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GSE78959

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Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Cell Model]

Organism: Homo sapiens
Platform: GPL16791
Samples: 24
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Mar 07 2016
Last Updated: May 15 2019
Status: Public on Jul 25 2016
Contact: Jitao David,,Zhang (F. Hoffmann-La Roche)

Relations

SubSeries of: GSE78961 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA314508 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP071232

Summary

Tuberous sclerosis complex (TSC) is a rare genetic disease characterized by mTOR hyperfunction induced benign tumor growths in multiple organs and neurological symptoms. Because the molecular pathology is highly complex and the etiology poorly understood we employed a defined human neuronal model with a single mTOR activating mutation to dissect the disease-relevant molecular responses driving the neuropathology. TSC2 deficient neural stem cells showed severely reduced neuronal functional maturation and characteristics of astrogliosis instead. Accordingly, transcriptome analysis uncovered an inflammatory response and increased metabolic activity, while ribosome profiling revealed excessive translation of ribosomal transcripts and higher synthesis rates of angiogenic growth factors. Treatment with mTOR inhibitors corrected translational alterations but not transcriptional dysfunction. These results extend our understanding of the molecular pathophysiology of TSC brain lesions, and suggest phenotype-tailored pharmacological treatment strategies.

Overall Design

Two TSC+/- cell lines and two TSC-/- cell lines were independently generated from wild-type human embryonic stem cells by genome editting with zinc finger nucleases. Two cell lines were handled in the same way but without any known human gene editted and they are used as negative controls. Two independent biological replicates of each of the six cell lines are profiled with ribosome profiling technique.

Analysis (3 steps)

View Data Processing
Processing steps for GSE78959
  1. Linker tags were removed from RNA sequencing and ribosome profiling reads by the FASTX Toolkit, v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/)
  2. All reads that mapped to rRNAs, tRNAs or mitochondrial rRNAs were removed, and the remaining reads were mapped to RefSeq (v38) by TopHat v2.0.13.
  3. Finally all read counts that mapped uniquely to genes were extracted for expression analysis with the help of samtools, v1.1.

Supplementary Files (2)

GSE78959_TSC2-cellModel_RNA.txt.gz Download
GSE78959_TSC2-cellModel_RPF.txt.gz Download
GEO Samples (24)

Dataset Citations (1)

Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model.
PMID 27655340 · 2016 · Genome medicine
Nils Grabole, Jitao David Zhang, Stefan Aigner, Nadine Ruderisch, Veronica Costa, Felix C Weber, Michel Theron, Nikolaos Berntenis, Olivia Spleiss, Martin Ebeling, Gene W Yeo, Ravi Jagasia, Anna Kiialainen

SRA Experiments (24) and Runs (24)

