title: 11-Mix-10-48: p53 & TGFBR2 siRNAs + IR

city: Seoul

first: Yoon-Jin

last: Lee

address: Nowon Gu

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: HUVEC

growth_protocol: HUVECs were cultured in Endothelial Cell Growth Medium 2 (Promocell).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Lexogen SENSE mRNA Library Preparation Kit standard protocols.

treatment_protocol: HUVECs were transfected with siRNAs using Lipofectamine 2000 (Invitrogen) and irradiated with gamma rays from a [137Cs] source at 3.81 Gy/min.

value: Human umbilical vein endothelial cells

tag: sirna transfection

value: p53 siRNA + TGFBR2 siRNA

tag: irradiation


title: Cultured L1210 cells [L1210serial_H09_S285]

status: Public on Oct 26 2018

type: SRA

city: Cambridge

first: Sanjay

last: Prakadan

state: MA

address: 77 Massachusetts Ave, E25-356

country: USA

institute: Massachusetts Institute of Technology

description:
L1210serial_H09_S285
l1210_rsem.txt

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
TopHat was used to align data
RSEM was used to generate estimates of transcripts per million reads for each single cell
Genome_build: human: hg19, mouse: mm10
Supplementary_files_format_and_content: cd8_rsem.txt: Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: gbmt_rsem.txt: Human Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: gbmut_rsem.txt: Human Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: l1201_rsem.txt: Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
Supplementary_files_format_and_content: fl5_rsem.txt: Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y

molecule: total RNA

organism: Mus musculus

source_name: Transcriptome of single L1210 leukemia cell following measurement with sSMR device

extract_protocol:
Smart-seq 2
Illumina Nextera XT

tag: cell type

value: Cultured L1210 cells


title: Cultured FL5.12 murine cells [FL51a_C01_S25]

description:
FL51a_C01_S25
fl5_rsem.txt

source_name: Transcriptome of single murine FL5.12 cell following measurement with sSMR device

value: Cultured FL5.12 murine cells


title: Cultured L1210 cells [L1210serial_H10_S286]

description:
L1210serial_H10_S286
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_H11_S287]

description:
L1210serial_H11_S287
l1210_rsem.txt


title: 9-p53-si-10-48: p53 siRNA + IR

organism: Homo sapiens

value: p53 siRNA


title: 10-TGFR-si-10-48: TGFBR2 siRNA + IR

value: TGFBR2 siRNA


title: Cultured L1210 cells [L1210serial_H08_S284]

description:
L1210serial_H08_S284
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_H06_S282]

description:
L1210serial_H06_S282
l1210_rsem.txt


title: 2-p53-si: p53 siRNA

value: No IR


title: 3-TGFR-si: TGFBR2 siRNA


title: Cultured L1210 cells [L1210serial_H07_S283]

description:
L1210serial_H07_S283
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_H05_S281]

description:
L1210serial_H05_S281
l1210_rsem.txt


title: 1-No-si: Control siRNA

value: Control siRNA


title: illu-HH1-2

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

description: YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression

library_source: genomic

data_processing:
Illumina HiSeq2500 single end sequencing
Sequenced reads were aligned to the hg19 genome assembly using the bowtie2 software suite with flag -X 2000
peak were called with MACS2 peak calling software with --nolambda flaq
common peak region and complementary region were optaine with bedtools suite were
Genome_build: hg19

molecule: genomic DNA

source_name: YB5 colon cancer cell line

growth_protocol: YB5 cell line was cultured in L-15 medium with 10% fetal bovine serum

extract_protocol: none provided by the submitter

treatment_protocol: Cells were treated with either DMSO or 10uM HH1 with a single dose for four days (one-dose and let the drug in the media for two days. Drug-free media were changed on day three before performing ATAC-seq on day four).

value: colon cancer cell line

tag: sample type

value: Dukes' type C, grade IV, colorectal adenocarcinoma

tag: gender

value: female


title: illu-HH1-3


title: Cultured L1210 cells [L1210serial_H03_S279]

description:
L1210serial_H03_S279
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_H01_S277]

description:
L1210serial_H01_S277
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_H02_S278]

description:
L1210serial_H02_S278
l1210_rsem.txt


title: illu-HH1-1


title: illu-ctl-3


title: illu-ctl-2


title: Cultured FL5.12 murine cells [FL51a_A01_S1]

description:
FL51a_A01_S1
fl5_rsem.txt


title: Cultured L1210 cells [L1210serial_G11_S275]

description:
L1210serial_G11_S275
l1210_rsem.txt


title: illu-ctl-1


title: 8-No-si: Control siRNA + IR


title: 4-Mix: p53 & TGFBR2 siRNAs


title: Cultured L1210 cells [L1210serial_G10_S274]

description:
L1210serial_G10_S274
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_G09_S273]

description:
L1210serial_G09_S273
l1210_rsem.txt


title: Deep Senescence rep3

city: Providence

first: John

last: Sedivy

state: RI

address: 70 Ship Street

institute: Brown University

data_processing:
Base calls were done by Beckman Coulter Genomics
Alignment to hg38 performed using HISAT2 version 2.0.5
Read counts for genes were assigned using featureCounts (subread package version 1.4.6)
Genome_build: hg38
Supplementary_files_format_and_content: processed files are in tab delimited txt format

source_name: lung fibroblast cells

growth_protocol: Proliferating: early passage normal diploid fibroblast during exponential growth; Early Senescence: after serial passaging and entrance in Replicative Senescence, 8 weeks; Deep Senescence: after serial passaging and entrance in Replicative Senescence, 16 weeks

extract_protocol:
Trizol extraction followed by PureLink RNA clean-up with on-column Dnase I treatment. Total RNA was sent to Beckman Coulter Genomics for library prep and sequencing.
Stranded Ribodepletion

value: ES-derived lung fibroblast cells

tag: state

value: late senescent

tag: molecule

value: ribodepleted RNA


title: Deep Senescence rep2


title: Cultured L1210 cells [L1210serial_G07_S271]

description:
L1210serial_G07_S271
l1210_rsem.txt


title: Early Senescence rep3

value: early senescent


title: Deep Senescence rep1


title: Early Senescence rep2


title: Cultured L1210 cells [L1210serial_H04_S280]

description:
L1210serial_H04_S280
l1210_rsem.txt


title: Early Senescence rep1


title: Cultured L1210 cells [L1210serial_G05_S269]

description:
L1210serial_G05_S269
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_G04_S268]

description:
L1210serial_G04_S268
l1210_rsem.txt


title: Proliferating rep3

value: proliferating


title: Proliferating rep2


title: Cultured L1210 cells [L1210serial_G06_S270]

description:
L1210serial_G06_S270
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_G12_S276]

description:
L1210serial_G12_S276
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_G01_S265]

description:
L1210serial_G01_S265
l1210_rsem.txt


title: Proliferating rep1


title: Cultured L1210 cells [L1210serial_G02_S266]

