title: TT_Input_ChIP-seq

data_processing:
Raw fastq files were aligned to human gneome using bowtie (VN:1.1.2) and duplicates were removed using picard.
Peaks were called using MACS2 with parameters -g hs --keep-dup 1 --bdg --SPMR --nomodel --extsize 200 -q 0.01
Bedgraph files generated by MACS2 were converted to bigWig files using ucsc bedGraphToBigWig tool.
Genome_build: hg19
Supplementary_files_format_and_content: bw files indicating pileup signal normalized to Reads Per Million. NarrowPeak files indicating peaks detected by MACS2

source_name: TT

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol

value: TT

tag: chip antibody


title: hPBMC_E_NS

status: Public on Sep 17 2018

type: SRA

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

description: mAb: NULL

library_source: transcriptomic

data_processing:
Data was separated by barcode and aligned using Tophat version 2.0.10 (Kim et al. 2013) with default settings.
Transcripts were quantified by the Broad Technology Labs computational pipeline using Cuffquant version 2.2.1 (Trapnell et al. 2012).
Data were processed through CuffNorm if 50% of the reads aligned and if at least 100,000 pairs were aligned per sample. Normalization used the default settings, including “geometric” normalization, and expression level information as FPKM (Fragments per kilobase of transcript per million mapped fragments) are provided.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including FPKM for each sample

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
RNA were extracted with RNA mini extraction kit according to manufacturer’s instructions (Qiagen). The quality and quantity of RNA were controlled by infrared spectrometry (Nanodrop) and Agilent bioanalyzer to obtain RNA integrity numbers (Agilent RNA 6000 Pico Kit)
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform according to the SmartSeq2 protocol (Picelli et al, 2013, 2014) with some modifications (Trombetta et al, 2014). Briefly, total RNA was purified using RNA-SPRI beads, polyA mRNA was converted to cDNA and amplified cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample. Sequencing was carried out as paired-end 2x25bp with an additional 8 cycles for each index.

treatment_protocol: Freshly isolated human PBMC were incubated 30 min at 37°C with 10µg/ml of anti-human IL7Rα mAbs, and then cultured alone or with 5 ng/ml of recombinant human IL7 (AbDSerotec) for 3 hours at 37°C. Reaction was stopped on ice, pellets were resuspended in RL-T buffer (Qiagen) containing 1% of β mercaptoethanol in RNase/DNase free condition and stored at -80°C before RNA extraction

tag: cell type

value: PBMC

tag: volunteer

value: E

tag: il7 treatment

value: Unstim

tag: mab incubation

tag: rin


title: hPBMC_A_7

description: mAb: NULL

value: A


title: TE5_SOX2_ChIP-seq

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

library_source: genomic

molecule: genomic DNA

growth_protocol: cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

tag: cell line

value: Esophageal squamous carcinoma cells

value: SOX2 [AF2018 (R&D System), ab59776 (Abcam) or 3579S (Cell  Signaling  Technology)]


title: TE5_Input_ChIP-seq


title: TE5_TP63_ChIP-seq

value: TP63 [sc-8431x or sc-8344 (Santa Cruz Biotechnologies)]


title: KYSE70_Input_ChIP-seq


title: hPBMC_C_7

description: mAb: NULL

value: C


title: TE5_H3K27Ac_ChIP-seq

value: H3K27Ac (Abcam, ab4729)


title: Rara KO 2

status: Public on Sep 16 2018

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

country: USA

institute: Purdue

data_processing:
Sequencing data were analyzed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control and mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner
Reads distribution across the genome was assessed using bamutils (from ngsutils)
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread) with the following parameters: “-s 2 –p –Q 10”. Quality control of sequencing and mapping results was summarized using MultiQC
Genes with read count per million (CPM) < 0.5 in more than 2 of the samples were removed. The data were normalized using the TMM (trimmed mean of M values) method
Differential expression analysis was performed using edgeR
Genome_build: MM 10
Supplementary_files_format_and_content: An Excel file (xlsx) includes raw counts and RPKM values of all 8 samples.

organism: Mus musculus

source_name: Cultured mouse bone marrrow cells

growth_protocol: BM cells were cultured for 3-5 days in complete RPMI-1640 medium supplemented with regular or charcoal-treated FBS (10%, Thermo-Fisher). GM-CSF (20 ng/ml) and hTGF-β1 (10 ng/ml) were added to generate LC-like cells.

extract_protocol:
CD11c+ cells from BM culture were isolated by magnetic sorting with biotin-CD11c (clone N418) and MojosortTM  streptavidin nanobeads (BioLegend; purity>90%). Total RNA was extracted using RNeasy Mini Kit (QIAGEN, Germantown, MD) and submitted to Purdue University Genomic Core Facility for sequencing.
The samples were processed with the Illumina TruSeq Standed mRNA Sample Prep Kit (Illumina Inc. San Diego, CA). Following quantification with KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA).
The libraries were sequenced with a HiSeq 2500 using v3 chemistry to generate paired-end 100 base reads.

treatment_protocol: At-RA was added at 1 nM.

tag: strain

tag: tissue

value: Cultured mouse bone marrrow cells

value: Bone marrow derived CD11c+ cells

tag: genotype

value: RARa-/-


title: TT_H3K27Ac_ChIP-seq


title: hPBMC_G_7

description: mAb: NULL

value: G


title: TE5-shp63-ma_RNA-seq

data_processing:
Raw fastq files were pseudoaligned to Ensemble version 82 transcripts using Kallisto (vn: 0.43.0)
Kallisto output files were later summarized into gene level abundance and counts using tximport Bioconductor package followed by DESeq2 to perform differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: abundance.tsv output from kallisto containing abundance in TPM and estimated fragment counts for all Ensemble 82 transcripts.

extract_protocol:
Total RNA was extracted by using RNeasy Kit (Qiagen).
Standard Illumina protocol

tag: genotype/variation

value: ShRNA mediated TP63 knock down


title: Rara KO 1


title: RA 2

value: wild type


title: WT 4


title: RA 1


title: KYSE140_H3K27Ac_ChIP-seq


title: WT 1


title: WT 3


title: WT 2


title: KYSE140_Input_ChIP-seq


title: A673_scrambled_3

city: Espoo

first: Kristiina

last: Iljin

address: Tietotie 2

country: Finland

institute: VTT

description: Scrambled siRNA, series 3

data_processing:
The base calling was done using bcl2fastq (v1.8.4)
Read alignment was done using TopHat (v2.0.10) to hg19 human genome reference
Genewise read counts were calculated using HTSeq (v0.5.4p3)
Genome_build: hg19
Supplementary_files_format_and_content: countdata.txt is a tab delimited text file and contains the genewise read counts across samples.

source_name: Ewing sarcoma cells

growth_protocol: Cells were grown in DMEM (high Glucose 4.5g/l) supplemented with 10% Tet system Approved Fetal Bovine Serum, L-glutamine, penicillin and streptomycin, 50 µg/ml Zeocin and 2 µg/ml blasticidine S hydrochloride.

extract_protocol:
RNA was isolated 48 hours after transfection from three independent experiments using RNeasy RNA isolation kit (Qiagen) with DNase treatment (Qiagen)
Library preparation was done according to Illumina TruSeq® RNA Sample Preparation v2 Guide

treatment_protocol: The siRNA molecules (final concentration 13 nM) were reverse transfected to the cells using siLentFect transfection reagent.

value: Ewing sarcoma


title: A673_siRNA6_1

description: siLRWD1-6, series 1


title: A673_scrambled_1

description: Scrambled siRNA, series 1


title: A673_siRNA5_3

description: siLRWD1-5, series 3


title: A673_siRNA6_3

description: siLRWD1-6, series 3


title: A673_siRNA6_2

description: siLRWD1-6, series 2


title: A673_siRNA5_2

description: siLRWD1-5, series 2


title: KYSE70_H3K27Ac_ChIP-seq


title: A673_scrambled_2

description: Scrambled siRNA, series 2


title: shNsd1.2_K27me3

status: Public on Sep 15 2018

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

description:
Sheared mouse genomic DNA, 250 bp
Immuno-precipitation of chromatin using a specific antibody against H3K27me3 (Cell signaling C36B11 9733)
N1-2_K27me3

data_processing:
Alignment: Short reads were mapped onto the mouse July, 2007 genome release (mm9) using Bowtie allowing to retain only reads with unique alignment.
Peaks: Peak calling was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for each ChIP-seq sample containing genome wide read intensity

source_name: E14/Drosophila spike-in

growth_protocol: Mouse ES cells were grown in feeder-free culture in the presence of LIF.

extract_protocol:
Cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with H3K27me3 and H3K36me2 antibody. For H3K27me3, ChIP with spike-in using sheared Drosophila melanogaster chromatin was performed. IPs were performed using Protein A Sepharose beads and recovered DNA was used for high-throughput sequencing.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: Cells were virally transduced, selected with puromycin and propagated for two passages before harvested for chromatin isolation.

value: Embryonic stem cells

tag: transduction

value: shRNA targeting Nsd1

value: H3K27me3 (Cell signaling C36B11 9733)


title: shNon-targeting control_K27me3

description:
Sheared mouse genomic DNA, 250 bp
Immuno-precipitation of chromatin using a specific antibody against H3K27me3 (Cell signaling C36B11 9733)
WT_K27me3

value: control


title: shNsd1.1_K36me2

description:
Sheared mouse genomic DNA, 250 bp
Immuno-precipitation of chromatin using a specific antibody against H3K36me2 (Abcam 9049)
N1-1_K36me2


title: MDA_RG-108, MDA-MB-231  (rna-seq 2)

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

description: Gene expression data from MDA-MB-231 cells treated with RG-108

data_processing:
Basecalls performed using Illumina CASAVA V1.8.4
Raw reads were aligned using TopHat (version 2.0.5; Kim et al., 2013) to build version hg19 of the human genome
Counts for UCSC annotated genes were calculated from the aligned reads using HTSeq (version 0.6.0, Anders et al., 2015)
Normalization and differential analysis were carried out using edgeR package (Robinson  et al., 2010) and R (version 3.0.0)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph coverage files (http://genome.ucsc.edu/goldenpath/help/bedgraph.html) were generated using bedtools genomecov function (version 2.15.0)

growth_protocol: MDA MB 231 cells were cultured in DMEM:F12 + 10% FBS.

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA-seq libraries were prepared with TruSeq Stranded Total RNA with Ribo-Zero GOLD (Illumina), according to manufacturer’s instructions.

treatment_protocol: All compounds were resuspended in DMSO and added to culture medium (1uM) for 24h.

value: MDA-MB-231 breast cancer cells

tag: treatment


title: MDA_Flavopiridol, MDA-MB-231  (rna-seq 2)

description: Gene expression data from MDA-MB-231 cells treated with Flavopiridol

source_name: Flavopiridol, MDA-MB-231

value: Flavopiridol


title: shNsd1.2_K36me2

description:
Sheared mouse genomic DNA, 250 bp
Immuno-precipitation of chromatin using a specific antibody against H3K36me2 (Abcam 9049)
N1-2_K36me2


title: shNsd1.1_K27me3

description:
Sheared mouse genomic DNA, 250 bp
Immuno-precipitation of chromatin using a specific antibody against H3K27me3 (Cell signaling C36B11 9733)
N1-1_K27me3


title: MDA_C646, MDA-MB-231  (rna-seq 2)

description: Gene expression data from MDA-MB-231 cells treated with C646


title: MDA_JQ1, MDA-MB-231  (rna-seq 2)

description: Gene expression data from MDA-MB-231 cells treated with JQ1

source_name: JQ1, MDA-MB-231


title: JQ1_rep1 (rna-seq 1)

data_processing:
Basecalls performed using CASAVA version 1.8.4
Raw reads were aligned using TopHat (version 2.0.5; Kim et al., 2013) to build version hg19 of the human genome
Counts for UCSC annotated genes were calculated from the aligned reads using HTSeq (version 0.6.0, Anders et al., 2015)
Normalization and differential analysis were carried out using edgeR package (Robinson  et al., 2010) and R (version 3.0.0)
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing cpm values for each sample

growth_protocol: MDA-MB-231 cells were cultured in DMEM:F12 + 10% FBS.

