title: TAB-seq_dr_24hpf

description: TAB-seq

data_processing: Single-read TAB-seq libraries were sequenced on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome (danRer7) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 1. Supplementary_files_format_and_content: For "*.allC" processed data files the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - hmc: number of reads supporting a hydroxymethylated cytosine.column 6 - h: total number of reads at that position.

growth_protocol: Danio rerio embryos used for TAB-Seq were obtained from a natural mating procedure and dechorionated by pronase treatment prior to gDNA isolation.

extract_protocol: For DNA extraction, embryos were lysed in 20 mM Tris pH 8.0, 100 mM NaCl, 15 mM EDTA, 1% SDS, 0.5 mg/ml proteinase K, for 3h at 55ºC. This was followed by two Phenol/Chlorophorm/Isoamylalcohol (25:24:1, PCI) extractions and subsequent centrifugation (5 minutes at 13,000 rpm). The DNA was then precipitated by adding 1/5 volumes of 4 M NH4Ac and 3 volumes of 96% ethanol. The reaction was left on ice for a minimum of 30 minutes. The DNA precipitate was centrifuged for 20 minutes at 4°C (13,000 rpm) and the pellet was washed with 500 μL of 70% ethanol and centrifuged for 5 minutes (13,000 rpm) at room temperature. The pellet was then resuspended in 200 μL of TE buffer and 1 μl of RNAse A (20 μg/μl) was added. The reaction was left to proceed for 30 minutes at room temperature after which it was precipitated with 0.1 volumes of 4 M NH4Ac and 1 volume of isopropanol on ice for 2 h. The reaction was then centrifuged for 30 minutes at 4°C (13,000 rpm) and the pellet resuspended in TE buffer. TAB-seq library generation was performed with the 5hmC TAB-seq Kit (WiseGene, USA - Cat# K001) as per manufacturer’s instructions, with minor modifications related to the amount of starting material (400 ng).


title: MethylC-seq_dr_24hpf_sox10

status: Public on Jan 29 2016

type: SRA

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

library_source: genomic

data_processing:
MethylC-seq libraries were sequenced in single-end mode on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome (danRer7) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 0.
Supplementary_files_format_and_content: For "*.allC" processed data files (for MethylC-Seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - mc: number of reads supporting a methylated cytosine.column 6 - h: total number of reads at that position.

molecule: genomic DNA

organism: Danio rerio

source_name: embryo

extract_protocol: Neural crest cells were isolated from 24hpf zebrafish transgenic embryos, expressing mCherry under the control of the sox10 regulatory locus (TgBAC(Sox10:Cherry)), using Fluorescence Activated Cell Sorting (FACS). Embryos were dissociated to a single cell suspension using collagenase (20mg/ml)/trypsin (0.05%) solution at 30°C for 12 mins with three intermittent homogenization steps. The reaction was stopped with Hank’s blocking solution (1X HBSS Ca-, Mg-, phenol red-free, 0.25% BSA, 10mM Hepes pH 8.0), cells collected by centrifugation at 500 x g for 10 mins, re-suspended in Hanks solution and passed through a cell strainer to remove the cell aggregates. Single cells, concentrated by another centrifugation were resuspended in ~500ul of Hank’s solution and processed by FACS. Genomic DNA for further analysis was isolated from collected mCherry-positive, sox10-expressing neural crest cells using Purelink Genomic DNA Mini Kit (#K182002, Life Technologies). MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 200 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 6 cycles of amplification.

tag: tissue

value: sox10+ cells

tag: developmental stage

value: 24 hpf (pharyngula)

tag: transgenic embryos

value: YES


title: MethylC-seq_dr_24hpf_tet123

growth_protocol: Danio rerio embryos used for MethylC-Seq were obtained from a natural mating procedure and dechorionated by pronase treatment prior to gDNA isolation.

extract_protocol: For DNA extraction, embryos were lysed in 20 mM Tris pH 8.0, 100 mM NaCl, 15 mM EDTA, 1% SDS, 0.5 mg/ml proteinase K, for 3h at 55ºC. This was followed by two Phenol/Chlorophorm/Isoamylalcohol (25:24:1, PCI) extractions and subsequent centrifugation (5 minutes at 13,000 rpm). The DNA was then precipitated by adding 1/5 volumes of 4 M NH4Ac and 3 volumes of 96% ethanol. The reaction was left on ice for a minimum of 30 minutes. The DNA precipitate was centrifuged for 20 minutes at 4°C (13,000 rpm) and the pellet was washed with 500 μL of 70% ethanol and centrifuged for 5 minutes (13,000 rpm) at room temperature. The pellet was then resuspended in 200 μL of TE buffer and 1 μl of RNAse A (20 μg/μl) was added. The reaction was left to proceed for 30 minutes at room temperature after which it was precipitated with 0.1 volumes of 4 M NH4Ac and 1 volume of isopropanol on ice for 2 h. The reaction was then centrifuged for 30 minutes at 4°C (13,000 rpm) and the pellet resuspended in TE buffer. MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 200 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 6 cycles of amplification.

value: whole embryo

tag: genetic background

value: mixed AB and Tübingen

value: Morpholino against Tet1/Tet2/Tet3


title: MethylC-Seq_dr_48hpf

value: 48hpf (hatching)

value: NO


title: MethylC-Seq_dr_24hpf


title: Sample_2S7

city: Milwaukee

first: Liang

last: Wang

state: Wisconsin

address: 8701 Watertown Plank Rd.

department: Pathology

country: USA

institute: Medical College of Wisconsin

description: exRNA seq

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to different RNA species using bowtie v1.1.1 with parameters -l 18, -v 1, -m 2, and --norc --best --strata
An iterative alignment strategy was ued: unmapped sequences from the previous alignment were used for the mapping of the next RNA reference species. The sequential alignment followed the order of mature miRNA, precursor miRNA, piwiRNA, siRNA, lncRNA, mRNA, pseudo genes, antisense RNA, rRNA, snRNA, snoRNA, misc-RNA, other transcribed RNA, FLJ human cDNA, and predicted RNA.
Reads per Megabase of library size (RPM) were calculated.
For detail, please see Yuan T et al. eRNA: A graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. BMC Genomics, 2014, 15:176.  PMCID: PMC4029068
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: plasma microvesicles

extract_protocol:
microvesicles were isolated from 250 μL of plasma using the ExoQuick exosome precipitation solution (System Biosciences, Mountain View, CA, USA). Microvesicle RNA was prepared using a miRNeasy Micro Kit (QIAGEN, Valencia, CA, USA)
Libraries were prepared according to NEBNext multiplex small RNA library preparation kit (NEB, New England Biolab, Ipswich, MA, USA). For detail, see Huang X at al. Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics, 2013; 14:319. PMCID: PMC3653748

tag: Sex

value: Female

tag: age (years)

tag: disease status

value: Cancer

tag: disease type

value: Colorectal Cancer


title: Sample_2S4

description: exRNA seq


title: Sample_2S1

description: exRNA seq


title: Sample_N25

description: exRNA seq

value: Normal

value: Healthy Control


title: Sample_N31

description: exRNA seq


title: Sample_N43

description: exRNA seq


title: MethylC-Seq_dr_epiboly

extract_protocol: For DNA extraction, the embryos were lysed in 20 mM Tris pH 8.0, 100 mM NaCl, 15 mM EDTA, 1% SDS, 0.5 mg/ml proteinase K, for 3h at 55ºC. This was followed by two Phenol/Chlorophorm/Isoamylalcohol (25:24:1, PCI) extractions and subsequent centrifugation (5 minutes at 13,000 rpm). The DNA was then precipitated by adding 1/5 volumes of 4 M NH4Ac and 3 volumes of 96% ethanol. The reaction was left on ice for a minimum of 30 minutes. The DNA precipitate was centrifuged for 20 minutes at 4°C (13,000 rpm) and the pellet was washed with 500 μL of 70% ethanol and centrifuged for 5 minutes (13,000 rpm) at room temperature. The pellet was then resuspended in 200 μL of TE buffer and 1 μl of RNAse A (20 μg/μl) was added. The reaction was left to proceed for 30 minutes at room temperature after which it was precipitated with 0.1 volumes of 4 M NH4Ac and 1 volume of isopropanol on ice for 2 h. The reaction was then centrifuged for 30 minutes at 4°C (13,000 rpm) and the pellet resuspended in TE buffer. MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 200 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 6 cycles of amplification.

value: 80% epiboly (gastrula)


title: Sample_2S16

description: exRNA seq


title: Sample_N13

description: exRNA seq


title: Sample_N1

description: exRNA seq


title: Sample_N7

description: exRNA seq


title: Sample_4S17

description: exRNA seq

value: Male


title: Sample_4S8

description: exRNA seq


title: Sample_4S14

description: exRNA seq


title: Sample_4S2

description: exRNA seq


title: Sample_4S5

description: exRNA seq


title: Sample_1S24

description: exRNA seq


title: Sample_1S18

description: exRNA seq


title: MethylC-seq_xt_brain

data_processing:
MethylC-seq libraries were sequenced in single-end mode on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome (JGI 7.1) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 0.
Supplementary_files_format_and_content: For "*.allC" processed data files (for MethylC-Seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - mc: number of reads supporting a methylated cytosine.column 6 - h: total number of reads at that position.

organism: Xenopus tropicalis

source_name: tissue

extract_protocol: For DNA extraction, the isolated brain was lysed in 20 mM Tris pH 8.0, 100 mM NaCl, 15 mM EDTA, 1% SDS, 0.5 mg/ml proteinase K, for 3h at 55ºC. This was followed by two Phenol/Chlorophorm/Isoamylalcohol (25:24:1, PCI) extractions and subsequent centrifugation (5 minutes at 13,000 rpm). The DNA was then precipitated by adding 1/5 volumes of 4 M NH4Ac and 3 volumes of 96% ethanol. The reaction was left on ice for a minimum of 30 minutes. The DNA precipitate was centrifuged for 20 minutes at 4°C (13,000 rpm) and the pellet was washed with 500 μL of 70% ethanol and centrifuged for 5 minutes (13,000 rpm) at room temperature. The pellet was then resuspended in 200 μL of TE buffer and 1 μl of RNAse A (20 μg/μl) was added. The reaction was left to proceed for 30 minutes at room temperature after which it was precipitated with 0.1 volumes of 4 M NH4Ac and 1 volume of isopropanol on ice for 2 h. The reaction was then centrifuged for 30 minutes at 4°C (13,000 rpm) and the pellet resuspended in TE buffer. MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 200 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 6 cycles of amplification.

value: brain

value: adult


title: Sample_1S15

description: exRNA seq


title: Sample_1S6

description: exRNA seq


title: Sample_1S9

description: exRNA seq


title: Sample_1S3

description: exRNA seq


title: Sample_N37

description: exRNA seq


title: TAB-seq_xt_st30

description: TAB-seq

data_processing: Single-read TAB-seq libraries were sequenced on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome (JGI 7.1) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 1. Supplementary_files_format_and_content: For "*.allC" processed data files (for TAB-seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - hmc: number of reads supporting a hydroxymethylated cytosine.column 6 - h: total number of reads at that position.

growth_protocol: Xenopus tropicalis embryos were obtained from a natural mating procedure after human chorion gonadotropin injection, dejellied in 3% cysteine and collected at the indicated stage.


title: LpM spib 1

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

data_processing:
reads were aligned to Mouse Ensembl genes using the STAR version 2.3.0 software
Differential expression was determined by use of the Cufflinks software with default settings
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mus musculus

source_name: mucosa area of the intestine

extract_protocol:
Intestine was removed, lamina propria and muscularis layers were mechanically separeted, the tissue was digested with Collagenase D. Macrophages were sorted directly in trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: intestine

tag: age

value: 8-10 weeks old


title: Sample_1S12

description: exRNA seq


title: MM spib 2

source_name: muscularis area of the intestine


title: Sample_N19

description: exRNA seq


title: MethylC-seq_xt_st30

data_processing: MethylC-seq libraries were sequenced in single-end mode on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome (JGI 7.1) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 0. Supplementary_files_format_and_content: For "*.allC" processed data files (for MethylC-Seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - mc: number of reads supporting a methylated cytosine.column 6 - h: total number of reads at that position.

