title: 3h Serratia marcescens infection 2

city: Strasbourg

first: Dominique

last: Ferrandon

address: 15, rue René Descartes

country: France

institute: UPR9022 CNRS

description: DB11 od10 3h 3

data_processing:
Base calling : Image analysis and base calling were performed using CASAVA 1.7.0 (Sucrose control samples) or CASAVA 1.8.0 (Serratia marcescens infection samples).
Alignment : Reads were mapped to BDGP5.25 assembly of Drosophila genome using Tophat v1.4.1
Quantification : Gene expression was quantified using HTSeq v0.5.3p3 using the “intersection non-empty” mode and gene annotations from Ensembl release 66.
Normalization : Data normalization was performed with DESeq v1.6.1 Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: text file with the following columns : Ensembl gene id, Gene name and one column for each sample containing the normalized read counts

source_name: 3h Serratia marcescens infection

extract_protocol:
At least 10 midguts were dissected per point and immediately placed in TRI Reagent® RT (Molecular Research Center) and crushed. RNAs were then extracted according to the manufacturer's protocol.
A library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “Truseq RNA sample preparation low throughput” protocol with some modifications. Briefly, mRNA was purified from 2 µg total RNA using oligo-dT magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers, then the second strand of the cDNA was synthesized using Polymerase I and RNase H. The next steps of RNA-Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit (ref A84801, Beckman Coulter, Inc) with the SPRI-TE instrument (Beckman Coulter, Inc). Briefly, in this system double stranded cDNA fragments were blunted, phosphorylated and ligated to indexed adapter dimers, and fragments in the range of ~200-400 bp were size selected. The automated steps were followed by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 13 cycles; 5 min at 72°C), then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).

treatment_protocol: Flies were fed on sucrose (50mM) or on sucrose (50mM)/Serratia marcescens Db11 (od10) infection solution for three hours.

tag: tissue

value: midgut

tag: fed on

value: sucrose (50mM)/S. marcescens Db11 (od10) infection solution for 3hrs


title: 3h Serratia marcescens infection 3

status: Public on Nov 22 2016

type: SRA

description: DB11 od10 3h 7

library_source: transcriptomic

molecule: total RNA

organism: Drosophila melanogaster

tag: strain


title: 3h Serratia marcescens infection 1

description: DB11 od10 3h 9


title: ssm_15120802_NC14_12_rep1

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

country: USA

institute: Northwestern University

library_source: genomic

data_processing:
Sequenced reads were barcode-split and adapters were removed using TrimGalore.
Trimmed reads were mapped to the Drosophila melanogaster genome (dm6) using BWA with default parameters.
Alignments were converted to .bam format, duplicates were marked with Picard MarkDuplicates, and reads were filtered for quality score (>= 30), duplication, and were required to be mapped, properly paired, and non secondary alignments.
Only reads corresponding to chr2L, chr2R, chr3L, chr3R, chr4, and chrX were considered for further analysis.
Paired end read fragments <= 98 bp were considered to have originated from 'open' chromatin. Replicates were pooled, and average coverage over open regions was calculated over 10 bp discrete windows. These data are provided as .wig formatted files in the processed data file deposit.
Peaks were called with Zinba on pooled biological replicates spanning either the entire timecourse (per genotype) or spanning entire cell cycles (NC11, NC12, NC13, per genotype). The peaks are provided as a tab-delimited table with annotations.
Nucleosomes within 2500bp regions flanking the maximum open position as called by Zinba were called using NucleoATAC. Both smoothed nucleosome profiles and dyad position/occupancy scores are provided in the processed data file deposit.
Genome_build: dm6
Supplementary_files_format_and_content: Peaks are provided as a tab-delimited text file with additional logical indexers that indicate categories of peak as determined by analysis. Coverage of reads originating from open chromatin are provided as .wig files for each timepoint and genotype. Predicted nucleosome positions are provided in two formats: smoothed nucleosome profiles from NucleoATAC are provided in bedgraph format, and dyad positions and estimated occupancy are provided in a .bed format.

molecule: genomic DNA

growth_protocol: Adults were allowed to lay eggs on yeasted apple juice agar plates. Adults were between 4 and 12 days old for embryo collection.

extract_protocol:
Embryos were observed under a fluorescent microscope until they reached the desired timepoint. Embryos were dechorionated in 4% bleach for 1 minute, washed extensively with water, and macerated in a small volume of extraction buffer. Nuclear pellets were collected and briefly frozen on dry ice.
Frozen nuclear pellets were thawed and fragmented using the Nextera Tn5 transposase solution (Illumina), 2.5 ul per 10 ul reaction. Fragmentation was for 30 minutes at 37 degrees with shaking. Samples were cleaned up with a Qiagen minelute kit and subjected to limited PCR amplification with barcoded primers.

value: w ssm[185b]; His2Av-GFP

value: haploid (sesame)

tag: timepoint

tag: sex type

value: haploid

value: Pool 2

value: CGTACTAG


title: 3h Sucrose control 3

description: Sucrose 3h 8

source_name: 3h Sucrose control

value: sucrose (50mM) for 3hrs


title: ssm_15120804_NC14_03_rep1

value: Pool 3

value: TCCTGAGC


title: ssm_15120901_NC14_03_rep2

value: Pool 1

value: CTCTCTAC


title: 3h Sucrose control 2

description: Sucrose 3h 6


title: ssm_15082504_NC13_12_rep2


title: ssm_15082203_NC13_12_rep1


title: 3h Sucrose control 1

description: Sucrose 3h 3


title: ssm_15082604_NC13_12_rep3

value: GTAGAGGA


title: ssm_15081303_NC13_09_rep3

value: Pool 4

value: AGGCAGAA


title: ssm_15081302_NC13_09_rep2


title: ssm_15082602_NC13_06_rep3

value: CGAGGCTG


title: 80_BSPCR_NS_needle_rep1

city: Fuzhou

first: Haifeng

last: Wang

state: Fujian

address: Shangxia dian

country: China

institute: Fujian Agriculture and Forestry University

data_processing:
BS-seq libraries were sequenced on a HiSeq 2500 system (Illumina) to obtain single-end 100 bp reads.
All BS-seq reads were aligned against the Norway spruce reference genome, as well as the chloroplast genome, using Bismark v0.13.0 with following parameters: -q --score_min L,0,-0.3 -most_valid_alignments 1 --bowtie2.
For BSPCR-seq analysis, only reads with correct BSPCR primers were kept. Primers were then trimmed with custome perl script. Then reads were alinged to the Norway spruce reference genome, as well as the chloroplast genome, using BSMAP(version 2.74) by allowing 2 mismatches(-v2) unique mapped reads (-w1). Then only cytosines over correct PCR regions and PCR strands were kept. Methylation ratio were calculated using #C/(#C+#T).

Genome_build: Norway spruce reference genome.
Supplementary_files_format_and_content: wig files were generated by custom perl script, and show each cytosine methylation levels by #C/(#C+#T).

organism: Picea abies

source_name: needle

extract_protocol:
DNA was extracted from needles of the sequenced Z4006 Picea abies genotype, as described in Nystedt et al 2013 Nature. For the SE culture sample, material was collected at the proliferation stage, as described in Businge et al 2012 Tree Physiol, and DNA extracted as for the needle samples. The culture was generated from seeds obtained from the sequenced ‘Z4006’ genotype.
BS-seq libraries were prepared using the TruSeq DNA LT kit (Illumina) as described previously Du J et al., (2014) Mol Cell, except that EZ DNA Methylation-Lightning Kit (Qiagen) was used for bisulfite conversion of the DNA. BS-Seq libraries were sequenced on a HiSeq 2500 system (Illumina) to obtain single-end 100bp reads per manufacture instructions.
For BSPCR-seq, genomic DNA were bisulfite treated by EZ DNA Methylation-Lightning Kit (Zymo) and then amplified by locus-specific primers. Amplification products were used for library generation. Libraries in repliate 1 were generated by Ovation Ultralow V2 kit (NuGen) and libraries in replicate 2 were generated by TruSeq Nano DNA LT kit (illumina). BSPCR-seq libraries were sequenced on a HiSeq 2000 system (Illumina) to obtain single-end 100bp reads per manufacture instructions.

tag: clone

tag: cell type

value: needle

tag: Stage

value: young needle


title: ssm_15081301_NC13_09_rep1

value: TAAGGCGA


title: 81_BSPCR_NS_needle_rep2


title: ssm_15082503_NC13_06_rep2

value: w ssm[185b]; His2Av-GFP

value: TAGGCATG


title: 78_BSPCR_NS_culture_rep1

source_name: culture

value: somatic embryogenesis

value: proliferation stage


title: 79_BSPCR_NS_culture_rep2


title: ssm_15081402_NC13_06_rep1

value: haploid (sesame)

value: haploid

value: GGACTCCT


title: 77_BSPCR_NS_buds_rep2

source_name: buds

value: bud


title: ssm_15120801_NC14_06_rep1

value: Pool 1


title: 75_BS-seq_needle_rep2


title: 76_BSPCR_NS_buds_rep1


title: ssm_15082603_NC13_03_rep3

value: Pool 2

value: AAGAGGCA


title: ssm_15081704_NC13_03_rep2

value: Pool 4

value: GTAGAGGA


title: 74_BS-seq_needle_rep2


title: ssm_15082502_NC12_09_rep3


title: 73_BS-seq_needle_rep2


title: ssm_15081403_NC12_09_rep2


title: 71_BS-seq_needle_rep2


title: 70_BS-seq_needle_rep2


title: 69_BS-seq_needle_rep2


title: ssm_15081401_NC12_09_rep1

value: TCCTGAGC


title: ssm_15082104_NC12_06_rep2

value: Pool 3


title: ssm_15082601_NC12_03_rep3

value: CAGAGAGG


title: 67_BS-seq_needle_rep2

value: needle

value: young needle


title: ssm_15081703_NC12_06_rep1

value: w ssm[185b]; His2Av-GFP


title: ssm_15082102_NC12_03_rep2

value: ACCACTGT


title: 66_BS-seq_needle_rep2


title: 64_BS-seq_needle_rep2


title: 65_BS-seq_needle_rep2


title: ssm_15082101_NC12_03_rep1

value: GTCGTGAT


title: 63_BS-seq_needle_rep2


title: WT_15042802_NC13_18_rep3

value: w; His2Av-GFP

value: Wild type (diploid)

value: m

value: AGGCAGAA


title: 62_BS-seq_needle_rep2


title: WT_15042404_NC13_18_rep2

value: f

value: CGTACTAG


title: WT_15042806_NC13_15_rep3

value: AAGAGGCA


title: WT_15042201_NC13_18_rep1

value: Pool 1

value: CTCTCTAC


title: 61_BS-seq_needle_rep2


title: 60_BS-seq_needle_rep2


title: ssm_15081701_NC13_03_rep1

value: haploid (sesame)

value: haploid

value: Pool 2


title: WT_15042403_NC13_15_rep2

value: Pool 3

value: GTAGAGGA


title: 72_BS-seq_needle_rep2

value: needle

value: young needle


title: 59_BS-seq_needle_rep2


title: WT_15042105_NC13_15_rep1

value: TCCTGAGC


title: ssm_15082501_NC12_06_rep3

value: w ssm[185b]; His2Av-GFP

value: CCGTTTGT


title: 68_BS-seq_needle_rep2


title: WT_15042305_NC13_12_rep2

value: w; His2Av-GFP

value: Wild type (diploid)