treatment_protocol: Cells were transcfected with YAP/TAZ siRNA or BRD siRNA with Lipofectamine RNAiMAX reagent (Thermo Fisher Scientific) 48h or 72h before harvesting, respectively. 1 µM JQ1 was added to culture medium for 24h.


title: JQ1_rep2 (rna-seq 1)


title: shNon-targeting control_K36me2

description:
Sheared mouse genomic DNA, 250 bp
Immuno-precipitation of chromatin using a specific antibody against H3K36me2 (Abcam 9049)
WT_K36me2


title: MDA_OTX015, MDA-MB-231  (rna-seq 2)

description: Gene expression data from MDA-MB-231 cells treated with OTX015


title: siBRD_mixB_rep2 (rna-seq 1)

description: Gene expression data from MDA-MB-231 cells depleted of endogenous BRD 2/3/4 by siRNA (mix B)

source_name: siBRD_mixB, MDA-MB-231

value: BRD siRNA #mix B

value: BRD depletion


title: A673_siRNA5_1

description: siLRWD1-5, series 1


title: siBRD_mixB_rep1 (rna-seq 1)


title: DMSO_ctrl_rep1 (rna-seq 1)

description: Gene expression data from control MDA-MB-231 cells (treated with DMSO)

source_name: DMSO_ctrl, MDA-MB-231

value: DMSO


title: DMSO_ctrl_rep2 (rna-seq 1)


title: MDA_DMSO, MDA-MB-231  (rna-seq 2)

description: Gene expression data from control MDA-MB-231 cells

source_name: DMSO, MDA-MB-231


title: siBRD_mixA_rep2 (rna-seq 1)

description: Gene expression data from MDA-MB-231 cells depleted of endogenous BRD 2/3/4 by siRNA (mix A)

source_name: siBRD_mixA, MDA-MB-231

value: BRD siRNA #mix A


title: siBRD_mixA_rep1 (rna-seq 1)


title: siYAPTAZ_mix1_rep2 (rna-seq 1)

description: Gene expression data from MDA-MB-231 cells depleted of endogenous YAP and TAZ by siRNA mix #1

source_name: siYAPTAZ_mix1, MDA-MB-231

value: YAP/TAZ siRNA #1

value: YAP/TAZ depletion


title: MDA_THZ1, MDA-MB-231  (rna-seq 2)

description: Gene expression data from MDA-MB-231 cells treated with THZ1

source_name: THZ1, MDA-MB-231


title: siYAPTAZ_mix2_rep1 (rna-seq 1)

description: Gene expression data from MDA-MB-231 cells depleted of endogenous YAP and TAZ by siRNA mix #2

source_name: siYAPTAZ_mix2, MDA-MB-231

value: YAP/TAZ siRNA #2


title: siAS_ctrl_rep2 (rna-seq 1)

description: Gene expression data from MDA-MB-231 cells transfected with control siRNA

source_name: siAS_ctrl, MDA-MB-231

value: Control siRNA


title: siAS_ctrl_rep1 (rna-seq 1)


title: siYT_H3K122ac_rep1 (chip-seq)

description:
Pooling of siYT_Input_rep3 and siYT_Input_rep4 was used as control for MACS2
MACS_SPMR_siYT_H3K122ac.bw

data_processing:
Basecalls performed using CASAVA version v1.8.4
Raw reads were aligned using Bowtie (version 0.12.7)  (Langmead et al., 2009) to build version hg19 of the human genome retaining only uniquely mapped reads.  Redundant reads were removed using SAMtools
MACS2 version 2.0.10 (Zhang et al., 2008) callpeak function was used to generate bedGraph files for pooled replicates using the -B --SPMR parameters and appropriate control samples.
BedGraph files were converted to bigWig format with UCSC bedGraphToBigWig utility.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files (http://genome.ucsc.edu/goldenPath/help/bigWig.html) are signal files containing fragment pileup per million reads

source_name: siYT_H3K122ac, MDA-MB-231

extract_protocol:
Cross-linked chromatin was sheared by sonication and immunoprecipitated with antibodies. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
NuGEN Ovation Ultralow Library Prep System kit

treatment_protocol: Cells were transfected with YAP/TAZ siRNA with Lipofectamine RNAiMAX reagent (Thermo Fisher Scientific) 48h before harvesting. 1 µM JQ1 was added to culture medium for 6h for BRD4 ChIP-seq, or 24h for RNA-PolII and H3K122ac ChIP-seq.

value: Histone H3 Acetyl K122 (abcam, ab33309, lot GR284790-3)

value: siYAPTAZ


title: siYAPTAZ_mix2_rep2 (rna-seq 1)


title: siYT_H3K122ac_rep2 (chip-seq)


title: siYT_Input_rep3 (chip-seq)

source_name: siYT_Input, MDA-MB-231

value: input


title: JQ1_H3K122ac_rep2 (chip-seq)

description:
Pooling of JQ1_Input_rep3 and JQ1_Input_rep4 was used as control for MACS2
MACS_SPMR_JQ1_H3K122ac.bw


title: siYT_Input_rep4 (chip-seq)


title: JQ1_Input_rep3 (chip-seq)

source_name: JQ1_Input, MDA-MB-231


title: JQ1_Input_rep4 (chip-seq)


title: DMSO_Input_rep4 (chip-seq)

source_name: DMSO_Input, MDA-MB-231


title: DMSO_H3K122ac_rep2 (chip-seq)

description:
Pooling of DMSO_Input_rep3 and DMSO_Input_rep4 was used as control for MACS2
MACS_SPMR_DMSO_H3K122ac.bw

source_name: DMSO_H3K122ac, MDA-MB-231


title: JQ1_H3K122ac_rep1 (chip-seq)


title: DMSO_Input_rep3 (chip-seq)


title: siYT_Pol2_rep1 (chip-seq)

description:
Pooling of siYT_Input_rep1 and siYT_Input_rep2 was used as control for MACS2
MACS_SPMR_siYT_Pol2.bw

source_name: siYT_Pol2, MDA-MB-231

value: RNA polymerase II 8WG16 (abcam, ab817, lot GR271062-1)


title: siYT_Input_rep2 (chip-seq)


title: DMSO_H3K122ac_rep1 (chip-seq)


title: JQ1_Pol2_rep2 (chip-seq)

description:
Pooling of JQ1_Input_rep1 and JQ1_Input_rep2 was used as control for MACS2
MACS_SPMR_JQ1_Pol2.bw

source_name: JQ1_Pol2, MDA-MB-231


title: JQ1_Input_rep2 (chip-seq)


title: DMSO_Pol2_rep2 (chip-seq)

description:
Pooling of DMSO_Input_rep1 and DMSO_Input_rep2 was used as control for MACS2
MACS_SPMR_DMSO_Pol2.bw

source_name: DMSO_Pol2, MDA-MB-231


title: JQ1_Input_rep1 (chip-seq)


title: siYAPTAZ_mix1_rep1 (rna-seq 1)


title: JQ1_Pol2_rep1 (chip-seq)


title: DMSO_Pol2_rep1 (chip-seq)


title: siYT_BRD4_rep2 (chip-seq)

description:
Pooling of siYT_IgG_rep1 and siYT_IgG_rep2 was used as control for MACS2
MACS_SPMR_siYT_BRD4.bw

source_name: siYT_BRD4, MDA-MB-231

value: BRD4 (Bethyl Laboratories, A301-985A, lot A301-985A100-5)


title: siYT_BRD4_rep1 (chip-seq)


title: siYT_IgG_rep1 (chip-seq)

source_name: siYT_IgG, MDA-MB-231

value: Rabbit IgG (Sigma, I5006)


title: DMSO_Input_rep1 (chip-seq)


title: JQ1_BRD4_rep1 (chip-seq)

description:
Pooling of JQ1_IgG_rep1 and JQ1_IgG_rep2 was used as control for MACS2
MACS_SPMR_JQ1_BRD4.bw

source_name: JQ1_BRD4, MDA-MB-231


title: JQ1_IgG_rep2 (chip-seq)

source_name: JQ1_IgG, MDA-MB-231


title: JQ1_BRD4_rep2 (chip-seq)


title: DMSO_BRD4_rep1 (chip-seq)

description:
Pooling of DMSO_IgG_rep1 and DMSO_IgG_rep2 was used as control for MACS2
MACS_SPMR_DMSO_BRD4.bw

source_name: DMSO_BRD4, MDA-MB-231


title: JQ1_IgG_rep1 (chip-seq)


title: DMSO_IgG_rep1 (chip-seq)

source_name: DMSO_IgG, MDA-MB-231


title: 3T3-L1; FLAG-tagged FTO (CLIP-Seq)

status: Public on Sep 14 2018

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

data_processing:
Library strategy: CLIP-seq
Gene structure annotations were downloaded from UCSC mm10 RefSeq/Repeatmasker. For CLIP-seq, we used a modified version of PARalyzer(Corcoran et al. 2011) to allow for all mutations, rather than just T to C mutations, forpeak calling. Consensusmotif was determined using HOMER (Heinz et al. 2010). For tRNA, the reads in each tRNA genes were counted.
Genome_build: mm10
Supplementary_files_format_and_content: txt， reads counts

source_name: 3T3-L1 cell

growth_protocol: Cells were maintained in DMEM (Gibco, #11965) with 10% fetal bovine serum (FBS, Gibco, 10438-026) and 1× Pen/Strep (Gibco, 15140).

extract_protocol:
After irradiation, cells were harvested and then lysed in RIPA lysis buffer (Sigma, R2078) at 4 ℃ for 2 h. Subsequently, the lysis mixture was centrifuged at 17,000 g at 4 °C for 30 min and the supernatant was carefully collected. 50 μl of antibody-conjugated Dynabeads Protein A was added into the supernatant and mixed gently at 4°C for 4 h. The supernatant was then discarded and the beads were washed for 3 times with 1 ml of high salt buffer and another 8 times with 1 ml of wash buffer (Wang et al., 2009). The RNAs were then isolated by proteinase K digestion following the manufacture’s protocol.
For CLIP-seq, NEB small RNA library kit

treatment_protocol: In brief, for each cell line, 5 plates of cells in 15 cm style dish were grown until 80% confluency (∼107 cells). The medium was aspirated and the cells were washed with PBS once and irradiated once with 400 mJ/cm2 at 254 nm in Stratalinker on ice.

value: fibroblast


title: DMSO_IgG_rep2 (chip-seq)

value: MDA-MB-231 breast cancer cells


title: siYT_Pol2_rep2 (chip-seq)


title: DMSO_Input_rep2 (chip-seq)


title: Post-PH 72 hrs replicate 1

city: Copenhagen

first: Leonor

last: Rib

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

data_processing:
Read mapping: The selected reads were mapped by using Tophat 2.0.13 (Kim et al. 2013), which in turn reuses the Bowtie2 mapper (Langmead et al. 2012). Reads were first mapped onto coding sequences annotated in the mm9 mouse annotation and, the non-mapped,
Read mapping: The selected reads were mapped by using Tophat 2.0.13 (Kim et al. 2013), which in turn reuses the Bowtie2 mapper (Langmead et al. 2012). Reads were first mapped onto coding sequences annotated in the mm9 mouse annotation and, the non-mapped, were aligned onto the genome.
Gene quantifications: The mapped reads were sorted by using samtools 0.1.19 (Li et al. 2009) and they were assigned to genes by using the ‘featureCounts’ function from the ‘Rsubread’ R package (Liao et al. 2013; R Core Team 2013).  Reads falling within genes with strand-specificity were assigned to the genes. Those reads mapping on unique genomic positions were counted as 1, whereas those reads mapping onto multiple genomic positions where assigned a score of 1 divided by the number of different positions they were mapped. Finally Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated on a log2 scale and used for analysis. All the handling of the data was done with the UNIX shell, Perl and the R software (R Core Team 2013).
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated table containing the log2(RPKMs) assigned to each annotated gene

molecule: polyA RNA

source_name: Liver

extract_protocol:
RNA-seq libraries were prepared with the TruSeq Stranded mRNA Library Prep kit from Illumina
Total RNA from individual livers was used for RNA-seq. Strand-specific libraries were prepared with the TruSeq Stranded mRNA Library Prep kit from Illumina. 100 nucleotides at the fragment ends were sequenced with single-end sequencing technology from HiSeq 2100 (Illumina).