Total: 27361 MB
SRX1617533 SRP071232 RNA-Seq SINGLE
GSM2082509: Total RNA of TSC2+/+ control generated from hESC cell line 2, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326936
BioProject: PRJNA314508
BioSample: SAMN04536260
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/+ control generated from hESC cell line 2, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/+
parental cell line id: hESC.2
assayed molecule: mRNA
Original files (1)
TSC2+/+ control generated from hESC cell line 2, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208852 27206936 1387553736 829.0 2T15_ATCACG_L002_R1_001.fastq.gz, SRR3208852, SRR3208852.sralite SRA
SRX1617534 SRP071232 RNA-Seq SINGLE
GSM2082510: Total RNA of TSC2+/+ control generated from hESC cell line 2, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326937
BioProject: PRJNA314508
BioSample: SAMN04536261
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/+ control generated from hESC cell line 2, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/+
parental cell line id: hESC.2
assayed molecule: mRNA
Original files (1)
TSC2+/+ control generated from hESC cell line 2, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208853 27598129 1407504579 837.08 2T16_CGATGT_L002_R1_001.fastq.gz, SRR3208853, SRR3208853.sralite SRA
SRX1617535 SRP071232 RNA-Seq SINGLE
GSM2082511: Total RNA of TSC2+/- cell line generated from hESC cell line 2, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326935
BioProject: PRJNA314508
BioSample: SAMN04536262
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/- cell line generated from hESC cell line 2, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/-
parental cell line id: hESC.2
assayed molecule: mRNA
Original files (1)
TSC2+/- cell line generated from hESC cell line 2, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208854 26937206 1373797506 820.74 2T17_TTAGGC_L002_R1_001.fastq.gz, SRR3208854, SRR3208854.sralite SRA
SRX1617536 SRP071232 RNA-Seq SINGLE
GSM2082512: Total RNA of TSC2+/- cell line generated from hESC cell line 2, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326934
BioProject: PRJNA314508
BioSample: SAMN04536263
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/- cell line generated from hESC cell line 2, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/-
parental cell line id: hESC.2
assayed molecule: mRNA
Original files (1)
TSC2+/- cell line generated from hESC cell line 2, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208855 29132915 1485778665 888.67 2T18_TGACCA_L002_R1_001.fastq.gz, SRR3208855, SRR3208855.sralite SRA
SRX1617537 SRP071232 RNA-Seq SINGLE
GSM2082513: Total RNA of TSC2-/- cell line generated from hESC cell line 2, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326933
BioProject: PRJNA314508
BioSample: SAMN04536264
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2-/- cell line generated from hESC cell line 2, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2-/-
parental cell line id: hESC.2
assayed molecule: mRNA
Original files (1)
TSC2-/- cell line generated from hESC cell line 2, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208856 27274066 1390977366 835.99 2T19_GCCAAT_L002_R1_001.fastq.gz, SRR3208856, SRR3208856.sralite SRA
SRX1617538 SRP071232 RNA-Seq SINGLE
GSM2082514: Total RNA of TSC2-/- cell line generated from hESC cell line 2, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326932
BioProject: PRJNA314508
BioSample: SAMN04536265
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2-/- cell line generated from hESC cell line 2, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2-/-
parental cell line id: hESC.2
assayed molecule: mRNA
Original files (1)
TSC2-/- cell line generated from hESC cell line 2, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208857 24345466 1241618766 741.58 2T20_CTTGTA_L002_R1_001.fastq.gz, SRR3208857, SRR3208857.sralite SRA
SRX1617539 SRP071232 RNA-Seq SINGLE
GSM2082515: Total RNA of TSC2+/+ control generated from hESC cell line 3, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326930
BioProject: PRJNA314508
BioSample: SAMN04536266
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/+ control generated from hESC cell line 3, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/+
parental cell line id: hESC.3
assayed molecule: mRNA
Original files (1)
TSC2+/+ control generated from hESC cell line 3, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208858 31884822 1626125922 1005.62 3T15_ATCACG_L003_R1_001.fastq.gz, SRR3208858, SRR3208858.sralite SRA
SRX1617540 SRP071232 RNA-Seq SINGLE
GSM2082516: Total RNA of TSC2+/+ control generated from hESC cell line 3, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326931
BioProject: PRJNA314508
BioSample: SAMN04536267
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/+ control generated from hESC cell line 3, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/+
parental cell line id: hESC.3
assayed molecule: mRNA
Original files (1)
TSC2+/+ control generated from hESC cell line 3, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208859 30832779 1572471729 983.51 3T16_CGATGT_L003_R1_001.fastq.gz, SRR3208859, SRR3208859.sralite SRA
SRX1617541 SRP071232 RNA-Seq SINGLE
GSM2082517: Total RNA of TSC2+/- cell line generated from hESC cell line 3, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326929
