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GSE106493

GSE GEO
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Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

Organism: Homo sapiens
Platform: GPL11154
Samples: 27
Experiment Types:
Other
Submitted: Nov 03 2017
Last Updated: May 24 2019
Status: Public on Dec 14 2017
Contact: William,,Mallard (Harvard University)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA417050 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP123582

Summary

The spatial organization of RNA within cells is a crucial factor influencing a wide range of biological functions throughout all kingdoms of life. However, a general understanding of RNA localization has been hindered by a lack of simple, high-throughput methods for mapping the transcriptomes of subcellular compartments. Here, we develop such a method, termed APEX-RIP, which combines peroxidase-catalyzed, spatially restricted in situ protein biotinylation with RNA-protein chemical crosslinking. We demonstrate that, using a single protocol, APEX-RIP can isolate RNAs from a variety of subcellular compartments, including the mitochondrial matrix, nucleus, bulk cytosol, and endoplasmic reticulum (ER), with specificity and sensitivity that rival or exceed those of conventional approaches. We further identify candidate RNAs localized to mitochondria-ER junctions and nuclear lamina, two compartments that are recalcitrant to classical biochemical purification. Since APEX-RIP is simple, versatile, and does not require special instrumentation, we envision its broad application in a variety of biological contexts.

Overall Design

27 samples total, from five experimental courses (negative controls, and mitochondrial, nuclear, cytosolic, and endoplasmic reticulum-targeted APEX-RIP). Negative controls: 4 samples (2 replicates, with paired inputs and mock RIPs); Mitochondrial APEX-RIP: 6 samples (3 replicates, with paired inputs and RIPs); Nuclear APEX-RIP: 6 samples (3 replicates, with paired inputs and RIPs); Cytosolic APEX-RIP: 6 samples (6 replicates, with paired inputs and RIPs); ER-targeted APEX-RIP ("KDEL"): 4 samples (2 replicates, with paired inputs and RIPs).

Analysis (4 steps)

View Data Processing
Processing steps for GSE106493
  1. Reads were mapped to human genome using TopHat v2.1.1 with the flags, "--no-coverage-search" and "--GTF gencode.v19.annotation.gtf".
  2. Gene expression was quantified against the Gencode v19 reference transcriptome (gencode.v19.annotation.gtf, genecodegenes.org) with Cufflinks v2.2.1.
  3. The statistical significance of differential expression was assessed using CuffDiff2, with the flags, "--dispersion-method per-condition" and "--seed 42".
  4. ROC analysis was perfomed in Microsoft Excel, using true positive and false positive gene lists culled from the literature.

Supplementary Files (4)

GSE106493_KDEL-HRP.gene_exp.diff.gz Download
GSE106493_Mito-APEX2.gene_exp.diff.gz Download
GSE106493_NES-APEX2.gene_exp.diff.gz Download
GSE106493_NLS-APEX2.gene_exp.diff.gz Download
GEO Samples (27)
GSM2838982 GSM2838983 GSM2838984 GSM2838985 GSM2838986 GSM2838987 GSM2838988 GSM2838989 GSM2838990 GSM2838991 GSM2838992 GSM2838993 GSM2838994 GSM2838995 GSM2838996 GSM2838997 GSM2838998 GSM2838999 GSM2839000 GSM2839001 GSM2839002 GSM2839003 GSM2839004 GSM2839005 GSM2839006 GSM2839007 GSM2839008

Dataset Citations (1)

PubMed citation (PMID 29239719)

SRA Experiments (27) and Runs (54)

