title: RNA seq of cell line D341 infected with shGFP.1

first: Sowmya

last: Iyer

department: Pathology

institute: Massachusetts General Hospital

description: Sample name: D341_shGFP.1

data_processing:
RNA-seq reads were mapped using STAR. Counts were generated using HT-seq and normalized to sequencing depth. We used Cufflinks to calculate FPKMs
Genome_build: hg19
Supplementary_files_format_and_content: text file with raw counts or fpkm.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA (Clontech).  1 μg of total RNA was treated with Ribogold zero to remove ribosomal RNA. Remaining RNA was used to construct Illumina sequencing libraries with random primers according to manufacturer instructions using the Truseq Stranded RNA LT Kit.
RNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: cell line

tag: source type

value: cell line


title: RNA seq of cell line D341 infected with shOTX2.1393.1

status: Public on Feb 21 2017

type: SRA

city: Boston

state: MA

country: USA

description: Sample name: D341_shOTX2.1393.1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: RNA seq of cell line D341 infected with shGFP.2

description: Sample name: D341_shGFP.2


title: ATAC seq for D283 cell line

library_source: genomic

data_processing:
Paired end reads were aligned to hg19 using BWA. Read start sites were adjusted to represent the center of the transposon binding event (+4 bp in the plus strand and -5 bp in the minus strand). Signal densities were calculated over a sliding 150 bp window at 20 bp steps and normalized to 10M reads in each experiment.
Genome_build: hg19

molecule: genomic DNA

extract_protocol:
5x10^4 cells for each condition were first incubated in hypotonic buffer then resuspended in lysis buffer, centrifugated and resuspended in Transposase reaction mix for additional 30 min at 37C, following manufacturer recommendations (Nextera DNA sample Prep Kit, Illumina).
DNA was purified and adaptor sequences were added to the fragmented DNA by PCR to construct Illumina sequencing libraries. Purified PCR products were sequenced using the Illumina Nextseq device.


title: D283_shNEUROD1.1154_NEUROD1

data_processing:
ChIP-seq reads were aligned to the reference genome (hg19) using BWA
Genome_build: hg19
Supplementary_files_format_and_content: We extended aligned reads to 200 bp to approximate fragment sizes and derived 25-bp resolution density maps by counting the number of fragments overlapping each position with IGVtools. All density maps were normalized to 10M reads.

source_name: NEUROD1 ChIP-seq in D283 cell line infected with shNEUROD1.1154

extract_protocol:
Chromatin from formaldehyde-fixed cells (3-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: chip antibody


title: D283_shOTX2.1393_OTX2

source_name: OTX2 ChIP-seq in D283 cell line infected with shOTX2.1393


title: D283_shOTX2.1393_H3K27ac

source_name: H3K27ac ChIP-seq in D283 cell line infected with shOTX2.1393


title: D283_shNEUROD1.1579_H3K27ac

source_name: H3K27ac ChIP-seq in D283 cell line infected with shNEUROD1.1579


title: RNA seq of cell line D341 infected with shOTX2.1393.2

description: Sample name: D341_shOTX2.1393.2


title: D283_shNEUROD1.1154_H3K27ac

source_name: H3K27ac ChIP-seq in D283 cell line infected with shNEUROD1.1154


title: D283_shGFP_H3K27ac

source_name: H3K27ac ChIP-seq in D283 cell line infected with shGFP


title: D341_shNEUROD1.1154_H3K27ac_3

source_name: H3K27ac ChIP-seq in D341 cell line infected with shNEUROD1.1154


title: D283_shNEUROD1.1579_NEUROD1

source_name: NEUROD1 ChIP-seq in D283 cell line infected with shNEUROD1.1579


title: D283_shGFP_OTX2

source_name: OTX2 ChIP-seq in D283 cell line infected with shGFP


title: D341_shNEUROD1.1579_NEUROD1_3

source_name: NEUROD1 ChIP-seq in D341 cell line infected with shNEUROD1.1579


title: D341_shNEUROD1.1579_H3K27ac_3

source_name: H3K27ac ChIP-seq in D341 cell line infected with shNEUROD1.1579


title: D283_shGFP_NEUROD1

source_name: NEUROD1 ChIP-seq in D283 cell line infected with shGFP


title: D341_shNEUROD1.1154_NEUROD1_3

source_name: NEUROD1 ChIP-seq in D341 cell line infected with shNEUROD1.1154


title: D341_CRISPR.OTX2.4_OTX2

source_name: OTX2 ChIP-seq in D341 cell line infected with CRISPR.OTX2.4


title: D341_CRISPR.OTX2.2_OTX2

source_name: OTX2 ChIP-seq in D341 cell line infected with CRISPR.OTX2.2


title: D341_CRISPR.OTX2.4_H3K27ac

source_name: H3K27ac ChIP-seq in D341 cell line infected with CRISPR.OTX2.4


title: D341_CRISPR.OTX2.2_H3K27ac

source_name: H3K27ac ChIP-seq in D341 cell line infected with CRISPR.OTX2.2


title: D341_CRISPR.GFP2_OTX2

source_name: OTX2 ChIP-seq in D341 cell line infected with CRISPR.GFP2


title: D341_shGFP_H3K27ac_3

source_name: H3K27ac ChIP-seq in D341 cell line infected with shGFP


title: D341_CRISPR.GFP2_H3K27ac

source_name: H3K27ac ChIP-seq in D341 cell line infected with CRISPR.GFP2


title: D341_CRISPR.GFP1_OTX2

source_name: OTX2 ChIP-seq in D341 cell line infected with CRISPR.GFP1


title: D341_CRISPR.GFP1_H3K27ac

source_name: H3K27ac ChIP-seq in D341 cell line infected with CRISPR.GFP1


title: D341_shOTX2.1393_OTX2_2

source_name: OTX2 ChIP-seq in D341 cell line infected with shOTX2.1393


title: D341_shOTX2.1393_H3K27ac_2

source_name: H3K27ac ChIP-seq in D341 cell line infected with shOTX2.1393


title: D341_shOTX2.1393_H3K27ac_1


title: D341_shGFP_OTX2_2

source_name: OTX2 ChIP-seq in D341 cell line infected with shGFP


title: D341_shGFP_NEUROD1_3

source_name: NEUROD1 ChIP-seq in D341 cell line infected with shGFP


title: D341_shOTX2.1393_OTX2_1


title: D341_shGFP_H3K27ac_2


title: D341_shGFP_H3K27ac_1


title: 4CM1

city: Shanghai

first: Junfang

last: Zhang

address: Huchenghuan Road 999

department: College of fishery and life science

country: China

institute: Shanghai Ocean University

data_processing:
Library strategy: 4C-Seq
Illumina Casava1.7 software was used for basecalling.
The fastx-toolkit program was used to filter off low quality sequences from raw sequencing data.
Sequencing reads were aligned to the mouse genome (Mus musculus NCBIM37) by BWA alignment
Analysis of cross-linking frequency with Seqmonk software.
Genome_build: mm9
Supplementary_files_format_and_content: excel file

organism: Mus musculus

source_name: bone-marrow

growth_protocol: M1 cells were maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum

extract_protocol:
4C assay was performed followed a standard protocol (Gondor et al 2008)
4C DNA was purified for paired-end sequencing according to the manufacturer Illumina.

treatment_protocol: For cell differentiation, M1 cells were seeded at a density of 1-2 x 105 cells / ml in medium containing interleukin-6 (IL-6) for 4-5 days.

tag: cell type

value: Murine myeloid progenitor M1 cells

tag: passages

tag: treatment with il-6

value: No


title: D341_INPUT

source_name: INPUT ChIP-seq in D341 cell line

value: INPUT


title: D341_H3K4m3

source_name: H3K4m3 ChIP-seq in D341 cell line


title: D341_shGFP_OTX2_1


title: D341_H3K27ac

source_name: H3K27ac ChIP-seq in D341 cell line


title: A5701-transduced B721.221 cells

first: Catherine

middle: J

last: Wu

address: 450 Brookline Ave.

institute: Dana Farber Cancer Institute

data_processing:
bowtie2-2.2.1 alignment to UCSC hg19 transcriptome; default parameters
rsem-1.2.19; default parameters
Genome_build: hg19
Supplementary_files_format_and_content: .isoforms.results.txt (RSEM transcript-level expression estimates; tab-delimited with headers)

growth_protocol: 721-221 cells were cultured in DMEM supplemented with 10% FBS, Penicillin and streptomycin.

extract_protocol:
Qiagen RNeasy mini kit protocol
We employed Nextera XT kit from Illumina and the Smart-seq2 protocol to generate full length cDNA and sequencing libraries.

treatment_protocol: G418, 400microgram/ml

tag: tissue

tag: genotype/variation


title: D341_H3K27m3

source_name: H3K27m3 ChIP-seq in D341 cell line


title: D341_NEUROD1

source_name: NEUROD1 ChIP-seq in D341 cell line


title: D341_OTX2

source_name: OTX2 ChIP-seq in D341 cell line


title: D341_OTX2.abcam

source_name: OTX2.abcam ChIP-seq in D341 cell line


title: D341_H3K4m1

source_name: H3K4m1 ChIP-seq in D341 cell line


title: D283_INPUT

source_name: INPUT ChIP-seq in D283 cell line


title: A5101-transduced B721.221 cells


title: D283_H3K27m3

source_name: H3K27m3 ChIP-seq in D283 cell line


title: D283_H3K27ac

source_name: H3K27ac ChIP-seq in D283 cell line


title: D283_H3K4m3

source_name: H3K4m3 ChIP-seq in D283 cell line


title: A2902-transduced B721.221 cells


title: D283_H3K4m1

source_name: H3K4m1 ChIP-seq in D283 cell line


title: A5401-transduced B721.221 cells


title: D283_OTX2.abcam

source_name: OTX2.abcam ChIP-seq in D283 cell line


title: Scapula muscle

city: Hohhot

first: Xinfeng

last: Liu

address: 24 Zhaojun Road

institute: Inner Mongolia University

data_processing:
RNA libraries were sequenced on the Illumina HiSeq 2500 platform.
Raw data (raw reads) of fastq format was firstly processed through in-house perl scripts.
The clean data with high quality which were aligned to the UMD3.1.75 Bos taurus reference genome using TopHat (version 2.0.9) with default parameters.
The mapped reads were assembled using Cufflinks version 2.1.1.
Genome_build: UMD3.1.75 Bos taurus reference genome
Supplementary_files_format_and_content: text file with FPKM abundance measurments

organism: Bos taurus

source_name: Skeletal muscle

growth_protocol: Four types of skeletal muscle samples (LT, SM, G and IM) were taken from three Hereford cattle which had not experienced any diseases in the past 3 months and had no closely relationship between each other (for at least 4 generations).  The cattle were fattened in a single feedlot and fed ad libidum with wet corn silage, and humanely sacrificed in an accredited commercial slaughterhouse when they reached 18 months to collect the skeletal muscle samples. All the samples were immediately frozen in liquid nitrogen and then storage at －80℃ until analysis.