description:
L1210serial_G02_S266
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F12_S264]

description:
L1210serial_F12_S264
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_G03_S267]

description:
L1210serial_G03_S267
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F11_S263]

description:
L1210serial_F11_S263
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F09_S261]

description:
L1210serial_F09_S261
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_G08_S272]

description:
L1210serial_G08_S272
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F08_S260]

description:
L1210serial_F08_S260
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F07_S259]

description:
L1210serial_F07_S259
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F06_S258]

description:
L1210serial_F06_S258
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F04_S256]

description:
L1210serial_F04_S256
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E10_S250]

description:
L1210serial_E10_S250
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E08_S248]

description:
L1210serial_E08_S248
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F03_S255]

description:
L1210serial_F03_S255
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F05_S257]

description:
L1210serial_F05_S257
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F02_S254]

description:
L1210serial_F02_S254
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F01_S253]

description:
L1210serial_F01_S253
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E11_S251]

description:
L1210serial_E11_S251
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E01_S241]

description:
L1210serial_E01_S241
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E03_S243]

description:
L1210serial_E03_S243
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E02_S242]

description:
L1210serial_E02_S242
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E06_S246]

description:
L1210serial_E06_S246
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E05_S245]

description:
L1210serial_E05_S245
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E07_S247]

description:
L1210serial_E07_S247
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D11_S239]

description:
L1210serial_D11_S239
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_F10_S262]

description:
L1210serial_F10_S262
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D10_S238]

description:
L1210serial_D10_S238
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D06_S234]

description:
L1210serial_D06_S234
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D05_S233]

description:
L1210serial_D05_S233
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D12_S240]

description:
L1210serial_D12_S240
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D07_S235]

description:
L1210serial_D07_S235
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D09_S237]

description:
L1210serial_D09_S237
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D03_S231]

description:
L1210serial_D03_S231
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D04_S232]

description:
L1210serial_D04_S232
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E09_S249]

description:
L1210serial_E09_S249
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D01_S229]

description:
L1210serial_D01_S229
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D02_S230]

description:
L1210serial_D02_S230
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C12_S228]

description:
L1210serial_C12_S228
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_E04_S244]

description:
L1210serial_E04_S244
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C11_S227]

description:
L1210serial_C11_S227
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C08_S224]

description:
L1210serial_C08_S224
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C10_S226]

description:
L1210serial_C10_S226
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C09_S225]

description:
L1210serial_C09_S225
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C07_S223]

description:
L1210serial_C07_S223
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C06_S222]

description:
L1210serial_C06_S222
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_D08_S236]

description:
L1210serial_D08_S236
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C03_S219]

description:
L1210serial_C03_S219
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C05_S221]

description:
L1210serial_C05_S221
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C04_S220]

description:
L1210serial_C04_S220
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C02_S218]

description:
L1210serial_C02_S218
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_C01_S217]

description:
L1210serial_C01_S217
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B11_S215]

description:
L1210serial_B11_S215
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B12_S216]

description:
L1210serial_B12_S216
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B09_S213]

description:
L1210serial_B09_S213
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B10_S214]

description:
L1210serial_B10_S214
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B08_S212]

description:
L1210serial_B08_S212
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B06_S210]

description:
L1210serial_B06_S210
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B04_S208]

description:
L1210serial_B04_S208
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B05_S209]

description:
L1210serial_B05_S209
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B03_S207]

description:
L1210serial_B03_S207
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B07_S211]

description:
L1210serial_B07_S211
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B02_S206]

description:
L1210serial_B02_S206
l1210_rsem.txt


title: SAMR1 vs SAMP8 hippocampus samples with 9 months of age

type: RNA

city: Barcelona

first: Christian

middle: Griñán

last: Ferré

state: Barcelona

address: Joan XIII, s/n

department: Pharmacology, Toxicology and Therapeutic Chemistry

country: Spain

institute: University of Barcelona

hyb_protocol: For cDNA synthesis 10ug of total RNA was used as the template, incorporating dUTP-Cy3 or dUTP-Cy5. Incorporation of the fluorophore was analysed by evaluating the absorbance at 555 nm for Cy3 and 655 nm for Cy5

scan_protocol: Equal quantities of the labeled cDNA were hybridized to the Mus musculus 22 thousand 65-mer Oligo Library from Sigma-Genosys Array images were acquired and quantified in a ScanArray 4000 using the accompanying software (Packard BioChips). All images were captured at a 50% scan rate using 65% PMT gain, 70 to 75% laser power and 10 um resolution.For each spot, the Cy3 and Cy5 mean density value and background value were calculated with ArrayPro Analyzer software.

data_processing:
Microarray data analysis were analyzed with the GenArise software, developed by the Computing Unit at the Cellular Physiology Institute of the UNAM. GenArise carries out a number of transformations: background correction, lowest normalization, intensity filter, replicate analysis, and selection of differentially expressed genes. The goal of GenArise is to provide evidence that genes are differentially expressed, and it has been successfully used in other studies. The software identifies differentially expressed genes by calculating an intensity-dependent z-score. It uses a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and it defines a z-score that measures the number of standard deviations a data point is from the mean: zi = (Ri - mean(R)) / sd(R), where zii is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. Applying these criteria, the elements with a z-score > 2 standard deviations correspond to genes that are likely to be differentially expressed.
z-score measures the number of standard deviations a data point is from the mean: zi = (Ri - mean(R)) / sd(R), where zii is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio.
Submitter declares complete normalized data are no longer available.

source_name: SAMR1, 9 months

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

extract_protocol: Total RNA was isolated from the hippocampus of each mouse, as described previously. Briefly, tissue was homogenized in the presence of Trizol reagent (Invitrogen). Chloroform was added and the RNA was precipitated from the aqueous phase with isopropanol at 4ºC. RNA were constituted in RNase-free water, and the quantified and checked for RNA integrity with an Agilent 2100 Bionalyzer.

tag: condition

value: Senescent-Accelerated Resistant

tag: age

value: 9 months

tag: tissue

value: Hippocampus

source_name: SAMP8, 9 months

value: Senescent-Accelerated Prone


title: Cultured L1210 cells [L1210serial_E12_S252]

description:
L1210serial_E12_S252
l1210_rsem.txt

value: Cultured L1210 cells


title: Cultured L1210 cells [L1210serial_A12_S204]

description:
L1210serial_A12_S204
l1210_rsem.txt


title: SAMR1 vs SAMP8 hippocampus samples with 2 months of age

source_name: SAMR1, 2 months

value: 2 months

source_name: SAMP8, 2 months


title: Cultured L1210 cells [L1210serial_A11_S203]

description:
L1210serial_A11_S203
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_A07_S199]

description:
L1210serial_A07_S199
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_A08_S200]

description:
L1210serial_A08_S200
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_A05_S197]

description:
L1210serial_A05_S197
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_A04_S196]

description:
L1210serial_A04_S196
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_A03_S195]

description:
L1210serial_A03_S195
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_A01_S193]

description:
L1210serial_A01_S193
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_A02_S194]

description:
L1210serial_A02_S194
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_B01_S205]

description:
L1210serial_B01_S205
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_A10_S202]

description:
L1210serial_A10_S202
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_A09_S201]

description:
L1210serial_A09_S201
l1210_rsem.txt


title: Cultured L1210 cells [L1210serial_A06_S198]

description:
L1210serial_A06_S198
l1210_rsem.txt


title: monocyte_treated_exosomes_rep4

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina DASL hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were log2-transformed and normalized with robust spline normalization using the lumi package from Bioconductor.