tag: experiment

value: RNA-Seq

tag: age (weeks)


title: Post-PH 60 hrs replicate 1


title: Post-PH 4 weeks replicate 2


title: Post-PH 4 weeks replicate 1


title: Post-PH 1 week replicate 1


title: Post-PH 72 hrs replicate 2


title: Post-PH 72 hrs replicate 3


title: Post-PH 4 weeks replicate 3


title: Post-PH 1 week replicate 2


title: Post-PH 1 week replicate 3


title: Post-PH 60 hrs replicate 2


title: siYT_IgG_rep2 (chip-seq)


title: Post-PH 48 hrs replicate 3


title: Post-PH 48 hrs replicate 5


title: Post-PH 48 hrs replicate 4


title: Post-PH 48 hrs replicate 1


title: Post-PH 44 hrs replicate 2


title: Post-PH 44 hrs replicate 3


title: Post-PH 44 hrs replicate 1


title: Post-PH 36 hrs replicate 6


title: Post-PH 36 hrs replicate 5


title: Post-PH 36 hrs replicate 3


title: Post-PH 36 hrs replicate 1


title: Post-PH 60 hrs replicate 3


title: siYT_Input_rep1 (chip-seq)


title: Post-PH 28 hrs replicate 3


title: Post-PH 48 hrs replicate 2


title: Post-PH 20 hrs replicate 4


title: Post-PH 20 hrs replicate 5


title: Post-PH 28 hrs replicate 2


title: Post-PH 28 hrs replicate 1


title: Post-PH 20 hrs replicate 2


title: Post-PH 10 hrs replicate 2


title: Post-PH 20 hrs replicate 1


title: Post-PH 20 hrs replicate 6


title: Post-PH 10 hrs replicate 4


title: Post-PH 4 hrs replicate 4


title: Post-PH 4 hrs replicate 5


title: Post-PH 10 hrs replicate 1


title: Post-PH 10 hrs replicate 5


title: Post-PH 10 hrs replicate 3


title: Post-PH 36 hrs replicate 4


title: Post-PH 4 hrs replicate 2


title: Post-PH 4 hrs replicate 1


title: Post-PH 1 hr replicate 6


title: Post-PH 1 hr replicate 5


title: Post-PH 10 hrs replicate 6


title: Post-PH 1 hr replicate 3


title: Post-PH 4 hrs replicate 6


title: Post-PH 1 hr replicate 4


title: Post-PH 1 hr replicate 2


title: Post-PH 1 hr replicate 1


title: Sham control 48 hrs replicate 3


title: Post-PH 36 hrs replicate 2


title: Post-PH 4 hrs replicate 3


title: Sham control 48 hrs replicate 1


title: Sham control 48 hrs replicate 2


title: Sham control 20 hrs replicate 2


title: Sham control 4 hrs replicate 3


title: Sham control 20 hrs replicate 1


title: Sham control 20 hrs replicate 3


title: Sham control 4 hrs replicate 5


title: Sham control 10 hrs replicate 1


title: Sham control 4 hrs replicate 1


title: Sham control 10 hrs replicate 2


title: Sham control 4 hrs replicate 2


title: Sham control 10 hrs replicate 3


title: Sham control 1 hr replicate 6


title: Sham control 4 hrs replicate 4


title: Sham control 1 hr replicate 1


title: Sham control 1 hr replicate 3


title: Sham control 1 hr replicate 4


title: Sham control 1 hr replicate 5


title: Sham control 1 hr replicate 2


title: Control 4 hrs replicate 2


title: Control 4 weeks replicate 2


title: Control 4 hrs replicate 1


title: Control 0 hr replicate 9


title: Control 4 hrs replicate 3


title: Control 0 hr replicate 8


title: Control 4 weeks replicate 1


title: Control 0 hr replicate 7


title: Control 0 hr replicate 6


title: Control 0 hr replicate 3


title: Control 0 hr replicate 2


title: Control 0 hr replicate 1


title: ChIP-Seq Input (control), 72 hrs, Series 2 CCC_s2_INPUT_TP72

description: Liver homogenate of mice

data_processing:
Alignment: The extreme 50 bp of the sequenced paired-ends were mapped onto the mouse (mm9) and human genome (hg19) with Elandv2e.  Only fragments whose two reads had good sequencing quality (i.e., quality of the first 25 bp higher than Q20, as specified by Illumina) and mapping on unique genomic locations were kept.  For further analysis fragment sizes between 50 and 500 bp were taken and only one copy of redundant fragments was kept.
Quantifications: To quantify the density of epitopes in the mouse genome, the 50 bp in the center of the sequenced fragments were used. Pol2 quantifications were done in the promoter proximal region of +/- 250 bp around annotated TSS. H3K4me3 quantifications were done in the promoter regions of +/- 1 kb around TSS. Also Pol2 and H3K36me3 quantifications in the body of annotated transcription units were done on a region of 500 bp downstream of the TSS to 2 kb downstream the PolyA signal. The same quantifications were done on the Input libraries as a control. All quantifications were scaled to the number of fragments analyzed per library. 500 pseudo-counts (i.e., 10 fragments with 50 bp displayed) were added to the quantifications to stabilize the variance in low scores.  Finally, the log2 ratios between ChIP and Input quantifications were calculated. Among the multiple transcription units associated to a given gene, the one containing the maximum Pol2 occupancy across time points in the promoter proximal region was used for analysis.
Genome_build: Ensembl 67/NCBI 37
Supplementary_files_format_and_content: Density of central 50 bp of sequenced fragments at a nucleotide resolution

extract_protocol:
ChIP-seq was performed with the ‘MicroPlex Library Preparation’ kit, from Diagenode
10 ng of immunoprecipitated material was used for sequencing library preparation. Total input was also prepared for sequencing at each time point and replicate. Paired-end sequencing libraries were prepared with the ‘MicroPlex Library Preparation’ kit, from Diagenode, following the instructions of the manufacturer (Diagenode, catalog no C05010011).  No size selection was performed and the chromatin was amplified with 14 cycles of PCR. 100 nucleotides at the fragment ends were sequenced with paired-end sequencing technology from HiSeq 2100 (Illumina).

value: ChIP-Seq


title: ChIP-Seq Input (control), 60 hrs, Series 2 CCC_s2_INPUT_TP60

description: Liver homogenate of mice


title: Control 0 hr replicate 5


title: ChIP-Seq Input (control), 28 hrs, Series 2 CCC_s2_INPUT_TP28

description: Liver homogenate of mice


title: ChIP-Seq Input (control), 44 hrs, Series 2 CCC_s2_INPUT_TP44

description: Liver homogenate of mice


title: ChIP-Seq Input (control), 20 hrs, Series 2 CCC_s2_INPUT_TP20

description: Liver homogenate of mice


title: ChIP-Seq Input (control), 10 hrs, Series 2 CCC_s2_INPUT_TP10

description: Liver homogenate of mice


title: ChIP-Seq Input (control), 36 hrs, Series 2 CCC_s2_INPUT_TP36

description: Liver homogenate of mice


title: ChIP-Seq Input (control), 1 hr, Series 2 CCC_s2_INPUT_TP01

description: Liver homogenate of mice


title: ChIP-Seq Input (control), Sham (control) 20 hrs, Series 2 CCC_s2_INPUT_S10

description: Liver homogenate of mice


title: ChIP-Seq Input (control), Sham (control) 1 hr, Series 2 CCC_s2_INPUT_S01

description: Liver homogenate of mice


title: ChIP-Seq Input (control), 4 hrs, Series 2 CCC_s2_INPUT_TP04

description: Liver homogenate of mice


title: ChIP-Seq Input (control), 0 hr, Series 2 CCC_s2_INPUT_TP00

description: Liver homogenate of mice


title: ChIP-Seq Input (control), Sham (control) 10 hrs, Series 2 CCC_s2_INPUT_S04

description: Liver homogenate of mice


title: ChIP-Seq Input (control), Sham (control) 20 hrs, Series 2 CCC_s2_INPUT_S20

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 1 week, Series 2 CCC_s2_H3K4ME3_TP1W

description: Liver homogenate of mice


title: Control 0 hr replicate 4


title: ChIP-Seq H3K4me3, 44 hrs, Series 2 CCC_s2_H3K4ME3_TP44

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 36 hrs, Series 2 CCC_s2_H3K4ME3_TP36

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 72 hrs, Series 2 CCC_s2_H3K4ME3_TP72

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 28 hrs, Series 2 CCC_s2_H3K4ME3_TP28

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 60 hrs, Series 2 CCC_s2_H3K4ME3_TP60

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 48 hrs, Series 2 CCC_s2_H3K4ME3_TP48

description: Liver homogenate of mice


title: ChIP-Seq Input (control), 1 week, Series 2 CCC_s2_INPUT_TP1W

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 10 hrs, Series 2 CCC_s2_H3K4ME3_TP10

description: Liver homogenate of mice


title: DMSO_BRD4_rep2 (chip-seq)


title: ChIP-Seq Input (control), 48 hrs, Series 2 CCC_s2_INPUT_TP48

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 20 hrs, Series 2 CCC_s2_H3K4ME3_TP20

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 1 hr, Series 2 CCC_s2_H3K4ME3_TP01

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, Sham (control) 20 hrs, Series 2 CCC_s2_H3K4ME3_S20

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 4 hrs, Series 2 CCC_s2_H3K4ME3_TP04

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, Sham (control) 10 hrs, Series 2 CCC_s2_H3K4ME3_S04

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, Sham (control) 1 hr, Series 2 CCC_s2_H3K4ME3_S01

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 0 hr, Series 2 CCC_s2_H3K4ME3_TP00

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 72 hrs, Series 2 CCC_s2_H3K36ME3_TP72

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 1 week, Series 2 CCC_s2_H3K36ME3_TP1W

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 48 hrs, Series 2 CCC_s2_H3K36ME3_TP48

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 44 hrs, Series 2 CCC_s2_H3K36ME3_TP44

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 36 hrs, Series 2 CCC_s2_H3K36ME3_TP36

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 20 hrs, Series 2 CCC_s2_H3K36ME3_TP20

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 28 hrs, Series 2 CCC_s2_H3K36ME3_TP28

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, Sham (control) 20 hrs, Series 2 CCC_s2_H3K36ME3_S20

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, Sham (control) 10 hrs, Series 2 CCC_s2_H3K36ME3_S10

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 4 hrs, Series 2 CCC_s2_H3K36ME3_TP04

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 1 hr, Series 2 CCC_s2_H3K36ME3_TP01

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, Sham (control) 1 hr, Series 2 CCC_s2_H3K36ME3_S04

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 0 hr, Series 2 CCC_s2_H3K36ME3_S01

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, Sham (control) 20 hrs, Series 2  CCC_s2_H3K36ME3_TP00

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 1 week, Series 2 CCC_s2_POLR2B_TP1W

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, Sham (control) 20 hrs, Series 2 CCC_s2_H3K4ME3_S10

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 72 hrs, Series 2 CCC_s2_POLR2B_TP72

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 60 hrs, Series 2 CCC_s2_H3K36ME3_TP60

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 60 hrs, Series 2 CCC_s2_POLR2B_TP60

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 36 hrs, Series 2 CCC_s2_POLR2B_TP36

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 20 hrs, Series 2 CCC_s2_POLR2B_TP20

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 44 hrs, Series 2 CCC_s2_POLR2B_TP44

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 28 hrs, Series 2 CCC_s2_POLR2B_TP28

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 48 hrs, Series 2 CCC_s2_POLR2B_TP48

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 10 hrs, Series 2 CCC_s2_POLR2B_TP10

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 0 hr, Series 2 CCC_s2_POLR2B_TP00

description: Liver homogenate of mice


title: ChIP-Seq Pol II, Sham (control) 20 hrs, Series 2 CCC_s2_POLR2B_S10

description: Liver homogenate of mice


title: ChIP-Seq Pol II, Sham (control) 20 hrs, Series 2 CCC_s2_POLR2B_S20

description: Liver homogenate of mice


title: ChIP-Seq Pol II, Sham (control) 1 hr, Series 2 CCC_s2_POLR2B_S01

description: Liver homogenate of mice


title: ChIP-Seq Pol II, Sham (control) 10 hrs, Series 2 CCC_s2_POLR2B_S04

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 1 hr, Series 2 CCC_s2_POLR2B_TP01

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 10 hrs, Series 2 CCC_s2_H3K36ME3_TP10