value: st30 (pharyngula)


title: Sample_4S20

description: exRNA seq


title: MethylC-seq_xt_st12

value: whole embryo

value: st12 (gastrula)


title: MM spib 1


title: Sample_4S23

description: exRNA seq


title: Sample_4S11

description: exRNA seq


title: LpM control 2


title: MM control 2


title: MethylC-seq_xt_st43


title: MethylC-seq_xt_st9

value: st9 (blastula)


title: LpM control 1


title: Sample_1S21

description: exRNA seq


title: CM cardiac derivatives of ieCPCs (replicate 3)

city: San Francisco

first: Gladstone

last: Bioinformatics

state: CA

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

description:
These cells were collected after ieCPCs were exposed to cardiac differentiation condition for 25 days.
CM_cardiac_derivatives_of_ieCPCs--replicate_3_bc15_GTGGCC

data_processing:
Alignment: Aligned to mouse genome build "mm9" using the program Tophat 2.0.13. Gene annotation (GTF file) used was Ensembl version 65. Specific settings: --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --microexon-search  --mate-inner-dist=150 --no-discordant --no-mixed
Reads to gene-level counts: Aligned reads were assigned to genes to arrive at per-gene counts using "featureCounts" (Liao et al., 2014), part of the Subread suite (http://subread.sourceforge.net/).
Any genes where there were not at least two samples with a CPM (counts per million) value between 0.5 and 5000 were filtered out ("NA" values for CPM and FPKM) in preparation for potential future differential expression analysis, which was not performed in these files.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and raw count data, tables in both Excel format and plain-text format.

source_name: Cardiac derivatives of ieCPCs

growth_protocol: 2nd MEFs were cultured in MEF medium; 2nd MEFs at day 9 of reprogramming were cultured with reprogramming medium for 6 days, transdifferentiation medium for 2 days, and then ieCPC basal medium with BACS for 1day; ieCPCs were cultured in ieCPC basal medium with BACS; Cardiac derivatives were cultured in serum-free differenitation medium.

extract_protocol:
Total RNA was prepared using the RNeasy Plus Mini Kit with Qiashredder columns  (Qiagen). Potentially residual DNA was removed by on-column DNase digestion with  RNase-free DNase (Qiagen). Total RNA was quantified on Nanodrop and quality was checked by electropherogram.
Total RNA (10 μg) was used as input material for  preparing the RNA sequencing (RNA-seq) libraries following the standard Illumina RNASeq  protocol as previously described (Wamstad et al., 2012)
Amplified libraries were sequenced on an Illumina GAIIx sequencer.

treatment_protocol: 2nd MEFs at day 9 of reprogramming were cultured with reprogramming medium for 6 days, transdifferentiation medium for 2 days, and then ieCPC basal medium with BACS for 1day;ieCPCs were cultured for passages after sorting on day 13 of cardiac reprogramming; Cardiac derivatives were collected after ieCPCs were exposed to cardiac differenitation medium for 25 days.

value: mixed background of C57BL/6 and 129J/SvE

tag: genotype/variation

value: Wildtype (WT)

tag: barcode

value: GTGGCC

tag: cell type

value: cardiac derivatives

tag: protocol

value: 25 days of cardiac differentiation from ieCPCs

tag: replicate number

value: Replicate 3


title: CM cardiac derivatives of ieCPCs (replicate 2)

description:
These cells were collected after ieCPCs were exposed to cardiac differentiation condition for 25 days.
CM_cardiac_derivatives_of_ieCPCs--replicate_2_bc14_CACCTC

value: CACCTC

value: Replicate 2


title: CM cardiac derivatives of ieCPCs (replicate 1)

description:
These cells were collected after ieCPCs were exposed to cardiac differentiation condition for 25 days.
CM_cardiac_derivatives_of_ieCPCs--replicate_1_bc13_ACAAAC

value: ACAAAC

value: Replicate 1


title: ieCPCs at Passage 12 (replicate 2)

description:
The ieCPCs were collected at passage 12.
ieCPCs_at_Passage_12--replicate_2_bc11_GTGTTA

source_name: ieCPCs at Passage 12

value: GTGTTA

value: cardiac progenitors

tag: passage


title: ATAC-seq_tet123_wt_rep2

data_processing: The ATAC-seq library was sequenced on the Illumina Hi-seq 2000 sequencing platform. Reads were aligned using zebrafish July 2010 assembly (danRer7) as the reference genome. Duplicated pairs or those ones separated by more than 2Kb were removed. The enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.

extract_protocol: ATAC-seq experiments were performed as previously described (Buenrostro et al. 2013). Briefly, 10 zebrafish embryos were manually dechorionated and disrupted in 500 µl of Ginzburg Fish Ringers (55 mM NaCl, 1.8 mM KCl, 1.25 mM NaHCO3). After washing with cold PBS, 75.000 cells were lysed (lysis buffer: 10 µM Tris pH7.4, 10 µM NaCl, 3 µM MgCl2, 0.1% IGEPAL) and incubated for 30 min at 37ºC with the TDE1 enzyme. The sample was then purified with Qiagen Minelute kit, and a PCR was performed with 13 cycles using Ad1F and Ad2.1R primers and KAPA HiFi hotstart enzyme (Kapa Biosystems).

value: mixed AB and Tübingen

value: NO


title: ieCPCs at Passage 12 (replicate 3)

description:
The ieCPCs were collected at passage 12.
ieCPCs_at_Passage_12--replicate_3_bc12_TGTGAA

value: TGTGAA


title: ieCPCs at Passage 12 (replicate 1)

description:
The ieCPCs were collected at passage 12.
ieCPCs_at_Passage_12--replicate_1_bc10_CACACA

value: CACACA


title: LpM spib 2

value: intestine

value: 8-10 weeks old


title: ieCPCs at Passage 3 (replicate 1)

description:
The induced expandable cardiovascular progenitor cells (ieCPCs) were collected at passage 3.
ieCPCs_at_Passage_3--replicate_1_bc7_GGATGT

source_name: ieCPCs at Passage 3

value: mixed background of C57BL/6 and 129J/SvE

value: Wildtype (WT)

value: GGATGT


title: 2nd MEFs at Day 9 of reprog (replicate 3)

description:
These cells were collected at the day 9 of cardiac reprogramming from 2nd MEFs.
2nd_MEFs_at_Day_9_of_reprog--replicate_3_bc6_CCTCGG

source_name: 2nd MEFs at Day9 of reprogramming

value: CCTCGG

value: reprogramed fibroblasts

value: 9 days of cardiac reprogramming from 2nd MEFs


title: 2nd MEFs at Day 9 of reprog (replicate 1)

description:
These cells were collected at the day 9 of cardiac reprogramming from 2nd MEFs.
2nd_MEFs_at_Day_9_of_reprog--replicate_1_bc4_TTCAGC

value: TTCAGC


title: ieCPCs at Passage 3 (replicate 2)

description:
The induced expandable cardiovascular progenitor cells (ieCPCs) were collected at passage 3.
ieCPCs_at_Passage_3--replicate_2_bc8_TTCGCT

value: TTCGCT

value: Replicate 2


title: 2nd MEFs at Passage 3 (replicate 3)

description:
The secondary mouse embryonic fibroblasts (2nd MEFs) were derived as previously described by Wernig et al.in 2008
2nd_MEFs_at_Passage_3--replicate_3_bc3_GGACCC

source_name: 2nd MEFs at Passage 3

value: GGACCC

value: fibroblasts

value: Replicate 3


title: ieCPCs at Passage 3 (replicate 3)

description:
The induced expandable cardiovascular progenitor cells (ieCPCs) were collected at passage 3.
ieCPCs_at_Passage_3--replicate_3_bc9_ACACGA

value: ACACGA

value: cardiac progenitors


title: 2nd MEFs at Passage 3 (replicate 1)

description:
The secondary mouse embryonic fibroblasts (2nd MEFs) were derived as previously described by Wernig et al.in 2008
2nd_MEFs_at_Passage_3--replicate_1_bc1_AAGGGA

value: AAGGGA

value: Replicate 1


title: ATAC-seq_tet123_MO_rep2

description: ATAC-seq

data_processing: ATAC-seq library was sequenced on the Illumina Hi-seq 2000 sequencing platform. Reads were aligned using zebrafish July 2010 assembly (danRer7) as the reference genome. Duplicated pairs or those ones separated by more than 2Kb were removed. The enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.

value: whole embryo

value: mixed AB and Tübingen

value: Morpholino against Tet1/Tet2/Tet3


title: ATAC-seq_tet123_MO_rep1

description: ATAC-seq


title: CK-1 (wild type)

city: wuhan

first: Yanna

last: Gao

address: hongshan area, shizishan street

country: China

institute: Huazhong agricultural university

data_processing:
Illumina HiSeq 2000 used for RNA-Seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Solanum lycopersicum whole genome by Tophat.
Fragment Per Kilobase of exon model per Million mapped reads (FPKM) were calculated using a protocol from Trapnell, Cole, et al (2010).
Genome_build: Solanum lycopersicum
Supplementary_files_format_and_content: tab-delimited text files include the number of FPKM values of each gene for each Sample…

organism: Solanum lycopersicum

source_name: leaf

extract_protocol:
The young primary leaf samples harvested  were frozen in liquid nitrogen and kept at -80°C until use. Total RNA was extracted using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Wild type

value: young primary leaf

value: seedling


title: ATAC-seq_tet123_wt_rep1

description: ATAC-seq

tag: tissue

value: NO


title: 2nd MEFs at Passage 3 (replicate 2)

description:
The secondary mouse embryonic fibroblasts (2nd MEFs) were derived as previously described by Wernig et al.in 2008
2nd_MEFs_at_Passage_3--replicate_2_bc2_CCTTCA

value: mixed background of C57BL/6 and 129J/SvE

value: Wildtype (WT)

value: CCTTCA


title: ID60.siE2F1

status: Public on Jan 28 2016

city: Singapore

first: Walter

last: Stunkel

address: 30 Medical Drive, Brenner Centre Lvl 4

country: Singapore

institute: Singapore Institute for Clinical Sciences

description: siE2F1 RNA-seq in ID60 AGA MSCs

data_processing:
Alignment: sequence reads were obtained using the Illumina HiSeq 2000 (or 2500) Pipeline (instrument model specified in raw files section)
For ChIP-seq and genomic input: reads were mapped using bowtie -m 5 --phred33-quals -5 0 -3 0 --best -n 2 -l 28 -B 1 -S -p 4
For E2F1 ChIP-seq: MACS2 was used to call the peaks with respective genomic input and default parameter of q-value 0.05
DiffBind R Package was used to generate consensus peaks for all E2F1 ChIP-seq and output to [E2F1_consensus.bed]
For RNA-seq: ID01.basal ID56.basal ID75.basal ID44.basal ID57.basal ID60.basal ID01.siCTRL ID56.siCTRL ID75.siCTRL ID44.siCTRL ID57.siCTRL ID60.siCTRL ID01.siE2F1 ID56.siE2F1 ID75.siE2F1 ID44.siE2F1 ID57.siE2F1 ID60.siE2F1
bigWig for histone marks and E2F1 ChIP-seq were generated using bamcompare against their respective genomic input reads.  Command used: bamCompare --scaleFactorsMethod SES -bs 20 -b1 (chip reads bam file) -b2 (respective genomic input reads bam file)
bigWig in AGA group were averaged and output as [AGA.(CHIPNAME).bigWig]
bigWig in SGA group were averaged and output as [SGA.(CHIPNAME).bigWig]
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: bigWig generated using bamcompare Signal Extraction Scaling against respective input
Supplementary_files_format_and_content: genecounts.xls: gene counts for all RNA-seq experiments against ENSEMBL GENCODE19 annotation
Supplementary_files_format_and_content: E2F1_consensus.bed: consensus of all E2F1 peak files using DiffBind

source_name: umbilical cord wharton's jelly

growth_protocol:
UC-MSCs were cultured in Dulbecco’s modified Eagle’s medium containing high glucose which was further supplemented with 20% fetal bovine serum, 1 X Insulin-Transferrin-Selenium G, 5 ng/ml basic fibroblast growth factor, 1 X Antibiotic/antimycotic mix and 0.1 mmol/l beta-mercaptoethanol.
UC-MSCs were cultured in Dulbecco’s modified Eagle’s medium containing high glucose which was further supplemented with 20% fetal bovine serum, 1 X Insulin-Transferrin-Selenium G, 5 ng/ml basic fibroblast growth factor, 1 X Antibiotic/antimycotic mix and 0.1 mmol/l beta-mercaptoethanol.