label: biotin

source_name: monocyte co-cultured with melanoma exosomes

label_protocol: According to whole genome DASL assay (Illumina)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with Ambion miRVANA kit according to the protocol provided by the manufacturer.

treatment_protocol: 300,000 CD14+ cells were co-cultured for 24 hours with 50 µg of exosomes isolated from the INT12 melanoma cell line generated in our laboratory

tag: subject status

value: healthy donor

value: CD14+ monocytes

tag: cocultivated with

value: 50 µg exosomes isolated from the INT12 melanoma cell line


title: monocyte_treated_exosomes_rep5


title: monocyte_treated_exosomes_rep2


title: monocyte_untreated_rep4

source_name: untreated monocyte

value: none (untreated control)


title: monocyte_treated_exosomes_rep1


title: monocyte_untreated_rep2


title: monocyte_untreated_rep3


title: monocyte_untreated_rep5


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H11_S287]

description:
T48hr_H11_S287
cd8_rsem.txt

source_name: Transcriptome of single T-cell following measurement with sSMR device


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H10_S286]

description:
T48hr_H10_S286
cd8_rsem.txt


title: monocyte_treated_exosomes_rep3


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H12_S288]

description:
T48hr_H12_S288
cd8_rsem.txt


title: monocyte_untreated_rep1


title: LNCap OE-OC2 3

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description: LNCaP enforced expression of ONECUT2

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data was normalized by GCRMA method.

label: Biotin

source_name: LNCap OE-OC2

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

growth_protocol: Cells were grown in RPMI-1640 media (Gibco) supplemented with 10% FBS and penicillin/streptomycin

extract_protocol: Total RNA was extracted using the RNeasy Kit (Qiagen) and hybridized to the Human U133plus2.0 Array Hybridization (Affymetrix) at the UCLA Clinical Microarray Core.

treatment_protocol: The OC2 overexpression plasmid was obtained by cloning the full-length OC2 cDNA (NM_004852) into the pLenti-C-Myc-DDK-IRES-Puro (Origene). For the knockdown of OC2, two validated shRNA clones (TRCN0000013443, TRCN0000013445) in the vector pLKO1 were purchased from Sigma. A non-mammalian shRNA Control Plasmid (TRC2-pLKO-puro non-target shRNA #1, Sigma) was used as a control. Cells were subsequently transduced in the presence of 5μg/mL of polybrene and selected on 5μg/ml puromycin to create the stable line.

tag: cell line

value: Prostate cancer cell line LNCaP

tag: treatment

value: ONECUT2 overexpression construct


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H06_S282]

description:
T48hr_H06_S282
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H09_S285]

description:
T48hr_H09_S285
cd8_rsem.txt


title: LNCaP Control 3

description: LNCaP Control sample

source_name: LNCaP Control

value: Vehicle


title: LNCap OE-OC2 2

description: LNCaP enforced expression of ONECUT2


title: LNCap OE-OC2 1

description: LNCaP enforced expression of ONECUT2


title: LNCaP Control 1

description: LNCaP Control sample


title: LNCaP Control 2

description: LNCaP Control sample


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H05_S281]

description:
T48hr_H05_S281
cd8_rsem.txt


title: 22RV1 sh43-1

description: 22Rv1 knock-down of ONECUT2

value: Prostate cancer cell line 22Rv1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H08_S284]

description:
T48hr_H08_S284
cd8_rsem.txt


title: 22RV1 sh202-3

description: 22Rv1 shRNA scramble

value: shRNA scramble


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H01_S277]

description:
T48hr_H01_S277
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H02_S278]

description:
T48hr_H02_S278
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H04_S280]

description:
T48hr_H04_S280
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_G12_S276]

description:
T48hr_G12_S276
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H07_S283]

description:
T48hr_H07_S283
cd8_rsem.txt


title: 22RV1 sh202-2

description: 22Rv1 shRNA scramble


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_G11_S275]

description:
T48hr_G11_S275
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_G10_S274]

description:
T48hr_G10_S274
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_G07_S271]

description:
T48hr_G07_S271
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_G06_S270]

description:
T48hr_G06_S270
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_G05_S269]

description:
T48hr_G05_S269
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_G04_S268]

description:
T48hr_G04_S268
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_H03_S279]

description:
T48hr_H03_S279
cd8_rsem.txt


title: 22RV1 sh43-3

description: 22Rv1 knock-down of ONECUT2


title: 22RV1 sh43-2

description: 22Rv1 knock-down of ONECUT2


title: 22RV1 OC2-OE3

description: 22Rv1 enforced expression of ONECUT2

source_name: 22RV1 OC2-OE


title: 22RV1 sh202-1

description: 22Rv1 shRNA scramble


title: 22RV1 OC2-OE2

description: 22Rv1 enforced expression of ONECUT2


title: 22RV1 Control 3

description: 22Rv1 Control sample

source_name: 22RV1 Control


title: 22RV1 Control 2

description: 22Rv1 Control sample


title: 617-16H 2

description: Small molecular inhibitor treatment for 16h in 22Rv1 prostate cancer cell line

label: Bioin

treatment_protocol: 22Rv1 cells treated for 4, 6 and 16 hours with the small compound

value: 22Rv1 prostate cancer cell line

value: Small molecular inhibitor

tag: time


title: 22RV1 OC2-OE1

description: 22Rv1 enforced expression of ONECUT2


title: 617-16H 1


title: 617-10-6h 3

description: Small molecular inhibitor treatment for 6h in 22Rv1 prostate cancer cell line


title: 617-16H 3


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_G02_S266]

description:
T48hr_G02_S266
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F12_S264]

description:
T48hr_F12_S264
cd8_rsem.txt


title: 617-10-6h 2


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_G01_S265]

description:
T48hr_G01_S265
cd8_rsem.txt


title: 22RV1 Control 1

description: 22Rv1 Control sample


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F10_S262]

description:
T48hr_F10_S262
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F08_S260]

description:
T48hr_F08_S260
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F09_S261]

description:
T48hr_F09_S261
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F11_S263]

description:
T48hr_F11_S263
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_G03_S267]

description:
T48hr_G03_S267
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F06_S258]

description:
T48hr_F06_S258
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F07_S259]

description:
T48hr_F07_S259
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F04_S256]