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 4 hrs, Series 2 CCC_s2_POLR2B_TP04

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 44 hrs, Series 1 CCC_s1_INPUT_TP44

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 28 hrs, Series 1 CCC_s1_INPUT_TP28

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 1 hr, Series 1 CCC_s1_INPUT_TP01

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 10 hrs, Series 1 CCC_s1_INPUT_TP10

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 36 hrs, Series 1 CCC_s1_INPUT_TP36

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 20 hrs, Series 1 CCC_s1_INPUT_TP20

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 0 hr, Series 1 CCC_s1_INPUT_TP00

description: Liver homogenate of mice


title: ChIP-Seq H3K36me2, 60 hrs, Series 1 CCC_s1_H3K36ME2_TP60

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 48 hrs, Series 1 CCC_s1_H3K36ME3_TP48

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 44 hrs, Series 1 CCC_s1_H3K36ME3_TP44

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 60 hrs, Series 1 CCC_s1_H3K36ME3_TP60

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 60 hrs, Series 1 CCC_s1_INPUT_TP60

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 10 hrs, Series 1 CCC_s1_H3K36ME3_TP10

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 20 hrs, Series 1 CCC_s1_H3K36ME3_TP20

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 36 hrs, Series 1 CCC_s1_H3K36ME3_TP36

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 48 hrs, Series 1 CCC_s1_INPUT_TP48

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 44 hrs, Series 1 CCC_s1_POLR2B_TP44

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 28 hrs, Series 1 CCC_s1_POLR2B_TP28

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 0 hr, Series 1 CCC_s1_H3K36ME3_TP00

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 36 hrs, Series 1 CCC_s1_POLR2B_TP36

description: Liver homogenate of mice


title: ChIP-Seq H3K36me3, 1 hr, Series 1 CCC_s1_H3K36ME3_TP01

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 48 hrs, Series 1 CCC_s1_POLR2B_TP48

description: Liver homogenate of mice


title: P7_CTX_cKO_DJ44

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Single-end reads (quality checked, filtered and adapter trimmed) were aligned to reference sequences (mm10 from UCSC) using STAR allowing three mismatches.
RNA-seq counts were quantified using HTSeq python suite. Reference gene model (mm10 GTF from Gencode vM11) were provided to assist the counting.
RNA-seq CPM values were then quantified using EdgeR (R package).
Gene-level CPM quantifications were used for all downstream processing.
Genome_build: UCSC Mouse GRCm38 / mm10

source_name: Cortex

extract_protocol:
Brain regions were dissected out and immediately flash frozen in liquid nitrogen. Total RNA was then purified from these samples, using an mRNeasy kit (Qiagen), following the manufacturer's instructions.
For P0 samples, Library construction was performed as a service by BGI America (Cambridge, MA). For P7 samples, mRNA was purified via poly(A) selection from 2ug of total RNA. Purified mRNA was then utilized to generated cDNA libraries using previously published protocols (Takahashi et al., 2015).
Pooled libraries of P0 and P7 brains were separately sequenced as 50 bp single-end on BGISEQ-500, a BGI in-house sequencer at BGI or as 75 bp single-end on Illumina NextSeq 500 at UT Southwestern Medical Center respectively.

tag: age

value: postnatal day 7

value: conditional knock-out

tag: hemisphere

value: right


title: ChIP-Seq Pol II, 0 hr, Series 1 CCC_s1_POLR2B_TP00

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 20 hrs, Series 1 CCC_s1_POLR2B_TP20

description: Liver homogenate of mice


title: P7_CTX_cKO_DJ48


title: P7_CTX_cKO_DJ42


title: P7_CTX_CTL_DJ47

value: control


title: P7_CTX_cKO_DJ41


title: P7_CTX_CTL_DJ45


title: P7_CTX_CTL_DJ46


title: ChIP-Seq Pol II, 10 hrs, Series 1 CCC_s1_POLR2B_TP10

description: Liver homogenate of mice


title: P7_CTX_CTL_DJ43


title: ChIP-Seq H3K36me3, 28 hrs, Series 1 CCC_s1_H3K36ME3_TP28

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 60 hrs, Series 1 CCC_s1_POLR2B_TP60

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 1 hr, Series 1 CCC_s1_POLR2B_TP01

description: Liver homogenate of mice


title: P0_CTX_cKO_NU08

value: postnatal day 0


title: P0_CTX_cKO_NU03


title: P0_CTX_cKO_NU07


title: P0_CTX_CTL_NU05


title: H3K27Ac_rep2

city: La Jolla

first: Marcelo

last: Rivas

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: University of California San Diego

data_processing:
Sequence reads were obtained and mapped to reference genomes (mm9) using Bowtie.  Among aligned duplicated all but one alignment were removed.
All libraries plus MNase-seq data from Carone et al (http://dx.doi.org/10.1016/j.devcel.2014.05.024) were pooled and the resulting library was used to call nucleosomes positions using iNPs (default parameters).
For each histone mark replicated were pooled and the number of reads per nucleosome were counted.
Genome_build: mm9
Supplementary_files_format_and_content: Counts of MNChIP-seq reads per nucleosome (BED format), and expected counts of MNChIP-seq reads per nucleosome stratified by counts of MNase-seq reads over nucleosome (tab-delimited format).

growth_protocol: E14(mESC) were plated onto gelatin-coated dishes in Dulbecco's modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM -mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Millipore ESG1107) in incubator set at 37 ºC in 5% CO2.

extract_protocol:
Except for minor modifications to decrease the reaction volume for subsequent ChIP procedure, the chromatin digestion by micrococcal nuclease (MNase) was performed as described by Ozsolak et al (doi:10.1038/nbt1279). E14 mouse embryonic stem cells were harvested and dissociated by Trypsin. Dissociated cells were then resuspended by solution A (300 mM sucrose, 60 mM KCl, 35 mM HEPES pH 7.4, 5 mM K2HPO4, 5 mM MgCl2, 0.5 mM CaCl2) and diluted by solution B (300 mM sucrose, 60 mM KCl, 15 mM NaCl, 35 mM HEPES pH 7.4, 5 mM K2HPO4, 5 mM MgCl2, 3 mM CaCl2) in a 5 millions cells/1.5ml ratio. NP-40 at 0.05% was added to the cell suspension and mixed by pipetting. The lysate of cytoplasm and naked nucleus were checked under microscope. We added either 600U or 1200 U of MNase (New England Biolabs) to the lysate before incubating it at 25◦ C for 15 or 45 min. After this, the MNase digestion was slowed down by putting the lysate on ice, and the nucleus were collected by centrifugation at 3000 rcf at 4◦ C for 10 min. We re-suspended the nucleus on solution C (100 mM EDATA 4% SDS) in a 5 millions cell/150μL ratio. Then, we added 100 mL of solution C to stop the MNase digestion and lysate the nucleus membranes. The lysates were treated with RNase and proteinase K, and 1/5 of it was kept for DNA purification. Nucleosomal DNA was purified by phenol chloroform and precipitated by isopropanol.
MNase-digested DNA coupled with ChIP-seq  (MNChIP-seq)

treatment_protocol: Once MNase digestion of the chromatin was completed, chromatin immuno-precipitation was performed as described by Xiao et al (doi:10.1016/j.cell.2012.04.029). Briefly, the MNase digested chromatin was diluted five times in IP buffer and precleared by incubation with slurry beds for 3 hours. Cleared chromatin was incubated with antibody overnight at 4◦ C and pulled down by incubation with slurry beads for additional 3 hours. Enriched DNA was purified by mini elute columns (Qiagen) and size selected on a E-Gel EX (life technology). We selected fragment sizes between 145-175 b length according to the ladder bands( 25bp ladder ) and Gel purified by mini Elution kit(Qiagen). Libraries were constructed by KAPA High-Throughput Library Preparation Kit (Cat. No. KK8234) and sequenced in 100 b paired-end by Illumina HiSeq2500.

value: Mouse embryonic stem cells

tag: developmental stage


title: H3K9me3

tag: cell type


title: H3K4me3_rep2


title: H3K27me3_rep1


title: P0_CTX_cKO_NU04


title: H3K27Ac_rep1


title: P0_CTX_CTL_NU02


title: H3K27me3_rep2


title: P0_CTX_CTL_NU06


title: ice1-2-C_RNAseq

status: Public on Sep 13 2018

city: Shanghai

first: Juan

last: Lin

address: 2005 Songhu Road

country: China

institute: Fudan University

data_processing:
Raw reads generated by high-throughput sequencing were cleaned by removing adaptor sequences, empty reads, and low-quality sequences (Ns > 5)
RNA-seq reads were mapped to the Arabidopsis genome downloaded from TAIR10 (ftp://ftp.arabidopsis.org/home/tair/ Sequences/whole_chromosomes/) by TopHat software (http://tophat.cbcb.umd.edu)
The expression level of each unigene was normalized by calculating the Fragments Per Kilobase of transcript per Million mapped reads (FPKM)
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM

organism: Arabidopsis thaliana

source_name: anther

growth_protocol: All plants were grown in greenhouses under long day growth conditions (16 hours light/8 hours dark) at 22℃.

extract_protocol:
Total RNA was extracted from collected stage 9-13 anther using ZR Plant RNA MiniPrepTM Kit (ZYMO Research Corp., USA) and purified using RNAeasy Plant Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
The constructed libraries were sequenced using the HiSeqTM 2000 Sequencing System (Illumina, San Diego, CA, USA) with single-end technology in a single run at Shanghai Genergy Biotechnology (Shanghai) Co., Ltd. (Shanghai, China) and subjected to 100 cycles of paired-end (2×100 bp) sequencing.

value: anther

value: anther stage 9-13

tag: ecotype


title: ice1-2-A_RNAseq


title: ice1-2-B_RNAseq


title: 10038559:Treg

city: Boston

first: Ilya

last: Korsunsky

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

data_processing:
Transcript counts and tpm quantified with Kallisto.
Identified one technical outlier D12, with low read depth.
Filtered transcripts that did not have at least 5 counts in at least 10 samples.
Summed transcripts mapping to identical HGNC symbols.
Log2p1 transformed tpm values.
Regressed out donor batch effect using Limma removeBatchEffect function.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized, batch regressed log2 tpm values for each sample.

source_name: CD4 T

extract_protocol:
Synovial samples were acquired after removal as part of standard of care during arthroplasty surgery. Synovial tissue was isolated by careful dissection, minced, and digested with 100μg/mL LiberaseTL and 100μg/mL DNaseI (both Roche) in RPMI (Life Technologies) for 15 minutes, inverting every 5 minutes. Cells were passed through a 70μm cell strainer, washed, subjected to red blood cell lysis, and cryopreserved in Cryostor CS10 (BioLife Solutions) for batched analyses.
Seven RA case samples and six OA control samples were flow sorted into the following seven subsets for low-input RNA-Sequencing: Central Memory T cells (TCM), Naïve T cells (TN), Regulatory T cells (TReg), DR+27+ Effector T cells (DR+27+), DR+27- Effector T Cells (DR+27-), DR-27+ Effector T Cells (DR-27+), and DR-27- Effector T Cells (DR-27-). We rapidly thawed the case and control samples of cryopreserved peripheral blood mononuclear cells, and MACS enriched the samples for CD4+ T cells (Miltenyi 130-096-533). We rested the samples overnight in complete RPMI/10% FBS. Following the rest, we prepared the samples for fluorescence activated cell sorting (FACS). We washed the cells once in cold PBS, and incubated them with eBioscience human FC Receptor Binding Inhibitor (Thermo #14-9161-73). Subsequently, we stained the samples in PBS/5% FBS for 45 minutes with the following antibodies: FITC CD27 (Biolegend #302806), PE CD25 (Biolegend #356104), Pe/Cy7 CD127(IL-7Ra) (Biolegend #351320), Brilliant Violet 510 HLA-DR (Biolegend #307646), Brilliant Violet 605 CD45RA (Biolegend #304134), APC CD62L (Biolegend #304810), Alexa Fluor 700 CD4 (Biolegend #300526), APC/Cy7 CD14 (Biolegend #367108), and APC/Cy7 CD19 (Biolegend #302217). Post-stain, we washed the cells in cold PBS, passed them through a 70-micron filter, and acquired the samples on a BD FACSAria Fusion cytometer. 1000 cells from each subset were sorted and collected into 5ul of TCL Lysis Buffer (Qiagen #1031576) with 1% b-me. We processed and collected the samples uniformly in batches containing both cases and controls, and randomized the samples within the plate. We prepared sequencing libraries using the Smart-Seq2 protocol. Sequenced libraries were pooled and sequenced with the Illumina HiSeq 2500 using 25bp paired-end reads. We removed one outlier with low read depth. The remaining libraries were sequenced to a depth of 6-19M reads.