extract_protocol:
Cells were cross-linked then sonicated to generate chromatin fragment sizes between 250-500bp. For E2F1 and histone ChIP-seq, the chromatin was immunoprecipitated with appropriate amounts of antibody. For genomic input, the chromatin was not subjected to antibody pull-down.
ChIP-enriched DNA was first quantified with the Quant-iT™ PicoGreen® dsDNA Assay Kit (Invitrogen, P11496) and ChIP-seq libraries were prepared from 5 ng of ChIP DNA using the TruSeq ChIP Sample Preparation Kit Set A (Illumina, IP-202-1012) according to the manufacturer’s protocol with some modifications. Adapter-ligated DNA was amplified with 13 cycles using the Primer Cocktail and Master Mix provided in the kit. Amplified products of appropriate sizes were excised from agarose gel stained with SYBR® Gold Nucleic Acid Gel Stain (Invitrogen, S11494) and purified using the MinElute Gel Extraction Kit (Qiagen, 28604). The DNA libraries were then checked for quality and quantified using the Agilent 2100 Bioanalyzer and DNA 1000 Kit (Agilent Technologies, 5067-1504). The histone modification ChIP-seq libraries were sequenced by a local NGS service provider (Genome Institute of Singapore, Singapore) whereas the E2F1 ChIP-seq libraries were sent for sequencing to the Beijing Genomics Institute (BGI). All ChIP-seq libraries were sequenced as 36-bp single-end reads using the Illumina HiSeq 2000 according to standard manufacturer’s procedures.
Total cellular RNA from UC-MSCs was extracted using TRIzol® Reagent (Invitrogen, 15 596-026) and chloroform before purifying with miRNeasy Mini Kit (Qiagen, 217004) according to the manufacturer’s instructions.
RNA integrity was checked and concentration was determined using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Kit (Agilent Technologies, 5067-1511). 2 µg of total cellular RNA from the UC-MSCs was depleted of ribosomal RNA (rRNA) using the Ribo-ZeroTM Magnetic Gold Kit (Epicentre, MRZG126) as per manufacturer’s instructions and purified via ethanol precipitation. The removal of rRNA was confirmed using Agilent 2100 Bioanalyzer and RNA 6000 Pico Kit (Agilent Technologies, 5067-1513). WT RNA-Seq libraries were then constructed using the TruSeq Stranded Total RNA LT Kit A (Illumina, RS-122-2201) according to manufacturer’s protocol. Adapter-ligated cDNA was amplified with 10 cycles using the PCR Primer Cocktail and PCR Master Mix provided in the kit. cDNA libraries were similarly checked for quality and quantified using the Agilent 2100 Bioanalyzer and DNA 1000 Kit as mentioned earlier before. The libraries were sent to Beijing Genomics Institute (China) for sequencing as 76-bp paired-end reads on the Illumina HiSeq 2000 according to standard manufacturer’s procedures.

tag: knockdown

value: Mesenchymal stem cells

tag: agasga

value: AGA


title: ID57.siE2F1

description: siE2F1 RNA-seq in ID57 AGA MSCs


title: MM control 1

value: intestine

value: 8-10 weeks old


title: ID44.siE2F1

description: siE2F1 RNA-seq in ID44 AGA MSCs


title: OV-5-1

value: Overexpression of SlRBZ transgenic plants

tag: developmental stage


title: ID60.siCTRL

description: siCTRL RNA-seq in ID60 AGA MSCs

value: siCTRL


title: ID01.siE2F1

description: siE2F1 RNA-seq in ID01 SGA MSCs

value: SGA


title: MethylC-seq_dr_brain

value: brain

value: adult

tag: genetic background

tag: transgenic embryos


title: ID57.siCTRL

description: siCTRL RNA-seq in ID57 AGA MSCs


title: ID56.siE2F1

description: siE2F1 RNA-seq in ID56 SGA MSCs


title: ID75.siCTRL

description: siCTRL RNA-seq in ID75 SGA MSCs


title: ID44.siCTRL

description: siCTRL RNA-seq in ID44 AGA MSCs


title: ID56.siCTRL

description: siCTRL RNA-seq in ID56 SGA MSCs


title: 2nd MEFs at Day 9 of reprog (replicate 2)

description:
These cells were collected at the day 9 of cardiac reprogramming from 2nd MEFs.
2nd_MEFs_at_Day_9_of_reprog--replicate_2_bc5_AAGACG

value: AAGACG

value: reprogramed fibroblasts

value: 9 days of cardiac reprogramming from 2nd MEFs

value: Replicate 2


title: ID01.siCTRL

description: siCTRL RNA-seq in ID01 SGA MSCs


title: ID56.Input

description: ID56 SGA MSCs Genomic Input DNA Sequencing

tag: chip antibody


title: ID44.Input

description: ID44 AGA MSCs Genomic Input DNA Sequencing


title: ID57.Input

description: ID57 AGA MSCs Genomic Input DNA Sequencing


title: ID60.Input

description: ID60 AGA MSCs Genomic Input DNA Sequencing


title: ID57.H3K4me3

description: H3K4me3 ChIP sequencing in ID57 AGA MSCs

value: H3K4me3 (5ug Abcam, AB8580)

tag: number of cells

value: 1.5 million


title: ID56.H3K4me3

description: H3K4me3 ChIP sequencing in ID56 SGA MSCs


title: ID60.H3K4me3

description: H3K4me3 ChIP sequencing in ID60 AGA MSCs


title: ID44.H3K4me3

description: H3K4me3 ChIP sequencing in ID44 AGA MSCs


title: ID57.H3K4me1

description: H3K4me1 ChIP sequencing in ID57 AGA MSCs

value: H3K4me1 (2ug Abcam, AB8895)


title: ID44.H3K4me1

description: H3K4me1 ChIP sequencing in ID44 AGA MSCs


title: ID01.Input

description: ID01 SGA MSCs Genomic Input DNA Sequencing


title: ID60.H3K4me1

description: H3K4me1 ChIP sequencing in ID60 AGA MSCs


title: ID01.H3K4me3

description: H3K4me3 ChIP sequencing in ID01 SGA MSCs


title: ID01.H3K4me1

description: H3K4me1 ChIP sequencing in ID01 SGA MSCs


title: ID75.H3K4me3

description: H3K4me3 ChIP sequencing in ID75 SGA MSCs


title: ID56.H3K4me1

description: H3K4me1 ChIP sequencing in ID56 SGA MSCs


title: ID75.H3K4me1

description: H3K4me1 ChIP sequencing in ID75 SGA MSCs


title: ID44.H3K36me3

description: H3K36me3 ChIP sequencing in ID44 AGA MSCs

value: H3K36me3 (2ug Abcam, AB9050)


title: ID75.H3K36me3

description: H3K36me3 ChIP sequencing in ID75 SGA MSCs

value: Mesenchymal stem cells


title: ID56.H3K36me3

description: H3K36me3 ChIP sequencing in ID56 SGA MSCs


title: ID60.H3K27me3

description: H3K27me3 ChIP sequencing in ID60 AGA MSCs

value: H3K27me3 (20ug Millipore, 07-449)

value: 3 million

value: AGA


title: ID01.H3K36me3

description: H3K36me3 ChIP sequencing in ID01 SGA MSCs


title: ID44.H3K27me3

description: H3K27me3 ChIP sequencing in ID44 AGA MSCs


title: ID75.H3K27me3

description: H3K27me3 ChIP sequencing in ID75 SGA MSCs


title: ID57.H3K27me3

description: H3K27me3 ChIP sequencing in ID57 AGA MSCs


title: ID56.H3K27me3

description: H3K27me3 ChIP sequencing in ID56 SGA MSCs


title: ID01.H3K27me3

description: H3K27me3 ChIP sequencing in ID01 SGA MSCs


title: ID75.Input

description: ID75 SGA MSCs Genomic Input DNA Sequencing


title: ID60.H3K27ac

description: H3K27ac ChIP sequencing in ID60 AGA MSCs

value: H3K27ac (2ug Abcam, AB4729)


title: ID44.H3K27ac

description: H3K27ac ChIP sequencing in ID44 AGA MSCs


title: ID60.E2F1

description: E2F1 ChIP sequencing in ID60 AGA MSCs

value: E2F1 (10ug Santa Cruz, sc-193X)

value: 8 million


title: ID57.E2F1

description: E2F1 ChIP sequencing in ID57 AGA MSCs


title: ID44.E2F1

description: E2F1 ChIP sequencing in ID44 AGA MSCs


title: ID01.E2F1

description: E2F1 ChIP sequencing in ID01 SGA MSCs

value: SGA


title: ID56.H3K27ac

description: H3K27ac ChIP sequencing in ID56 SGA MSCs


title: ID75.E2F1

description: E2F1 ChIP sequencing in ID75 SGA MSCs


title: ID01.H3K27ac

description: H3K27ac ChIP sequencing in ID01 SGA MSCs


title: M_002062977862_KY

city: Seoul

first: Minseok

last: Seo

address: Kwan-ak ro 1

department: Interdisciplinary program of bioinformatics

country: South Korea

institute: Seoul National University

data_processing:
We employed Trimmomatic (Bolger et al. 2014) with following option : PE -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 MINLEN:75 2 for making clean reads.
We mapped such clean reads into genome reference (BosTau7) from USSC database using Bowtie2, implemented in tophat2
For making the SAM file from the BAM file, we used a SAMtools
We used HTseq package (Anders 2010) for estimating mapped reads count on each of annotated genes from Bos taurus7 gene transfer format (.GTF) file.
Genome_build: BosTau7
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample

organism: Bos taurus

source_name: Male(Bull) Muscle

extract_protocol:
All animal procedures were approved by the National Institute of Animal Science Institutional Animal Use and Care Committee (NIASIAUCC), Republic of Korea, and performed in accordance with the animal experimental guidelines provided by NIASIAUCC as above described. We used Korean cattle from the Dae Kwan Ryung experimental branches of the National Institute of Animal Science (NIAS). These cattle were slaughtered at age of (> 22 months) and carcass weight was 353 ± 36 kg after slaughter. Abdominal adipose tissue, liver, intact longissimus dorsi muscle, and pituitary gland tissue samples were immediately separated after slaughter. Tissue sample were stored at -80°C. Total RNA was isolated from four tissues using the TRIzol reagent (Invitrogen) based on the manufacturer's instructions. The extracted total RNA was stored at -80°C or assessed for RNA-sequencing.
Libraries were prepared using  illimina manual and platform.

tag: Sex

value: Male

value: Muscle


title: M_002062977862_NS

source_name: Male(Bull) Pituitary-gland

value: Pituitary-gland


title: M_002062977862_JB

source_name: Male(Bull) Fat

value: Fat


title: ID57.H3K36me3

description: H3K36me3 ChIP sequencing in ID57 AGA MSCs


title: ID56.E2F1

description: E2F1 ChIP sequencing in ID56 SGA MSCs


title: M_002059653722_KY


title: M_002062977862_G

source_name: Male(Bull) liver

value: Liver


title: M_002059653722_G


title: M_002059653722_JB


title: M_002059653722_NS


title: M_002057817341_KY


title: ID75.H3K27ac

description: H3K27ac ChIP sequencing in ID75 SGA MSCs


title: M_002057817341_G


title: M_002057817341_JB


title: M_002056819043_NS


title: M_002056819043_JB


title: M_002056819043_KY


title: M_002056819043_G


title: M_002056410964_KY


title: UF_B19

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

description: 3' adapter sequence: TGTGTTCGTATGCCGTCTTCTGCTTG

data_processing:
Illumina GA IIx standard base-calling
RNAworld in-house allingment and annotation pipeline (see PMID: 22836126)
Genome_build: hg19

source_name: urine

extract_protocol:
TRIzol-based (see PMID: 24489795)
ligation/gel-based small RNA cDNA library (see PMID: 24489795)

tag: void

value: B

tag: fraction

value: extracellular vesicles (Evs)

value: F


title: UF_B20

description: 3' adapter sequence: TTGGTTCGTATGCCGTCTTCTGCTTG


title: UF_B17

description: 3' adapter sequence: TGATGTCGTATGCCGTCTTCTGCTTG


title: FM_002056944375_NS

source_name: Female(Cow) Pituitary-gland

value: Female


title: UF_B15

description: 3' adapter sequence: TAGGATCGTATGCCGTCTTCTGCTTG

value: M


title: FM_002056944375_KY

source_name: Female(Cow) Muscle


title: UF_B14

description: 3' adapter sequence: TAGAGTCGTATGCCGTCTTCTGCTTG


title: M_002057817341_NS


title: UF_B16

description: 3' adapter sequence: TATCATCGTATGCCGTCTTCTGCTTG


title: M_002056410964_JB


title: UF_B13

description: 3' adapter sequence: TAATATCGTATGCCGTCTTCTGCTTG


title: FM_002045323314_NS


title: ID75.siE2F1

description: siE2F1 RNA-seq in ID75 SGA MSCs

value: Mesenchymal stem cells


title: FM_002056944375_G

source_name: Female(Cow) liver


title: UF_B11

description: 3' adapter sequence: TTAAGTCGTATGCCGTCTTCTGCTTG


title: ID60.H3K36me3

description: H3K36me3 ChIP sequencing in ID60 AGA MSCs

value: H3K36me3 (2ug Abcam, AB9050)