Total: 45858 MB
SRX3359940 SRP123582 RIP-Seq PAIRED
GSM2838982: Mito_Input_rep1; Homo sapiens; RIP-Seq
Sample: SRS2658903
BioProject: PRJNA417050
BioSample: SAMN07975327
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: Mito-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253019 12560521 1256052100 698.73 JR1072__Mito-APEX2_Input_rep1.R1.Lane1.fastq.gz, JR1072__Mito-APEX2_I… SRA
SRR6253020 12163553 1216355300 673.79 JR1072__Mito-APEX2_Input_rep1.R1.Lane2.fastq.gz, JR1072__Mito-APEX2_I… SRA
SRX3359941 SRP123582 RIP-Seq PAIRED
GSM2838983: Mito_Input_rep2; Homo sapiens; RIP-Seq
Sample: SRS2658904
BioProject: PRJNA417050
BioSample: SAMN07975353
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: Mito-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253021 13196454 1319645400 739.46 JR1073__Mito-APEX2_Input_rep2.R2.Lane1.fastq.gz, SRR6253021, SRR62530… SRA
SRR6253022 12752760 1275276000 710.77 JR1073__Mito-APEX2_Input_rep2.R1.Lane2.fastq.gz, JR1073__Mito-APEX2_I… SRA
SRX3359942 SRP123582 RIP-Seq PAIRED
GSM2838984: Mito_Input_rep3; Homo sapiens; RIP-Seq
Sample: SRS2658905
BioProject: PRJNA417050
BioSample: SAMN07975352
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: Mito-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253023 17184031 1718403100 954.04 JR1074__Mito-APEX2_Input_rep3.R1.Lane1.fastq.gz, JR1074__Mito-APEX2_I… SRA
SRR6253024 16643625 1664362500 920.03 JR1074__Mito-APEX2_Input_rep3.R1.Lane2.fastq.gz, JR1074__Mito-APEX2_I… SRA
SRX3359943 SRP123582 RIP-Seq PAIRED
GSM2838985: Mito_RIP_rep1; Homo sapiens; RIP-Seq
Sample: SRS2658907
BioProject: PRJNA417050
BioSample: SAMN07975351
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: Mito-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253025 15075869 1507586900 838.51 JR1075__Mito-APEX2_RIP_rep1.R1.Lane1.fastq.gz, JR1075__Mito-APEX2_RIP… SRA
SRR6253026 14640111 1464011100 811.18 JR1075__Mito-APEX2_RIP_rep1.R1.Lane2.fastq.gz, JR1075__Mito-APEX2_RIP… SRA
SRX3359944 SRP123582 RIP-Seq PAIRED
GSM2838986: Mito_RIP_rep2; Homo sapiens; RIP-Seq
Sample: SRS2658906
BioProject: PRJNA417050
BioSample: SAMN07975350
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: Mito-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253027 15842950 1584295000 891.59 JR1076__Mito-APEX2_RIP_rep2.R1.Lane1.fastq.gz, JR1076__Mito-APEX2_RIP… SRA
SRR6253028 15365806 1536580600 860.88 JR1076__Mito-APEX2_RIP_rep2.R2.Lane2.fastq.gz, SRR6253028, SRR6253028… SRA
SRX3359945 SRP123582 RIP-Seq PAIRED
GSM2838987: Mito_RIP_rep3; Homo sapiens; RIP-Seq
Sample: SRS2658908
BioProject: PRJNA417050
BioSample: SAMN07975349
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: Mito-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253029 12194091 1219409100 676.03 JR1077__Mito-APEX2_RIP_rep3.R1.Lane1.fastq.gz, JR1077__Mito-APEX2_RIP… SRA
SRR6253030 11822475 1182247500 652.96 JR1077__Mito-APEX2_RIP_rep3.R1.Lane2.fastq.gz, JR1077__Mito-APEX2_RIP… SRA
SRX3359946 SRP123582 RIP-Seq PAIRED
GSM2838988: Mito_Input_NegCtrl_rep1; Homo sapiens; RIP-Seq
Sample: SRS2658909
BioProject: PRJNA417050
BioSample: SAMN07975348
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: Mito-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253031 14336043 1433604300 803.11 JR1078__Mito-APEX2_Input_NegCtrl_rep1.R1.Lane1.fastq.gz, JR1078__Mito… SRA
