title: WGBS from forebrain (ENCLB706LDH)

description:
https://www.encodeproject.org/experiments/ENCSR007JSP/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 12.5 day mouse forebrain
experiment encode accession: ENCSR007JSP
assay title: WGBS
assembly: mm10
encode release date: 2016-03-14
lab: Joe Ecker, Salk
library encode accession: ENCLB706LDH
size range: 180-500

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (12.5 days)

value: Forebrain from 68 embryonic 12.5 day mice

value: ENCBS617DPG at ENCODE; https://www.encodeproject.org/ENCBS617DPG/


title: WGBS from forebrain (ENCLB423YAC)

status: Public on Jun 22 2016

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR007JSP/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 12.5 day mouse forebrain
experiment encode accession: ENCSR007JSP
assay title: WGBS
assembly: mm10
encode release date: 2016-03-14
lab: Joe Ecker, Salk
library encode accession: ENCLB423YAC
size range: 180-500

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Mus musculus

value: forebrain

value: tissue

tag: description

value: Forebrain from 120 embryonic 12.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS974GPH at ENCODE; https://www.encodeproject.org/ENCBS974GPH/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: WGBS from forebrain (ENCLB378ISE)

description:
https://www.encodeproject.org/experiments/ENCSR007JSP/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 12.5 day mouse forebrain
experiment encode accession: ENCSR007JSP
assay title: WGBS
assembly: mm10
encode release date: 2016-03-14
lab: Joe Ecker, Salk
library encode accession: ENCLB378ISE
size range: 180-500


title: ChIP-seq from heart (ENCLB193JDK)

description:
https://www.encodeproject.org/experiments/ENCSR007XTC/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on embryonic 14.5 day mouse heart
experiment encode accession: ENCSR007XTC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR840PFW
encode release date: 2016-02-18
lab: Bing Ren, UCSD
library encode accession: ENCLB193JDK
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap heart tissue mixed sex embryo (14.5 days)

tag: antibody

value: heart

value: Heart from pooled embryonic 14.5 day mice

value: ENCBS566AAA at ENCODE; https://www.encodeproject.org/ENCBS566AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: P28_input

status: Public on Jun 21 2016

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 30

data_processing:
Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering.
ChIP-seq reads were aligned to the GRCm38 genome assembly using Genomatix Mining Station.
ChIP-seq peaks were called using SICER v1.1 with the following parameters: window 200 nt, gap 400 nt, input as control, redundancy threshold 1, FDR=1E-2.
Peak summaries were annotated according to the type of feature they overlapped. Annotation was based on ENSEMBL GRCm38.73 (sep 2013), downloaded from their web-based Biomart interface.  Annotation was performed in R 3.0.1
Annoated summary files were combined into a master file where each row contains a called peak, information from each sample's summary file as well as combined read count, average fold change vs. input, and average p-value. Performed in R 3.0.1
Genome_build: GRCm38.p1 with Ensembl 73
Supplementary_files_format_and_content: BED files containg the ChIP-seq peaks and a .txt file containing the annotated summary of the ChIP-seq results.

source_name: retina

extract_protocol:
Flow-sorted cells were lysed using lysis buffer and sonicated using Covaris. Cellular debris was removed by centrigugation, and clear chromatin solution was reconstituted to RIPA buffer. Pre-cleared chromatin solution was then incubated with anti-H3K4me3 (ab8580, Abcam, MA, USA), anti-H3K27me3 (07-449, Millipore, MA, USA) or normal IgG (12-370, Millipore) with constant rotation at 4°C overnight. Thoroughly washed immunoprecipitation complexes were then digested, and the cross-link was reversed by incubation in 50 l of TE, pH 8 supplemented with 0.3% SDS and 1 mg/ml proteinase K at 65 °C for 6 hrs. The carried-over RNA was digested by 1 hr incubation at 37°C with RNase cocktail (Ambion, Life Technologies), and the immunoprecipitated DNA was then purified using Agencourt AMPure XP beads (Beckman Coulter, CA, USA).
Libraries were prepared using TruSeq DNA Sample Preparation kit v2 (Illumina, FC-121-2001; FC-121-2002) according to Illumina's instructions with the following modifications. 1.  As amount of total ChIP DNA obtained from each ChIP experiment is estimated to be only 400 pg to 1 ng, entire ChIP DNA was used for ChIP-seq library construction Instead of 1 ug DNA as recommended by Illumina. 2. For adapter ligation, 1/100 dilution of adapter was used to avoid having access adapter-adapter dimer. 3. After adapter ligation, double-sided SPRI technique (200-500 nt fragments were selected with 0.55x left /0.75x right) was used for size-selection in order to minimize a sample loss. 4. 18 cycles of PCR amplification were performed on all ChIP-seq libraries.

treatment_protocol: Retinal cells were dissociated using papain for 10 min at 28'C, washed, and cross-linked in 1% formaldehyde for 15 min at room teperature. GFP-positive cells were flow-sorted using FACSAria II.

tag: strain

tag: genotype

value: Nrlp-GFP

tag: chip antibody


title: ChIP-seq from embryonic facial prominence (ENCLB547PMP)

description:
https://www.encodeproject.org/experiments/ENCSR008WOQ/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on embryonic 13.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR008WOQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR742ZUI
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB547PMP
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (13.5 days)

value: embryonic facial prominence

value: Embryonic facial prominence from embryonic 13.5 day mice

value: ENCBS764ZZN at ENCODE; https://www.encodeproject.org/ENCBS764ZZN/


title: ChIP-seq from heart (ENCLB038KYL)

description:
https://www.encodeproject.org/experiments/ENCSR007XTC/
***************
biological replicate number: 1
technical replicate number: 1,2,3
description: H3K9me3 ChIP-seq on embryonic 14.5 day mouse heart
experiment encode accession: ENCSR007XTC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR840PFW
encode release date: 2016-02-18
lab: Bing Ren, UCSD
library encode accession: ENCLB038KYL
size range: 300-500

value: ENCBS563AAA at ENCODE; https://www.encodeproject.org/ENCBS563AAA/


title: P10_input

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 12


title: P10_H3K4me3

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 11

value: H3K4me3 (Abcam, ab8580)


title: P28_H3K4me3

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 29


title: P28_K3K27me3

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 28

value: H3K27me3 (Millipore, 07-449)


title: WGBS from forebrain (ENCLB255SGE)

description:
https://www.encodeproject.org/experiments/ENCSR007JSP/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 12.5 day mouse forebrain
experiment encode accession: ENCSR007JSP
assay title: WGBS
assembly: mm10
encode release date: 2016-03-14
lab: Joe Ecker, Salk
library encode accession: ENCLB255SGE
size range: 180-500

value: forebrain

value: tissue

value: Forebrain from 68 embryonic 12.5 day mice

value: embryonic

value: ENCBS617DPG at ENCODE; https://www.encodeproject.org/ENCBS617DPG/


title: P10_K3K27me3

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 10


title: P2_H3K4me3

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 3


title: P2_input

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 4


title: P2_K3K27me3

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 2


title: P28_mDNA_rep3

description: RRBS of flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 28

data_processing:
Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering.
Pass filter reads were adapter trimmed using Trim Galore v0.2.7 (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) prior to bisulfite alignment to the GRCm38 assembly using Genomatix Mapper v3.7.5 on the Genomatix Mining Station (Genomatix, GmBH, Munich Germany). The methylation call files exported from Genomatix were further analyzed using the methylKit package (Akalin et al. 2012) in R.
Genome_build: GRCm38.p1
Supplementary_files_format_and_content: Methylation call file from the Genomatix anlysis export (90_methylation file).

growth_protocol: The retina was dissected from Nrlp-GFP mice at different postnatal stages of development in Hank’s Balanced Salt Solution (HBSS; Life Technologies, NY, USA), followed by dissociation in Accutase (Life Technologies) at 37°C for 10 min with constant agitation. After removing cell clumps by filtration, 4 ml of PBS (GIBCO, Life Technologies) was added to dissociated cells. The cells were collected by centrifugation at 800g for 5 min and re-suspended in 1 ml of PBS. GFP-positive cells were isolated by fluorescence-activated cell sorting (FACS) using FACS Aria II (Becton Dickinson, CA, USA) with a stringent precision setting to maximize the purity of the sorted cells.

extract_protocol:
DNA was extracted by Purelink gDNA isolation kit (Life Tech).
The libraries were constructed as previously described (Gu et al. 2011), with several modifications to optimize the protocol for smaller sample sizes and for sequencing on Illumina platform. Briefly, 50 ng of isolated genomic DNA was digested with 20 U of MspI (New England Biolabs, MA) at 37°C for varied digestion times - 5 min, 10 min, 30 min and 60 min to retrieve diverse length of digested gDNA fragments. TE buffer (10 mM Tris-HCl, pH 8.0 and 1 mM EDTA) (150 ml) and UltraPure phenol/chloroform/isoamyl alcohol (Life Technologies)(200 ml) were added to isolated fragmented gDNA and four samples with varied digestion times were pooled together. Fragmented gDNA in the aqueous phase was purified by ethanol precipitation (100% ethanol, 100 mM NaCl, 20 ng of Glycogen). TruSeq DNA sample preparation kit (Illumina) was then used to construct sequencing libraries with one modification: the use of 1/10 dilution of TruSeq index adapters for to avoid having an access amount of adapter-adapter dimers. Subsequently, bisulfite modification was performed using Epitech kit (Qiagen) on size-selected adapter ligated DNA fragments, and the resulting libraries were amplified for 18 cycles using KAPA Uracil+ 2X polymerase mixture (KAPA Biosystems, MA).

tag: age (days post-natal)

tag: tissue

value: retina

tag: cell type

value: GFP positive retina cells


title: P28_mDNA_rep5


title: P28_mDNA_rep1


title: P10_mDNA_rep4

description: RRBS of flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 10


title: P28_mDNA_rep2


title: P28_mDNA_rep4


title: P10_mDNA_rep3


title: P10_mDNA_rep1


title: P10_mDNA_rep2


title: P2_mDNA_rep1

description: RRBS of flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 2


title: P2_mDNA_rep4


title: P14KO_rep2_seq

description: flow sorted Nrlp-GFP positive cells in Nrl-/- retina at post natal day 14