BioProject: PRJNA314508
BioSample: SAMN04536268
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/- cell line generated from hESC cell line 3, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/-
parental cell line id: hESC.3
assayed molecule: mRNA
Original files (1)
TSC2+/- cell line generated from hESC cell line 3, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208860 33453490 1706127990 1052.41 3T17_TTAGGC_L003_R1_001.fastq.gz, SRR3208860, SRR3208860.sralite SRA
SRX1617542 SRP071232 RNA-Seq SINGLE
GSM2082518: Total RNA of TSC2+/- cell line generated from hESC cell line 3, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326928
BioProject: PRJNA314508
BioSample: SAMN04536269
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/- cell line generated from hESC cell line 3, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/-
parental cell line id: hESC.3
assayed molecule: mRNA
Original files (1)
TSC2+/- cell line generated from hESC cell line 3, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208861 31558788 1609498188 989.34 3T18_TGACCA_L003_R1_001.fastq.gz, SRR3208861, SRR3208861.sralite SRA
SRX1617543 SRP071232 RNA-Seq SINGLE
GSM2082519: Total RNA of TSC2-/- cell line generated from hESC cell line 3, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326927
BioProject: PRJNA314508
BioSample: SAMN04536270
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2-/- cell line generated from hESC cell line 3, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2-/-
parental cell line id: hESC.3
assayed molecule: mRNA
Original files (1)
TSC2-/- cell line generated from hESC cell line 3, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208862 35240391 1797259941 1112.53 3T19_GCCAAT_L003_R1_001.fastq.gz, SRR3208862, SRR3208862.sralite SRA
SRX1617544 SRP071232 RNA-Seq SINGLE
GSM2082520: Total RNA of TSC2-/- cell line generated from hESC cell line 3, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326926
BioProject: PRJNA314508
BioSample: SAMN04536271
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2-/- cell line generated from hESC cell line 3, total RNA
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2-/-
parental cell line id: hESC.3
assayed molecule: mRNA
Original files (1)
TSC2-/- cell line generated from hESC cell line 3, total RNA
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208863 31494149 1606201599 993.79 3T20_CTTGTA_L003_R1_001.fastq.gz, SRR3208863, SRR3208863.sralite SRA
SRX1617545 SRP071232 RNA-Seq SINGLE
GSM2082521: Ribosome protected fragments (RPF) of TSC2+/+ control generated from hESC cell line 2, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326925
BioProject: PRJNA314508
BioSample: SAMN04536272
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/+ control generated from hESC cell line 2, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/+
parental cell line id: hESC.2
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2+/+ control generated from hESC cell line 2, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208864 38379872 1957373472 1153.9 2R15_CAGATC_L005_R1_001.fastq.gz, SRR3208864, SRR3208864.sralite SRA
SRX1617546 SRP071232 RNA-Seq SINGLE
GSM2082522: Ribosome protected fragments (RPF) of TSC2+/+ control generated from hESC cell line 2, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326924
BioProject: PRJNA314508
BioSample: SAMN04536273
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/+ control generated from hESC cell line 2, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/+
parental cell line id: hESC.2
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2+/+ control generated from hESC cell line 2, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208865 39165304 1997430504 1178.09 2R16_CTTGTA_L005_R1_001.fastq.gz, SRR3208865, SRR3208865.sralite SRA
SRX1617547 SRP071232 RNA-Seq SINGLE
GSM2082523: Ribosome protected fragments (RPF) of TSC2+/- cell line generated from hESC cell line 2, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326923
BioProject: PRJNA314508
BioSample: SAMN04536274
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/- cell line generated from hESC cell line 2, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/-
parental cell line id: hESC.2
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2+/- cell line generated from hESC cell line 2, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208866 41927164 2138285364 1283.45 2R17_ACAGTG_L006_R1_001.fastq.gz, SRR3208866, SRR3208866.sralite SRA
SRX1617548 SRP071232 RNA-Seq SINGLE
GSM2082524: Ribosome protected fragments (RPF) of TSC2+/- cell line generated from hESC cell line 2, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326922
BioProject: PRJNA314508
BioSample: SAMN04536275
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/- cell line generated from hESC cell line 2, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/-
parental cell line id: hESC.2
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2+/- cell line generated from hESC cell line 2, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208867 40751703 2078336853 1256.87 2R18_GCCAAT_L006_R1_001.fastq.gz, SRR3208867, SRR3208867.sralite SRA
SRX1617549 SRP071232 RNA-Seq SINGLE
GSM2082525: Ribosome protected fragments (RPF) of TSC2-/- cell line generated from hESC cell line 2, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326920
