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GSE109423

GSE GEO
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A transcriptome-wide divergence in protein translation scales with LIN28B expression

Organism: Mus musculus
Platform: GPL20301
Samples: 30
Experiment Types:
Other Non-coding RNA profiling by high throughput sequencing
Submitted: Jan 19 2018
Last Updated: Jan 07 2022
Status: Public on Dec 13 2018
Contact: Gene,,Yeo (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA430874 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP131042

Summary

We report the mapping of LIN28B binding to RNA in HEK293A at various LIN28B expression levels using enhanced CLIP. We provide small RNA sequencing data regarding miRNA expression in HEK293A and those miRNAs bound by AGO2. We also profile the effect of LIN28B expression on transcriptome-wide ribosome occupancy in HEK293A via RNA-seq. Finally, we provide orthogonal regulatory data by profiling the effect of LIN28B expression on transcriptome-wide ribosome occupancy in NIH3T3 via RNA-seq.

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 5 LIN28B expression conditions. X0 is lin28b knockout. X1 through X4 are increasing levels of lin28b expression (X1 < X2 < X3 < X4). X1 through X4 lie within the naturally occurring spectrum of lin28b expression from other cell types such as HepG2, NTera2 and iPSC. Examination of small RNAs expressed in HEK293A and those specifically bound by AGO2, in the presence or absence of LIN28B or transfected let-7a miRNA, single replicate. Examination of changes in transcriptome-wide ribosome occupancy in HEK293A via total RNA (2 replicates) and ribosome-bound RNA (2 replicates) for 5 different LIN28B expression conditions. Experimental design for examining changes in transcriptome-wide ribosome occupancy in NIH3T3 were the same as for HEK293A.

Analysis (6 steps)

View Data Processing
Processing steps for GSE109423
  1. Library strategy: ribosome profiling
  2. Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
  3. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences.
  4. Remaining reads were mapped to the appropriate genome build using STAR aligner
  5. RPKM values were calculated for all polysome and rnaseq samples.
  6. For eCLIP samples, read densities were calculated to identify eCLIP peaks. eCLIP peaks were identified using clipper

Supplementary Files (4)

GSE109423_Polysomes_Let7_RPKM.csv.gz Download
GSE109423_human_polysome_samples_rpkms.txt.gz Download
GSE109423_human_small_rnaseq_counts.txt.gz Download
GSE109423_mouse_polysome_samples_rpkms.txt.gz Download
GEO Samples (30)
GSM2942714 GSM2942715 GSM2942716 GSM2942717 GSM2942718 GSM2942719 GSM2942720 GSM2942721 GSM2942722 GSM2942723 GSM2942724 GSM2942725 GSM2942726 GSM2942727 GSM2942728 GSM2942729 GSM2942730 GSM2942731 GSM2942732 GSM2942733 GSM2942734 GSM2942735 GSM2942736 GSM2942737 GSM2942738 GSM2942739 GSM2942740 GSM2942741 GSM2942742 GSM2942743

Dataset Citations (2)

A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.
PMID 30527666 · 2019 · Molecular cell
Frederick E Tan, Shashank Sathe, Emily C Wheeler, Julia K Nussbacher, Samson Peter, Gene W Yeo
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 (30) and Runs (30)

