← All datasets

GSE178259

GSE GEO
View on GEO Export SRA CSV

Non-microRNA Binding Competitively Inhibits LIN28 Regulation

Organism: Mus musculus
Platform: GPL20301
Samples: 38
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jun 15 2021
Last Updated: Jan 08 2022
Status: Public on Jan 07 2022
Contact: Gene,,Yeo (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA738154 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP324158

Summary

RNA binding protein (RBP) expression is finite. For RBPs that are vastly outnumbered by their potential target sites, a simple competition for binding can set the magnitude of post-transcriptional control. Here we show that LIN28, best known for its direct regulation of let-7 miRNA biogenesis, is also indirectly regulated by its widespread binding of non-miRNA transcripts. Approximately 99% of LIN28 binding sites are found on non-miRNA transcripts, like protein coding and ribosomal RNAs. These sites are bound specifically and strongly, but they do not appear to mediate direct post-transcriptional regulation. Instead, non-miRNA sites act to sequester LIN28 protein and effectively change its functional availability, thus impeding the regulation of let-7 in cells. Together, these data show that the binding properties of the transcriptome broadly influence the ability of an RBP to mediate changes in RNA metabolism and gene expression.

Overall Design

Examination of LIN28B binding using enhanced CLIP via 2 biological replicates of RNA fragments derived from LIN28B immunoprecipitation and 2 control input replicates for 4 LIN28B expression conditions in HEK293A (LIN28B_X1, LIN28B_X2, LIN28B_X3, LIN28B_X4). Examination of LIN28B binding using enhanced CLIP via 2 biological replicates of RNA fragments derived from Lin28A immunoprecipitation and 2 control input replicates in mouse ESCs with (HPK_mESCs) and without (V6_5_mESCs) sponge expression. Examination of changes in transcriptome-wide ribosome occupancy in mouse ESCs via total RNA (2 replicates, T) and ribosome-bound RNA (2 replicates, P) for several experimental conditions: (dd-Cit = double Dicer knockout ESCs expressing mock Citrine), (dd-HpK = double Dicer knockout ESCs expressing LIN28 sponge), (V6_5_mock = V6.5 ESCs expressing mock Citrine), (Hpk_mock = V6.5 ESCs expressing LIN28 sponge).

Analysis (6 steps)

View Data Processing
Processing steps for GSE178259
  1. Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
  2. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences.
  3. Remaining reads were mapped to the appropriate genome build using STAR aligner
  4. RPKM values were calculated for all polysome samples.
  5. For eCLIP samples, read densities were calculated to identify eCLIP peaks.
  6. eclip data processing pipeline can be requested from the following link : https://github.com/YeoLab/eclip

Supplementary Files (1)

GSE178259_RAW.tar Download
GEO Samples (38)
GSM5385970 GSM5385971 GSM5385972 GSM5385973 GSM5385974 GSM5385975 GSM5385976 GSM5385977 GSM5385978 GSM5385979 GSM5385980 GSM5385981 GSM5385982 GSM5385983 GSM5385984 GSM5385985 GSM5385986 GSM5385987 GSM5385988 GSM5385989 GSM5385990 GSM5385991 GSM5385992 GSM5385993 GSM5385994 GSM5385995 GSM5385996 GSM5385997 GSM5385998 GSM5385999 GSM5386000 GSM5386001 GSM5386002 GSM5386003 GSM5386004 GSM5386005 GSM5386006 GSM5386007

Dataset Citations (1)

Non-microRNA binding competitively inhibits LIN28 regulation.
PMID 34380031 · 2021 · Cell reports
Frederick E Tan, Shashank Sathe, Emily C Wheeler, Gene W Yeo

SRA Experiments (38) and Runs (38)