extract_protocol:
Total RNA was extracted using TRK-1002 total RNA purification kit (LC Science, Houston, TX) following the manufacturer's procedure. Equal amount of total RNA of the same muscle samples from the three cattle were mixed into a pool.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: skeletal muscle

tag: muscle name

value: Scapula muscle

tag: Sex

value: Female

tag: age

value: 18 months

tag: breed

value: Hereford


title: Longissimus thoraci

value: Longissimus thoraci


title: D283_OTX2

source_name: OTX2 ChIP-seq in D283 cell line


title: Intercostal muscle

value: Intercostal muscle


title: Pycnoporus sanguineus, xylan-galactomannan rep1

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

country: France

institute: INRAE - Aix Marseille University

description:
Liquid cultures of P. sanguineus CIRM-BRFM 1264 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), a mixture of xylans and galacto-mannans (15 g.l-1 )
raw_counts_CIRM-BRFM1264
norm_counts_CIRM-BRFM1264

data_processing:
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline.
QCed reads from each library were aligned to the reference genome Pycnoporus coccineus BRFM 310 v1.0, Pycnoporus cinnabarinus BRFM 137, or Pycnoporus sanguineus BRFM 1264 v1.0,available via Mycocosm JGI portal, using TopHat2 (Galaxy Tool Version 0.7-INRA MIGALE bioinformatics platform) with only unique mapping allowed.
Read counts were determined by HTSeq  (Galaxy Tool Version 0.3.2-INRA MIGALE bioinformatics platform)
Read counts were normalized using ddsNorm from the DESeq Bioconductor package (version 1.5)
Supplementary_files_format_and_content: File "raw_counts_CIRM-BRFM310"  includes read count values for each sample
Supplementary_files_format_and_content: File "rnorm_counts_CIRM-BRFM310"  includes normalized read count values for each sample

organism: Trametes sanguinea

source_name: mycelium

extract_protocol:
Total RNA was extracted from 100 mg tissue ground with FastPrep Lysis Matrix A (MP Biomedicals) in 1 ml TRIZOL (Ambion). Nucleic acids were precipitated with isopropanol, resuspended in water and treated with RNase-Free DNase I (QIAGEN). Total RNA was precipitated with LiCl and resuspended in DEPC-treated water. RNA quantity and quality were determined using the Experion RNA StdSens kit (QIAGEN).
Double stranded cDNAs were synthesized from Poly A RNA and fragmented (200-300bp) before construction of the sequencing libraries (Kapa Library Amplification Kit ; Kapa Biosystems).
Illumina HighSeq-2500 JGI platform generating paired end reads of 150bp each.

treatment_protocol: Mycelium and remaining solid substrate were immediately frozen in liquid nitrogen and stored at -80°C before RNA extraction.

tag: strain

value: CIRM-BRFM 1264

tag: agent

value: xylan-galactomannan

tag: time

value: day 3


title: Pycnoporus sanguineus, xylan-galactomannan rep2


title: Pycnoporus sanguineus, Avicel rep3

description:
Liquid cultures of P. sanguineus CIRM-BRFM 1264 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), Avicel (15 g.l-1 )
raw_counts_CIRM-BRFM1264
norm_counts_CIRM-BRFM1264

value: Avicel


title: Pycnoporus sanguineus, wheat straw rep2

description:
Liquid cultures of P. sanguineus CIRM-BRFM 1264 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted wheat straw (15 g.l-1 )
raw_counts_CIRM-BRFM1264
norm_counts_CIRM-BRFM1264

value: wheat straw


title: Pycnoporus sanguineus, wheat straw rep3


title: Pycnoporus sanguineus, Avicel rep2


title: Pycnoporus sanguineus, maltose rep2

description:
Liquid cultures of P. sanguineus CIRM-BRFM 1264 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (20 g.l-1)
raw_counts_CIRM-BRFM1264
norm_counts_CIRM-BRFM1264

value: maltose


title: Pycnoporus sanguineus, aspen rep2

description:
Liquid cultures of P. sanguineus CIRM-BRFM 1264 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), 1 mm Wiley-milled aspen (15 g.l-1 )
raw_counts_CIRM-BRFM1264
norm_counts_CIRM-BRFM1264

value: aspen


title: Pycnoporus sanguineus, aspen rep1


title: UV-24h

city: London

first: Laura

last: Williamson

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: GRO-seq

data_processing:
Reads were aligned to the hg19 genome assembly using BWA v0.5.9 (Li and Durbin, 2009) with default settings.
Reads were extended to 250 bp, and each sample was normalized to a read depth of 20 million.
A subset of the protein-coding human Ensembl transcriptome was created by filtering for transcripts ≥30 kb, selecting only the largest transcript per gene. Base pair level coverage of the region 2 kb upstream, to 120 kb downstream, of each transcript's TSS was calculated for each sample. Average gene profiles were generated by taking a trimmed mean (0.05) of read depth over each base pair.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.avg_gene_profile.txt: Tab-delimited text files containing the average gene read depth profile. Positions are given relative to TSS.

source_name: MRC5VA cells, UV, 24hr

growth_protocol: Standard growth conditions in DMEM.

extract_protocol:
Trizol
Preparation of strand-specific RNA libraries using standard Illumina protocols and sequenced on an Illumina HiSeq 2000 sequence analyzer as single-end 51 bp reads.

treatment_protocol: GRO-Seq. Permeabilized nuclei isolated from untreated or UV-treated cells were supplemented with ATP, CTP, GTP and BrUTP to allow for transcription run on for 5 minutes, followed by DNA digestion by DNase I. Alkaline-digested BrU-labelled nascent RNA was purified using anti-BrU resin and extracted using Trizol.

tag: treatment

value: UVC irradiated

value: 24 hours


title: Pycnoporus sanguineus, wheat straw rep1


title: Pycnoporus coccineus, wheat straw rep2

description:
Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted wheat straw (15 g.l-1 )
raw_counts_CIRM-BRFM310
norm_counts_CIRM-BRFM310

organism: Trametes coccinea

value: CIRM-BRFM 310


title: Pycnoporus sanguineus, maltose rep3


title: UV-12h

description: GRO-seq

source_name: MRC5VA cells, UV, 12hr

value: 12 hours


title: Pycnoporus sanguineus, maltose rep1


title: UV-5h

description: GRO-seq

source_name: MRC5VA cells, UV, 5hr

value: 5 hours


title: Pycnoporus sanguineus, aspen rep3


title: D283_NEUROD1

source_name: NEUROD1 ChIP-seq in D283 cell line

value: cell line


title: Gluteus

value: skeletal muscle

value: Gluteus

value: Female

value: 18 months


title: UV-8h

description: GRO-seq

source_name: MRC5VA cells, UV, 8hr

value: 8 hours


title: UV-2h

description: GRO-seq

source_name: MRC5VA cells, UV, 2hr

value: 2 hours


title: Pycnoporus coccineus, wheat straw rep1

value: day 3


title: Pycnoporus coccineus, xylan-galactomannan rep1

description:
Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), a mixture of xylans and galacto-mannans (15 g.l-1 )
raw_counts_CIRM-BRFM310
norm_counts_CIRM-BRFM310

value: xylan-galactomannan


title: Pycnoporus coccineus, xylan-galactomannan rep2


title: Pycnoporus coccineus, xylan-galactomannan rep3

description:
Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), wheat straw (15 g.l-1 )
raw_counts_CIRM-BRFM310
norm_counts_CIRM-BRFM310


title: Pycnoporus coccineus, Avicel rep3

description:
Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), Avicel (15 g.l-1 )
raw_counts_CIRM-BRFM310
norm_counts_CIRM-BRFM310

value: Avicel


title: Pycnoporus sanguineus, Avicel rep1

value: CIRM-BRFM 1264


title: Untreated

description: GRO-seq

source_name: MRC5VA cells, untreated, 0hr

value: Untreated

value: 0 hours


title: UV+.t40

description: DRB GRO-seq

data_processing:
Reads were aligned to the hg19 genome assembly using BWA v0.5.9 (Li and Durbin, 2009) with default settings.
Reads were extended to 200 bp, and each sample was normalized to a read depth of 20 million.
A subset of the protein-coding human Ensembl transcriptome was created by filtering for transcripts ≥30 kb, selecting only the largest transcript per gene. Base pair level coverage of the region 2 kb upstream, to 120 kb downstream, of each transcript's TSS was calculated for each sample. Average gene profiles were generated by taking a trimmed mean (0.05) of read depth over each base pair.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.avg_gene_profile.txt: Tab-delimited text files containing the average gene read depth profile. Positions are given relative to TSS.

source_name: MRC5VA cells, DRB, UV, 40min

value: UVC irradiated

value: 40 minutes


title: Pycnoporus coccineus, Avicel rep2

value: CIRM-BRFM 310


title: Pycnoporus coccineus, wheat straw rep3

value: wheat straw


title: Pycnoporus coccineus, aspen rep3

description:
Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), 1 mm Wiley-milled aspen (15 g.l-1 )
raw_counts_CIRM-BRFM310
norm_counts_CIRM-BRFM310

value: aspen


title: Pycnoporus coccineus, Avicel rep1


title: Pycnoporus coccineus, pine rep3

description:
Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted pine wood fragments < 2 mm (15 g.l-1)
raw_counts_CIRM-BRFM310
norm_counts_CIRM-BRFM310

value: pine


title: UV+.t25

description: DRB GRO-seq

source_name: MRC5VA cells, DRB, UV, 25min

value: 25 minutes


title: Pycnoporus coccineus, pine rep2


title: Pycnoporus sanguineus, xylan-galactomannan rep3


title: Pycnoporus coccineus, aspen rep1


title: UV+.t10

description: DRB GRO-seq

source_name: MRC5VA cells, DRB, UV, 10min

value: 10 minutes


title: Pycnoporus coccineus, pine rep1


title: UV-10h

description: GRO-seq

source_name: MRC5VA cells, UV, 10hr

value: 10 hours


title: Pycnoporus coccineus, maltose rep3

description:
Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (20 g.l-1)
raw_counts_CIRM-BRFM310
norm_counts_CIRM-BRFM310

value: maltose


title: Pycnoporus coccineus, maltose rep2


title: UV-.t40

description: DRB GRO-seq

source_name: MRC5VA cells, DRB, untreated, 40min


title: UV-.t10

description: DRB GRO-seq

source_name: MRC5VA cells, DRB, untreated, 10min


title: Pycnoporus coccineus, maltose rep1


title: UV-t25

description: DRB GRO-seq

source_name: MRC5VA cells, DRB, untreated, 25min


title: DHS-seq-M1+IL-6

data_processing:
Illumina Casava1.7 software was used for basecalling.
The fastx-toolkit program was used to filter off low quality sequences from raw sequencing data.
DHS-seq reads were aligned to the mouse genome (Mus musculus NCBIM37) by BWA alignment
Analysis of DHS sites with Seqmonk software.
Genome_build: mm9
Supplementary_files_format_and_content: .txt

source_name: bone-marrow

extract_protocol:
Intact nuclei were isolated from M1 and IL-6 treated M1 cells and restrictedly digested with DNase I according to a standard protocol (Sabo et al., 2006).
Fractions containing small DNA fragments representing two-hit DNase I cutting events were precipitated, pooled, and prepared for Illumia sequencing according to the manufacturer Illumina.

value: Murine myeloid progenitor M1 cells

value: Yes


title: DHS-seq-M1

value: No


title: Pycnoporus coccineus, aspen rep2

value: day 3


title: Untreated replicate 1

description:
Untreated_1
Processed data file: genelevel.rawcounts.txt

data_processing:
The 72-bp paired-end read data were aligned to the hg19 version of the human genome using Tophat2 (version 2.0.8, Kim et al., 2013). A transcriptome guide file derived from the knownGene annotation table available from the University of California, Santa Cruz (UCSC) Genome Bioinformatics site was provided to focus alignments towards characterized transcripts. Non-unique alignments were removed prior to further analysis.
We identified putative alternative splicing events using Miso (Katz et al., 2010). Miso's hg19 gff3 annotation files was used to test possible events. Events were identified for pairwise comparisons between UV treated and untreated sample pairs within the two replicate groups.
Miso's post processing filters were then used to help reduce false positives.
Gene-level read quantifications were generated using the summarizeOverlaps function within the GenomicAlignments package, Bioconductor (mode="IntersectionStrict", singleEnd=FALSE ).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: genelevel.rawcounts.txt: Tab-delimited text file containing raw gene-level read quantifications.
Supplementary_files_format_and_content: *miso.txt: Miso-compare filtered output files.