Total: 27876 MB
SRX3586130 SRP131042 OTHER SINGLE
GSM2942714: Lin28B_X0_Polysome_Human; Homo sapiens; OTHER
Sample: SRS2854823
BioProject: PRJNA430874
BioSample: SAMN08379262
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Lin28B_X0_Polysome_Human
cell line: HEK293A
Original files (1)
Lin28B_X0_Polysome_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497056 17231076 861553800 279.92 b8p37_a9_polysome_S16_L004_R1_001.fastq.gz, SRR6497056, SRR6497056.sr… SRA
SRX3586131 SRP131042 OTHER SINGLE
GSM2942715: Lin28B_X1_Polysome_Human; Homo sapiens; OTHER
Sample: SRS2854827
BioProject: PRJNA430874
BioSample: SAMN08379261
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Lin28B_X1_Polysome_Human
cell line: HEK293A
Original files (1)
Lin28B_X1_Polysome_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497057 17336036 866801800 284.31 b8p37_x1_polysome_S17_L004_R1_001.fastq.gz, SRR6497057, SRR6497057.sr… SRA
SRX3586132 SRP131042 OTHER SINGLE
GSM2942716: Lin28B_X2_Polysome_Human; Homo sapiens; OTHER
Sample: SRS2854819
BioProject: PRJNA430874
BioSample: SAMN08379260
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Lin28B_X2_Polysome_Human
cell line: HEK293A
Original files (1)
Lin28B_X2_Polysome_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497058 13174871 658743550 214.49 b8p37_x2_polysome_S18_L004_R1_001.fastq.gz, SRR6497058, SRR6497058.sr… SRA
SRX3586133 SRP131042 OTHER SINGLE
GSM2942717: Lin28B_X3_Polysome_Human; Homo sapiens; OTHER
Sample: SRS2854826
BioProject: PRJNA430874
BioSample: SAMN08379259
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Lin28B_X3_Polysome_Human
cell line: HEK293A
Original files (1)
Lin28B_X3_Polysome_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497059 21054078 1052703900 344.35 b8p37_x3_polysome_S19_L004_R1_001.fastq.gz, SRR6497059, SRR6497059.sr… SRA
SRX3586134 SRP131042 OTHER SINGLE
GSM2942718: Lin28B_X4_Polysome_Human; Homo sapiens; OTHER
Sample: SRS2854824
BioProject: PRJNA430874
BioSample: SAMN08379258
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Lin28B_X4_Polysome_Human
cell line: HEK293A
Original files (1)
Lin28B_X4_Polysome_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497060 15671864 783593200 255.71 b8p37_x4_polysome_S20_L004_R1_001.fastq.gz, SRR6497060, SRR6497060.sr… SRA
SRX3586135 SRP131042 RNA-Seq SINGLE
GSM2942719: Lin28B_X0_Total_RNA_Human; Homo sapiens; RNA-Seq
Sample: SRS2854852
BioProject: PRJNA430874
BioSample: SAMN08379257
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Lin28B_X0_Total_RNA_Human
cell line: HEK293A
Original files (1)
Lin28B_X0_Total_RNA_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497061 56230384 2811519200 912.46 b8p37_a9_input_S11_L004_R1_001.fastq.gz, SRR6497061, SRR6497061.srali… SRA
SRX3586136 SRP131042 RNA-Seq SINGLE
GSM2942720: Lin28B_X1_Total_RNA_Human; Homo sapiens; RNA-Seq
Sample: SRS2854850
BioProject: PRJNA430874
BioSample: SAMN08379256
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Lin28B_X1_Total_RNA_Human
cell line: HEK293A
Original files (1)
Lin28B_X1_Total_RNA_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497062 52958116 2647905800 862.37 b8p37_x1_input_S12_L004_R1_001.fastq.gz, SRR6497062, SRR6497062.srali… SRA
SRX3586137 SRP131042 RNA-Seq SINGLE
GSM2942721: Lin28B_X2_Total_RNA_Human; Homo sapiens; RNA-Seq
Sample: SRS2854830
BioProject: PRJNA430874
BioSample: SAMN08379255
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Lin28B_X2_Total_RNA_Human
cell line: HEK293A
Original files (1)