library_source: transcriptomic

data_processing:
Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering.
The reference assembly GRCm38.p1 with transcript annotation Ensembl 73 was used for alignment and quantitation. Transcript quantitation was accomplished by streaming read alignment from Bowtie2 (Langmead and Salzberg, 2012) to eXpress (Roberts and Pachter, 2013; Roberts et al., 2013).  Bowtie2 alignment settings were used as previously described (Roberts et al., 2013) and eXpress setting –r-stranded was used for directional transcript analysis.  Bias corrected effective counts were used for downstream normalization and differential expression analysis. Read alignments used for viewing in Integrated Genomics Viewer (IGV) (Thorvaldsdottir et al., 2013) were performed using a 2-step alignment strategy employing TopHat2 (Kim et al., 2013) splice junction mapper keeping the alignment with the best alignment score.  Reads were first aligned to the annotation GTF prior to aligning to the genome reference assembly using the default settings with the exception of the following options: -g 1 –library-type fr-firststrand –G <gtf file>.
Effective counts from eXpress were used to filter and to normalize the data via library size correction using the TMM method within the R package edgeR. Prior to normalization, transcripts showing at least 1 Fragment Per Kilobase Per Million (FPKM) from the eXpress output in all replicates of any timepoint/genotype group were kept for further analysis. Normalized counts were used for differential expression analysis, whereas, normalized FPKM values were used for cluster analysis.
Differential expression analysis was performed using limma v3.20.9 to compare Nrl-KO with wild type samples at each time point. A generalized linear model was set up with time and genotype as factors, dispersion estimation performed using the voom function, and appropriate contrast statistics employed using eBayes function. Transcripts having greater than two-fold change and an FDR of <0.05 in any Nrl-KO vs WT comparison at any time point were considered significantly differentially expressed and used for further analysis.
Genome guided de novo transcript assembly was performed to generate a catalog of novel transcripts expressed throughout the development of Nrlp-GFP and Nrlp-GFP;Nrl-KO photoreceptors. Pass filter reads were aligned to GRCm38.p3/Ensembl v78 assembly and annotated using TopHat2 v2.0.11. The de novo assembly was performed with Cufflinks v2.2.1 with the following options to improve the accuracy: –multi-read-correct –frag-bias-correct –GTF-guide. Subsequently, the GTF files generated in the de novo assembly were merged using Cuffmerge. The merged GTF file was compared with Ensembl v78 GTF file using Cuffcompare to identify novel isoforms of known genes and novel transcripts in intergenic regions.
Genome_build: GRCm38.p1 with Ensembl 73
Supplementary_files_format_and_content: Excel files contain tables of count, FPKM, or differential expression analysis results. The Gene Transfer Format (GTF) file contains the entire output of transcripts from the de novo assembly analysis.
Supplementary_files_format_and_content: Seq_eXpress_counts.xlsx: Quantitation output from eXpress of effective counts.
Supplementary_files_format_and_content: Seq_eXpress_fpkm.xlsx: Quantitation output from eXpress of fpkm values.
Supplementary_files_format_and_content: Seq_Norm_fpkm.xlsx: TMM normalized fpkm values.
Supplementary_files_format_and_content: Seq_Analysis.xlsx: Differential expression results from sequencing.
Supplementary_files_format_and_content: Seq_de.novo.eXpress_counts.xlsx: Quantitation output from eXpress of effective counts from de novo assembly.
Supplementary_files_format_and_content: Seq_de.novo.eXpress_fpkm.xlsx: Quantitation output from eXpress of fpkm values from de novo assembly.
Supplementary_files_format_and_content: de.novo.assembly.gtf: GTF of de novo assembly transcripts.

molecule: total RNA

growth_protocol: The retina was dissected from Nrlp-GFP or Nrlp-GFP;Nrl-KO mice at different postnatal stages of development in Hank’s Balanced Salt Solution (HBSS; Life Technologies, NY, USA), followed by dissociation in Accutase (Life Technologies) at 37°C for 10 min with constant agitation. After removing cell clumps by filtration, 4 ml of PBS (GIBCO, Life Technologies) was added to dissociated cells. The cells were collected by centrifugation at 800g for 5 min and re-suspended in 1 ml of PBS. GFP-positive cells were isolated by fluorescence-activated cell sorting (FACS) using FACS Aria II (Becton Dickinson, CA, USA) with a stringent precision setting to maximize the purity of the sorted cells.

extract_protocol:
Total RNA was extracted by Trizol LS (Life Tech).
Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.
Stranded mRNA-seq (dUTP method)

value: Nrlp-GFP;Nrl-/-


title: P14KO_rep1_seq


title: P10KO_rep3_seq

description: flow sorted Nrlp-GFP positive cells in Nrl-/- retina at post natal day 10


title: P10KO_rep1_seq


title: P6KO_rep3_seq

description: flow sorted Nrlp-GFP positive cells in Nrl-/- retina at post natal day 6


title: P2_mDNA_rep2


title: P6KO_rep2_seq


title: P2_mDNA_rep3


title: P28KO_rep2_seq

description: flow sorted Nrlp-GFP positive cells in Nrl-/- retina at post natal day 28


title: P4KO_rep2_seq

description: flow sorted Nrlp-GFP positive cells in Nrl-/- retina at post natal day 4


title: P4KO_rep1_seq


title: P28_rep4_seq


title: P6KO_rep1_seq


title: P2KO_rep1_seq

description: flow sorted Nrlp-GFP positive cells in Nrl-/- retina at post natal day 2


title: P2KO_rep2_seq


title: P28_rep2_seq


title: P28_rep1_seq


title: P10_rep3_seq


title: P10_rep2_seq


title: P10KO_rep2_seq


title: P10_rep1_seq


title: P6_rep2_seq

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 6


title: P6_rep3_seq


title: P14_rep2_seq

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 14


title: P4_rep2_seq


title: P28_rep3_seq

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 28


title: P2_rep2_seq


title: P2_rep1_seq


title: Cbx8 knockdown_MMTV-Myc cells

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description:
Myc_shCbx8_RNAseq_Cuffdiff.txt
MMTV-Myc_shCBX8

data_processing:
Sequencing reads were first quality checked by FastQC (version 0.10.0) and then mapped to the reference genome (mouse mm9) by TopHat (version 1.4.0) using the following parameters: maximum alignment number = 20, mismatch allowed = 2.
Transcripts were assembled by Cufflinks program (version 1.3.0) (Trapnell et al., 2010) with quartile normalization and bias correction functions.
Differential expression analysis was performed by Cuffdiff (version 0.0.7) program with the following parameters: library normalization method = geometric, dispersion estimation = blind, FDR = 0.05, minimum alignment count = 10, bias correction = on.
Genome_build: mm9
Supplementary_files_format_and_content: txt files contain gene expression information (FPKM) in each sample

molecule: polyA RNA

source_name: MMTV-Myc cells

growth_protocol: MMTV-Myc cells were cultured in DMEM/F12 (Cellgro) with 2% FBS, 10μg/ml insulin, 1X glutamine, 10mM HEPES, 1X nonessential amino acids and 1X Penicillin/Streptomycin. MS were cultured in DMEM/F12 (Cellgro) or MEBM (Lonza) with 20ng/ml EGF, 20ng/ml bFGF, 1X Gem21 supplement (Gemini Bio-products) and 1X Penicillin/Streptomycin on Ultra-low attachment plates (Corning) at a density <1X106 cells per 10ml media. MS were dissociated with trypsin into single cells and passaged every 4 days.

extract_protocol:
Total RNA was extracted with the QIAGEN RNeasy Mini Kit
RNA samples were quality checked (RIN score of 8 or higher) using the RNA 6000 Nano chip on a 2100 Bioanalyzer (Agilent). mRNA was then isolated using Sera-Mag oligo-dT beads (Thermo Fisher Scientific), and cDNA library was synthesized by SuperScript II (Invitrogen) with random primers. The cDNA library was quality checked.
Pooled libraries were loaded on high throughput HiSeq 2500 flow cells, using v3 reagents, and sequenced 100nt, single-end.

treatment_protocol: Lentiviral infections with pLKO.1 based Cbx8 shRNAs, 2 days after infection cells were selected with 2ug/ml of puromycin for at least 4 days. Cells were passaged with constant selection under 2ug/ml puromycin.

tag: cell line

value: MMTV-Myc

value: Cbx8 knockdown (sh68)


title: control_MMTV-Myc cells

description:
Myc_shCbx8_RNAseq_Cuffdiff.txt
MMTV-Myc_shScr

value: wild type (shLuc)


title: Bulk cells_MMTV-Myc cells

description:
Myc_bulkvsMS_RNAseq_Cuffdiff.txt
MMTV-Myc_Bulk

value: bulk cells (day 0)

value: wild type


title: P28KO_rep1_seq


title: P14_rep1_seq

value: Nrlp-GFP


title: H3K27me3 ChIP in Cbx8KD_MMTV-Myc cells

description:
MMTV-Myc_shCbx8_H3K27me3
MNase-ChIPed mononucleosome DNA

data_processing:
Sequencing reads were quality checked by FastQC (version 0.10.0) and NGS-QC generator (version 1.5.1).
Sequence reads were then aligned to the NCBI Build 37 mouse genome (mm9) for MMTV-myc cells and human genome (hg19) for MDA-MB-231L cells with Bowtie (version 1.0.0) using the following parameters: seed length (l) = 70 bp, maximum mismatch (n) = 2, suppression (m) = 20, and reported alignments (k) = 1. Read difference between the control and Cbx8 knockdown samples of each ChIP were normalized by random selection of bed tags in the sample with higher reads to match that of the lower read sample (to normalize for read differences between samples).
MACS2 (version 2.1.0) was used to generate Bedgraph files that show fold change enrichment of ChIP over input. Bedgraph files were then converted into BigWig files by BedClip program and uploaded onto UCSC genome browser for visualization and plotting.
SICER-df was used to reveal significantly changed peaks between the control and Cbx8 knockdown MMTV-Myc cells using the following parameters: window size = 50bp, gap size = 400bp, island calling = FDR<5x10-55 (H3K4me3) and FDR<1x10-4 (H3K27ac and H3K27me3), WT vs KD FDR<1x10-8, WT vs KD fold change >1.8. For MDA-MB-231-Luc cells: window size = 50 bp, gap size = 400 bp, island calling = FDR<1x10-55, WT vs KD FDR<2x10-3.
Genome_build: mm9 (MMTV-Myc) or hg19 (MDA-MB-231-Luc)
Supplementary_files_format_and_content: BED files include all the differential peaks calculated by SICER-df
Supplementary_files_format_and_content: BigWig files include the RPKM fold enrichment of each sample over input.

growth_protocol: MMTV-Myc cells were cultured in DMEM/F12 (Cellgro) with 2% FBS, 10μg/ml insulin, 1X glutamine, 10mM HEPES, 1X nonessential amino acids and 1X Penicillin/Streptomycin. MDA-MB-231-Luc cells were cultured in DMEM with 10% FBS and 1X Penicillin/Streptomycin.

extract_protocol:
Chromatin from control (shScr) and shCbx8 tranduced MMTV-Myc cells and MDA-MB-231-Luc cells was digested with micrococcal nuclease (MNase) and used for ChIP with indicated antibodies, essentially as described (Gaspar-Maia et al., 2013). Sequencing libraries were generated and barcoded for multiplexing as previously described (Gaspar-Maia et al., 2013) and resulting libraries were submitted for 100-bp, single-end Illumina sequencing on a HiSeq 2500 instrument.
Total of 10ng MNase-ChIPed mononucleosome DNA was gel extracted for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2500 illumina platform.

treatment_protocol: Lentiviral infections with pLKO.1 based Cbx8 shRNAs,  2 days after infection cells were selected with 2ug/ml of puromycin for at least 4 days. Cells were passaged with constant selection under 2ug/ml puromycin.

value: Cbx8 knockdown

value: anti-H3K27me3 (Millipore, catalog#  07-449, lot# 2194165)


title: H3K4me3 ChIP in control_MMTV-Myc cells

description:
MMTV-Myc_shScr_H3K4me3
MNase-ChIPed mononucleosome DNA

value: anti-H3K4me3 (Abcam, catalog# ab1012, lot# GR187380-1)


title: H3K27ac ChIP in Cbx8KD_MMTV-Myc cells

description:
MMTV-Myc_shCbx8_H3K27ac
MNase-ChIPed mononucleosome DNA

value: anti-H3K27ac (Abcam, catalog# ab4729, lot# GR183919-2)


title: H3K27me3 ChIP in control_MMTV-Myc cells

description:
MMTV-Myc_shScr_H3K27me3
MNase-ChIPed mononucleosome DNA


title: Input control_MMTV-Myc cells

description:
MMTV-Myc_shScr_Input
MNase-ChIPed mononucleosome DNA


title: H3K27ac ChIP in control_MMTV-Myc cells

description:
MMTV-Myc_shScr_H3K27ac
MNase-ChIPed mononucleosome DNA


title: P6_rep1_seq


title: H3K4me3 ChIP in Cbx8KD_MMTV-Myc cells

description:
MMTV-Myc_shCbx8_H3K4me3
MNase-ChIPed mononucleosome DNA


title: 5L

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the human genome (UCSC build hg19) using the TopHat aligner.
Mapped reads were analyzed using the Cufflinks package (using fragment bias and multi-read correction).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file contains FPKM values for each sample.