description:
T48hr_F04_S256
cd8_rsem.txt


title: 617-10-6h 1


title: 617-10-4h 2

description: Small molecular inhibitor treatment for 4h in 22Rv1 prostate cancer cell line


title: 617-10-4h 3


title: VE-10 2

description: Vehicle treatment in 22Rv1 prostate cancer cell line


title: 617-10-4h 1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F03_S255]

description:
T48hr_F03_S255
cd8_rsem.txt


title: VE-10 1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F02_S254]

description:
T48hr_F02_S254
cd8_rsem.txt


title: VE-10 3


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_E12_S252]

description:
T48hr_E12_S252
cd8_rsem.txt


title: 24: P14_129_WT

city: Chicago

first: Jennifer

last: Kearney

state: IL

address: 320 East Superior Street, Searle 8-510

department: Pharmacology

institute: Northwestern University

description: pooled hippocampi from 12-16 mice

data_processing:
Illunima Casava
FastQ files were groomed with FastQ groomer v. 1.0.4
Aligned to mm10 mouse genome with Tophat2 v. 2.1.0
Counts of aligned that overlap GFF features were calculated with HTSeq v 0.6.1p1 (union overlap mode)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimted text files with counts for each feature

source_name: Hippocampus

extract_protocol:
Hippocampi were removed, flash frozen on dry ice, and RNA was prepared using TRIzol reagent
Samples were prepared  TruSeq RNA Library Preparation Kit v2

tag: strain

value: hippocampus

tag: tag

value: post natal day 14

tag: genotype

value: wild type

tag: phenotype

value: no seizures


title: 25: P14_129_WT

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_E07_S247]

description:
T48hr_E07_S247
cd8_rsem.txt

tag: cell type


title: 21: P14_129_KO

description: pooled hippocampi from 12-16 mice


title: 22: P14_129_KO

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_E11_S251]

description:
T48hr_E11_S251
cd8_rsem.txt


title: 23: P14_129_KO

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_E06_S246]

description:
T48hr_E06_S246
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_E10_S250]

description:
T48hr_E10_S250
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_F05_S257]

description:
T48hr_F05_S257
cd8_rsem.txt


title: 20: P14_F1_WT

description: pooled hippocampi from 12-16 mice

value: [129S6/SvEvTac x C57BL/6]F1


title: 19: P14_F1_WT

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_E04_S244]

description:
T48hr_E04_S244
cd8_rsem.txt


title: 18: P14_F1_WT

description: pooled hippocampi from 12-16 mice


title: HIV stimulated 2

city: Miami

first: Emmanuel

last: Thomas

state: FL

address: 1550 NW 12th Ave, Papanicolaou Bldg., RM. PAP 514

department: Schiff Center for LIver Diseases

institute: University Of Miami School of Medicine

description: Gene expression data from primary kupffer cells...with HIV.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA nomalization by GeneSpring Software GX 13.0 and basline was transformed to median of all samples

source_name: Human Primary Kupffer Cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary Kupfer Cells Were Isolated and Plated on 12 well plates at the University of Pittsburgh in the Laboratory of Dr. David Geller and provided through the NIH funded Liver Tissue and Cell Distribution System (LTCDS)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: RNA was isolated after treatment with HIV (HIV-IIIB)  for 24 hours (m.o.i=2).

value: Liver

value: Kupffer Cells

value: HIV


title: HIV stimulated 1

description: Gene expression data from primary kupffer cells….with HIV.


title: HIV stimulated 3

description: Gene expression data from primary kupffer cells…with HIV.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_E05_S245]

description:
T48hr_E05_S245
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_E02_S242]

description:
T48hr_E02_S242
cd8_rsem.txt


title: Cont HIV 1

description: Gene expression data from primary kupffer cells.  Control without HIV.

value: control HIV


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D12_S240]

description:
T48hr_D12_S240
cd8_rsem.txt


title: Cont HIV 3

description: Gene expression data from primary kupffer cells. Control without HIV.


title: 14: P24_129_WT

description: pooled hippocampi from 12-16 mice

value: post natal day 24


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_E03_S243]

description:
T48hr_E03_S243
cd8_rsem.txt


title: Cont HIV 2


title: 15: P14_F1_KO

description: pooled hippocampi from 12-16 mice


title: 16: P14_F1_KO

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D11_S239]

description:
T48hr_D11_S239
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_E01_S241]

description:
T48hr_E01_S241
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D10_S238]

description:
T48hr_D10_S238
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D08_S236]

description:
T48hr_D08_S236
cd8_rsem.txt


title: 12: P24_129_WT

description: pooled hippocampi from 12-16 mice


title: 13: P24_129_WT

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D07_S235]

description:
T48hr_D07_S235
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D09_S237]

description:
T48hr_D09_S237
cd8_rsem.txt


title: 11: P24_129_KO

description: pooled hippocampi from 12-16 mice


title: 8: P24_F1_WT

description: pooled hippocampi from 12-16 mice


title: 9: P24_129_KO

description: pooled hippocampi from 12-16 mice


title: 10: P24_129_KO

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D06_S234]

description:
T48hr_D06_S234
cd8_rsem.txt


title: 7: P24_F1_WT

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D03_S231]

description:
T48hr_D03_S231
cd8_rsem.txt


title: 17: P14_F1_KO

description: pooled hippocampi from 12-16 mice


title: 6: P24_F1_WT

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D04_S232]

description:
T48hr_D04_S232
cd8_rsem.txt


title: 5: P24_F1_KO

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D05_S233]

description:
T48hr_D05_S233
cd8_rsem.txt


title: 3: P24_F1_KO_Sz

description: pooled hippocampi from 3-4 mice

value: Seizures


title: 1: P24_F1_KO_Sz

description: pooled hippocampi from 3-4 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D02_S230]

description:
T48hr_D02_S230
cd8_rsem.txt


title: 2: P24_F1_KO_Sz

description: pooled hippocampi from 3-4 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C11_S227]

description:
T48hr_C11_S227
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C10_S226]

description:
T48hr_C10_S226
cd8_rsem.txt


title: 4: P24_F1_KO

description: pooled hippocampi from 12-16 mice


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C09_S225]

description:
T48hr_C09_S225
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C12_S228]

description:
T48hr_C12_S228
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C07_S223]

description:
T48hr_C07_S223
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C05_S221]

description:
T48hr_C05_S221
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C06_S222]

description:
T48hr_C06_S222
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C04_S220]

description:
T48hr_C04_S220
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_D01_S229]

description:
T48hr_D01_S229
cd8_rsem.txt


title: pulldown T20 rep1

city: Berkeley

first: Alejandro

last: Padron

address: University of California, Berkeley

department: MCB

institute: UC Berkeley

description:
Streptavidin Pulldown RNA
Sample name:
pT20_1

data_processing:
Library strategy: APEX-seq
Fastq preprocessing performed with cutadapt
reads were aligned using hisat2
count tables were generated using featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file with counts