Lin28B_X2_Total_RNA_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497063 78651688 3932584400 1269.68 b8p37_x2_input_S13_L004_R1_001.fastq.gz, SRR6497063, SRR6497063.srali… SRA
SRX3586138 SRP131042 RNA-Seq SINGLE
GSM2942722: Lin28B_X3_Total_RNA_Human; Homo sapiens; RNA-Seq
Sample: SRS2854828
BioProject: PRJNA430874
BioSample: SAMN08379254
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Lin28B_X3_Total_RNA_Human
cell line: HEK293A
Original files (1)
Lin28B_X3_Total_RNA_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497064 73015716 3650785800 1187.76 b8p37_x3_input_S14_L004_R1_001.fastq.gz, SRR6497064, SRR6497064.srali… SRA
SRX3586139 SRP131042 RNA-Seq SINGLE
GSM2942723: Lin28B_X4_Total_RNA_Human; Homo sapiens; RNA-Seq
Sample: SRS2854832
BioProject: PRJNA430874
BioSample: SAMN08379253
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Lin28B_X4_Total_RNA_Human
cell line: HEK293A
Original files (1)
Lin28B_X4_Total_RNA_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497065 60634166 3031708300 987.25 b8p37_x4_input_S15_L004_R1_001.fastq.gz, SRR6497065, SRR6497065.srali… SRA
SRX3586140 SRP131042 OTHER PAIRED
GSM2942724: Lin28B_X0_Polysome_Mouse; Mus musculus; OTHER
Sample: SRS2854833
BioProject: PRJNA430874
BioSample: SAMN08379252
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Lin28B_X0_Polysome_Mouse
cell line: NIH3T3
Original files (1)
Lin28B_X0_Polysome_Mouse
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497066 22141076 4428215200 1863.89 PX0_S52_L006_R1_001.fastq.gz, PX0_S52_L006_R2_001.fastq.gz, SRR649706… SRA
SRX3586141 SRP131042 OTHER PAIRED
GSM2942725: Lin28B_X1_Polysome_Mouse; Mus musculus; OTHER
Sample: SRS2854834
BioProject: PRJNA430874
BioSample: SAMN08379264
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Lin28B_X1_Polysome_Mouse
cell line: NIH3T3
Original files (1)
Lin28B_X1_Polysome_Mouse
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497067 17636294 3527258800 1499.7 PX1_S53_L006_R1_001.fastq.gz, PX1_S53_L006_R2_001.fastq.gz, SRR649706… SRA
SRX3586142 SRP131042 OTHER PAIRED
GSM2942726: Lin28B_X2_Polysome_Mouse; Mus musculus; OTHER
Sample: SRS2854835
BioProject: PRJNA430874
BioSample: SAMN08379263
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Lin28B_X2_Polysome_Mouse
cell line: NIH3T3
Original files (1)
Lin28B_X2_Polysome_Mouse
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497068 20649943 4129988600 1732.3 PX2_S54_L006_R1_001.fastq.gz, PX2_S54_L006_R2_001.fastq.gz, SRR649706… SRA
SRX3586143 SRP131042 OTHER PAIRED
GSM2942727: Lin28B_X3_Polysome_Mouse; Mus musculus; OTHER
Sample: SRS2854836
BioProject: PRJNA430874
BioSample: SAMN08379248
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Lin28B_X3_Polysome_Mouse
cell line: NIH3T3
Original files (1)
Lin28B_X3_Polysome_Mouse
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497069 19331417 3866283400 1724.35 PX3_S55_L006_R1_001.fastq.gz, PX3_S55_L006_R2_001.fastq.gz, SRR649706… SRA
SRX3586144 SRP131042 OTHER PAIRED
GSM2942728: Lin28B_X4_Polysome_Mouse; Mus musculus; OTHER
Sample: SRS2854838
BioProject: PRJNA430874
BioSample: SAMN08379247
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Lin28B_X4_Polysome_Mouse
cell line: NIH3T3
Original files (1)
Lin28B_X4_Polysome_Mouse
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497070 17887092 3577418400 1502.07 PX4_S56_L006_R1_001.fastq.gz, PX4_S56_L006_R2_001.fastq.gz, SRR649707… SRA
SRX3586145 SRP131042 RNA-Seq PAIRED
GSM2942729: LIN28B_X0_Total_RNA_Mouse; Mus musculus; RNA-Seq
Sample: SRS2858978
BioProject: PRJNA430874
BioSample: SAMN08379265