tag: number input cells

value: Treg

tag: disease status

value: oa

tag: donor id


title: 10043449:DR+27-


title: 10024253:DR-27+

value: ra


title: Post-PH 20 hrs replicate 3


title: WT-B_RNAseq

value: wild type


title: 10040772:TCM

value: TCM


title: WT-A_RNAseq


title: 10024301:DR+27+


title: H3K4me3_rep1


title: 10038559:Tnaive

value: Tnaive


title: 10030474:DR+27-


title: 10030474:DR-27-


title: 10043467:Treg


title: 10040772:DR-27+


title: 10043467:DR+27+


title: 28778769:Treg


title: 10024301:Treg


title: Empty:Empty (D10)

value: Empty


title: 10018377:DR-27+


title: 10040772:DR+27+


title: 10029272:Tnaive


title: 10029272:DR+27+


title: 10029272:TCM


title: 10008438:TCM


title: 10008438:DR+27-


title: 10029276:DR+27+


title: WT-C_RNAseq


title: 10043467:DR-27+


title: 10024253:Tnaive


title: 28778769:DR+27+


title: 10024253:DR+27-


title: 10024302:TCM


title: 10043467:DR-27-


title: 10024253:DR+27+


title: 10018377:DR-27-


title: 10029272:Treg


title: 10024302:Treg


title: 10043449:Tnaive


title: 10024301:TCM


title: 10018377:Tnaive


title: 10029276:DR+27-


title: 10040772:Tnaive


title: 10043467:TCM


title: 10024302:DR-27-


title: 10043449:DR-27-


title: 10038559:TCM


title: 10018377:Treg


title: Empty:Empty (F07)


title: 10043467:DR+27-


title: 10029276:DR-27+


title: 10029276:DR-27-


title: 10024301:DR-27+


title: 10030474:DR-27+


title: P0_CTX_CTL_NU01


title: 28778769:DR-27+


title: 10029272:DR-27+


title: 10040772:DR-27-


title: 10024253:Treg


title: Empty:Empty (H06)


title: 10024253:DR-27-


title: 10043449:TCM


title: 10029276:Treg


title: 10043449:DR-27+


title: 10024302:DR+27+


title: 10024302:DR-27+


title: 10008438:Treg


title: 10043449:Treg


title: 10040772:Treg


title: Empty:Empty (G04)


title: 10024301:DR-27-


title: 10024301:DR+27-


title: 10038559:DR-27+


title: 10024302:Tnaive


title: 10029272:DR-27-


title: Empty:Empty (C04)


title: 10008438:DR-27-


title: 10018377:TCM


title: 10024301:Tnaive


title: 10024253:TCM


title: 10008438:DR+27+


title: 10029276:Tnaive


title: 10030474:Treg


title: 10043449:DR+27+


title: 10038559:DR+27-


title: 10018377:DR+27-


title: 28778769:DR+27-


title: 10024302:DR+27-


title: 10008438:DR-27+


title: 10043467:Tnaive


title: 28778769:TCM


title: 28778769:DR-27-


title: 10018377:DR+27+


title: 10038559:DR+27+


title: 10029276:TCM


title: 10030474:Tnaive


title: 10008438:Tnaive


title: 10030474:DR+27+


title: 10029272:DR+27-


title: 10040772:DR+27-


title: 7279_PP_RNA

city: Dresden

first: Alexander

last: Herrmann

address: Fetscherstraße 74

department: Clinic of Internal Medicine I

country: Germany

institute: Technical University Dresden, University Hospital Carl Gustav Carus

data_processing:
RRBS: Reads were trimmed with Trim Galore! (v0.4.2, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for adapter contamination and 3' ends with base quality below 20 in RRBS mode.
RRBS: The reads were then aligned to the 1000 genomes version of the human GRCh37 reference (PMID: 26432245) with the BWA (v0.6.2) (PMID: 19451168) wrapper methylCtools (v0.9.2) (PMID: 24847876).
RRBS: Samtools (v1.3) (PMID: 19505943) and Picard tools (v1.115) (http://broadinstitute.github.io/picard/) were utilized for converting, merging and indexing of alignment files.
RRBS: Bis-SNP was used for SNP (dbSNP, v138, http://www.ncbi.nlm.nih.gov/SNP) aware realignment, quality recalibration and methylation calls.
RNA-seq: Reads were trimmed with Trim Galore! (v0.4.2) http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for adapter contamination and 3' ends with base quality below 20.
RNA-seq: The reads were then aligned to the 1000 genomes version of the human GRCh37 reference (PMID: 26432245) with the STAR (v2.5.2a) (PMID: 23104886) and the per-sample 2-pass mapping strategy processing all reads in both passes as described in the documentation.
RNA-seq: Read counts were summarized to Gencode gene models (v19) (PMID: 22955987) with featureCounts (v1.5.0-p3) (PMID: 24227677) counting primary alignments only.
Genomic tracks (bigwig and bed) were generated using bedtools (PMID: 20110278) and UCSC tools (PMID:22908213).
Genome_build: hg19
Supplementary_files_format_and_content: RRBS: bed files contain genomic coordinates, methylation values and coverage of all covered CpGs of a sample; bigwig files (.CG.bw) contain methylation values and bigwig files (coverage_ct.bw) coverage information. RNA-seq: bigwig files contain coverage information.

source_name: hepatocytes

extract_protocol:
RRBS: The frozen tissue was cut in 20 µm slices, mounted on precooled glass-slides and dried at room temperature for 30 minutes. In sum, an area of 200.000 µm2 per sample was microdissected using a ZEISS PALM MicroBeam LCM in Auto-LPC mode. Tissue pieces subjected for RRBS were frozen and maintained at -80° C. RNA-seq: The frozen tissue was cut in 20 µm slices and mounted on precooled glass-slides. Immediately after mounting, the tissue was fixed by incubation in 70% EtOH for 2 min and stained by incubation in a cresyl violet/50% EtOH solution for 30 sec with two short subsequent wash steps in 70% EtOH, followed by a 2 min air-drying step. All steps were performed on ice. In sum, an area of 500.000 µm2, from of 5-10 periportal fields and intermediate zones or hepatozytes surrounding 15-20 central veins per sample, were microdissected using a ZEISS PALM MicroBeam LCM in Auto-LPC mode. Tissue pieces subjected for RRBS were frozen and maintained at -80° C. Samples subjected for RNA-Seq were immediately processed.
RRBS: Cell lysis of microdissected material was done directly in the caps of the capturing tubes by treatment with 8 µl lysis buffer (10 mM Tris-HCl, 5 mM EDTA) and 2 µl Proteinase K (1 mg/ml, NEB) at 55 °C for 3 hours. For proteinase inactivation 0.5 µl Pefabloc (21 mM, Sigma) was added for 1 hour at room temperature. Restriction was performed using the methylation insensitive enzymes HaeIII (25 U, NEB) and AluI (5 U, NEB) supplemented with 1.5 µl CutSmart buffer (10 X, NEB), 1 µl MgAce (5 mM) and 1 µl yeast tRNA (100 ng) at 37 °C for 18 hours. Enzymes were inactivated at 80 °C for 20 min. A-Tailing was achieved with 1 µl Klenow Fragment (3′ → 5′ exo−, 5 U/µl, NEB) and 1 µl dATP (10 mM, NEB) at 37 °C for 30 min followed by enzyme inactivation at 75 °C for 20 min. Methylated Illumina TruSeq sequencing adapters (adapter 1: ACACTCTTTCCCTACACGACGCTCT TCCGATCT, adapter 2: GATCGGAA GAGCACACGTCTGAACTCCAGTCAC) were ligated using 1 µl pre-annealed adapters (100 µM), 0.5 µl T4 Ligase (2,000,000 U/µl, NEB) and 2 µl ATP (10 mM, NEB) at 16 °C for 22 hours. Subsequent bisulfite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo). Adapter ligated fragments were amplified by PCR using 0.5 µl each of indexed TruSeq primers (10 µM, Primer I5: AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTC CCTACACGACGCTCTTCCGAT,Primer I7: GATCGGAAGAGCACACGTCTGAACTC CAGTCAC[i7]ATCTCGTATGCCGTCTTCTGCTTG), 3 µl PCR Buffer (10 X, Qiagen), 1.2 µl MgCl2 (25 mM), 2.4 µl dNTPs (10 mM) and 0.5 µl Hot Start Taq (5 U / µl, Qiagen) in a 30 µl reaction with 95 °C for 15 min, 22 cycles of 95 °C for 30 sec, 60 °C for 30 sec, 72 °C for 1 min and final elongation at 72 °C for 7 min. After purification with 0.8 X Ampure XP Beads (Beckman Coulter) libraries were sequenced on a HiSeq2500 (Illumina) using TruSeq SBS Kit v3 – HS chemistry in a single read run with 90 bp read length.  RNA-seq: After microdissection, RNA was isolated using the RNeasy Micro Kit (Qiagen, Hilden, Germany).  Concentration and RNA Quality was obtained by using an Agilent BioAnalyzer (Agilent, Santa Clara, CA). The typical yield was between 4.5 ng and a RIN between 8 and 9. The RNA was reverse transcribed and amplified with the SMARTer Universal Low Input RNA Kit for Sequencing (Takara/Clontech) and 1 ng of RNA.  Libraries for next generation sequencing were constructed with the Nextera DNA Library Prep Kit (Illumina) and sequenced on a HiSeq2500 Sequencer.

value: liver

tag: hepatic zone

value: periportal (PP)

tag: isolation

value: laser capture microdissection


title: 7252_PP_RNA

tag: tissue


title: 7344_PP_RNA


title: 7251_PP_RNA


title: 28778769:Tnaive


title: 7230_PP_RNA


title: 7213_PP_RNA


title: 7194_PP_RNA


title: 7173_PP_RNA


title: 7188_PP_RNA


title: 7157_PP_RNA


title: 7172_PP_RNA


title: 7041_PP_RNA


title: 6967_PP_RNA


title: 7012_PP_RNA


title: 10038559:DR-27-


title: 10030474:TCM


title: 7344_IZ_RNA

value: intermediate (IZ)


title: 6758_PP_RNA


title: 6610_PP_RNA


title: 6922_PP_RNA


title: 7252_IZ_RNA


title: 7279_IZ_RNA


title: 7194_IZ_RNA


title: 7181_PP_RNA


title: 7251_IZ_RNA


title: 7230_IZ_RNA


title: GapR_2hr_g60

city: Seattle

first: Monica

middle: S

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

description:
gDNA
Cells were lysed with lysozyme and SDS, and proteins were removed by Proteinase K. CTAB was added and DNAs were extracted by phenol:chloroform:isoamyl alcohol and precipitated. DNA was sheared to 300-800 bp fragments using a Bioruptor Plus sonicator (Diagenode). RNase A (Qiagen) was added and the fragments were electrophoresed, and 300-600 bp fragments were size selected, purified with Gel Extraction Kit (Qiagen), and resuspended in 50 µL EB. Sequencing reads were aligned to NC_011916.1 offset by 1 MB.

data_processing:
Reads were aligned to Caulobacter NC_011916.1 (NA1000) with bowtie (single-end reads) or bowtie2 (paired end reads) allowing for 1 mismatch
Bowtie alignments were converted to wiggle files by mapping the center of each read.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: wig files were generated using custom python scripts, tab delimited files, first column represents genome position, second column represents value of position

organism: Caulobacter vibrioides NA1000

source_name: Caulobacter crescentus NA1000

growth_protocol: Caulobacter crescentus was grown to OD 0.2-0.4 before treatment or harvest

extract_protocol: Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with either Phusion (NEB) or Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 250-600 bp.