organism: Homo sapiens

source_name: A375 cell line

extract_protocol:
Total RNA was extracted using RNeasy Qiagen extraction kit according to the manufacturer's instructions.
Libraries were prepared using the mammalian RiboZero magnetic rRNA depletion kit (Epicenter, Madison, WI) following the manufacturer’s protocol.  Five nanograms of RiboZero-treated RNA were used to construct a library using Epicenter’s ScriptSeq v2 RNASeq Library Preparation Kit.

tag: treatment

value: Control


title: 34R


title: 34L


title: 5R


title: P4_rep1_seq

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 4


title: 33R


title: 33L


title: 2L


title: 2R


title: 29L


title: Th17 KO duplicate 1

city: La Jolla

first: Changchun

last: Xiao

state: California

address: 10550 North Torrey Pines Road

department: Immunology & Microbial Science

institute: The Scripps Research Institute

description: F; Not Transduced

data_processing:
Basecalls performed using Illumina bcl2fastq/2.16.0.10
Reads were aligned to Pre-built STAR 2.3.0  indexed Mouse genome, M. musculus UCSC mm10,
Generation of gene counts was performed using Partek® software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.
These data were filtered to exclude transcripts for which the maximum number of reads for all samples was <40 reads.
The mRNA-Seq data was analyzed using R Bioconductor package edgeR [Robinson et al., 2010], using the traditional GLM approach.
The results are first filtered with False Discovery Rate (FDR) >0.15 and then by log Counts Per Million (log2(CPM)) > 4.0.
Genome_build: mm10
Supplementary_files_format_and_content: microsoft excel,RefSeq mRNAs, gene read count.

source_name: Th17 KO

growth_protocol: Control vector- or miR-96-overexpressing T cells and miR-183C+/+ or miR-183C-/- T cells were cultured under the Th17(23) condition and were harvested on day 4-5. Cell sorting was performed using a FACSAria cell sorter to obtain GFP-positive cells. Total RNA was extracted using the TRIzol reagent, enriched for polyA-containing RNAs and submitted to RNA-Seq.

extract_protocol:
RNA was extracted using Trizol reagent.
RNAseq libraries were prepared using 500ng - 1.0 ug total RNA with the polyA selection module of the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following manufacturer’s protocol.

tag: strain background

tag: genotype/variation

value: Th17 T cell


title: Mammosphere cells day 20_MMTV-Myc cells

description:
Myc_bulkvsMS_RNAseq_Cuffdiff.txt
MMTV-Myc_D20_MS

value: mammosphere cells (day 20)


title: 19R

value: vemurafenib


title: 26L


title: 26R


title: 16R


title: 19L


title: 16L


title: 40_1000_A

city: los angeles

first: matteo

last: pellegrini

address: 610 charles young drive east

institute: UCLA

description: replicate A

data_processing:
genome index building: a synthetic genome comprised of lambda genomic DNA and 15 telomeric repeats (heptad: TTTAGGG) was built using BS-Seeker2 v2.0.8 - Sept 5, 2014
reads alignment: reads were aligned using BS-Seeker2 v2.0.8 - Sept 5, 2014 with default parameters
methylation call: methylation for each single cytosine was calculated using BS-Seeker2 v2.0.8 - Sept 5, 2014
Genome_build: lambda gemone: GeneBank Accession J02459
Supplementary_files_format_and_content: wig files: UCSC format
Supplementary_files_format_and_content: CGmap files: https://github.com/BSSeeker/BSseeker2

molecule: other

organism: synthetic construct

source_name: annealed oligos

extract_protocol:
Equal amounts of oligos containing the sequences (TTTAGGG)15 and (CCCTAAA)15 were mixed, heated to 98ºC for 10 minutes and allowed to cool down at room temperature for 15 minutes. Then, the annealed DNA fragments were gel purified and their quality assessed using the D1000 assay on the TapeStation 2200 (Agilent Technologies).
End repair, A-tailing and adapter ligation was performed on the annealed oligos according to the Illumina TruSeq Nano kit protocol (cat # 15041759, Illumina, CA).  Adapter-ligated oligos were denatured in the presence of bisulfite (Zymo Lightning MagPrep, cat # D5046, Zymo Research, CA) at 98°C for 8 minutes and two temperatures were used for the conversion step: 54°C (manufacturer’s suggested temperature) and 40°C. Desulfonation was performed according to manufacturer’s instructions. Converted DNA was amplified using MyTaq Mix (Bioline, Taunton, MA,) and Illumina TruSeq PCR Primer Cocktail according to the following protocol: initial denaturation at 98°C for 30 s; 12 cycles of 98°C for 15 s, 60°C for 30 s, 72°C for 30 s; final extension at 72°C for 5 min. AMPure XP beads were used to clean up the final PCR reactions before sequencing.

value: synthetic genome comprised of lambda other and 15 telomeric repeats (heptad:TTTAGGG)

value: 1:1000 dilution

value: bisulfite treatment 40C


title: 40_1000_B

description: replicate B


title: 54_1000_A

description: replicate A

value: bisulfite treatment 54C


title: 40_100_A

description: replicate A

value: 1:100 dilution


title: 29R


title: 40_100_B

description: replicate B


title: 54_100_B

description: replicate B


title: 54_100_A

description: replicate A


title: 54_1000_B

description: replicate B


title: Input control_MDA-MB-231-Luc cells

description:
MDA-MB-231-Luc_shScr_Input
MNase-ChIPed mononucleosome DNA

source_name: MDA-MB-231-Luc cells


title: H3K4me3 ChIP in CBX8KD_MDA-MB-231-Luc cells

description:
MDA-MB-231-Luc_shCBX8_H3K4me3
MNase-ChIPed mononucleosome DNA

value: CBX8 knockdown


title: miR-372 replicate A

city: Stockholm

first: Janne

last: Lehtiö

state: Stockholm

address: SciLifeLab

department: Department of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
1. Mapping: Reads were mapped with Tophat/2.0.4 to the Human genome assembly, build GRCh37.
2. Merging: Bamfiles from samples run on different lanes were merged with samtools.
3. Sorting and Marking duplicates: Merged bam files were sorted and duplicates removed using picard-tools/1.29.
4. Counts for genes: Gene counts were generated using htseq/0.6.1 on bam files with duplicates included
Genome_build: GRCh37
Supplementary_files_format_and_content: read counts

source_name: U1810 NSCLC cell line

growth_protocol: Cells were cultured in RPMI-1640 AQmedium supplemented with 10% FBS and 1% Penicillin Streptomycin

extract_protocol:
RNEasy
TruSeq Stranded mRNA

treatment_protocol: 24h after seeding cells were transfected with miR-372-3p mimic or non-targeting siRNA control using RNAiMAX. 30h post transfection cells were harvested and total RNA was extracted.

value: NSCLC

value: miR-372-3p mimic


title: Control replicate A

description: CTRLA

value: non-targeting control siRNA


title: miR-372 replicate B


title: H3K4me3 ChIP in control_MDA-MB-231-Luc cells

description:
MDA-MB-231-Luc_shScr_H3K4me3
MNase-ChIPed mononucleosome DNA

value: wild type


title: 5504C-Brca1mp_p53mp_CRC-1

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

description: processed data file: 5504CD_FPKM_table.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc), and contaminated adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/project/trim_galore).
Paired-end sequenced reads were aligned to the mouse reference genome (mm9 assembly) using TopHat.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from homogenized mammary glands using Trizol (Invitrogen) and 300μl chloroform (Thermo Fisher Scientific, Waltham, MA) for phase separation, precipitated with 650μl isopropanol (Thermo Fisher Scientific) and purified using an RNeasy Plus Mini Kit (Qiagen, Valencia, CA).
Polyadenylated (polyA) RNA was isolated from 1ug total RNA and converted to cDNA using SuperScript II (Invitrogen). A TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) was used to generate sequencing libraries according to the manufacturer’s instructions. Libraries were independently sequenced by the paired-end method using HiSeq 2000 (Illumina).

tag: gender type

value: nulliparous female

value: Brca1fl 11/WT/MMTV-Cre/Trp53-/+

value: mammary glands


title: 5504D-Brca1mp_p53mp_EpiC-2


title: 5504D-Brca1mp_p53mp_CRC-2


title: 5504D-Brca1mp_p53mp_Cancer-2


title: 5504C-Brca1mp_p53mp_Cancer-1


title: miR-372 replicate C


title: AlloBrca1mp_p53mp_EpiC-4C

description: processed data file: Cuffnorm_FPKM_table.txt

value: Host:NU (NCr)-Foxn1nu/Cells:C57Bl/6

value: Allograft generated in mammary gland


title: 5504C-Brca1mp_p53mp_EpiC-1


title: AlloBrca1mm_p53mp_CRC-1


title: WGBS from liver (ENCLB502JLY)

description:
https://www.encodeproject.org/experiments/ENCSR033PGF/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 11.5 day mouse liver
experiment encode accession: ENCSR033PGF
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB502JLY
size range: 180-500

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (11.5 days)

extract_protocol:
general protocol: https://www.encodeproject.org/documents/665c8f16-3724-4ab7-aa29-688f396bcd4f/@@download/attachment/Ecker_Protocol_Summary.png
general protocol: https://www.encodeproject.org/documents/862389c9-38b6-4e76-8b84-d82fb9a4c6cf/@@download/attachment/Ecker_Replication_Summary.png
extraction method: Qiagen DNeasy Blood and Tissue Kit
general protocol: https://www.encodeproject.org/documents/9d5f346e-88d3-45e2-b28a-2b26f537490f/@@download/attachment/Ecker_Methyl_protocol_v030114.pdf

value: liver

value: tissue

tag: description

value: Liver from pooled embryonic 11.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS522YOW at ENCODE; https://www.encodeproject.org/ENCBS522YOW/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: AlloBrca1mp_p53mp_EpiC-5A


title: AlloBrca1mp_p53mp_CRC-11C


title: AlloBrca1mm_p53mp_CRC-12


title: AlloBrca1mp_p53mp_CRC-10C


title: Control replicate C

description: CTRLC

value: NSCLC


title: AlloBrca1mm_p53mp_CRC-2


title: AlloBrca1mp_p53mp_CRC-10B


title: Control replicate B

description: CTRLB

value: non-targeting control siRNA


title: AlloCYP19A1_p53mp_EpiC-7B


title: AlloCYP19A1_p53mp_CRC-6C


title: H1_SNE2

city: Chicago

first: Alex

last: Ruthenburg

address: 920 E. 58th Street

institute: University of Chicago

data_processing:
Tophat2 was used to align reads to the genome.
Cuffdiff was used to quantify and determine differential abundance between fractions
Genome_build: hg38
Supplementary_files_format_and_content: gene name, location, and FPKM in both SNE and CPE

source_name: H1 hESC

extract_protocol:
Extraction of RNA was performed as in Werner & Ruthenburg, Cell Reports. 2015
Illumina NEBnext ultra stranded

value: H1 hESC

tag: molecule

value: soluble nuclear RNA


title: Brca1mm_p53mp_CRC

value: nulliparous female


title: H1_CPE2

value: chromatin RNA


title: Brca1mp_p53mp_EpiC

value: Brca1fl 11/WT/MMTV-Cre/Trp53-/+

value: mammary glands


title: H1_SNE1


title: Brca1mm_p53mp_EpiC


title: H1_CPE3


title: CYP19A1_p53mp_EpiC


title: H1_CPE1


title: K562_plusHemin_SNE1

source_name: K562 cell line

value: plus 50 µM Hemin


title: K562_plusHemin_SNE2


title: Brca1mp_p53mp_CRC


title: K562_plusHemin_CPE2


title: K562_SNE2


title: K562_plusHemin_CPE1


title: K562_SNE3


title: K562_CPE3


title: K562_CPE2


title: K562_CPE1


title: Th17 KO duplicate 2

description: H; Not Transduced

value: Th17 T cell


title: Th17 WT duplicate 2

description: G; Not Transduced

source_name: Th17 WT


title: Th17 Control duplicate 2

description: C; Transduced with control vector

source_name: Th17 Control

value: control vector-expressing


title: H1_SNE3


title: Th17 WT duplicate 1

description: E; Not Transduced


title: Th17 miR O.E. duplicate 1

description: B; Transduced with miR-96

source_name: Th17 miR O.E.