growth_protocol: Standard growing procedures.

extract_protocol:
RNeasy Kit (Qiagen).
Preparation of mRNA libraries using standard Illumina protocols and sequenced on an Illumina GA IIX sequence analyzer as paired-end 72 bp reads.

treatment_protocol: UVC irradiation was performed using Stratalinker 2400.


title: UV 8 hr replicate 2

description:
UV_8_hr_2
Processed data file: genelevel.rawcounts.txt

value: 8 hours


title: UV 8 hr replicate 1

description:
UV_8_hr_1
Processed data file: genelevel.rawcounts.txt


title: Liver Day 28 Heat Stress Library 1325

city: Newark

first: Carl

last: Schmidt

state: DE

address: 601 Sincock Ln

institute: University of Delaware

data_processing:
Bowtie
TopHat
Cufflinks
Genome_build: Gallus gallus ver 4 - 2015

molecule: polyA RNA

organism: Gallus gallus

source_name: heat stress

growth_protocol: Birds were raised following grower standards outlined by our AACUC protocol (#(27)03-12-14R). Briefly, birds were raised on litter with ad libitum access to feed and water. First week house temperature: 35 degrees C with 5 degrees C decrease each week until 25 degrees celsius was reached. Thermoneutral/Control house maintained this temperature through completion of the trial while heat stress (experimental) house began a cyclical heat stress scheme detaield below through completion of the trial at day 28. Both houses received 23 hours of light and 1 hour of dark for the entirety of the study. A necropsy was performed on day 28. Matched controls were collected at this time point.

extract_protocol:
Birds were euthanized via cervical dislocation and necropsied on day 28. Approximately 1 square centimeter samples from the left lobe of the liver were collected and flash frozen with liquid nitrogen.
Libraries were constructed using the illumina Truseq Stranded mRNA Sample Prep Kit as per manufacturer instructions

treatment_protocol: Temperature in the experimental house was increased each day from 25 degrees celsius to approximately 35-37 degrees celsius from 7 am to 3 pm each day starting on day 21. This cyclical heat stress scheme continued through day 28, completion of the trial.

value: Left Lobe of Liver

value: Ross 708 broiler

value: 28 days


title: Liver Day 28 Heat Stress Library 1328


title: UV 24 hr replicate 1

description:
UV_24_hr_1
Processed data file: genelevel.rawcounts.txt

value: UVC irradiated

value: 24 hours


title: Liver Day 28 Heat Stress Library 1327


title: Liver Day 28 Heat Stress Library 1324


title: Liver Day 28 Heat Stress Library 1323


title: Liver Day 28 Heat Stress Library 1322


title: Liver Day 28 Heat Stress Library 1321


title: Liver Day 28 Heat Stress Library 1326


title: Liver Day 28 Control Library 1334

source_name: control


title: Liver Day 28 Control Library 1337


title: Rex1_2i_Rep2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: Whole genome bisulfite sequencing, WGBS-Seq

data_processing:
Raw sequence reads were trimmed to remove both poor quality calls and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.3.3, default parameters).
Remaining sequences were mapped to the mouse genome (build NCBIM37) using Bismark (Krueger and Andrews, 2011) (v0.12.3, parameters --bowtie2); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts.
Genome_build: NCBIM37
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: 2i population

growth_protocol: ES cell lines carrying the RGd2 reporter were derived from embryos using previously described protocols (Nichols et al., 2009). For routine maintenance ES cells were plated at 2-3 x 10^4 cells cm-2 in 2i on 0.1% gelatine-coated dishes (Sigma, G1890) and passaged every 3 days following dissociation with Accutase (PAA, L11-007). 2i consists of N2B27 (NDiff N2B27 base medium, Stem Cell Sciences Ltd, Cat. SCSSF-NB-02) or homemade N2B27, supplemented with PD0325901 (1 μM) and CHIR99021 (3 μM).

extract_protocol:
Genomic DNA was isolated using Gentra Puregene Cell Kit (Qiagen)
Genomic DNA was fragmented by sonication (Covaris) and adaptor ligated using Illumina supplied methylated adaptors and NEBnext library preparation kit. Subsequently DNA was bisulfite-treated using the Sigma Imprint kit according to the manufacturer’s instructions (one step protocol). Final library amplification (11 cycles) was done using KAPA Uracil+ (KAPA Biosystems), after which the libraries were purified using Ampure beads (x1).

treatment_protocol: Cells were plated at 1.5 x 104 cells cm-2 in 2i and medium was replaced with N2B27 or fresh 2i after 20-24 h. Prior to sorting cells were washed, pelleted and resuspended in the respective culture medium. For dissociation of 2i-cells 2i inhibitors were added into Accutase. ToPro-3 (Invitrogen) was added at a concentration of 0.05 nM to label membrane compromised cells. Cells were sorted in MoFlo flow sorter (Beckman Coulter). From 2i -and 16h-cultures all ToPro-3-negative cells, and to obtain Rex1-high and –low fractions from 25h-cultures, cells with highest and lowest 15% GFP expression were collected

value: Rex1-GFPd2 (1903.4 line)


title: Liver Day 28 Control Library 1332


title: Rex1_2i_Rep1


title: Liver Day 28 Control Library 1331


title: Rex1_25h-Low_Rep1

source_name: Rex1-low population 25h post-2i withdrawal


title: Untreated replicate 2

description:
Untreated_2
Processed data file: genelevel.rawcounts.txt

value: Untreated

value: 0 hours


title: UV 24 hr replicate 2

description:
UV_24_hr_2
Processed data file: genelevel.rawcounts.txt

source_name: MRC5VA cells, UV, 24hr


title: Rex1_25h-Low_Rep3


title: Rex1_25h-Low_Rep2


title: Liver Day 28 Control Library 1330


title: Liver Day 28 Control Library 1335


title: Liver Day 28 Control Library 1333


title: Rex1_25h-High_Rep2

source_name: Rex1-high population 25h post-2i withdrawal


title: Rex1_25h-High_Rep3


title: Rex1_16h_Rep3

source_name: 16h population post-2i withdrawal


title: Memory_H3K27me3_rep1

city: Stanford

first: Howard

middle: Y

last: Chang

state: California

address: 269 Campus Drive

institute: Stanford University

data_processing:
Reads were aligned to mm10 by BWA
Reads with low quality (MAPQ < 30) were filtered out. If multiple reads were mapped to the exact same location, only one read was kept.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: KLRG1loIL7Rhi memory CD8 T cells

extract_protocol:
Splenocytes were isolated and specific CD8 T cell subsets were sorted by FACS
ATAC-seq library was constructed by Nextera DNA Sample Prep Kit (Illumina). For ChIP-seq library, DNA was end-repaired using End-it End-repair kit (Epicentre) and then added an “A” base to the 3’ end of DNA fragments using Klenow (NEB). Then DNA was ligated with adaptors using quick DNA ligase (NEB) at 25°C for 15 min followed by size selection of 200-400 bp using AMPure SPRI beads (Beckman Coulter). The adaptor ligated DNA was amplified using NEBNext High-Fidelity 2X PCR master mix (NEB).

treatment_protocol: OT1 transfer and Lm-OVA infection for 8 days or >60 days

value: six to seven weeks

value: Spleen


title: Liver Day 28 Control Library 1336


title: Rex1_2i_Rep3


title: MP_H3K27me3_rep2

source_name: KLRG1loIL7Rhi memory precursor CD8 T cells


title: Pycnoporus cinnabarinus, wheat straw rep2

description:
Liquid cultures of P. cinnabarinus CIRM-BRFM 137 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted wheat straw (15 g.l-1 )
raw_counts_CIRM-BRFM137
norm_counts_CIRM-BRFM137

organism: Trametes cinnabarina

source_name: mycelium

value: wheat straw


title: Rex1_16h_Rep2


title: Pycnoporus cinnabarinus, xylan-galactomannan rep2

description:
Liquid cultures of P. cinnabarinus CIRM-BRFM 137 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), a mixture of xylans and galacto-mannans (15 g.l-1 )
raw_counts_CIRM-BRFM137
norm_counts_CIRM-BRFM137

value: xylan-galactomannan


title: Rex1_16h_Rep1


title: TE_H3K27me3_rep2

source_name: KLRG1hiIL7Rlo terminal effector CD8 T cells


title: TE_H3K27me3_rep1


title: Pycnoporus cinnabarinus, xylan-galactomannan rep3


title: Pycnoporus cinnabarinus, xylan-galactomannan rep1


title: Pycnoporus cinnabarinus, wheat straw rep3


title: TN_H3K27me3_rep2

source_name: naive CD8 T cells


title: Pycnoporus cinnabarinus, Avicel rep1

description:
Liquid cultures of P. cinnabarinus CIRM-BRFM 137 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), Avicel (15 g.l-1 )
raw_counts_CIRM-BRFM137
norm_counts_CIRM-BRFM137

value: Avicel


title: Pycnoporus cinnabarinus, pine rep3

description:
Liquid cultures of P. cinnabarinus CIRM-BRFM 137were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted pine wood fragments < 2 mm (15 g.l-1)
raw_counts_CIRM-BRFM137
norm_counts_CIRM-BRFM137

value: pine


title: Pycnoporus cinnabarinus, pine rep2


title: Pycnoporus cinnabarinus, aspen rep2

description:
Liquid cultures of P. cinnabarinus CIRM-BRFM 137 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), 1 mm Wiley-milled aspen (15 g.l-1 )
raw_counts_CIRM-BRFM137
norm_counts_CIRM-BRFM137

value: aspen


title: Pycnoporus cinnabarinus, aspen rep1

value: day 3


title: TN_H3K27me3_rep1


title: Rex1_25h-High_Rep1


title: Pycnoporus cinnabarinus, pine rep1


title: Pycnoporus cinnabarinus, maltose rep2

description:
Liquid cultures of P. cinnabarinus CIRM-BRFM 137 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (20 g.l-1)
raw_counts_CIRM-BRFM137
norm_counts_CIRM-BRFM137

value: maltose


title: MP_H3K27me3_rep1


title: Pycnoporus cinnabarinus, maltose rep1


title: MPSY T20 RNAseq rep2

city: Beijing

first: Xingzhong

address: NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China

department: The State Key Laboratory of Mycology

institute: Institute Of Microbiology Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mrakia psychrophila whole genome using tophat v2.1.0
FPKM was culculated using Cufflinks v2.2.1
Genome_build: Mrakia psychrophila BioProject: PRJNA304674
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all samples as matrix table. Text files with CDS sequence and protein sequence are available on the series records.

organism: Mrakia psychrophila

source_name: Yeast cultured on PDA_20C

growth_protocol: cultured on PDA

extract_protocol:
RNA is extract with RNeasy® Plant Mini Kit (QIAGEN)
Sequencing libraries were generated using a NEBNext®Ultra™ RNA Library Prep Kit for Illumina®(NEB, USA) following the manufacturer’s recommendations.