tag: growth stage

value: exponential phase

tag: genotype

value: delta-gapR Pxyl-gapR

tag: media

value: PYE + 0.2% glucose

tag: growth treatment

value: grown 2hr in 0.2% glucose, 60 mins post synchrony in 0.2% glucose


title: 7188_IZ_RNA


title: GapR_2hr_g40

value: grown 2hr in 0.2% glucose, 40 mins post synchrony in 0.2% glucose


title: 7213_IZ_RNA


title: 7181_IZ_RNA


title: GapR_2hr_g0

value: grown 2hr in 0.2% glucose, 0 mins post synchrony in 0.2% glucose


title: GapR_g80

value: grown in 0.3% xylose, 80 mins post synchrony in 0.2% glucose


title: GapR_g60

value: grown in 0.3% xylose, 60 mins post synchrony in 0.2% glucose


title: 7173_IZ_RNA


title: GapR_2hr_g20

value: grown 2hr in 0.2% glucose, 20 mins post synchrony in 0.2% glucose


title: 7137_PP_RNA


title: GapR_g40

value: grown in 0.3% xylose, 40 mins post synchrony in 0.2% glucose


title: GapR_g0

value: grown in 0.3% xylose, 0 mins post synchrony in 0.2% glucose


title: WT_g80

value: wild type

value: grown in 0.2% glucose, 80 mins post synchrony in 0.2% glucose


title: WT_g60

value: grown in 0.2% glucose, 60 mins post synchrony in 0.2% glucose


title: GapR_2hr_g80

value: grown 2hr in 0.2% glucose, 80 mins post synchrony in 0.2% glucose


title: WT_g20

value: grown in 0.2% glucose, 20 mins post synchrony in 0.2% glucose


title: 7137_IZ_RNA

value: liver

value: intermediate (IZ)

value: laser capture microdissection


title: WT_g40

value: exponential phase

value: PYE + 0.2% glucose

value: grown in 0.2% glucose, 40 mins post synchrony in 0.2% glucose


title: WT_g0

value: grown in 0.2% glucose, 0 mins post synchrony in 0.2% glucose


title: 7012_IZ_RNA


title: 7041_IZ_RNA


title: GapR-3xFlag

description:
mRNA
RNA was extracted by hot trizol lysis and Direct-zol RNA MiniPrep (Zymo). rRNAs were removed using the Ribo-Zero Kit for Gram-negative bacteria (Illumina) and mRNAs were then fragmented with RNA fragmentation reagents (Ambion). First-strand cDNA synthesis was performed with random primers (Invitrogen) and Superscript III. After purifying cDNAs by phenol:chloroform:isoamyl alcohol extraction and precipitation, second-strand synthesis occurred with dUTP (Promega) instead of dTTP and RNase H (NEB), E.coli DNA ligase (NEB), and DNA Pol I (NEB). Sequencing libraries were built as with other libraries, except that the second strand was digested with USER (NEB) after the addition of Y-adaptors.


title: 6967_IZ_RNA


title: GapR depletion in glucose 6h

value: delta-gapR Pxyl-gapR


title: Rif treated GapR-3xFLAG ChIP-seq

description:
gDNA
Cells were fixed with 1% formaldehyde and quenched with glycine. Cells were lysed with lysozyme and sonication, and cell debris cleared by centrifugation. Supernatants were diluted to use 500 μg of protein was used for ChIP and pre-cleared with 50 μL of Protein-A Dynabeads (Life Technologies) pre-blocked in ChIP buffer + 0.01% SDS and 100 μg ultrapure BSA (Ambion). Beads were pelleted and 90 μL of the supernatant was removed as input DNA. Remaining pre-cleared supernatant was incubated with 1 µL of FLAG antibody (Sigma), and immune complexes were captured with pre-blocked Protein-A Dynabeads. Beads were then washed and complexes eluted. Crosslinking was reversed at 65 °C in the presence of RNase A, and treated with Proteinase K (NEB). gDNA was recovered by phenol:chloroform:isoamyl alcohol extraction and precipitation.

value: PYE

value: 25 µg/mL of rifampicin was added for 20 min prior to fixation


title: 7172_IZ_RNA


title: 6922_IZ_RNA


title: GapR-3xFLAG ChIP-seq


title: WT grown in glucose 6h


title: Negative control ChIP-seq


title: 7344_CV_RNA

value: pericentral (CV)


title: 6758_IZ_RNA


title: 6610_IZ_RNA


title: 7279_CV_RNA


title: 7252_CV_RNA


title: 7213_CV_RNA


title: 7157_IZ_RNA


title: 7251_CV_RNA


title: 7194_CV_RNA


title: GapR_g20

value: grown in 0.3% xylose, 20 mins post synchrony in 0.2% glucose


title: 7230_CV_RNA


title: 7188_CV_RNA


title: 7181_CV_RNA


title: 7172_CV_RNA


title: 7157_CV_RNA


title: 7173_CV_RNA


title: 7012_CV_RNA


title: 7137_CV_RNA


title: 7041_CV_RNA


title: LHY_input

city: Coventry

first: Isabelle

last: Carre

address: Gibbet Hill

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

data_processing:
ChIP-seq reads were aligned to the TAIR9 genome assembly using bowtie, allowing only unique alignments to be retained.
Peaks were called using MACS2, release 2.0.10.09132012. Window size (-bw) was set to 200 and the q value threshold (-q) was set to 0.01
Genome_build: TAIR9
Supplementary_files_format_and_content: Peaks were called using MACS2

growth_protocol: For each chromatin preparation, approximately 500µl of seed were sterilized and sown over two 90mm square plates. Seedlings were grown for 2 weeks and samples collected 2h after dawn

extract_protocol:
Samples were cross-linked by vacuum-infiltration in 1% formaldehyde for 10 min. The cross-linking reaction was quenched by adding 1.3 mls of 2 M glycine and infiltrating for a further 5 min. Each sample was homogenized in 30 mls of Extraction Buffer 1 (0.4 M sucrose, 10 mM Tris-HCl pH 8, 5mM beta-mercaptoethanol, 1 mM PMSF and protease inhibitors (Roche complete protease inhibitor cocktail)) using a Polytron Status X120. Debris was removed by filtration through miracloth and the sample was centrifuged at 4°C. The resulting pellet was gently resuspended in 1ml of Extraction Buffer 2 (0.25 M sucrose, 10 mM Tris-HCl pH 8, 10 mM MgCl2, 1% Triton X-100, 5 mM beta-mercaptoethanol, 1 mM PMSF and protease inhibitors) and the nuclei collected by centrifugation. The nuclei were lysed in 500 µl of Nuclear Lysis Buffer (50 mM Tris-Hcl pH 8, 10 mM EDTA, 1% SDS, 1 mM PMSF and protease inhibitors) and sonicated to give chromatin fragment sizes ranging from 100 to 1000bp. For each immunoprecipitation, 250 µl of chromatin was added to 2 mls of ChIP dilution buffer (167 mM NaCl, 16.7 mM Tris-HCl pH8, 1.2 mM EDTA, Triton X-100, 1 mM PMSF and protease inhibitors) and pre-cleared with protein A Dynabeads (Invitrogen). Samples were incubated overnight at 4°C with either anti-LHY (1:200)  antibody. The immuno-complexes were isolated by incubation with protein A Dynabeads for 2 h at 4°C. The beads were washed as described by Haring et al.,  2007 with the addition of three extra high salt buffer washes. Protein A beads were then resuspended in 100 μl of TE and treated with RNase at 37°C for 20 minutes. SDS was added to a final concentration of 0.5% and the samples digested with proteinase K for 2 h at 50°C. To reverse cross-linking, 8 μl of 5 M NaCl was added and the samples were incubated overnight at 65°C. The DNA was then purified using the MinElute PCR purification kit (Qiagen).
Four independent ChIP samples were pooled for the generation of a library. Four corresponding samples of input DNA (i.e., DNA that was not submitted to the immunoprecipitation procedure) were also combined for the preparation of an input DNA library.  Library preparation and sequencing was conducted at the University of Utah’s Bioinformatic Core facility using an Illumina GAII sequencer. The libraries were prepared using the Illumina Tru Seq DNA sample prep kit according to the instructions of the manufacturer.

tag: chip antibody

value: Col

value: seedling


title: 6922_CV_RNA


title: LHY_IP

value: LHY antiserum


title: 6967_CV_RNA


title: 6758_CV_RNA


title: 7344_PP_RRBS

description: HaeIII / AluI restriction

value: periportal (PP)


title: 6610_CV_RNA


title: 7252_PP_RRBS

description: HaeIII / AluI restriction


title: 7279_PP_RRBS

description: HaeIII / AluI restriction


title: 7230_PP_RRBS

description: HaeIII / AluI restriction


title: 7213_PP_RRBS

description: HaeIII / AluI restriction


title: 7251_PP_RRBS

description: HaeIII / AluI restriction


title: ES2i_oX

city: Barcelona

first: Thomas

last: Graf

address: c/Dr. Aiguader, 88. PRBB Building

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: CRG (Center for Genomic Regulation)

data_processing:
We used the GEM mapper (Marco-Sola et al., 2012) with two modified versions each of the mouse (GRCm38) and viral reference genomes: one with all C’s changed to T’s and another with all G’s changed to A’s. Reads were fully converted in silico prior to mapping to the modified reference genomes, and the original reads were restored after mapping.
The first few bases from each read have been shown to have a slightly higher probability of being called as methylated (Schultz et al., 2015), so we trimmed the first ten bases from each read. Heterozygous positions, positions with a genotype error probability greater than 0.01, and positions with a read depth greater than 250 were filtered out. Only cytosines with six or more reads informative for methylation status were considered. On average, half of the reads from either strand will be informative for methylation status at a given position, so minimum coverage is tipically greater than 12.
Methylated and unmethylated cytosine conversion rates were determined from spiked-in bacteriophage DNA (fully methylated phage T7 and unmethylated phage lambda).
Methylated non-CGs were defined as those cytosines with at least two unconverted reads and a methylation probability greater than two SDs, where the probability of the following base being a guanine was at least two orders of magnitude smaller than the most probable base
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files used for browser exploration of the data.

source_name: embryo (inner cell mass)

growth_protocol: B and Ba cells were grown in 20%FBS-RPMI+IL7; D1-D4 in N2B27 medium. ES2i in N2B27+2i medium. ESserum in 15%FBS+LIF conditions.  All cells were grown on feeders (mitomycin-C treated mouse embryonic fibroblasts)

extract_protocol:
Cells were collected, seperated from feeders by pre-plating and genomic DNA was extracted using the Blood & Cell Culture DNA Mini kit (Qiagen).
High molecular weight DNA (400ng) was spiked with unmethylated bacteriophage λ DNA (5 ng of λ DNA per microgram of genomic DNA; Promega), with methylated T7 phage DNA (5 ng of T7 DNA per microgram of genomic DNA) and also with the manufacture’s digestion and sequencing control (each 20 ng per microgram of genomic DNA). Genomic DNA with the spike-in controls was sheared using Covaris LE220 focused-ultrasonicator to a mean fragment size of 800bp, purified, denatured and the sample was evenly split for the oxidation reaction and the mock-oxidation reaction where the oxidant solution was replaced by water. Both aliquots were then processed in parallel for all stages of the protocol. Illumina compatible adapters and library specific indexes were incorporated through ten PCR cycles. The quality control of the library was monitored using the Agilent 2100 Bioanalyzer DNA 7500 assay, and the concentration was estimated using the KAPA Library Quantification Kit for Illumina® Platforms, v1.14 (Kapa Biosystems).
WGBS and oxWGBS following the workflow of  CEGX TrueMethyl® Whole Genome kit, v3.1 (Cambridge Epigenetix) in HydroxyMethyl mode

treatment_protocol: To activate C/EBPa cultures were treated for 18h with 100nM b-Estradiol (E2), resulting in Ba cells. After E2 washout, the cultures were treated with 2μg/ml of doxycycline to activate OSKM.