SRR6253032 13895202 1389520200 774.45 JR1078__Mito-APEX2_Input_NegCtrl_rep1.R1.Lane2.fastq.gz, JR1078__Mito… SRA
SRX3359947 SRP123582 RIP-Seq PAIRED
GSM2838989: Mito_Input_NegCtrl_rep2; Homo sapiens; RIP-Seq
Sample: SRS2658911
BioProject: PRJNA417050
BioSample: SAMN07975347
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: Mito-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253033 16561497 1656149700 921.97 JR1079__Mito-APEX2_Input_NegCtrl_rep2.R1.Lane1.fastq.gz, JR1079__Mito… SRA
SRR6253034 16037637 1603763700 888.85 JR1079__Mito-APEX2_Input_NegCtrl_rep2.R1.Lane2.fastq.gz, JR1079__Mito… SRA
SRX3359948 SRP123582 RIP-Seq PAIRED
GSM2838990: Mito_RIP_NegCtrl_rep1; Homo sapiens; RIP-Seq
Sample: SRS2658910
BioProject: PRJNA417050
BioSample: SAMN07975346
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: Mito-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253035 11495253 1149525300 640.6 JR1080__Mito-APEX2_RIP_NegCtrl_rep1.R1.Lane1.fastq.gz, JR1080__Mito-A… SRA
SRR6253036 11111436 1111143600 616.64 JR1080__Mito-APEX2_RIP_NegCtrl_rep1.R1.Lane2.fastq.gz, JR1080__Mito-A… SRA
SRX3359949 SRP123582 RIP-Seq PAIRED
GSM2838991: Mito_RIP_NegCtrl_rep2; Homo sapiens; RIP-Seq
Sample: SRS2658912
BioProject: PRJNA417050
BioSample: SAMN07975345
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: Mito-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253037 11473718 1147371800 643.07 JR1081__Mito-APEX2_RIP_NegCtrl_rep2.R1.Lane1.fastq.gz, JR1081__Mito-A… SRA
SRR6253038 11158251 1115825100 622.61 JR1081__Mito-APEX2_RIP_NegCtrl_rep2.R1.Lane2.fastq.gz, JR1081__Mito-A… SRA
SRX3359950 SRP123582 RIP-Seq PAIRED
GSM2838992: KDEL_Input_rep1; Homo sapiens; RIP-Seq
Sample: SRS2658913
BioProject: PRJNA417050
BioSample: SAMN07975344
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: KDEL-HRP
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253039 14147612 1414761200 768.82 JR1260__KDEL-HRP_Input_rep1.R1.Lane1.fastq.gz, JR1260__KDEL-HRP_Input… SRA
SRR6253040 13778444 1377844400 746.75 JR1260__KDEL-HRP_Input_rep1.R2.Lane2.fastq.gz, SRR6253040, SRR6253040… SRA
SRX3359951 SRP123582 RIP-Seq PAIRED
GSM2838993: KDEL_Input_rep2; Homo sapiens; RIP-Seq
Sample: SRS2658914
BioProject: PRJNA417050
BioSample: SAMN07975343
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: KDEL-HRP
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253041 14817177 1481717700 802.62 JR1261__KDEL-HRP_Input_rep2.R1.Lane1.fastq.gz, JR1261__KDEL-HRP_Input… SRA
SRR6253042 14437124 1443712400 780.1 JR1261__KDEL-HRP_Input_rep2.R1.Lane2.fastq.gz, JR1261__KDEL-HRP_Input… SRA
SRX3359952 SRP123582 RIP-Seq PAIRED
GSM2838994: KDEL_Input_rep3; Homo sapiens; RIP-Seq
Sample: SRS2658915
BioProject: PRJNA417050
BioSample: SAMN07975342
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: KDEL-HRP
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253043 17796796 1779679600 968.42 JR1262__KDEL-HRP_Input_rep3.R1.Lane1.fastq.gz, JR1262__KDEL-HRP_Input… SRA
SRR6253044 17314765 1731476500 939.05 JR1262__KDEL-HRP_Input_rep3.R1.Lane2.fastq.gz, JR1262__KDEL-HRP_Input… SRA
SRX3359953 SRP123582 RIP-Seq PAIRED
GSM2838995: KDEL_RIP_rep1; Homo sapiens; RIP-Seq
Sample: SRS2658916
BioProject: PRJNA417050
BioSample: SAMN07975341
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: KDEL-HRP