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: LIN28B_X0_Total_RNA_Mouse
cell line: NIH3T3
Original files (1)
LIN28B_X0_Total_RNA_Mouse
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497071 24922656 4984531200 2092.9 TX0_S47_L006_R1_001.fastq.gz, TX0_S47_L006_R2_001.fastq.gz, SRR649707… SRA
SRX3586146 SRP131042 RNA-Seq PAIRED
GSM2942730: LIN28B_X1_Total_RNA_Mouse; Mus musculus; RNA-Seq
Sample: SRS2854837
BioProject: PRJNA430874
BioSample: SAMN08379251
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: LIN28B_X1_Total_RNA_Mouse
cell line: NIH3T3
Original files (1)
LIN28B_X1_Total_RNA_Mouse
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497072 17582777 3516555400 1457.47 TX1_S48_L006_R1_001.fastq.gz, TX1_S48_L006_R2_001.fastq.gz, SRR649707… SRA
SRX3586147 SRP131042 RNA-Seq PAIRED
GSM2942731: LIN28B_X2_Total_RNA_Mouse; Mus musculus; RNA-Seq
Sample: SRS2858965
BioProject: PRJNA430874
BioSample: SAMN08379250
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: LIN28B_X2_Total_RNA_Mouse
cell line: NIH3T3
Original files (1)
LIN28B_X2_Total_RNA_Mouse
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497073 16014565 3202913000 1340.66 TX2_S49_L006_R1_001.fastq.gz, TX2_S49_L006_R2_001.fastq.gz, SRR649707… SRA
SRX3586148 SRP131042 RNA-Seq PAIRED
GSM2942732: LIN28B_X3_Total_RNA_Mouse; Mus musculus; RNA-Seq
Sample: SRS2854839
BioProject: PRJNA430874
BioSample: SAMN08379249
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: LIN28B_X3_Total_RNA_Mouse
cell line: NIH3T3
Original files (1)
LIN28B_X3_Total_RNA_Mouse
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497074 20300501 4060100200 1684.5 TX3_S50_L006_R1_001.fastq.gz, TX3_S50_L006_R2_001.fastq.gz, SRR649707… SRA
SRX3586149 SRP131042 RNA-Seq PAIRED
GSM2942733: LIN28B_X4_Total_RNA_Mouse; Mus musculus; RNA-Seq
Sample: SRS2854840
BioProject: PRJNA430874
BioSample: SAMN08379246
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: LIN28B_X4_Total_RNA_Mouse
cell line: NIH3T3
Original files (1)
LIN28B_X4_Total_RNA_Mouse
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497075 22493378 4498675600 1875.94 TX4_S51_L006_R1_001.fastq.gz, TX4_S51_L006_R2_001.fastq.gz, SRR649707… SRA
SRX3586150 SRP131042 RIP-Seq SINGLE
GSM2942734: LIN28B_KO_let7_ip_smallRNA; Homo sapiens; RIP-Seq
Sample: SRS2854841
BioProject: PRJNA430874
BioSample: SAMN08379288
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: LIN28B_KO_let7_ip
cell line: HEK293A
antibody: anti-AGO2 Clone 9E8.2, Millipore, Cat# 04-642
Original files (1)
LIN28B_KO_let7_ip
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497076 11438118 857858850 335.91 b8p100_smallrnaseq_hek293_ko_l7_ip_S27_L002_R1_001.fastq.gz, SRR64970… SRA
SRX3586151 SRP131042 ncRNA-Seq SINGLE
GSM2942735: LIN28B_KO_let7_total_smallRNA; Homo sapiens; ncRNA-Seq
Sample: SRS2854842
BioProject: PRJNA430874
BioSample: SAMN08379287
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: LIN28B_KO_let7_total
cell line: HEK293A
Original files (1)
LIN28B_KO_let7_total
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497077 15054801 1129110075 457.61 b8p100_smallrnaseq_hek293_ko_l7_total_S23_L002_R1_001.fastq.gz, SRR64… SRA
SRX3586152 SRP131042 RIP-Seq SINGLE
GSM2942736: LIN28B_KO_wt_ip_smallRNA; Homo sapiens; RIP-Seq
Sample: SRS2854844
BioProject: PRJNA430874
BioSample: SAMN08379289
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: LIN28B_KO_wt_ip
cell line: HEK293A
antibody: anti-AGO2 Clone 9E8.2, Millipore, Cat# 04-642
Original files (1)
LIN28B_KO_wt_ip