value: GGACTCCT


title: WT_15042902_NC13_12_rep3

value: m


title: 56_BS-seq_needle_rep1


title: 57_BS-seq_needle_rep2


title: 55_BS-seq_needle_rep1


title: WT_15042308_NC13_09_rep2

value: Pool 4

value: CAGAGAGG


title: 54_BS-seq_needle_rep1


title: WT_15042805_NC13_09_rep3

value: f

value: Pool 1


title: 53_BS-seq_needle_rep1


title: 52_BS-seq_needle_rep1


title: WT_15042206_NC13_06_rep2


title: 51_BS-seq_needle_rep1


title: WT_15042307_NC13_09_rep1

value: CTCTCTAC


title: WT_15042704_NC13_06_rep3

value: Pool 2


title: 50_BS-seq_needle_rep1


title: WT_15042804_NC13_03_rep3


title: 49_BS-seq_needle_rep1


title: 47_BS-seq_needle_rep1


title: 48_BS-seq_needle_rep1


title: WT_15042306_NC13_03_rep2

value: TAGGCATG


title: WT_15042103_NC13_06_rep1

value: CGTACTAG


title: 46_BS-seq_needle_rep1

value: needle


title: 45_BS-seq_needle_rep1

value: young needle


title: WT_15042205_NC13_03_rep1

value: AAGAGGCA


title: 58_BS-seq_needle_rep2


title: WT_15042803_NC12_12_rep4

value: CGAGGCTG


title: 44_BS-seq_needle_rep1


title: WT_15042304_NC12_12_rep2

value: TCCTGAGC


title: WT_15042702_NC12_12_rep3

value: w; His2Av-GFP


title: WT_15042204_NC13_12_rep1

value: Wild type (diploid)


title: 43_BS-seq_needle_rep1


title: 41_BS-seq_needle_rep1


title: WT_15042701_NC12_09_rep3

value: Pool 3

value: GGACTCCT


title: WT_15042104_NC12_12_rep1

value: m

value: AGGCAGAA


title: WT_15042303_NC12_09_rep2


title: 40_BS-seq_needle_rep1


title: WT_15042107_NC12_09_rep1

value: f


title: 39_BS-seq_needle_rep1


title: 38_BS-seq_needle_rep1


title: WT_15042405_NC12_06_rep3

value: TAAGGCGA


title: 36_BS-seq_culture_rep2

value: somatic embryogenesis

value: proliferation stage


title: 37_BS-seq_culture_rep2


title: 35_BS-seq_culture_rep2


title: WT_15042302_NC12_03_rep3


title: WT_15042202_NC12_03_rep2

value: CAGAGAGG


title: 34_BS-seq_culture_rep2


title: WT_15042102_NC12_06_rep1


title: WT_15042401_NC12_06_rep2

value: Pool 1


title: 31_BS-seq_culture_rep2


title: 32_BS-seq_culture_rep2


title: 42_BS-seq_needle_rep1

value: needle


title: 30_BS-seq_culture_rep2


title: WT_15121604_NC11_09_rep2

value: mixed


title: WT_15042106_NC12_03_rep1

value: Pool 4


title: WT_15121603_NC11_06_rep2

value: Pool 2


title: WT_15121801_NC11_06_rep3

value: TAGGCATG


title: 28_BS-seq_culture_rep2


title: WT_15121802_NC11_03_rep3

value: w; His2Av-GFP

value: CTCTCTAC


title: 27_BS-seq_culture_rep2


title: WT_15121602_NC11_03_rep2

value: Wild type (diploid)

value: Pool 3


title: WT_15121504_NC11_06_rep1


title: WT_15121503_NC11_09_rep1

value: CCACTCCT


title: 26_BS-seq_culture_rep2


title: 25_BS-seq_culture_rep2


title: WT_15121502_NC11_03_rep1

value: TTGACCCT


title: 23_BS-seq_culture_rep2


title: 24_BS-seq_culture_rep2


title: 22_BS-seq_culture_rep2


title: 33_BS-seq_culture_rep2


title: 21_BS-seq_culture_rep2


title: 20_BS-seq_culture_rep2


title: 5-8

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

description:
ribosome-depleted RNA
DOPP5.csv

data_processing:
Unmapped BAM files were imported into CLC Genomics Workbench (7.0.4, CLC bio, Aarhus, Denmark). Sequence quality was verified by inspection of quality control reports and samples were processed using CLC Genomics Server (6.0, CLC bio).
Reads were quality trimmed (error probability 0.01) with default parameters in CLC Genomics Workbench.
Trimemd reads were mapped to the RefSeq assembly (Mus musculus GRCm38.p1) and BAM files were exported.
The number of reads mapped to the exon sequences of annotated genes was determined using FeatureCounts (Liao et al. 2014).
Differential expression analyses between sample groups were performed by fitting the expression data to a generalized linear model using edgeR-robust.
Genome_build: GRCm38.p1
Supplementary_files_format_and_content: Comma separated values output from edgeR with NCBI gene accession, gene symbol, gene name and read counts.

organism: Mus musculus

source_name: endometrium

growth_protocol: Female PUGKO mice were produced as prevously described. Briefly, all C57BL/6J females in a litter received subcutaneous injections of progesterone (50 μg/g body weight in sesame oil) from postnatal days 2 through 10 (day 0 = birth). Adult (6-10 week old) C57BL/6J wildtype and PUGKO females were mated with vasectomized males to induce pseudopregnancy.

extract_protocol:
Qiagen RNeasy Plus Mini kit was used to extract total RNA. Samples of total RNA (5 μg) were depleted of ribosomal RNA using Ribominus Eukaryote System v2 (Ambion).
Ion Total RNA-seq Kit v2 (Life Technologies) was used to construct strand-specific sequencing libraries from ribosomal-depleted samples (20 ng).

tag: time point (day)

tag: genotype/variation

value: PUGKO


title: WT_15121804_NC11_09_rep3

value: CGAGGCTG


title: 5-5

description:
ribosome-depleted RNA
DOPP5.csv


title: 5-6

description:
ribosome-depleted RNA
DOPP5.csv


title: 5-7

description:
ribosome-depleted RNA
DOPP5.csv


title: 5-4

description:
ribosome-depleted RNA
DOPP5.csv

value: Wild-type


title: 19_BS-seq_culture_rep1

value: somatic embryogenesis

value: proliferation stage


title: 17_BS-seq_culture_rep1


title: 5-1

description:
ribosome-depleted RNA
DOPP5.csv


title: 18_BS-seq_culture_rep1


title: 29_BS-seq_culture_rep2


title: 5-2

description:
ribosome-depleted RNA
DOPP5.csv


title: 16_BS-seq_culture_rep1


title: 5-3

description:
ribosome-depleted RNA
DOPP5.csv


title: 14_BS-seq_culture_rep1


title: CR

city: Nicosia

first: Antonis

last: Kirmizis

address: 1 University Avenue, PO BOX 20537

department: Department  of Biological Sciences

country: Cyprus

institute: University of Cyprus

data_processing:
Quality of the sequenced reads was checked by FastQC 0.11.1. The reads were mapped to the reference yeast genome sequence sacCer3 (UCSC/SGD Apr2011) using GSNAP 2014-09-30.
Only uniquely mapped reads were considered for further analysis. Mapped reads were post-processed using SAMtools 0.1.16
Gene abundance was quantified using HTSeq-count 0.6.1, with the Ensembl gene annotation (release 78) and with taking strandeness of the sequencing protocol into the account.
Gene expression analysis was performed using Bioconductor R package edgeR 3.8.2. Differential gene expression was calculated using information from each condition using generalized linear model with tagwise dispersion and FDR correction according to the edgeR vignette.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include RPKM

organism: Saccharomyces cerevisiae

source_name: Wild-type cells grown in 0.1% glucose

growth_protocol: Cells were grown overnight in liquid rich (YPAD) medium at 30°C. Cultures were then diluted to O.D. 0.1 in medium with either 2% or 0.1% glucose and grown to mid-exponential phase (O.D. 0.8). Cells were collected and processed immediately in downstream applications.

extract_protocol:
Total RNA from logarithmically grown (O.D. 0.8) yeast cells was isolated using the hot phenol extraction method [Schmitt ME et al., Nucleic Acids Res 1990] and then treated with TURBO DNA-free DNase kit (Ambion, AM1907).
cDNA libraries were prepared from 10μg of total RNA using the Illumina mRNA-Seq-Sample Prep Kit according to manufacturer's instructions. cDNA fragments of ~400 bp were purified from each library and confirmed for quality by Agilent 2100 Bioanalyzer.

tag: growth phase

value: Exponential

value: wild-type


title: NCR

source_name: Wild-type cells grown in 2% glucose


title: 15_BS-seq_culture_rep1


title: 4-7

description:
ribosome-depleted RNA
DOPP4.csv


title: 4-6

description:
ribosome-depleted RNA
DOPP4.csv


title: 4-8

description:
ribosome-depleted RNA
DOPP4.csv


title: Input DNA

city: Birmingham

first: Saverio

last: Brogna

address: Edgbaston

country: United Kingdom

institute: University Birmingham

data_processing:
Reads were then filtered for high quality reads where read quality was greater than 15 using Samtools.
ChIP reads were mapped to the Drosophila genome (BDGP R5/dm3 Assembly) using the bioscope mapping tool (Life Technologies).
ChIP peaks were called using MACS and MACS ChIP wiggle tracks were then generated.
Genome_build: BDGP R5/dm3 Assembly
Supplementary_files_format_and_content: .wig files

source_name: S2 cells

growth_protocol: Drosophila embryo driven S2 cells were cultured in Insect–XPRESS medium (Lonza) supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin-Glutamine mix (P/S/G) (Invitrogen) at 27°C.

extract_protocol:
Chromatin was purified using AMPure XP beads (Beckman Coulter). ChIP and input DNA were further fragmented to 250 bp fragment size using a Covaris S2 focused ultrasonicator prior to library preparation
Library preparation, sequencing  was using SOLiD 4 genome technology, using a SOLiD Fragment Library Construction Kit (Life Technologies).
ChIP DNA was barcoded using the SOLiD Fragment Library Barcoding Kit Module 1–16. Sequencing libraries were run on a SOLiD 4 genome analyzer.

value: S2 cells

tag: antibodu

value: none, Input


title: nat4D

source_name: Cells deleted in Nat4

value: Nat4-deletion mutant


title: 4-5

description:
ribosome-depleted RNA
DOPP4.csv


title: WT

source_name: Wild-type cells


title: 4-4

description:
ribosome-depleted RNA
DOPP4.csv


title: Y14 ChIP

value: Y14 ChIP


title: 13_BS-seq_culture_rep1


title: os2HS

city: Saint Paul

first: Nora

last: Plesofsky

state: MN

address: 1479 Gortner Avenue

department: Plant Biology

institute: University of Minnesota

data_processing:
Primary analysis was performed with Illumina's CASAVA software 1.8.2
De-multiplexing was performed with Illumina's CASAVA software 1.8.2
Quality of sequence data was checked with FastQC, using Galaxy program through the University of Minnesota MSI
Reads were aligned by TopHat to the Neurospora crassa 74a_12 supercontigs reference genome and to the 74a_12 transcripts.gtf
Cufflinks was used to normalize transcript expression levels
Cuffdiff was used to compare differentially expressed transcripts between strains and treatments
Genome_build: 74a_12 Supercontigs

organism: Neurospora crassa

source_name: germinating (5 hr) conidia

growth_protocol: Fresh water-harvested conidia were cultured for 5 hr in liquid Vogel's medium, containing 0.05% glucose, in a 30 degree shaking water bath

extract_protocol:
RNAzolRT from MRC
Illumina's Truseq RNA Sample Preparation Kit, including oligo-dT purification and reverse transcription to create cDNA, which was fragmented, blunt-ended, and ligated to indexed (barcoded) adaptors.