tag: temperature

value: 20 degree centigrade


title: Memory_H3K27me3_rep2


title: MPSY T20 RNAseq rep3


title: Pycnoporus cinnabarinus, maltose rep3


title: Pycnoporus cinnabarinus, wheat straw rep1


title: MPSY T12 RNAseq rep3

source_name: Yeast cultured on PDA_12C

value: 12 degree centigrade


title: MPSY T20 RNAseq rep1


title: MPSY T12 RNAseq rep1


title: MPSY T12 RNAseq rep2


title: MPSY T4 RNAseq rep1

source_name: Yeast cultured on PDA_4C

value: 4 degree centigrade


title: MPSY T4 RNAseq rep3


title: Pycnoporus cinnabarinus, Avicel rep3


title: Pycnoporus cinnabarinus, aspen rep3


title: Lap1 Testis ChIP-seq replicate 1, technical replicate 1

status: Public on Feb 20 2017

city: Canberra

first: David

last: Tremethick

state: ACT

address: 131 Garran Rd

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

description: ChIP-seq

data_processing:
3' adapter sequences were  trimmmed using Trimmomatic-0.36
ChIP-seq and CLIP-seq reads were mapped to  UCSC mouse mm9 using bowtie2. mRNA-seq paired-end reads were mapped to UCSC mouse mm9 genome assembly using Tophat.
Supplementary_files_format_and_content: bw files with mapping alignments were generated

source_name: Testis

extract_protocol:
Chromatin preparation for ChIP and RNA-IP: Mononucleosomes were prepared from testicular tubules as described (Soboleva et al. 2012). To prepare chromatin from hippocampal tissues, 10 Balb/c male mice (6-10 weeks old) were decapitated and hippocampi were surgically removed into ice cold Hank's Balanced Salt Solution (HBSS, Sigma) buffered with 50mM Hepes pH-7.6 and supplemented with 0.2 mM PMSF and EDTA-free protein inhibitor cocktail (Roche)). Hippocampal slices were homogenised in a Dounce homogeniser with 5-10 strokes using pestle A with 4 ml of ice-cold HBSS. Cells were counted and the subsequent preparation of mononucleosomes was identical to that described above for testicular tubules using 2-5 x 107 cells. To prepare sonicated chromatin fragments (∼ 300 base pairs long) from testis for RNA-IP Seq experiments, purified nuclei were re-suspended in 2ml of sonication buffer (50mM Hepes pH-7.6, 1mMEDTA, 05mM EGTA, 0.1% (w/v) SDS, 0.1% (w/v) sodium deoxycholate, 0.2 mM PMSF, Roche EDTA-free protein inhibitor cocktail) and sonicated for 15 minutes (30 seconds intervals on/off at high settings) at 40C using a Bioraptor Sonicator (Diagenode). After sonication, the sheared chromatin was cleared by centrifugation at 10000 g for 5 minutes, dialysed against 10 mM Tris-HCl pH 7.6, 1 mM EDTA, 0.5 mM EGTA, 4% (v/v) glycerol and stored at -80°C.
Antibodies used were as follows. Anti-H2A.B.3[1], Anti-H2A.Z[2] , Anti-Smith Antigen [Y12] (abcam (ab) 3138); Anti-H2A (ab18255), anti-H3 (ab1791), anti-RNA PolII (phospho S2) (ab5095), anti-RNA PolII (phospho S5) (ab5131), anti-Rent1 (ab109363), anti-Snrpa1  (ab128937), anti-U1A (ab155054), anti-SPT6 (ab32820), anti-Symplekin (ab80274), anti-SAP18 (ab31748) and anti-Sf3b155 (ab66774), all from Abcam. Anti-DDX39A (PA5-31220, Pierce), anti-sheep-HRP (AP324R; Chemicon), anti-rabbit-HRP (AP322P; Chemicon)
[1] Soboleva TA, Nekrasov M, Pahwa A, Williams R, Huttley GA, et al. (2012) A unique H2A histone variant occupies the transcriptional start site of active genes. Nat Struct Mol Biol 19: 25-30.
[2] Rangasamy D, Berven L, Ridgway P, Tremethick DJ (2003) Pericentric heterochromatin becomes enriched with H2A.Z during early mammalian development. EMBO J 22: 1599-1607.
Chromatin immunoprecipitations were performed with affinity purified H2A.B.3, H2A.Z and H3K36me3. ChIP-seq Libraries were prepared for the first biological replicate using the Sample Prep Kit (Illumina) according to the manufacturer's protocol for single end sequencing of DNA. The second biological replicate used the ChIP-Seq Library Prep (New England Biolabs) with barcodes and paired end adaptors. Quality and concentration of the libraries were assessed on Agilent Technologies 2100 Bioanalyzer and using qPCR with adaptor specific primers (ABI Prism 7900HT) according to Illumina's recommendations. DNA was sequenced on HiSeq 2000 or HiSeq 2500 (rapid run mode) (Illumina) using 100 base pairs single– or paired–end reads. RNA-IP libraries were prepared from these low molecular weight RNA-protein complexes and sequenced using 100 base pair paired–end reads.

value: Balb/c

tag: gender

value: male

value: Testis


title: H2A_Z Testis ChIP-seq replicate 1, technical replicate 2

description: ChIP-seq


title: WT rep1

city: La Jolla

first: Shenghong

last: Ma

state: CA

address: 2880 TORREY PINES SCENIC DR, Sanford Consortium

institute: UCSD

description: wild-type control sample

data_processing:
Illumina Casava1.7 software used for basecalling.
Trimmomatic for adaptor trim and low quality read trim.
Tophat2 for RNAseq alignment
cufflinks for gene-level and transcript-level FPKM calculation
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: widl type_brain

extract_protocol:
brain were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: FVB

value: wild type

value: 2-month old (post natal month 2)

value: brain


title: WT rep2

description: wild-type control sample


title: L2hgdh-KO rep1

description: L2hgdh gene knockout mice sample

value: L2hgdh-KO;  L2hgdh-/-


title: Lap1 Testis ChIP-seq replicate 1, technical replicate 2

description: ChIP-seq


title: MPSY T4 RNAseq rep2


title: H2A_Z Testis ChIP-seq replicate 1, technical replicate 1

description: ChIP-seq


title: L2hgdh-KO rep2

description: L2hgdh gene knockout mice sample


title: WT rep3

description: wild-type control sample


title: 3H8

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using STAR version 2.4.1b with the following options --outFilterMultimapNmax 10  --outFilterMultimapScoreRange 1 --limitOutSJoneRead --outFilterScoreMin 3  --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66  --outFilterMismatchNoverLmax 0.3 and the other parameter kept as default
BAM files of sample1-11 are downsampled, if needed, using samtools to ensure sample 1-4, sample 5-8, sample 9-11 have same read numbers.
for sample 1-4: peaks were called using MACS version 1.4.2 using sample 5-8 as backgournd, with the following setting -g mm --nomodel --nolambda and others as default.
for sample 9-11: tag directories were first generated by HOMER makeTagDirectory with -keepOne -tbp 1 and other options as default.
for sample 9 and 11: peakd were call by HOMER findpeak using sample 12 as background and -style factor -size 100 -fragLength 50 with other options as default
for sample 10: peakd were call by HOMER findpeak using sample 12 as background and -style histone -fragLength 50 -size 200 -minDist 1000 -L 0 with other options as default
for sample 13-16: transcript count were generated by kallisto version 0.42.4 using GENCODE GRCm38.p4 transcriptome as reference, with the following parameter: -l 200 -s 20 --single and other setting as default
For all Single Cell Samples the following processing steps apply:
Single-cell RNA-seq data pre-processing. Single-cell mRNA sequencing data from 256 murine CD8+ T cells were processed with a bioinformatics pipeline focusing on quality control (QC) and robust expression quantification.  For each cell, raw RNA-seq reads were: checked for quality metrics with fastqc (v0.10.1); poly-A and adaptor-trimmed with cutadapt (v1.8.1); quantified by kallisto (v0.42.1) to a reference transcriptome (Gencode vM3) without bias correction; and aligned by STAR (v2.4.1b) to the reference mouse genome (mm10) with default parameters for quality control and downstream analysis. Next, the transcript per million (TPM) outputs of kallisto for all cells were combined into a cell-by-gene expression matrix (C=288 cells=rows, G=22425 genes=columns) by summing the expression values for all quantified transcripts of a given gene. Finally, the TPM value for each cell c and gene g was natural log-transformed to yield a normalized expression value: EXPRc,g = ln(1+TPMc,g).
Dimensionality reduction and cell heterogeneity visualization. To reduce the dimensionality of the cell-by-gene expression matrix EXPR and visualize the diversity of gene expression among CD8+ T cells of different subtypes in a 2-dimensional scatter plot, we applied the t-distributed Stochastic Neighborhood Embedding (tSNE) algorithm via its Barnes-Hut approximation (bhSNE). We first applied standard Principal Components Analysis (PCA) to reduce the dimensionality down to D=10, and only then applied bhSNE to visualize in D=2 (with perplexity=30 and theta=0.75 parameters).
Differential gene expression analysis. We performed differential gene expression analysis between all pairs of T cell sub-populations from two non-overlapping sets of rows in the log-transformed expression matrix EXPR. Since single-cell gene expression does not conform to the usual negative binomial distribution and can even be bimodal due to dropout we used two non-parametric statistical tests for heterogeneity of expression: Mann Whitney Wilcoxon (MWW, also known as MWU) which is a rank-sum test but relies on a large sample to approximate normality, and Kolmogorov-Smirnov 2-sample (KS2) test which finds the largest difference between the empirical cumulative distributions, even between two small samples such as our 1st division sub-types Div1TE (n =36) and Div1MEM (n =24).
Cell type classifier. We trained two binary T cell classifiers to identify gene expression signatures that not only differentiate the examined T cell sub-populations (like the differential gene expression described above) but can also be used to predict the ‘memory-‘ or ‘effector-ness’ of previously unseen cells. Each classifier constructed an independent ensemble of Extremely Randomized Trees. Using the terminally differentiated effector and memory (TCM, TEM) populations, we built a training set for a fate classifier for CD8+ T cells. Using the newly observed segregation of daughter T cells into Div1TE and Div1MEM subpopulations after the first division, we built a second training set for another early state classifier. Both classifiers were fed their respective training sets using 10-fold cross-validation
After both the fate and early state classifiers were trained on their respective subpopulations, they were both applied on previously unseen intermediate Day 4 CD8+ T cells. Their predicted ‘memory-ness’ scores were scatter-plotted and shown to correlate in Fig. 3f.  For each T cell, its ‘effector-ness’ scores is 1 minus the ‘memory-ness’ score and is redundant for this analysis. The signature genes for each classifier were selected from all G=22,425 genes by their GINI score.
Temporal expression trajectories through inferred lineage paths. To understand the temporal dynamics of expression for key genes along the effector and memory lineages, we constructed hypothetical differentiation time-courses for each lineage. Briefly, we sampled with replacement 50 cells from each population and constructed all trajectories through the cross-product of populations ordered in a particular lineage. These orders were determined a priori based on our earlier work with similar timecourses of RT-qPCR study (Arsenio et. al. Nature Immunology 2014). Specifically, the ‘effector lineage’ starts from the naïve population, and progresses through the Div1TE subpopulation, then onto Day 4, and finally Day 7. In contrast, the ‘effector memory’ and ‘central memory lineages’ start from naïve, through the Div1MEM subpopulation, ending with TEM and TCM respectively. These bootstrapped trajectories were visually summarized by a seaborn timeseries plot which links the average expression for each population sample with a solid line segment and represents the 95% confidence interval by a shaded area around it.
Genome_build: mm10
Supplementary_files_format_and_content: peak BED files generated from MACS and HOMER. Transcript Expression CSV tables generated from kallisto.

