title: Sf-2 root, biological replicate 2

description:
Barcode for sample: CATT
sf-2_root_br2
polyA RNA


title: Mt-0 root, biological replicate 2

status: Public on Dec 11 2013

type: SRA

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

country: USA

institute: University of Utah

description:
Barcode for sample: CATT
mt-0_root_br2
polyA RNA

library_source: transcriptomic

data_processing:
Read data was acquired from an Illumina Genome IIx sequencer using the SR_Amplification_Linearization_Blocking_PrimerHyb_v7 protocol and base calling was performed with the Illumina version SCS2.6 software. For the "Real Time Analysis (RTA)" that is implemented in the SCS control software, we used "per lane" parameters for basecalling.
Barcode splitting was performed as described by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
Reads from FASTQ files that were the output of the Illumina SCS analysis pipeline were aligned to the genome and processed with TopHat 2.0.9, Bowtie2 2.1.0, SAMtools 0.1.19-44428cd, and Cufflinks 2.1.1 for calculation of gene expression levels (the TAIR10 annotation was used for assessing gene expression).
Genome_build: TAIR10
Supplementary_files_format_and_content: A single text file per sample with the output of Cufflinks 2.1.1. The files are tab-delimited.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 10-day-old root, Mt-0

growth_protocol: Plants were germinated on plates and grown for 10 days under standard long day conditions (16 hours light 8 hours dark, at 20C).

extract_protocol:
Tissue was frozen in liquid nitrogen, ground to a fine power in liquid nitrogen, and RNA was extracted with the Plant Reagent (Invitrogen using the manufacturer's recommendations). Specific details are as given in Gan et al. 2011. Nature, 477:419-23; see Supplementary Information Section 7, page 13.
Illumina non-strand-specific (a minor adaptation of the Illumina mRNA-seq methods as reported by Gan et al. 2011. Nature, 477:419-23; see Supplementary Information Section 7, page 13).

tag: accession

tag: tissue

value: whole root

tag: age

value: 10 days

tag: replicate

value: biological replicate 2


title: Ler-0 root, biological replicate 1

description:
Barcode for sample: TGCT
ler-0_root_br1
polyA RNA

source_name: 10-day-old root, Ler-0

value: biological replicate 1


title: Mt-0 root, biological replicate 1

description:
Barcode for sample: GTAT
mt-0_root_br1
polyA RNA


title: Kn-0 root, biological replicate 1

description:
Barcode for sample: GTAT
kn-0_root_br1
polyA RNA

source_name: 10-day-old root, Kn-0


title: Hi-0 root, biological replicate 2

description:
Barcode for sample: CATT
hi_0_root_br2
polyA RNA

source_name: 10-day-old root, Hi-0


title: Hi-0 root, biological replicate 1

description:
Barcode for sample: CATT
hi-0_root_br1
polyA RNA


title: Ws-0 root, biological replicate 1

description:
Barcode for sample: ACGT
ws-0_root_br1
polyA RNA

source_name: 10-day-old root, Ws-0


title: Wu-0 root, biological replicate 1

description:
Barcode for sample: CATT
wu-0_root_br1
polyA RNA

source_name: 10-day-old root, Wu-0


title: Edi-0 root, biological replicate 2

description:
Barcode for sample: ACGT
edi-0_root_br2
polyA RNA

source_name: 10-day-old root, Edi-0


title: Edi-0 root, biological replicate 1

description:
Barcode for sample: ACGT
edi-0_root_br1
polyA RNA


title: Col-0 root, biological replicate 2

description:
Barcode for sample: GTAT
col-0_root_br2
polyA RNA

source_name: 10-day-old root, Col-0


title: Col-0 root, biological replicate 1

description:
Barcode for sample: GTAT
col-0_root_br1
polyA RNA


title: HadjurLab-ChIPSeq-mNSC-Rad21 IP 2

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

department: Cancer biology

country: United Kingdom

institute: Ucl

library_source: genomic

data_processing:
Read alignment using Bowtie v1.0.0 with the parameters as "-n 3 -a -m 1 --best --strata".
Peak calling using MACS v2.0.9 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: The encodePeak files were generated using MACS.

molecule: genomic DNA

organism: Mus musculus

source_name: neural stem cell

growth_protocol: Cells were grown in serum-free media containing EGF+FGF (for NSCs) or BMP+FGF (for ASTs) and Laminin

extract_protocol:
DNA was extracted using phenol chlorophorm. Cells were accutased, washed and immediately fixed with 1% formaldehyde. Chromatin was sonicated and immunoprecipitated with Rad21 antibody and PGS beads.
Immunoprecipitated material was ligated to PE adapters. Libraries were amplified, checked on Bioanalyser and sequenced.

treatment_protocol: cells did not undergo any treatments

tag: cell type

value: neural stem cell

tag: antibody

tag: antibody vendor/catalog#

value: Abcam 992


title: Ct-1 root, biological replicate 1

description:
Barcode for sample: TGCT
ct-1_root_br1
polyA RNA

source_name: 10-day-old root, Ct-1


title: Ct-1 root, biological replicate 2

description:
Barcode for sample: TGCT
ct-1_root_br2
polyA RNA


title: Tsu-0 root, biological replicate 1

description:
Barcode for sample: GTAT
tsu-0_root_br1
polyA RNA

source_name: 10-day-old root, Tsu-0


title: Can-0 root, biological replicate 1

description:
Barcode for sample: CATT
can-0_root_br1
polyA RNA

source_name: 10-day-old root, Can-0


title: Can-0 root, biological replicate 2

description:
Barcode for sample: CATT
can-0_root_br2
polyA RNA


title: No-0 root, biological replicate 1

description:
Barcode for sample: ACGT
no-0_root_br1
polyA RNA

source_name: 10-day-old root, No-0


title: No-0 root, biological replicate 2

description:
Barcode for sample: ACGT
no-0_root_br2
polyA RNA


title: Bur-0 root, biological replicate 2

description:
Barcode for sample: ACGT
bur-0_root_br2
polyA RNA

source_name: 10-day-old root, Bur-0


title: Kn-0 root, biological replicate 2

description:
Barcode for sample: GTAT
kn-0_root_br2
polyA RNA


title: Arabidopsis thaliana Zu-0 root, biological replicate 1

description:
zu-0_rt_br_1
Whole seedling root
polyA RNA

data_processing:
Read data was acquired from an Illumina Genome IIx sequencer using the SR_Amplification_Linearization_Blocking_PrimerHyb_v7 protocol and base calling was performed with the Illumina version SCS2.6 software. For the "Real Time Analysis (RTA)" that is implemented in the SCS control software, we used "per lane" parameters for basecalling.
Reads from FASTQ files that were the output of the Illumina SCS analysis pipeline were aligned to the genome and processed with TopHat 2.0.9, Bowtie2 2.1.0, SAMtools 0.1.19-44428cd, and Cufflinks 2.1.1 for calculation of gene expression levels (the TAIR10 annotation was used for assessing gene expression).
Genome_build: TAIR10
Supplementary_files_format_and_content: A single text file per sample with the output of Cufflinks 2.1.1. The files are tab-delimited.

source_name: 10-day-old root, Zu-0

growth_protocol: Plants were germinated on soil (seedling and floral bud samples) or plates (root samples) and grown for approximately 10 or 11 days under standard long day conditions (16 hours light 8 hours dark, at 20C) for seedling and root samples or until stage 12 floral bud for flower samples.

extract_protocol:
Tissue was frozen in liquid nitrogen, ground to a fine power in liquid nitrogen, and RNA was extracted with the Plant Reagent (Invitrogen using the manufacturer's recommendations). Specific details are as given in Gan et al. 2011. Nature, 477:419-23; see Supplementary Information Section 7, page 13.
Libraries were generated by adapting the Illumina small RNA protocol to use fragmented mRNA as input for library construction (Gan et al. 2011. Nature, 477:419-23; see Supplementary Information Section 7.5, page 15).