value: 1.5 million


title: FM_002045323314_KY


title: UF_B9

description: 3' adapter sequence: TCTCCTCGTATGCCGTCTTCTGCTTG


title: UF_B10

description: 3' adapter sequence: TCTGATCGTATGCCGTCTTCTGCTTG


title: UF_B8

description: 3' adapter sequence: TCTAGTCGTATGCCGTCTTCTGCTTG


title: M_002056410964_NS


title: FM_002031791453_NS


title: UF_B7

description: 3' adapter sequence: TCGCGTCGTATGCCGTCTTCTGCTTG


title: M_002056410964_G


title: UF_B6

description: 3' adapter sequence: TCGATTCGTATGCCGTCTTCTGCTTG


title: FM_002031791453_KY


title: FM_002031791453_G


title: UF_B2

description: 3' adapter sequence: TCATCTCGTATGCCGTCTTCTGCTTG


title: FM_002031790233_JB

source_name: Female(Cow) Fat


title: FM_002031790233_KY


title: UF_B12

description: 3' adapter sequence: TAACGTCGTATGCCGTCTTCTGCTTG


title: UF_B5

description: 3' adapter sequence: TCCTATCGTATGCCGTCTTCTGCTTG


title: UF_B4

description: 3' adapter sequence: TCCGTTCGTATGCCGTCTTCTGCTTG


title: FM_002056944375_JB


title: UF_A20

description: 3' adapter sequence: TTGGTTCGTATGCCGTCTTCTGCTTG

value: A


title: UF_B3

description: 3' adapter sequence: TCCACTCGTATGCCGTCTTCTGCTTG


title: FM_002031789184_NS


title: FM_002031790233_G


title: UF_A19

description: 3' adapter sequence: TTACATCGTATGCCGTCTTCTGCTTG


title: FM_002031790233_NS


title: FM_002031789184_KY


title: UF_A17

description: 3' adapter sequence: TGATGTCGTATGCCGTCTTCTGCTTG


title: FM_002045323314_JB


title: FM_002045323314_G


title: FM_002031789184_G


title: UF_A16

description: 3' adapter sequence: TATCATCGTATGCCGTCTTCTGCTTG


title: FM_002031789184_JB


title: UF_A14

description: 3' adapter sequence: TAGAGTCGTATGCCGTCTTCTGCTTG


title: UF_A15

description: 3' adapter sequence: TAGGATCGTATGCCGTCTTCTGCTTG


title: FM_002031791453_JB


title: UF_A13

description: 3' adapter sequence: TAATATCGTATGCCGTCTTCTGCTTG


title: UF_A12


title: UF_B1

description: 3' adapter sequence: TCACTTCGTATGCCGTCTTCTGCTTG


title: UF_A11

description: 3' adapter sequence: TTAAGTCGTATGCCGTCTTCTGCTTG


title: UF_A10

description: 3' adapter sequence: TCTGATCGTATGCCGTCTTCTGCTTG


title: UF_A8

description: 3' adapter sequence: TCTAGTCGTATGCCGTCTTCTGCTTG


title: UF_A6

description: 3' adapter sequence: TCGATTCGTATGCCGTCTTCTGCTTG


title: UF_A7

description: 3' adapter sequence: TCGCGTCGTATGCCGTCTTCTGCTTG


title: UF_A9

description: 3' adapter sequence: TCTCCTCGTATGCCGTCTTCTGCTTG


title: UF_A18

description: 3' adapter sequence: TGTGTTCGTATGCCGTCTTCTGCTTG


title: UF_A3


title: cells_B20

value: cells


title: UF_A2

description: 3' adapter sequence: TCATCTCGTATGCCGTCTTCTGCTTG


title: cells_B17


title: UF_A1


title: cells_B19


title: UF_A5

description: 3' adapter sequence: TCCTATCGTATGCCGTCTTCTGCTTG


title: cells_B18


title: cells_B16


title: cells_B13


title: cells_B11


title: cells_B15


title: cells_B14


title: cells_B12

description: 3' adapter sequence: TAACGTCGTATGCCGTCTTCTGCTTG


title: Esamlo_ITD_2

city: Ithaca

first: Colleen

last: Lau

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
Base-calling was performed by bcl2fastq (v 1.8.4).
Fastq files were aligned to mm10 genome using the Galaxy wrapper for Fastq Groomer (v 1.0.4) and Bowtie2 (v 0.4).
Mapped reads were counted using the summarizeOverlaps function from the GenomicAlignments package (v 1.4.2) and the TxDb.Mmusculus.UCSC.mm10.ensGene package (v 3.1.2).
DESeq2 package (v 1.8.2) was used to generate normalized counts.
Downstream differential expression was done using default parameters of DESeq2, controlling for experimental batches. Genes that had 1 or no counts were excluded from analysis.
Genome_build: mm10
Supplementary_files_format_and_content: DC_all_rawcounts.csv: Raw counts of all samples listed by Ensembl Gene ID.  DC_all_normcounts.csv: Normalized counts of all samples as computed by DESeq2, listed by Ensembl Gene ID. Genes that had 1 or no raw counts are excluded.

source_name: Spleen

extract_protocol:
Splenic DCs were sorted by flow cytometry and pelleted. RNA was isolated using the Arcturus PicoPure RNA Kit as directed, or by Trizol reagent followed by the Arcturus PicoPure RNA Kit.
cDNA was prepared using the Clontech SMART-seq v4 Ultra Low Input RNA Kit, and library prep was prepared using the Clontech Low Input Library Prep Kit, both per manufacturer's instructions.

tag: strain

value: C57BL/6 x FVB/N F1

value: spleen

tag: dc subset

value: Esam-lo CD11b+

value: Flt3 ITD/+

tag: experiment batch

value: D


title: cells_B9


title: cells_B10


title: cells_B8


title: Esamlo_WT_2


title: UF_A4

description: 3' adapter sequence: TCCGTTCGTATGCCGTCTTCTGCTTG


title: Esamlo_ITD_1

value: C


title: cells_B7


title: cells_B6


title: Esamlo_WT_1


title: Esamhi_ITD_1

value: Esam-hi CD11b+


title: cells_B5

value: B


title: Esamhi_WT_2


title: Esamhi_WT_1


title: cells_B3

description: 3' adapter sequence: TCCACTCGTATGCCGTCTTCTGCTTG


title: cells_B4


title: Esamhi_ITD_2


title: NC_CD8_ITD_2

value: Non-canonical CD8+


title: NC_CD8_ITD_1


title: NC_CD8_WT_2


title: NC_CD8_ITD_3


title: C_CD8_ITD_3

value: Canonical CD8+


title: C_CD8_ITD_2


title: cells_B2

value: F


title: NC_CD8_WT_3


title: NC_CD8_WT_1


title: cells_A20

description: 3' adapter sequence: TTGGTTCGTATGCCGTCTTCTGCTTG


title: C_CD8_ITD_1


title: C_CD8_WT_2


title: C_CD8_WT_3


title: cells_B1


title: cells_A19

description: 3' adapter sequence: TTACATCGTATGCCGTCTTCTGCTTG


title: C_CD8_WT_1


title: cells_A18


title: cells_A17

description: 3' adapter sequence: TGATGTCGTATGCCGTCTTCTGCTTG


title: PDC_ITD_2

value: PDC


title: cells_A16

description: 3' adapter sequence: TATCATCGTATGCCGTCTTCTGCTTG


title: PDC_ITD_1


title: KMT2D ChIP-Exo 2

first: Siang-Yun

last: Ang

institute: Gladstone Institute of Cardiovascular Disease

description: Differentiated using a protocol from Wamstad et al., Cell, 2012.

data_processing:
Sequencing reads were de-multiplexed using CASAVA version 1.8.2.
Reads are trimmed using the fastq-mcf program (https://code.google.com/p/ea-utils/).
The filtered reads are analyzed using the Fastqc program (ttp://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The reads are aligned to the genome assembly of choice using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2).
Samtools is used to keep only the reads that do not map uniquely to the genome (mapq score >= 30) (http://samtools.sourceforge.net/).
bam2bed is used to convert bam files into bed files, the genome-wide shift between + and - strand tags is calculated in a manner adapted from the Kundaje method (Neph et al, Nature, 2012; Landt et al., Genome Res, 2012; http://bedops.readthedocs.org).
The genome is divided into 20bp bins. The tag density is defined as the number of tags that map to within 75bp of each genomic bin (Landt et al., Genome Res, 2012).
If input chromatin is provided, then the tag density of input is calculated identically. Tag densities are normalized as follows: tagDensity = #binsInGenome * ((#tags/#totalTags) - (#inputTags/#totalInputTags))
If input chromatin is not provided, then the tag densities are normalized as follows: tagDensityOfGenomicBin = #tagsAtBin(step06.1) * #binsInEntireGenome / #totalTagsInDataset
Bins representing either 6-fold enrichment over input (tag density ≥ 30) for H3K4me1/2/3 or roughly 6.64-fold over background (tag density ≥ 100) for KMT2D are accepted as peaks.
Enriched bins ("peaks") are merged together throughout the genome, merged bins representing signal peaks spanning multiple genomic bins are retained.
In order to compare peak scores and perform differential enrichment, peaks are annotated with total tag density within the peak region (Paige et al, Cell, 2012).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files contain tag density data displayable as a continuous graph.  BigBed files contain genomic intervals defined as "peaks" (see manuscript) stored in an indexed binary format; plain bed files contain the same but in plain text format.

source_name: Cardiomyocytes

growth_protocol: Male mice with a heterozygous Kmt2d floxed allele and expressing the Tnnt2::Cre recombinase (Tnnt2::Cre; Kmt2d fl/+) were crossed to female mice homozygous for Kmt2d floxed alleles and the Rosa26-Cre reporter mTmG (Kmt2d fl/fl; mTmG/mTmG). The females will carry litters with the WT control genotype (Tnnt2::Cre; Kmt2d fl/+; mTmG/+) and the mutant genotype (Tnnt2::Cre; Kmt2d fl/fl; mTmG/+).

extract_protocol:
ChIP-Exo Library Prep: All adapter and primer sequences were obtained from Serandour et al., Genome Biology, 2013.  Briefly, immunoprecipitation was performed using a mixture of Protein G magnetic beads, anti-KMT2D antibody, and crosslinked KMT2D-DNA complexes.  Beads were collected using a magnet and all supernatant (containing unbound material) was removed.  Several enzymatic reactions were then performed while the immunoprecipitated KMT2D-DNA complexes were still bound to the beads; a number of washes preceded each step.  First, complexes were treated with T4 DNA polymerase, E. coli Pol I large (Klenow) fragment, and T4 polynucleotide kinase to ensure all dsDNA fragments were blunt-ended with 5' phosphates.  Next, P7 adapter was ligated to each fragment using T4 DNA ligase.  Following ligation, nicks were repaired using Phi29 polymerase.  KMT2D-DNA complexes were then digested with Lambda exonuclease, which acts only in the 5' to 3' direction.  This step leaves behind single-stranded DNA except where crosslinked protein protects the DNA from digestion.  Following this first digestion, a second digestion was performed using RecJf, a fusion protein of RecJ and maltose binding protein.  This enzyme specifically digests single-stranded DNA in the 5' to 3' direction.  Finally, immunoprecipitated KMT2D-DNA complexes were eluted and crosslinks were reversed overnight (65C, 0.54M NaCl).  DNA was isolated from each sample.  Complimentary strand synthesis was completed by denaturing the DNA and then treating with Phi29 polymerase following the addition of a primer complimentary to the P7 adapter sequence.  DNA was isolated and P5 adapter was ligated to each strand using T4 DNA ligase.  DNA was again isolated and amplified using a pair of universal and barcoded primers.  Amplified fragments between 200 and 400bp were isolated from an agarose gel and purified.  This DNA was then clustered on an Illumina flow cell and sequenced on an Illumina HiSeq 4000.
Both WT and mutant hearts were thawed on ice and pooled into 3 replicates of 30 hearts each. Samples were crosslinked with 1% formaldehyde, lysed with cell lysis and nuclei lysis buffer, and sonicated to shear chromatin into 200-600 bp fragments. Each replicate was further split into input and 3 samples. Chromatin immunoprecipitation was performed with 3 ug of anti-H3K4me1/2/3 antibody (Abcam) overnight with Protein G Dynabead (Life Technologies). After washing, DNA was eluted, reverse-crosslinked and precipitated with AmPure XP magnetic beads (Beckman Coulter).