title: Th17 miR O.E. duplicate 2

description: D; Transduced with miR-96


title: inducible Treg (iTreg) cells, 1

data_processing:
Basecalls performed using CASAVA version 1.8
FastX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit) for conversion to FASTA format, removing the adaptors, collapsing the identical sequences into uniquely tagged reads with number of counts for each tag, and discarding reads shorter than 18 nucleotide in length.
Reads were aligned to Pre-built Bowtie indexed Mouse genome, M. musculus UCSC mm9, using Bowtie short read aligner (http://bowtie-bio.sourceforge.net/index.shtml).
known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) ).
Genome_build: mm9
Supplementary_files_format_and_content: microsoft excel, known and novel miRNAs, read count, mature miRNA sequence, precursor sequence, and other miRDeep2 parameters

source_name: spleen and lymph node

extract_protocol:
RNA was harvested using Trizol reagent.
Approximately 1 µg of total RNA was used for Next Generation Sequencing following the Illumina protocol, TruSeq_SmallRNA_SamplePrep_Guide_15004197_C.pdf, using 12 cycles of PCR. The prepared library was then loaded onto an Illumina HiSeq v2 single-read flowcell, standard cluster generation was performed on a Cbot and sequenced for 40 bases of the insert and 7 bases of the index read using standard HiSeq sequencing reagents. Reads were then processed using CASAVA 1.8 and demultiplexed based on index sequences.

value: spleen and lymph node


title: CYP19A1_p53mp_CRC


title: Th17 Control duplicate 1

description: A; Transduced with control vector


title: Th17 cells, 2


title: Th17 cells, 1


title: Th1 cells, 2

value: Ifngyfp


title: inducible Treg (iTreg) cells, 2


title: Naïve CD4 T cells, 2

value: wild type


title: K562_SNE1


title: Alp13-del_G2 arrest_mRNA-seq_1

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

institute: KAIST

data_processing:
Prepared libraries were sequenced on a HiSeq2500 with single-end method (50-bp reads).
ChIP-seq reads were aligned to the S.pombe genome (ASM294v2) using NovoAlign (Novocraft technologies, Malaysia).
Significantly enriched peaks were identified using Homer and mapped reads were quantified using DeepTools and bwtool.
For mRNA-seq analysis, raw reads were aligned to S. pombe genome (ASM294v2) using STAR aligner.
The number of mapped reads was further analyzed using HOMER and DESeq
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: RNA-seq : tab-delimited text files include RPKM values for each Sample, ChIP-seq : bed files including peak position

organism: Schizosaccharomyces pombe

source_name: yeast cells

growth_protocol: Histone trunover experiment : Grow up cells in 4% sucrose PMG medium at 37°C  ChIP-seq and mRNA-seq : Grow up cells in  YES medium at 37°C

extract_protocol: ChIP-seq libraries for genome-wide sequencing were prepared using 10 ng of input DNA or 1 to 10 ng of eluted ChIP DNA using NEXTflex ChIP-Seq kit, Bioo Scientific (cat.5143).  mRNA-seq libraries were made using NEXTflexTM Rapid RNA-Seq kit (cat. 5138) from isolated mRNA.


title: Set2-del_G2 arrest_mRNA-seq_2


title: Alp13-del_G2 arrest_mRNA-seq_2


title: Naïve CD4 T cells, 1


title: Set2-del_G2 arrest_mRNA-seq_1


title: WT_G2 arrest_mRNA-seq_2


title: WT_G2 arrest_mRNA-seq_1


title: Alp13-del_H4K20me3 ChIP-seq 2

tag: antibody


title: Alp13-del_H4K20me3 ChIP-seq 1


title: Alp13-del_H4K20me1 ChIP-seq 1


title: Alp13-del_H3K56Ac ChIP-seq 2


title: Set2-del_H4K20me3 ChIP-seq 2


title: Alp13-del_H3 ChIP-seq 2


title: Alp13-del_H3K56Ac ChIP-seq 1


title: Set2-del_H4K20me3 ChIP-seq 1


title: Set2-del_H4K20me1 ChIP-seq 1


title: Th1 cells, 1

tag: strain


title: Set2-del_H3K56Ac ChIP-seq 1

tag: genotype


title: Set2-del_H3K56Ac ChIP-seq 2


title: Set2-del_H3 ChIP-seq 2


title: WT_H4K20me3 ChIP-seq 1


title: WT_H4K20me1 ChIP-seq 2


title: WT_H4K20me3 ChIP-seq 2


title: WT_H3K56Ac ChIP-seq 1


title: WT_H3 ChIP-seq 2


title: WT_H4K20me1 ChIP-seq 1


title: histone turnover_H3 ChIP-seq 2


title: Alp13-del_H4K20me1 ChIP-seq 2


title: histone turnover_H3 ChIP-seq 1


title: Set2-del_H4K20me1 ChIP-seq 2


title: WT_H3K56Ac ChIP-seq 2


title: histone turnover_Flag ChIP-seq 1

value: anti-Flag


title: histone turnover_Flag ChIP-seq 2


title: Alp13-del_H3 ChIP-seq 1


title: Dlip3

status: Public on Jun 20 2016

city: Los Angeles

first: Edward

middle: M

last: De Robertis

address: 615 Charles E. Young Drive South

department: Biological chemistry

institute: HHMI/UCLA

data_processing:
After sequencing, adaptors were first trimmed from the RNA reads and RNA reads of low quality filtered. The clean RNA reads were mapped using Tophat (Version 2.09, default parameters) against the Xenopus laevis JGI9.1 (Xenbase) transcript sequences.
Transcripts counts were normalized using DESeq package in R. RPKM (Reads Per Kilobase per Million mapped reads) for transcripts was calculated in R.
Human gene names were assigned to transcripts using an annotation file obtained by blasting the JGI9.1 peptide sequences to human reference protein sequences.
Genome_build: Xenbase Xenopus Laevis J-strain Version 9.1
Supplementary_files_format_and_content: Excel tables include RPKM and fold-induction values of genes for each sample.

organism: Xenopus laevis

source_name: embryo, dorsal lips

growth_protocol: The embryos were cultured in 0.1x Marc's Modified Ringers (MMR) and staged according to Nieuwkoop and Faber (1967).

extract_protocol:
RNA from wild type whole embryos or dorsal lips or ventral lips was isolated with an Absolutely RNA miniprep Kit (Agilent).
Libraries were constructed with the Illumina TruSeq RNA Library Preparation Kit V2 according to manufacturer's protocol. Briefly, 1 µg total RNA from stage 10.5 wild type embryos, dorsal lips or ventral lips was used for input RNA. Then mRNA was purified through polyA+ selection. After fragmentation of the mRNA, first strand and second strand synthesis, double strand cDNA (ds cDNA) was obtained. The ds cDNA was then further processed for A-tailing, end repair and ligation of appropriate adaptors. Finally, the ds cDNA with adaptors was amplified by PCR to generate libraries. After measurement of the length and concentration of the libraries by Bioanalyser and Qubit, the libraries were sent for sequencing on Illumina Hi-Seq 2000 using standard methods to generate 100-bp single end reads by the Broad Stem Cell Research Center at UCLA.

treatment_protocol: Dorsal and ventral lips were dissected at stage 10.5 in 1x Barth's solution.

tag: strain/background

value: Nasco

tag: developmental stage

value: dorsal lips


title: Vlip2

source_name: embryo, ventral lips

tag: tissue

value: ventral lips


title: Dlip2


title: WE

source_name: embryo, whole

value: whole embryo


title: Dlip1


title: SGC shSCRAM Rep 2

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: Replicate 2

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the human genome (G1k V37) using tophat2 and bowtie2
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genes with a false discovery rate below 0.05 and a fold‐change greater than 2 were considered significantly differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of normalised expression values for all Samples

source_name: MV4;11 cell line

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with 20% fetal calf serum, penicillin (100 units/mL) and streptomycin (100 ug/mL)

extract_protocol:
RNA was prepared using the Qiagnen RNeasy kit
TruSeq RNA Sample Preparation protocol (Illumina)

treatment_protocol: Cell lines were transduced with a BRD4 or scramble shRNA with DMSO or 5uM of SGC0946

value: peripheral blood

tag: cell type

value: macrophage


title: Set2-del_H3 ChIP-seq 1


title: SGC shSCRAM Rep 1

description: Replicate 1

tag: cell line


title: SGC shBRD4 Rep 3

description: Replicate 3


title: DMSO shSCRAM Rep 3

description: Replicate 3


title: SGC shBRD4 Rep 1

description: Replicate 1


title: DMSO shSCRAM Rep 1

description: Replicate 1


title: DMSO shSCRAM Rep 2

description: Replicate 2


title: WT_H3 ChIP-seq 1


title: SGC shBRD4 Rep 2

description: Replicate 2


title: DMSO shBRD4 Rep 3

description: Replicate 3


title: DMSO shBRD4 Rep 2

description: Replicate 2


title: I-BET + SGC0946 Rep 2

description: Replicate 2

extract_protocol:
Total RNA was isolated from with TRIzol® reagent
TruSeq RNA Sample Preparation protocol (Illumina)

treatment_protocol: Cell lines were grown in 0.1% DMSO, 500nM of I-BET151 and/or 5uM of SGC0946 and labelled for 60 minutes with 200μM 4sU at the end of inhibitor treatment


title: I-BET + SGC0946 Rep 1

description: Replicate 1


title: Vlip3


title: DMSO shBRD4 Rep 1

description: Replicate 1


title: SGC0946 treated Rep 1

description: Replicate 1


title: HDMEC_P1

city: Delhi

first: Debarka

last: Sengupta

state: Delhi

address: IIIT Delhi, Okhla Phase 3

department: Computational Biology and Computer Science

country: India

institute: Indraprastha Institute of Information Technology

data_processing:
BAM files produced using TopHat v1.4.1 with hg19 as  the reference genome.
FPKM values are obtained using cufflinks v2.0.2.
The refseq genes are tracked for analysis.
Genome_build: hg19
Supplementary_files_format_and_content: The .xlsx file contains the FPKM table of all samples involved in this study.

source_name: Dermal microvasculature

extract_protocol:
Single cell clusters were lysed using SMARTer Ultra Low RNA Kit (Clontech Laboratories). Whole tissue and cell lines RNA was extracted using RNeasy mini kit (Qiagen). RNA from LCM samples was extracted using RNAqueous-Micro Total RNA Isolation Kit (Ambion)
cDNA was synthesised from single cell clusters, 10 pg of whole tissue, 10pg laser-dissected endothelial cells or 10pg primary endothelial cell RNA. To this end, we used the SMARTer Ultra Low RNA Kit (Clontech Laboratories) and long-distance PCR (LDPCR), for 25 cycles, 18, 18 cycles and 18 cycles, respectively. For each sample, cDNA was sheared using the Adaptive Focused Acoustics system (Covaris). Libraries were constructed using NEBNext DNA Library Prep Master Mix Kit (New England Biolabs). All libraries were barcoded using unique indexes and pooled for RNA sequencing

tag: diagnosis

value: normal

value: Dermal microvasculature

tag: sample type

value: Primary cells from culture

tag: patient

tag: patient treatment status


title: P21_lcm_tumor

source_name: Colorectal tumor microvasculature

value: colorectal cancer

value: Colorectal tumor microvasculature

value: Laser-capture microdissected sample

value: Patient 21

value: Treatment-naïve


title: Vlip1

tag: genotype/variation


title: HPrMEC_P1

source_name: Prostate microvasculature

value: Prostate microvasculature


title: SGC shSCRAM Rep 3

description: Replicate 3


title: P21_lcm_normal

source_name: Colonic mucosa microvasculature

value: Colonic mucosa microvasculature


title: DMSO Rep 2

description: Replicate 2


title: I-BET treated Rep 1

description: Replicate 1


title: P20_lcm_tumor

value: Patient 20


title: DMSO Rep 1

description: Replicate 1


title: P20_lcm_normal


title: I-BET treated Rep 2

description: Replicate 2


title: P19_lcm_metastasis

source_name: Colorectal metastasis microvasculature

value: Colorectal metastasis microvasculature

value: Patient 19


title: PA1 poly(A)- RNA-seq

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

data_processing:
Basecalling using Illumina Casava1.8.2 software.
Map to human genome hg19 using Tophat (v 2.0.9).
Bam to Bedgraph using genomeCoverageBed.
Bedgraph to bigwig using UCSC bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: PA1 cells

growth_protocol: PA1 cells were maintained on plates coated with Matrigel (BD Biosciences) in either defined mTeSR medium (StemCell Technologies Inc.) or conditioned medium (CM) with irradiated mouse embryo fibroblasts supplemented with 4 ng/mL human Basic Fibroblast Growth Factor (bFGF).