treatment_protocol:
2 hr at 45 degrees (HS)
Control cultures were kept an additional hr at 30 degrees, whereas the stress treatments (either heat shock or dual stress) were administered for 2 hr in a 45 degree shaking water bath

tag: developmental stage

value: germinating (5 hr) conidia

value: UCLA 80A

tag: hrs of germination

value: 5 hr at 30 degrees

tag: genotype

value: os230 mutant


title: os2DS

treatment_protocol:
2 hr at 45 degrees plus 2-DG (DS)
Control cultures were kept an additional hr at 30 degrees, whereas the stress treatments (either heat shock or dual stress) were administered for 2 hr in a 45 degree shaking water bath


title: 4-3

description:
ribosome-depleted RNA
DOPP4.csv


title: 11_BS-seq_culture_rep1


title: os230

treatment_protocol:
1 hr at 30 degrees (contrtol)
Control cultures were kept an additional hr at 30 degrees, whereas the stress treatments (either heat shock or dual stress) were administered for 2 hr in a 45 degree shaking water bath


title: 4-2

description:
ribosome-depleted RNA
DOPP4.csv


title: 10_BS-seq_culture_rep1


title: wtHS

value: wild type


title: wtDS


title: wt30


title: 9_BS-seq_culture_rep1


title: 4-1

description:
ribosome-depleted RNA
DOPP4.csv


title: 6_BS-seq_culture_rep1


title: 7_BS-seq_culture_rep1


title: 3-6

description:
ribosome-depleted RNA
DOPP3.csv


title: 3-8

description:
ribosome-depleted RNA
DOPP3.csv


title: 8_BS-seq_culture_rep1


title: 3-4

description:
ribosome-depleted RNA
DOPP3.csv


title: 3-7

description:
ribosome-depleted RNA
DOPP3.csv


title: 3-3

description:
ribosome-depleted RNA
DOPP3.csv


title: 5_BS-seq_culture_rep1


title: 4_BS-seq_culture_rep1


title: 3-5

description:
ribosome-depleted RNA
DOPP3.csv


title: S13176_788532_hOKT3_NR_24mo_WB

status: Public on Nov 21 2016

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

data_processing:
Reads were aligned using Omicsoft Sequence Aligner (OSA, v.1.7.3) with OShell (v.6.1.0.2) using default parameters and a gene models index provided for Ensembl version 66.
Read counts per Ensembl gene ID were estimated using htseq-count (v.0.5.4p3).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Samples were selected for further analysis by using these criteria: log10(PF_ALIGNED_BASES)>6.5, MEDIAN_CV_COVERAGE<1 & MEDIAN_CV_COVERAGE >0.4.
Genes expressed (counts per million >1) in less than 3 samples were removed. Data normalization (TMM) and differential expression analysis were performed in R using "edgeR" package.
Genome_build: GRCh37
Supplementary_files_format_and_content: combined_ABATE_raw_counts_after_qc_063016_not_collapsed.txt is a tab-delimited matrix. The first column contains the Ensembl gene ID. The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.
Supplementary_files_format_and_content: metrics_ABATE_after_qc_063016.txt is a tab-delimited matrix. The first column contains library ID, remaining columns include RNA sequencing and alignment metrics.

molecule: polyA RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Total RNA was globin reduced with GLOBINclear (Ambion, TX) according to manufacturer’s instructions.
Libraries were prepared from globin reduced RNA samples using the TruSeq RNA Sample Preparation kit v2 according to manufacturer's instructions (Illumina, San Diego, CA).

tag: samplelabel

tag: sampleID

tag: status

value: NR

tag: itn name

tag: studysiteshort

value: YALE

tag: age

tag: gender

value: Male

tag: treatmentgroup

tag: race

value: White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

value: TruSeq RNA v2

tag: projectid

tag: seqsite

value: Covance

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3

tag: lane


title: 1_BS-seq_culture_rep1

tag: clone

tag: cell type

value: somatic embryogenesis

tag: Stage

value: proliferation stage


title: 12_BS-seq_culture_rep1


title: 3-1

description:
ribosome-depleted RNA
DOPP3.csv

tag: time point (day)

tag: genotype/variation

value: Wild-type


title: S13177_229085_hOKT3_NR_24mo_WB

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race


title: 2_BS-seq_culture_rep1


title: S13173_738493_hOKT3_R_24mo_WB

value: R

value: Female

value: White; White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: S13174_166103_Control_C_24mo_WB

tag: samplelabel

tag: sampleID

value: C

value: Control

tag: runchemistry

tag: lane


title: S13172_283344_hOKT3_R_24mo_WB

tag: status

tag: itn name

tag: studysiteshort

tag: age


title: S13171_266365_hOKT3_R_24mo_WB

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode


title: S13167_838213_hOKT3_R_24mo_WB

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tag: visitmonth

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title: S13168_618372_hOKT3_R_24mo_WB

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tag: samplelabel

tag: sampleID

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tag: lane


title: S13170_678610_hOKT3_NR_24mo_WB

tag: status

tag: itn name

tag: studysiteshort

tag: age


title: 3_BS-seq_culture_rep1

tag: clone

tag: cell type

tag: Stage


title: S13165_161201_Control_C_24mo_WB

tag: gender

tag: treatmentgroup

tag: race

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tag: siteandparticipantcode

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title: S13164_595950_hOKT3_NR_24mo_WB

tag: samplelabel

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title: S13163_229642_hOKT3_NR_24mo_WB

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title: S13158_666079_hOKT3_R_24mo_WB

value: PNRI

tag: gender

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tag: race

value: White; American Indian or Alaska Native

tag: trunkbarcode


title: S13161_689968_Control_C_24mo_WB

tag: samplelabel

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth


title: 3-2

description:
ribosome-depleted RNA
DOPP3.csv

tag: time point (day)

tag: genotype/variation


title: S13157_623229_Control_C_24mo_WB

tag: sampleID

value: Black or African American; White

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: S13156_642173_hOKT3_NR_24mo_WB

tag: status

value: NR

tag: itn name

tag: studysiteshort

value: BRI-VM

tag: age

tag: runchemistry

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title: S13159_693516_hOKT3_NR_24mo_WB

tag: samplelabel

tag: gender

value: Male

tag: treatmentgroup

tag: race

value: White

tag: trunkbarcode

tag: siteandparticipantcode


title: S13160_314565_Control_C_24mo_WB

tag: sampleID

tag: visitnumber

tag: visitmonth

tag: libraryid

value: TruSeq RNA v2

value: Covance


title: S13155_785228_hOKT3_R_24mo_WB

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

value: TruSeq SBS Kit v3


title: S13175_921524_hOKT3_NR_24mo_WB

tag: status

tag: itn name

tag: studysiteshort

value: YALE

tag: age


title: 4533C5

city: Atlanta

first: Mehul

middle: Shamal

last: Suthar

state: GA

address: 954 Gatewood Road, Office 2022

institute: Emory University

data_processing:
Bam files generated using TopHat alignment software using Illumina's Basespace
Samples were filtered with normalized read counts across all samples >1
One read count was added to each of the genes across all samples.  This provides a value to genes which show no read counts and allows for appropriate calculations of fold change.  As a result, low abundance transripts are more influenced by highly expressed transcripts.
The processed data file was processed using Tibco Spotfire version 7.0 with OmicsOffice. We used the NGS SeqSolve function.  This sofware utilizes Cufflinks to generate raw read counts.  Read counts were normalized using DESeq2 through R software and data was imported into Tibco Spotfire version 7.0 for further data analysis.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: text file with DESeq-normalized read counts.

source_name: CD8+ T cells (P14)

extract_protocol:
Total RNA was prepared using the QIAGEN RNEasy Micro Kit.
Libraries were generated using the CLONTECH SMARTer HV kit, barcoding and sequencing primers were added using NexteraXT DNA kit.  Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.

tag: strain

tag: timepoint

tag: tissue

value: Splenic red pulp

tag: cell type

value: CD8+ T cells (P14)


title: 4333C3


title: S13151_770569_hOKT3_R_24mo_WB

tag: samplelabel

value: R

tag: gender

tag: treatmentgroup

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tag: runchemistry

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title: S13153_214040_hOKT3_NR_24mo_WB

tag: sampleID

value: Female

value: American Indian or Alaska Native; White

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: 4433C4

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: S13152_289534_hOKT3_NR_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race


title: S13150_800847_hOKT3_R_24mo_WB

tag: sampleID

value: COLORADO

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: runchemistry

tag: lane


title: 3415C4

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: 3515C5


title: S13149_268024_hOKT3_R_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: S13166_781179_Control_C_24mo_WB

tag: sampleID

value: C

tag: age

tag: gender

tag: treatmentgroup

value: Control

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: 3315C3

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: 3215C2


title: S13154_555647_Control_C_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: visitmonth

tag: libraryid

tag: runchemistry

tag: lane


title: S13148_612273_hOKT3_NR_24mo_WB

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: 3115C1

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: S13147_325907_hOKT3_NR_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S13162_604690_Control_C_24mo_WB

tag: sampleID

value: MC GEORGIA

tag: age

tag: gender

tag: treatmentgroup

tag: visitmonth

tag: libraryid

tag: runchemistry

tag: lane


title: S13146_156104_Control_C_24mo_WB

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: 2411C4

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: 2111C1


title: 157C5


title: 2211C2


title: 2311C3


title: S13140_768498_hOKT3_R_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

value: UCSF

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S13142_692210_Control_C_24mo_WB

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

value: White; Asian

tag: visitmonth

tag: libraryid

tag: runchemistry

tag: lane


title: S13141_255654_hOKT3_R_24mo_WB

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: S13143_676063_hOKT3_R_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort


title: S13144_445249_Control_C_24mo_WB

value: Male

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S13137_106306_hOKT3_R_24mo_WB

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup


title: 117C1

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: S13136_537789_Control_C_24mo_WB

value: White

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: 50C5


title: S13138_479125_Control_C_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

value: TruSeq RNA v2


title: 40C4

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: S13135_869009_hOKT3_NR_24mo_WB

tag: sampleID

value: NR

tag: age

tag: gender

tag: treatmentgroup

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid

value: Covance


title: S13134_122083_hOKT3_NR_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

value: Black or African American; White

tag: seqsite

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3

tag: lane


title: 2511C5

tag: strain

tag: timepoint

tag: tissue

value: Splenic red pulp

tag: cell type

value: CD8+ T cells (P14)


title: 30C3


title: S13145_443762_hOKT3_NR_24mo_WB

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S13133_475166_Control_C_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

value: Female

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid


title: S13132_333398_hOKT3_R_24mo_WB

value: R

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: 10C1

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: 5033T5

value: Splenic white pulp


title: 20C2


title: S13139_464149_hOKT3_R_24mo_WB

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: 137C3


title: S13131_397935_hOKT3_NR_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

value: White; Other

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid


title: 4933T4

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: 4833T3


title: S13129_326726_hOKT3_NR_24mo_WB

tag: sampleID

value: COLUMBIA

tag: age

tag: gender

tag: treatmentgroup

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: 147C4


title: 4733T2


title: S13130_242972_Control_C_24mo_WB

tag: samplelabel

tag: status

value: C

tag: itn name

tag: studysiteshort

value: Control

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S13128_406442_hOKT3_NR_24mo_WB