value: whole seedling root


title: Arabidopsis thaliana Zu-0 seedling, biological replicate 1

description:
zu-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Zu-0

value: aerial seedling

value: 11 days

tag: developmental stage

value: emergence of 4th true leaf


title: Arabidopsis thaliana Ws-0 seedling, biological replicate 1

description:
ws-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Ws-0


title: Arabidopsis thaliana Wu-0 seedling, biological replicate 1

description:
wu-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Wu-0


title: Arabidopsis thaliana Wu-0 root, biological replicate 1

description:
wu-0_rt_br_1
Whole seedling root
polyA RNA


title: Arabidopsis thaliana Ws-0 floral bud, biological replicate 1

description:
ws-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Ws-0

value: whole floral bud

value: stage 12


title: Arabidopsis thaliana Wil-2 seedling, biological replicate 1

description:
wil-2_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Wil-2


title: Arabidopsis thaliana Tsu-0 seedling, biological replicate 1

description:
tsu-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Tsu-0


title: Arabidopsis thaliana Wil-2 root, biological replicate 1

description:
wil-2_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Wil-2


title: Arabidopsis thaliana Tsu-0 floral bud, biological replicate 1

description:
tsu-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Tsu-0


title: Arabidopsis thaliana Sf-2 root, biological replicate 1

description:
sf-2_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Sf-2


title: Arabidopsis thaliana Wil-2 floral bud, biological replicate 1

description:
wil-2_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Wil-2


title: Arabidopsis thaliana Sf-2 floral bud, biological replicate 1

description:
sf-2_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Sf-2


title: Arabidopsis thaliana Sf-2 seedling, biological replicate 1

description:
sf-2_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Sf-2


title: Arabidopsis thaliana Tsu-0 root, biological replicate 1

description:
tsu-0_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Tsu-0


title: Arabidopsis thaliana Rsch-4 root, biological replicate 1

description:
rsch-4_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Rsch-4


title: Arabidopsis thaliana Po-0 seedling, biological replicate 1

description:
po-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Po-0


title: Arabidopsis thaliana Rsch-4 seedling, biological replicate 1

description:
rsch-4_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Rsch-4


title: Arabidopsis thaliana Rsch-4 floral bud, biological replicate 1

description:
rsch-4_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Rsch-4


title: Arabidopsis thaliana Po-0 root, biological replicate 1

description:
po-0_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Po-0


title: Arabidopsis thaliana Oy-0 seedling, biological replicate 1

description:
oy-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Oy-0


title: Arabidopsis thaliana Ws-0 root, biological replicate 1

description:
ws-0_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Ws-0


title: Arabidopsis thaliana Oy-0 root, biological replicate 1

description:
oy-0_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Oy-0


title: Arabidopsis thaliana Oy-0 floral bud, biological replicate 1

description:
oy-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Oy-0


title: Arabidopsis thaliana Zu-0 floral bud, biological replicate 1

description:
zu-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Zu-0


title: Arabidopsis thaliana No-0 seedling, biological replicate 1

description:
no-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, No-0


title: Arabidopsis thaliana Wu-0 floral bud, biological replicate 1

description:
wu-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Wu-0


title: Arabidopsis thaliana No-0 root, biological replicate 1

description:
no-0_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, No-0


title: Arabidopsis thaliana Mt-0 seedling, biological replicate 1

description:
mt-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Mt-0


title: Arabidopsis thaliana No-0 floral bud, biological replicate 1

description:
no-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, No-0


title: Arabidopsis thaliana Mt-0 root, biological replicate 1

description:
mt-0_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Mt-0


title: Arabidopsis thaliana Mt-0 floral bud, biological replicate 1

description:
mt-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Mt-0


title: Arabidopsis thaliana Kn-0 floral bud, biological replicate 1

description:
kn-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Kn-0


title: Arabidopsis thaliana Ler-0 floral bud, biological replicate 1

description:
ler-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Ler-0


title: Arabidopsis thaliana Ler-0 root, biological replicate 1

description:
ler-0_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Ler-0


title: Bur-0 root, biological replicate 1

description:
Barcode for sample: ACGT
bur-0_root_br1
polyA RNA

source_name: 10-day-old root, Bur-0


title: Arabidopsis thaliana Kn-0 root, biological replicate 1

description:
kn-0_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Kn-0


title: Arabidopsis thaliana Kn-0 seedling, biological replicate 1

description:
kn-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Kn-0


title: Arabidopsis thaliana Ler-0 seedling, biological replicate 1

description:
ler-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Ler-0


title: Arabidopsis thaliana Hi-0 floral bud, biological replicate 1

description:
hi-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Hi-0


title: Arabidopsis thaliana Edi-0 floral bud, biological replicate 1

description:
edi-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Edi-0


title: Arabidopsis thaliana Ct-1 seedling, biological replicate 1

description:
ct-1_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Ct-1


title: Arabidopsis thaliana Ct-1 root, biological replicate 1

description:
ct-1_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Ct-1


title: Arabidopsis thaliana Edi-0 root, biological replicate 1

description:
edi-0_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Edi-0


title: input_BVSC

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

data_processing:
ChIP-seq reads were aligned on mm9 genome assembly using bowtie-0.12.8 with "-n 3 -m 1" settings.
2kb binned reads in every 1kb were counted and created BED and WIG files using sql and perl based scripts.
Genome_build: mm9
Supplementary_files_format_and_content: TDF files were created using IGVTools-2.3.5 with "-w 25 -e 250" settings.
Supplementary_files_format_and_content: Bed files were using perl based script.
Supplementary_files_format_and_content: Wig files were using perl based script.

source_name: EpiLC

growth_protocol: ESCs were induced into EpiLCs as described previously (Hayashi et. al., 2011).  1×105 ESCs were cultured in a well of a 12-well plate coated with human plasma fibronectin (Merck Millipore) (16.7 mg/ml) in N2B27 medium containing Activin A (20 ng/ml; Peprotech), bFGF (12 ng/ml; Invitrogen), and KSR (1 %).  Medium was changed 24 hrs later, and the cells were cultured for another 24 hrs.  The resultant EpiLCs were then cultured under a floating condition by plating 2 x 103 cells in a well of a lipidure coated U-bottom 96-well plate (Thermo Scientific, Waltham, MA) in a GK15+LIF medium in the presence or absence of the cytokines [BMP4 (500 ng/ml), WNT3A (50 ng/ml)].

extract_protocol:
Cells were trypsinized, washed, and collected by centrifugation.  For crosslinking, the pellet was resuspended in PBS containing 1% formaldehyde, incubated for 10 min, and quenched with 125 mM glycine.  The fixed cells were resuspended in 1 ml of cold LB1 (20 mM Tris, 10 mM NaCl, 2.5 mM MgCl2, 0.2% NP-40, and 1 mM PMSF [pH 7.5]), rotated for 10 min at 4 oC, and pelleted by centrifugation at 1,500×g for 5 min.  The pellet was resuspended in 1 ml of LB2 (20 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 1 mM PMSF [pH 8.0]) and rotated for 10 min at 4 oC.
The nuclei were pelleted by centrifugation at 1,500×g for 5 min at 4 oC and lysed in 400 ml of LB3 (20 mM Tris, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1mM PMSF).  The lysed nuclei were sonicated using the following conditions: Bioruptor with high power output; 10 cycles (30 s ON and 60 s OFF at 4 oC).
Protein-DNA complexes were immunoprecipitated for 15 hrs at 4 oC using 4 μg of antibodies bound to 50 μl of Dynabeads Protein G (Invitrogen).  Immunoprecipitates were sequentially washed with 200 μl of Low salt buffer (0.1 % SDS, 1 % TritonX100, 2 mM EDTA,20 mM Tris, and 150 mM NaCl [pH 8.0]), High salt buffer (0.1 % SDS, 1 % TritonX100, 2 mM EDTA,20 mM Tris, and 500 mM NaCl [pH 8.0]), RIRA buffer (50 mM HEPES-KOH, 0.5 M LiCl, 1 mM EDTA, 0.5% Na-Deoxycholate, and 1% NP-40 [pH 7.4]), and TE buffer (10 mM Tris and 10 mM EDTA [pH 8.0]).  For collection of the protein-DNA complexes, beads were resuspended with 50 μl of elution buffer (100 mM NaHCO3, 1 % SDS, and 10 mM DTT).  The crosslink for both the immunoprecipitated and input DNA fragments was reversed by incubating at 65 oC for 6 hr.  After Proteinase K digestion, the DNA was purified by using PCR purification Kit (Qiagen), and dissolved with TE buffer.
DNA of between 2000 and 350 bp, purified using an Agencourt AMPureXP Kit, was sequenced on a Life Technologies SOLiD 5500xl platform to generate single-end 50 bp reads.

tag: strain

tag: chip antibody

tag: genotype

value: Blimp1-mVenus reporter (BV)

value: EpiLC


title: Arabidopsis thaliana Po-0 floral bud, biological replicate 1

description:
po-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Po-0


title: Arabidopsis thaliana Edi-0 seedling, biological replicate 1

description:
edi-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Edi-0


title: Arabidopsis thaliana Hi-0 seedling, biological replicate 1

description:
hi-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Hi-0


title: Arabidopsis thaliana Hi-0 root, biological replicate 1

description:
hi-0_rt_br_1
Whole seedling root
polyA RNA

source_name: 10-day-old root, Hi-0


title: Arabidopsis thaliana Ct-1 floral bud, biological replicate 1

description:
ct-1_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Ct-1


title: TCF1


title: input_PV

value: Prdm14-mVenus reporter (PV)


title: T_brachyury


title: SMAD1_36h_PV


title: Arabidopsis thaliana Bur-0 root, biological replicate 1

description:
bur-0_rt_br_1
Whole seedling root
polyA RNA


title: Arabidopsis thaliana Bur-0 seedling, biological replicate 1

description:
bur-0_sd_br_1
Aerial seedling, emergence of 4th true leaf
polyA RNA

source_name: 11-day-old seedling, Bur-0


title: SMAD1_24h


title: SMAD1_36h_BV


title: Arabidopsis thaliana Bur-0 floral bud, biological replicate 1

description:
bur-0_fb_br_1
Whole floral buds, stage 12
polyA RNA

source_name: Floral bud stage 12, Bur-0


title: ChIP-seq_IgG_mock

status: Public on Dec 10 2013

city: Copenhagen

first: Bo

middle: Torben

last: Porse

address: Ole Maaloes vej 5

department: BRIC/Finsen Laboratory

country: Denmark

institute: University of Copenhagen/Rigshospitalet

data_processing:
GMP peaks were called using MACS2 (https://github.com/taoliu/MACS/downloads) with the following specifications: macs2 callpeak –t GMP.tagAlign.gz -c IgG_mock.tagAlign.gz -f BED-n GMP_vs_IgG -g mm -p 1e-3 --to-large.  Overlapping peaks were subjected to filtration based on the p-value given by MACS2 (min 10-14), and by peak heightwhen comparing with   the individual global sample background (peak heightshould be greater   than the background height of the 0.01% highest randomregions). Regions with high IgG levels were filtered out.
Genome_build: mm9
Supplementary_files_format_and_content: Raw data files in fastq and Cebpa peakcalling in GMPs at bedfile

source_name: Haematopoietic progenitor cells

extract_protocol:
Chromatin from 100.000 preGMs or 500.000 GMPs was incubated with antibodies for histone marks (H3K4me3 and H3K27me3) or C/EBPa, respectively. The antibody-bound chromatin was captured with Protein-A sepharose beads, washed, de-cross-linked and precipitated. DNA was extracted using standard phenol-chloroform extraction
Precipitated DNA were mixed with 2 ng E. Coli DNA and amplified using NEB Next ChIP-seq sample prep reagent set 1 (New England Biolabs) according to manufacturers protocol.