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497078 10460416 784531200 304.56 b8p100_smallrnaseq_hek293_ko_wt_ip_S25_L002_R1_001.fastq.gz, SRR64970… SRA
SRX3586153 SRP131042 ncRNA-Seq SINGLE
GSM2942737: LIN28B_KO_wt_total_smallRNA; Homo sapiens; ncRNA-Seq
Sample: SRS2854843
BioProject: PRJNA430874
BioSample: SAMN08379245
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: LIN28B_KO_wt_total
cell line: HEK293A
Original files (1)
LIN28B_KO_wt_total
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497079 18036398 1352729850 563.75 b8p100_smallrnaseq_hek293_ko_wt_total_S21_L002_R1_001.fastq.gz, SRR64… SRA
SRX3586154 SRP131042 RIP-Seq SINGLE
GSM2942738: LIN28B_X3_let7_ip_smallRNA; Homo sapiens; RIP-Seq
Sample: SRS2854846
BioProject: PRJNA430874
BioSample: SAMN08379290
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: LIN28B_X3_let7_ip
cell line: HEK293A
antibody: anti-AGO2 Clone 9E8.2, Millipore, Cat# 04-642
Original files (1)
LIN28B_X3_let7_ip
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497080 8183880 613791000 241.03 b8p100_smallrnaseq_hek293_x3_l7_ip_S28_L002_R1_001.fastq.gz, SRR64970… SRA
SRX3586155 SRP131042 ncRNA-Seq SINGLE
GSM2942739: LIN28B_X3_let7_total_smallRNA; Homo sapiens; ncRNA-Seq
Sample: SRS2854845
BioProject: PRJNA430874
BioSample: SAMN08379283
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: LIN28B_X3_let7_total
cell line: HEK293A
Original files (1)
LIN28B_X3_let7_total
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497081 16804977 1260373275 509.15 b8p100_smallrnaseq_hek293_x3_l7_total_S24_L002_R1_001.fastq.gz, SRR64… SRA
SRX3586156 SRP131042 RIP-Seq SINGLE
GSM2942740: LIN28B_X3_wt_ip_smallRNA; Homo sapiens; RIP-Seq
Sample: SRS2858966
BioProject: PRJNA430874
BioSample: SAMN08379282
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: LIN28B_X3_wt_ip
cell line: HEK293A
antibody: anti-AGO2 Clone 9E8.2, Millipore, Cat# 04-642
Original files (1)
LIN28B_X3_wt_ip
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497082 11834223 887566725 341.56 b8p100_smallrnaseq_hek293_x3_wt_ip_S26_L002_R1_001.fastq.gz, SRR64970… SRA
SRX3586157 SRP131042 ncRNA-Seq SINGLE
GSM2942741: LIN28B_X3_wt_total_smallRNA; Homo sapiens; ncRNA-Seq
Sample: SRS2854847
BioProject: PRJNA430874
BioSample: SAMN08379281
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: LIN28B_X3_wt_total
cell line: HEK293A
Original files (1)
LIN28B_X3_wt_total
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497083 20111442 1508358150 617.84 b8p100_smallrnaseq_hek293_x3_wt_total_S22_L002_R1_001.fastq.gz, SRR64… SRA
SRX3586158 SRP131042 OTHER SINGLE
GSM2942742: LIN28B_X0_let7_transfection_Polysome_Human; Homo sapiens; OTHER
Sample: SRS2854848
BioProject: PRJNA430874
BioSample: SAMN08379280
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: LIN28B_X0_let7_transfection_Polysome_Human
cell line: HEK293A
Original files (1)
LIN28B_X0_let7_transfection_Polysome_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497084 15779005 788950250 274.66 b8p37_a9_polysome_let7_S6_L003_R1_001.fastq.gz, SRR6497084, SRR649708… SRA
SRX3586159 SRP131042 RNA-Seq SINGLE
GSM2942743: LIN28B_X0_let7_transfection_Total_RNA_Human; Homo sapiens; RNA-Seq
Sample: SRS2854849
BioProject: PRJNA430874
BioSample: SAMN08379286
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: LIN28B_X0_let7_transfection_Total_RNA_Human
cell line: HEK293A
Original files (1)
LIN28B_X0_let7_transfection_Total_RNA_Human
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6497085 51344176 2567208800 857.62 b8p37_a9_input_let7_S1_L003_R1_001.fastq.gz, SRR6497085, SRR6497085.s… SRA