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid


title: 4633T1

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: S13124_853089_Control_C_24mo_WB

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S13126_209864_hOKT3_NR_24mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S13127_493934_hOKT3_NR_24mo_WB

value: Black or African American

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid


title: 3715T2

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: 3615T1


title: 3915T4


title: 3815T3


title: 2911T4


title: 3011T5


title: S12648_738493_hOKT3_R_6mo_WB

tag: sampleID

value: YALE

tag: age

tag: gender

tag: treatmentgroup

value: White; White

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S12647_283344_hOKT3_R_6mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: race

value: White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

value: TruSeq RNA v2


title: 2811T3

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: 2711T2


title: S12646_678610_hOKT3_NR_6mo_WB

tag: sampleID

value: NR

tag: age

tag: gender

tag: treatmentgroup

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid

value: Covance


title: S12645_229085_hOKT3_NR_6mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

value: Male

tag: seqsite

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3

tag: lane


title: 2611T1

tag: strain

tag: timepoint

tag: tissue

tag: cell type

value: CD8+ T cells (P14)


title: S12643_838213_hOKT3_R_6mo_WB

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S12644_618372_hOKT3_R_6mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

value: Female

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid


title: 207T5

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: 197T4


title: 187T3


title: S12641_161201_Control_C_6mo_WB

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S12642_781179_Control_C_6mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S13125_137567_hOKT3_R_24mo_WB

value: R

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid


title: 167T1

tag: strain

tag: timepoint

tag: tissue

value: Splenic white pulp

tag: cell type


title: S12650_788532_hOKT3_NR_6mo_WB

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: 100T5


title: 4015T5


title: S12639_604690_Control_C_6mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

value: MC GEORGIA

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S12640_595950_hOKT3_NR_6mo_WB

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid


title: 90T4

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: S12638_371894_hOKT3_R_6mo_WB

tag: sampleID

value: PNRI

tag: age

tag: gender

tag: treatmentgroup

value: Other

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S12649_921524_hOKT3_NR_6mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: 80T3

tag: strain

tag: timepoint

tag: tissue

tag: cell type


title: S12637_689968_Control_C_6mo_WB

tag: sampleID

value: C

tag: age

tag: gender

tag: treatmentgroup

value: Control

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid


title: S12635_693516_hOKT3_NR_6mo_WB

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S12633_555647_Control_C_6mo_WB

value: BRI-VM

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber


title: S12632_214040_hOKT3_NR_6mo_WB

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

value: American Indian or Alaska Native; White


title: S33359_618372_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Samples were selected for further analysis by using these criteria: log10(PF_ALIGNED_BASES)>6.5, MEDIAN_CV_COVERAGE<1 & MEDIAN_CV_COVERAGE >0.4.
Genes expressed (counts per million >1) in less than 3 samples were removed. Data normalization (TMM) and differential expression analysis were performed in R using "edgeR" package.
Genome_build: GRCh38
Supplementary_files_format_and_content: AbATE_P54_bulk_raw_counts.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.
Supplementary_files_format_and_content: AbATE_P54_bulk_keep_R_qc.txt is a tab-delimited matrix. The first column contains library ID, remaining columns include RNA sequencing and alignment metrics.

source_name: CD8+ sorted T-cells

extract_protocol:
Full-length cDNA was prepared from 500-1000 cells using SMARTer Ultra Low Input RNA Kit for Sequencing - v3 according to manufacturer’s instructions (Clontech, Mountain View, CA).
Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer’s instructions (Illumina, San Diego, CA).

value: YALE

value: White

tag: visitmonth

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT+ KLRG1+

tag: stim

value: anti-CD3 anti-CD28 Stimulated + PVR-fc treated

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

value: SMARTer v3

tag: libraryprep

value: NexteraXT

tag: projectid

value: BRI

value: HiSeq SBS Kit v4


title: S33358_618372_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: samplelabel

tag: status

value: R

tag: itn name

tag: studysiteshort

value: Female

tag: race

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: 70T2

tag: strain

tag: timepoint

tag: tissue

value: Splenic white pulp

tag: cell type

value: CD8+ T cells (P14)


title: S33355_618372_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: sortmarkers

tag: stim

value: anti-CD3 anti-CD28 Stimulated

tag: numcellssorted

tag: samplebarcode

tag: libraryid


title: 60T1

tag: strain


title: S33360_618372_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: samplelabel

tag: status

tag: itn name

tag: studysiteshort

tag: race

tag: cdnasynthesis

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S33354_618372_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_tr

tag: sampleID

tag: age

tag: gender

tag: treatmentgroup

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT- KLRG1-

tag: stim


title: S12627_612273_hOKT3_NR_6mo_WB

tag: samplelabel

tag: status

value: NR

tag: itn name

tag: studysiteshort

value: COLORADO

value: Male

tag: race

tag: libraryid

value: TruSeq RNA v2

value: Covance

value: TruSeq SBS Kit v3


title: S12626_325907_hOKT3_NR_6mo_WB

value: White

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: S12631_289534_hOKT3_NR_6mo_WB

tag: sampleID

value: BRI-VM

tag: age

tag: gender

tag: treatmentgroup

tag: trunkbarcode

tag: siteandparticipantcode


title: S33357_618372_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: samplelabel

tag: status

value: YALE

tag: visitnumber

tag: visitmonth

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT+ KLRG1+

tag: stim

value: anti-CD3 anti-CD28 Stimulated + PVR-fc treated

tag: numcellssorted

tag: samplebarcode

tag: cdnasynthesis

value: SMARTer v3

value: NexteraXT


title: S33350_618372_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr

value: R

tag: itn name

tag: studysiteshort

value: Female

tag: race

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

value: BRI

tag: flowcellid

tag: runchemistry

value: HiSeq SBS Kit v4


title: S12630_770569_hOKT3_R_6mo_WB

tag: samplelabel

tag: sampleID

tag: status

tag: age

tag: gender

tag: treatmentgroup

tag: trunkbarcode

tag: siteandparticipantcode

tag: lane


title: S33352_618372_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_tr

tag: itn name

tag: studysiteshort

tag: visitnumber

tag: visitmonth

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT- KLRG1-

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: cdnasynthesis


title: S12636_314565_Control_C_6mo_WB

tag: samplelabel

tag: sampleID

value: C

value: PNRI

value: Control

tag: race

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry


title: S33356_618372_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: trunkbarcode

tag: siteandparticipantcode

tag: lane


title: S12629_800847_hOKT3_R_6mo_WB

tag: samplelabel

tag: sampleID

value: COLORADO

value: Male

tag: visitnumber

tag: visitmonth

value: TruSeq RNA v2

value: Covance


title: S33348_618372_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr

value: YALE

tag: race

value: White

tag: sortmarkers

tag: stim

value: anti-CD3 anti-CD28 Stimulated

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

tag: projectid


title: S12622_443762_hOKT3_NR_6mo_WB

tag: status

value: NR

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: seqsite

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3


title: S33353_618372_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: samplelabel

tag: sampleID

value: R

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT+ KLRG1+

value: SMARTer v3

value: NexteraXT

tag: lane


title: S33351_618372_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: status

tag: itn name

value: Female

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

tag: projectid

value: BRI

value: HiSeq SBS Kit v4


title: S33290_838213_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: samplelabel

tag: sampleID

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

value: White; White

value: anti-CD3 anti-CD28 Stimulated + PVR-fc treated

tag: seqsite

tag: flowcellid

tag: runchemistry


title: S12624_707556_Control_C_6mo_WB

tag: status

value: C

tag: itn name

value: COLORADO

value: Male

value: Control

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: lane


title: S33349_618372_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: samplelabel

value: YALE

value: White

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

tag: projectid


title: S12617_479125_Control_C_6mo_WB

tag: sampleID

tag: status

tag: studysiteshort

value: UCSF

tag: age

tag: gender

tag: treatmentgroup

value: TruSeq RNA v2

tag: seqsite

value: Covance

tag: flowcellid

tag: runchemistry


title: S12623_445249_Control_C_6mo_WB

tag: samplelabel

tag: itn name

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

value: TruSeq SBS Kit v3

tag: lane


title: S12634_785228_hOKT3_R_6mo_WB

tag: sampleID

value: R

value: BRI-VM

tag: libraryid

tag: libraryprep

tag: projectid


title: S33347_618372_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: status

tag: studysiteshort

tag: age

tag: gender

value: Female

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT+ KLRG1+

tag: stim

value: anti-CD3 anti-CD28 Stimulated

tag: numcellssorted

tag: samplebarcode

tag: cdnasynthesis

value: SMARTer v3

value: NexteraXT


title: S12614_122083_hOKT3_NR_6mo_WB

tag: samplelabel

value: NR

tag: itn name

tag: treatmentgroup

tag: race

value: Black or African American; White

tag: trunkbarcode

tag: siteandparticipantcode

tag: seqsite

tag: flowcellid

tag: runchemistry


title: S12621_768498_hOKT3_R_6mo_WB

tag: sampleID

tag: status

tag: studysiteshort

value: Male

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid

tag: lane


title: S33282_838213_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: samplelabel

tag: itn name

tag: age

tag: gender

value: White; White

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: cdnasynthesis

value: BRI

value: HiSeq SBS Kit v4


title: S12612_333398_hOKT3_R_6mo_WB

tag: sampleID

tag: status

value: UCSF

tag: treatmentgroup

tag: race

value: White

tag: trunkbarcode

tag: siteandparticipantcode

tag: seqsite

tag: flowcellid

tag: runchemistry


title: S12628_268024_hOKT3_R_6mo_WB

tag: samplelabel

tag: itn name

tag: studysiteshort

value: COLORADO

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

value: TruSeq RNA v2

tag: projectid

value: Covance

tag: lane


title: S33280_838213_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: sampleID

tag: status

value: R

value: YALE

tag: age

tag: gender

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: cdnasynthesis


title: S12620_692210_Control_C_6mo_WB

tag: samplelabel

value: C

tag: itn name

value: Female

tag: treatmentgroup

value: Control

tag: race

value: White; Asian

tag: trunkbarcode

tag: siteandparticipantcode

tag: seqsite

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3


title: S12619_676063_hOKT3_R_6mo_WB

tag: sampleID

tag: status

tag: studysiteshort

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid

tag: lane


title: S33289_838213_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: samplelabel

tag: itn name

tag: age

tag: gender

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT+ KLRG1+

tag: stim

value: anti-CD3 anti-CD28 Stimulated + PVR-fc treated

tag: numcellssorted

tag: samplebarcode

tag: cdnasynthesis

value: SMARTer v3

value: NexteraXT


title: S12610_242972_Control_C_6mo_WB

tag: sampleID

tag: status

value: Male

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: seqsite

tag: flowcellid

tag: runchemistry


title: S33288_838213_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: samplelabel

tag: itn name

tag: studysiteshort

value: White; White

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid

value: BRI

value: HiSeq SBS Kit v4

tag: lane


title: S12618_464149_hOKT3_R_6mo_WB

tag: sampleID

tag: status

value: UCSF

tag: age

tag: gender

value: White

value: TruSeq RNA v2


title: S12625_156104_Control_C_6mo_WB

value: COLORADO

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

value: Covance


title: S33278_838213_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: samplelabel