source_name: CD8+ T cell

growth_protocol: 5 x 103 P14 CD45.1+ CD8+ T cells were adoptively transferred into congenic wild-type CD45.2+ recipient mice, followed by intraperitoneal infection (i.p.) 1 day later with 2 x105 plaque forming units (pfu) per mouse of LCMV-Arm.  Splenocytes were isolated from recipient mice at 7 d post-infection (n=4) and splenocytes and lymph nodes were harvested at 42 d (n=40) post-infection.  For the isolation of CD8+ T cells at 4 d post infection, 5 x 104 P14 CD8+ T cells per mouse were adoptively transferred into 24 recipient mice.

extract_protocol:
The C1 Single-Cell Auto Prep System (Fluidigm) was used to perform whole transcriptome amplification (WTA) of up to 96 single cells simultaneously. After cell isolation, FACS sorted 2.5 x 105 to 2 x 106 P14 CD8+ T cells were loaded onto the C1 Single-Cell Auto Prep mRNA Array IFC for single-cell capture on chip. Live/dead stain (Invitrogen) was included to exclude dead cells. Viable single cells captured on chip were manually imaged. Cell lysis and RT-PCR were performed on chip.
SMARTer chemistry (Clontech) WTA was performed according to the manufacturer’s instructions. Illumina Nextera XT single-cell complementary DNA (cDNA) libraries were generated according to the manufacturer’s instructions (Illumina). Quality control measures of the single-cell cDNA libraries were performed on the 2100 Bioanalyzer (Agilent Technologies), Qubit 3.0 Fluorometer (Thermo Fisher Scientific), and MiSeq Sequencing System (Illumina). Single-cell cDNA libraries were sequenced (paired-end 100 or single-end 100) on the HiSeq2500 Sequencing System at the UCSD Institute for Genomics Medicine (IGM) Center.

treatment_protocol: For the isolation of CD8+ T cells that had undergone their first cell division, 2 x 106 P14 CD8+ T cells were first labeled with carboxyfluorescein diacetate succinimidyl ester (CFSE) prior to adoptive transfer into recipient mice (n=24) and harvested 2 d post LCMV-Arm infection.

tag: subtype

tag: library strategy

value: Single Cell RNAseq


title: L2hgdh-KO rep3

description: L2hgdh gene knockout mice sample


title: 3H6

tag: replicate


title: 3H7


title: 3H2

value: Tcm


title: 3H1


title: 3H11


title: 3H12


title: 3H4

value: Tem


title: 3H10


title: 3G9


title: 3G8


title: 3G6

value: Naive


title: 3G7


title: 3G5


title: 3G3


title: 3G2


title: 3G1


title: 3G11


title: 3G4


title: 3H5


title: 3F9


title: 3G10


title: 3F7


title: 3G12


title: 3F8


title: 3H9


title: 3H3


title: 3F6


title: 3F4


title: 3F1


title: 3E9


title: 3F10


title: 3F3


title: 3E5


title: 3E6


title: 3E4


title: 3F11


title: 3E1


title: 3E12


title: 3E2


title: 3E3


title: 3E11


title: 3E10


title: 3F2


title: 3D2


title: 3D3


title: 3D4


title: 3D5


title: 3E7


title: 3E8


title: 3F12


title: 3D12


title: 3D7


title: 3D8


title: 3D1


title: 3D10


title: 3D9


title: 3D11


title: 3C5


title: 3C2


title: 3C6


title: 3C1


title: 3C9


title: 3C11


title: 3C8


title: 3C4


title: 3D6


title: 3C7


title: 3C10


title: 3B8


title: 3B4


title: 3B5


title: 3B7


title: 3B2


title: 3B3


title: 3B1


title: 3B12


title: 3C3


title: 3B11


title: 3B10


title: 3A9


title: 3B9


title: 3C12


title: 3A5


title: 3A4


title: 3A2


title: 3A3


title: 3A6


title: 3A11


title: 3A1


title: 3B6


title: 2H11


title: 3A7


title: 2H12


title: 2G12


title: 2F12


title: 2G11


title: 3A8


title: 2F11


title: 2C11


title: 2D12


title: 2A12


title: 2D11


title: 2E11


title: 2E12


title: 2A11


title: 2H10


title: 2C12


title: 2B11


title: 3A12


title: 3A10


title: 2F9


title: 2G10


title: 2H9


title: 2G9


title: 2F10


title: 2E10


title: 2E9


title: 2B12


title: 2C9


title: 2B9


title: 2A10


title: 2D10


title: 2B10


title: 2A9


title: 2F8


title: 2H8


title: 2G7


title: 2G8


title: 2E8


title: 2F7


title: 2H7


title: 2C7


title: 2E7


title: 2C8


title: 2D8


title: 2B7


title: 2H5


title: 2A7


title: 2D7


title: 2B8


title: 2D9


title: 2G6


title: 2A8


title: 2C10


title: 2E6


title: 2F5


title: 2D6


title: 2C5


title: 2C6


title: 2F6


title: 2B5


title: 2H3


title: 2A5


title: 2E5


title: 2F3


title: 2D5


title: 2A6


title: 2F4


title: 2G3


title: 2H4


title: 2D3


title: 2E4


title: 2E3


title: 2G4


title: 2D4


title: 2H6


title: 2G5


title: 2C4


title: 2C3


title: 2B4


title: 2B3


title: 2H1


title: 2A4


title: 2A3


title: 2G2


title: 2G1


title: 2H2


title: 2F2


title: 2F1


title: 2E1


title: 2E2


title: 2D1


title: 2D2


title: 2B2


title: 2C1


title: 2C2


title: 2A2


title: 1H9


title: 1H6


title: 1H5


title: 2A1


title: 1H4


title: 1H3


title: 1H2


title: 1H1


title: 1G6


title: 1G5


title: 1H11


title: 1G7


title: 1G1


title: 1G12


title: 1G10


title: 1G11


title: 1H10


title: 1H12


title: 1G8


title: 1F7


title: 1G4


title: 1F10


title: 1F12


title: 1G3


title: 1H8


title: 1G2


title: 2B1


title: 1F9


title: 1F8


title: 1F6


title: 1F5


title: 1H7


title: 1F4


title: 1E5


title: Day4Input

description: Growth Protocol: Wild-type CD8+ T cells were activated in vitro with plate-bound anti-CD3 and anti-CD28 antibodies for 4 days and sorted by flow cytometry to exclude dead cells. Extraction Protocol: Cells were cross-linked with formaldehyde and ChIP performed using the EZ-Magna ChIP kit (Millipore) according to the manufacturer’s instructions.  Library Construction Protocol: Sequence-indexed libraries were prepared from immunoprecipitated DNA and input controls (1%) using the NEB Next ChIP Library Preparation Reagent Set (NEB), according to the manufacturer’s instructions.

tag: antibody


title: 1F3


title: 1F2


title: 1F1


title: 1F11


title: RNA-seq KO rep2

description:
Growth Protocol: 50000 P14 WT or Ezh2-deficient CD8 + T cells were adoptively transferred into recipient mice followed by infection with LCMV and sorted by flow cytometry at 4 days post-infection. Library Construction Protocol: mRNA stranded cDNA libraries were generated according to the manufacturer’s instructions (Illumina).
CW08_S8_L002_R1
bulkRNA_count.csv

value: Ezh2 fl/fl Cd4Cre

value: Bulk RNA-Seq


title: RNA-seq KO rep1

description:
Growth Protocol: 50000 P14 WT or Ezh2-deficient CD8 + T cells were adoptively transferred into recipient mice followed by infection with LCMV and sorted by flow cytometry at 4 days post-infection. Library Construction Protocol: mRNA stranded cDNA libraries were generated according to the manufacturer’s instructions (Illumina).
CW07_S7_L002_R1
bulkRNA_count.csv


title: 1G9


title: 1E9


title: Day4PolII


title: 1E2


title: 1E4


title: input DNA KO rep2


title: 1E8


title: RNA-seq WT rep2

description:
Growth Protocol: 50000 P14 WT or Ezh2-deficient CD8 + T cells were adoptively transferred into recipient mice followed by infection with LCMV and sorted by flow cytometry at 4 days post-infection. Library Construction Protocol: mRNA stranded cDNA libraries were generated according to the manufacturer’s instructions (Illumina).
CW06_S6_L002_R1
bulkRNA_count.csv

value: Ezh2 fl/fl Cd4wt


title: RNA-seq WT rep1

description:
Growth Protocol: 50000 P14 WT or Ezh2-deficient CD8 + T cells were adoptively transferred into recipient mice followed by infection with LCMV and sorted by flow cytometry at 4 days post-infection. Library Construction Protocol: mRNA stranded cDNA libraries were generated according to the manufacturer’s instructions (Illumina).
CW05_S5_L002_R1
bulkRNA_count.csv


title: 1E6


title: Day4H3K27me3

value: H3K27me3 antibody (Millipore, 07-449, lot 2652971)


title: input DNA KO rep1


title: 1E3


title: Day4Ezh2

value: Ezh2 antibody (Santa Cruz H-80,sc-25383,H0213)


title: 1E1


title: 1E7


title: input DNA WT rep2


title: H3K27me3_ChIPSeq KO rep2


title: H3K27me3_ChIPSeq KO rep1


title: 1D8


title: 1E11


title: H3K27me3_ChIPSeq WT rep2


title: 1D7


title: H3K27me3_ChIPSeq WT rep1


title: 1D6


title: 1D5


title: 1E12


title: 1D1


title: 1D3


title: 1D11


title: 1D12


title: 1D10


title: 1C7


title: 1C9


title: 3F5


title: 1D2


title: 1D9


title: 1E10


title: 1C5


title: 1C6


title: 1C4


title: 1C3


title: 1C2


title: 1C12


title: 1C11


title: 1B7


title: 1B8


title: 1B9


title: 1C10


title: 1B6


title: 1B5


title: 1D4


title: 1C8


title: 1B4


title: 1B2


title: 1B3


title: 1B1


title: mRNA-seq Testis replicate 2

description: mRNA-seq

extract_protocol:
For RNA-seq libraries, Total RNA was isolated using TRIzol (Invitrogen) and the RNeasy Mini kit (Qiagen). Samples were treated with TURBO™ DNase (Life Technologies).
library construction protocol not provided.