extract_protocol:
Total RNAs were prepared using Trizol Reagent and treatment with DNase I. 20μg of total RNAs were separated into polyadenylated and nonpolyadenylated fraction by oligo(dT) magnetic beads (Invitrogen). Ribosomal RNAs were further depleted in nonpolyadenylated fraction by using RiboMinus kit (Invitrogen) to get the poly(A)-/ribo- RNA population. Poly(A)-/ribo- RNAs were further incubated with 5U of RNase R (Epicentre) for 3h at 37℃ and then were subjected to Trizol extraction (Invitrogen).
An aliquot of poly(A)-/ribo- enriched and RNase R digested RNA was used for library preparation with Illumina TruSeq Stranded Total RNA HT Sample Prep Kit (P/N 15031048), and then subjected to 1x100 deep sequencing with Illumina HiSeq 2000.

tag: rna population

value: poly(A)-


title: PA1 poly(A)-/RNaseR RNA-seq

value: poly(A)-/RNaseR


title: PA1 poly(A)+ RNA-seq

value: poly(A)+


title: RANK-negative 4

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Image analysis was performed by the HiSeq Control Software (HCS) v2.2.38 and Real Time Analysis (RTA) v1.18.61. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Reads were aligned to the human genome by Rsubread version 1.16.1
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: hg19 (build 37.2)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapped to that gene

source_name: Normal human breast (wild-type)

extract_protocol:
FACS sorted cells were lysed for RNA preparation using the QIAGEN RNEasy plus micro-kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fresh breast tissue

tag: immunophenotype

value: luminal progenitor

tag: cell population

value: RANK-negative


title: HUVEC_P1

source_name: Humbilical vein

value: normal

value: human umbilical vein

value: Primary cells from culture


title: P19_lcm_tumor

value: colorectal cancer

value: Colorectal tumor microvasculature

value: Laser-capture microdissected sample


title: P19_lcm_normal

value: Treatment-naïve


title: P18_lcm_tumor

value: Patient 18


title: SGC0946 treated Rep 2

description: Replicate 2

value: peripheral blood

value: macrophage


title: RANK-negative 3


title: P10_lcm_tumor

value: Patient 10


title: RANK-positive 1

value: RANK-positive


title: P08_lcm_normal

value: Colonic mucosa microvasculature

value: Patient 08


title: P01_lcm_tumor

value: Patient 01


title: RANK-positive 3

value: fresh breast tissue

value: luminal progenitor


title: P08_lcm_tumor


title: P21_tissue_tumor

source_name: Colorectal tumor

value: Colorectal tumor

value: Whole tissue

value: Patient 21


title: P10_lcm_normal

value: normal


title: P01_lcm_normal


title: RANK-negative 2

value: RANK-negative


title: P21_tissue_normal

source_name: Colonic mucosa

value: Colonic mucosa


title: RANK-positive 2


title: P18_lcm_normal

value: Laser-capture microdissected sample

value: Treatment-naïve


title: RANK-positive 4


title: RANK-negative 1


title: ES_H31_6h_2

city: Cambridge

first: Aimee

last: Deaton

state: MA

address: 360 Binney St

institute: Amgen Inc

description: time-ChIP 6h timepoint

data_processing: Reads were mapped to mm9 genome using bowtie. Where tags had 5 or more reportable alignments, one was reported at random. Genomic positions with the numbers of mapped tags above the significance threshold of z-score = 7 were identified as anomalous, and the tags mapped to such positions were discarded. The genome was divided into 1kb bins and, for each sample, the number of tags per bin was calculated as reads per million to normalize for library size. Data for each time point was then input subtracted. For each 1kb bin, turnover index (TI) was calculated by fitting the number of reads for each time point to a simple linear regression model. A Kendall rank correlation test was used to assess how well points fit the linear model. The slope of the line fitted by linear regression was weighted by multiplying by 1-p-value from the Kendall test. The sign of the slope was reversed such that positive TI values represented high turnover. The mean H3.3 TI of three biological replicates was used for further analysis. Genome Build: mm9.

source_name: ESC time-ChIP 6h timepoint

growth_protocol: ESCs were maintained on mitomycin-C inactivated embryonic fibroblast feeders in DMEM supplemented with 15% fetal bovine serum and 1000U/ml of leukemia inhibitory factor. NSCs were derived by injecting H3.3_SNAP ESCs into blastocysts, harvesting E13.5 embryos and deriving NSCs from embryonic brains. NSCs were maintained on poly-l-ornithine coated plates in DMEM:F12 containing B-27 and N-2 supplements (Gibco) and EGF+FGF-2 (10ng/ml).

extract_protocol:
Cells were harvested and nuclei isolated. Nuclei were digested with 120-140U MNase in the presence of 3mM CaCl2 for 20min at 25°C. Reactions were stopped and the MNase digested chromatin was centrifuged at 12,000g for 5min. The resulting supernatant was added to 15µl streptavidin magnetic beads and incubated for 1h at 4°C. Beads were washed and DNA eluted and purified according to standard protocols.
Sequencing libraries were prepared as described in Bowman et al. (Bowman et al., 2013).

treatment_protocol: 48h (ESCs) or 72h (NSCs) prior to labeling, H3.3_SNAP was induced with 500ng/ml doxycycline (H3.1_SNAP was induced with 50ng/ml doxycycline). For labeling, 0.5-2x108 cells were incubated in 500µl complete medium supplemented with 10µM CP-Biotin (NEB) for 40min at 37°C then washed twice. Cells were then resuspended in 10ml complete medium and incubated for 20min at 37°C to remove any unbound CP-biotin. After a final wash, one-fifth of the labeled cells were harvested as the 0h time point and the rest plated for harvest at 3h, 6h or 12h.

value: ESC

value: A2lox.Cre (derived from E14)

tag: replicate


title: ES_H31_12h_2

description: time-ChIP 12h timepoint

source_name: ESC time-ChIP 12h timepoint


title: P20_tissue_tumor

value: colorectal cancer

value: Patient 20


title: ES_H31_0h_2

description: time-ChIP 0h timepoint

source_name: ESC time-ChIP 0h timepoint


title: P19_tissue_metastasis

source_name: Colorectal ovarian metastasis

value: Colorectal ovarian metastasis

value: Patient 19


title: ES_H31_inp_2

description: time-ChIP input

source_name: ESC time-ChIP input (for replicate 2)


title: ES_H31_12h_1

description: time-ChIP 12h timepoint


title: ES_H31_3h_2

description: time-ChIP 3h timepoint

source_name: ESC time-ChIP 3h timepoint


title: ES_H31_6h_1

description: time-ChIP 6h timepoint


title: P19_tissue_tumor


title: P19_tissue_normal


title: P18_tissue_tumor

value: Patient 18


title: P20_tissue_normal


title: P18_tissue_normal


title: ES_H31_0h_1

description: time-ChIP 0h timepoint


title: P08_tissue_tumor

value: Patient 08


title: ES_H31_3h_1

description: time-ChIP 3h timepoint


title: P10_tissue_normal

value: Patient 10


title: P08_tissue_normal


title: DMSO shSCRAM Rep 2

description: Replicate 2

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the mouse genome (mm10) using tophat2 and bowtie2
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genes with a false discovery rate below 0.05 and a fold‐change greater than 2 were considered significantly differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of normalised expression values for all Samples

source_name: c-Kit+ MLL-AF9

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with 20% fetal calf serum, penicillin (100 units/mL), streptomycin (100 ug/mL), amphotericin B (250ng/mL) and gentamycin (50 ug/mL)

treatment_protocol: Cell lines were transduced with a BRD4 or scramble shRNA with/without DMSO or 5uM of SGC0946

value: bone marrow

value: c-Kit+ bone marrow haematopoietic progenitors transduced with MLL-AF9

tag: shRNA

value: scramble

tag: treatment

value: DMSO


title: P01_tissue_tumor_superficial

value: Colorectal tumor

value: Whole tissue

value: Patient 01


title: SGC shSCRAM Rep 1

description: Replicate 1

tag: strain


title: ES_H33_HA_inp

source_name: ESC input for HA ChIP

tag: antibody

value: non


title: ES_H31_inp_1

description: time-ChIP input

source_name: ESC time-ChIP input (for replicate 1)

value: ESC


title: P01_tissue_tumor_deep

value: Treatment-naïve


title: shBRD4 Rep 2

description: Replicate 2


title: ES_H33_HA

source_name: ESC HA ChIP

value: A2lox.Cre (derived from E14)

value: ChIP with anti-HA (Abcam, ab9110)


title: shBRD4 Rep 3

description: Replicate 3


title: shBRD4 Rep 1

description: Replicate 1


title: shSCRAM Rep 1

description: Replicate 1


title: P01_tissue_normal

value: normal

value: Colonic mucosa


title: NS_H33_12h_3

source_name: NSC time-ChIP 12h timepoint

value: NSC

tag: time point


title: NS_H33_6h_3

source_name: NSC time-ChIP 6h timepoint


title: P01_tissue_tumor_center

value: colorectal cancer

tag: tissue


title: NS Ring1b

description: Chromatin immunoprecipitation for Ring1b

data_processing:
Reads were mapped to mm9 genome using BWA and filtered for uniquely mapped reads. PCR duplicates were removed.
To determine regions of tag enrichment, tag counts were analyzed in 1 Kb window sliding with the step of 200 bp. Statistical significance of enrichment of ChIP vs input counts was assessed using negative binomial distribution. Adjacent significantly enriched windows separated by 1 Kb or less were merged into regions of significant enrichment.

source_name: NSC Ring1b ChIP

growth_protocol: J1 ESCs were maintained on mitomycin-C inactivated embryonic fibroblast feeders in DMEM supplemented with 15% fetal bovine serum and 1000U/ml of leukemia inhibitory factor.  NSCs were derived by in vitro differentiation of J1 ESCs and maintained on gelatin in NS media + 10ng/ml EGF and FGF as described in Pollard et al. (2006).

extract_protocol:
Cells were harvested and MEFs depleted from ESC cultures. ESCs and NSCs were crosslinked in 1% formaldehyde for 10 minutes at room temperature. ChIP was carried out as described in Illingworth et al. (2015). Briefly, cells were lysed and sonicated to an average fragment length of 250bp using a Qsonica. Chromatin was incubated with protein A dynabeads pre-bound with antibody overnight at 4C. Beads were washed and DNA eluted.
Sequencing libraries were prepared as described in Bowman et al. (Bowman et al., 2013).