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253045 12063183 1206318300 668.99 JR1264__KDEL-HRP_RIP_rep1.R2.Lane1.fastq.gz, SRR6253045, SRR6253045.s… SRA
SRR6253046 11762752 1176275200 650.66 JR1264__KDEL-HRP_RIP_rep1.R1.Lane2.fastq.gz, SRR6253046.sralite, SRR6… SRA
SRX3359954 SRP123582 RIP-Seq PAIRED
GSM2838996: KDEL_RIP_rep2; Homo sapiens; RIP-Seq
Sample: SRS2658918
BioProject: PRJNA417050
BioSample: SAMN07975340
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: KDEL-HRP
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253047 11077810 1107781000 612.65 JR1265__KDEL-HRP_RIP_rep2.R1.Lane1.fastq.gz, JR1265__KDEL-HRP_RIP_rep… SRA
SRR6253048 10852263 1085226300 598.89 JR1265__KDEL-HRP_RIP_rep2.R1.Lane2.fastq.gz, JR1265__KDEL-HRP_RIP_rep… SRA
SRX3359955 SRP123582 RIP-Seq PAIRED
GSM2838997: NLS_Input_rep1; Homo sapiens; RIP-Seq
Sample: SRS2658917
BioProject: PRJNA417050
BioSample: SAMN07975339
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NLS-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253049 13601006 1360100600 736.98 JR1266__NLS-APEX2_Input_rep1.R1.Lane1.fastq.gz, JR1266__NLS-APEX2_Inp… SRA
SRR6253050 13236162 1323616200 715.4 JR1266__NLS-APEX2_Input_rep1.R2.Lane2.fastq.gz, SRR6253050, SRR625305… SRA
SRX3359956 SRP123582 RIP-Seq PAIRED
GSM2838998: NLS_Input_rep2; Homo sapiens; RIP-Seq
Sample: SRS2658921
BioProject: PRJNA417050
BioSample: SAMN07975338
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NLS-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253051 13996213 1399621300 766.33 JR1267__NLS-APEX2_Input_rep2.R1.Lane1.fastq.gz, SRR6253051, SRR625305… SRA
SRR6253052 13640067 1364006700 744.5 JR1267__NLS-APEX2_Input_rep2.R1.Lane2.fastq.gz, JR1267__NLS-APEX2_Inp… SRA
SRX3359957 SRP123582 RIP-Seq PAIRED
GSM2838999: NLS_Input_rep3; Homo sapiens; RIP-Seq
Sample: SRS2658919
BioProject: PRJNA417050
BioSample: SAMN07975337
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NLS-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253053 14439052 1443905200 788.77 JR1268__NLS-APEX2_Input_rep3.R1.Lane1.fastq.gz, JR1268__NLS-APEX2_Inp… SRA
SRR6253054 14068156 1406815600 766.9 JR1268__NLS-APEX2_Input_rep3.R1.Lane2.fastq.gz, JR1268__NLS-APEX2_Inp… SRA
SRX3359958 SRP123582 RIP-Seq PAIRED
GSM2839000: NLS_RIP_rep1; Homo sapiens; RIP-Seq
Sample: SRS2658920
BioProject: PRJNA417050
BioSample: SAMN07975336
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NLS-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253055 20393659 2039365900 1156.85 JR1269__NLS-APEX2_RIP_rep1.R1.Lane1.fastq.gz, JR1269__NLS-APEX2_RIP_r… SRA
SRR6253056 20741064 2074106400 1180.0 JR1269__NLS-APEX2_RIP_rep1.R1.Lane2.fastq.gz, JR1269__NLS-APEX2_RIP_r… SRA
SRX3359959 SRP123582 RIP-Seq PAIRED
GSM2839001: NLS_RIP_rep2; Homo sapiens; RIP-Seq
Sample: SRS2658922
BioProject: PRJNA417050
BioSample: SAMN07975335
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NLS-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253057 15082100 1508210000 857.19 JR1270__NLS-APEX2_RIP_rep2.R1.Lane1.fastq.gz, SRR6253057, SRR6253057.… SRA
SRR6253058 15312756 1531275600 872.93 SRR6253058, SRR6253058.sralite, JR1270__NLS-APEX2_RIP_rep2.R2.Lane2.f… SRA
SRX3359960 SRP123582 RIP-Seq PAIRED
GSM2839002: NLS_RIP_rep3; Homo sapiens; RIP-Seq
Sample: SRS2658923
BioProject: PRJNA417050
BioSample: SAMN07975334