treatment_protocol: Both WT and mutant embryos were harvested at embryonic day E11.5 and embryonic hearts were dissected in cold PBS. Hearts were flash frozen in liquid nitrogen and kept at -80˚C.

tag: antibody

tag: cell type

value: ES-cell derived cardiomyocytes

tag: replicate

value: replicate 2

value: E14 Tg(Nkx2-5-EmGFP) mouse ES cells


title: KMT2D ChIP-Exo 3

value: replicate 3

tag: genotype


title: PDC_WT_2

tag: tissue


title: cells_A15

description: 3' adapter sequence: TAGGATCGTATGCCGTCTTCTGCTTG

value: A

value: cells

value: M


title: KMT2D ChIP-Exo 1

value: replicate 1


title: Liver

city: Bunkyo-ku

first: chaninya

last: wongwarangkana

state: Tokyo

address: 1-1-1 Yayoi

department: aquatic bioscience

country: Japan

institute: the university of tokyo

data_processing:
low quality reads and 3′ sequencing adapters were eliminated and trimmed, respectively, by our own Perl script.
Small RNAs (18–25 nt) were Blast-searched against mature miRNAs deposited in miRBase 19.0 (www.mirbase.org/), using CLC genomics workbench software (CLC bio, Aarhus, Denmark).
Genome_build: miRBase 19.0
Supplementary_files_format_and_content: tab-delimited text files containing sequence, expression values, length, count, name, resource, match type and mismatches.

organism: Takifugu rubripes

source_name: Liver

extract_protocol:
Total RNA was extracted using a  mirVana miRNA Isolation Kit (Applied Biosystems).
Nine small RNA libraries were constructed, using Small 415 RNA Library Preparation for SOLiD Sequencing (Applied Biosystems)

value: Liver

value: wild type


title: cells_A14

description: 3' adapter sequence: TAGAGTCGTATGCCGTCTTCTGCTTG


title: Testis

source_name: Testis

value: Testis


title: cells_A13

description: 3' adapter sequence: TAATATCGTATGCCGTCTTCTGCTTG


title: Slow muscle

source_name: Slow muscle

value: Slow muscle


title: mutant 3 H3K4me3 ChIP-Seq

description: Embryonic heart harvested at E11.5

source_name: E11.5 embryonic hearts

extract_protocol:
ChIP-Seq Library Prep: Immunoprecipitated complexes were washed and isolated.  Crosslinks were reversed overnight (65C, 0.54M NaCl).  DNA was then isolated and treated with T4 DNA polymerase, E. coli Pol I large (Klenow) fragment, and T4 polynucleotide kinase to ensure all dsDNA fragments are blunt-ended with 5' phosphates.  DNA then repurified and treated with Klenow 3' -> 5' exo minus and dATP to adenylate the 3' end of each fragment.  DNA was repurified and ligated to Illumina TruSeq indexed adapters containing a T-overhang using T4 DNA ligase.  DNA was repurified and PCR amplified using primers complimentary to the Illumina TruSeq adapter sequence.  Amplified fragments between 200 and 500bp were isolated from an agarose gel and purified.  This DNA was then clustered on an Illumina flow cell and sequenced on an Illumina HiSeq 2500.
Both WT and mutant hearts were thawed on ice and pooled into 3 replicates of 30 hearts each. Samples were crosslinked with 1% formaldehyde, lysed with cell lysis and nuclei lysis buffer, and sonicated to shear chromatin into 200-600 bp fragments. Each replicate was further split into input and 3 samples. Chromatin immunoprecipitation was performed with 3 ug of anti-H3K4me1/2/3 antibody (Abcam) overnight with Protein G Dynabead (Life Technologies). After washing, DNA was eluted, reverse-crosslinked and precipitated with AmPure XP magnetic beads (Beckman Coulter).

value: heart

value: Mutant Tnnt2::Cre; Kmt2d(fl/fl)


title: mutant 3 H3K4me2 ChIP-Seq

description:
Embryonic heart harvested at E11.5
H3K4me2_decreased.bed


title: Ovary

source_name: Ovary

value: Ovary


title: PDC_WT_1

value: C57BL/6 x FVB/N F1

value: spleen


title: cells_A12


title: Heart

source_name: Heart

value: Heart


title: Eye

source_name: Eye

value: Eye


title: mutant 3 input DNA

description: Embryonic heart harvested at E11.5

value: input


title: cells_A10

description: 3' adapter sequence: TCTGATCGTATGCCGTCTTCTGCTTG


title: Intestine

source_name: Intestine

value: Intestine


title: mutant 3 H3K4me1 ChIP-Seq

description:
Embryonic heart harvested at E11.5
H3K4me1_decreased.bed


title: Brain

source_name: Brain

value: Brain


title: cells_A9

description: 3' adapter sequence: TCTCCTCGTATGCCGTCTTCTGCTTG

value: A

value: cells


title: cells_A8

description: 3' adapter sequence: TCTAGTCGTATGCCGTCTTCTGCTTG

value: M


title: mutant 2 H3K4me3 ChIP-Seq

description: Embryonic heart harvested at E11.5

value: replicate 3


title: cells_A7

description: 3' adapter sequence: TCGCGTCGTATGCCGTCTTCTGCTTG

value: F


title: cells_A6

description: 3' adapter sequence: TCGATTCGTATGCCGTCTTCTGCTTG


title: cells_A5

description: 3' adapter sequence: TCCTATCGTATGCCGTCTTCTGCTTG


title: Fast muscle

source_name: Fast muscle

value: Fast muscle

value: wild type


title: MukBDA 22°C

city: Oxford

first: Sophie

last: Nolivos

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: Oxford University

data_processing:
Illumina Casava v1.8 used for basecalling.
Reads were adapter removed and trimmed to 40Bp using trimmomatic 0.32 with parameters ILLUMINACLIP:/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa:2:30:10 HEADCROP:8 CROP:40 SLIDINGWINDOW:6:5 MINLEN:40
Sequences were mapped to NC_000913.2 using bowtie2 v2.2.2 with parameters -N 0 --sensitive --minins 130 --maxins 780 -q --no-mixed --no-discordant  --no-unal
MACS v2.0.10.20131216 was used for peak calling with parameters --llocal=10000 -g 4639675 --bw 300 -p 0.05 --slocal=1000 --keep-dup=20
Genome_build: NC_000913.2
Supplementary_files_format_and_content: MACS v2.0.10.20131216 peaks file

organism: Escherichia coli K-12

source_name: E. coli

growth_protocol: Cells were grown in LB at 22°C or 37°C, as indicated.

extract_protocol:
Cells were resuspended in Lysis buffer (10mM tris, 20% sucrose, 50mM NaCl, 10mM EDTA, 10mg/ml lysosyme, 0.1mg/ml EDTA, 0.1mg/ml RNaseA) and subsequently incubated for 30min at 37C. Next, IP buffer was added (50mM Hepes, 150mM NaCl, 1mM EDTA, 1%triton, 0.1% sodium deoxycholate, 0.1% SDS). Cells have been sonicated, centrifugated, and the supernatent was used for the immunoprecipitation.
Sequencing libraries were constructed using the NEBNext Ultra DNA Library Prep Kit for Illumina (#E7370, NEB) for samples 1 to 3 (37 C) and the WaferGen PrepX ILM ChiP-Seq Library Kit (#400075, WaferGen) on the Apollo 324 System for samples 4 to 10 (22 C).

treatment_protocol: Crosslinking was performed using 1% of forlmaldehyde

tag: growth temperature

value: anti-Flag

tag: genotype/variation

value: AB1157 mukBDA-3xflag


title: cells_A11

description: 3' adapter sequence: TTAAGTCGTATGCCGTCTTCTGCTTG

source_name: urine


title: MukBEQ deltamatP 22°C

value: AB1157 mukBEQ-3xflag deltamatP


title: cells_A4

description: 3' adapter sequence: TCCGTTCGTATGCCGTCTTCTGCTTG


title: cells_A2

description: 3' adapter sequence: TCATCTCGTATGCCGTCTTCTGCTTG


title: mutant 1 H3K4me3 ChIP-Seq

description: Embryonic heart harvested at E11.5

value: heart

tag: developmental stage

value: Mutant Tnnt2::Cre; Kmt2d(fl/fl)


title: MukBEQ 22°C

value: AB1157 mukBEQ-3xflag


title: mutant 1 H3K4me2 ChIP-Seq

value: replicate 2


title: mutant 1 H3K4me1 ChIP-Seq

value: replicate 1


title: WT3 H3K4me3 ChIP-Seq

description:
Embryonic heart harvested at E11.5
H3K4me1_2_or_3_peaks.bed

value: Het control Tnnt2::Cre; Kmt2d(fl/+)


title: cells_A1

description: 3' adapter sequence: TCACTTCGTATGCCGTCTTCTGCTTG


title: mutant 1 input DNA

description: Embryonic heart harvested at E11.5

value: input


title: WT3 H3K4me1 ChIP-Seq

description:
Embryonic heart harvested at E11.5
H3K4me1_2_or_3_peaks.bed
H3K4me1_decreased.bed


title: WT3 H3K4me2 ChIP-Seq

description:
Embryonic heart harvested at E11.5
H3K4me1_2_or_3_peaks.bed
H3K4me2_decreased.bed


title: WT 22°C


title: MukB 22°C

value: AB1157 mukB-3xflag


title: MukB deltamatP 22°C

value: AB1157 mukB-3xflag deltamatP


title: WT3 input DNA

description: Embryonic heart harvested at E11.5


title: mutant 2 H3K4me1 ChIP-Seq


title: WT2 H3K4me3 ChIP-Seq


title: mutant 2 H3K4me2 ChIP-Seq


title: mutant 2 input DNA

description: Embryonic heart harvested at E11.5


title: WT2 H3K4me2 ChIP-Seq


title: deltamatP 22°C

value: AB1157 deltamatP


title: MukB 37°C


title: cells_A3

description: 3' adapter sequence: TCCACTCGTATGCCGTCTTCTGCTTG

value: A

value: cells


title: WT 37°C


title: WT2 H3K4me1 ChIP-Seq


title: WT2 input DNA

description: Embryonic heart harvested at E11.5


title: ID60.basal

description: basal RNA-seq in ID60 AGA MSCs

source_name: umbilical cord wharton's jelly

value: Mesenchymal stem cells

tag: agasga

value: AGA


title: Rpb2-HTP_clr4∆

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

institute: The Australian National University

description: Rpb2 CRAC in clr4∆ cells

data_processing:
Library protocol: CRAC-seq
Demultiplexing and removal of 3prime adapter conatmination and poly-A sequences was done in one step.
Reads were mapped to S. pombe genome, version ASM294v1.17, with Tophat2 software. (Tophat-2.0.14)
PCR duplicates were filtered out and genome-wide coverage was calculated using R Bioconductor packages.
Datasets were normalised for mean coverage over mRNA.
Genome_build: ASM294v1.17
Supplementary_files_format_and_content: BigWig format containing normalised genome-wide coverage

organism: Schizosaccharomyces pombe

source_name: Yeast RNA

growth_protocol: Cultures were grown in full media (YEA) at 30ºC to O.D. of 2.0.

extract_protocol:
For extraction and library preparation protocol please refer to the Materials and Methods section.
For extraction and library preparation protocol please refer to the Materials and Methods section.