treatment_protocol: standard growth conditions

tag: cell type

value: anti-RNF2 (Bethyl, A302-869A)


title: ES Ring1b

source_name: ESC Ring1b ChIP


title: NS input Ring1b

description: input DNA for Chromatin immunoprecipitation

source_name: NSC input for Ring1b ChiP


title: shSCRAM Rep 2

description: Replicate 2

value: bone marrow


title: NS_H33_3h_3

source_name: NSC time-ChIP 3h timepoint


title: shSCRAM Rep 3

description: Replicate 3

value: c-Kit+ bone marrow haematopoietic progenitors transduced with MLL-AF9


title: SGC shSCRAM Rep 2

description: Replicate 2

value: scramble


title: ES input Ring1b

source_name: ESC input for Ring1b ChIP


title: P20_CTM16

source_name: TECC/CTM

value: TECC/CTM

value: Single cell cluster

value: Patient 20


title: P21_CTM11

value: Patient 21


title: NS_H33_0h_3

source_name: NSC time-ChIP 0h timepoint


title: NS_H33_inp_2

source_name: NSC time-ChIP input (for replicates 2 and 3)

value: input


title: P20_CTM15


title: P20_CTM14


title: ES Ezh2

description: Chromatin immunoprecipitation for Ezh2

source_name: ESC ChIP for Ezh2

value: ESC

value: anti-Ezh2(D2C9) (Cell Signaling, 5246S)


title: DMSO shSCRAM Rep 1

description: Replicate 1

value: DMSO


title: NS_H33_12h_2

value: A2lox.Cre (derived from E14)


title: NS input

source_name: NSC input for ChIP (H3K27me3)


title: ES H3K27me3

description: Chromatin immunoprecipitation for H3K27me3

source_name: ESC ChIP for H3K27me3

value: anti-H3K27me3 (Millipore, 07-449)


title: ES Cbx2

description: Chromatin immunoprecipitation for Cbx2

source_name: ESC ChIP for Cbx2

value: anti-Cbx2 (Santa Cruz, sc-19297)


title: ES input

source_name: ESC input for ChIP (H3K27me3, Cbx2, Ezh2)


title: NS H3K27me3

source_name: NSC ChIP for H3K27me3

value: NSC


title: P19_CTM2

value: colorectal cancer

value: Patient 19

value: Treatment-naïve


title: P18_CTM6

value: Patient 18


title: NS_H33_6h_2


title: GCB RNA-seq_r2

first: Salvatore

last: Loguercio

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

description:
GCB RNA-seq, replicate 2
mGCB_H132

data_processing:
Raw data were aligned to the mouse reference genome (mm9) using TopHat 2.1.0 and Bowtie2 2.2.6.
Reads were counted with HTseq (parameters: -s no -m intersection-nonempty)
A quasi-likelihood negative binomial generalized log-linear model was fitted to count data using the R/Bioconductor package EdgeR (v. 3.8.6) with simple design
Differentially expressed genes were called using a nominal FDR threshold of 0.1
Genome_build: mm9
Supplementary_files_format_and_content: format: tsv | content: matrix of raw read counts (genes x samples) as generated by Htseq (gene annotation: UCSC mm9)

source_name: GC B cells

growth_protocol: Bone marrow and spleen cells were isolated from 6- to 14-wk old B6 mice, including both males and females.

extract_protocol:
For bone marrow subset purification we used B6.RAG1-/-mice to obtain pro-B cells. Pro-B YY1 KO was obtained with RAG-/-YY1f/f x mb1-Cre pro-B cells. B6.RAG-/-µ+ mice bearing a rearranged IgM transgene were used to obtain pre-B cells. follicular B cells were sorted from 5-8 week old spleen as CD19+AA4- CD21loCD23hi. Germinal center B cells were obtained from spleens of mice 8 days after IP immunization with 100 mg OVA and 10 mg of LPS in alum.  GC B cells were identified as CD19+Fas+GL7+
Directional RNASeq. For each sample approximately 0.5 ug total RNA was depleted of ribosomal RNA using RiboMinus (Life Technologies). Ribodepleted RNA was prepared for sequencing using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs) for Illumina following manufacturer’s recommend protocols with 15 cycles of PCR. Final libraries were size selected on 2% agarose gels to obtain products with library sizes between 280-380 bases in length. The prepared libraries were loaded onto an Illumina HiSeq2000 for single-end 100 base reads with 7 bases of the index read. Data was processed to generate Fastq files using CASAVA 1.8 and demultiplexed based on index sequences.

tag: age

value: 6-14 weeks

tag: gender

value: pooled male and female

value: spleen

value: GC B cells


title: GCB RNA-seq_r1

description:
GCB RNA-seq, replicate 1
mGCB_H128


title: P18_CTM5

tag: diagnosis

value: TECC/CTM

tag: sample type

value: Single cell cluster


title: FOB RNA-seq_r1

description:
FOB RNA-seq, replicate 1
mFOB_H132

source_name: Follicular B cells

value: Follicular B cells


title: P18_CTM4

tag: patient

tag: patient treatment status


title: pre-B RNA-seq_r2

description:
pre-B RNA-seq, replicate 2
preB_H105

source_name: RAG-/-µ+ pre-B cells

value: bone marrow

value: Pre-B cells

tag: genotype

value: RAG-/- mu+


title: NS_H33_inp_1

source_name: NSC time-ChIP input (for replicate 1)

value: A2lox.Cre (derived from E14)

value: input


title: P10_tissue_tumor

source_name: Colorectal tumor

value: Colorectal tumor

value: Whole tissue

value: Patient 10


title: P18_CTM2

value: colorectal cancer

value: Treatment-naïve


title: pro-B YY1 KO RNA-seq_r2

description:
pro-B YY1 KO RNA-seq, replicate 2
proB_yy1KO_H132

source_name: RAG-/- YY1f/f x mb1-Cre pro-B cells

value: 6-14 weeks

value: Pro-B cells

value: RAG-/- YY1f/f x mb1-Cre


title: NS_H33_0h_2

value: NSC


title: NS_H33_3h_2

source_name: NSC time-ChIP 3h timepoint


title: P16_CTM2

value: TECC/CTM

value: Patient 16


title: NS_H33_12h_1

source_name: NSC time-ChIP 12h timepoint


title: pro-B YY1 KO RNA-seq_r1

description:
pro-B YY1 KO RNA-seq, replicate 1
proB_yy1KO_H128

value: pooled male and female


title: NS_H33_6h_1

source_name: NSC time-ChIP 6h timepoint


title: P10_CTM10

source_name: TECC/CTM

value: Single cell cluster


title: pro-B RNA-seq_r3

description:
pro-B RNA-seq, replicate 3
proB_H150

source_name: RAG1-/-pro-B cells

value: bone marrow


title: pro-B RNA-seq_r2

description:
pro-B RNA-seq, replicate 2
proB_H87_2


title: pre-B RNA-seq_r1

description:
pre-B RNA-seq, replicate 1
preB_H87

value: Pre-B cells

value: RAG-/- mu+


title: pro-B YY1 KO RNA-seq_r3

description:
pro-B YY1 KO RNA-seq, replicate 3
proB_yy1KO_H150


title: pro-B RNA-seq_r1

description:
pro-B RNA-seq, replicate 1
proB_H87_1


title: H3K4me1 pro-B input ChIP-seq

description: H3K4me1 pro-B input ChIP-seq

data_processing:
Duplicated reads were removed before mapping.
Experimental and input control fastaq tags were aligned to the mouse reference genome (mm9) using Bowtie 0.12.9. Alignment parameters used:-a -v 2 -m 3 --best --strata
All reads mapping with their best alignment score at more than 3 sites in the genome were discarded.
For YY1, confident peaks were called using MACS (version 1.4.2), with FDR<= 1% and the default p value (1E-5). For H3K4me1 and H3K27me3, significant regions were called using HOMER (version 4.7) with parameter-style histone.
Genome_build: mm9
Supplementary_files_format_and_content: file format: bed; content: confident peaks (as called by MACS) | file format: txt; content: significant regions (as called by HOMER)

growth_protocol: Bone marrow and spleen cells were isolated from 6 to 14 wk old C57BL/6 mice, including both males and females.

extract_protocol:
For bone marrow subset purification we used B6 RAG1-/-mice to obtain pro-B cells.  B6.RAG-/-µ+ mice bearing a rearranged IgM transgene were used to obtain pre-B cells. follicular B cells were sorted from 5-8 week old spleen as CD19+AA4- CD21loCD23hi. Germinal center B cells were obtained from spleens of mice 8 days after IP immunization with 100 mg OVA and 10 mg of LPS in alum.  GC B cells were identified as CD19+Fas+GL7+
For each sample 1 - 10 ng of IP material or input control sample was prepared into sequencing libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina following manufacturers protocol. Samples were amplified using 18 cycles of PCR and then size selected on 2% EX agarose gels (Thermo Fisher) and bands cut at 300bps (+ 25 bps) and cleaned up using DNA Clean & Concentrator-25  (Zymo Research). The prepared libraries were loaded onto an Illumina HiSeq2000 for single-end 100 base reads with 7 bases of the index read. Data was processed to generate Fastq files using CASAVA 1.8 and demultiplexed based on index sequences.


title: FOB RNA-seq_r2

description:
FOB RNA-seq, replicate 2
mFOB_H136

value: spleen

value: Follicular B cells


title: P08_CTM11

value: Patient 08


title: H3K4me1 pro-B ChIP-seq

description: H3K4me1 pro-B ChIP-seq


title: NS_H33_3h_1

value: A2lox.Cre (derived from E14)


title: H3K27me3 GCB input ChIP-seq

description: H3K27me3 GCB input ChIP-seq

value: GC B cells


title: P08_CTM10

value: colorectal cancer

value: Treatment-naïve


title: NS_H33_0h_1

source_name: NSC time-ChIP 0h timepoint


title: H3K27me3 GCB ChIP-seq

description: H3K27me3 GCB ChIP-seq

value: 6-14 weeks


title: ES_H33_12h_3

source_name: ESC time-ChIP 12h timepoint

value: ESC


title: P08_CTM7


title: ES_H33_6h_3

source_name: ESC time-ChIP 6h timepoint


title: H3K27me3 FOB ChIP-seq

description: H3K27me3 FOB ChIP-seq


title: H3K27me3 FOB input ChIP-seq

description: H3K27me3 FOB input ChIP-seq


title: P01_CTM1

value: Patient 01


title: P01_CTM3

value: TECC/CTM


title: H3K27me3 pre-B ChIP-seq

description: H3K27me3 pre-B ChIP-seq


title: H3K27me3 pre-B input ChIP-seq

description: H3K27me3 pre-B input ChIP-seq


title: P01_CTM4


title: S110.utr

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

data_processing: RNA-seq reads were mapped to the human genome using TopHat2. Gene expression levels were calculated using HTseq-count utility using Genecode gene annotations (v19). Only genes that were readily detected in the dataset (covered by at least 20 reads; 14,647 genes) were included in subsequent analyses.  Quantile normalization was used to normalize expression levels across samples. After normalization, floor expression level was set to 20.0

source_name: untreated control

growth_protocol: Human islets were received 2–6 days following isolation. Islets from individual donors were dissociated into single cells and cultured in regular growth medium: CMRL 1066 medium containing 5.6 mM glucose and supplemented with 10% fetal bovine serum (FBS; HyClone, Logan, UT), 100 units/ml penicillin, 100 µg/ml streptomycin, 100 µg/ml gentamycin sulphate, and 5 µg/ml amphotericin B . The medium was replaced twice a week, and the cells were split 1:2 once a week.

extract_protocol:
Total RNA was extracted using the ZR RNA MiniPrep RNA Isolation Kit (Zymo Research), and treated with RNase-free DNase I (Thermo Scientific). cDNA libraries were constructed following TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) for next-generation sequencing. Briefly, 400 ng total RNA was used as starting material and PolyA-selected mRNAs were purified, size-fractioned, and subsequently transcribed into single-stranded cDNA by random hexamer priming.
Following second-strand synthesis, double-stranded cDNAs were blunt-end fragmented and indexed using adapter ligation, after which they were amplified and sequenced according to manufacturer's protocol (Illumina).