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NLS-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253059 16768281 1676828100 955.77 JR1271__NLS-APEX2_RIP_rep3.R1.Lane1.fastq.gz, JR1271__NLS-APEX2_RIP_r… SRA
SRR6253060 17076863 1707686300 976.1 JR1271__NLS-APEX2_RIP_rep3.R1.Lane2.fastq.gz, JR1271__NLS-APEX2_RIP_r… SRA
SRX3359961 SRP123582 RIP-Seq PAIRED
GSM2839003: NES_Input_rep1; Homo sapiens; RIP-Seq
Sample: SRS2658926
BioProject: PRJNA417050
BioSample: SAMN07975333
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NES-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253061 19042463 1904246300 1081.41 JR1272__NES-APEX2_Input_rep1.R1.Lane1.fastq.gz, JR1272__NES-APEX2_Inp… SRA
SRR6253062 19358792 1935879200 1102.58 JR1272__NES-APEX2_Input_rep1.R1.Lane2.fastq.gz, JR1272__NES-APEX2_Inp… SRA
SRX3359962 SRP123582 RIP-Seq PAIRED
GSM2839004: NES_Input_rep2; Homo sapiens; RIP-Seq
Sample: SRS2658924
BioProject: PRJNA417050
BioSample: SAMN07975332
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NES-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253063 18375126 1837512600 1057.15 JR1273__NES-APEX2_Input_rep2.R1.Lane1.fastq.gz, JR1273__NES-APEX2_Inp… SRA
SRR6253064 18702364 1870236400 1079.06 JR1273__NES-APEX2_Input_rep2.R1.Lane2.fastq.gz, JR1273__NES-APEX2_Inp… SRA
SRX3359963 SRP123582 RIP-Seq PAIRED
GSM2839005: NES_Input_rep3; Homo sapiens; RIP-Seq
Sample: SRS2658925
BioProject: PRJNA417050
BioSample: SAMN07975331
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NES-APEX2
input or rip: Input
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253065 17762445 1776244500 1011.13 JR1274__NES-APEX2_Input_rep3.R1.Lane1.fastq.gz, JR1274__NES-APEX2_Inp… SRA
SRR6253066 18097229 1809722900 1033.61 JR1274__NES-APEX2_Input_rep3.R1.Lane2.fastq.gz, SRR6253066, SRR625306… SRA
SRX3359964 SRP123582 RIP-Seq PAIRED
GSM2839006: NES_RIP_rep1; Homo sapiens; RIP-Seq
Sample: SRS2658927
BioProject: PRJNA417050
BioSample: SAMN07975330
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NES-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253067 17096346 1709634600 988.33 JR1275__NES-APEX2_RIP_rep1.R1.Lane1.fastq.gz, JR1275__NES-APEX2_RIP_r… SRA
SRR6253068 17347880 1734788000 1005.98 JR1275__NES-APEX2_RIP_rep1.R1.Lane2.fastq.gz, JR1275__NES-APEX2_RIP_r… SRA
SRX3359965 SRP123582 RIP-Seq PAIRED
GSM2839007: NES_RIP_rep2; Homo sapiens; RIP-Seq
Sample: SRS2658928
BioProject: PRJNA417050
BioSample: SAMN07975329
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NES-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253069 17850274 1785027400 1029.97 JR1276__NES-APEX2_RIP_rep2.R1.Lane1.fastq.gz, JR1276__NES-APEX2_RIP_r… SRA
SRR6253070 18147262 1814726200 1050.68 JR1276__NES-APEX2_RIP_rep2.R1.Lane2.fastq.gz, JR1276__NES-APEX2_RIP_r… SRA
SRX3359966 SRP123582 RIP-Seq PAIRED
GSM2839008: NES_RIP_rep3; Homo sapiens; RIP-Seq
Sample: SRS2658938
BioProject: PRJNA417050
BioSample: SAMN07975328
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T cells
cell line: HEK293T cells
expression construct: NES-APEX2
input or rip: RIP
Original files (1)
HEK293T cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR6253071 17587963 1758796300 1001.65 JR1277__NES-APEX2_RIP_rep3.R1.Lane1.fastq.gz, JR1277__NES-APEX2_RIP_r… SRA
SRR6253072 17904252 1790425200 1023.0 JR1277__NES-APEX2_RIP_rep3.R1.Lane2.fastq.gz, JR1277__NES-APEX2_RIP_r… SRA