Linked Publications (2)

Non-microRNA binding competitively inhibits LIN28 regulation.
Cell reports · 2021
A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.
Molecular cell · 2019

Potentially Related Publications (3)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.
Nature methods · 2021
Non-microRNA binding competitively inhibits LIN28 regulation.
Cell reports · 2021
A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.
Molecular cell · 2019

Data Files (71)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— b8p100_smallrnaseq_hek293_ko_l7_total_S23_L002_R1_001.… ncRNA-Seq 457.6 MB link
— b8p100_smallrnaseq_hek293_ko_wt_total_S21_L002_R1_001.… ncRNA-Seq 563.8 MB link
— b8p100_smallrnaseq_hek293_x3_l7_total_S24_L002_R1_001.… ncRNA-Seq 509.1 MB link
— b8p100_smallrnaseq_hek293_x3_wt_total_S22_L002_R1_001.… ncRNA-Seq 617.8 MB link
— SRR6497077_GSM2942735 ncRNA-Seq 457.0 MB link
— SRR6497079 ncRNA-Seq 563.8 MB link
— SRR6497079_GSM2942737 ncRNA-Seq 563.0 MB link
— SRR6497081 ncRNA-Seq 509.1 MB link
— SRR6497081_GSM2942739 ncRNA-Seq 509.0 MB link
— SRR6497083 ncRNA-Seq 617.8 MB link
— SRR6497083_GSM2942741 ncRNA-Seq 617.0 MB link
— b8p37_a9_polysome_let7_S6_L003_R1_001.fastq.gz OTHER 274.7 MB link
— b8p37_a9_polysome_S16_L004_R1_001.fastq.gz OTHER 279.9 MB link
— b8p37_x1_polysome_S17_L004_R1_001.fastq.gz OTHER 284.3 MB link
— b8p37_x2_polysome_S18_L004_R1_001.fastq.gz OTHER 214.5 MB link
— b8p37_x3_polysome_S19_L004_R1_001.fastq.gz OTHER 344.3 MB link
— b8p37_x4_polysome_S20_L004_R1_001.fastq.gz OTHER 255.7 MB link
— PX0_S52_L006_R1_001.fastq.gz OTHER 1.8 GB link
— PX1_S53_L006_R1_001.fastq.gz OTHER 1.5 GB link
— PX2_S54_L006_R1_001.fastq.gz OTHER 1.7 GB link
— PX3_S55_L006_R1_001.fastq.gz OTHER 1.7 GB link
— PX4_S56_L006_R1_001.fastq.gz OTHER 1.5 GB link
— PX4_S56_L006_R2_001.fastq.gz OTHER 1.5 GB link
— SRR6497056_GSM2942714 OTHER 279.0 MB link
— SRR6497057_GSM2942715 OTHER 284.0 MB link
— SRR6497058 OTHER 214.5 MB link
— SRR6497058_GSM2942716 OTHER 214.0 MB link
— SRR6497059 OTHER 344.3 MB link
— SRR6497059_GSM2942717 OTHER 344.0 MB link