extract_protocol:
APEX labeling reaction of RNAs were carried out using 500 µM biotin-phenol and incubating for 30 min followed by a 1 minute 1 mM H2O2 treatment. RNAs were extracted by treating cells with TRIzol. Biotinylated RNAs were enriched using streptavidin beads
Libraries were constructed using NEBnext Ultra II Directional RNA sequencing from NEB

tag: construct

tag: stress condition

value: Heatshock


title: pulldown APEX-eIF4A DMSO rep2

description:
Streptavidin Pulldown RNA
Sample name:
p4A2

value: DMSO


title: pulldown T0 rep2

description:
Streptavidin Pulldown RNA
Sample name:
pT0_2

value: Naive


title: pulldown T0 rep1

description:
Streptavidin Pulldown RNA
Sample name:
pT0_1


title: pulldown T4 rep1

description:
Streptavidin Pulldown RNA
Sample name:
pT4


title: pulldown T20 rep2

description:
Streptavidin Pulldown RNA
Sample name:
pT20_2


title: pulldown APEX-eIF4A DMSO rep1

description:
Streptavidin Pulldown RNA
Sample name:
p4A1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C03_S219]

description:
T48hr_C03_S219
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C01_S217]

description:
T48hr_C01_S217
cd8_rsem.txt


title: pulldown hip rep1

description:
Streptavidin Pulldown RNA
Sample name:
pHIP1

value: Hippuristanol


title: pulldown hip rep2

description:
Streptavidin Pulldown RNA
Sample name:
pHIP2


title: pulldown APEX-eIF4E rep1

description:
Streptavidin Pulldown RNA
Sample name:
p4E_1


title: pulldown APEX-eIF4E rep2

description:
Streptavidin Pulldown RNA
Sample name:
p4E_2


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B10_S214]

description:
T48hr_B10_S214
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B11_S215]

description:
T48hr_B11_S215
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B09_S213]

description:
T48hr_B09_S213
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C02_S218]

description:
T48hr_C02_S218
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B08_S212]

description:
T48hr_B08_S212
cd8_rsem.txt


title: pulldown APEX-eIF4A rep2

description:
Streptavidin Pulldown RNA
Sample name:
p4A_2


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B12_S216]

description:
T48hr_B12_S216
cd8_rsem.txt


title: pulldown APEX-eIF4A rep1

description:
Streptavidin Pulldown RNA
Sample name:
p4A_1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B07_S211]

description:
T48hr_B07_S211
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_C08_S224]

description:
T48hr_C08_S224
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B06_S210]

description:
T48hr_B06_S210
cd8_rsem.txt


title: pulldown APEX-GFP rep1

description:
Streptavidin Pulldown RNA
Sample name:
pGFP_1

value: APEX-GFP


title: pulldown APEX-GFP rep2

description:
Streptavidin Pulldown RNA
Sample name:
pGFP_2


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B05_S209]

description:
T48hr_B05_S209
cd8_rsem.txt


title: pulldown C1-APEX rep1

description:
Streptavidin Pulldown RNA
Sample name:
p34_1


title: pulldown APEX-CBX1 rep2

description:
Streptavidin Pulldown RNA
Sample name:
pCBX_2


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B03_S207]

description:
T48hr_B03_S207
cd8_rsem.txt


title: pulldown APEX-CBX1 rep1

description:
Streptavidin Pulldown RNA
Sample name:
pCBX_1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A12_S204]

description:
T48hr_A12_S204
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A11_S203]

description:
T48hr_A11_S203
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B01_S205]

description:
T48hr_B01_S205
cd8_rsem.txt


title: input T4 rep1

description:
Sample name:
iT4


title: input T20 rep2

description:
Sample name:
iT20_2


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A10_S202]

description:
T48hr_A10_S202
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B02_S206]

description:
T48hr_B02_S206
cd8_rsem.txt


title: input hip rep2

description:
Sample name:
iHIP2


title: input hip rep1

description:
Sample name:
iHIP1


title: input T0 rep2

description:
Sample name:
iT0_2


title: input T0 rep1

description:
Sample name:
iT0_1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A08_S200]

description:
T48hr_A08_S200
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A07_S199]

description:
T48hr_A07_S199
cd8_rsem.txt


title: input T20 rep1

description:
Sample name:
iT20_1


title: pulldown C1-APEX rep2

description:
Streptavidin Pulldown RNA
Sample name:
p34_2


title: input APEX-eIF4A rep1

description:
Sample name:
i4A_1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A06_S198]

description:
T48hr_A06_S198
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A05_S197]

description:
T48hr_A05_S197
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A09_S201]

description:
T48hr_A09_S201
cd8_rsem.txt


title: input APEX-eIF4E rep1

description:
Sample name:
i4E_1


title: input APEX-eIF4E rep2

description:
Sample name:
i4E_2


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A03_S195]

description:
T48hr_A03_S195
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_B04_S208]

description:
T48hr_B04_S208
cd8_rsem.txt


title: input APEX-eIF4A rep2

description:
Sample name:
i4A_2


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A02_S194]

description:
T48hr_A02_S194
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A04_S196]

description:
T48hr_A04_S196
cd8_rsem.txt


title: input APEX-eIF4A DMSO

description:
Sample name:
i4A_2


title: input APEX-GFP rep1

description:
Sample name:
iGFP_1


title: input C1-APEX rep2

description:
Sample name:
i34_2


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 48 hrs [T48hr_A01_S193]

description:
T48hr_A01_S193
cd8_rsem.txt


title: input APEX-CBX1 rep1

description:
Sample name:
iCBX_1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H11_S191]

description:
T24hr_H11_S191
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H09_S189]

description:
T24hr_H09_S189
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H10_S190]

description:
T24hr_H10_S190
cd8_rsem.txt


title: input C1-APEX rep1

description:
Sample name:
i34_1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H08_S188]

description:
T24hr_H08_S188
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H07_S187]

description:
T24hr_H07_S187
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H06_S186]

description:
T24hr_H06_S186
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H04_S184]

description:
T24hr_H04_S184
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H02_S182]

description:
T24hr_H02_S182
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H12_S192]

description:
T24hr_H12_S192
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H01_S181]

description:
T24hr_H01_S181
cd8_rsem.txt


title: input APEX-CBX1 rep2

description:
Sample name:
iCBX_2


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G11_S179]

description:
T24hr_G11_S179
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G10_S178]