Linked Publications (1)

Transcriptome regulation by PARP13 in basal and antiviral states in human cells.
iScience · 2024

Data Files (54)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— JR1072__Mito-APEX2_Input_rep1.R1.Lane1.fastq.gz RIP-Seq 698.7 MB link
— JR1072__Mito-APEX2_Input_rep1.R1.Lane2.fastq.gz RIP-Seq 673.8 MB link
— JR1073__Mito-APEX2_Input_rep2.R1.Lane2.fastq.gz RIP-Seq 710.8 MB link
— JR1073__Mito-APEX2_Input_rep2.R2.Lane1.fastq.gz RIP-Seq 739.5 MB link
— JR1074__Mito-APEX2_Input_rep3.R1.Lane1.fastq.gz RIP-Seq 954.0 MB link
— JR1074__Mito-APEX2_Input_rep3.R1.Lane2.fastq.gz RIP-Seq 920.0 MB link
— JR1075__Mito-APEX2_RIP_rep1.R1.Lane1.fastq.gz RIP-Seq 838.5 MB link
— JR1075__Mito-APEX2_RIP_rep1.R1.Lane2.fastq.gz RIP-Seq 811.2 MB link
— JR1076__Mito-APEX2_RIP_rep2.R1.Lane1.fastq.gz RIP-Seq 891.6 MB link
— JR1076__Mito-APEX2_RIP_rep2.R2.Lane2.fastq.gz RIP-Seq 860.9 MB link
— JR1077__Mito-APEX2_RIP_rep3.R1.Lane1.fastq.gz RIP-Seq 676.0 MB link
— JR1077__Mito-APEX2_RIP_rep3.R1.Lane2.fastq.gz RIP-Seq 653.0 MB link
— JR1078__Mito-APEX2_Input_NegCtrl_rep1.R1.Lane1.fastq.gz RIP-Seq 803.1 MB link
— JR1078__Mito-APEX2_Input_NegCtrl_rep1.R1.Lane2.fastq.gz RIP-Seq 774.4 MB link
— JR1079__Mito-APEX2_Input_NegCtrl_rep2.R1.Lane1.fastq.gz RIP-Seq 922.0 MB link
— JR1079__Mito-APEX2_Input_NegCtrl_rep2.R1.Lane2.fastq.gz RIP-Seq 888.8 MB link
— JR1080__Mito-APEX2_RIP_NegCtrl_rep1.R1.Lane1.fastq.gz RIP-Seq 640.6 MB link
— JR1080__Mito-APEX2_RIP_NegCtrl_rep1.R1.Lane2.fastq.gz RIP-Seq 616.6 MB link
— JR1081__Mito-APEX2_RIP_NegCtrl_rep2.R1.Lane1.fastq.gz RIP-Seq 643.1 MB link
— JR1081__Mito-APEX2_RIP_NegCtrl_rep2.R1.Lane2.fastq.gz RIP-Seq 622.6 MB link
— JR1260__KDEL-HRP_Input_rep1.R1.Lane1.fastq.gz RIP-Seq 768.8 MB link
— JR1260__KDEL-HRP_Input_rep1.R2.Lane2.fastq.gz RIP-Seq 746.8 MB link
— JR1261__KDEL-HRP_Input_rep2.R1.Lane1.fastq.gz RIP-Seq 802.6 MB link
— JR1261__KDEL-HRP_Input_rep2.R1.Lane2.fastq.gz RIP-Seq 780.1 MB link
— JR1262__KDEL-HRP_Input_rep3.R1.Lane1.fastq.gz RIP-Seq 968.4 MB link