value: R

value: YALE

tag: sortmarkers

tag: stim

value: anti-CD3 anti-CD28 Stimulated

tag: numcellssorted

tag: samplebarcode

tag: cdnasynthesis

tag: seqsite

tag: flowcellid

tag: runchemistry


title: S33287_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_tr

tag: sampleID

tag: itn name

tag: studysiteshort

tag: visitnumber

tag: visitmonth

value: CD8+ CD45R0+ TIGIT- KLRG1-

tag: libraryid

tag: libraryprep

tag: projectid

tag: lane


title: S33286_838213_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: samplelabel

tag: status

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT+ KLRG1+


title: S12616_106306_hOKT3_R_6mo_WB

tag: sampleID

tag: itn name

value: Female

value: American Indian or Alaska Native; White

tag: seqsite

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3


title: S33285_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_tr

tag: studysiteshort

value: Male

tag: visitnumber

tag: visitmonth

tag: stim

value: anti-CD3 anti-CD28 Stimulated + PVR-fc treated

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

value: SMARTer v3

tag: libraryprep

value: NexteraXT


title: S12615_537789_Control_C_6mo_WB

tag: samplelabel

tag: status

value: C

value: UCSF

tag: age

tag: gender

tag: treatmentgroup

value: Control

tag: race

tag: trunkbarcode

tag: projectid

tag: lane


title: S33284_838213_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: sampleID

tag: itn name

tag: studysiteshort

value: White; White

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: seqsite

value: BRI

tag: flowcellid

tag: runchemistry

value: HiSeq SBS Kit v4


title: S33283_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr

tag: samplelabel

tag: status

value: R

value: YALE

tag: visitmonth

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

tag: libraryprep


title: S32729_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: sampleID

tag: itn name

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: projectid

tag: lane


title: S32728_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_tr

tag: samplelabel

tag: status

tag: studysiteshort

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT- KLRG1-

tag: seqsite

tag: flowcellid

tag: runchemistry


title: RNA-seq_HCT116_arid1aMM1

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

data_processing:
The sequenced reads from each sample were aligned to the human genome+transcriptome assembly GRCh37.72 using TopHat v2.0.8 with default parameters except turning off novel junction search ( -G <gtf> --no-novel-juncs).
Genomic coverage was calculated in R using BioConductor packages Rsamtools and Granges
Genome_build: hg19
Supplementary_files_format_and_content: wig file showing unnormalized RNA-seq coverage

growth_protocol: HCT116 isogenic cell lines were cultured in RPMI 1640 with 10% FBS as per provider's instructions (Horizon Discovery Catalog # HD104-031, #HD 104-04).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and further purified using RNeasy MinElute Cleanup Kit (Qiagen).
2 μg of total RNA was used to make the RNA-Seq library using TruSeq Total RNA Sample Prep Kit  (Illumina) and sequenced with the Hi-Seq Illumina genome analyzer.

treatment_protocol: No treatment.

tag: cell line

tag: cell type

value: colorectal carcinoma derived cell line

tag: genotype/variation

value: Homozygous ARID1A-KO


title: RNA-seq_HCT116_arid1aPM2

value: Heterozygous ARID1A-KO


title: S32725_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr

tag: sampleID

tag: itn name

tag: age

tag: gender

value: Female

tag: treatmentgroup

value: American Indian or Alaska Native; White

tag: visitmonth

tag: stim

value: anti-CD3 anti-CD28 Stimulated

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

tag: libraryprep


title: S12613_475166_Control_C_6mo_WB

tag: samplelabel

tag: status

tag: studysiteshort

tag: race

value: White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

value: TruSeq RNA v2

tag: projectid

tag: seqsite

value: Covance

tag: flowcellid

value: TruSeq SBS Kit v3

tag: lane


title: S33281_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr

tag: sampleID

tag: itn name

tag: age

tag: gender

value: Male

tag: treatmentgroup

tag: visitmonth

tag: sortmarkers

tag: stim

value: SMARTer v3

value: NexteraXT

tag: runchemistry


title: S32727_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: samplelabel

tag: status

tag: studysiteshort

value: UCSF

tag: race

value: CD8+ CD45R0+ TIGIT+ KLRG1+

value: anti-CD3 anti-CD28 Stimulated + PVR-fc treated

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

tag: libraryprep

value: BRI

value: HiSeq SBS Kit v4


title: S12611_397935_hOKT3_NR_6mo_WB

tag: sampleID

value: NR

tag: itn name

value: White; Other

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: projectid

tag: seqsite

tag: flowcellid

tag: lane


title: S33279_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr

tag: samplelabel

tag: status

value: R

value: YALE

tag: age

tag: gender

tag: treatmentgroup

value: White; White

tag: visitmonth

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT- KLRG1-

tag: stim

tag: runchemistry


title: S32723_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr

tag: sampleID

tag: itn name

tag: studysiteshort

value: Female

tag: race

value: American Indian or Alaska Native; White

value: anti-CD3 anti-CD28 Stimulated

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

tag: libraryprep


title: S12609_326726_hOKT3_NR_6mo_WB

tag: samplelabel

tag: status

value: COLUMBIA

value: White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

value: TruSeq RNA v2

tag: projectid

tag: seqsite

value: Covance

tag: flowcellid

value: TruSeq SBS Kit v3

tag: lane


title: S12608_853089_Control_C_6mo_WB

tag: sampleID

value: C

tag: itn name

tag: age

tag: gender

value: Male

tag: treatmentgroup

value: Control

tag: visitmonth

tag: runchemistry


title: S33277_838213_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr

tag: studysiteshort

tag: race

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

value: SMARTer v3

tag: libraryprep

value: NexteraXT

value: BRI

value: HiSeq SBS Kit v4


title: RNA-seq_HCT116_WT1

tag: cell line

tag: cell type

value: colorectal carcinoma derived cell line

tag: genotype/variation

value: Parental


title: S12607_406442_hOKT3_NR_6mo_WB

tag: samplelabel

tag: sampleID

tag: status

value: NR

tag: itn name

tag: age

value: Female

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: projectid

tag: seqsite

tag: flowcellid

tag: lane


title: S33276_838213_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

value: R

tag: studysiteshort

value: YALE

tag: gender

tag: treatmentgroup

tag: race

value: White; White

tag: visitmonth

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT+ KLRG1+

tag: stim

value: anti-CD3 anti-CD28 Stimulated

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

tag: runchemistry


title: S32731_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_tr

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

value: UCSF

tag: age

value: American Indian or Alaska Native; White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

value: CD8+ CD45R0+ TIGIT- KLRG1-

value: anti-CD3 anti-CD28 Stimulated + PVR-fc treated

tag: libraryprep


title: ChIP-seq_HCT116_Homozygous_inputIII

data_processing:
The sequenced reads were aligned to the hg19 genome assembly using Bowtie 0.12.6, allowing up to 10 matches (‘-m 10 --best’ options).
Reads on the 24 assembled chromosomes excluding the encode blacklisted regions were kept for downstream analysis.
For batches with low library complexity (<70% in any sample), only one read was preserved mapping to each position (denoted "1read")
Peaks of cross-correlation profiles were identified to estimate the typical fragment size for each sample.  Each read was considered to represent a signal at half typical fragment size from the 5' end.
Genomic profiles for visualization were generated using a sigma=100bp Gaussian smoothing after library size normalization
Genome_build: hg19
Supplementary_files_format_and_content: wig files depict genomic profiles after a sigma=100bp Gaussian smoothing.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Cat.# IP-202-1012)

tag: cell line

tag: cell type

tag: genotype/variation

value: Homozygous ARID1A-KO


title: S12605_209864_hOKT3_NR_6mo_WB

tag: studysiteshort

value: COLUMBIA

tag: gender

value: Male

tag: treatmentgroup

tag: race

value: White

tag: visitmonth

value: TruSeq RNA v2

tag: projectid

tag: seqsite

value: Covance

tag: flowcellid

value: TruSeq SBS Kit v3

tag: lane


title: S32730_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: age

value: Female

tag: sortmarkers

tag: stim

tag: numcellssorted

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

value: SMARTer v3

value: NexteraXT

value: BRI

tag: runchemistry

value: HiSeq SBS Kit v4


title: S12604_137567_hOKT3_R_6mo_WB

value: R

tag: studysiteshort

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryprep


title: ChIP-seq_HCT116_Homozygous_inputII

tag: cell line

tag: cell type

value: colorectal carcinoma derived cell line

tag: genotype/variation


title: S32695_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1neg_stim_tr

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

value: UCSF

tag: age

value: American Indian or Alaska Native; White

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT+ KLRG1-

tag: stim

tag: numcellssorted

tag: projectid

tag: seqsite

tag: flowcellid

tag: lane


title: S32724_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: studysiteshort

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

value: CD8+ CD45R0+ TIGIT+ KLRG1+

value: anti-CD3 anti-CD28 Stimulated

tag: samplebarcode

tag: libraryid

tag: cdnasynthesis

tag: runchemistry


title: RNA-seq_HCT116_arid1aMM2

tag: cell line

tag: cell type

tag: genotype/variation

value: Homozygous ARID1A-KO


title: S32697_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: age

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT- KLRG1-

tag: stim

tag: numcellssorted

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: RNA-seq_HCT116_WT2

value: Parental


title: S12603_505125_hOKT3_R_6mo_WB

tag: studysiteshort

value: COLUMBIA

tag: gender

value: Male

tag: treatmentgroup

tag: race

value: White; White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

value: TruSeq RNA v2

value: Covance

tag: lane


title: S32726_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: age

value: Female

tag: sortmarkers

tag: samplebarcode

tag: cdnasynthesis

value: SMARTer v3

value: NexteraXT

value: BRI

tag: runchemistry


title: S12606_493934_hOKT3_NR_6mo_WB

value: NR

tag: studysiteshort

tag: gender

tag: treatmentgroup

value: Black or African American

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

value: TruSeq SBS Kit v3


title: S32694_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

value: R

value: UCSF

tag: race

value: American Indian or Alaska Native; White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

value: CD8+ CD45R0+ TIGIT+ KLRG1+

tag: stim

value: anti-CD3 anti-CD28 Stimulated + PVR-fc treated

tag: numcellssorted

tag: libraryid

value: HiSeq SBS Kit v4

tag: lane


title: S32722_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: age

tag: sortmarkers

value: anti-CD3 anti-CD28 Stimulated

tag: samplebarcode

tag: cdnasynthesis

tag: runchemistry


title: S32692_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_tr

tag: studysiteshort

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

value: CD8+ CD45R0+ TIGIT- KLRG1-

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: S32698_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1pos_stim_untr

tag: samplelabel

tag: sampleID

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

value: CD8+ CD45R0+ TIGIT- KLRG1+

tag: stim

tag: numcellssorted

tag: libraryid

tag: lane


title: ChIP-seq_HCT116_Homozygous_SMARCA4III

tag: cell line

tag: cell type

value: colorectal carcinoma derived cell line

tag: genotype/variation

value: Homozygous ARID1A-KO

tag: chip antibody

value: SMARCA4/BRG1 (Abcam, EPNCIR111A, ab110641)


title: ChIP-seq_HCT116_Parental_input

value: Parental


title: RNA-seq_HCT116_arid1aPM1

value: Heterozygous ARID1A-KO


title: ChIP-seq_HCT116_Parental_inputIII


title: ChIP-seq_HCT116_Parental_inputII


title: ChIP-seq_HCT116_Homozygous_input


title: S32690_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

value: Female

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: sortmarkers

tag: samplebarcode

tag: cdnasynthesis

value: SMARTer v3

tag: libraryprep

value: NexteraXT

value: BRI

tag: runchemistry


title: S32689_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: samplelabel

tag: sampleID

value: R

value: UCSF

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: stim

tag: numcellssorted

tag: libraryid

tag: projectid

tag: seqsite

tag: flowcellid

tag: lane


title: ChIP-seq_HCT116_Parental_SMARCA4III

tag: cell line

tag: cell type

tag: genotype/variation

tag: chip antibody


title: S32696_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_tr

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

value: American Indian or Alaska Native; White

tag: trunkbarcode

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT+ KLRG1+

tag: samplebarcode

tag: cdnasynthesis

tag: libraryprep

tag: runchemistry


title: S32687_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: samplelabel

tag: sampleID

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: stim

tag: numcellssorted

tag: libraryid

tag: projectid

tag: seqsite

tag: flowcellid

value: HiSeq SBS Kit v4

tag: lane


title: ChIP-seq_HCT116_Homozygous_H3K4me1II

tag: cell line

tag: cell type

tag: genotype/variation

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: S32686_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1pos_stim_untr