treatment_protocol: The washed cells were UV-crossliked for 3 minutes at 254nm, then pelleted and flash frozen in liquid nitrogen

value: clr4_delta + Rpb2-HTP


title: ID57.basal

description: basal RNA-seq in ID57 AGA MSCs


title: ID44.basal

description: basal RNA-seq in ID44 AGA MSCs


title: WT1 H3K4me3 ChIP-Seq

value: replicate 3


title: ID75.basal

description: basal RNA-seq in ID75 SGA MSCs

value: SGA


title: Rpb2-HTP_Dhp1-1_rep2

description: Rpb2 CRAC in dhp1-1 mutant cells, rep2

value: Dhp1-1 + Rpb2-HTP


title: WT1 H3K4me1 ChIP-Seq

value: heart


title: Rpb2-HTP_Dhp1-1_rep1

description: Rpb2 CRAC in dhp1-1 mutant cells, rep1


title: MatP 37°C

tag: chip antibody

value: anti-Flag

value: AB1157 matP-3xflag


title: ID56.basal

description: basal RNA-seq in ID56 SGA MSCs


title: Rpb2-HTP_WT_rep2

description: Rpb2 CRAC in Wild Type cells, rep2

value: WildType + Rpb2-HTP


title: WGBS_J1_2iVitC

status: Public on Jan 27 2016

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: bisulfite converted genomic DNA

data_processing:
The first eight base pairs of the reads were trimmed using FASTX-Toolkit v0.0.13
Adapter sequences were removed with Cutadapt v1.3 and reads shorter than 16pb were discarded.
Cleaned sequences were aligned to the mouse genome (mm10) Using Bismark v0.12.5 and default parameters
Only reads mapping uniquely on the genome were conserved. Methylation calls were extracted after duplicates removal. Only CG dinucleotides covered by a minimum of 10 reads were conserved for the rest of the analysis.
The residually methylated regions (RMRs) In 2i+vitC sample were identified using the MethPipe pipeline (Song et al., 2013) With default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bed file is the output of methpipe pipeline. It represents residually methylated regions
Supplementary_files_format_and_content: Txt file represents for each CG, The coverage and the % Of methylation

source_name: ES cell in 2i+vitC

growth_protocol: ES cells were grown for two weeks in 2i medium in presence of vitaimin C : 50% neurobasal medium (Gibco), 50% DMEM/F12 (Gibco), 2mM L-glutamine (Gibco), 0.1mM β-mercaptoethanol, Ndiff Neuro2 supplement (Milipore), B27 serum-free supplement (Gibco), 1000U/mL LIF, 3μM Gsk3 inhibitor CT-99021, 1μM MEK inhibitor PD0325901, 100μg/mL vitamin C (Sigma). All 2i ES cells were grown in gelatin coated plates and passaged every two or three days using accutase (Gibco).

extract_protocol:
Genomic DNA was isolated using the GenElute Mammalian Genomic DNA Miniprep Kit from Sigma, with RNase treatment
Whole Genome Bisulfite sequencing library was prepared from 50ng of genomic DNA with the EpiGnome/Truseq DNA Methylation Kit (Illumina) following the manufacturer instructions.

value: J1 WT mouse ES cell

tag: culture medium


title: Rpb2-HTP_WT_rep1

description: Rpb2 CRAC in Wild Type cells, rep1


title: ID57.H3K27ac

description: H3K27ac ChIP sequencing in ID57 AGA MSCs

value: H3K27ac (2ug Abcam, AB4729)

tag: number of cells

value: 1.5 million


title: WT1 H3K4me2 ChIP-Seq

value: replicate 2

value: Het control Tnnt2::Cre; Kmt2d(fl/+)


title: RNA_J1_2iVitC_D13_rep1

data_processing:
Paired-end 2x100bp reads were mapped to the Mouse reference genome (mm10) Using Tophat v2.0.6 and the Refseq gene annotation allowing 5 mismatches.
Gene-scaled quantification was performed with HTSeq v0.6.1
Reads mapping to ribosomal RNA (rRNA) Sequences were first removed with Bowtie v1.0.0 allowing 3 mismatches.
The rRNA depleted libraries were then mapped on the Mouse reference genome (mm10) Using Bowtie v1.0.0 allowing zero mismatch and 10 000 best alignments per read. Exonic reads were removed.
In order to count reads mapping to transposable elements, Read were weighted by the number of mapping sites and each library was intersected with the reconstructed RepeatMasker annotation, Conserving only reads overlapping at least at 80% With a given transposon.
Genome_build: mm10
Supplementary_files_format_and_content: Text files represent gene or transposon-scaled expression value in log

source_name: ES cell

growth_protocol: ES cells initially cultivated in serum medium were grown for two weeks in 2i medium in presence of vitaimin C. Serum: Glasgow medium (Sigma), 15% FBS (Gibco), 2mM L-Glutamine, 0.1mM MEM non essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 0.1mM β-mercaptoethanol, 1000U/mL leukemia inhibitory factor (LIF, Miltenyi). ES cells were grown in feeder-free condition on gelatin-coated plates and passaged with TrypLE Express Enzyme (Life technology). 2i+vitC: 50% neurobasal medium (Gibco), 50% DMEM/F12 (Gibco), 2mM L-glutamine (Gibco), 0.1mM β-mercaptoethanol, Ndiff Neuro2 supplement (Milipore), B27 serum-free supplement (Gibco), 1000U/mL LIF, 3μM Gsk3 inhibitor CT-99021, 1μM MEK inhibitor PD0325901, 100μg/mL vitamin C (Sigma). All 2i ES cells were grown in gelatin coated plates and passaged every two or three days using accutase (Gibco).

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) and Dnase treatment performed with Turbo Dnase (Ambion)
RNA-seq libraries were prepared from 500ng of DNase-treated RNA with the TruSeq Stranded mRNA kit from Illumina

tag: day of convserion


title: RNA_J1_2iVitC_D0_rep2

value: Serum


title: RNA_J1_2iVitC_D6_rep2


title: RNA_J1_2iVitC_D13_rep2


title: ID01.basal

description: basal RNA-seq in ID01 SGA MSCs


title: RNA_J1_2iVitC_D6_rep1


title: H3K27me3_J1_2iVitC_D15_rep2

data_processing:
Paired-end 2x50bp reads were mapped to the Mouse reference genome (mm10) using Bowtie v1.0.0 allowing 3 mismatches.
One hit was randomly reported. Duplicate reads were removed using Picard v1.65
Tracks were created using HOMER software v4.7
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

extract_protocol:
Cells were cross-linked directly in the culture plate with 1% formaldehyde (culture medium supplemented with 1% formaldehyde, 0.015M NaCl, 0.15mM EDTA, 0.075mM EGTA, 15mM Hepes pH 8). Formaldehyde was quenched with 0.125M glycine and cells were washed in PBS and pelleted. Cells were then rotated at 4°C for 10 minutes in buffer 1 (Hepes-KOH pH 7.5 50mM, NaCl 140mM, EDTA pH 8.0 1mM, glycerol 10% NP-40 0.5%, Triton X-100 0.25% and the protease inhibitors: PMSF 1mM, Aprotinin 10μg/ml, leupeptin 1μg/ml and pepstatin1μg/ml), resuspended and rotated at room temperature for 10 minutes in buffer 2 (NaCl 200mM, EDTA pH 8.0 1mM, EGTA pH 8.0 0.5mM and 10mM Tris pH 8 and the same protease inhibitors as buffer 1) and then resuspended in buffer 3 (EDTA pH 8.0 1mM, EGTA pH 8.0 0.5mM, Tris pH8 10mM, N-lauroyl-sarcosine 0.5% and the protease inhibitors as buffer 1). Chromatin was sonicated with a Bioruptor (Diagenode) to reach a fragment size around 200bp. Chromatin corresponding to 10μg of DNA was incubated overnight at 4°C with 3-5μg of antibody in incubation buffer (buffer 3 supplemented with 0.5 volume of 3% Triton, 0.3% sodium deoxycholate, 15mM EDTA and protease inhibitors as in buffer 1). 5% of chromatin extracts were taken aside for inputs. Chromatin bound to the antibody was recovered using Active Motif Protein G Agarose Columns. Briefly, the antibody-chromatin mix was incubated in the column for 4 hours, washed eight times with modified RIPA buffer (Hepes pH7.6 50mM, EDTA pH 8.0 10mM, sodium deoxycholate 0.7%, NP-40 1%, LiCl 500mM, PMSF 1 mM, 1μg/ml leupeptin and 1μg/ml pepstatin), and washed one last time with TE-NaCl (50mM Tris pH 8.0, 10mM EDTA, 50mM NaCl). Chromatin was eluted with pre-warmed TE-SDS (50mM Tris pH 8.0, 10mM EDTA, 1% SDS). ChIP-enriched sample and inputs were then reverse cross-linked at 65°C overnight and treated with RNase A and proteinase K. DNA was extracted with phenol/chloroform/isoamyl alcohol, precipitated with glycogen in sodium acetate and ethanol and finally resuspended in TE.
20ng of ChIP- or input-DNA were used for ChIP-seq. Remaining large DNA fragment were first eliminated using SPRIselect beads (Beckman Coulter) and libraries were prepared using the TruSeq ChIP Sample Prep kit from Illumina.

tag: day of conversion

value: Cell Signaling C36B11


title: H3K27me3_J1_2iVitC_D0_rep2


title: H3K27me3_J1_2iVitC_D6_rep2


title: Input_J1_rep4

value: input


title: H3K27me3_J1_2iVitC_D6_rep1


title: WT1 input DNA

description: Embryonic heart harvested at E11.5

tag: strain


title: Input_J1_rep3


title: H3K9me3_J1_2iVitC_D15_rep2

value: Abcam ab8898


title: H3K9me3_J1_2iVitC_D0_rep2


title: H3K9me3_J1_2iVitC_D15_rep1


title: H3K9me3_J1_2iVitC_D6_rep1


title: Input_J1_rep1


title: H3K9me3_J1_2iVitC_D0_rep1


title: Input_J1_rep2


title: RNA_J1_2iVitC_D0_rep1


title: serumfree_female_C10

city: Gent

first: Dieter

last: De Coninck

address: J. Plateaustraat 22

department: Applied Ecology and Environmental Biology

country: Belgium

institute: Ghent University

data_processing:
Illumina Cassava 1.8 software used for basecalling
12bp from the 5' end from each read were trimmed. Additional read quality trimming was performed based on the Phred base quality scores and a limit setting equal to 0.03 using the CLC Genomics Workbench v7.0.4 software
Reads were aligned to the Bos taurus UMD3.1 v75 reference genome using the CLC Genomics Workbench 7.0.4 software at standard settings. Particular imprinted genes of interest were added to the reference genome annotation file: USP29 (NCBI Gene ID: 788661), PEG3 (444864), APEG3 (100169896), MEG3 (100335527), H19 (100126192) and XIST (338325)
The number of uniquely mapping exonic reads were considered in subsequent analyses
Genome_build: UMD3.1 v75
Supplementary_files_format_and_content: Tab-delimited text file contains then number of uniquely mapped exonic reads for each gene and sample

source_name: early blastocyst

growth_protocol: In vitro early bovine blastocysts (n =16) were produced by routine in vitro methods [6]. Briefly, ovaries from Holstein cows were collected at a local slaughterhouse and processed within 2 h. Cumulus oocyte complexes were aspirated from follicles between 4 and 8 mm in diameter and matured in groups of 60 in 500 µL of maturation media consisting of modified TCM-199 medium (GIBCO-BRL Life Technologies) supplemented, depending on the experimental set up, with either 20 ng/mL EGF (Epidermal Growth Factor; Sigma E4127) and 50 µg/mL gentamycine (serum-free conditions) or 20 % FBS (Fetal Bovine Serum; Biochrom AG, Berlin, Germany), 50 µg/mL gentamycine, 0.4 mM L-Glutamine and 2 mM Na-pyruvate (serum conditions) for 22 h at 38.5°C in 5 % CO2 in air. Frozen-thawed sperm from the same Holstein bull of proven fertility used to obtain the in vivo derived embryos (to minimize variation throughout the experiments) was separated through a discontinuous Percoll gradient (45 and 90 % (v/v); VWR International). The final sperm concentration of 1x106 spermatozoa/mL was adjusted in IVF-TALP, consisting of bicarbonate buffered Tyrode solution, supplemented with 6 mg/mL BSA (Sigma A8806) and 20 µg/mL heparin (Sigma). Matured oocytes were washed with WAS-TALP, consisting of HEPES buffered Tyrode solution supplemented with 0.34 mg/mL BSA (Sigma A6003) and incubated with the sperm for 21 h. Presumptive zygotes were vortexed for 3 minutes to remove rests of cumulus cells and spermatozoa, washed with WAS-TALP, and cultured in 50 µL drops of SOF supplemented with essential and non-essential amino acids and, depending on the experimental set up, 5% of FBS (serum conditions) or 0.4% BSA (Sigma A9647) and ITS (5 µg/mL Insulin + 5 µg/mL Transferrin + 5 ng/mL Selenium) (serum-free conditions) in both cases under mineral oil in groups of 25 at 38.5°C in 5% CO2, 5% O2 and 90% N2. Blastocysts were collected, between day 6 and 7 post insemination, from three independent in vitro experiments. The 8 in vivo derived blastocysts were obtained from three Holstein cows. The animals were superovulated with a total of 480 µg of FSH (Follicle-stimulating hormone; Stimufol) administered in eight decreasing doses every 12 h over 4 days. Prostaglandin injection (37.5 mg Enzaprost) was administered 48 h after the start of the superovulatory treatment. Two inseminations with the same Holstein bull of proven fertility used for the in vitro experiments were performed in 12 h intervals starting between 8-12 h after the assessment of the estrus. Seven days after insemination, both uterine horns underwent a non-surgical uterine horn flushing for embryo recovery.