value: Balb/c

tag: tissue


title: 1A9


title: 1B11


title: 1B10


title: 1B12


title: mRNA-seq Hippocampus replicate 3

description: mRNA-seq

source_name: Hippocampus

value: male

value: Hippocampus


title: 1A8


title: mRNA-seq Testis replicate 1

description: mRNA-seq

value: Testis


title: mRNA-seq Hippocampus replicate 1

description: mRNA-seq


title: 1A6


title: H2A_Z CLIP-seq Testis replicate 2

description:
iCLIP-seq
merged bigwig over 3 replicates, plus/minus bigwigs are available on GSM2437149

extract_protocol:
RNA-IP Seq: A single cell suspension prepared from testicular tubules was washed 3 times with cold DPBS-GL (DPBS (Gibco) supplemented with 5.6mM D-glucose, 5.4mM DL-lactate, 0.5mM DTT, 0.2mM PMSF, EDTA-free protein inhibitor cocktail (Roche), pH-7.1). These cells were then resuspended into 6 ml at a density of 4-6x106 cells per ml in the same buffer and UV-irradiated with 75mJ/cm2 at 254 nm (Stratalinker 1800, Stratagene). Purified nuclei were sonicated and sheared chromatin (∼ 300 base pairs in size) was prepared as described for ChIP-Seq experiments (Soboleva et al. 2012). The RNA-IP procedure to detect H2A.B.3 associated RNA was carried out as described (Konig et al. 2011) using 300μg of sheared testis chromatin with some modifications. To minimize non- specific RNA carryover by eluted IgGs, 20μg of antibody was covalently linked to dynabeads (Life Technologies). As a control, we also performed this procedure using affinity purified H2A.Z antibodies. Immunopurified H2A.B.3 revealed several RNA-protein complexes (that were less than 70 Kd) that were not present in chromatin immunopurified with H2A.Z (data not shown), which were chosen and combined for further analysis.
Antibodies used were as follows. Anti-H2A.B.3[1], Anti-H2A.Z[2] , Anti-Smith Antigen [Y12] (abcam (ab) 3138); Anti-H2A (ab18255), anti-H3 (ab1791), anti-RNA PolII (phospho S2) (ab5095), anti-RNA PolII (phospho S5) (ab5131), anti-Rent1 (ab109363), anti-Snrpa1  (ab128937), anti-U1A (ab155054), anti-SPT6 (ab32820), anti-Symplekin (ab80274), anti-SAP18 (ab31748) and anti-Sf3b155 (ab66774), all from Abcam. Anti-DDX39A (PA5-31220, Pierce), anti-sheep-HRP (AP324R; Chemicon), anti-rabbit-HRP (AP322P; Chemicon)
[1] Soboleva TA, Nekrasov M, Pahwa A, Williams R, Huttley GA, et al. (2012) A unique H2A histone variant occupies the transcriptional start site of active genes. Nat Struct Mol Biol 19: 25-30.
[2] Rangasamy D, Berven L, Ridgway P, Tremethick DJ (2003) Pericentric heterochromatin becomes enriched with H2A.Z during early mammalian development. EMBO J 22: 1599-1607.
Chromatin immunoprecipitations were performed with affinity purified H2A.B.3, H2A.Z and H3K36me3. ChIP-seq Libraries were prepared for the first biological replicate using the Sample Prep Kit (Illumina) according to the manufacturer's protocol for single end sequencing of DNA. The second biological replicate used the ChIP-Seq Library Prep (New England Biolabs) with barcodes and paired end adaptors. Quality and concentration of the libraries were assessed on Agilent Technologies 2100 Bioanalyzer and using qPCR with adaptor specific primers (ABI Prism 7900HT) according to Illumina's recommendations. DNA was sequenced on HiSeq 2000 or HiSeq 2500 (rapid run mode) (Illumina) using 100 base pairs single– or paired–end reads. RNA-IP libraries were prepared from these low molecular weight RNA-protein complexes and sequenced using 100 base pair paired–end reads.


title: H2A_Z CLIP-seq Testis replicate 3


title: mRNA-seq Hippocampus replicate 2

description: mRNA-seq


title: Lap1 CLIP-seq Testis replicate 3

description:
iCLIP-seq
merged bigwig over 3 replicates, plus/minus bigwigs are available on GSM2437146


title: 1A5


title: H2A_Z CLIP-seq Testis replicate 1


title: Lap1 CLIP-seq Testis replicate 1


title: Lap1 CLIP-seq Testis replicate 2


title: 1A4


title: mRNA-seq Testis replicate 3

description: mRNA-seq


title: Lap1 Testis ChIP-seq replicate 1

description: ChIP-seq


title: 1A3


title: Lap1 Hippocampus ChIP-seq replicate 1

description: ChIP-seq


title: H3K36Me3 Hippocampus ChIP-seq replicate 1

description: ChIP-seq


title: 1A2


title: H3K36Me3 Testis ChIP-seq replicate 1

description: ChIP-seq


title: H3K36Me3 Hippocampus ChIP-seq replicate 2

description: ChIP-seq


title: H2A_Z Testis ChIP-seq replicate 2

description: ChIP-seq


title: 1A1


title: Input Hippocampus ChIP-seq replicate 1

description: ChIP-seq


title: 1A7


title: H2A_Z Hippocampus ChIP-seq replicate 1

description: ChIP-seq


title: input DNA WT rep1


title: 1A12


title: 1C1


title: H3K36Me3 Testis ChIP-seq replicate 2

description: ChIP-seq


title: Input Testis ChIP-seq replicate 1

description: ChIP-seq


title: 1A11


title: 7583 E2-2 wildtype

city: New York

first: Emily

last: Hsu

state: NY

address: 1130 St. Nicholas Ave.

department: ICG

institute: Columbia University

data_processing:
Libraries were pooled and sequenced on an Illumina HiSeq2000 with 100 bp single or paired end reads.
CASAVA (version 1.8.2) was used for base calling and adaptor trimming.
Alignment of sequencing reads to the mouse reference genome (Genome browser  Build 9) was performed using TopHat version 2.0.4  (Trapnell, Hendrickson et al. 2013) with standard parameters of 4 allowable mismatches and 10 maximum multiple hits.
The relative abundance of genes was estimated using Cufflinks version 2.0.2  (Trapnell, Hendrickson et al. 2013), with default settings.
For comparing the two sample groups, overexpression was defined as a ≥1.1 mean fold change and underexpression as a ≤ 0.9 mean fold change.
Genes showing RPKM values < 5 were excluded from further analysis. The mean RPKM ratio of E2-2/Itf2/Tcf4 deleted tumors compared to E2-2/Itf2/Tcf4 wild type controls  for every gene was calculated and filtered using a criteria of unpaired T-test, p-values <0.05 and mean RPKM ratio cutoff of 30% fold change over or underexpression.
Genome_build: Mouse reference genome (Genome browser Build 9)

source_name: Cultured fetal mouse kidney

growth_protocol: Fetal kidneys were dissected at 10.5dpc, then grown in culture for 3-4 days.

extract_protocol:
Total RNA from cultured mouse embryonic kidneys was prepared using Trizol reagent.
Poly-A pull-down was used to enrich for mRNAs, and libraries were prepared using the Illumina TruSeq RNA kit.

treatment_protocol: Pregnant mice were intraperitoneally injected with tamoxifen (2mg/40g body weight) at 10.5 dpc. After dissection, kidneys were grown on 12-well TranswellTM membranes saturated with  F12 medium/DMEM (1:1) containing 5ug/mL transferrin, 5ug/mL insulin and 5ng/mL selenium.

tag: genotype/variation

value: beta-catenin activated, E2-2 wildtype


title: 5455 E2-2 wildtype


title: 2B6


title: 1A10


title: 7532 E2-2 deleted

value: beta-catenin activated, E2-2 deleted


title: 7184 E2-2 deleted


title: 7531 E2-2 wildtype


title: Input_ChIP

city: Bethesda

first: Stacie

last: Loftus

address: 49 Convent Dr

institute: National Human Genome Research Institute

data_processing:
ChIP-Seq peaks for each experimental replicate were called independently using the Model-based Analysis for ChIP-Seq (MACS v1.4.2) algorithm by applying default settings and a significance p-value threshold of 1.00e-05 and >10-fold enrichment over background.
Only ChIP-Seq profiles that showed reproducible overlap between both experimental samples were used for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using MACS and scores represent tag pileup over each position.   Text files represent narrow peak file ouput from MACS

growth_protocol: According to guidelines from Bennett et al. 1987 (PMID 3102392), cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), 200 nM 12-O-tetradecanoylphorbol 13-acetate (Sigma-Aldrich, St Louis, MO, USA) and 200 pM cholera toxin (Sigma- Aldrich, St Louis, MO, USA) at 37°C in humidified air.

extract_protocol:
Approximately 2 x 10^7 cells were harvested and crosslinked at room temperature with 1% formaldehyde for 9 minutes. Crosslinking reaction was quenched with the addition of glycine to a final concentration of 125 mM for at least 15 minutes. Crosslinked cells were lysed on ice using 1 ml low-salt ChIP buffer (150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.5% NP-40, 1.0%Triton X-100) and sonicated using a Qsonica Sonicator Q500 (Newtown, CT 0647) with the following settings: 70% amplitude; 10 seconds on/20 seconds off cycles; total sonication time of 15 minutes to yield fragments of 500-100 bp. Sonicated samples were centrifuged and the soluble chromatin (supernatant) was used for chromatin immunoprecipiation reactions. Briefly, 200 µl of lysate (~ 2 x 106 cells) was incubated with each antibody, 10µg / IP of HIF1A antibody #AF1935 Immunoprecipitated chromatin was recovered using recombinant protein G beads or magnetic Dynabeads® (Invitrogen). ChIP samples were reverse crosslinked and DNA was purified using the phenol-chloroform extraction method.
Illumina ChIP Seq libraries were prepared as follows: ChIP-isolated DNA was size selected by 2% Agarose Nusieve gel, and a 200-500bp region was excised and purified using Qiaquick gel extraction kit. Adapter linker attachment was performed by PCR using 30ng of DNA and 2X Phusion master mix and primers, using conditions of 30 sec, 98°C, followed by 10 sec, 98°C, 30 sec, 65°C and 30 sec, 72°C with cycle number empirically determined, followed by a final 5 min, 72°C extension step. Adapter ligated PCR reactions were purified using Agencourt Ampure XP PCR Purification Beads per manufacturer’s protocol.

treatment_protocol: Cells were grown in 1% oxygen for 24hr prior to crosslinking

value: Cdkn2a tm1RDp/tm1RDp mice

tag: cell line

tag: cell type

value: immortalized melanocyte cell line

tag: chip antibody

value: none (input)


title: HIF1A_ChIPrep2


title: 7533 E2-2 deleted


title: HIF1A_ChIPrep1


title: Stressed_GRChIP_r1

city: Bristol

first: John

middle: Robert

last: Pooley

address: Dorothy Hodgkin Building, Whitson Street

department: Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology

institute: University of Bristol

description:
GR ChIP Stressed replicate 1
processed data file : RepConcordant_Cort_Stressed_Hotspots.csv
processed data file : Thresholded_Merged_Cort_NSC_Stressed_Hotspots.csv
Cort_stressed_rn5_nodup_simple_pooled_hs_fdr0.0_input_adjusted.bgr.gz

data_processing:
RTA 1.12.42 was used for Basecalling.
Alignment was performed by Bowtie2 software with the rn5 reference genome.
Replicate concordant areas of enrichment were identified using DNase2Hotspots software modified to remove PCR-duplicated tags (https://sourceforge.net/projects/dnase2hotspots/).
Hotspots with FDR = 0% were manually inspected in a genome browser and based on this the top 20% from each group carried forward for analysis.
Signal density graphs (BedGraphs) were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands. Values for tag densities were normalized to 10 million reads to adjust for differences in the sequencing depth between samples.
Genome_build: rn5
Supplementary_files_format_and_content: Comma-delimited (CSV) text files include genomic locations (chromosome, start, end ), z-score, p-value and the maximum tag density of hotspots. Bedgraph files contain genomic locations and tag density profiles calculated as above.

organism: Rattus norvegicus

source_name: Whole hippocampus

growth_protocol: Rats were 7 weeks old on arrival and 9 weeks old at the time of the experiments described.