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: sortmarkers

value: anti-CD3 anti-CD28 Stimulated

tag: samplebarcode

tag: cdnasynthesis

tag: libraryprep

tag: runchemistry


title: ChIP-seq_HCT116_Parental_H3K4me3II

tag: cell line

value: H3K4me3 (Millipore, 07-473)


title: ChIP-seq_HCT116_Parental_H3K4me1II

tag: cell type

value: colorectal carcinoma derived cell line


title: S32685_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_stim_untr

tag: samplelabel

tag: sampleID

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

value: CD8+ CD45R0+ TIGIT- KLRG1-

tag: stim

tag: numcellssorted

tag: libraryid

tag: projectid

tag: seqsite

tag: flowcellid

tag: lane


title: ChIP-seq_HCT116_Heterozygous_input

tag: genotype/variation


title: ChIP-seq_HCT116_Heterozygous_H3K27Ac

tag: chip antibody

value: H3K27ac (Cell Signaling Technology, D5E4, 8173)


title: S32682_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1pos_unstim_untr

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT- KLRG1+

value: Unstimulated

tag: samplebarcode

tag: cdnasynthesis

tag: libraryprep

tag: runchemistry


title: S32681_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_unstim_untr

tag: samplelabel

tag: sampleID

value: Female

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: stim

tag: numcellssorted

tag: libraryid

tag: projectid

tag: seqsite

tag: flowcellid


title: S32680_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1neg_unstim_untr

tag: status

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

value: CD8+ CD45R0+ TIGIT+ KLRG1-

value: SMARTer v3

tag: lane


title: S32679_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_unstim_untr

tag: samplelabel

tag: sampleID

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: samplebarcode

tag: cdnasynthesis

tag: libraryprep

value: NexteraXT

value: BRI

tag: runchemistry


title: RNA-seq_TM87_DoxII

growth_protocol: G401 and BT16 cells were cultured in DMEM with 10% FBS; TTC549 cells were cultured in RPMI with 10% FBS. G402 and TM87cells were cultured in McCoy’s with 10% FBS; BT12 cells were cultured in Opti-MEM with 5% FBS; All cell lines are maintained with Tet-System Approved FBS (Clonetech, cat.# 631106)

treatment_protocol: Cells were treated with doxycycline to induce SNF5 re-expression for 48 hours.

tag: cell line

tag: cell type

value: retroperitoneum rhabdoid tumor derived cell line

tag: treatment/condition

value: Doxycycline induced SMARCB1 reexpresion


title: S32693_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1pos_stim_tr

tag: status

value: R

tag: itn name

tag: studysiteshort

value: UCSF

tag: age

tag: gender

value: American Indian or Alaska Native; White

tag: visitmonth

tag: stim

value: anti-CD3 anti-CD28 Stimulated + PVR-fc treated

tag: numcellssorted

tag: libraryid

tag: projectid

tag: seqsite

tag: flowcellid


title: ChIP-seq_HCT116_Homozygous_SMARCC1III

tag: genotype/variation

value: Homozygous ARID1A-KO

tag: chip antibody

value: SMARCC1/BAF155 (Santa Cruz, R-8, sc-9746)


title: RNA-seq_TM87_DoxIII

tag: cell line


title: Input DNA

city: La Jolla

first: ANJANA

last: RAO

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

data_processing:
Sequencing reads were mapped against mm9 using Bowtie.
Tet3-enriched regions were identified by MACS peak-calling software (version 1.4.2).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: .bed files

source_name: Neural progenitor cells, input

extract_protocol:
Chromatin was sheared using truChIP High Cell Chromatin Shearing Kit with Non-ionic Shearing Buffer (Covaris).
ChIP-seq libraries were constructed using 5500 SOLiD Fragment 48 Library Core Kit. Libraries were sequenced on the SOLiD 5500 platforms according to the manufacturer's instructions.

tag: strain/background

tag: cell type

value: ES-derived neural progenitor cells


title: Tet3 ChIPSeq

description: Antibody is a gift from Dr. Guoliang Xu (PMID: 21892189).

source_name: Neural progenitor cells, Tet3 ChIP


title: S32676_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1neg_unstim_untr

tag: samplelabel

tag: sampleID

tag: status

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

tag: samplebarcode

tag: cdnasynthesis

tag: libraryprep

tag: runchemistry

value: HiSeq SBS Kit v4

tag: lane


title: EB WT 10d

description:
Tet3 KO mouse ESCs were generated in-house. They were from mice (C57BL/6-background) bearing the Tet3 floxed alleles, followed by excision of the floxed exon by transient expression of Cre recombinase.
Processed data file: ES_Cell_RPKM.txt

data_processing:
Bulk RNA-Seq data was mapped against the mouse mm9 reference genome using tophat43 (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome Bioinformatics Site. Sequencing read coverage per gene was counted using HTSeqcount (-m union -s yes -t exon -i gene_id, http://www-huber.embl.de/users/anders/HTSeq/).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: ES_Cell_RPKM.txt: Tab-delimited text file includes RPKM values for each sample.

source_name: mES cells, WT, 10d

growth_protocol: WT and Tet3 KO mESCs differentiating into neuroectoderm under SFEB culture (days 6 and 10). Control and Tet3-overexpressing mESCs in non-permissive neural differentiation conditions containing FBS (days 4 and 7).

extract_protocol:
For mES cell samples, total RNA was extracted using RNeasy Plus Mini Kit (Qiagen).
For mES cell samples, multiplexed libraries were constructed using SOLiD Total RNA-seq kit. Libraries were sequenced on the SOLiD 5500 platforms according to the manufacturer's instructions.

tag: genotype/variation

value: WT

value: embryonic stem cells

tag: time point


title: S32691_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1neg_stim_tr

tag: itn name

tag: studysiteshort

tag: age

tag: gender

value: Female

tag: visitmonth

tag: stim

tag: numcellssorted

tag: libraryid

tag: projectid

tag: seqsite

tag: flowcellid


title: ChIP-seq_HCT116_Parental_SMARCC1III

tag: cell line

tag: cell type

value: colorectal carcinoma derived cell line

value: Parental

tag: chip antibody


title: RNA-seq_BT12_DoxIII

value: brain rhabdoid tumor derived cell line

tag: treatment/condition


title: S32688_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1neg_stim_untr

tag: samplelabel

tag: sampleID

tag: status

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT+ KLRG1-

value: anti-CD3 anti-CD28 Stimulated

tag: samplebarcode

tag: cdnasynthesis

value: SMARTer v3

tag: libraryprep

value: NexteraXT

value: BRI

tag: runchemistry

tag: lane


title: ChIP-seq_HCT116_Homozygous_H3K4me3II

tag: cell line

tag: cell type

tag: genotype/variation

value: H3K4me3 (Millipore, 07-473)


title: EB Tet3 4d

source_name: mES cells, Tet3-overexpressing, 4d

tag: strain/background

tag: time point


title: EB CTL 7d

source_name: mES cells, control, 7d

value: CTL


title: EB CTL 4d

source_name: mES cells, control, 4d


title: RNA-seq_BT12_NoDoxIII

tag: treatment/condition

value: untreated


title: ChIP-seq_HCT116_Homozygous_H3K27Ac

value: Homozygous ARID1A-KO

tag: chip antibody

value: H3K27ac (Cell Signaling Technology, D5E4, 8173)


title: RNA-seq_BT12_DoxI

value: Doxycycline induced SMARCB1 reexpresion


title: S32683_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_stim_untr

tag: samplelabel

tag: sampleID

tag: status

value: R

tag: itn name

tag: studysiteshort

value: UCSF

tag: age

tag: gender

tag: treatmentgroup

tag: race

value: American Indian or Alaska Native; White

tag: visitmonth

value: CD8+ CD45R0+ TIGIT+ KLRG1+

tag: stim

tag: numcellssorted

tag: libraryid

tag: projectid

tag: seqsite

tag: flowcellid

value: HiSeq SBS Kit v4


title: RNA-seq_G402_NoDoxIII

tag: cell line

tag: cell type

value: kidney rhabdoid tumor derived cell line

tag: treatment/condition


title: RNA-seq_G402_NoDoxI


title: RNA-seq_G402_DoxIII


title: ChIP-seq_HCT116_Parental_H3K27Ac

value: colorectal carcinoma derived cell line

tag: genotype/variation

value: Parental

tag: chip antibody


title: RNA-seq_TTC549_NoDoxIII

value: liver rhabdoid tumor derived cell line


title: RNA-seq_TTC549_NoDoxII


title: RNA-seq_G402_NoDoxII


title: RNA-seq_TM87_DoxI

value: retroperitoneum rhabdoid tumor derived cell line


title: RNA-seq_TTC549_NoDoxI


title: S32678_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1pos_unstim_untr

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

value: Female

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT- KLRG1+

value: Unstimulated

tag: samplebarcode

tag: cdnasynthesis

value: SMARTer v3

tag: libraryprep

value: NexteraXT

value: BRI

tag: runchemistry

tag: lane


title: ChIP-seq_TTC549_NoDox_H3K27Ac

data_processing:
The sequenced reads were aligned to the hg19 genome assembly using Bowtie 0.12.6, allowing up to 10 matches (‘-m 10 --best’ options).
Reads on the 24 assembled chromosomes excluding the encode blacklisted regions were kept for downstream analysis.
Peaks of cross-correlation profiles were identified to estimate the typical fragment size for each sample.  Each read was considered to represent a signal at half typical fragment size from the 5' end.
Genomic profiles for visualization were generated using a sigma=100bp Gaussian smoothing after library size normalization
Genome_build: hg19
Supplementary_files_format_and_content: wig files depict genomic profiles after a sigma=100bp Gaussian smoothing.