value: C57BL/6 cebpa flox/flox

tag: chip-antibody

value: IgG:Sigma, I8140


title: ChIP-seq_Cebpa_GMP_replicate

value: Cebpa:Santa Cruz 14-AA


title: SMAD1_12h


title: ChIP-seq_Cebpa_GMP


title: ChIP-seq_K27me3_preGM_CebpaKO_replicate

value: C57BL/6 cebpa flox/flox;Mx1Cre

value: H3K27Me3:Cell Signaling, C36B11


title: ChIP-seq_K4me3_preGM_CebpaWT_replicate

value: H3K4Me3:Cell Signaling, C42D8


title: ChIP-seq_K4me3_preGM_CebpaKO_replicate


title: ChIP-seq_K27me3_preGM_CebpaWT


title: ChIP-seq_K27me3_preGM_CebpaWT_replicate


title: ChIP-seq_K4me3_preGM_CebpaKO


title: P448_H3K27AC

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Chromatin immunoprecipitation against H3K27Ac

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

organism: Homo sapiens

source_name: Diffuse Large B-Cell Lymphoma

extract_protocol:
Primary tissue samples from DLBCL tumors, normal lymph node, or normal tonsil that were flash-frozen and stored in OCT were collected in 10 slices at 20 ¼m. Frozen biopsy specimens of newly diagnosed, previously untreated primary DLBCLs with >80% tumor involvement and known transcriptional subtyping (Monti et al., 2012) were obtained according to Institutional Review Board (IRB)-approved protocols  (Brigham & Women Hospital, and Dana-Farber Cancer Institute). A waiver to obtain informed consent was granted by the local IRBs because otherwise discarded tissue was used. After two washes and spin downs in PBS (300g, 5 min), tissue slices were then cross-linked with 1.1% formaldehyde in PBS for 10 min. The formaldehyde was quenched by adding 60 ul/ml of 2.5 M glycine. Glycine and fixative were removed with two washes in cold PBS. Samples were homogenized with a Dounce homogenizer using 10 strokes with pestle A and 10 strokes pestle B in a solution of 10 mM Tris HCl pH8, 10 mM NaCl, 3 mM MgCl2, and 1% NP40. Sample was then transferred to a 15 ml conical tube and rotated in the cold room for 60 min. After this incubation, nuclei were spun down at 1350g for 10 min and transferred to a 3.5 ml tube in 50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.7% SDS. Samples were then sonicated on ice for 10 cycles at 30 s (18 W) with 60 s on ice between cycles. All lysis and sonication buffers contain Complete protease inhibitor cocktail (Roche). Sonicated lysates were cleared by centrifuging at 20,000g for 10 min and incubated overnight on a spinning wheel at 4oC with magnetic beads prebound with antibody after diluting sample to 0.1% SDS final. 100 _l of Dynal magnetic beads per sample (Invitrogen) were blocked with 0.5% BSA (w/v) in PBS. Magnetic beads were loaded with 10 _g of each antibody overnight at 4oC. Antibodies used were as follows: Histone H3K27Ac: Abcam ab4729 ; BRD4: Bethyl A301-985A.
Beads were washed three times with sonication buffer, one time with sonication buffer supplemented with 500 mM NaCl, one time with LiCl wash buffer (20 mM Tris pH 8.0, 1 mM EDTA, 250 mMLiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and once with TE. DNA was eluted in elution buffer (50 mM Tris-HCl pH 8, 10mM EDTA, and 1% SDS). Cross-links were reversed overnight at 65oC. RNA and protein were digested with 0.2mg/mL RNase A for two hr followed by 0.2 mg/ml Proteinase K for one hr. DNA was purified with phenol chloroform extraction and ethanol precipitation.

tag: antibody catalog number

value: Abcam AB4729

value: primary diffuse large B-cell lymphoma tumor


title: P14A_H3K27AC

value: primary normal tonsil


title: P14A_WCE

description: Whole cell extract input control for ChIP

value: None - whole cell extract input control


title: P286_H3K27AC


title: P397_H3K27AC


title: P107A_WCE

value: primary normal lymph node


title: P397_WCE


title: TOLEDO_WCE

growth_protocol: RPMI 1640+FBS

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: TOLEDO


title: P265_WCE


title: P265_H3K27AC


title: TOLEDO_H3K27AC


title: LY4_WCE


title: LY3_WCE


title: LY3_H3K27AC


title: ChIP-seq_K27me3_preGM_CebpaKO


title: HBL1_H3K27AC


title: DHL6_WCE


title: DHL6_H3K27AC


title: LY1_E2F1_DMSO

description: Chromatin IP against E2F1 in Ly1 + DMSO

treatment_protocol: Cells treated with DMSO for 24 hours

tag: chip antibody catalog number

tag: chip antibody manufacturer

value: Cell Signaling

tag: cell line

tag: time

value: 24 hours

tag: concentration

tag: treatment

value: DMSO


title: LY1_RNA_POL2_JQ1

description: Chromatin IP against RNA Pol2 in Ly1 + JQ1

treatment_protocol: Cells treated with 500nM JQ1 for 24 hours

value: RNA Pol II (Rpb1 N-terminus)

value: Santa


title: LY1_WCE_JQ1

description: Whole cell extract - Ly1 + JQ1

value: WCE


title: LY1_WCE_DMSO

description: Whole cell extract - Ly1 + DMSO


title: LY1_BRD4_JQ1

description: Chromatin IP against Brd4 ChIP + JQ1

value: Bethyl


title: LY1_RNA_POL2_DMSO

description: Chromatin IP against RNA Pol2 in Ly1 + DMSO


title: LY1_H3K4ME3_DMSO

description: Chromatin IP against H3K4me3 in Ly1 + DMSO

value: Millipore


title: LY1_H3K27AC_DMSO

description: Chromatin IP against H3K27Ac in Ly1 + DMSO

value: Abcam


title: LY1_H3K27AC_JQ1

description: Chromatin IP against H3K27Ac in Ly1 + JQ1


title: LY1_H3K4ME3_JQ1

description: Chromatin IP against H3K4me3 in Ly1 + JQ1


title: HBL1_WCE


title: LY4_H3K27AC


title: HMLE_Parental_DREAM

city: Illkirch

first: Gabriel

middle: G

last: Malouf

address: 1 rue Laurent Fries

department: Cancer and functional genomics

country: France

institute: IGBMC

description: One DREAM library

data_processing:
library strategy: Digital restriction enzyme analysis of methylation (DREAM)-seq
Sequencing tags were mapped to SmaI sites in the human genome (hg18) and signatures corresponding to methylated (starting with CCGGG…) and unmethylated CpG (starting with GGG…) were enumerated for each SmaI/XmaI site.
The methylation value was calculated as (number of tags starting with CCGGG + 0.5)/(total number of tags mapped to a given SmaI/XmaI site + 1).
Genome_build: hg18
Supplementary_files_format_and_content: The columns of the processed file are: SmaI_ID(SmaI site ID), Chrom(chromosome of the SmaI site), Pos(position of the SmaI site), MetReads(observed number of tags corresponding to methylated CpG), UnmetReads(observed number of tags corresponding to unmethylated CpG), Methylation(methylation value).

source_name: Human mammary epithelial cells

extract_protocol:
DNA was isolated using the DNeasy Blood & Tissue Kit from Quiagen according to manufacturer's instructions
Five micrograms of genomic DNA were digested with 5 µl of FastDigest SmaI endonuclease (Fermentas, Glen Burnie, MD) for 3 hours at 37°C. Subsequently, 50 units (5 µl) of XmaI endonuclease (NEB, Ipswich, MA) were added and the digestion was continued for additional 16 hours. The digested DNA was purified using QIAquick PCR purification kit (Qiagen, Valencia, CA). The recesses at 3’ DNA ends created by XmaI digestion were filled in and 3’ dA tails were added by Klenow DNA polymerase lacking 3’-5’ exonuclease activity (NEB) and dCTP, dGTP and dATP mix (0.4 mM of each). Illumina paired-end sequencing adapters were ligated using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose gel. A slice corresponding to 250-500 bp size window based on DNA ladder was cut out and DNA is extracted from agarose. Eluted DNA was amplified with Illumina paired-end PCR primers for 13-15 cycles using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA). Resulting sequencing library was cleaned with AMPure magnetic beads (Agencourt, Beverly, MA) and then ready for paired-end sequencing on Illumina Genome Analyzer II.