description:
T24hr_G10_S178
cd8_rsem.txt


title: Fascin bulk RNAseq_2

city: Atlanta

first: Alberto

last: Stolfi

state: Georgia

address: 950 Atlantic Dr

department: School of Biological Sciences

institute: Georgia Institute of Technology

description:
THxFascinCounts.dedup.matrix.full.txt
fasc2

data_processing:
Single-cell data processing (fastq generation, alignment, counting, etc) was performed using CellRanger version 2.0.0
Fastq files were generated using “cellranger mkfastq” with default arguments
Counting was done by “cellranger count” using KyotoHoya (KH) gene models, with default arguments except “--force-cells=3000”
For bulk RNA-seq, raw fastq files were first processed by STAR 2.5.2b and mapped to the Ciona robusta (formerly Ciona intestinalis type A) genome
The output bam files were then processed using Rsubread/featureCounts with the parameter "ignoreDup=TRUE" to remove reads duplication caused by library amplification
After duplication removal, the reads which mapped to the exons of KyotoHoya (KH) gene models were counted for downstream differential expression analysis
Differential expression between TH+ and Fascin+ replicates was measured by EdgeR (https://osf.io/vjq95/?view_only=18df57e03275448d88c9dd78611f7cfc)
Genome_build: Genome used was Ciona intestinalis (KH2012, Ghost Database) (Dehal et al., 2002; Satou et al., 2008). Gene model used was KyotoHoya (KH) gene model (Satou et al., 2008)
Supplementary_files_format_and_content:
[scRNAseq]  Gene-barcode matrices and per-molecule information for all molecules in HDF5 format and molecule information (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/overview)
[bulk RNAseq]  raw counts file (processed data)

organism: Ciona robusta

source_name: FACS-isolated cells

growth_protocol: Ciona robusta embryos grown in filtered buffered artificial sea water

extract_protocol: RNA extracted using RNAqueous micro kit (ThermoFisher), cDNA libraries prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech/Takara), and sequencing libraries prepared using Ovation Ultralow Library kit (NuGEN)

treatment_protocol: Dissociation using calcium/magnesium-free sea water + trypsin, FACS using BD FacsAria I

value: brain

value: Fascin>tagRFP/Unc-67::GFP+ cells (brain + contaminants)

tag: developmental stage

value: 24 hours post-fertilization, 18C


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G09_S177]

description:
T24hr_G09_S177
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G07_S175]

description:
T24hr_G07_S175
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G08_S176]

description:
T24hr_G08_S176
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H03_S183]

description:
T24hr_H03_S183
cd8_rsem.txt


title: TH bulk RNAseq_1

description:
THxFascinCounts.dedup.matrix.full.txt
th1

value: TH>GFP+ cells (DA cells)


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G06_S174]

description:
T24hr_G06_S174
cd8_rsem.txt


title: stim_39h

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

description: RNA expression value derived from Affymetrix Launcher software

hyb_protocol: Samples were hybridized with Clarioum S Human Arrays (Affymetrix) and scanned at the HUJI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed in R for background correction and RMA normalization. Normalized expression data were log-transformed.

source_name: MNT-1 melanoma line

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: MNT-1 melanoma cells were grown in 10% serum DMEM.

extract_protocol: RNA was isolated from MNT-1 cells using Trizol (Qiagen), according to the manufacturer’s instructions. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA.

treatment_protocol: MNT-1 melnaoma cells were serum depleted for 48 hours perior to treatment with 20uM Forskolin for 30 minutes, followed by replacment of medium with serum depleted medium. RNA was extracted at the indicated time points following stimulaiton.


title: stim_27h


title: Fascin bulk RNAseq_1

description:
THxFascinCounts.dedup.matrix.full.txt
fasc1


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_H05_S185]

description:
T24hr_H05_S185
cd8_rsem.txt


title: stim_33h


title: stim_15h


title: baseline 96

type: genomic

city: Cantanhede

first: Helena

last: Vazao

address: Biocant Park Nucleo4, 4A

department: HeartGenetics

country: Portugal

institute: HeartGenetics

description:
BL96
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.

hyb_protocol: Not applicable

scan_protocol: The status of 171 mutations (by the reading of 61 positions) in 6 genes (OncoAlvo® Panel) was assessed using a high-throughput DNA Microchip platform, the iPLEX® system (Agena Bioscience, Inc). This array platform allows an optimal genetic analysis by combining the benefits of accurate primer extension chemistry with MALDI-TOF mass spectrometry. The different masses of each generated PCR product are then converted into mutational status information.

data_processing: The processed data (attached as 14 .txt files) were generated by software computing analysis. The processing was made by normalizing the peak intensity (converted into fraction of mutant alleles) of each genetic variant of each sample by the peak intensity of the correspondent variant of the average of 96 baseline samples. As the baseline samples serve as the minimum threshold, the computer software does not give a processed data file for them; thus, there are no processed data .txt files for these 96 samples. The processed data files only show the positive results.

source_name: colorectal healthy sample

label_protocol: Not applicable

growth_protocol: FFPE human colon adenocarcinoma.

extract_protocol: A commercial kit was used to perform DNA extraction and purification from FFPE colon adenocarcinoma. DNA concentration and quality were evaluated with MultiskanGo spectrophotometer (Thermo Scientific).

treatment_protocol: No treatment applied.

value: FFPE colorectal healthy sample

tag: sample type

value: Baseline


title: baseline 95

description:
BL95
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G05_S173]

description:
T24hr_G05_S173
cd8_rsem.txt


title: stim_19h


title: stim_11h


title: baseline 94

description:
BL94
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: stim_23h


title: unstim


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G12_S180]

description:
T24hr_G12_S180
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G04_S172]

description:
T24hr_G04_S172
cd8_rsem.txt


title: stim_7h


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G03_S171]

description:
T24hr_G03_S171
cd8_rsem.txt


title: baseline 93

description:
BL93
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: TH bulk RNAseq_2

description:
THxFascinCounts.dedup.matrix.full.txt
th2


title: stim_4h


title: baseline 92

description:
BL92
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G02_S170]

description:
T24hr_G02_S170
cd8_rsem.txt


title: baseline 91

description:
BL91
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_G01_S169]

description:
T24hr_G01_S169
cd8_rsem.txt


title: baseline 90

description:
BL90
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F12_S168]

description:
T24hr_F12_S168
cd8_rsem.txt


title: baseline 88

description:
BL88
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F11_S167]

description:
T24hr_F11_S167
cd8_rsem.txt


title: baseline 86

description:
BL86
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F09_S165]

description:
T24hr_F09_S165
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F10_S166]

description:
T24hr_F10_S166
cd8_rsem.txt


title: baseline 85

description:
BL85
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F06_S162]

description:
T24hr_F06_S162
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F07_S163]

description:
T24hr_F07_S163
cd8_rsem.txt


title: baseline 84

description:
BL84
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 82

description:
BL82
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 81

description:
BL81
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F05_S161]

description:
T24hr_F05_S161
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F04_S160]

description:
T24hr_F04_S160
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F02_S158]

description:
T24hr_F02_S158
cd8_rsem.txt


title: baseline 80

description:
BL80
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 79

description:
BL79
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F03_S159]

description:
T24hr_F03_S159
cd8_rsem.txt


title: baseline 78

description:
BL78
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F01_S157]