extract_protocol:
Hippocampi were fixed from fresh in 1% formaldehyde. Lysates were clarified from sonicated nuclei and GR-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Rats were adrenalectomised to remove endogenous corticosterone and implanted with a cannula into the jugular vein. Supplemental corticosterone provided in drinking saline during recovery was withdrawn 12 hours prior to experiments and replaced with saline only. Random assignment to two groups, stressed or non-stressed control. Both groups receive corticosterone infusion via jugular cannula to model a stress-like rise in hormone secretion. Stressed animals cocomitantly undergo 30 min restraint stress in perspect restrainers. Non-stressed controls remained in their home cage. Both groups killed immediately after the 30 min infusion/restraint and hippocampus dissected.

value: Whole hippocampus

value: Sprague-Dawley

tag: age

value: 9 weeks

value: anti-GR cocktail (2µg Santa Cruz sc-1004 X, 4µl Thermo PA1-510A, 4µg Thermo PA1-511A)


title: Stressed_GRChIP_r2

description:
GR ChIP Stressed replicate 2
processed data file : RepConcordant_Cort_Stressed_Hotspots.csv
processed data file : Thresholded_Merged_Cort_NSC_Stressed_Hotspots.csv
Cort_stressed_rn5_nodup_simple_pooled_hs_fdr0.0_input_adjusted.bgr.gz

tag: strain


title: Stressed_Input_r2

description:
Input control for Stressed replicate 2
processed data file : RepConcordant_Cort_Stressed_Hotspots.csv
processed data file : Thresholded_Merged_Cort_NSC_Stressed_Hotspots.csv
Cort_stressed_rn5_nodup_simple_pooled_hs_fdr0.0_input_adjusted.bgr.gz


title: Stressed_Input_r1

description:
Input control for Stressed replicate 1
processed data file : RepConcordant_Cort_Stressed_Hotspots.csv
processed data file : Thresholded_Merged_Cort_NSC_Stressed_Hotspots.csv
Cort_stressed_rn5_nodup_simple_pooled_hs_fdr0.0_input_adjusted.bgr.gz


title: NSC_Input_r2

description:
Input control for NSC replicate 2
processed data file : RepConcordant_Cort_NSC_Hotspots.csv
processed data file : Thresholded_Merged_Cort_NSC_Stressed_Hotspots.csv
Cort_basal_rn5_nodup_simple_pooled_hs_fdr0.0_input_adjusted.bgr.gz


title: NSC_GRChIP_r1

description:
GR ChIP NSC replicate 1
processed data file : RepConcordant_Cort_NSC_Hotspots.csv
processed data file : Thresholded_Merged_Cort_NSC_Stressed_Hotspots.csv
Cort_basal_rn5_nodup_simple_pooled_hs_fdr0.0_input_adjusted.bgr.gz


title: PMEN3_uninduced_T6h

city: Oxford

first: Angela

middle: B

last: Brueggemann

address: Peter Medawar Building for Pathogen Research

department: Nuffield Department of Medicine

institute: University of Oxford

data_processing:
The sequenced forward and reverse reads were paired and mapped to reference genomes using Bowtie2 with the highest sensitivity option.
Differential gene expression was assessed in Geneious using the DESeq method.
Genes with an adjusted P value <0.05 were deemed to be differentially expressed.
Genome_build: PMEN3 Reference Sequence
Supplementary_files_format_and_content: comma-delimited text files include the ratio of the normalized values between the control and mitomycin C for all genes at each time point (Log 2 of Differential Expression Ratio) and a p-value indicating the confidence that each gene is differentially expressed (Differential Expression p-value)

organism: Streptococcus pneumoniae

source_name: broth culture

extract_protocol:
RNA was immediately extracted from the samples using the Promega Maxwell® 16 Instrument and LEV simplyRNA Cells purification kit, following the manufacturer’s protocol.
RNA extracts were sent to the Oxford Genomics Centre where library preps were made using RNA-Seq Ribozero kits (Illumina, Inc)

value: PMEN3 (Spain9V-3)

tag: timepoint

value: 6 hour

tag: condition

value: Control


title: PMEN3_mitomycinC_T5h

value: 5 hour

value: Induced with mitomycin C


title: 7339 E2-2 wildtype


title: PMEN3_uninduced_T5h


title: PMEN3_uninduced_T4h

value: 4 hour


title: ERa ChIP-Seq E2+ICI

first: Joshua

middle: D

last: Stender

address: 9500 Gillman

institute: University of California at San Diego

description:
Sample 53
DSG and formaldehyde cross-linked.

data_processing:
For ChIP-Seq, RNA-Seq, and Gro-Seq samples, reads were aligned to the hg19 genome using default parameter for bowtie (RNA-Star, respectively).
Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif- and other analyses in the study.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), expression text files (RNA-Seq expression data, using default HOMER parameters). All genomic coordinates are relative to hg19 human assembly.

source_name: MCF7 cells, E2+ICI, ERa ChIP

extract_protocol:
ChIP-Seq: Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adapter ligation as previously described (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 12-15 cycles, size selected by gel extraction and sequenced on a HiSeq 2000 (Illumina) for 51 cycles.
RNA-Seq: Enriched mRNA was hydrolyzed with Fragmentation Buffer (Ambion) for 10 min at 70°C and re-buffered to 10 mM Tris pH 7.4 using P-30 size exclusion columns (Bio-Rad). RNA was then de-capped for 2 h at 37°C with 0.5 µl (10 U/µl) TAP (Epicentre) in 20 µl TAP buffer containing 1 U/µl SUPERase-IN. Samples were 3’ dephosphorylated for 50’ at 37°C with 1 µl PNK (Enzymatics), 0.5 µl 10x TAP buffer, 1.5 µl water, 0.5 ul 0.25 M MgCl2 (3 mM free Mg2+ final), 0.5 µl 10 mM ATP (0.2 µM final to protect PNK). Subsequently, RNA was 5’-phosphorylated for 60 min at 37°C by adding 2 µl (10 U/µl) PNK, 10 ul 10x T4 DNA ligase buffer and 63 µl water. RNA was extracted with Trizol LS, precipitated in the presence of Glycoblue (Ambion), and dissolved in 4.5 µl water. 0.5 µl 9 µM of a 5’-adenylated sRNA3'MPX adapter /5Phos/AG ATC GGA AGA GCA CAC GTC TGA /3AmMO/ (IDT, desalted; adenylated with Mth ligase (NEB) according to the manufacturer’s instructions, phenol-chloroform/chloroform-extracted, ethanol-precipitated with glycogen and dissolved in water at 9 µM) were heat-denatured together with the RNA for 2 minutes at 70°C, and ligated with 100 U truncated T4RNA ligase 2 K227Q (NEB) in 10 µl 1x T4 RNA ligase buffer without ATP, containing 10 U SUPERase-In and 15% PEG8000 for 2 hours at 16°C. To reduce adapter dimer formation, 0.5 µl 10 µM MPX_ RT primer 5’-GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3’ (IDT, desalted) was added and annealed to the ligation product by incubating at 75°C for 2 minutes, then 37°C for 30 minutes, then 25°C for 15 minutes. Finally, 0.5 µl 5 µM hybrid DNA/RNA sRNA5'h adapter 5’-GTT CAG AGT TCT ACA rGrUrC rCrGrA rCrGrA rUrC-3’ (IDT) were ligated to previously capped RNA 5’ ends by adding 2 µl T4 RNA ligase buffer, 6 µl 50% PEG8000 (15% final), 1 µl 10 mM ATP, 9.5 µl water and 0.5 µl (5 U) T4 RNA ligase 1 for 90 minutes at 20°C. To 15 µl ligation reaction, an additional 0.5 µl 10 µM MPX_ RT primer were added, reactions were denatured at to 70°C for 1 minute, then placed on ice. RNA was reverse-transcribed by adding 3 µl 10x first strand buffer, 4.5 µl water, 1.5 µl 10 mM dNTP, 3 µl 0.1 M DTT, 1.5 µl RNaseOUT and 1 µl Superscript III reverse transcriptase (Invitrogen), and incubating for 30 minutes at at 50°C. Complementary DNA was isolated by adding 35 µl AMPure XL beads (Beckman), binding and washing according to manufacturer’s instructions and dissolved in 40 µl TET. Libraries were PCR-amplified for 13 cycles with 0.75 µM primers oNTI201 (5'-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAC G-3' and TruSeq-compatible indexed primers (e.g. 5’-CAA GCA GAA GAC GGC ATA CGA GAT iii iii GTG ACT GGA GTT CAG ACG TGT GCT CTT-3’ (desalted, IDT, i signifies index nucleotides) using Phusion Hot Start II (Thermo Scientific) in HF buffer containing 0.5 M betaine (98°C, 30s/12x(98°C, 10s/57°C, 25s/72°C, 20s)/ 72°C, 1min/4°C, ?), 175-225 bp fragments were size-selected on 10% PAGE gels and sequenced for 51 cycles on a HiSeq 2000 sequencer (Illumina) with small RNA sequencing primer 5’-CGA CAG GTT CAG AGT TCT ACA GTC CGA CGA TC-3’ and TruSeq Index sequencing primer (Illumina).
Gro-Seq: Nuclei were extracted from 8-12 million cells grown on 10 cm plates and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 10-16 cycles. The final product was run on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.

treatment_protocol: See above

value: breast cancer cell line

tag: treatment

value: ERa (Vendor:Santa Cruz, cat# sc-543, lot# C2114)


title: Gro-Seq TNFa Rep2

description:
Sample 52
Run-On RNA
Processed data file: GeneExpressionGroSeq.txt.gz

data_processing:
Library strategy: Gro-Seq
For ChIP-Seq, RNA-Seq, and Gro-Seq samples, reads were aligned to the hg19 genome using default parameter for bowtie (RNA-Star, respectively).
Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif- and other analyses in the study.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), expression text files (RNA-Seq expression data, using default HOMER parameters). All genomic coordinates are relative to hg19 human assembly.

source_name: MCF7 cells, TNFa, 30m

value: TNFa for 30m


title: Gro-Seq TNFa Rep1

description:
Sample 51
Run-On RNA
Processed data file: GeneExpressionGroSeq.txt.gz


title: p65 ChIP-Seq IL1b+ICI

description:
Sample 56
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, IL1b+ICI, ERa ChIP


title: ERa ChIP-Seq IL1b+ICI

description:
Sample 54
DSG and formaldehyde cross-linked.


title: Gro-Seq E2 Rep2

description:
Sample 48
Run-On RNA
Processed data file: GeneExpressionGroSeq.txt.gz

source_name: MCF7 cells, E2, 30m

value: E2 for 30m


title: p65 ChIP-Seq E2+ICI

description:
Sample 55
DSG and formaldehyde cross-linked.