value: human mammary epithelial cells

tag: transfected with

value: none (parental)

tag: culture type

value: monolayer


title: LY1_BRD4_DMSO

description: Chromatin IP against Brd4 in Ly1 + DMSO


title: HMLE_GFP_DREAM

description: One DREAM library

tag: cell type

value: GFP


title: HMLE_Twist3D_DREAM

description: One DREAM library

value: sphere


title: HMLE_Twist3D_H3K4me3_rep2

description:
Chromatin IP against H3K4me3
processed data file: HMLE_Twist3D_H3K4me3_peaks.txt

data_processing:
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
Unique reads mapped to a single genomic location were called peaks using the MACS software (version 1.3.7.1) for H3K4me3 marks (the windows was 400 bp, and the p-value cutoff was 1e-5).
For peak calling of H3K27me3, SICER (version 1.03) was used to detect peaks and enriched domains as the peaks were large and not as sharp as for H3K4me3. The window size was set as 200 bp as default. The gap size was determined as recommended by Zang et al., or at most 2 kb, since the performance worsens as the gap size increases beyond more than 10 times the window size. Following Wang et al., E-value was set at FDR≤5%, which was estimated as E-value (the expected number of significant domains under the random background) divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text file records the position of each peak

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
For each chromatin immunoprecipitation (ChIP) reaction, 0.5 million cells were used. ChIP was performed using Dynabeads Protein G (Invitrogen, Carlsbad, CA) as per manufacturer’s protocol. ChIP libraries for sequencing were prepared as per Illumina’s standard protocol (Illumina, San Diego, CA) with minor modifications. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow enzyme (DNA Polymerase I Large Fragment) and T4 polynucleotide kinase (NEB, Ipswich, MA). The blunt phosphorylated DNA fragments were treated with Klenow fragment (3’ to 5’ exo minus) (NEB) and dATP to add an ‘A’ base to the 3’ end. Sequencing adapters were ligated to the ends of the DNA fragments using Quick T4 DNA Ligase (Enzymatics, Beverly, MA) and Genomic Adapter Oligo Mix (Illumina, part # 1000521). The ligation products were size selected by electrophoresis in a 2% agarose gel. A slice corresponding to 300 (± 25) bp size window based on DNA ladder was cut out and DNA is extracted from agarose. Eluted DNA was amplified by 14 cycles of PCR using Phusion High-Fidelity DNA Polymerase (NEB) and Illumina’s PCR primer 1.1 and PCR primer 2.1. Resulting sequencing library was cleaned with AMPure magnetic beads (Agencourt, Beverly, MA) and ready for single-read sequencing on Illumina Genome Analyzer II.

tag: chip antibody vendor

tag: chip antibody cat. #

tag: antibody lot. #


title: HMLE_Twist3D_H3

description: Chromatin IP against H3, as a control


title: HMLE_Twist3D_H3K4me3_rep1


title: HMLE_Twist3D_H3K27me3_rep2

description:
Chromatin IP against H3K27me3
processed data file: HMLE_Twist3D_H3K27me3_peaks.txt


title: HMLE_Twist3D_H3K27me3_rep1


title: LY1_BCL6_DMSO

description: Chromatin IP against Bcl6 in Ly1 + DMSO

value: Santa Cruz


title: HMLE_Twist2D_H3K27me3

description:
Chromatin IP against H3K27me3
processed data file: HMLE_Twist2D_H3K27me3_peaks.txt


title: HMLE_Twist2D_H3

description: Chromatin IP against H3, as a control


title: HMLE_Parental_H3K27me3_rep1

description:
Chromatin IP against H3K27me3
processed data file: HMLE_Parental_H3K27me3_peaks.txt


title: HMLE_Twist2D_H3K4me3

description:
Chromatin IP against H3K4me3
processed data file: HMLE_Twist2D_H3K4me3_peaks.txt


title: HMLE_Parental_H3K4me3

description:
Chromatin IP against H3K4me3
processed data file: HMLE_Parental_H3K4me3_peaks.txt


title: HMLE_Parental_H3

description: Chromatin IP against H3, as a control


title: HMLE_Twist2D_DREAM

description: One DREAM library


title: Input_H3K4me3_CAT

city: Bethesda

first: Marei

last: Dose

state: MD

address: 9000 Rockville Pk

institute: National Institutes of Health

data_processing:
base-calling: Illumina
alignment: bowtie-0.12.8/bowtie -S -m 1 -p 20 -a --best --strata -n 2
filtering (uniquely aligned reads): samtools-0.1.18/samtools view -S -b -F4
normalized tag density: custom script, maximum 2 reads with the same start position allowed
Genome_build: mm9
Supplementary_files_format_and_content: .wig files contain tag counts in 100 nt windows divided by windowsize and library size in millions to obtain normalized read counts (rpkm)

source_name: thymus

extract_protocol:
1e08 WT or CAT thymocytes were fixed in 3ml of RPMI containing 1% formaldehyde for 10 min at room temperature. The fixative was quenched with glycine, samples were washed twice with ice cold PBS and cells were lysed in RIPA buffer for 10 min on ice. Samples were then sonicated using Diagnode's Bioruptor water bath sonicator (desired fragment size=200bp, conditions vary). Lysates were cleared by centrifugation and incubated overnight with Tcf-1 antibodies [a kind gift of Hiroshi Kawamoto (Riken Yokohama Institute, Yokohama, Japan)] or H3K4me3 antibodies coupled to Protein G Dynabeads (Life Technologies). Immunoprecipitation and input samples were de-cross-linked overnight at 65 °C in elution buffer [50 mM Tris·HCl (pH 8)/10 mM EDTA/1% SDS/ 0.3 M NaCl]. DNA was extracted with phenol/chloroform, quantified, and quality-checked for enrichment of known target regions of Tcf-1 by real-time PCR. ChIP-Seq libraries were prepared from 10 ng of immunoprecipitated material according to an Illumina ChIP DNA library preparation kit.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

tag: strain

value: CD4Cre;CtnnbdEx3fl/fl ('CAT')

tag: age

value: 4-6 weeks

tag: antibody

value: none, input


title: H3K4me3_CAT

tag: genotype

tag: antibody catalog

tag: antibody vendor

tag: antibody lot


title: HMLE_Parental_RNASeq

description: RNA library

data_processing:
Short reads were mapped to the human reference genome (hg19) and exon junctions using the ABI Bioscope (version 1.21) pipeline with default parameters.
Only the tags that mapped to the hg19 reference at full 35-nt length were used. Tags that aligned to multiple positions were excluded.
Tags mapped to RefSeq genes were counted to derive a measure of gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file records number of tags mapped to each gene

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard SoLID protocols


title: HMLE_Twist2D_RNASeq

description: RNA library

value: Twist


title: Tcf1_CAT

tag: antibody provider

value: antiserum provided by Dr. Kawamoto


title: Input_Tcf1_CAT


title: Control group

status: Public on Dec 09 2013

city: Brisbane

first: Renato

last: de Souza Pinto Lemgruber

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd

country: Australia

institute: University of Queensland

data_processing:
Error correction of the tags was done by using the SOLiD(TM) Accuracy Enhancer Tool (SAET) v.2.3
A script in Perl language was developed to translate the csfasta to fasta files.
Blastn was used for tags identifications (word size 14, strand minus, max target seqs 1, gap penalty -3, gap open 5, gap extend 2, reward 1)
The bioconductor (version 2.11-  packages annotate and edge R) were used for gene annotation and differential expression analysis, respectively.
Supplementary_files_format_and_content: tab-delimited text files with tag counts, logFC, and pValue.

organism: Symphysodon aequifasciata

source_name: Liver

extract_protocol:
Total RNA was extracted from S. aequifasciatus liver (20-30 mg) using 500μL of TRIzol® (Invitrogen) according to the instructions of the manufacturer.
RNA SAGE libraries were prepared for sequencing using SOLiD v.3 Plus protocols

treatment_protocol: Twelve adult specimens of discus fish (Symphysodon aequifasciatus) were obtained from a local commercial dealer (“Prestige Aquário”, Manaus, AM, Brazil). They were acclimated in the laboratory using INPA´s aerated groundwater for two weeks in 500L tanks. During the acclimation period, animals were fed dry food pellets with 36% protein content (Purina) once a day. Forty-eight hours before the beginning of the experiments, feeding was suspended and fish were transferred to four 150L-tanks, three fish per tank, where the experiment was performed. Fish remained without the addition of the contaminants for another 24 hours. Tanks 1 and 2 were set as control, where the fish were not exposed to any contaminants. Tanks 3 and 4 hold the fish exposed to combined sublethal levels of benzo[a]pyrene and phenanthrene.  The concentrations of benzo[a]pyrene (SIGMA 40071) and phenanthrene (SIGMA 442753) were 0.5µg/L and 50µg/L, respectively, both dissolved in DMSO (Dimethyl sulfoxide) (0.1ml/L – 0.01%). The same amount of DMSO (0.1ml/L) was also added to the tanks 1 and 2 (control).