extract_protocol:
The developmental stage and the quality of the blastocysts, according to IETS standards, was determined for all the embryos by the same three trained individuals. Only early blastocysts of quality 1 were selected for the study. Selected blastocysts were washed three times in RNase free PBS (Phosphate buffered saline; Ambion), placed individually in 2 µL of lysis buffer consisting in 5mM DTT (DT-Dithiothreitol; Promega), 4U/ µL RNasin Plus RNase inhibitor (Promega) and 0.64 µM Igepal (Sigma) in RNase free water (Sigma) and immediately stored on -80°C. RNA was extracted using the RNeasy micro kit (Qiagen) excluding RNase treatment. Manufacturer´s instructions were followed with a single modification performed in the elution step, when 14 µL of RNase free water was passed through the column two times.
Concentration and quality of the total RNA extracted were examined using Quant-iT RiboGreen RNA Assay kit (Life Technologies) and RNA 6000 Pico Chip (Agilent Technologies), respectively. Subsequently, 1 ng of RNA was used to start the library preparation. First, cDNA was synthesized using the 'SMARTer Ultra low input RNA for Illumina, High Volume kit' (Clontech) mainly following to manufacturer's instructions. For the PCR reaction 12 cycles were chosen. Second, the 'Low input library prep kit' (Clontech) was used to prepare the libraries for sequencing. Libraries were prepared according to manufacturer's instructions, 4+6 cycles were chosen during the PCR reaction in the protocol. Libraries were quantified by qPCR, according to Illumina's protocol 'Sequencing Library qPCR Quantification protocol guide', version February 2011. A high sensitivity DNA chip (Agilent Technologies) was used to control the size, distribution and quality of the libraries. Sequencing was performed by a rapid run on 2 lanes of the Illumina Hiseq-2000 sequencer using 2x100 bp paired-end reads; twelve samples were run per lane in equimolar quantities.

tag: growth condition

value: In vitro serum-free

tag: breed

value: Holstein

tag: Sex

value: female


title: serumfree_male_C1

value: male


title: serumfree_female_C3


title: serumfree_male_C6


title: serumfree_male_C4


title: serumfree_male_C7


title: serumfree_male_C2


title: serumfree_female_C8


title: H3K27me3_J1_2iVitC_D15_rep1

tag: cell type

tag: antibody


title: serum_male_B5

value: In vitro serum


title: serum_female_B6


title: serum_female_B8


title: serum_male_B7


title: H3K27me3_J1_2iVitC_D0_rep1


title: serum_female_B3


title: serum_male_B1


title: in_vivo_femaleA9

value: in vivo


title: serum_female_B2


title: H3K9me3_J1_2iVitC_D6_rep2


title: serum_female_B4


title: in_vivo_male_A8


title: in_vivo_female_A6


title: in_vivo_female_A7


title: in_vivo_male_A4


title: in_vivo_male_A1


title: in_vivo_male_A2


title: in vivo_male_A3


title: starved

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

description: small RNA

data_processing:
An artificial hexamer (ACATCG) was present at the 5’ end of 6-8% of all reads, so a custom Perl script was used to trim these occurrences.
We then used reaper (PMID:23816787) to process the FASTQ files, and remove the Illumina sRNA 3’ adapter sequence (ATCTCGTATGCCGTCTTCTGCTTGC).
Since we were interested in microRNAs, only cleaned reads between 16 and 28 nucleotides were kept. These sequences were collapsed to unique reads using tally (PMID:23816787), assigning their total counts to each sequence identifier.
Genome_build: The full genome, as well as all protein-coding and non-coding transcripts were downloaded form WormBase version WS235 in FASTA format (Yook et al. 2012). Sequences for all known C. elegans microRNA hairpins were obtained from miRBase version 19 (Kozomara & Griffiths-Jones, 2011). Mature sequences were also obtained from this database, but a Perl script was used to extend them by 3 bases at the 5’ end and 5 bases at the 3’ end, when permitted by the length of the hairpin. This extension facilitates sRNA-seq reads to map directly to mature miRNAs. All FASTA sequences were then concatenated to produce the final reference set.
Supplementary_files_format_and_content: Processed fasta files contain unique sequences after trimming, the total count of each unique sequence is added to the end of the identifier line.

organism: Caenorhabditis elegans

source_name: starved L4 worms

growth_protocol: The wild type strain N2 of C. elegans was grown under standard conditions (Wood, W.B., 1988) at 20 degrees Celsius. The worms were synchronized by killing of all the larval and adult worms by immersion in sodium hypochlorite, conditions in which only eggs can survive (Wood, W.B., 1988). Worms were then left to develop until larval stage L4.

extract_protocol:
Small RNAs were purified using the miRNeasy mini kit (Qiagen), following manufacturer’s instructions.
The cDNA libraries were prepared from 5 ug of small RNA. Preparation of cDNA libraries for the Illumina deep sequencing experiment was performed using the DGE-Small RNA Sample Prep Kit ver. 1.0 (Illumina) according to the manufacturer’s instructions.

treatment_protocol: L4 larvae were cleaned from bacteria in sucrose cushions and separated in two fractions. One fraction was immediately frozen (well-fed L4 worms), while the other fraction was incubated in a Petri dish without bacteria for 12 hrs, and then quickly frozen (starved L4 worms).

tag: stress

value: starved


title: wellfed

description: small RNA

source_name: well-fed L4 worms

value: well-fed


title: 0.7M sucrose, w1118, D2, cg_20

city: Binghamton

first: Laura

middle: Palanker

last: Musselman

address: 4400 Vestal Parkway East

department: Biological Sciences

institute: Binghamton University

data_processing:
To produce bed alignments, sequenced reads were aligned to the D. melanogaster UCSC dm3 assembly using Tophat (v1.3.2) and Bowtie (v0.12.7). Default Tophat settings were used.
Gene expression was quantified by processing the Tophat produced bam alignments with Cufflinks (v1.1.0) and the modENCODE MB8 annotation.
Expression was normalized by applying upper-quartile normalization as defined in "Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments", Bullard et al. BMC Bioinformatics. 2010; 11: 94
Genome_build: MB8
Supplementary_files_format_and_content: "GEO upload processed data.txt" file containing normalized RPKM for each raw dataset, indexed by gene Accession (CG number)

organism: Drosophila melanogaster

source_name: fat body

growth_protocol: Wild-type males (VDRC's w1118 or 60100 control stocks) were crossed to GAL4 driver line virgin females to produce offspring that serve as controls for various RNAi lines (not in this dataset). Larval offspring were collected at the end of larval development (also known as the wandering third instar stage)

extract_protocol:
Fat bodies were homogenized in Trizol and total RNA isolated after DNAse digestion.
RiboZero subtraction was used to remove rRNA and then reverse transcription, size exclusion, amplification, and bar coding produced the final library.
Reads using bar-coded cDNA were generated by Illumina Hi-Seq analyzer.

treatment_protocol: Larvae were reared on control (0.15M) or high-sugar (0.7M) diets using a modified Bloomington semi-defined food as previously described (J Biol Chem 288(12):8028-42). Fat bodies were isolated by fine dissection or by shearing and separation by centrifugation.

value: wandering third instar larva

tag: tissue

value: fat body

tag: strain/genotype

value: VDRC's 60000 stock crossed with a UAS-Dcr2 (X); cg-GAL4 stock


title: 0.7M sucrose, w1118, D2, r4_61

value: VDRC's 60000 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock


title: 0.7M sucrose, w1118, D2, cg_52


title: 0.7M sucrose, w1118, D2, r4_62


title: 0.7M sucrose, w1118, D2, cg_21


title: 0.7M sucrose, w1118, D2, cg_53


title: 0.7M sucrose, 60100, D2, r4_91

value: VDRC's 60100 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock


title: 0.7M sucrose, w1118, D2, cg_54


title: 0.15M sucrose, w1118, D2, r4_57


title: 0.15M sucrose, w1118, D2, r4_56


title: 0.15M sucrose, w1118, D2, r4_55


title: 0.7M sucrose, 60100, D2, r4_75


title: 0.15M sucrose, w1118, D2, cg_50


title: 0.15M sucrose, w1118, D2, cg_13


title: 0.15M sucrose, w1118, D2, cg_49


title: 0.15M sucrose, w1118, D2, cg_51


title: 0.7M sucrose, w1118, D2, r4_63


title: 0.15M sucrose, w1118, D2, cg_15


title: 0.7M sucrose, 60100, D2, r4_92


title: 0.15M sucrose, 60100, D2, r4_84


title: 0.15M sucrose, w1118, D2, cg_14


title: 0.15M sucrose, 60100, D2, r4_83


title: 0.15M sucrose, 60100, D2, r4_68


title: Saline 3

city: New York

first: Immanuel

last: Purushothaman

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Basecalls performed using CASAVA
Adapter (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) sequences were removed from 3' end by fastx.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat with options --frag-bias-correct and --multi-read-correct. Novel transcript assembly was not attempted.
Differential analysis was performed by Cuffdiff. An FDR<10% was used as cutoff.
Genome_build: Ensembl NCBIM37.62
Supplementary_files_format_and_content: An Excel spreadsheet of the differential analysis results

source_name: Brain Tissue

extract_protocol: NAc tissue was dissected.  Mice were housed in group of 5 mice per cage, and all mice in a cage were injected with either saline or cocaine and thus there was no counter-balancing between groups.

tag: tisue

value: brain

tag: treatment

value: Repeated Saline  I.P. injection for 1w

tag: age

tag: gender


title: 0.15M sucrose, 60100, D2, r4_67

tag: developmental stage


title: Saline 2


title: 0.7M sucrose, w1118, D2, cg_19


title: Cocaine 3

value: Repeated cocaine I.P. injection for 1w at 20mg/kg


title: Saline 1


title: 0.7M sucrose, 60100, D2, r4_76


title: Cocaine 1


title: RNA-seq_GATA3_Rep3

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

data_processing:
Reads were filtered based on a mean base quality score >20. Reads were mapped to hg19 genome using Bowtie 0.12.8
For ATAC-seq data processing, we performed Trim Galore! to remove adapter sequence contamination. The offset parameters suggested by Buenrostro et al were applied to each mapped read.
Peak calling was performed with HOMER v4.1 at default parameters.  Peaks were then adjusted to 200-mers centered on the midpoint of the HOMER calls.
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
All paired-end reads were converted to a single fragment.  After normalization within each data set, bigWig files were generated to visualize the genomic coverage.
For RNA-seq data processing, read counts per gene per sample were collected by HTSeq-Count.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, bed

growth_protocol: Cells were grown on 15 cm plats in high glucose DMEM medium with 10% FBS

extract_protocol: Libraries were prepared according to Illumina or BIOO SCIENTIFIC instruction. ATAC-seq libraries were prepared by following the original protocol (Buenrostro et al., 2013) with several modifications (as described above)

treatment_protocol:
ChIP-Seq: Cells were lysed with Tris-HCl pH 8.0 based buffer with appropriate concentration of SDS. Chromatin fragmentation was performed by sonication with Bioruptor or Covaris. DNA was precipitated with antibody against each target protein.
MNase-seq: Cells were treated with a hypotonic buffer. Isolated nuclei were digested with MNase. DNA Mononucleosomal DNA was extracted by using a ZYMO RESEARCH cleanup column and QIAGEN Gel extraction kit.
ATAC-seq: Cells were treated with CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100), and then chromatin tagmentation was performed by Tn5 transposase (5 µl in 25 µl total reaction, Nextera DNA Library Preparation Kit from Illumina).

tag: genotype/variation

value: GATA3 expressed

tag: passages


title: RNA-seq_GATA3_Rep2


title: RNA-seq_control_Rep2

value: Control cells (GFP expressed)


title: RNA-seq_GATA3_Rep1


title: BG880 PARE

first: David

middle: H

last: Bechhofer

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Department of Pharmacology and Systems Therapeutics

description: PARE

data_processing:
Base-calling was performed by Illumina CASAVA software.
Reads from fastq files were aligned to Bacillus subtilis genome by Bowtie 2 with --local option.
SAMtools and BEDtools were used to count reads mapped to specific genes for regular RNA-seq. Gene annotation reference was obtained from NCBI database. Homemade Python scripts were used to count read coverage at each base and to pick the peaks with >100 reads per position and >25nt in length for PARE experiments.
For regular RNA-seq, homemade Python script was used to normalize and compare the read abundance (reads/base) of each transcript as described in a previous study (Liu, B., et al. 2014 PMID: 25099370).
For PARE, homemade Python script was used to calculate an RR ratio for each peak found in BG880, which is the ratio of read coverage in the specific peak region in BG880 and BG879 normalized by the expression data of this region from regular RNA-seq (peak_100_RR.txt)
Genome_build: NC_000964.3
Supplementary_files_format_and_content: Tab-delimited txt files contain peaks (peaks_10_BG*.txt) or read abundance for genes (expression.txt)

organism: Bacillus subtilis

growth_protocol: The cells were cultured in LB medium at 37°C until mid-log phase.