— SRR6497060 OTHER 255.7 MB link
— SRR6497060_GSM2942718 OTHER 255.0 MB link
— SRR6497066_GSM2942724 OTHER 1.8 GB link
— SRR6497067_GSM2942725 OTHER 1.5 GB link
— SRR6497068_GSM2942726 OTHER 1.7 GB link
— SRR6497069_GSM2942727 OTHER 1.7 GB link
— SRR6497070_GSM2942728 OTHER 1.5 GB link
— SRR6497084_GSM2942742 OTHER 274.0 MB link
— b8p100_smallrnaseq_hek293_ko_l7_ip_S27_L002_R1_001.fas… RIP-Seq 335.9 MB link
— b8p100_smallrnaseq_hek293_ko_wt_ip_S25_L002_R1_001.fas… RIP-Seq 304.6 MB link
— b8p100_smallrnaseq_hek293_x3_l7_ip_S28_L002_R1_001.fas… RIP-Seq 241.0 MB link
— b8p100_smallrnaseq_hek293_x3_wt_ip_S26_L002_R1_001.fas… RIP-Seq 341.6 MB link
— SRR6497076_GSM2942734 RIP-Seq 335.0 MB link
— SRR6497078_GSM2942736 RIP-Seq 304.0 MB link
— SRR6497080_GSM2942738 RIP-Seq 241.0 MB link
— SRR6497082_GSM2942740 RIP-Seq 341.0 MB link
— b8p37_a9_input_let7_S1_L003_R1_001.fastq.gz RNA-Seq 857.6 MB link
— b8p37_a9_input_S11_L004_R1_001.fastq.gz RNA-Seq 912.5 MB link
— b8p37_x1_input_S12_L004_R1_001.fastq.gz RNA-Seq 862.4 MB link
— b8p37_x2_input_S13_L004_R1_001.fastq.gz RNA-Seq 1.2 GB link
— b8p37_x3_input_S14_L004_R1_001.fastq.gz RNA-Seq 1.2 GB link
— b8p37_x4_input_S15_L004_R1_001.fastq.gz RNA-Seq 987.2 MB link
— SRR6497061_GSM2942719 RNA-Seq 912.0 MB link
— SRR6497062_GSM2942720 RNA-Seq 862.0 MB link
— SRR6497063_GSM2942721 RNA-Seq 1.2 GB link
— SRR6497064_GSM2942722 RNA-Seq 1.2 GB link
— SRR6497065_GSM2942723 RNA-Seq 987.0 MB link
— SRR6497071 RNA-Seq 2.0 GB link
— SRR6497071_GSM2942729 RNA-Seq 2.0 GB link
— SRR6497072_GSM2942730 RNA-Seq 1.4 GB link
— SRR6497073_GSM2942731 RNA-Seq 1.3 GB link
— SRR6497074 RNA-Seq 1.6 GB link
— SRR6497074_GSM2942732 RNA-Seq 1.6 GB link
— SRR6497075 RNA-Seq 1.8 GB link
— SRR6497075_GSM2942733 RNA-Seq 1.8 GB link
— SRR6497085 RNA-Seq 857.6 MB link
— SRR6497085_GSM2942743 RNA-Seq 857.0 MB link
— TX0_S47_L006_R1_001.fastq.gz RNA-Seq 2.0 GB link
— TX1_S48_L006_R1_001.fastq.gz RNA-Seq 1.4 GB link
— TX2_S49_L006_R1_001.fastq.gz RNA-Seq 1.3 GB link
— TX3_S50_L006_R1_001.fastq.gz RNA-Seq 1.6 GB link
— TX4_S51_L006_R1_001.fastq.gz RNA-Seq 1.8 GB link