tag: tissue

value: Hepatic

value: adult


title: HMLE_Parental_H3K27me3_rep2

tag: chip antibody


title: tumor_rep1_total RNA_total RNA

city: Seattle

first: Paul

last: Valdmanis

state: WA

address: 1705 NE Pacific St, HSB J-309

department: Medicine

institute: University of Washington

data_processing:
RNA-seq reads were aligned to the mm9 genome using TopHat version 1.3.3 with parameters -r 100 --mate-std-dev 100 --segment length 20 -library-type fr-unstranded
supplementary_files_format_and_content: FPMK values were calculated using the CuffDiff program version 1.3.0
Genome_build: mm9

source_name: lung adenocarcinoma - total RNA

growth_protocol: Kras G12D 129S4 male mice were crossed with 129S4 or MOLF females.  F1 offspring either bore a G12D or wildtype Kras allele.  Tumors were initiated by intranasal viral-Cre delivery

extract_protocol:
Large RNA samples were homogenized and extracted by Trizol; ribosomal sequences were removed using RiboRemoval kit
Large RNA Libraries were prepared in a strand-specific manner using a ScriptSeq kit v1 starting with a 900ng of riboremoved RNA

value: lung adenocarcinoma

value: 129S4 x MOLF


title: tumor_rep2_total RNA_total RNA


title: tumor_lung_rep3_small RNA_small RNA

data_processing:
small RNA sequencing reads were sorted by barcode, barcode removed (4nt), linker1 clipped and aligned to mouse hairpins from mirBase release 17 using bowtie version 0.12.7 with 2 mismatches and command -- best
supplementary_files_format_and_content: FPMK values were calculated using the CuffDiff program version 1.3.0
Genome_build: mm9

source_name: lung adenocarcinoma - small RNA

extract_protocol:
small RNA samples were extracted using a miRvana microRNA isolation kit
small RNAs were ligated to Linker-1 (IDT) in the absence of ATP with T4 RNA ligase 1 (New England Biolabs). Ligated RNA was size selected (based on an 18-36nt small RNA fraction) on 15% PAGE. The 5’ ends RNA were ligated to barcoded adapters. Dual-ligated RNA was reverse transcribed; PCR amplified and size selected on 4% NuSieve (Lonza) agarose.  Small RNA sequencing was performed on the Illumina/GAII platform.


title: tumor_rep3_total RNA_total RNA


title: normal_lung_rep3_total RNA_total RNA

source_name: lung - total RNA

value: lung


title: tumor_lung_rep2_small RNA_small RNA


title: normal_lung_rep1_total RNA_total RNA


title: normal_lung_rep2_total RNA_total RNA


title: hTERT overexpression induced immortalized hMEC

city: Beijing

first: lina

last: ma

address: No.7 Beitucheng West Road, Chaoyang District

country: China

institute: Beijing Institute of Genomics,Chinese Academy of Sciences

description: 1ug of total RNA  was used to isolate poly(A)+ mRNA by using Oligotex (QIAGEN)

data_processing: Sequence alignments were generated with Corona_lite_v4.0r2.0 (SOLiDâ¢ System Analysis Pipeline Tool; http://solidsoftwaretools.com/gf/project/corona/). A database contains splice junctions was generated for tag mapping, where the 3' 50bp from every exon is joined to 5' 50bp from the next exon for every gene locus. The sequencing reads in full-length (50bp) were first mapped to the genome assembly, allowing for five color base mismatches. Reads that cannot be mapped were then mapped to splice junctions, with the same standard. After the first round of mapping, reads that cannot be mapped to the splice junctions were trimmed to 45bp for the second round of mapping, with four mismatches. Then, a series of stringency reductions were performed for salvaging more data: 40bp with four mismatches, 35bp with three mismatches, 30bp with three mismatches, and 25 bp with three mismatches. Mapped reads were sorted into multiple and unique hits and unique mapped reads were annotated to genes from Ensembl database (HomoSapiens.GRCh37).

source_name: immortalized hMEC

growth_protocol: Normal human mammary epithelial cells (hMEC) were purchased from Clonetics BioWhittaker (Walkersville, MD) and maintained in serum-free mammary epithelial basal medium supplemented with growth factors.

extract_protocol: Total RNA was extracted by using Trizol (Invitrogen) reagent. RNA samples in triplex were pooled and 1ug of total RNA from each pool was used to isolate poly(A)+ mRNA by using Oligotex (QIAGEN). The libraries were prepared according to the instruction from the manufacturer for RNA-seq (updated 4/29/09; http://solid.appliedbiosystems.com; Life Technologies, Foster City, CA).

treatment_protocol: hMEC cells at the second passage were infected with retroviral vector containing hTERT cDNA, and the resultant cells had been cultured for over 100 PDs. Therefore, hTERT immortalized hMEC cells (I_hMEC) has been established. The I_hMEC cells were then irradiated with a single dose of 60 cGy of heavy ions produced at Brook Heaven National laboratory, USA. The irradiated cells were continuously cultured for 3-4 months and then injected subcutaneously into the left flank of 4â6 week old male Nu/Nu mice (Harlan SpragueâDawley, Indianapolis, IN) at 5-106cells/site. The same passages of unirradiated I_hMEC cells were used as control. Only heavy ion-irradiated cells can form progressively growing tumors at four weeks post injection in nude mice. The tumorigenic cell lines (T_hMEC) were then established from the above tumor nodules.

value: mammary epithelial cell

tag: tumor formation

value: no


title: heavy ions radiation induced tumorigenic hMEC based on I_hMEC

source_name: tumorigenic hMEC

value: yes


title: tumor_lung_rep1_small RNA_small RNA


title: normal_lung_rep3_small RNA_small RNA

source_name: lung - small RNA


title: normal_lung_rep1_small RNA_small RNA


title: normal_lung_rep2_small RNA_small RNA


title: HMLE_Twist3D_RNASeq

description: RNA library

value: human mammary epithelial cells

tag: transfected with


title: S4L-SCLB

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

data_processing:
Image analysis, base calling and FASTQ generation were performed using the genome analyzer pipeline software CASAVA (version 1.8.2).
Inline demultiplexing was performed using software fastq_multx (Aronesty 2011)
Sequencing reads were mapped to hg19 of the human reference genome (NCBI genome build 37.2) plus human ribosomal 5S, 18S and 28S sequences using Novoalign (Novocraft Technologies v.2.08, Selangor, Malaysia) paired-end base default parameters.
The relative abundance of each transcript was calculated using Genomatix software (www.genomatix.de) and presented as FPKM (fragments per kilobase exon per million fragments mapped).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include each read's mapping location on reference genome

source_name: Fertile mature sperm

extract_protocol:
Semen samples was collected in liquefied fraction, or pelleted fraction, then treated with PureSperm gradient centrifugation through a 50% PureSperm cushion, or Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100).
The RNA-Seq libraries for each sperm sample were prepared in two stages using the Nugen Ovation kit (Nugen Inc., San Carlos, CA) for cDNA synthesis and amplification plus the Nugen Encore system for library preparation. The cDNA samples were subject to single primer isothermal amplification (SPIA) prior to sequencing library preparation. In brief, 20 ng of total RNA was subject to reverse-transcription. The cDNA synthesis used oligo dT and random hexamer primers followed by isothermal amplification (SPIA). The amplified cDNA was then fragmented by covaris sonicator and the fragment ends were repaired. The Illumina compatible PE adaptors with inline barcodes were ligated onto the cDNA products followed by 15 cycles of PCR enrichment.

tag: storage method

value: Liquefied storage

tag: purification method

value: Somatic Cell Lysis Buffer


title: S4P-PS

value: Pelleted storage

value: PureSperm cushion


title: Experimental group


title: S3P-SCLB


title: Lsh_E13.5_RNASeq

city: Edinburgh

first: Donncha

middle: S

last: Dunican

address: Western General Hospital

institute: IGMM / MRC HGU

description: Processed data files are tabular files generated from  fastq raw files and input into EdgeR

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were groomed using Fastqgroomer and filtered for read quality.
Reads were mapped using TopHat v1.4.0 using the settings: -p 4 -r 24 -a 8 -m 0 -I 70 -l 500000 -g 20 --library-type fr-firststrand --no-novel-indels --no-coverage-search --no-closure-search --mate-std-dev 27 --initial-read-mismatches 0 --segment-mismatches 0 -segment
Galaxy pipeline was used to filter for unique hits generating interval files which were used to create read pile-ups by the Galaxy inner join package.
Read pile-up files were input into EdgeR to calculate differential expression between libraries and also pile-ups were converted to bed files for this submission.
Genome_build: Mouse mm9
Supplementary_files_format_and_content: abundance

source_name: Mouse  embryo stage E13.5

growth_protocol: Tailtip fibroblasts were cultured in 89% DMEM, 10% FCS and 1% penicillin-streptomycin.  E13.5 embryos were isolated using standard techniques.

extract_protocol:
Total RNA was extracted from fibroblasts and embryos using TriZol Reagent.
Paired-end strand-specific RNA-Seq libraries were prepared from fibroblast and embryo RNA using the dUTP method and libraries were sequenced using the Illumina HiSeq instrument.

value: Lsh-/-

value: E13.5 mouse embryos


title: S4L-PS


title: S3P-PS


title: WT_E13.5_RNASeq

value: WT


title: Lsh_fib_RNASeq

source_name: Tailtip fibroblasts

tag: cell type

value: adult tailtip fibroblasts


title: S3L-PS


title: 3b--_HELP

description: Processed data files are bed files generated from  fastq raw files

data_processing:
Raw data was analysed using the WASP online automated piepline (McLellan AS, 2012, Genomics; 100(6); p345-51)
Raw HELP reads were mapped to the mouse genome (mm9) using Bowtie
Alignments were overlapped with repeatmasker annotated murine repetitive DNA elements in Galaxy.
Using custom Perl scripts, reads were counted in respective repeat classes,  2x2 contingency table odds-ratios (OR) were computed using the Text-NSP-1.03 CPAN package.
Finally, signficance was measured between tester and driver lines using Fisher's exact tests and Bonferroni correction for multiple testing.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated by read pileups in Galaxy.