treatment_protocol: Redifferentiation of expanded islet cells. Expanded human islet cells or sorted beta-cells derived (BCD) cells were infected with ARX shRNA or control shRNA viruses. Six days following infection, cells were trypsinized, pelleted, and seeded at 4x104 cells/cm2 in ultra-low attachment plates (Corning, NY) in CMRL 1066 medium containing 5.6 mM glucose and supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin, 100 µg/ml gentamycin sulphate, 1% BSA fraction V (Sigma-Aldrich), 1X insulin/transferrin/selenium (ITS; Gibco Life Technologies, Grand Island, NY), D-Glucose (final concentration 25 mM), 8 nM exendin-4 (Acris, Herford, Germany or Sigma-Aldrich), 8 nM activin A (PeproTech, Rocky Hill, NJ), 1X B27 supplement (Stem Cell Technologies, Vancouver, Canada or Gibco), and 10 mM nicotinamide (Sigma-Aldrich) (Redifferentiation Cocktail, RC) for 4-8 days. Half-volume medium changes were performed every other day.. ARX shRNAs (accession numbers TRCN00000163-33 and -34) and a control empty shRNA (SHC001) cloned in pLKO.1-PURO lentiviral vector (Sigma-Aldrich) were used to produce virus particles. Cells were infected at MOI 2:1 in CMRL 1066 medium containing 8 µg/ml polybrene (Sigma-Aldrich) overnight. The medium was then replaced with regular growth medium. Three days following infection the cells were selected with 1 µg/ml puromycin (Invivogen, Toulouse, France) for 3 days

value: Human islet cells

tag: donor

value: Donor 3


title: GCB input control

description: GCB input control

value: pooled male and female


title: H3K27me3 pro-B ChIP-seq

description: H3K27me3 pro-B ChIP-seq

value: bone marrow

value: Pro-B cells


title: ES_H33_12h_2


title: ES_H33_0h_3

source_name: ESC time-ChIP 0h timepoint


title: FOB input control

description: FOB input control


title: ES_H33_3h_3

source_name: ESC time-ChIP 3h timepoint


title: ES_H33_6h_2


title: 0.05nM_MeHg_r2

city: Versoix

first: Rebecca

last: Beauvais-Flueck

address: 10 route de Suisse - CP 416

department: Institut F.-A. Forel

country: Switzerland

institute: University of Geneva

description:
Sample name: M10.2
artificial exposure medium
MeHg_10-11_2

data_processing:
Samples were aligned with TopHat2 to the Creiinhardtii 236 V.9.0 available at phytozome.org.
Reads were counted using the Python package HTSeq.
Genome_build: C. reinhardtii 236 V.9.0
Supplementary_files_format_and_content: The .txt files report raw counts

organism: Chlamydomonas reinhardtii

source_name: cell culture exposed to metal

growth_protocol: Algal cells were exposed in an artificial freshwater medium.

extract_protocol:
Total RNA was extracted using TRI Reagent® protocol.
RNA libraries were prepared using Illumina TruSeq Stranded mRNA kit.
RNA libraries were sequenced on a Illumina HiSeq 2500 System.

treatment_protocol: Algal pellets were frozen in liquid nitrogen and cells were broken using glass beads in the presence of TRI Reagent.

tag: genotype/variation

value: wild type

value: 0.05 nM CH3Hg

tag: time (exposure)


title: YY1 GCB ChIP-seq

description: YY1 GCB ChIP-seq

source_name: GC B cells

value: spleen


title: Pre-B input control

description: Pre-B input control

source_name: RAG-/-µ+ pre-B cells

value: Pre-B cells

value: RAG-/- mu+


title: H3K27me3 pro-B input ChIP-seq

description: H3K27me3 pro-B input ChIP-seq


title: Pro-B input control

description: Pro-B input control


title: 0.05nM_MeHg_r1

description:
Sample name: M10.1
artificial exposure medium
MeHg_10-11_1


title: ES_H33_3h_2

value: A2lox.Cre (derived from E14)

tag: replicate


title: 0.05nM_MeHg_r3

description:
Sample name: M10.3
artificial exposure medium
MeHg_10-11_3

tag: treatment


title: S110.rc.siARX

source_name: Redifferentiation Cocktail + ARX shRNA


title: 0.5nM_MeHg_r3

description:
artificial exposure medium
MeHg_10-10_3

data_processing:
Samples were aligned with TopHat2 to the Creiinhardtii 236 V.9.0 available at phytozome.org.
Reads were counted using the Python package HTSeq.
Analysis of differential gene expression was computed using CLC Main Workbench (Version 7, CLC bio, QIAGEN, Denmark).
Genome_build: Creiinhardtii 236 V.9.0 (ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Creinhardtii)

source_name: cells

extract_protocol:
Total RNA was extracted using TRI Reagent® protocol.
RNA libraries were prepared using Illumina TruSeq Stranded mRNA kit.

tag: strain

value: 0.5 nM MeHg

tag: exposure


title: S106.rc.siARX

value: Donor 2


title: YY1 FOB ChIP-seq

description: YY1 FOB ChIP-seq

source_name: Follicular B cells

value: 6-14 weeks

value: Follicular B cells


title: YY1 pre-B ChIP-seq

description: YY1 pre-B ChIP-seq


title: YY1 pro-B ChIP-seq

description: YY1 pro-B ChIP-seq


title: ENSC.vest

data_processing:
Reads were aligned to the mouse genome (mm9) using tophat
Gene expression levels were calculated using Htseq-count based on Ensembl gene annotations (v67)
Gene expression levels were next normalized across samples using quantile normalization
Only genes with at least 40 reads in at least one sample were included in the analysis
Prior to quantile normalization, genes with less than 20 counts were set to 20.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each sample.

source_name: Vestibular ENSCs

growth_protocol: mouse inner ear tissue

extract_protocol:
RNeasy Plus Micro Kit (Qiagen)
NuGEN Ovation

treatment_protocol: cells obtained by cell sorting

tag: strain background

value: Vestibular system

value: epithelial non-sensory cells (ENSCs)


title: S106.utr

value: Human islet cells


title: S110.rc

source_name: Redifferentiation Cocktail + control shRNA

value: Donor 3


title: 0.5nM_MeHg_r2

description:
artificial exposure medium
MeHg_10-10_2


title: ES_H33_3h_1

value: ESC

tag: time point


title: ND.rc.siARX

tag: cell type

value: Donor 1


title: Control r2

description:
artificial exposure medium
Control_2

value: Control


title: Control r3

description:
artificial exposure medium
Control_3

value: wild type


title: ES_H33_6h_1


title: ES_H33_12h_1


title: 0.5nM_MeHg_r1

description:
artificial exposure medium
MeHg_10-10_1


title: ES_H33_0h_2


title: HC.vest

source_name: Vestibular HCs

tag: tissue

value: hair-cells (HCs)


title: ENSC.coch

source_name: Cochlear ENSCs

value: cochlea


title: Control r1

description:
artificial exposure medium
Control_1


title: HC.coch

source_name: Cochlear HCs


title: ES_H33_0h_1


title: Postmortem Sample 1 (sample 12)

status: Public on Jun 19 2016

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: Postmortem Sample 1

data_processing:
Base calling and de-multipexing was performed using CASAVA version 1.8
RNAseq reads were aligned to UCSC hg19 using TopHat2 (v 2.0.12), allowing for 2 mismatches.
For each sample, a count table for all genes was generated using R function summarizeOverlaps from the R/Bioconductor package GenomicAlignments (v 1.7.3) using only the primary alignments of each read.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Postmortem

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). Total RNA was converted into libraries of double stranded cDNA molecules as a template for high throughput sequencing following the manufacturer’s recommendations using the Illumina TruSeq RNA Sample Preparation Kit v2
RNA libraries were prepared for sequencing using standard Illumina protocols

value: non-tumor CD11b+ microglia samples


title: Postmortem Sample 4 (sample 15)

description: Postmortem Sample 4


title: Postmortem Sample 2 (sample 13)

description: Postmortem Sample 2


title: Postmortem Sample 5 (sample 16)

description: Postmortem Sample 5


title: Postmortem Sample 3 (sample 14)

description: Postmortem Sample 3


title: ND.rc


title: ES_H33_inp_1

source_name: ESC time-ChIP input (for replicate 1)

value: input


title: S106.rc


title: ND.utr


title: Epilepsy Sample 3 (sample 11)

description: Epilepsy Sample 3

source_name: Epilepsy


title: Epilepsy Sample 2 (sample 10)

description: Epilepsy Sample 2


title: Epilepsy Sample 1 (sample 9)

description: Epilepsy Sample 1


title: GBM Sample 2 (sample 2)

description: GBM Sample 2

source_name: GBM

value: CD11b+ human glioblastoma-associated microglia/monocytes


title: GBM Sample 4 (sample 4)

description: GBM Sample 4


title: GBM Sample 3 (sample 3)

description: GBM Sample 3


title: GBM Sample 5 (sample 5)

description: GBM Sample 5


title: GBM Sample 7 (sample 7)

description: GBM Sample 7


title: GBM Sample 1 (sample 1)

description: GBM Sample 1


title: GBM Sample 6 (sample 6)

description: GBM Sample 6


title: cas_RNAA

city: Beijing

first: Feng

last: Zhao

address: No. 17 Qinghua East Road, Haidian District

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

data_processing:
Base calling performed using  Illumina GA pipeline 1.6.
The clean reads obtained were aligned to the genome sequence of E. coli O157:H7 EDL933 using SOAP2
The raw reads were ﬁltered for removing dirty raw reads which contain adapters, unknown or low quality bases.
All those uniquely mapped reads were used to calculate the gene expression level by the RPKM method, which is able to eliminate the influence of different gene length and sequencing discrepancy on the calculation of gene expression and thus the calculated gene expression level can be directly used for comparing the difference of gene expression among samples.
Genome_build: ASM666v1; NC_002655.2
Supplementary_files_format_and_content: Microsoft excel spreadsheet files include RPKM values for each gene of sample

organism: Escherichia coli

source_name: Bacterium

growth_protocol: The strain was stocked in tryptic soy broth (TSB) with 25% glycerol at -80℃, and was activated by streaking onto TSA plate and incubating at 37℃ for 24 h. And then, a single colony was picked and used to inoculate TSB and incubated at 37℃ for 12 h with shaking at 200 rpm. This overnight culture was transferred to TSB at a dilution of 1:100 and grew to the exponential phase (OD550=0.93).

extract_protocol:
Total RNA was isolated from the VBNC cells and the exponential-phase cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA samples were treated with DNase Ⅰ (Invitrogen) to remove residual genomic DNA.
10 μg of total RNA sample was subjected to puriﬁcation for discarding rRNA via the MICROBExpress kit (Ambion) according to the manufacturer’s protocol. Following purification, the RNA was interrupted into short fragments using divalent cations under elevated temperature and the short fragments were used for the cDNA synthesis using a SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) according to the manufacturer’s instructions. These cDNA fragments were purified with a QIAquick PCR purification kit (Qiagen), and then went through end reparation, adding poly(A) and ligation of sequencing adaptors. These products were purified with agarose gel electrophoresis and fragments in the size of 200-250 bp were selected for PCR amplification to construct the cDNA library.

treatment_protocol: In order to generate the VBNC state in E. coli O157:H7, 20 mL of the exponential-phase cell suspensions in a 50 mL sterile glass tube was treated by HPCD at 5 MPa and 25℃ for 40 min.