growth_protocol: G401, BT16 cells were cultured in DMEM with 10% FBS;  TTC549 cells were cultured in RPMI with 10% FBS. All cell lines are maintained with Tet-System Approved FBS (Clonetech, cat.# 631106)

tag: cell line

tag: cell type

tag: treatment/condition

value: untreated

value: H3K27ac (Cell Signaling Technology, D5E4, 8173)


title: RNA-seq_BT16_DoxII

value: brain rhabdoid tumor derived cell line

value: Doxycycline induced SMARCB1 reexpresion


title: RNA-seq_BT16_DoxIII


title: RNA-seq_BT16_DoxI


title: RNA-seq_TM87_NoDoxIII


title: RNA-seq_BT16_NoDoxIII


title: S32684_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1neg_stim_untr

tag: samplelabel

value: R

value: UCSF

tag: age

tag: gender

tag: treatmentgroup

tag: race

value: American Indian or Alaska Native; White

tag: visitmonth

value: CD8+ CD45R0+ TIGIT+ KLRG1-

tag: stim

value: anti-CD3 anti-CD28 Stimulated

tag: numcellssorted

tag: libraryid

tag: projectid

tag: seqsite

tag: flowcellid


title: EB Tet3 KO 10d Dkk

description:
Dkk is a secreted protein that acts extracellularly to inhibit Wnt-receptor interactions.
Tet3 KO mouse ESCs were generated in-house. They were from mice (C57BL/6-background) bearing the Tet3 floxed alleles, followed by excision of the floxed exon by transient expression of Cre recombinase.
Processed data file: ES_Cell_RPKM.txt

source_name: mES cells, Tet3 KO, 10d

tag: strain/background

tag: genotype/variation

value: Tet3 KO

value: embryonic stem cells

tag: time point


title: RNA-seq_TM87_NoDoxII

tag: cell line

tag: cell type

value: retroperitoneum rhabdoid tumor derived cell line


title: S32677_106306_hOKT3_R_6mo_CD8_TIGITneg_KLRG1neg_unstim_untr

tag: samplelabel

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

value: Female

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: sortmarkers

value: CD8+ CD45R0+ TIGIT- KLRG1-

tag: samplebarcode

tag: cdnasynthesis

tag: libraryprep

tag: runchemistry

value: HiSeq SBS Kit v4

tag: lane


title: RNA-seq_G401_Dox2

value: kidney rhabdoid tumor derived cell line

tag: treatment/condition


title: RNA-seq_G401_NoDox2

tag: cell line


title: RNA-seq_G401_Dox1

tag: cell type


title: ChIP-seq_RT407_input

growth_protocol: primary tissue

extract_protocol:
lysis (SDS) of sonicated (Branson) nuclei, ChIP with antibodies and Dynabeads
single read Illumina

tag: tissue id

tag: tissue source/type

value: primary kidney rhabdoid tumor tissue


title: EB Tet3 KO 10d

tag: strain/background

tag: genotype/variation

tag: time point


title: RNA-seq_TM87_NoDoxI

value: untreated


title: EB Tet3 KO 6d Dkk

source_name: mES cells, Tet3 KO, 6d


title: EB Tet3 KO 6d


title: ChIP-seq_TTC549_Dox_input

value: liver rhabdoid tumor derived cell line


title: ChIP-seq_TTC549_NoDox_input


title: ChIP-seq_RT172_input

value: primary brain rhabdoid tumor tissue


title: RNA-seq_BT12_NoDoxII

value: brain rhabdoid tumor derived cell line


title: S32675_106306_hOKT3_R_6mo_CD8_TIGITpos_KLRG1pos_unstim_untr

tag: samplelabel

tag: sampleID

tag: status

value: R

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: visitmonth

value: CD8+ CD45R0+ TIGIT+ KLRG1+

tag: stim

value: Unstimulated

tag: numcellssorted

tag: libraryid

value: SMARTer v3

value: NexteraXT

tag: projectid

tag: seqsite

value: BRI

tag: flowcellid


title: EB Tet3 7d

source_name: mES cells, Tet3-overexpressing, 7d

tag: strain/background

tag: genotype/variation

tag: cell type

value: embryonic stem cells

tag: time point


title: ChIP-seq_BT16_NoDox_inputH

description: input for histone marks

tag: cell line

tag: treatment/condition


title: RNA-seq_BT12_NoDoxI


title: ChIP-seq_RT230_H3K36me3

tag: tissue id

tag: tissue source/type

tag: chip antibody

value: H3K36me3 (Abcam, ab9050)


title: EB WT 6d

source_name: mES cells, WT, 6d

value: WT


title: RNA-seq_BT12_DoxII

value: Doxycycline induced SMARCB1 reexpresion


title: ChIP-seq_RT407_H3K4me1

value: H3K4me1 (Abcam, ab8895)


title: RNA-seq_G402_DoxI

value: kidney rhabdoid tumor derived cell line


title: RNA-seq_TTC549_DoxII


title: RNA-seq_G402_DoxII


title: RNA-seq_TTC549_DoxIII


title: RNA-seq_TTC549_DoxI


title: ChIP-seq_RT262_H3K4me3

value: primary kidney rhabdoid tumor tissue

value: H3K4me3 (Millipore, 07-473)


title: RNA-seq_BT16_NoDoxII

value: untreated


title: ChIP-seq_RT262_H3K4me1


title: RNA-seq_BT16_NoDoxI


title: ChIP-seq_RT262_H3K27Ac

value: H3K27ac (Cell Signaling Technology, D5E4, 8173)


title: ChIP-seq_RT262_input


title: ChIP-seq_RT242_input


title: RNA-seq_G401_NoDox1


title: ChIP-seq_RT236_input

value: primary liver rhabdoid tumor tissue


title: ChIP-seq_TTC549_NoDox_H3K4me3

value: liver rhabdoid tumor derived cell line


title: ChIP-seq_RT242_H3K4me1


title: ChIP-seq_RT230_input

value: primary brain rhabdoid tumor tissue


title: ChIP-seq_BT16_Dox_inputH

description: input for histone marks

value: brain rhabdoid tumor derived cell line


title: ChIP-seq_RT236_H3K4me3


title: ChIP-seq_RT407_H3K36me3


title: ChIP-seq_BT16_Dox_input

description: input for SMARCA4/SMARCC1


title: ChIP-seq_RT172_H3K36me3


title: ChIP-seq_RT236_H3K27Ac


title: ChIP-seq_TTC549_Dox_SMARCC1

value: SMARCC1/BAF155 (Santa Cruz, R-8, sc-9746)


title: ChIP-seq_BT16_NoDox_input

description: input for SMARCA4/SMARCC1


title: ChIP-seq_G401_NoDox_input


title: ChIP-seq_RT407_H3K4me3


title: ChIP-seq_RT407_H3K27Ac


title: ChIP-seq_RT230_H3K4me1


title: ChIP-seq_BT16_Dox_H3K4me1


title: ChIP-seq_TTC549_Dox_H3K4me3


title: si-Suz12_R2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: RNAseq (Suz12 knock-down 2)

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. RNAseq analysis: Alignment: The reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. Cufflinks (PubMed ID 22383036) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIP profiles were produced by MACS in BedGraph. Peaks were reported in BED format.
Genome_build: mm9

source_name: Undifferentiated ES cells

growth_protocol: E14TG2a mouse ES cells were kept under feeder-free, 20% serum conditions with LIF on 0.1% gelatin coated dishes, as in (Morey et al., 2012)

extract_protocol:
ChIP experiments used about 20 million cells, using a protocol adapted from (Stock et al., 2007). For all ChIPs except those against EloB, cells were washed 2´ with PBS, and crosslinking was started by adding 1% formaldehyde in PBS to the plate, stopped by adding 0.125 M glycine, and cells were harvested by scraping and then pelleted. For ChIPs against EloB, cells were washed 2x with PBS, protein-protein crosslinking was performed with 40 ml ChIP Crosslink Gold (Diagenode, C01019027) or 2 mM DSP (ThermoFisher, cat 22586) in 10 ml PBS for 30 min, followed by two washes with PBS. Protein-DNA crosslinking (1% formaldehyde in PBS) was then performed on the plate for 10 min, stopped by 0.125 M glycine and cells were harvested by scraping and then pelleted. Cell pellets were resuspended and incubated for 10 min in 2 ml swelling buffer (25 mM HEPES [pH 7.9], 1.5 mM MgCl2, 10 mM KCl, 0.1% NP40, protein and phosphatase inhibitors) and the suspension was homogeneized (tight pestle, 50x). Nuclei were pelleted (3,000 g, 5 min) and resuspended in 1.3 ml sonication buffer (50 mM HEPES [pH 7.9], 140 mM Nacl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, protease and phosphatase inhibitors). Sonication (Diagenode Bioruptor, 30 s ON/30 s OFF, high potency, 2x 8 cycles with fresh ice in between). Insoluble material was pelleted, and chromatin concentration and sonication efficiency was determined in the supernatant by DNA quantification or agarose gel after decrosslinking the extracts overnight. ChIPs were performed O.N. using 20-30 μg of DNA, 4 μg antibody (the amount of antibody for reaching full enrichment was titrated) and 25 μl of protein A dynabeads in 500 μl of sonication buffer. ChIPs were washed once with sonication buffer, once with buffer wash buffer A (50 mM HEPES [pH 7.9], 500 mM Nacl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, protease and phosphatase inhibitors), once with  wash buffer B (20 mM Tris-Cl [pH 8.0], 250 mM LiCl, 1 mM EDTA, 0.5% Triton MP40, 0.5% Na-deoxycholate, protease and phosphatase inhibitors) twice with 1x TE pH 8.0 and eluted in 200 μl TE pH 8.0, 1% SDS followed by decrosslinking (O.N) and RNAse treatment. DNA was finally purified over PCR (Qiagen) and eluted in 55 μl water.
Libraries were prepared according to Illumina instructions.

treatment_protocol: To generate stable cell lines expressing shRNA targeted against C17orf96 , lentivirus was produced in 293T cells by calcium phosphate-mediated transfection of 5 mg plasmid. To generate stable C17orf96 –/– cell lines, 5 ug plasmids encoding sgRNAs were transfected using Lipofectamine 2000 (Invitrogen), according to the manufacturer´s instruction. Puromycin selection was performed for 1 day at 2 mg/ml, 1000 cells were split into a 10-cm dish, and clones were picked 10 days later. Clones were expanded into 6-well dishes, and C17orf96 expression was checked by Western blot. Supernatant was harvested after 48 hr, diluted 1:4, and used to infect E14 cells. Puromycin (2 mg/ml) was added for 2 days for selection. For siRNA experiments, 100,000 cells were seeded in 6-well plates and transfected 24 hr later with 20 μM siRNA using 7 μl Lipofectamine RNAimax (Invitrogen) and Optimem, according to manufacturer’s instructions. Transfections were repeated one day later, and cells were harvested after an additional 24 hr (i.e., 48 hr after the first transfection). Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen) using protocol Appendix D. For siRNA experiments followed by ChIP, 1.2 million cells were seeded, and siRNA was transfected twice at 20 μM using using 70 μl Lipofectamine RNAimax (Invitrogen) and Optimem, according to manufacturer’s instructions. Transfections were repeated one day later, and cells were harvested after additional 24 hr (i.e. 48 hr after the first transfection).