source_name: Mouse embryonic fibroblasts

growth_protocol: Tailtip fibroblasts and mouse embryonic fibroblasts were cultured in 89% DMEM, 10% FCS and 1% penicillin-streptomycin.

extract_protocol:
Total genomic DNA was extracted from fibroblasts using established SDS lysis protocols.
Single ended HELP seq libraries were prepared from fibroblast DNA and sequenced on the Illumina HiSeq instrument using the method of Jing et al., Meth. Mol. Biol. V815, 2012, pp 79-87.

value: Mouse embryonic fibroblasts


title: S2P-PS


title: S2L-SCLB


title: 3b+-_HELP


title: S2P-SCLB


title: S2L-PS


title: S3L-SCLB


title: Lsh_fib_HELP rep3

value: Tailtip fibroblasts


title: S1P-SCLB


title: WT_fib_RNASeq


title: S4P-SCLB


title: WT_HELP rep3


title: WT_HELP rep2


title: S1P-PS


title: S1L-PS


title: S1L-SCLB


title: WT_HELP rep1


title: Mliver_B1T1HS

status: Public on Dec 07 2013

city: Chicago

first: Danielle

last: Maatouk

address: 303 E. Superior St., Lurie 7-250

institute: Northwestern University

data_processing:
Illumina CASAVA1.8.2 software used for basecalling.
Sequenced reads were trimmed to the first 20bp to remove adaptor sequence using custom scripts, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using BWA version 0.6.1-r104 with default indexing (index -a bwtsw) and aln parameters (aln -t 8) to create alignment SAI files.
SAM files were created from the SAI files using bwa samse with default parameters, then filtered for alignments with greater than 4 mismatches using custom scripts.
The SAM files (after filtering for mismatches >4) were converted to BAM format using "samtools view", then sorted via chromosome using "samtools sort", then converted to BED format using "bedtools bamtobed".
Sharp sequence pileups introduced by PCR amplification artifacts or potential misalignments were filtered out to reflect a maximum acceptable read count for a peaks region based on a Poisson distribution.
Genome_build: mm9
Supplementary_files_format_and_content: F-seq (Boyle AP, et al. Bioinformatics 2008; 24(21):2537-2538) was used to generate both base-pair signal Parzen score (wig format - later converted to bigWig) and discrete peaks (bed format) corresponding to DNaseI hypersensitive (DHS) sites.

source_name: Whole liver

extract_protocol:
Mouse tissues (kidney, liver, heart, and brain) were collected from adult B6 mice,flash frozen and then pulverized before use. FACS sorted pre-Sertoli cells were pelleted and resuspended in 250uL of Recovery-Cell Culture Freezing Media (Gibco) and slowly frozen to -80°C before use. Mouse ES and fibroblast cell lines were grown in culture then pelleted before immediately proceeding to DNase-seq library preparations.  All DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106) with few exceptions.  Incubation of FACS purified pre-Sertoli cells with low concentrations of exogenous DNaseI enzyme was found to severely degrade the DNA; therefore DNase digestion was performed using endogenous nucleases. Briefly, cells were lysed and incubated at 37°C for various times (5 min to 1 hour) and optimal DNase digestion was confirmed by pulsed field gel electrophoresis (Song L and Crawford GE. Cold Spring Harbor protocols 2010(2):pdb prot5384).
DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106).

value: Whole liver

tag: developmental stage

value: adult


title: Fibroblast_M_B3T1

description: The mouse fibroblast cell line was derived from adult B6 mice (Jackson Labs) and grown as described in (Shibata Y, et al.  PLoS Genet. 2012; doi:10.1371/journal.pgen.1002789).

source_name: Skin fibroblast

value: Primary fibroblast cell culture

value: cell culture


title: Lsh_fib_HELP rep1


title: P286_WCE

description: Whole cell extract input control for ChIP

tag: antibody catalog number

value: None - whole cell extract input control

value: primary diffuse large B-cell lymphoma tumor


title: E15.5_Sox9CFP

description: Pre-Sertoli cells were collected from the testes of E15.5 mouse embryos (Sox9 Heterozygous male embryos conceived from transgenic homozygous Sox9-ECFP C57BL/6J male mice mated to female CD-1 (Charles River) females)

source_name: PreSertoli cells

tag: strain

value: Testes

value: E15.5 embryos


title: Mkidney_B1T1HS

source_name: Whole kidney

value: Whole kidney


title: Lsh_fib_HELP rep2


title: Mheart_B2T1HS

source_name: Whole heart

value: Whole heart


title: BSO30_mRNA

status: Public on Dec 06 2013

city: Rochester

first: Krishna

middle: R

last: Kalari

state: MN

address: 200 1st ST SW

department: Department of Biomedical Statistics and Informatics

institute: Mayo Clinic

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (NCBI 37 build) genomes using BWA and tophat 1.3 alignment. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: Gene counts were obtained using HTSeq
Variant callng is done using eSNV Detect Pipeline
Genome_build: hg19
Supplementary_files_format_and_content: Text file with raw gene counts for all the samples(tab seperated)

source_name: Benign cell lines (HMEC)

growth_protocol: All the tumors and cell lines were grown under conditions recommended by ATCC and RNA and DNA were extracted from mid log phase populations of low passage number cultures.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA extraction was performed using Exiqon's miRCURY RNA Isolation Kit. Long-read mRNA-seq cDNA libraries were prepared from 1ug of total RNA using a modification of the Illumina mRNA-seq protocol.  Briefly, mRNA was resolved using poly-dT oligonucleotides attached to magnetic beads, fragmented using divalent cations under elevated temperatures, and converted to cDNA using random primers. After conversion of the cleaved fragments into cDNA, the cDNA underwent blunt end repair, addition of an 'A' base to the 3' blunt ends, and ligation of adapter molecules which will be used for PCR amplification, bridge amplification, and sequencing. The cDNA library was resolved by gel electrophoresis using conventional Illumina protocols except that we cut from the gel those cDNA fragments in the range of 300-400bp. The increased fragment length is necessary to accommodate paired end sequence analysis. The gel purified cDNA fragments were amplified by PCR and sequenced using the Illumina Cluster Station and Genome Analyzer. Paired-end sequence analysis (51 cycles/end) was carried out using sequencing primers that correspond to either end of the bridge-amplified cDNA fragments so as to obtain 50nt of sequence from either end of every cDNA fragment.

tag: tissue type

value: Benign cell lines (HMEC)


title: Mbrain_B2T1HS

source_name: Whole brain

value: Whole brain


title: BSO29_mRNA


title: DHF168_mRNA


title: BSO19B_mRNA


title: BSO37_mRNA


title: ChIP-seq_K4me3_preGM_CebpaWT

source_name: Haematopoietic progenitor cells

value: C57BL/6 cebpa flox/flox

tag: chip-antibody

value: H3K4Me3:Cell Signaling, C42D8


title: BSO36_mRNA


title: ES_JM8_B3T1HS

description: ESCs were kindly provided by Ute Hochgeschwender (Duke University) and were grown on gelatinized plates in the absence of a feeder layer or matrigel. To harvest ESCs, plates were washed with 1X PBS and treated with 0.25% Trypsin-EDTA for 7-10 minutes at 37°C. An equal volume of medium (containing 10% FBS) was then added to the plates to stop trypsinization. Cells were collected and pipetted up/down to get a single cell suspension and were centrifuged at ~1.2 krpm for 10 minutes. All medium was removed from the cell pellet.

source_name: Embryonic stem cells

value: ES cell culture


title: OP-535_mRNA

source_name: Breast tumor

value: Triple Negative Breast Tumor


title: BSO32N_mRNA


title: BRS-73_mRNA


title: BRS-129_mRNA


title: BCT40_mRNA

value: HER2+ Breast Tumor


title: BCT39_mRNA


title: B-LCL-2.1

status: Public on Dec 08 2013

city: Montreal

first: Diana

middle: Paola

last: Granados

state: Quebec

address: C.P. 6128, succursale Centre-ville

department: Medecine

country: Canada

institute: IRIC

description: HLA-identical female sibling.

data_processing:
Ilumina Casava 1.8.1 software was used for base calling.
Sequence data were mapped to the human reference genome (hg19) using the Casava 1.8.1 and the Eland v2e mapping softwares (Illumina).
The *.bcl files were converted into compressed FASTQ files, following by demultiplexing of separate multiplexed sequence runs by index. Single reads were aligned to the human reference genome using the multiseed and gapped alignment method. The following criteria were applied: i) a read contains at least one seed that matches with at most 2 mismatches without gaps and ii) gaps were allowed for the whole read, as long as they correct at least five mismatches downstream.
Reads that mapped at 2 or more locations (multireads) were not included in further analyses. An additional alignment was performed against splice junctions and contaminants (mitochondrial and ribosomal RNA). Sequences mapping to contaminants were discarded whereas reads uniquely mapping to splice junctions were kept and converted back to genome coordinates.
Reads were re-aligned around candidate indels using Casava 1.8.1 software (Ilumina) to improve the quality of variant calls and site coverage summaries.
Genome_build: GRCh37
Supplementary_files_format_and_content: RPKM-genes*: Tab-delimited text files include RPKM values per gene (gene symbol) for each sample, as well as the chromosomal location, the start and the end coordinates of the gene.
Supplementary_files_format_and_content: RPKM-exons*: Tab-delimited text files include RPKM values per exon for each sample, as well as the chromosomal location, the start and the end coordinates of the exons.