value: embryo (inner cell mass)

value: low passage (p<10)

tag: cell subtype

value: 2i E14TG2 cells


title: 7194_PP_RRBS

description: HaeIII / AluI restriction

value: liver

value: laser capture microdissection


title: D4_oX

source_name: bone marrow

value: bone marrow

value: cultured primary cells (short term)

value: Ba cells + 4 days after OSKM activation


title: Bcell_oX

value: B cells


title: D1_oX

value: Ba cells + 1 day after OSKM activation


title: D2_oX

value: Ba cells + 2 days after OSKM activation


title: 7188_PP_RRBS

description: HaeIII / AluI restriction


title: Ba_oX

value: B cells exposed to C/EBPa during 18 h


title: D4_BS


title: 7181_PP_RRBS

description: HaeIII / AluI restriction


title: ES2i_BS


title: D2_BS


title: D1_BS


title: Ba_BS


title: 7172_PP_RRBS

description: HaeIII / AluI restriction


title: 7157_PP_RRBS

description: HaeIII / AluI restriction


title: RNA_KO_Day9_R1

first: Enrique

last: Blanco

address: Dr. Aiguader 88

institute: Center for Genomic Regulation (CRG)

description: Processed data file: Day9_OH-TAM_FPKMs.txt

data_processing:
RNAseq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. DeSeq2 (PubMed ID 25516281) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Files *FPKMs..txt: Tab-delimited text, FPKMs.

source_name: EBs derived from mESCs

growth_protocol: The Mll2F/F:CreERT2/+ ESCs were established from blastocysts of C57Bl/6 mice as previously described (Denissov et al., Development 2014). Cells were cultured in feeder-free 0.1% gelatin-coated dishes in DMEM (SIGMA G5154) supplemented with 20% FBS (HyClone), with 0.2% β-mercaptoethanol (Gibco), 1% Pen/Strep (Gibco), 1% sodium pyruvate (Gibco), 1% non-essential amino acids (MEM NEAA, Gibco), 1% GlutaMAX™ (Gibco) and 1,000U/ml recombinant LIF (Millipore). Wild-type and Mll2KO (treated with carrier or 10-6 M 4-hydroxytamoxifen for 96h, respectively, corresponding to Day0) mESCs were differentiated into embryoid bodies (EBs) with the “hanging drops” method as previously described (Morey et al., Cell Stem Cell 2012).

extract_protocol:
RNAseq: RNA was extracted using RNeasy kit (Qiagen).
Libraries were prepared according to Illumina instructions.

treatment_protocol: Induction of Cre-recombination was achieved by treating cells with 10-6 M 4-hydroxytamoxifen during 96 hours as previously described (Glaser et al., Epigenetics Chromatin 2009).

tag: strain/background

tag: mll2 status

value: KO

value: Embryoid bodies

tag: differentiation time point

value: Day 9


title: RNA_KO_Day9_R2

tag: cell type


title: Bcell_BS


title: RNA_KO_Day6_R1

description: Processed data file: Day6_OH-TAM_FPKMs.txt

value: Day 6


title: 7137_PP_RRBS

description: HaeIII / AluI restriction

value: periportal (PP)


title: RNA_KO_Day6_R2


title: 7041_PP_RRBS

description: HaeIII / AluI restriction


title: RNA_KO_Day3_R2

description: Processed data file: Day3_OH-TAM_FPKMs.txt

value: Day 3


title: RNA_KO_Day0_R2

description: Processed data file: Day0_OH-TAM_FPKMs.txt

value: Day 0


title: RNA_KO_Day0_R1


title: RNA_KO_Day3_R1


title: 7173_PP_RRBS

description: HaeIII / AluI restriction


title: RNA_WT_Day9_R1

value: WT


title: RNA_WT_Day3_R2

data_processing:
RNAseq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. DeSeq2 (PubMed ID 25516281) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq.
Genome_build: mm9 (MGSCv37).
Supplementary_files_format_and_content: Files *FPKMs..txt: Tab-delimited text, FPKMs.


title: RNA_WT_Day9_R2


title: RNA_WT_Day6_R1

growth_protocol: The Mll2F/F:CreERT2/+ ESCs were established from blastocysts of C57Bl/6 mice as previously described (Denissov et al., Development 2014). Cells were cultured in feeder-free 0.1% gelatin-coated dishes in DMEM (SIGMA G5154) supplemented with 20% FBS (HyClone), with 0.2% β-mercaptoethanol (Gibco), 1% Pen/Strep (Gibco), 1% sodium pyruvate (Gibco), 1% non-essential amino acids (MEM NEAA, Gibco), 1% GlutaMAX™ (Gibco) and 1,000U/ml recombinant LIF (Millipore).


title: RNA_WT_Day6_R2


title: 6967_PP_RRBS

description: HaeIII / AluI restriction

value: liver


title: 6922_PP_RRBS

description: HaeIII / AluI restriction

value: laser capture microdissection


title: 6758_PP_RRBS

description: HaeIII / AluI restriction


title: RNA_WT_Day3_R1


title: RNA_WT_Day0_R2


title: RNA_WT_Day0_R1

data_processing:
RNAseq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. DeSeq2 (PubMed ID 25516281) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq. .
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Files *FPKMs..txt: Tab-delimited text, FPKMs.


title: 7344_IZ_RRBS

description: HaeIII / AluI restriction

value: intermediate (IZ)


title: ATAC_KO_R3

data_processing:
ATACseq analysis: Sequence reads were mapped to the mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the options -m 1, --chunkmbs 2000 and -X 2000.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ATACseq profiles were produced by MACS in BedGraph format. Peaks were reported in BED format.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Files *.bedgraph.gz: BedGraph, genome-wide ChIP profiles.
Supplementary_files_format_and_content: Files *.bed: BED, signal-enriched regions.

source_name: mouse Embryonic Stem Cells (mESCs)

extract_protocol: ATAC-seq libraries for Mll2WT and Mll2KO (treated 96h with 10-6 M 4-hydroxytamoxifen) cells were generated following the Buenrostro et al, Curr Protoc Mol Biol 2015 protocol.

value: Embryonic stem cells


title: 7279_IZ_RRBS

description: HaeIII / AluI restriction


title: ATAC_KO_R2


title: ATAC_KO_R1


title: 7012_PP_RRBS

description: HaeIII / AluI restriction


title: reChIP_H3K27me3-IgG

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIPseq and ATACseq profiles were produced by MACS in BedGraph format. Peaks were reported in BED format.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Files *.bedgraph.gz: BedGraph, genome-wide ChIP profiles.
Supplementary_files_format_and_content: Files *.bed: BED, signal-enriched regions.

extract_protocol: Re-ChIP-seq experiments were performed using Re-ChIP-IT kit (Active Motif, 53016) following manufacturer's instructions.

value: H3K27me3 (Millipore, 07-449)


title: ATAC_WT_R1


title: ATAC_WT_R2


title: ATAC_WT_R3


title: reChIP_H3K27me3-H3K4me3

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIPseq profiles were produced by MACS in BedGraph format. Peaks were reported in BED format.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Files *.bedgraph.gz: BedGraph, genome-wide ChIP profiles.
Supplementary_files_format_and_content: Files *.bed: BED, signal-enriched regions.

extract_protocol:
Re-ChIP-seq experiments were performed using Re-ChIP-IT kit (Active Motif, 53016) following manufacturer's instructions.
Libraries were prepared according to Illumina instructions.

value: H3K4me3(Diagenode C15410003), H3K27me3 (Millipore, 07-449)


title: 7252_IZ_RRBS

description: HaeIII / AluI restriction


title: 7251_IZ_RRBS

description: HaeIII / AluI restriction


title: reChIP_H3K4me3-H3K27me3


title: ChIP_RPB1_KO

extract_protocol: ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013).

value: RPB1 (Cell Signaling Technologies, Rabbit mAb #14958 (D8L4Y))


title: 6610_PP_RRBS

description: HaeIII / AluI restriction


title: 7230_IZ_RRBS

description: HaeIII / AluI restriction


title: reChIP_H3K4me3-IgG

value: H3K4me3(Diagenode C15410003)


title: 7213_IZ_RRBS

description: HaeIII / AluI restriction


title: ChIP_RPB1_WT


title: ChIP_CTCF_KO

value: CTCF (Millipore, 07-729)


title: ChIP_H3K27ac_KO

value: KO

value: H3K27ac (Millipore 07-360)


title: ChIP_H3K27ac_WT


title: ChIP_H3K36me3_WT

value: H3K36me3 (Abcam, ab9050)


title: ChIP_H3K36me3_KO


title: ChIP_CTCF_WT


title: 7188_IZ_RRBS

description: HaeIII / AluI restriction


title: 7172_IZ_RRBS

description: HaeIII / AluI restriction


title: 7157_IZ_RRBS

description: HaeIII / AluI restriction


title: ChIP_Ring1b_WT

data_processing:
Sequence reads were mapped to a synthetic genome constituted of the mouse and the human chromosomes (mm9+hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIPseq genome-wide profiles are normalized by the total number of human reads of each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bedgraph.gz: BedGraph, genome-wide ChIP profiles.
Supplementary_files_format_and_content: Files .bed: BED, signal enriched regions.

extract_protocol:
ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013).
This ChIPseq includes spike-in control from human K562 cell line:  0.75ug (2.5%) of chromatin from crosslinked K562 cells was added to 30 ug of ESCs chromatin, together with 4ug of homemade RING1B-specific antibody during immunoprecipitation reactions. Libraries were prepared according to Illumina instructions.

value: Ring1b (Homemade (PubMed id:22226355))


title: 7173_IZ_RRBS

description: HaeIII / AluI restriction


title: ChIP_Suz12_WT

value: Suz12 (Abcam, ab12073)


title: ChIP_Suz12_KO


title: ChIP_IgG_KO


title: 7137_IZ_RRBS

description: HaeIII / AluI restriction


title: ChIP_Pol2Ser5P_KO

value: Pol2Ser5P (clone CTD4H8; Mouse Monoclonal, Covance, MMS-128P)


title: 7041_IZ_RRBS

description: HaeIII / AluI restriction


title: 7194_IZ_RRBS

description: HaeIII / AluI restriction


title: ChIP_Mll2_KO

value: Mll2 (Generated in Shilatifard lab (PubMed id:23934151))


title: 7181_IZ_RRBS

description: HaeIII / AluI restriction


title: ChIP_IgG_WT

value: WT


title: ChIP_Pol2Ser5P_WT


title: 7012_IZ_RRBS

description: HaeIII / AluI restriction

value: liver


title: ChIP_H3_KO

value: H3 (Abcam, ab1791)


title: 6967_IZ_RRBS

description: HaeIII / AluI restriction

value: intermediate (IZ)

value: laser capture microdissection


title: ChIP_H3K27me3_KO

value: Embryonic stem cells

value: H3K27me3 (Millipore, 07-449)


title: ChIP_H3K27me3_WT


title: ChIP_Ring1b_KO

extract_protocol: ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). This ChIPseq includes spike-in control from human K562 cell line:  0.75ug (2.5%) of chromatin from crosslinked K562 cells was added to 30 ug of ESCs chromatin, together with 4ug of homemade RING1B-specific antibody during immunoprecipitation reactions. Libraries were prepared according to Illumina instructions.


title: 6922_IZ_RRBS

description: HaeIII / AluI restriction


title: ChIP_H3K4me3_WT

value: H3K4me3 (Generated in Shilatifard lab (PubMed id:23934151))


title: 7344_CV_RRBS

description: HaeIII / AluI restriction

value: pericentral (CV)


title: 6758_IZ_RRBS

description: HaeIII / AluI restriction


title: 6610_IZ_RRBS

description: HaeIII / AluI restriction


title: 7252_CV_RRBS

description: HaeIII / AluI restriction


title: 7279_CV_RRBS

description: HaeIII / AluI restriction


title: 7251_CV_RRBS

description: HaeIII / AluI restriction


title: 7188_CV_RRBS

description: HaeIII / AluI restriction


title: 7213_CV_RRBS

description: HaeIII / AluI restriction


title: 7194_CV_RRBS

description: HaeIII / AluI restriction


title: 7230_CV_RRBS

description: HaeIII / AluI restriction


title: ChIP_H3_WT


title: ChIP_Mll2_WT


title: 7173_CV_RRBS

description: HaeIII / AluI restriction


title: 7172_CV_RRBS

description: HaeIII / AluI restriction


title: 7157_CV_RRBS

description: HaeIII / AluI restriction


title: 7041_CV_RRBS

description: HaeIII / AluI restriction


title: ChIP_H3K4me3_KO


title: 7012_CV_RRBS

description: HaeIII / AluI restriction


title: 7137_CV_RRBS

description: HaeIII / AluI restriction


title: 6610_CV_RRBS

description: HaeIII / AluI restriction


title: 6758_CV_RRBS

description: HaeIII / AluI restriction


title: RT4 input rep2 (JP507)