value: Suz12 knock-down 2


title: ChIP-seq_RT230_H3K27Ac


title: ChIP-seq_TTC549_Dox_SMARCA4

value: SMARCA4/BRG1 (Abcam, EPNCIR111A, ab110641)


title: ChIP-seq_TTC549_Dox_H3K4me1


title: ChIP-seq_G401_Dox_input


title: ChIP-seq_RT242_H3K4me3


title: ChIP-seq_TTC549_Dox_H3K27Ac


title: ChIP-seq_TTC549_NoDox_H3K4me1


title: ChIP-seq_RT242_H3K27Ac


title: ChIP-seq_TTC549_NoDox_SMARCA4


title: ChIP-seq_BT16_NoDox_H3K4me3


title: ChIP-seq_RT236_H3K4me1


title: ChIP-seq_BT16_NoDox_H3K4me1


title: ChIP-seq_TTC549_NoDox_SMARCC1


title: C17orf96 KO-3A

description: RNAseq (C17 knock-out 2)

value: C17 knock-out 2


title: ChIP-seq_BT16_Dox_SMARCA4


title: ChIP-seq_BT16_Dox_H3K27Ac


title: C17orf96 KO-1A

description: RNAseq (C17 knock-out 1)

value: C17 knock-out 1


title: ChIP-seq_BT16_Dox_SMARCC1


title: ChIP-seq_BT16_Dox_H3K4me3


title: ChIP-seq_BT16_NoDox_H3K27Ac


title: ChIP-seq_RT230_H3K4me3


title: si-ct_R1

description: RNAseq (control 1)

value: control 1


title: wt

description: RNAseq (control)

value: control


title: si-EloB_R2

description: RNAseq (EloB knock-down 2)

value: EloB knock-down 2


title: si-Suz12_R1

description: RNAseq (Suz12 knock-down 1)

value: Suz12 knock-down 1


title: ChIP-seq_RT172_H3K4me3


title: H3K4me3 upon ElonginB knock-down

description: chromatin IP against H3K4me3


title: ChIP-seq_G401_NoDox_H3K4me1

value: kidney rhabdoid tumor derived cell line

value: H3K4me1 (Abcam, ab8895)


title: H3K4me3 replicate 1

description: chromatin IP against H3K4me3


title: ChIP-seq_RT172_H3K4me1


title: H3K4me3 upon C17orf96 knock-down

description: chromatin IP against H3K4me3


title: ElonginB upon C17orf96 knock-down replicate 2

description: chromatin IP against EloB


title: ElonginB replicate 2

description: chromatin IP against EloB


title: ChIP-seq_BT16_NoDox_SMARCA4

value: untreated


title: H3K4me3 replicate 2

description: chromatin IP against H3K4me3


title: ChIP-seq_BT16_NoDox_SMARCC1


title: si-ct_R2

description: RNAseq (control 2)

value: control 2


title: ChIP-seq_G401_Dox_SMARCA4

value: Doxycycline induced SMARCB1 reexpresion


title: ChIP-seq_G401_NoDox_H3K4me3

value: H3K4me3 (Millipore, 07-473)


title: ElonginB upon C17orf96 knock-down replicate 1

description: chromatin IP against EloB

value: bethyl  A304-008A Lot -1


title: ChIP-seq_G401_NoDox_SMARCC1


title: H3K27me3

description: chromatin IP against H3K27me3

value: Active Motif 39155 Lot 23813016


title: RNA-seq_Rhabdoid_RT236

extract_protocol:
Total RNA was purified using RNeasy Kit (Qiagen).
2 μg of total RNA were used to fragment and polyA isolate the 3’ends of mRNA transcripts. Illumina sequencing libraries were constructed.

tag: tissue type/source

value: primary liver rhabdoid tumor tissue


title: ChIP-seq_G401_NoDox_H3K27Ac

value: H3K27ac (Cell Signaling Technology, D5E4, 8173)


title: Suz12 upon EloB knock-down

description: chromatin IP against Suz12


title: ChIP-seq_G401_Dox_H3K4me3


title: RNA-seq_Rhabdoid_RT242

value: primary kidney rhabdoid tumor tissue


title: ElonginB replicate 1

description: chromatin IP against EloB


title: ChIP-seq_G401_Dox_H3K4me1


title: ChIP-seq_RT308_H3K36me3

value: primary brain rhabdoid tumor tissue

value: H3K36me3 (Abcam, ab9050)


title: H3K27me3 upon C17orf96 knock-down

description: chromatin IP against H3K27me3


title: IgG

description: chromatin IP against C17orf96


title: ChIP-seq_RT307_H3K4me3


title: Suz12 upon C17orf96 knock-down

description: chromatin IP against Suz12


title: ChIP-seq_G401_Dox_H3K27Ac


title: C17orf96 replicate 1

description: chromatin IP against C17orf96

value: home-made against aa 1-240 Lot1


title: Suz12 replicate 2

description: chromatin IP against Suz12


title: ChIP-seq_G401_Dox_SMARCC1

value: SMARCC1/BAF155 (Santa Cruz, R-8, sc-9746)


title: Suz12 replicate 1

description: chromatin IP against Suz12


title: ChIP-seq_RT308_H3K4me1


title: ChIP-seq_G401_NoDox_SMARCA4

value: SMARCA4/BRG1 (Abcam, EPNCIR111A, ab110641)


title: RNA-seq_Colon_ColonF

data_processing:
The sequenced reads from each sample were aligned to the mouse genome+transcriptome assembly NCBIM37.67 using TopHat v2.0.8 with default parameters except turning off novel junction search ( -G <gtf> --no-novel-juncs).
Genomic coverage was calculated in R using BioConductor packages Rsamtools and Granges
Genome_build: mm9
Supplementary_files_format_and_content: wig file showing unnormalized RNA-seq coverage

source_name: wild type_colon

growth_protocol: Primary colon epithelial cells were isolated from wildtype and Villin Cre-ERT2 ARID1A(fl/fl) mice 2 months post-injection with Tamoxifen.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and further purified using RNeasy MinElute Cleanup Kit (Qiagen) and Turbo DNase kit (Ambien).
2 μg of total RNA was used to make the RNA-Seq library using TruSeq Total RNA Sample Prep Kit  (Illumina) and sequenced with the Hi-Seq Illumina genome analyzer.

treatment_protocol: EDTA chelation treatment was used to dissociate epithelial cells.

tag: strain background

value: WT

tag: tissue

value: colon

value: primary colon epithetial cells


title: TKO embryo, replicate 4

description:
TKO_4
Processed data file: EmbryoCell_RPKM.txt

data_processing:
Bulk RNA-Seq data was mapped against the mouse mm9 reference genome using tophat43 (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome Bioinformatics Site. Sequencing read coverage per gene was counted using HTSeqcount (-m union -s yes -t exon -i gene_id, http://www-huber.embl.de/users/anders/HTSeq/).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: EmbryoCell_RPKM.txt: Tab-delimited text file includes RPKM values for each sample.

source_name: E6.75 embryo, Tet1/2/3 TKO

extract_protocol:
Single embryos were lysed and converted into double stranded cDNA using SMARTer ultra-low RNA kit for Illumina sequencing (Clontech).
For single embryo samples, 1 ng of cDNA for each sample was used for preparing libraries using Nextera XT DNA sample preparation kit (IIlumina). Libraries were sequenced on Illumina HiSeq 2500 platforms according to the manufacturer's instructions.

value: Tet1/2/3 TKO

tag: age

value: Whole embryo


title: ChIP-seq_RT308_H3K27Ac


title: RNA-seq_Rhabdoid_RT262


title: C17orf96 knock-down replicate 2

description: chromatin IP against C17orf96

value: home-made against aa 1-240 Lot2


title: RNA-seq_Colon_ColonE


title: RNA-seq_Colon_ColonD


title: RNA-seq_Colon_ColonB

value: ARID1A KO


title: C17orf96 replicate 2

description: chromatin IP against C17orf96


title: CTL embryo, replicate 4

description:
123WT_4
Processed data file: EmbryoCell_RPKM.txt

source_name: E6.75 embryo, control

value: Control


title: ChIP-seq_ColonARID1A_input

data_processing:
The sequenced reads were aligned to the mm9 genome assembly using Bowtie 0.12.6, allowing up to 10 matches (‘-m 10 --best’ options).
Reads on the 19 autosomal chromosomes excluding blacklisted regions were kept for downstream analysis. Blacklist regions were identified in an accompanying project.
Only one read was preserved mapping to each position to remove PCR artifacts.
Peaks of cross-correlation profiles were identified to estimate the typical fragment size for each sample.  Each read was considered to represent a signal at half typical fragment size from the 5' end.
Genomic profiles for visualization were generated using a sigma=100bp Gaussian smoothing after library size normalization
Genome_build: mm9
Supplementary_files_format_and_content: wig files depict genomic profiles after a sigma=100bp Gaussian smoothing.

value: Primary colon epithelial cells


title: C17orf96 knock-down replicate 1

description: chromatin IP against IgG


title: ChIP-seq_RT307_H3K4me1

value: H3K4me1 (Abcam, ab8895)


title: ChIP-seq_RT172_H3K27Ac

value: H3K27ac (Cell Signaling Technology, D5E4, 8173)


title: CTL embryo, replicate 3

description:
123WT_3
Processed data file: EmbryoCell_RPKM.txt


title: ChIP-seq_WT_PolIIinput

description: processed data files: MEF_blacklist.bed; MEF_transcribed.bed

data_processing:
The sequenced reads were aligned to the mm9 genome assembly using Bowtie 0.12.6, allowing up to 10 matches (‘-m 10 --best’ options).
1kb sized bins with more than mean+3standard deviation signal in any of the input samples were marked as noisy blacklist regions (total 287kb).
Reads on the 19 autosomal chromosomes excluding blacklisted regions were kept for downstream analysis.
For batches with low library complexity (<70% in any sample), only one read was preserved mapping to each position (denoted "PCRclean" or "clean1" in file names)
Peaks of cross-correlation profiles were identified to estimate the typical fragment size for each sample.  Each read was considered to represent a signal at half typical fragment size from the 5' end.
Genomic profiles for visualization were generated using a sigma=100bp Gaussian smoothing after library size normalization
The genome was segmented using multi-sample BICSeq comparing PolII sample and matching input, with parameter l=1; Transcribed regions were identified as segments with IP>input*log2(0.1)
Genome_build: mm9
Supplementary_files_format_and_content: wig files depict genomic profiles after a sigma=100bp Gaussian smoothing.
Supplementary_files_format_and_content: bed files depict blacklisted regions and regions identified as transcribed.

growth_protocol: MEFs were cultured in DMEM with 10% FBS

treatment_protocol: Cells were infected with retrovisur expressing Cre, and selected with puromycine. 72 hours post selection, cells were harvested and used to extract chromatin.

tag: strain

value: mouse embryonic fibroblast


title: CTL embryo, replicate 2

description:
123WT_2
Processed data file: EmbryoCell_RPKM.txt


title: ChIP-seq_RT307_H3K36me3

value: primary brain rhabdoid tumor tissue


title: ChIP-seq_WT_PolII

value: PolII (Santa Cruz, N-20, sc-899X, lot#C0813)


title: CTL embryo, replicate 1

description:
123WT_1
Processed data file: EmbryoCell_RPKM.txt


title: TKO embryo, replicate 2

description:
TKO_2
Processed data file: EmbryoCell_RPKM.txt


title: RNA-seq_Colon_ColonC


title: ChIP-seq_ColonWT_input


title: TKO embryo, replicate 1

description:
TKO_1
Processed data file: EmbryoCell_RPKM.txt


title: RNA-seq_MEF_Smarcb1II

treatment_protocol: Cells were infected with retrovisur expressing Cre, and selected with puromycine. 72 hours post selection, cells were harvested and used.


title: ChIP-seq_ColonARID1A_H3K27Ac


title: ChIP-seq_ColonWT_H3K4me3

value: H3K4me3 (Millipore, 07-473)


title: ChIP-seq_ColonWT_H3K27Ac


title: RNA-seq_MEF_Smarca4II