title: PMEN3_mitomycinC_T2h

value: 2 hour


title: Gro-Seq IL1b Rep2

description:
Sample 50
Run-On RNA
Processed data file: GeneExpressionGroSeq.txt.gz

source_name: MCF7 cells, IL1b, 30m

value: IL1b for 30m


title: PMEN3_mitomycinC_T4h


title: Gro-Seq IL1b Rep1

description:
Sample 49
Run-On RNA
Processed data file: GeneExpressionGroSeq.txt.gz


title: Gro-Seq E2 Rep1

description:
Sample 47
Run-On RNA
Processed data file: GeneExpressionGroSeq.txt.gz


title: Gro-Seq Veh Rep2

description:
Sample 46
Run-On RNA
Processed data file: GeneExpressionGroSeq.txt.gz

source_name: MCF7 cells, Veh

value: vehicle


title: RNA-Seq E2+TOT+TNFa_Expt3 Rep2

description:
Sample 44
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, E2+TOT+TNFa, Expt3


title: NSC_GRChIP_r2

description:
GR ChIP NSC replicate 2
processed data file : RepConcordant_Cort_NSC_Hotspots.csv
processed data file : Thresholded_Merged_Cort_NSC_Stressed_Hotspots.csv
Cort_basal_rn5_nodup_simple_pooled_hs_fdr0.0_input_adjusted.bgr.gz

value: Whole hippocampus

value: male


title: PMEN3_mitomycinC_T6h


title: Gro-Seq Veh Rep1

description:
Sample 45
Run-On RNA
Processed data file: GeneExpressionGroSeq.txt.gz


title: RNA-Seq E2+TOT+TNFa_Expt3 Rep1

description:
Sample 43
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: NSC_Input_r1

description:
Input control for NSC replicate 1
processed data file : RepConcordant_Cort_NSC_Hotspots.csv
processed data file : Thresholded_Merged_Cort_NSC_Stressed_Hotspots.csv
Cort_basal_rn5_nodup_simple_pooled_hs_fdr0.0_input_adjusted.bgr.gz

value: Sprague-Dawley

value: 9 weeks


title: RNA-Seq E2+TOT+IL1b_Expt3 Rep2

description:
Sample 42
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, E2+TOT+IL1b, Expt3


title: RNA-Seq E2+TOT_Expt3 Rep2

description:
Sample 40
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, E2+TOT, Expt3


title: PMEN3_mitomycinC_T3h

value: PMEN3 (Spain9V-3)

value: 3 hour


title: RNA-Seq E2+TOT_Expt3 Rep1

description:
Sample 39
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: PMEN3_uninduced_T3h

value: Control


title: PMEN3_uninduced_T2h


title: RNA-Seq E2_Expt3 Rep1

description:
Sample 37
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, E2, Expt3


title: RNA-Seq Veh_Expt3 Rep2

description:
Sample 36
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, Veh, Expt3


title: RNA-Seq_TNFa+ICI_Expt2 Rep2

description:
Sample 34
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, TNFa+ICI, 3h, Expt2

value: TNFa+ICI for 3h


title: RNA-Seq Veh_Expt3 Rep1

description:
Sample 35
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: RNA-Seq_TNFa_Expt2 Rep1

description:
Sample 31
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, TNFa, 3h, Expt2

value: TNFa for 3h


title: RNA-Seq Veh_Expt2 Rep1

description:
Sample 29
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, Veh, Expt2


title: RNA-Seq Veh_Expt2 Rep2

description:
Sample 30
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: RNA-Seq_TNFa+ICI_Expt2 Rep1

description:
Sample 33
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: RNA-Seq_TNFa_Expt2 Rep2

description:
Sample 32
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: RNA-Seq IL1b+ICI_Expt1 Rep1

description:
Sample 27
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, IL1b+ICI, 3h, Expt1

value: IL1b+ICI for 3h


title: tor1Δ RNA-seq

first: Vyacheslav

last: Labunskyy

state: Massachusetts

address: 609 Albany Street

department: Department of Dermatology

institute: Boston University School of Medicine

data_processing:
De-multiplexing and base-calling was performed by Harvard University Bauer Center Sequencing Core
3' adapter trimming using custom scripts
rRNA alignment with bowtie v1.1.2
Transcriptome alignment with bowtie v1.1.2
Read quantitation using custom scripts
Genome_build: R64-2-1
Supplementary_files_format_and_content: Tab-delimited txt files with 3 columns: 1. SGD ORF name, 2. transcript length, 3. rpkm

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Yeast cultures were grown to OD600 = 0.5 in 500 ml of standard YPD medium

extract_protocol:
Lysates were subjected to ribosome footprinting by RNAse I treatment. After sucrose density gradient fractionation ribosome-protected fragments were purified from 80S peak fractions. In parallel, mRNA was isolated with Dynabeads mRNA Purification Kit (Life technologies) and subjected to alkaline hydrolysis. Fragments of 50-75 nt were used for library preparation.
The RNA-seq and Ribo-seq libraries were prepared using ARTseq Ribosome Profiling kit (Illumina)

treatment_protocol: Yeast extracts were prepared by cryogrinding with BioSpec cryomill. Extracts were resuspended in buffer containging cycloheximide, and aliquots of cell lysates were used for footprint extraction and isolation of total RNA.

tag: rna type

value: intact mRNA


title: RNA-Seq IL1b+ICI_Expt1 Rep2

description:
Sample 28
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

value: breast cancer cell line


title: RNA-Seq E2+TOT+IL1b_Expt3 Rep1

description:
Sample 41
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: rpl22aΔ RNA-seq


title: tor1Δ ribo-seq, replicate 1

description: ribosome profiling

value: ribosome protected fragment


title: RNA-Seq IL1b_Expt1 Rep1

description:
Sample 25
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, IL1b, 3h, Expt1

value: IL1b for 3h


title: rpl22aΔ ribo-seq, replicate 2

description: ribosome profiling


title: rpl22aΔ ribo-seq, replicate 1

description: ribosome profiling


title: RNA-Seq E2+ICI Rep2

description:
Sample 24
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, E2+ICI, 3h, Expt1

value: E2+ICI for 3h


title: RNA-Seq E2+ICI Rep1

description:
Sample 23
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: can1Δ RNA-seq, replicate 2


title: RNA-Seq E2_Expt3 Rep2

description:
Sample 38
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: RNA-Seq E2_Expt1 Rep2

description:
Sample 22
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, E2, 3h, Expt1

value: E2 for 3h


title: wild-type RNA-seq, replicate 2

value: wild-type


title: RNA-Seq E2_Expt1 Rep1

description:
Sample 21
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: wild-type RNA-seq, replicate 1


title: RNA-Seq Veh_Expt1 Rep1

description:
Sample 19
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz

source_name: MCF7 cells, Veh, Expt1

value: vehicle


title: RNA-Seq Veh_Expt1 Rep2

description:
Sample 20
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: can1Δ ribo-seq, replicate 3

description: ribosome profiling


title: tor1Δ ribo-seq, replicate 2

description: ribosome profiling


title: RNA-Seq IL1b_Expt1 Rep2

description:
Sample26
PolyA RNA
Processed data file: GeneExpressionPolyA.txt.gz


title: p65 ChIP-Seq TNFa Rep2

description:
Sample 18
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, TNFa, 45m, p65 ChIP

value: TNFa for 45m

value: p65 (Vendor:Santa Cruz, cat# sc-372, lot# D0604)


title: wild-type ribo-seq, replicate 3

description: ribosome profiling


title: p65 ChIP-Seq IL1b Rep2

description:
Sample 16
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, IL1b, 45m, p65 ChIP

value: IL1b for 45m


title: p65 ChIP-Seq IL1b Rep1

description:
Sample 15
DSG and formaldehyde cross-linked.


title: p65 ChIP-Seq E2 Rep2

description:
Sample 14
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, E2, 45m, p65 ChIP

value: E2 for 45m


title: can1Δ ribo-seq, replicate 1

description: ribosome profiling


title: wild-type ribo-seq, replicate 2

description: ribosome profiling


title: ERa ChIP-Seq IL1b+IKK7

description:
Sample 10
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, IL1b+IKK7, ERa ChIP

value: ERa (Vendor:Santa Cruz, cat# sc-543, lot# C2114)


title: p65 ChIP-Seq TNFa Rep1

description:
Sample 17
DSG and formaldehyde cross-linked.


title: p65 ChIP-Seq E2 Rep1

description:
Sample 13
DSG and formaldehyde cross-linked.


title: ERa ChIP-Seq Veh+IKK7

description:
Sample 9
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, IKK7, ERa ChIP


title: p65 ChIP-Seq Veh Rep2

description:
Sample 12
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, Veh, p65 ChIP


title: ERa ChIP-Seq TNFa Rep2

description:
Sample 8
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, TNFa, 45m, ERa ChIP


title: ERa ChIP-Seq TNFa Rep1

description:
Sample 7
DSG and formaldehyde cross-linked.


title: p65 ChIP-Seq Veh Rep1

description:
Sample 11
DSG and formaldehyde cross-linked.


title: ERa ChIP-Seq IL1b Rep2

description:
Sample 6
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, IL1b, 45m, ERa ChIP


title: wild-type ribo-seq, replicate 1

description: ribosome profiling


title: ERa ChIP-Seq IL1b Rep1

description:
Sample 5
DSG and formaldehyde cross-linked.


title: can1Δ RNA-seq, replicate 1


title: ERa ChIP-Seq E2 Rep2

description:
Sample 4
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, E2, 45m, ERa ChIP


title: ERa ChIP-Seq E2 Rep1

description:
Sample 3
DSG and formaldehyde cross-linked.


title: can1Δ ribo-seq, replicate 2

description: ribosome profiling


title: PP2i-m2

first: Zhong-Dong

last: Shi

address: 430E 67th Street

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
The outputs data (FASTQ files) are mapped to the target genome using the rnaStar aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions.
We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done.
After mapping we compute the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq) and one of several possible gene model databases.
The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analysis differential expression between sample groups.
Genome_build: hg19
Supplementary_files_format_and_content: counts per gene for each sample

source_name: hESC-derived cells

growth_protocol: hESCs were differentiated into PDX1+NKX6.1+ pancreatic progenitor (PP2) stage and the cells were cultured in MCDB 131 medium containing 1X GlutaMAX, 2% BSA, 2.5 g/L NaHCO3 and 10 mM glucose.

extract_protocol:
Cells were lysed using TRIzol and total RNA was isolated using the miRNeasy Mini Kit (Qiagen, #217004).
RNA libraries were prepared for sequencing using standard Illumina protocols by the MSKCC Integrated Genomics Operation Core

treatment_protocol: The medium also contained 0.25 mM Vitamin C, 2 ng/ml FGF7, 0.25 uM SANT-1, 0.1 uM retinoic acid and 200 nM LDN-193189, 100 nM TPB and 1:200 ITS-X.

value: ESCs

tag: genotype


title: PP2i-w4

value: wild type


title: PP2i-w2


title: ERa ChIP-Seq Veh Rep1

description:
Sample 1
DSG and formaldehyde cross-linked.

source_name: MCF7 cells, Veh, ERa ChIP


title: PP2i-m5


title: ERa ChIP-Seq Veh Rep2

description:
Sample 2
DSG and formaldehyde cross-linked.


title: TIBA-pin - repeat 2

status: Public on Feb 19 2017

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were aligned to the tomato genome sequence SL2.50 (downloaded from the sol genomics network http://solgenomics.net/organism/Solanum_lycopersicum/genome) using Tophat (v2.0.10).
Counting reads on ITAG2.4 genes (downloaded from sol genomics network) was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Genome_build: SL2.50
Supplementary_files_format_and_content: Excel file including the normalized counts, ratios and p-values (and adjusted p-values).

organism: Solanum lycopersicum

source_name: tomato TIBA-induced pin

growth_protocol: Seedlings were grown in a greenhouse for 14-18 days.

extract_protocol:
RNeasy kit, QIAGEN, Cat. #74004
Truseq RNA Sample prep-Illumina

treatment_protocol: Seedlings were fixed in acetone and shoot apical meristems were dissected

value: pin-like shoot induced by 1mM TIBA spraying

value: The sample contains the shoot apical meristem (SAM).


title: lfs - repeat 2

source_name: lfs tomato shoot apical meristem (SAM)

value: lfs mutant