extract_protocol:
Total RNA was extracted with hot phenol method, and ribosomal RNA was removed with Ribo-Zero rRNA Removal Kit for bacteria
For regular RNA-seq, Libraries were constructed according to the standard Illumina RNA-seq protocol. For PARE, equal amounts of samples were used to construct the PARE libraries using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1). The manufacturer’s protocol was modified so that 5ʹ monophosphorylated ends that result from endonuclease cleavage or pyrophosphohydrolase activity were preferentially selected. Briefly, after 3ʹ SR Adaptor ligation, reverse transcriptase (RT) primer hybridization, and 5ʹ SR Adaptor ligation – performed as per the manufacturer’s protocol – the reaction mixture volume was brought to 100 μl and samples were cleaned up with the RNeasy MinElute Cleanup Kit (Qiagen). 12 μl of RNA was recovered following the manufacturer’s protocol. The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 minutes, and 2 μl of stop solution was added. After a second RNeasy MinElute cleanup, half of the RNA (6 μl) was again ligated to the 3ʹ SR Adaptor. Thus, after magnesium fragmentation only RNAs that retained their 5ʹ SR Adaptor (and original 5’ monophosphate) would undergo subsequent RT and PCR amplification. After addition of the RT primer, the reaction volume was adjusted to 30 μl and RT/PCR amplification reactions were performed as per the manufacturer’s protocol, using barcoded primers. One tenth of the PCR reaction was run on a 1.5% agarose gel to visualize the library, which consisted of cDNA ranging from 50 to ~500 nts. 20 μl of the cDNA library were prepared for Illumina sequencing using a 1.5X volume of Agencourt AMPure XP Beads (Beckman Coulter), according to the manufacturer’s instructions. The procedure was repeated twice, and the sample was eluted in a final volume of 20 µl.

tag: genotype (on ribonucleases)

value: 37°C LB medium to mid-log phase

tag: molecule subtype

value: Total RNA with rRNA removed


title: BG879 PARE

description: PARE

tag: strain

value: ΔrnjA::spec Δrnc::ery

tag: growth condition


title: BG578 PARE

description: PARE

value: Pspac-rnjA ery


title: Cocaine 2

value: male


title: KDM5c_Spikein_SMCX_333_ChIP_WT_CN_rep2

city: Ann Arbor

first: Saurabh

last: Agarwal

state: Michigan

address: 1241 E. Catherine St. 5815 Medical Science II

department: Human Genetics

institute: University of Michigan

data_processing:
Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline.
Drosophila (DM3) and Mouse (MM9) genomes were merged and indexed using bowtie 1
First 50 bases of the reads (to maintain consistency across different ChIP-Seq samples) were mapped to the merged genome and only uniquely mapping reads were selected.
Reads mapping only to mm9 were selected and PCR duplicates were removed using samtools rmdup utility.
Normalization of enrichment was not done as WT and KO samples showed similar fraction of drosphila reads.
Genome_build: mm9

growth_protocol: Cortices from E16.5 male mouse embryos were collected in HHGN dissection solution (Hanks' Balanced Salt Solution supplemented with 2.5 mM Hepes, 35 mM Glucose, 4 mM sodium bicarbonate). Cortices were incubated with 0.1% trypsin (Life Technologies) in HHGN for 20 min. at room temperature, quenched in Neurobasal media (Life Technologies) containing 10% fetal bovine serum (FBS), and triturated in Neurobasal media containing 0.01 mg/ml DNaseI.  Dissociated cells were suspended in Neurobasal media supplemented with 1x B27 solution (Life Technologies), 1x penicillin-streptomycin , 0.5 mM L-glutamine, and 25 mM 2-mercaptoethanol. Cells from one cortex were plated in a 10-cm tissue culture dish treated with 50 mg/ml Poly-D-lysine hydrobromide (Sigma, MW 30,000-70,000). Cultured are maintained in humidified incubators with 5% CO2 at 37°C. Half of culture media was replaced with new culture media every 3 days in vitro (DIV), and cells were harvested on 9 or 10 DIV.

extract_protocol:
A small amount of sonicated drosphila chromatin was spiked-in to chromatin from mouse neurons. Spiked-In Chromatin was spiked-in with an antibody specific to drosphila specific histone variant. Chromatin was immunoprecipitated (overnight, 4°C) with beads and antibody (KDM5c 333). After immunoprecipitation, beads were washed as described previously. Immune complexes were eluted from beads (65°C, 5 min; and room temperature, 15 min) with 50 mM Tris-HCl pH 8.0, 1 mM EDTA and 1% SDS. Elution was repeated and eluates pooled. Reverse cross-linking was carried out (16h, 65°C) with addition of NaCl and RNase A. EDTA was increased to 5 mM and samples were incubated with 200 μg/ml proteinase K (2h, 50°C). DNA was recovered by phenol-chloroform extraction and ethanol precipitation, and quantifed by Qubit (Life Technologies).
ChIP-Seq libraries were prepared through standard Illumina's procedure for library-preparation using NEBNext library reagents.
ChIP-seq libraries were prepared from 10 ng DNA using NEBNext DNA library preparation reagents (E6000) and the protocol and reagent concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. After PCR amplification, 300-600 bp DNA fragments were selected on an agarose gel. Libraries were quantified by Qubit (Invitrogen), and library size was assessed by Bioanalyzer (Agilent). Libraries were sequenced using a HiSeq 2000 (Illumina) to generate 50 base single-end reads. ChIP-seq libraries were generated from two biological repeats per antibody, and matched Input samples.

treatment_protocol: Chromatin preparation was performed as described in8 with some modifications. Cortical neurons were fixed in 1% formaldehyde (10 min for histone modifications, 20 mins for Kdm5c, RT). Fixation was stopped by addition of Glycine to 0.125M (5 min, RT). Cells were washed in cold PBS, before “swelling” buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl and 0.1% NP-40) was added to lyse the cells (10 min, 4°C). After resuspension in “sonication” buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and 0.1% SDS), nuclei were sonicated using a Misonix 3000 (Amplitude 60; 25 cycles; 15s ‘on’, 45s ‘off’; 4°C). The resulting material was centrifuged twice (10 min, 4°C) at 14,000 rpm. Swelling and sonication buffers were supplemented with 5 mM NaF, 1 mM PMSF, and protease inhibitor cocktail (Roche). Magnetic beads (Protein G dynabeads, Invitrogen) were washed with sonication buffer before use.

value: WT

value: mouse embryonic cortex

tag: culture

value: 10 Days in vitro

tag: chip antibody

value: KDM5c 333

value: ChIP-DNA


title: RNA-seq_control_Rep1

tag: antibody


title: KDM5c_Spikein_Input_Pooled_CN_rep1

value: Pooled Input (WT + SMCX KO)

value: Input-DNA


title: KDM5c_Spikein_Input_Pooled_CN_rep2


title: AMY_WT_3_2091

data_processing:
Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline.
RNA-Seq reads were mapped to mm9 build using TOPHAT v2.1.1 and Bowtie 2 allowing for upto 2 mismatches.
Aligned BAM files were normalized to the sequencing depth and converted to bigwig files in a strand-specific manner using bedtobedgraph and wigtobigwig utilities.
Genome_build: mm9

source_name: Adult Amygdala

extract_protocol:
Total RNA was purified through Purelink RNA Mini Kit (Life Technologies). rRNA was depleted using RiboMinus Eukaryote kit for RNA-Seq (Life Technologies).
RNA-Seq libraries were prepared by Direct Ligation of Adapters to First Strand cDNA (DLAF) where splinted adapters were ligated to single-stranded first strand cDNA. The novel method is described in a manuscript under revision and the reference will be updated soon.

treatment_protocol: KCl Treated' cortical neurons were treated with 50mM KCl for 60 minutes.

tag: genotype

tag: tissue type

value: Adult Amygdala


title: AMY_KO_2_783

value: SMCX KO


title: KDM5c_Spikein_SMCX_333_ChIP_WT_CN_rep1

tag: tissue


title: KDM5c_Spikein_SMCX_333_ChIP_KO_CN_rep2


title: AMY_KO_1_782


title: AMY_KO_3_2089


title: AMY_WT_2_785


title: AMY_WT_1_786


title: RNA-seq_control_Rep3


title: PFC_KO_1_782

source_name: Adult Pre-Frontal Cortex

value: Adult Pre-Frontal Cortex


title: PFC_WT_3_2091


title: PFC_KO_2_783


title: PFC_WT_2_785


title: PFC_WT_1_786


title: RNASEQ_mCN_SMCX_KO_KCl_Treated_60min_rep2

description: Ribominus depleted total RNA

data_processing:
Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline.
RNA-Seq reads were mapped to mm9 build using TOPHAT v2.0.9 allowing for upto 2 mismatches.
Genome_build: mm9

source_name: E16.5 mouse embryonic cortex

value: embryonic cortex


title: KDM5c_Spikein_SMCX_333_ChIP_KO_CN_rep1


title: CHIPSEQ_mCN_WT_H3K4me3_rep2

description: ChIP-DNA

data_processing:
Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline.
ChIP-Seq and Input reads were mapped to mm9 using bowtie v 0.12.8
Genome_build: mm9

extract_protocol:
Chromatin was immunoprecipitated (overnight, 4°C) with beads and antibody (H3K4me3 Millipore CMA304; H3K4me1 Diagenode pAb-037-050). After immunoprecipitation, beads were washed as described previously. Immune complexes were eluted from beads (65°C, 5 min; and room temperature, 15 min) with 50 mM Tris-HCl pH 8.0, 1 mM EDTA and 1% SDS. Elution was repeated and eluates pooled. Reverse cross-linking was carried out (16h, 65°C) with addition of NaCl and RNase A. EDTA was increased to 5 mM and samples were incubated with 200 μg/ml proteinase K (2h, 50°C). DNA was recovered by phenol-chloroform extraction and ethanol precipitation, and quantifed by Qubit (Life Technologies).
ChIP-Seq libraries were prepared through standard Illumina's procedure for library-preparation using NEBNext library reagents.
ChIP-seq libraries were prepared from 10 ng DNA using NEBNext DNA library preparation reagents (E6000) and the protocol and reagent concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. After PCR amplification, 300-600 bp DNA fragments were selected on an agarose gel. Libraries were quantified by Qubit (Invitrogen), and library size was assessed by Bioanalyzer (Agilent). Libraries were sequenced using a HiSeq 2000 (Illumina) to generate 50 base single-end reads. ChIP-seq libraries were generated from two biological repeats per antibody, and matched Input samples.

value: WT male


title: CHIPSEQ_mCN_WT_Input_rep2

description: Input-DNA


title: RNASEQ_mCN_SMCX_KO_Untreated_rep1

description: Ribominus depleted total RNA


title: RNASEQ_mCN_WT_Untreated_rep2

description: Ribominus depleted total RNA


title: RNASEQ_mCN_WT_Untreated_rep1

description: Ribominus depleted total RNA


title: RNASEQ_mCN_SMCX_KO_KCl_Treated_60min_rep1

description: Ribominus depleted total RNA


title: CHIPSEQ_mCN_WT_H3K4me1_rep2

description: ChIP-DNA


title: RNASEQ_mCN_WT_KCl_Treated_60min_rep2

description: Ribominus depleted total RNA


title: CHIPSEQ_mCN_SMCX_KO_Input_rep1

description: Input-DNA

value: SMCX KO male


title: RNASEQ_mCN_WT_KCl_Treated_60min_rep1

description: Ribominus depleted total RNA


title: RNASEQ_mCN_SMCX_KO_Untreated_rep2

description: Ribominus depleted total RNA


title: CHIPSEQ_mCN_SMCX_KO_Input_rep2

description: Input-DNA


title: CHIPSEQ_mCN_WT_Input_rep1

description: Input-DNA


title: CHIPSEQ_mCN_SMCX_KO_H3K4me3_rep1

description: ChIP-DNA


title: CHIPSEQ_mCN_WT_H3K4me1_rep1

description: ChIP-DNA


title: input_for_BRG1_ChIP-seq_TA1del_Rep3

value: Ty1-TA1del expressed


title: CHIPSEQ_mCN_WT_H3K4me3_rep1

description: ChIP-DNA


title: CHIPSEQ_mCN_SMCX_KO_H3K4me3_rep2

description: ChIP-DNA


title: input_for_BRG1_ChIP-seq_TA1del_Rep2


title: PFC_KO_3_2089