Total: 36976 MB
SRX11150347 SRP324158 RNA-Seq SINGLE
GSM5385970: dd-Cit-P-1; Mus musculus; RNA-Seq
Sample: SRS9212010
BioProject: PRJNA738154
BioSample: SAMN19714246
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: mESCs derived from Dicer(flox/flox) C57/BL6 mice
cell type: mESCs derived from Dicer(flox/flox) C57/BL6 mice
Original files (1)
mESCs derived from Dicer(flox/flox) C57/BL6 mice
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820418 39562745 3006768620 1190.94 dd-Cit-P-1_S5_L007_R1_001.fastq.gz, SRR14820418, SRR14820418.lite SRA
SRX11150348 SRP324158 RNA-Seq SINGLE
GSM5385971: dd-Cit-P-2; Mus musculus; RNA-Seq
Sample: SRS9212011
BioProject: PRJNA738154
BioSample: SAMN19714245
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: mESCs derived from Dicer(flox/flox) C57/BL6 mice
cell type: mESCs derived from Dicer(flox/flox) C57/BL6 mice
Original files (1)
mESCs derived from Dicer(flox/flox) C57/BL6 mice
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820419 45761285 3477857660 1376.0 dd-Cit-P-2_S6_L007_R1_001.fastq.gz, SRR14820419, SRR14820419.lite SRA
SRX11150349 SRP324158 RNA-Seq SINGLE
GSM5385972: dd-Cit-T-1; Mus musculus; RNA-Seq
Sample: SRS9212012
BioProject: PRJNA738154
BioSample: SAMN19714224
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: mESCs derived from Dicer(flox/flox) C57/BL6 mice
cell type: mESCs derived from Dicer(flox/flox) C57/BL6 mice
Original files (1)
mESCs derived from Dicer(flox/flox) C57/BL6 mice
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820420 38540565 2929082940 1169.7 dd-Cit-T-1_S1_L007_R1_001.fastq.gz, SRR14820420, SRR14820420.lite SRA
SRX11150350 SRP324158 RNA-Seq SINGLE
GSM5385973: dd-Cit-T-2; Mus musculus; RNA-Seq
Sample: SRS9212013
BioProject: PRJNA738154
BioSample: SAMN19714223
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: mESCs derived from Dicer(flox/flox) C57/BL6 mice
cell type: mESCs derived from Dicer(flox/flox) C57/BL6 mice
Original files (1)
mESCs derived from Dicer(flox/flox) C57/BL6 mice
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820421 48623209 3695363884 1481.71 dd-Cit-T-2_S2_L007_R1_001.fastq.gz, SRR14820421, SRR14820421.lite SRA
SRX11150351 SRP324158 RNA-Seq SINGLE
GSM5385974: dd-HpK-P-1; Mus musculus; RNA-Seq
Sample: SRS9212014
BioProject: PRJNA738154
BioSample: SAMN19714249
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: mESCs derived from Dicer(flox/flox) C57/BL6 mice
cell type: mESCs derived from Dicer(flox/flox) C57/BL6 mice
Original files (1)
mESCs derived from Dicer(flox/flox) C57/BL6 mice
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820422 41235719 3133914644 1244.5 dd-HpK-P-1_S7_L007_R1_001.fastq.gz, SRR14820422, SRR14820422.lite SRA
SRX11150352 SRP324158 RNA-Seq SINGLE
GSM5385975: dd-HpK-P-2; Mus musculus; RNA-Seq
Sample: SRS9212015
BioProject: PRJNA738154
BioSample: SAMN19714248
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: mESCs derived from Dicer(flox/flox) C57/BL6 mice