description:
T24hr_F01_S157
cd8_rsem.txt


title: baseline 77

description:
BL77
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E12_S156]

description:
T24hr_E12_S156
cd8_rsem.txt


title: baseline 89

description:
BL89
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 76

description:
BL76
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E11_S155]

description:
T24hr_E11_S155
cd8_rsem.txt


title: baseline 87

description:
BL87
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 75

description:
BL75
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 74

description:
BL74
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_F08_S164]

description:
T24hr_F08_S164
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E09_S153]

description:
T24hr_E09_S153
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E08_S152]

description:
T24hr_E08_S152
cd8_rsem.txt


title: baseline 83

description:
BL83
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E10_S154]

description:
T24hr_E10_S154
cd8_rsem.txt


title: baseline 73

description:
BL73
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 71

description:
BL71
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 72

description:
BL72
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 69

description:
BL69
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 70

description:
BL70
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E07_S151]

description:
T24hr_E07_S151
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E06_S150]

description:
T24hr_E06_S150
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E05_S149]

description:
T24hr_E05_S149
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E03_S147]

description:
T24hr_E03_S147
cd8_rsem.txt


title: baseline 68

description:
BL68
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E04_S148]

description:
T24hr_E04_S148
cd8_rsem.txt


title: baseline 66

description:
BL66
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E01_S145]

description:
T24hr_E01_S145
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D12_S144]

description:
T24hr_D12_S144
cd8_rsem.txt


title: baseline 65

description:
BL65
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 67

description:
BL67
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 64

description:
BL64
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D11_S143]

description:
T24hr_D11_S143
cd8_rsem.txt


title: baseline 62

description:
BL62
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 63

description:
BL63
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D09_S141]

description:
T24hr_D09_S141
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D10_S142]

description:
T24hr_D10_S142
cd8_rsem.txt


title: baseline 61

description:
BL61
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 60

description:
BL60
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 59

description:
BL59
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D06_S138]

description:
T24hr_D06_S138
cd8_rsem.txt


title: baseline 58

description:
BL58
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D04_S136]

description:
T24hr_D04_S136
cd8_rsem.txt


title: baseline 57

description:
BL57
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_E02_S146]

description:
T24hr_E02_S146
cd8_rsem.txt


title: baseline 56

description:
BL56
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D02_S134]

description:
T24hr_D02_S134
cd8_rsem.txt


title: baseline 54

description:
BL54
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C11_S131]

description:
T24hr_C11_S131
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C12_S132]

description:
T24hr_C12_S132
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D05_S137]

description:
T24hr_D05_S137
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C10_S130]

description:
T24hr_C10_S130
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C09_S129]

description:
T24hr_C09_S129
cd8_rsem.txt


title: baseline 51

description:
BL51
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D03_S135]

description:
T24hr_D03_S135
cd8_rsem.txt


title: baseline 52

description:
BL52
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C08_S128]

description:
T24hr_C08_S128
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D08_S140]

description:
T24hr_D08_S140
cd8_rsem.txt


title: baseline 50

description:
BL50
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 49

description:
BL49
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_D07_S139]

description:
T24hr_D07_S139
cd8_rsem.txt


title: baseline 53

description:
BL53
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C07_S127]

description:
T24hr_C07_S127
cd8_rsem.txt


title: baseline 48

description:
BL48
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C06_S126]

description:
T24hr_C06_S126
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C05_S125]

description:
T24hr_C05_S125
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C04_S124]

description:
T24hr_C04_S124
cd8_rsem.txt


title: baseline 46

description:
BL46
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C03_S123]

description:
T24hr_C03_S123
cd8_rsem.txt


title: baseline 55

description:
BL55
Raw data file: G1104148.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C02_S122]

description:
T24hr_C02_S122
cd8_rsem.txt


title: baseline 44

description:
BL44
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_C01_S121]

description:
T24hr_C01_S121
cd8_rsem.txt


title: baseline 43

description:
BL43
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 42

description:
BL42
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B11_S119]

description:
T24hr_B11_S119
cd8_rsem.txt


title: baseline 41

description:
BL41
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 39

description:
BL39
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B10_S118]

description:
T24hr_B10_S118
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B09_S117]

description:
T24hr_B09_S117
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B08_S116]

description:
T24hr_B08_S116
cd8_rsem.txt


title: baseline 36

description:
BL36
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B07_S115]

description:
T24hr_B07_S115
cd8_rsem.txt


title: baseline 47

description:
BL47
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 38

description:
BL38
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 35

description:
BL35
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B04_S112]

description:
T24hr_B04_S112
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B05_S113]

description:
T24hr_B05_S113
cd8_rsem.txt


title: baseline 34

description:
BL34
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B02_S110]

description:
T24hr_B02_S110
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B03_S111]

description:
T24hr_B03_S111
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B06_S114]

description:
T24hr_B06_S114
cd8_rsem.txt


title: baseline 33

description:
BL33
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 32

description:
BL32
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 45

description:
BL45
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 31

description:
BL31
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B01_S109]

description:
T24hr_B01_S109
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A12_S108]

description:
T24hr_A12_S108
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_B12_S120]

description:
T24hr_B12_S120
cd8_rsem.txt


title: baseline 40

description:
BL40
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 29

description:
BL29
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 28

description:
BL28
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A10_S106]

description:
T24hr_A10_S106
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A09_S105]

description:
T24hr_A09_S105
cd8_rsem.txt


title: baseline 37

description:
BL37
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 26

description:
BL26
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A08_S104]

description:
T24hr_A08_S104
cd8_rsem.txt


title: baseline 25

description:
BL25
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A07_S103]

description:
T24hr_A07_S103
cd8_rsem.txt


title: baseline 24

description:
BL24
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A06_S102]

description:
T24hr_A06_S102
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A05_S101]

description:
T24hr_A05_S101
cd8_rsem.txt


title: baseline 23

description:
BL23
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 22

description:
BL22
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 21

description:
BL21
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A04_S100]

description:
T24hr_A04_S100
cd8_rsem.txt


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A03_S99]

description:
T24hr_A03_S99
cd8_rsem.txt


title: baseline 19

description:
BL19
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A01_S97]

description:
T24hr_A01_S97
cd8_rsem.txt


title: baseline 30

description:
BL30
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 18

description:
BL18
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 17

description:
BL17
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: WT E12 Small Intestine RNA replicate2

city: Boston

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
E12 MG_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

data_processing:
Alignment: ATAC-seq and ChIP-seq: Bowtie2. RNA-seq: STAR aligner, version 2.5.3a.
ATAC-seq differential region identification: diffReps; Peak calling: MACS2; RNA-seq raw read counts: HTSeq
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: ATAC-Seq & ChIP-seq: bigwig file for visualizing aligned sequence tags (available in tar archives on the series record).
Supplementary_files_format_and_content: RNA-seq:  text file with raw read counts

source_name: Mouse small intestinal epithelial cells

extract_protocol:
E12 small intestines were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: No treatment