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
fastq files were obtained from CCHMC DNA core.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie with the following configurations: -S -m 1 --best
sam files were converted to bam files using samtools.
Reads were sorted and duplicates were removed using samtools.
HOMER was used as peak callers.
Genome_build: hg19
Supplementary_files_format_and_content: tdf files were generated using igvtools
Supplementary_files_format_and_content: peaks.bed files were generated using HOMER as a peak caller

source_name: RT4 cells

growth_protocol: McCoy 5A medium with 10% FBS

extract_protocol:
not applicable
Sequencing libraries were generated using Rubicon ThruPLEX DNA-seq kit.

treatment_protocol: not applicable

tag: tissue type

value: transitional cell papilloma

tag: Stage

value: adult

value: input DNA


title: RT4 input rep1 (JP498)


title: RT4 FoxA1 ChIP-seq rep1 (JP499)


title: 6922_CV_RRBS

description: HaeIII / AluI restriction


title: GLUCNAC_3

city: Helsinki

first: Krista

last: Kokki

address: Viikinkaari 9, Biocenter 1, Institute of Biotechnology P.O.Box. 56

department: Department of Biosciences (Genetics)

institute: University of Helsinki

description: glucnac rep 3

data_processing:
Sequenced reads were trimmed with Trimmomatic with parameters ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36
Sequences were mapped using TopHat (v2.1.0) to dmel R6.10 with parameter -p 4 and quantified with HTSeq (v2.7.6) with parameters -m HTSeq.scripts.count -m union -s reverse -a 10 -t exon -i Parent
Differentially expressed genes were calculated with R package limma with Benjamini-Hochberg correction, with genes with low counts (cpm<1 in more than one replicate) filtered
Genome_build: Flybase Drosophila melanogaster R6.10
Supplementary_files_format_and_content: tab delimited.txt file includes read counts for expressed genes for all samples and their statistics

organism: Drosophila melanogaster

source_name: whole larvae

growth_protocol: Mated females were maintained for seven days at 25°C with fly food containing agar 0.8% (w/v), syrup 4,4% (w/v), corn flour 8% (w/v), soya flour 1% (w/v), malt 8% (w/v), dry baker's yeast 1.8% (w/v), propionic acid 0.6% (v/v), phosphoric acid 0.06% (v/v) and Nipagin (methylparaben) 0.24% (v/v).

extract_protocol:
Intestines were dissected in PBS at room temperature and total RNA was extracted using the RNeasy kit (Qiagen).
Illumina TrueSeq stranded mRNA protocol

treatment_protocol: Flies were shifted to diluted fly food (0.25x of the maintenance diet while keeping the preservative concentration constant) for 24 hours with, or without for control animals, N-acetyl-D-Glucosamine (GlcNAc, MP Biomedicals, cat no:100068) in 0.1M concentration. Four independent samples from control (-GlcNAc) and experiment (+GlcNAc) were sampled in parallel.

value: intestine

tag: Sex

value: female

tag: treatment

value: glucosamine


title: GLUCNAC_4

description: glucnac rep 4


title: CTRL_4

description: control rep 4


title: 7181_CV_RRBS

description: HaeIII / AluI restriction

tag: hepatic zone


title: CTRL_3

description: control rep 3


title: CTRL_2

description: control rep 2


title: GLUCNAC_1

description: glucnac rep 1


title: CTRL_1

description: control rep 1


title: RNA-seq from control cells with treatment repeat 3

status: Public on Sep 12 2018

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

data_processing:
Sequences were quality trimmed , discarding those < 35 nt
alignment  genome with STAR
Summerization of reads with  featureCounts based on Ensmble v 75
Differential expression using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Spreadsheets with summary statistics and differential P values

source_name: liver

growth_protocol: Huh-7.5 cells and Huh7/FT3-7 cells  were cultured as described previously at Yi M, Ma Y, Yates J, Lemon SM: Compensatory mutations in E1, p7, NS2, and NS3 enhance yields of cell culture-infectious intergenotypic chimeric hepatitis C virus. J Virol 2007, 81:629-638.

extract_protocol:
Total RNA from HCV infected and non-infected Huh7/FT3-7 cells was purified using the RNeasy Mini Kit (Qiagene).
1 µg of total RNA was treated with the NEB Next poly (A) mRNA Magnetic Isolation Module (NEB). RNA-seq libraries were produced by using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB), and sequenced by Illumina HiSeq 2500 platform with single-end reads of 50 bp according to the manufacturer's instructions

treatment_protocol: For all experiments with Huh7/FT3-7, cells were infected with HJ3-5 chimeric virus at a MOI of 0.1 or 0.5 and passaged for two weeks until approximately 100% of the cells were HCV positive.


title: RNA-seq from control cells with treatment repeat 2


title: RNA-seq from HCV infected and cured cells repeat 3


title: 6967_CV_RRBS

description: HaeIII / AluI restriction

tag: isolation


title: RNA-seq from HCV infected and cured cells repeat 1

tag: tissue


title: RNA-seq from control cells with treatment repeat 1


title: RNA-seq from HCV infected and cured cells repeat 2


title: RNA-seq from HCV infected cells repeat 6


title: RNA- seq from non-infected cells repeat 5


title: RNA- seq from non-infected cells repeat 4


title: RT4 FoxA1 ChIP-seq rep2 (JP508)


title: RNA-seq from HCV infected cells repeat 4


title: RNA- seq from non-infected cells repeat 3


title: RNA-seq from HCV infected cells repeat 3


title: RNA-seq from HCV infected cells repeat 5


title: RNA- seq from non-infected cells repeat 1


title: RNA-seq from HCV infected cells repeat1


title: RNA-seq from HCV infected cells repeat 2


title: GLUCNAC_2

description: glucnac rep 2


title: H3K27Me3 ChIP-seq from HCV infected cells rapeat 3

data_processing:
Sequences were quality trimemed , discarding those < 35 nt
Alignment wiith bwa, duplicate alignments removed
Peak calling with MACS with an input sample as background - any region with > 2 peaks used downstream
Summerization of reads with  bedtools multi cov
Differential expression using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Spreadsheets with summary statistics and differentialP values

extract_protocol:
ChIP assays were performed using the Magna Chip G kit (Milipore) as described by the manufacturer instructions. In brief, HCV infected and non-infected Huh7/FT3-7 cells were fixed with 1% formaldehyde to cross-link proteins to DNA. After crosslinking, cells were then lysed, nuclei were purified, and chromatin was fragmented by sonication (Covaris S220) to generate DNA fragments of 200-1000 bp. Chromatin was incubated overnight with 5 µg of either specific antibodies against H3K9Ac ,H3K43Me,  H3K93Me and H3K273Me Abs (Milipore) or a normal Rabbit IgG Ab/ beads only (Milipore) as a negative control for the immunoprecipitation experiments. Immunoprecipitated chromatin was then washed and eluted. After reversal of the crosslinks the DNA was purified. The purified DNA was then used for qPCR and next generation sequencing (NGS)
Libraries were prepared by using NEBNext® Ultra TM DNA Library Prep Kit for Illumina® (NEB #E7370S/L)

value: ChIPAb Trimethyl-Histone H3 (Lys-27) 07-449 (Millipore)


title: H3K27Me3 ChIP- seq from non-infected cells rapeat 3


title: H3K27Me3 ChIP- seq from non-infected cells rapeat 2


title: H3K27Me3 ChIP-seq from HCV infected cells rapeat 2


title: H3K27Me3 ChIP- seq from non-infected cells rapeat 1


title: H3K9Me3 ChIP- seq from non-infected cells repeat 3

value: ChIPAb Trimethyl-Histone H3 (Lys-9) Purified 17-10242 (Millipore)


title: H3K9Me3 ChIP- seq from non-infected cells repeat 2


title: H3K27Me3 ChIP-seq from HCV infected cells rapeat 1


title: RNA- seq from non-infected cells repeat 6


title: H3K9Me3 ChIP-seq from HCV infected cells repeat 2


title: H3K9Me3 ChIP-seq from HCV infected cells repeat 1


title: H3K4Me3 ChIP-seq from HCV infected cells  repeat 3

value: ChIPAb Trimethyl-Histone H3 (Lys-4) 17-614 (Millipore)


title: H3K9Me3 ChIP- seq from non-infected cells repeat 1

value: liver


title: H3K4Me3 ChIP- seq from non-infected cells repeat 3

value: ChIPAb Trimethyl-Histone H3 (Lys-4)  17-614 (Millipore)


title: RNA- seq from non-infected cells repeat 2


title: H3K4Me3 ChIP- seq from non-infected cells repeat 2


title: V09081/2104_ingfat_L1

city: New York

first: Rui

last: Xiao

state: NY

address: 630 West 168th Street

department: Anesthesiology

institute: Columbia University

data_processing:
Read mapping was conducted with a proprietary algorithm by Expression Analysis (www.q2labsolutions.com) and RSEM method,  and read counts were used as input for differential expression analysis in DESeq2 version 1.10.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text matrix files include RSEM raw values and normalized values.
Supplementary_files_format_and_content: rsem_gcounts* files: gene raw count matrix with rsem method
Supplementary_files_format_and_content: rsem_gnorm* files: gene normalized count matrix with rsem method
Supplementary_files_format_and_content: rsem_icounts* files: isoform raw count matrix with rsem method
Supplementary_files_format_and_content: rsem_inorm* files: isoform normalized count matrix with rsem method

source_name: inguinal white adipose tissues

extract_protocol: Wild type (C57BL6/J – C57n:C57mt and C3H/HeN - C3Hn:C3Hmt) and MNX (C57n:C3Hmt and C3Hn:C57mt) mouse were weaned with Chor diet and continued with Chow or changed to high-fat diet from 6 to 12-13 weeks of age. RNA samples were isolated from white adipose tissues collected from epididymal (eWAT) and inguinal (iWAT) fat, representing visceral and subcutaneous fat depots, respectively with RNeasy kit (Qiagen).

value: C3H wt

tag: diet

value: High Fat Diet

value: inguinal white adipose tissues


title: H3K4Me3 ChIP- seq from non-infected cells repeat 1


title: H31244/4111_epifat_L1.D712_504

source_name: epididymal white adipose tissue

tag: genotype

value: epididymal white adipose tissue


title: H31244/3205_epifat_L1.D707_504


title: H31244/3112_ingfat_L1.D710_505

value: C57 wt


title: H31244/4109_epifat_L1.D701_505


title: H3K4Me3 ChIP-seq from HCV infected cells  repeat 2


title: H31244/3203_ingfat_L1.D712_505


title: H31244/4109_ingfat_L1.D704_506


title: H3K4Me3 ChIP-seq from HCV infected cells  repeat 1


title: H3K9Me3 ChIP-seq from HCV infected cells repeat 3


title: H31244/3111_ingfat_L1.D711_505


title: H3K9Ac ChIP-seq from HCV infected cells repeat 3

value: ChIPAb Acetyl-Histone H3 (Lys-9) Purified 17-658 (Millipore)


title: H31244/2204_ingfat_L1.D705_505


title: H3K9Ac ChIP- seq from non-infected cells repeat 2


title: H31243/4204_ingfat_L1.D709_505


title: H31244/2102_ingfat_L1.D707_505


title: H31243/4204_epifat_L1.D708_504


title: H3K9Ac ChIP-seq from HCV infected cells repeat 2


title: H31243/4110_ingfat_L1.D701_506


title: H3K9Ac ChIP- seq from non-infected cells repeat 1


title: H31244/4209_epifat_L1.D702_505


title: H31243/3209_epifat_L1.D704_504


title: H3K9Ac ChIP-seq from HCV infected cells repeat 1


title: H3K9Ac ChIP- seq from non-infected cells repeat 3


title: H31244/2205_epifat_L1.D702_504


title: H31243/3203_epifat_L1.D711_504


title: H31244/4208_ingfat_L1.D703_506


title: H31243/3205_ingfat_L1.D708_505


title: H31243/2205_ingfat_L1.D704_505


title: H31244/3111_epifat_L1.D710_504


title: H31243/2202_epifat_L1.D705_504


title: H31243/2202_ingfat_L1.D706_505


title: H31243/2204_epifat_L1.D703_504


title: H31243/2104_epifat_L1.D701_504


title: H31243/3112_epifat_L1.D709_504