source_name: B lymphoblasts

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples of 2 HLA-identical female siblings. B lymphoblastoid cell lines (B-LCLs) were derived from PBMCs with Ficoll-Paque Plus (Amersham )and infected with Epstein-Barr virus and as described by Tosato et al. (Tosato, G. & Cohen, J. I. Generation of Epstein-Barr Virus (EBV)-immortalized B cell lines. Curr. Protoc. Immunol. Chapter 7, Unit (2007)). Established B-LCLs were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 25 mM of HEPES, 2mM L-glutamine and penicillin-streptomycin. Cells were seeded at a density of 0.5 million cells per ml, 20 ml in total in a T75 flask, 18 hours before RNA extraction.

extract_protocol:
Total RNA was isolated from 5 million B-LCLs using RNeasy mini kit including DNase I treatment (Qiagen) according to the manufacturer's instructions. Total RNA was quantified using the NanoDrop 2000 (Thermo Scientific) and RNA quality was assessed with the 2100 Bioanalyzer (Agilent Technologies).
Transcriptome libraries were generated from 1 μg of total RNA using the TruSeq RNA Sample Prep Kit (v2) (Illumina) following the manufacturer's protocol. Briefly, poly-A mRNA was purified using poly-T oligo-attached magnetic beads using two rounds of purification. During the second elution of the poly-A RNA, the RNA was fragmented and primed for cDNA synthesis. Reverse transcription of the first strand was performed using random primers and SuperScript II (InvitroGene). A second round of reverse transcription was done to generate a double-stranded cDNA, which was then purified using Agencourt AMpure XP PCR purification system (Beckman Coulter). End repair of fragmented cDNA, adenylation of the 3' ends and ligation of adaptors were completed following the manufacturer's protocol. Enrichment of DNA fragments containing adapter molecules on both ends was done using 15 cycles of PCR amplification and the Illumina PCR mix and primers cocktail.

treatment_protocol: Cells were not treated.

value: EBV-infected human B lymphoblastoid cell line

tag: source tissue

value: peripheral blood mononuclear cells

tag: host sex

value: female


title: BCT38_mRNA


title: B-LCL-2.2

description: HLA-identical female sibling.


title: BCT37_mRNA


title: BCT35_mRNA


title: BCT34_mRNA


title: BSO28_mRNA


title: BCT33_mRNA


title: BCT30_mRNA


title: BCT32_mRNA


title: BCT31_mRNA


title: BRS-124_mRNA


title: BCT28_mRNA

value: ER+ Breast Tumor


title: BCT29_mRNA


title: BCT16_mRNA


title: BCT24_mRNA


title: BCT22_mRNA


title: BCT14_mRNA


title: BCT12_mRNA


title: BCT04_mRNA


title: BCT36_mRNA


title: 3-APC-iPSC-9 MeDIP sequencing

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute Of Biological Sciences, Beijing (NIBS)

description: Sample 9

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_9_peaks.bed: mm9

growth_protocol: ES cells and iPS cells were maintained in ES cell media containing 15% FBS and 1,000 Uml-1 of LIF.MEF and APCs were cultured in DMEM supplemented with 10% FBS and penicillin/streptomycin. HPCs was freshly isolated from bone marrow

extract_protocol: Genomic DNA was extracted from cell pellets and 5μg original gDNA were prepared for a library. DNA quality was analyzed by Qubit 2.0 Fluorometer (life technologies). gDNA was sonicated to 100-500bp, and repaired to overhang a 3’-dA; then the adapters were ligated to the end of DNA fragments according to the Paired-End DNA Sample Prep Kit (Illumina). For the immunoprecipitation, DNA was first denatured, followed by immunoprecipitated by 5mC antibody using Magnetic Methylated DNA Immunoprecipitation kit (Diagenod). Q-PCR was used to validate the efficiency of the enriched products. Then the pull-down DNA were amplified about 12-15 cycles, and fragments with proper size, usually 200-300bp, were gel-purified using Gel Extraction Kit (Qiagen) and quantified by 2100 Bioanalyzer (Agilent Technologies)

value: APC-derived induced pluripotent stem cells

tag: passage


title: 3-APC-iPSC-3 MeDIP sequencing

description: Sample 5

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_3_peaks.bed: mm9


title: 2-HPC MeDIP sequencing

description: Sample 12

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_HSC_peaks.bed: mm9

value: mouse hematopoietic progenitor cells (HPC)


title: 3-APC MeDIP sequencing

description: Sample 13

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_BSC_peaks.bed: mm9

value: mouse adipose progenitor cells (APC)


title: 2-HPC-iPSC-18 MeDIP sequencing

description: Sample 8

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_18_peaks.bed: mm9

value: HPC-derived induced pluripotent stem cells


title: 2-APC-iPSC-4 MeDIP sequencing

description: Sample 7

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_4_peaks.bed: mm9


title: 1-MEF MeDIP sequencing

description: Sample 10

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_MEF_peaks.bed: mm9

value: mouse embryonic fibroblast (MEF)


title: 1-MEF-iPSC-42 MeDIP sequencing

description: Sample 6

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_42_peaks.bed: mm9

value: MEF-derived induced pluripotent stem cells


title: 2-HPC-iPSC-16 MeDIP sequencing

description: Sample 4

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_16_peaks.bed: mm9


title: P448_WCE

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Diffuse Large B-Cell Lymphoma

extract_protocol:
Primary tissue samples from DLBCL tumors, normal lymph node, or normal tonsil that were flash-frozen and stored in OCT were collected in 10 slices at 20 ¼m. Frozen biopsy specimens of newly diagnosed, previously untreated primary DLBCLs with >80% tumor involvement and known transcriptional subtyping (Monti et al., 2012) were obtained according to Institutional Review Board (IRB)-approved protocols  (Brigham & Women Hospital, and Dana-Farber Cancer Institute). A waiver to obtain informed consent was granted by the local IRBs because otherwise discarded tissue was used. After two washes and spin downs in PBS (300g, 5 min), tissue slices were then cross-linked with 1.1% formaldehyde in PBS for 10 min. The formaldehyde was quenched by adding 60 ul/ml of 2.5 M glycine. Glycine and fixative were removed with two washes in cold PBS. Samples were homogenized with a Dounce homogenizer using 10 strokes with pestle A and 10 strokes pestle B in a solution of 10 mM Tris HCl pH8, 10 mM NaCl, 3 mM MgCl2, and 1% NP40. Sample was then transferred to a 15 ml conical tube and rotated in the cold room for 60 min. After this incubation, nuclei were spun down at 1350g for 10 min and transferred to a 3.5 ml tube in 50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.7% SDS. Samples were then sonicated on ice for 10 cycles at 30 s (18 W) with 60 s on ice between cycles. All lysis and sonication buffers contain Complete protease inhibitor cocktail (Roche). Sonicated lysates were cleared by centrifuging at 20,000g for 10 min and incubated overnight on a spinning wheel at 4oC with magnetic beads prebound with antibody after diluting sample to 0.1% SDS final. 100 _l of Dynal magnetic beads per sample (Invitrogen) were blocked with 0.5% BSA (w/v) in PBS. Magnetic beads were loaded with 10 _g of each antibody overnight at 4oC. Antibodies used were as follows: Histone H3K27Ac: Abcam ab4729 ; BRD4: Bethyl A301-985A.
Beads were washed three times with sonication buffer, one time with sonication buffer supplemented with 500 mM NaCl, one time with LiCl wash buffer (20 mM Tris pH 8.0, 1 mM EDTA, 250 mMLiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and once with TE. DNA was eluted in elution buffer (50 mM Tris-HCl pH 8, 10mM EDTA, and 1% SDS). Cross-links were reversed overnight at 65oC. RNA and protein were digested with 0.2mg/mL RNase A for two hr followed by 0.2 mg/ml Proteinase K for one hr. DNA was purified with phenol chloroform extraction and ethanol precipitation.

value: None - whole cell extract input control

value: primary diffuse large B-cell lymphoma tumor


title: BCT26_mRNA


title: 2-APC-iPSC-32 MeDIP sequencing

description: Sample 3

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_32_peaks.bed: mm9


title: 1-MEF-iPSC-37 MeDIP sequencing

description: Sample 2

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_37_peaks.bed: mm9


title: 1-MEF H3K4me2 ChIPseq

description: Sample 50

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_MEF_peaks.bed: mm9

source_name: MEF H3K4me2 ChIPseq

extract_protocol: 1.5x108 cells were resuspended in lysis buffer and digested with micrococcal nuclease about 5 minutes at 37℃.Then, the lysate was immunoprecipitated with antibody anti-H3K4me2, anti-H3K4me3, anti-H3K27me3; meanwhile, retaining a fraction of input ‘whole-cell extract’ as sequencing control. Immunoprecipitation-enrichment of chromatin fragments were defined and the bound DNA were purified using phenol:chloroform extractions. Chiped DNA was quantified by Qubit 2.0 Fluorometer (life technologies) and Q-PCR was performed to validate the enrichment efficiency. Then the enriched DNA was sonicated to 100-500bp fragments. DNA-end was repaired to overhang a 3’-dA, then adapters was ligated to the end DNA fragments. DNA fragments about 100-300bp, were recovered and amplified to construct the sequencing library. Thirty-nine ChIP library and thirteen input controls were used for sequencing.