BioProject: PRJNA314508
BioSample: SAMN04536276
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2-/- cell line generated from hESC cell line 2, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2-/-
parental cell line id: hESC.2
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2-/- cell line generated from hESC cell line 2, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208868 39809441 2030281491 1219.23 2R19_CAGATC_L006_R1_001.fastq.gz, SRR3208868, SRR3208868.sralite SRA
SRX1617550 SRP071232 RNA-Seq SINGLE
GSM2082526: Ribosome protected fragments (RPF) of TSC2-/- cell line generated from hESC cell line 2, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326921
BioProject: PRJNA314508
BioSample: SAMN04536277
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2-/- cell line generated from hESC cell line 2, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2-/-
parental cell line id: hESC.2
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2-/- cell line generated from hESC cell line 2, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208869 44599672 2274583272 1363.94 2R20_CTTGTA_L006_R1_001.fastq.gz, SRR3208869, SRR3208869.sralite SRA
SRX1617551 SRP071232 RNA-Seq SINGLE
GSM2082527: Ribosome protected fragments (RPF) of TSC2+/+ control generated from hESC cell line 3, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326919
BioProject: PRJNA314508
BioSample: SAMN04536278
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/+ control generated from hESC cell line 3, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/+
parental cell line id: hESC.3
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2+/+ control generated from hESC cell line 3, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208870 51303099 2616458049 1588.19 3R15_ACAGTG_L007_R1_001.fastq.gz, SRR3208870, SRR3208870.sralite SRA
SRX1617552 SRP071232 RNA-Seq SINGLE
GSM2082528: Ribosome protected fragments (RPF) of TSC2+/+ control generated from hESC cell line 3, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326918
BioProject: PRJNA314508
BioSample: SAMN04536279
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/+ control generated from hESC cell line 3, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/+
parental cell line id: hESC.3
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2+/+ control generated from hESC cell line 3, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208871 45979423 2344950573 1420.29 3R16_GCCAAT_L007_R1_001.fastq.gz, SRR3208871, SRR3208871.sralite SRA
SRX1617553 SRP071232 RNA-Seq SINGLE
GSM2082529: Ribosome protected fragments (RPF) of TSC2+/- cell line generated from hESC cell line 3, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326942
BioProject: PRJNA314508
BioSample: SAMN04536280
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/- cell line generated from hESC cell line 3, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/-
parental cell line id: hESC.3
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2+/- cell line generated from hESC cell line 3, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208872 46269146 2359726446 1462.3 3R17_CAGATC_L007_R1_001.fastq.gz, SRR3208872, SRR3208872.sralite SRA
SRX1617554 SRP071232 RNA-Seq SINGLE
GSM2082530: Ribosome protected fragments (RPF) of TSC2+/- cell line generated from hESC cell line 3, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326941
BioProject: PRJNA314508
BioSample: SAMN04536281
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2+/- cell line generated from hESC cell line 3, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2+/-
parental cell line id: hESC.3
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2+/- cell line generated from hESC cell line 3, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208873 40130053 2046632703 1219.47 3R18_CTTGTA_L007_R1_001.fastq.gz, SRR3208873, SRR3208873.sralite SRA
SRX1617555 SRP071232 RNA-Seq SINGLE
GSM2082531: Ribosome protected fragments (RPF) of TSC2-/- cell line generated from hESC cell line 3, Biological Replicate 1; Homo sapiens; RNA-Seq
Sample: SRS1326940
BioProject: PRJNA314508
BioSample: SAMN04536282
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2-/- cell line generated from hESC cell line 3, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2-/-
parental cell line id: hESC.3
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2-/- cell line generated from hESC cell line 3, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208874 50196119 2560002069 1600.04 3R19_ACAGTG_L008_R1_001.fastq.gz, SRR3208874, SRR3208874.sralite SRA
SRX1617556 SRP071232 RNA-Seq SINGLE
GSM2082532: Ribosome protected fragments (RPF) of TSC2-/- cell line generated from hESC cell line 3, Biological Replicate 2; Homo sapiens; RNA-Seq
Sample: SRS1326939
BioProject: PRJNA314508
BioSample: SAMN04536283
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: TSC2-/- cell line generated from hESC cell line 3, RPF
cell type: Embryonic stem cell-derived neurons
genotype/variation: TSC2-/-
parental cell line id: hESC.3
assayed molecule: Ribosome protected fragments
Original files (1)
TSC2-/- cell line generated from hESC cell line 3, RPF
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR3208875 47853945 2440551195 1524.68 3R20_GCCAAT_L008_R1_001.fastq.gz, SRR3208875, SRR3208875.sralite SRA