cell type: mESCs derived from Dicer(flox/flox) C57/BL6 mice
Original files (1)
mESCs derived from Dicer(flox/flox) C57/BL6 mice
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820423 42262665 3211962540 1278.35 dd-HpK-P-2_S8_L007_R1_001.fastq.gz, SRR14820423, SRR14820423.lite SRA
SRX11150353 SRP324158 RNA-Seq SINGLE
GSM5385976: dd-HpK-T-1; Mus musculus; RNA-Seq
Sample: SRS9212016
BioProject: PRJNA738154
BioSample: SAMN19714247
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: mESCs derived from Dicer(flox/flox) C57/BL6 mice
cell type: mESCs derived from Dicer(flox/flox) C57/BL6 mice
Original files (1)
mESCs derived from Dicer(flox/flox) C57/BL6 mice
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820424 51737163 3932024388 1578.16 dd-HpK-T-1_S3_L007_R1_001.fastq.gz, SRR14820424, SRR14820424.lite SRA
SRX11150354 SRP324158 RNA-Seq SINGLE
GSM5385977: dd-HpK-T-2; Mus musculus; RNA-Seq
Sample: SRS9212017
BioProject: PRJNA738154
BioSample: SAMN19714244
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: mESCs derived from Dicer(flox/flox) C57/BL6 mice
cell type: mESCs derived from Dicer(flox/flox) C57/BL6 mice
Original files (1)
mESCs derived from Dicer(flox/flox) C57/BL6 mice
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820425 52679801 4003664876 1595.94 dd-HpK-T-2_S4_L007_R1_001.fastq.gz, SRR14820425, SRR14820425.lite SRA
SRX11150355 SRP324158 RNA-Seq SINGLE
GSM5385978: Hpk_mock_1; Mus musculus; RNA-Seq
Sample: SRS9212018
BioProject: PRJNA738154
BioSample: SAMN19714243
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820426 31887732 2391579900 927.71 Hpk_mock_1_S5_L001_R1_001.fastq.gz, SRR14820426, SRR14820426.lite SRA
SRX11150356 SRP324158 RNA-Seq SINGLE
GSM5385979: Hpk_mock_1_poly; Mus musculus; RNA-Seq
Sample: SRS9212019
BioProject: PRJNA738154
BioSample: SAMN19714242
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820427 26985117 2023883775 793.05 Hpk_mock_1_poly_S7_L001_R1_001.fastq.gz, SRR14820427, SRR14820427.lite SRA
SRX11150357 SRP324158 RNA-Seq SINGLE
GSM5385980: Hpk_mock_2; Mus musculus; RNA-Seq
Sample: SRS9212020
BioProject: PRJNA738154
BioSample: SAMN19714241
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820428 30083977 2256298275 874.18 Hpk_mock_2_S17_L002_R1_001.fastq.gz, SRR14820428, SRR14820428.lite SRA
SRX11150358 SRP324158 RNA-Seq SINGLE
GSM5385981: Hpk_mock_2_poly; Mus musculus; RNA-Seq
Sample: SRS9212021
BioProject: PRJNA738154
BioSample: SAMN19714240
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820429 28640993 2148074475 841.97 Hpk_mock_2_poly_S19_L002_R1_001.fastq.gz, SRR14820429, SRR14820429.li… SRA
SRX11150359 SRP324158 RNA-Seq SINGLE
GSM5385982: V6_5_mock_1; Mus musculus; RNA-Seq
Sample: SRS9212022
BioProject: PRJNA738154
BioSample: SAMN19714239
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820430 30038391 2252879325 860.62 V6_5_mock_1_S1_L001_R1_001.fastq.gz, SRR14820430, SRR14820430.lite SRA
SRX11150360 SRP324158 RNA-Seq SINGLE