— JR1262__KDEL-HRP_Input_rep3.R1.Lane2.fastq.gz RIP-Seq 939.0 MB link
— JR1264__KDEL-HRP_RIP_rep1.R1.Lane2.fastq.gz RIP-Seq 650.7 MB link
— JR1264__KDEL-HRP_RIP_rep1.R2.Lane1.fastq.gz RIP-Seq 669.0 MB link
— JR1265__KDEL-HRP_RIP_rep2.R1.Lane1.fastq.gz RIP-Seq 612.6 MB link
— JR1265__KDEL-HRP_RIP_rep2.R1.Lane2.fastq.gz RIP-Seq 598.9 MB link
— JR1266__NLS-APEX2_Input_rep1.R1.Lane1.fastq.gz RIP-Seq 737.0 MB link
— JR1266__NLS-APEX2_Input_rep1.R2.Lane2.fastq.gz RIP-Seq 715.4 MB link
— JR1267__NLS-APEX2_Input_rep2.R1.Lane1.fastq.gz RIP-Seq 766.3 MB link
— JR1267__NLS-APEX2_Input_rep2.R1.Lane2.fastq.gz RIP-Seq 744.5 MB link
— JR1268__NLS-APEX2_Input_rep3.R1.Lane1.fastq.gz RIP-Seq 788.8 MB link
— JR1268__NLS-APEX2_Input_rep3.R1.Lane2.fastq.gz RIP-Seq 766.9 MB link
— JR1269__NLS-APEX2_RIP_rep1.R1.Lane1.fastq.gz RIP-Seq 1.1 GB link
— JR1269__NLS-APEX2_RIP_rep1.R1.Lane2.fastq.gz RIP-Seq 1.2 GB link
— JR1270__NLS-APEX2_RIP_rep2.R1.Lane1.fastq.gz RIP-Seq 857.2 MB link
— JR1271__NLS-APEX2_RIP_rep3.R1.Lane1.fastq.gz RIP-Seq 955.8 MB link
— JR1271__NLS-APEX2_RIP_rep3.R1.Lane2.fastq.gz RIP-Seq 976.1 MB link
— JR1272__NES-APEX2_Input_rep1.R1.Lane1.fastq.gz RIP-Seq 1.1 GB link
— JR1272__NES-APEX2_Input_rep1.R1.Lane2.fastq.gz RIP-Seq 1.1 GB link
— JR1273__NES-APEX2_Input_rep2.R1.Lane1.fastq.gz RIP-Seq 1.0 GB link
— JR1273__NES-APEX2_Input_rep2.R1.Lane2.fastq.gz RIP-Seq 1.1 GB link
— JR1274__NES-APEX2_Input_rep3.R1.Lane1.fastq.gz RIP-Seq 1011.1 MB link
— JR1274__NES-APEX2_Input_rep3.R1.Lane2.fastq.gz RIP-Seq 1.0 GB link
— JR1275__NES-APEX2_RIP_rep1.R1.Lane1.fastq.gz RIP-Seq 988.3 MB link
— JR1275__NES-APEX2_RIP_rep1.R1.Lane2.fastq.gz RIP-Seq 1006.0 MB link
— JR1276__NES-APEX2_RIP_rep2.R1.Lane1.fastq.gz RIP-Seq 1.0 GB link
— JR1276__NES-APEX2_RIP_rep2.R1.Lane2.fastq.gz RIP-Seq 1.0 GB link
— JR1277__NES-APEX2_RIP_rep3.R1.Lane1.fastq.gz RIP-Seq 1001.6 MB link
— JR1277__NES-APEX2_RIP_rep3.R1.Lane2.fastq.gz RIP-Seq 1023.0 MB link
— SRR6253058 RIP-Seq 872.9 MB link