value: CD1 wild type

value: Embryonic epithelial cells from the midgut

value: Wild-Type


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A11_S107]

description:
T24hr_A11_S107
cd8_rsem.txt


title: WT E12 Small Intestine RNA replicate1

description:
E12 MG_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: WT E12 HS RNA replicate2

description:
E12 HS_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

source_name: Mouse hindstomach epithelial cells

extract_protocol:
E12 hindstomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Embryonic epithelial cells from the hindstomach


title: baseline 16

description:
BL16
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 15

description:
BL15
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 27

description:
BL27
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: WT E12 HS RNA replicate1

description:
E12 HS_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: WT E12 FS RNA replicate2

description:
E12 FS_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

source_name: Mouse forestomach epithelial cells

extract_protocol:
E12 forestomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Embryonic epithelial cells from the forestomach


title: baseline 13

description:
BL13
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: WT E12 FS RNA replicate1

description:
E12 FS_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: baseline 12

description:
BL12
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 11

description:
BL11
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 14

description:
BL14
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: WT E14 Small Intestine RNA replicate1

description:
E14 MG_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

extract_protocol:
E14 small intestines were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: baseline 20

description:
BL20
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cultured CD8+ T cells stimulated with CD3/CD28, activated for 24 hrs [T24hr_A02_S98]

description:
T24hr_A02_S98
cd8_rsem.txt


title: WT E14 HS RNA replicate1

description:
E14 HS_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

extract_protocol:
E14 hindstomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: baseline 9

description:
BL9
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: WT E14 FS RNA replicate2

description:
E14 FS_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

extract_protocol:
E14 forestomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: baseline 8

description:
BL8
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: WT E14 HS RNA replicate2

description:
E14 HS_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: WT E14 Small Intestine RNA replicate2

description:
E14 MG_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: baseline 6

description:
BL6
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cdx2-/- (deleted at E10) Small Intestine RNA replicate3

description:
E16_MG_E10_Cdx2KO_RNA rep3
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

extract_protocol:
E16 small intestines were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: B6;129 mixed background

value: Embryonic epithelial cells from the small intestine

value: Cdx2f/f; Shh-Cre


title: WT E14 FS RNA replicate1

description:
E14 FS_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: baseline 5

description:
BL5
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cdx2-/- (deleted at E10) Small Intestine RNA replicate2

description:
E16_MG_E10_Cdx2KO_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: baseline 7

description:
BL7
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 3

description:
BL3
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cdx2-/- (deleted at E10) Small Intestine RNA replicate1

description:
E16_MG_E10_Cdx2KO_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: Cdx2-/- (deleted at E13) Small Intestine RNA replicate2

description:
E16_MG_E13_Cdx2KO_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

treatment_protocol: Mice were given an oral gavage of 5mg Tamoxifen

value: Cdx2f/f; Villin-Cre


title: baseline 2

description:
BL2
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: baseline 4

description:
BL4
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: Cdx2-/- (deleted at E13) Small Intestine RNA replicate1

description:
E16_MG_E13_Cdx2KO_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: baseline 1

description:
BL1
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: positive CTRL 10 5765

description:
5765
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

source_name: metastatic colorectal carcinoma

value: FFPE colon adenocarcinoma

value: Positive control


title: WT E16 Small Intestine RNA replicate1

description:
E16 MG_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: WT E16 Small Intestine RNA replicate2

description:
E16 MG_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: WT E16 HS RNA replicate2

description:
E16 HS_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

extract_protocol:
E16 hindstomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: positive CTRL 9 5764

description:
5764
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: baseline 10

description:
BL10
Raw data file: G1104131.xml
Processed data file: none
Belongs to a group of normal samples (non-mutated) used to set up the baseline threshold.


title: WT E16 HS RNA replicate1

description:
E16 HS_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: WT E16 FS RNA replicate2

description:
E16 FS_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

extract_protocol:
E16 forestomachs were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Negative CTRL 10 5762

description:
5762
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

value: Negative control


title: positive CTRL 8 5763

description:
5763
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: positive CTRL 7 5761

description:
5761
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E16 FS RNA replicate1

description:
E16 FS_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: Cdx2-/- (deleted at E15) Small Intestine RNA replicate2

description:
E18_MG_E15_Cdx2KO_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

extract_protocol:
Villi from E18 intestines were isolated by incubation in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were dissociated with 4X TrypLE in DMEM for 45 minutes at 37°C. Cells were immediately used for RNA isolation.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Negative CTR 9 5760

description:
5760
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E18 Small Intestine RNA replicate2

description:
E18 MG_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: positive CTRL 6 5758

description:
5758
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Negative CTR 8 5759

description:
5759
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Cdx2-/- (deleted at E15) Small Intestine RNA replicate1

description:
E18_MG_E15_Cdx2KO_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: positive CTRL 5 5757

description:
5757
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Cdx2-/- Adult Ileum Villus RNA-seq replicate2

description:
Adult Ileum_Cdx2KO_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

source_name: Mouse intestinal villus epithelial cells

extract_protocol:
Villi from distal 1/3rd (ileum) of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were used immediately for RNA extraction.
Total RNA from cells collected in TRIzol reagent (Thermo Fisher Sci.) was extracted with the RNeasy kit (Qiagen) and Dnase treatment.
The TruSeq RNA Sample Preparation Kit V2 (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected i.p. with 1mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre for recombination of conditional alleles, and were sacrificed 3 days after last injection.

value: Adult differentiated ileal epithelial cells; distal 1/3 of intestine

value: adult


title: WT E18 Small Intestine RNA replicate1

description:
E18 MG_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: positive CTRL 2 5753

description:
5753
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Cdx2-/- Adult Ileum Villus RNA-seq replicate1

description:
Adult Ileum_Cdx2KO_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: Negative CTR 7 5755

description:
5755
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: positive CTRL 3 5754

description:
5754
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT Adult Ileum Villus RNA-seq replicate2

description:
Adult Ileum_WT_RNA rep2
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt

treatment_protocol: Mice were injected i.p. with sunflower oil (vehicle for tamoxifen) for 5 consecutive days and were sacrificed 3 days after last injection.


title: WT Adult Ileum Villus RNA-seq replicate1

description:
Adult Ileum_WT_RNA rep1
supplementary file: RNAseq_RawRead_Counts_All_Samples.txt


title: positive CTRL 1 5752

description:
5752
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: WT E14 CDX2 ChIP-seq replicate 1

description:
E14 MG_CDX2 ChIP rep1
supplementary file: E14_CDX2.bw

extract_protocol:
E14 small intestines were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flow cytometry. Cells were immediately cross-linked and snap frozen for subsequent ChIP-seq.
Whole cell lysates were sonicated and incubated with 30 uL CDX2  antibody (#12306, Cell Signaling) overnight for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Negative CTR 6 5751

description:
5751
Raw data file: G1140105.xml
Processed data file: G1140105_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.