GSM5385983: V6_5_mock_1_poly; Mus musculus; RNA-Seq
Sample: SRS9212023
BioProject: PRJNA738154
BioSample: SAMN19714238
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820431 27170416 2037781200 785.09 V6_5_mock_1_poly_S3_L001_R1_001.fastq.gz, SRR14820431, SRR14820431.li… SRA
SRX11150361 SRP324158 RNA-Seq SINGLE
GSM5385984: V6_5_mock_2; Mus musculus; RNA-Seq
Sample: SRS9212024
BioProject: PRJNA738154
BioSample: SAMN19714237
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820432 30412964 2280972300 874.08 V6_5_mock_2_S13_L002_R1_001.fastq.gz, SRR14820432, SRR14820432.lite SRA
SRX11150362 SRP324158 RNA-Seq SINGLE
GSM5385985: V6_5_mock_2_poly; Mus musculus; RNA-Seq
Sample: SRS9212025
BioProject: PRJNA738154
BioSample: SAMN19714236
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820433 31374120 2353059000 910.91 V6_5_mock_2_poly_S15_L002_R1_001.fastq.gz, SRR14820433, SRR14820433.l… SRA
SRX11150363 SRP324158 RNA-Seq SINGLE
GSM5385986: HPK_mESCs_IN3; Mus musculus; RNA-Seq
Sample: SRS9212026
BioProject: PRJNA738154
BioSample: SAMN19714235
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820434 42822908 3254541008 1235.42 HPK_mESCs_IN7_mock_R1_merged.fastq.gz, SRR14820434, SRR14820434.lite SRA
SRX11150364 SRP324158 RNA-Seq SINGLE
GSM5385987: HPK_mESCs_IP3; Mus musculus; RNA-Seq
Sample: SRS9212028
BioProject: PRJNA738154
BioSample: SAMN19714234
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820435 41737975 3172086100 1424.01 HPK_mESCs_IP3_mock_S20_L007_R1_001.fastq.gz, SRR14820435, SRR14820435… SRA
SRX11150365 SRP324158 RNA-Seq SINGLE
GSM5385988: HPK_mESCs_IP7; Mus musculus; RNA-Seq
Sample: SRS9212027
BioProject: PRJNA738154
BioSample: SAMN19714233
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820436 42858230 3257225480 1263.76 HPK_mESCs_IP7_mock_R1_merged.fastq.gz, SRR14820436, SRR14820436.lite SRA
SRX11150366 SRP324158 RNA-Seq SINGLE
GSM5385989: V6_5_mESCs_IN1; Mus musculus; RNA-Seq
Sample: SRS9212029
BioProject: PRJNA738154
BioSample: SAMN19714260
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820437 38227921 2905321996 1077.0 V6_5_mESCs_IN1_mock_R1_merged.fastq.gz, SRR14820437, SRR14820437.lite SRA
SRX11150367 SRP324158 RNA-Seq SINGLE
GSM5385990: V6_5_mESCs_IP1; Mus musculus; RNA-Seq
Sample: SRS9212030
BioProject: PRJNA738154
BioSample: SAMN19714259
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820438 38547855 2929636980 1159.31 V6_5_mESCs_IP1_mock_S19_L007_R1_001.fastq.gz, SRR14820438, SRR1482043… SRA
SRX11150368 SRP324158 RNA-Seq SINGLE
GSM5385991: V6_5_mESCs_IP5; Mus musculus; RNA-Seq
Sample: SRS9212031
BioProject: PRJNA738154
BioSample: SAMN19714258
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: V6.5 mESCs
cell type: V6.5 mESCs
Original files (1)
V6.5 mESCs
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820439 46059656 3500533856 1387.77 V6_5_mESCs_IP5_mock_S21_L007_R1_001.fastq.gz, SRR14820439, SRR1482043… SRA
SRX11150369 SRP324158 RNA-Seq PAIRED