value: Treated by HPCD at 5 MPa and 25℃ for 40 min


title: P01_CTM8

source_name: TECC/CTM

value: colorectal cancer

value: TECC/CTM

value: Single cell cluster

value: Patient 01

value: Treatment-naïve


title: ES_H33_inp_2

source_name: ESC time-ChIP input (for replicates 2 and 3)

value: A2lox.Cre (derived from E14)


title: con_RNAA


title: GBM Sample 8 (sample 8)

description: GBM Sample 8


title: Fuji  125mg/kg Tazemetosta 7 day treatment BID 7Fuji-7_L5.D701

status: Public on Jun 18 2016

first: Igor

last: Feldman

address: 400 Technology Square

institute: Epizyme

data_processing: The raw read counts were transformed using voom and quantile normalized, which results in expression measures (summarized intensities) in log base 2.  Statistical analysis was subsequently performed using empirical Bayes from the limma R package.  Normalized data provide the input for statistical hypothesis testing, in which genes are identified that are statistically significantly different between sample groups, i.e. differences that are unlikely to be due to chance.  The degree of difference, i.e. the fold-change, is also accounted for.  In the output, the fold-changes (logFC) are given as log2 values, with a positive logFC representing up-regulation, and a negative logFC indicating down-regulation.  For each comparison (e.g. A-B, which is the same as 'A relative to B'), the first group (A) is the numerator, while the second group (B) is the denominator.  Thus, a positive logFC for the comparison 'A-B' indicates up-regulation in A relative to B.  Comparisons were undertaken using linear modelling.  Subsequently, empirical Bayesian analysis was applied (including vertical p-value adjustment for multiple testing, which controls for false discovery rate).  For each comparison, the null hypothesis was that there was no difference between the groups being compared.  Significant genes with adjusted P<0.05 from each comparison were analyzed for enrichment of KEGG and GO pathway membership using a hypergeometric test.  Enrichment (P<0.05) was assessed for up- and down-regulated genes separately.  The results from the three separate xenograft models were taken and a congruence analysis was performed to determine the extent of overlap between the differentially expressed genes and significantly enriched KEGG pathways and GO terms between cell lines.

source_name: Fuji Xenograft model

growth_protocol: All the procedures related to animal handling, care, and the treatment in this study were performed according to the guidelines approved by the Institutional Animal Care and Use Committee (IACUC) of Champions Oncology and Eisai Tsukuba following the guidance of the Association for Assessment and Accreditation of Laboratory Animal Care. HS-SY-II xenograft studies were performed at Eisai Tsukuba (pharmacodynamics study) and HAMRI Tsukuba Research center (efficacy study).  The protocols were approved by the IACUC of Eisai Tsukuba (Permit Number: 13-D-0307-001 for efficacy study and 13-D-0154-001 for pharmacodynamics study).  HS-SY-II cells were harvested during mid-log phase growth, and resuspended in PBS with 50% Matrigel (BD Biosciences).  Balb/C-nu mice (Charles River Laboratories Japan) received 1 × 107 cells (0.1 mL cell suspension) subcutaneously in the right flank.  Mice carrying tumors of approximately 170 mm3 for efficacy study (35 days after injection) or 220 mm3 for pharmacodynamics study (31 days after injection) were sorted into treatment groups with similar mean tumor volumes.  Tazemetostat or vehicle (0.5% methyl cellulose + 0.1% Tween-80 in water) was administered at the indicated doses on twice a day schedules for either 7 or 28 days by oral gavage.  As reference compound, doxorubicin HCl in saline was dosed at 10 mg/kg.  Each dose was delivered in a volume of 0.2 mL/20 g mouse (10 mL/kg), and adjusted for the last recorded weight of individual animals.  Mice were monitored for overall health status daily and their tumor volumes were monitored twice a week using a digital caliper throughout the experiment.  On day 7 (pharmacodynamics study) or day 28 (efficacy study), mice were sampled in a prespecified fashion.  Sampling included nonterminal bleeds (0.15 mL) from the retro-orbital venous plexus with anesthesia by isoflurane inhalation.  Fuji xenograft studies were performed at Eisai Tsukuba.  The protocols were approved by the IACUC of Eisai Tsukuba (Permit Number: 13-D-0307-002 for efficacy study and 14-D-0047-001 for pharmacodynamics study).  Fuji cells were harvested during mid-log phase growth, and resuspended in HBSS with 50% Matrigel.  Balb/C-nu mice received 1 × 107 cells (0.1 mL cell suspension) subcutaneously in the right flank.  Mice carrying tumors of approximately 200 mm3 for efficacy study (25 days after injection) or 260 mm3 for pharmacodynamics study (26 days after injection) were sorted into treatment groups with similar mean tumor volumes.

extract_protocol:
RNA extraction was performed as previously described Knutson SK, Wigle TJ, Warholic NM, Sneeringer CJ, Allain CJ, et al. (2012) A selective inhibitor of EZH2 blocks H3K27 methylation and kills mutant lymphoma cells. Nat Chem Biol 8: 890-896.
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina RS-122-2103).  Briefly, Total RNA samples are concentration normalized, and polyadenylated RNA is purified using oligo-dT attached to magnetic beads.  Purified mRNA is fragmented using heat in the presence of divalent cations. Fragmented RNA is converted into double-stranded cDNA, with dUTP utilized in place of dTTP in the second strand master mix.  A single 'A' base is added to the cDNA and forked adaptors that include index, or barcode, sequences are attached via ligation. The resulting molecules are amplified via polymerase chain reaction (PCR). During PCR the polymerase stalls when a dUTP base is encountered in the template. Since only the second strand includes the dUTP base, this renders the first strand the only viable template, thereby preserving the strand information.  Final libraries are quantified, normalized and pooled.  Pooled libraries are bound to the surface of a flow cell and each bound template molecule is clonally amplified up to 1000-fold to create individual clusters.  Four fluorescently labeled nucleotides are then flowed over the surface of the flow cell and incorporated into each nucleic acid chain.  Each nucleotide label acts as a terminator for polymerization, thereby ensuring that a single base is added to each nascent chain during each cycle.  Fluorescence is measured for each cluster during each cycle to identify the base that was added to each cluster. The dye is then enzymatically removed to allow incorporation of the next nucleotide during the next cycle.

treatment_protocol: Fuji xenograft studies were performed at Eisai Tsukuba.  Tazemetostat, EPZ011989 or vehicle (0.5% methylcellulose + 0.1% Tween-80 in water) was administered at the indicated doses on twice a day schedules for either 7, 29 or 35 days by oral gavage.  Each dose was delivered in a volume of 0.2 mL/20 g mouse (10 mL/kg), and adjusted for the last recorded weight of individual animals.  Mice were monitored for overall health status daily during the dosing period or twice a week after the dosing period, and their tumor volumes were monitored twice a week using a digital caliper throughout the experiment. PDX studies (CTG-0771, CTG-0331, and CTG-1169) were performed at Champions Oncology.  The protocols were approved by the IACUC of Champions Oncology (Permit Number:  CHA-003-2013).  Tumor fragments (5 mm x 5 mm x 5 mm) were harvested from donor animals, each implanted from a specific passage lot (CTG-0331 and CTG-0771 at P4).  NCr-nu mice (Taconic) received the fragment subcutaneously in the flank region.  Mice carrying tumors of approximately 100-300 mm3 were sorted into treatment groups with similar mean tumor volumes.  Tazemetostat or vehicle (0.5% sodium carboxymethylcellulose +0.1%Tween-80 in water) was administered at the indicated doses on twice a day schedules for 35 days by oral gavage.  As reference compound, doxorubicin HCl in saline was dosed at 3 mg/kg.  Each dose was delivered in a volume of 0.2 mL/20 g mouse (10 mL/kg), and adjusted for the last recorded weight of individual animals.  Mice were monitored for overall health status daily and their tumor volumes were monitored twice a week using a digital caliper throughout the experiment.  For the CTG-0771 and CTG-0331 models, 3 to 5 mice per group with the largest tumors were euthanized by carbon dioxide inhalation on day 35 for blood and tissue sampling, and the 7 remaining mice were followed for an additional 25 days as animal survival study.  Analgesics and anesthetics were not administered.  Mice were humanely euthanized by carbon dioxide inhalation if their body weights dropped more than 20% of the original weight for two consecutive measurements, more than 30% of the original weight for one measurement, their xenograft tumor grew larger than 2000 mm3, or they showed appear moribund at any time, while a tumor volume endpoint in Kaplan-Meier survival curve was 1200 mm3, with the exception of the slower growing CTG-1169 model for which 600 mm3 was used as an endpoint for Kaplan-Meier survival curve  Diet gel was provided ad libitum if their body weights dropped more than 10%.  The summary of deaths for the 3 models is as follows:  For CTG-0771 there was one animal found dead in 400-500 mg/kg group.  For CTG-0331 there was no dead animal.  For CTG-1169 there were four animals that were found dead in multiple groups, two animals in 125 mg/kg group, one animal in 500 mg/kg group, and one animal in doxorubicin group.  For the above cases, necropsies were performed and the causes of death were not clarified.

tag: model

value: Fuji Xenograft model

tag: cell or tumor type

value: synovial sarcoma

tag: xenograft or pdx

value: xenograft

tag: treatment time (days)


title: Fuji  125mg/kg Tazemetosta 7 day treatment BID 7Fuji-9_L5.D703


title: Fuji  Vehicle 7 day treatment BID 7Fuji-4_L4.D710


title: Fuji  500mg/kg Tazemetosta 7 day treatment BID 7Fuji-20_L7.D701


title: Fuji  Vehicle 7 day treatment BID 7Fuji-3_L4.D709


title: Fuji  125mg/kg Tazemetosta 7 day treatment BID 7Fuji-8_L5.D702


title: Fuji  500mg/kg Tazemetosta 7 day treatment BID 7Fuji-19_L6.D712


title: Fuji  250mg/kg Tazemetosta 7 day treatment BID 7Fuji-15_L6.D709


title: Fuji  500mg/kg Tazemetosta 7 day treatment BID 7Fuji-18_L6.D711


title: Fuji  Vehicle 7 day treatment BID 7Fuji-2_L4.D708


title: Fuji  500mg/kg Tazemetosta 7 day treatment BID 7Fuji-17_L6.D710


title: Fuji  250mg/kg Tazemetosta 7 day treatment BID 7Fuji-14_L6.D708


title: JIA patient 21_clinical_remission

city: BUFFALO

first: JAMES

last: JARVIS

address: 875 ELLICOTT STREET 8026

department: PEDIATRIC

institute: UNIVERSITY AT BUFFALO

description:
JIA patient with clinical remission on medication
CD4TCell_CRM_10

data_processing:
Sequences were excluded for adapter contamination and low quality bases
Sequences were aligned to hg19 human reference genome using Tophat version 2.0.13
Gene expression abundance was calculated by HTSeq count version 0.6.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each sample

source_name: CD4+ T cell

extract_protocol:
Total RNA was extracted using TRIzol™ reagent according to manufacturer's directions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA). RNA was quantified spectrophotometrically (Nanodrop, Thermo Scientific, Wilmington, DE) and assessed for quality by capillary gel electrophoresis (Agilent 2100 Bioanalyzer; Agilent Technologies, Inc., Palo Alto, CA)
Samples libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit according to the manufacture's recommended protocols

tag: disease stage

value: blood

value: CD4+ T cell


title: JIA patient 19_clinical_remission

description:
JIA patient with clinical remission on medication
CD4TCell_CRM_8


title: Fuji  Vehicle 7 day treatment BID 7Fuji-5_L4.D711


title: JIA patient 20_clinical_remission

description:
JIA patient with clinical remission on medication
CD4TCell_CRM_9


title: JIA patient 18_clinical_remission

description:
JIA patient with clinical remission on medication
CD4TCell_CRM_7


title: Fuji  125mg/kg Tazemetosta 7 day treatment BID 7Fuji-6_L4.D712


title: Fuji  250mg/kg Tazemetosta 7 day treatment BID 7Fuji-12_L5.D706


title: Fuji  250mg/kg Tazemetosta 7 day treatment BID 7Fuji-11_L5.D705


title: JIA patient 16_clinical_remission

description:
JIA patient with clinical remission on medication
CD4TCell_CRM_5


title: JIA patient 17_clinical_remission

description:
JIA patient with clinical remission on medication
CD4TCell_CRM_6