Linked Publications (1)

Data Files (25)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
2R15_CAGATC_L005_R1_001.fastq.gz RNA-Seq 1.1 GB link
2R16_CTTGTA_L005_R1_001.fastq.gz RNA-Seq 1.2 GB link
2R17_ACAGTG_L006_R1_001.fastq.gz RNA-Seq 1.3 GB link
2R18_GCCAAT_L006_R1_001.fastq.gz RNA-Seq 1.2 GB link
2R19_CAGATC_L006_R1_001.fastq.gz RNA-Seq 1.2 GB link
2R20_CTTGTA_L006_R1_001.fastq.gz RNA-Seq 1.3 GB link
2T15_ATCACG_L002_R1_001.fastq.gz RNA-Seq 829.0 MB link
2T16_CGATGT_L002_R1_001.fastq.gz RNA-Seq 837.1 MB link
2T17_TTAGGC_L002_R1_001.fastq.gz RNA-Seq 820.7 MB link
2T17_TTAGGC_L002_R1_001.fastq.gz RNA-Seq 820.7 MB link
2T18_TGACCA_L002_R1_001.fastq.gz RNA-Seq 888.7 MB link
2T19_GCCAAT_L002_R1_001.fastq.gz RNA-Seq 836.0 MB link
2T20_CTTGTA_L002_R1_001.fastq.gz RNA-Seq 741.6 MB link
3R15_ACAGTG_L007_R1_001.fastq.gz RNA-Seq 1.6 GB link
3R16_GCCAAT_L007_R1_001.fastq.gz RNA-Seq 1.4 GB link
3R17_CAGATC_L007_R1_001.fastq.gz RNA-Seq 1.4 GB link
3R18_CTTGTA_L007_R1_001.fastq.gz RNA-Seq 1.2 GB link
3R19_ACAGTG_L008_R1_001.fastq.gz RNA-Seq 1.6 GB link
3R20_GCCAAT_L008_R1_001.fastq.gz RNA-Seq 1.5 GB link
3T15_ATCACG_L003_R1_001.fastq.gz RNA-Seq 1005.6 MB link
3T16_CGATGT_L003_R1_001.fastq.gz RNA-Seq 983.5 MB link
3T17_TTAGGC_L003_R1_001.fastq.gz RNA-Seq 1.0 GB link
3T18_TGACCA_L003_R1_001.fastq.gz RNA-Seq 989.3 MB link
3T19_GCCAAT_L003_R1_001.fastq.gz RNA-Seq 1.1 GB link
3T20_CTTGTA_L003_R1_001.fastq.gz RNA-Seq 993.8 MB link