GSM5385992: LIN28B_X1_eCLIP_IP_Rep1_Human; Homo sapiens; RNA-Seq
Sample: SRS9212032
BioProject: PRJNA738154
BioSample: SAMN19714257
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
barcode: A01, B06
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820440 9483584 1016052099 460.81 LIN28B_PHI_1_CLIP_R1_S32_L002_R1_A01_B06.fastq.gz, LIN28B_PHI_1_CLIP_… SRA
SRX11150370 SRP324158 RNA-Seq PAIRED
GSM5385993: LIN28B_X1_eCLIP_IP_Rep2_Human; Homo sapiens; RNA-Seq
Sample: SRS9212033
BioProject: PRJNA738154
BioSample: SAMN19714256
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
barcode: A01, B06
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820441 6260754 669739738 305.61 LIN28B_PHI_1_CLIP_R2_S24_L002_R1_A01_B06.fastq.gz, LIN28B_PHI_1_CLIP_… SRA
SRX11150371 SRP324158 RNA-Seq PAIRED
GSM5385994: LIN28B_X2_eCLIP_IP_Rep1_Human; Homo sapiens; RNA-Seq
Sample: SRS9212034
BioProject: PRJNA738154
BioSample: SAMN19714255
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
barcode: C01, D08fixed
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820442 8760403 943211161 420.76 LIN28B_PHI_2_CLIP_R1_S31_L002_R1_C01_D08.fastq.gz, LIN28B_PHI_2_CLIP_… SRA
SRX11150372 SRP324158 RNA-Seq PAIRED
GSM5385995: LIN28B_X2_eCLIP_IP_Rep2_Human; Homo sapiens; RNA-Seq
Sample: SRS9212035
BioProject: PRJNA738154
BioSample: SAMN19714254
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
barcode: C01, D08fixed
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820443 7494740 804175075 361.67 LIN28B_PHI_2_CLIP_R2_S23_L002_R1_C01_D08.fastq.gz, LIN28B_PHI_2_CLIP_… SRA
SRX11150373 SRP324158 RNA-Seq PAIRED
GSM5385996: LIN28B_X3_eCLIP_IP_Rep1_Human; Homo sapiens; RNA-Seq
Sample: SRS9212036
BioProject: PRJNA738154
BioSample: SAMN19714250
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
barcode: A04, F05
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820444 9091434 965253306 439.3 LIN28B_PHI_3_CLIP_R1_S28_L002_R1_A04_F05.fastq.gz, LIN28B_PHI_3_CLIP_… SRA
SRX11150374 SRP324158 RNA-Seq PAIRED
GSM5385997: LIN28B_X3_eCLIP_IP_Rep2_Human; Homo sapiens; RNA-Seq
Sample: SRS9212037
BioProject: PRJNA738154
BioSample: SAMN19714232
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
barcode: A04, F05
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820445 8771308 926258292 424.98 LIN28B_PHI_3_CLIP_R2_S20_L002_R1_A04_F05.fastq.gz, LIN28B_PHI_3_CLIP_… SRA
SRX11150375 SRP324158 RNA-Seq PAIRED
GSM5385998: LIN28B_X4_eCLIP_IP_Rep1_Human; Homo sapiens; RNA-Seq
Sample: SRS9212038
BioProject: PRJNA738154
BioSample: SAMN19714231
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
barcode: X2A, X2B
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820446 9197274 968953681 445.58 LIN28B_PHI_4_CLIP_R1_S27_L002_R1_X2A_X2B.fastq.gz, LIN28B_PHI_4_CLIP_… SRA
SRX11150376 SRP324158 RNA-Seq PAIRED
GSM5385999: LIN28B_X4_eCLIP_IP_Rep2_Human; Homo sapiens; RNA-Seq
Sample: SRS9212039
BioProject: PRJNA738154
BioSample: SAMN19714230
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