value: mouse embryonic fibroblast

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat #

tag: chip antibody lot #


title: R1-ESC  MeDIP sequencing

description: Sample 1

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_R1_peaks.bed: mm9

value: embryonic stem cells


title: 2-HPC H3K4me2 ChIPseq

description: Sample 52

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_HSC_peaks.bed: mm9

source_name: HPC H3K4me2 ChIPseq

value: mouse hematopoietic progenitor cells

tag: chip antibody


title: 2-APC H3K4me2 ChIPseq

description: Sample 51

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_ASC_peaks.bed: mm9

source_name: APC H3K4me2 ChIPseq

value: mouse adipose progenitor cells


title: 2-HPC-iPSC-18 H3K4me2 ChIPseq

description: Sample 48

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_18_peaks.bed: mm9

source_name: HPC-iPSC H3K4me2 ChIPseq


title: 1-MEF-iPSC-42 H3K4me2 ChIPseq

description: Sample 46

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_42_peaks.bed: mm9

source_name: MEF-iPSC H3K4me2 ChIPseq


title: 2-APC-iPSC-4 H3K4me2 ChIPseq

description: Sample 47

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_4_peaks.bed: mm9

source_name: APC-iPSC H3K4me2 ChIPseq


title: 3-APC-iPSC-9 H3K4me2 ChIPseq

description: Sample 49

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_9_peaks.bed: mm9


title: 3-APC-iPSC-3 H3K4me2 ChIPseq

description: Sample 45

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_3_peaks.bed: mm9


title: 2-APC MeDIP sequencing

description: Sample 11

data_processing:
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_ASC_peaks.bed: mm9


title: 2-HPC-iPSC-16 H3K4me2 ChIPseq

description: Sample 44

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_16_peaks.bed: mm9


title: BDI23 Stem

city: NEWARK

first: Dong-Hoon

last: Jeong

state: DE

address: 15 Innovation Way

institute: University of Delaware

description: PARE (Parallel Analysis of RNA Ends) library

data_processing:
The raw sequencing data was converted to SCARF format, trimmed of adapters, matched to the Brachypodium Genome 8X Assembly (ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Bdistachyon/)  by custom Perl scripts
Genome_build: 8X
Supplementary_files_format_and_content: Text containing distinct small RNAs or mRNAs with their raw abundance after removing the adapter sequences

organism: Brachypodium distachyon

source_name: Stem

growth_protocol: Brachypodium (Line Bd21) was used for all libraries. For the BDI small RNA and PARE libraries, seeds were germinated in soil and the plants were grown in a growth chamber at a constant 20°C, under a 20 h-light, 4 h-dark cycle. Leaf, stem, and panicle tissues were harvested from six-week old plants. Leaf tissue was the blade of first and second leaf from the top, not including the leaf sheath.  Stem tissue was harvested from just above the first top node to just below the second node, including both nodes as well as the leaf sheath of the second leaf.  Panicle tissue was harvested from plants with immature, unfertilized flowers from the tip of the spikelet to just above, but not including, the panicle node at approximately 10 h into the subjective day. To collect root tissue, seeds were husked, surface-sterilized with a 50% bleach solution, rinsed with sterile water, and germinated on half-strength Murashige and Skoog (MS) medium containing 0.2% (w/v) Phytagel in sterile plastic boxes. Root tissue was harvested from three-week old plants from the tip of the root to just below, but not including the seed. For the OBD set of small RNA libraries from tissues, Brachypodium plants were grown with supplemental light on a 16 h photoperiod at 25°C. For OBD02, leaf and stem tissues were collected at day 7-8, 14-15, and 27-28 and pooled. Panicle tissue was collected at day 28-35 at 4 time point intervals of 0700 (dawn), 1300, 1900, 0100 hours. For OBD03 seedlings, the following whole seedlings including roots were pooled. Two samples were soil grown under a 16 h photoperiod and tissues were collected from 3- and 4-day old plants. Two additional samples included 5-day old etiolated seedlings and light-grown seedlings grown on moistened filter paper.

extract_protocol:
Total RNAs were isolated using Trizol reagent (Molecular Research Center).
Small RNA libraries were constructed as previously described (Lu et al., 2007) and PARE libraries were constructed as described (German et al., 2008). All the libraries were sequenced on llumina IIGX analyzer. Sequencing was performed at Illumina or the Delaware Biotechnology Institute.

treatment_protocol: Stress treatments and controls except phosphate starvation and its control for BDI small RNA libraries were done using three-week old plants planted in soil under normal growth conditions with a 20 h photoperiod as above. Stresses began 5-6 h after the lights came on.  For heat stress, plants were moved to 40°C for 12 h.  For cold stress, plants were moved to 4°C in a cold room for 12 h.  For drought stress, plants were removed from the soil and rinsed, blotted dry with paper towels, and air-dried for 12 h.  For salt stress, the base of the plant pot was submerged in 300mM NaCl solution for 12 h to the depth of approximately 1 inch, not covering the soil.  For submergence stress, plants were fully submerged in 20°C water for 24 h.  For phosphate starvation stress, seeds were planted in MS media with KH2PO4 omitted, and control plants were planted in MS media; plants were harvested at three weeks, 5-6 h after lights on.  Control plants were sampled at the same time as the stress treatments. For OBD04, tissues from plants treated with abiotic, biotic, and mechanical stresses were pooled. For abiotic stress, leaves and stems were collected from plants subjected to heat (37°C), cold (4°C), salt (200 mM NaCl), and osmotic (300 mM Mannitol) treatments. For biotic stress, leaves were collected from plants with the following treatments: Bacterial treatments were (Pseudomonas fluorescens and Pseudomonas syringae pv. tomato DC3000 [Pto DC3000]) delivered to 28-29 day old Brachypodium leaves under vacuum at 1x107 cfu/mL. Leaves of four-week old plants were placed in a 1.5 ml microcentrifuge tube containing 20 µg/mL victorin. Tissue was harvested 24 h after treatment with victorin. Mechanical stress was applied by crushing the leaves of 29-30 day old plants with tweezers. Unless otherwise indicated, libraries were made from a pool of samples collected every 4 h after the stress began, i.e. 4h+8h+12h+16h+20h+24h.

tag: tissue

value: stem

tag: plant line

tag: treatment

value: untreated


title: BDI25 Panicle

source_name: Panicle

value: panicle


title: BDI21 Leaf

source_name: Leaf

value: leaf


title: 2-APC-iPSC-32 H3K4me2 ChIPseq

description: Sample 43

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_32_peaks.bed: mm9

value: APC-derived induced pluripotent stem cells


title: 3-APC H3K4me3 ChIPseq

description: Sample 40

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_BSC_peaks.bed: mm9

source_name: APC H3K4me3 ChIPseq

value: abcam


title: R1-ESC H3K4me2 ChIPseq

description: Sample 41

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_R1_peaks.bed: mm9

source_name: ESC H3K4me2 ChIPseq


title: 1-MEF-iPSC-37 H3K4me2 ChIPseq

description: Sample 42

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_37_peaks.bed: mm9


title: 2-APC H3K4me3 ChIPseq

description: Sample 38

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_ASC_peaks.bed: mm9


title: 2-HPC H3K4me3 ChIPseq

description: Sample 39

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_HSC_peaks.bed: mm9

source_name: HPC H3K4me3 ChIPseq


title: BDI20 Root

source_name: Root

value: root


title: 3-APC H3K4me2 ChIPseq

description: Sample 53

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_BSC_peaks.bed: mm9


title: BDI19 Submergence-stressed shoot

description: small RNA

source_name: Shoot

value: shoot

value: submergence


title: BDI16 Phosphate-starved shoot

description: small RNA

value: Phosphate-starvation


title: BDI15 Shoot control for low phosphate

description: small RNA


title: 3-APC-iPSC-9 H3K4me3 ChIPseq

description: Sample 36

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_9_peaks.bed: mm9

source_name: APC-iPSC H3K4me3 ChIPseq


title: 1-MEF H3K4me3 ChIPseq

description: Sample 37

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_MEF_peaks.bed: mm9

source_name: MEF H3K4me3 ChIPseq


title: P107A_H3K27AC

description: Chromatin immunoprecipitation against H3K27Ac

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Diffuse Large B-Cell Lymphoma

value: Abcam AB4729

value: primary normal lymph node


title: BDI18 Heat-stressed shoot

description: small RNA

value: heat


title: 1-MEF-iPSC-42 H3K4me3 ChIPseq

description: Sample 33

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_42_peaks.bed: mm9

source_name: MEF-iPSC H3K4me3 ChIPseq

value: MEF-derived induced pluripotent stem cells


title: BDI17 Salt-stressed shoot

description: small RNA

value: salt


title: 2-HPC-iPSC-18 H3K4me3 ChIPseq

description: Sample 35

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_18_peaks.bed: mm9

source_name: HPC-iPSC H3K4me3 ChIPseq

value: HPC-derived induced pluripotent stem cells


title: 2-APC-iPSC-4 H3K4me3 ChIPseq

description: Sample 34

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_4_peaks.bed: mm9


title: 3-APC-iPSC-3 H3K4me3 ChIPseq

description: Sample 32

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_3_peaks.bed: mm9