barcode: X2A, X2B
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820447 16038453 1717087827 783.57 LIN28B_PHI_4_CLIP_R2_S19_L002_R1_X2A_X2B.fastq.gz, LIN28B_PHI_4_CLIP_… SRA
SRX11150377 SRP324158 RNA-Seq PAIRED
GSM5386000: LIN28B_X1_eCLIP_INPUT_Rep1_Human; Homo sapiens; RNA-Seq
Sample: SRS9212040
BioProject: PRJNA738154
BioSample: SAMN19714229
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820448 15052518 1471704217 1268.08 LIN28B_PHI_1_INPUT_R1_S29_L002_R1.fastq.gz, LIN28B_PHI_1_INPUT_R1_S29… SRA
SRX11150378 SRP324158 RNA-Seq PAIRED
GSM5386001: LIN28B_X1_eCLIP_INPUT_Rep2_Human; Homo sapiens; RNA-Seq
Sample: SRS9212041
BioProject: PRJNA738154
BioSample: SAMN19714228
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820449 9249273 869926529 786.15 LIN28B_PHI_1_INPUT_R2_S21_L002_R1.fastq.gz, LIN28B_PHI_1_INPUT_R2_S21… SRA
SRX11150379 SRP324158 RNA-Seq PAIRED
GSM5386002: LIN28B_X2_eCLIP_INPUT_Rep1_Human; Homo sapiens; RNA-Seq
Sample: SRS9212042
BioProject: PRJNA738154
BioSample: SAMN19714253
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820450 12726616 1240648973 1080.8 LIN28B_PHI_2_INPUT_R1_S30_L002_R1.fastq.gz, LIN28B_PHI_2_INPUT_R1_S30… SRA
SRX11150380 SRP324158 RNA-Seq PAIRED
GSM5386003: LIN28B_X2_eCLIP_INPUT_Rep2_Human; Homo sapiens; RNA-Seq
Sample: SRS9212043
BioProject: PRJNA738154
BioSample: SAMN19714252
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820451 11775338 1160091122 1009.72 LIN28B_PHI_2_INPUT_R2_S22_L002_R1.fastq.gz, LIN28B_PHI_2_INPUT_R2_S22… SRA
SRX11150381 SRP324158 RNA-Seq PAIRED
GSM5386004: LIN28B_X3_eCLIP_INPUT_Rep1_Human; Homo sapiens; RNA-Seq
Sample: SRS9212044
BioProject: PRJNA738154
BioSample: SAMN19714251
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820452 8304492 811584345 715.92 LIN28B_PHI_3_INPUT_R1_S25_L002_R1.fastq.gz, LIN28B_PHI_3_INPUT_R1_S25… SRA
SRX11150382 SRP324158 RNA-Seq PAIRED
GSM5386005: LIN28B_X3_eCLIP_INPUT_Rep2_Human; Homo sapiens; RNA-Seq
Sample: SRS9212045
BioProject: PRJNA738154
BioSample: SAMN19714227
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820453 12372015 1214011274 1054.19 LIN28B_PHI_3_INPUT_R2_S17_L002_R1.fastq.gz, LIN28B_PHI_3_INPUT_R2_S17… SRA
SRX11150383 SRP324158 RNA-Seq PAIRED
GSM5386006: LIN28B_X4_eCLIP_INPUT_Rep1_Human; Homo sapiens; RNA-Seq
Sample: SRS9212046
BioProject: PRJNA738154
BioSample: SAMN19714226
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820454 13347261 1318116125 1130.35 LIN28B_PHI_4_INPUT_R1_S26_L002_R1.fastq.gz, LIN28B_PHI_4_INPUT_R1_S26… SRA
SRX11150384 SRP324158 RNA-Seq PAIRED
GSM5386007: LIN28B_X4_eCLIP_INPUT_Rep2_Human; Homo sapiens; RNA-Seq
Sample: SRS9212047
BioProject: PRJNA738154
BioSample: SAMN19714225
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293A
cell type: HEK293A
Original files (1)
HEK293A
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14820455 11246687 1098178570 958.18 LIN28B_PHI_4_INPUT_R2_S18_L002_R1.fastq.gz, LIN28B_PHI_4_INPUT_R2_S18… SRA

Linked Publications (1)

Non-microRNA binding competitively inhibits LIN28 regulation.
Cell reports · 2021

Data Files (38)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— dd-Cit-P-1_S5_L007_R1_001.fastq.gz RNA-Seq 1.2 GB link
— dd-Cit-P-2_S6_L007_R1_001.fastq.gz RNA-Seq 1.3 GB link
— dd-Cit-T-1_S1_L007_R1_001.fastq.gz RNA-Seq 1.1 GB link
— dd-Cit-T-2_S2_L007_R1_001.fastq.gz RNA-Seq 1.4 GB link
— dd-HpK-P-1_S7_L007_R1_001.fastq.gz RNA-Seq 1.2 GB link
— dd-HpK-P-2_S8_L007_R1_001.fastq.gz RNA-Seq 1.2 GB link
— dd-HpK-T-1_S3_L007_R1_001.fastq.gz RNA-Seq 1.5 GB link
— dd-HpK-T-2_S4_L007_R1_001.fastq.gz RNA-Seq 1.6 GB link
— HPK_mESCs_IN7_mock_R1_merged.fastq.gz RNA-Seq 1.2 GB link
— HPK_mESCs_IP3_mock_S20_L007_R1_001.fastq.gz RNA-Seq 1.4 GB link
— HPK_mESCs_IP7_mock_R1_merged.fastq.gz RNA-Seq 1.2 GB link
— Hpk_mock_1_poly_S7_L001_R1_001.fastq.gz RNA-Seq 793.0 MB link
— Hpk_mock_1_S5_L001_R1_001.fastq.gz RNA-Seq 927.7 MB link
— Hpk_mock_2_poly_S19_L002_R1_001.fastq.gz RNA-Seq 842.0 MB link
— Hpk_mock_2_S17_L002_R1_001.fastq.gz RNA-Seq 874.2 MB link
— LIN28B_PHI_1_CLIP_R1_S32_L002_R1_A01_B06.fastq.gz RNA-Seq 460.8 MB link
— LIN28B_PHI_1_CLIP_R2_S24_L002_R1_A01_B06.fastq.gz RNA-Seq 305.6 MB link
— LIN28B_PHI_1_INPUT_R1_S29_L002_R1.fastq.gz RNA-Seq 1.2 GB link
— LIN28B_PHI_1_INPUT_R2_S21_L002_R1.fastq.gz RNA-Seq 786.1 MB link
— LIN28B_PHI_2_CLIP_R1_S31_L002_R1_C01_D08.fastq.gz RNA-Seq 420.8 MB link
— LIN28B_PHI_2_CLIP_R2_S23_L002_R1_C01_D08.fastq.gz RNA-Seq 361.7 MB link
— LIN28B_PHI_2_INPUT_R1_S30_L002_R1.fastq.gz RNA-Seq 1.1 GB link
— LIN28B_PHI_2_INPUT_R2_S22_L002_R1.fastq.gz RNA-Seq 1009.7 MB link
— LIN28B_PHI_3_CLIP_R1_S28_L002_R1_A04_F05.fastq.gz RNA-Seq 439.3 MB link
— LIN28B_PHI_3_CLIP_R2_S20_L002_R1_A04_F05.fastq.gz RNA-Seq 425.0 MB link
— LIN28B_PHI_3_INPUT_R1_S25_L002_R1.fastq.gz RNA-Seq 715.9 MB link
— LIN28B_PHI_3_INPUT_R2_S17_L002_R1.fastq.gz RNA-Seq 1.0 GB link
— LIN28B_PHI_4_CLIP_R1_S27_L002_R1_X2A_X2B.fastq.gz RNA-Seq 445.6 MB link
— LIN28B_PHI_4_CLIP_R2_S19_L002_R1_X2A_X2B.fastq.gz RNA-Seq 783.6 MB link
— LIN28B_PHI_4_INPUT_R1_S26_L002_R1.fastq.gz RNA-Seq 1.1 GB link
— LIN28B_PHI_4_INPUT_R2_S18_L002_R1.fastq.gz RNA-Seq 958.2 MB link
— V6_5_mESCs_IN1_mock_R1_merged.fastq.gz RNA-Seq 1.1 GB link
— V6_5_mESCs_IP1_mock_S19_L007_R1_001.fastq.gz RNA-Seq 1.1 GB link
— V6_5_mESCs_IP5_mock_S21_L007_R1_001.fastq.gz RNA-Seq 1.4 GB link
— V6_5_mock_1_poly_S3_L001_R1_001.fastq.gz RNA-Seq 785.1 MB link
— V6_5_mock_1_S1_L001_R1_001.fastq.gz RNA-Seq 860.6 MB link
— V6_5_mock_2_poly_S15_L002_R1_001.fastq.gz RNA-Seq 910.9 MB link
— V6_5_mock_2_S13_L002_R1_001.fastq.gz RNA-Seq 874.1 MB link