title: DPY28 Rep1 ChIPSeq

description:
DPY28_N2_MxEmb_average.wig
DPY28_N2_MxEmb_peaks.bed

value: DPY-28 SDQ4564 Rabbit polyclonal is against the antigen QQQPTRNNDGLSGFKSITEIIAEADNNIPSEQIDKDIDSFSSYSDISDWRGIPKFFPSLSSLSRRASTYENWENRFKVVDYLVSCSGALKDSVSDYVADY May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: DPY28 Rep2 ChIPSeq

status: Public on Sep 16 2013

type: SRA

city: New York

first: Sevinc

last: Ercan

state: NY

address: 12 Waverly Place

department: Biology

country: USA

institute: New York University

library_source: genomic

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 0.12.7 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.141 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Genome coverage was estimated using MACS version 1.4.141 with the following setting: genome size (-g ce), format (-f BAM), output in wiggle format (-w), whole genome output (-S), resolution (--space=1)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks per subunits, reads from the replicates were combined using the BEDTools utility mergeBam version 2.13.442, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
To get final peak sets representing condensinI-IDC and condensinII, we used a sliding window across the genome. Each base pair covered by at least two of the three non-SMC subunits (DPY-26, DPY-28, and CAPG-1 for condensinI-IDC, CAPG-2, HCP-6, and KLE-2 for condensinII) was included in the final peak set.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.0.2 using default parameters supplying gene annotations.
Genome_build: WS220
Supplementary_files_format_and_content: Wig files were generated using MACS version 1.4.141, normalized according to the genome-wide mean coverage and the input subtracted. Scores represent the average coverage of each replicate at each base position.
Supplementary_files_format_and_content: Bed files were generated by combining replicate reads and using MACS version 1.4.141 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value.
Supplementary_files_format_and_content: FPKM text file contains the FPKM values for each gene for each replicate.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed stage embryos (wild type N2) were isolated by bleaching gravid adults grown in liquid or plates at 20C temperature.

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.

tag: strain

tag: developmental stage

value: embryo

tag: matching input

tag: antibody


title: SMC4 Rep3 ChIPSeq

description:
SMC4_N2_MxEmb_average.wig
SMC4_N2_MxEmb_peaks.bed

value: SMC-4 KH-SMC4 Rabbit Polyclonal to 1519-1549 aa sequence CGSTPKRSPMKPLTPSSKKKEKAIVDDDDDME  (PMID:19119011)


title: IgG Rep3 ChIPSeq

description:
IgG_N2_Mxemb_average.wig
IgG_N2_Mxemb_peaks.bed

value: Rabbit IgG, Abcam antibody catalog number ab46540


title: SMC4 Rep2 ChIPSeq

value: SMC-4 OD0039 Rabbit polyclonal from Arshad Desai Lab


title: IgG Rep1 ChIPSeq


title: SMC4 Rep1 ChIPSeq


title: DPY27 Rep1 ChIPSeq

description:
DPY27_N2_MxEmb_average.wig
DPY27_N2_MxEmb_peaks.bed

value: DPY-27 JL00001 Rabbit polyclonal to 1-409 aa. (Ercan et al. Nat Genet. 2007) is against the antigen 1-409 aa


title: PQN85 TY1072 Rep2 ChIPSeq

description:
PQN85_TY1072_Mxemb_average.wig
PQN85_TY1072_Mxemb_peaks.bed

value: PQN-85 SDQ4481 Rabbit polyclonal is against the antigen QQQPVQQIQRQQPIAQPIPQHTIPPSTSNQFQQQIQSAASSIFDSSVISSHQKLYEEQCRQIEKERKEQEERKRKQELEEQRKRNEELKRLRIAEEKRLL May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: DPY26 Rep4 ChIPSeq

description:
DPY26_N2_Mxemb_average.wig
DPY26_N2_MxEmb_peaks.bed

value: DPY-26 SDQ4561 Rabbit polyclonal is against the antigen RVDRLHHDVRQIDSALSSGTVMRDSNGEEIHLTLESRKAKKKMAVVDGMNGMLDFLNNMDDALTTTELDADNDKNWKEDEENIAGEPRIDFKANSKDVDA May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: PQN85 TY1072 Rep1 ChIPSeq


title: DPY26 Rep5 ChIPSeq


title: HTZ Rep2 ChIPSeq

value: HTZ1 BK00001 mouse ascites polyclonal against HTZ-1 specific C-terminal peptide N-PGKPGAPGQGPQ-C (PMID:18787694)


title: KLE2 Rep3 ChIPSeq

description:
KLE2_N2_Mxemb_average.wig
KLE2_N2_Mxemb_peaks.bed

value: KLE-2 SDQ3942 Rabbit polyclonal is against the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: DPY26 Rep2 ChIPSeq

value: DPY-26 SDQ4496 Rabbit polyclonal is against the antigen RVDRLHHDVRQIDSALSSGTVMRDSNGEEIHLTLESRKAKKKMAVVDGMNGMLDFLNNMDDALTTTELDADNDKNWKEDEENIAGEPRIDFKANSKDVDA May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: HCP6 TY1072 Rep2 ChIPSeq

description:
HCP6_TY1072_Mxemb_average.wig
HCP6_TY1072_MxEmb_peaks.bed

value: HCP-6 KH-HCP6 Rabbit Polyclonal to 1708-1722 aa sequence CKSAQAYHLHNIFEEDEES  (PMID:19119011)


title: 9597_RNA-seq

city: Berne

first: Martin

middle: H

last: Braunschweig

state: Berne

address: Bremgartenstrasse 109A

department: Vetsuisse Faculty

country: Switzerland

institute: University of Bern

description: suppl_diet 1

library_source: transcriptomic

data_processing:
The quality of the sequence reads was assessed using fastQC version 0.9
Ribosomal RNA contaminations were removed by mapping the 100bp single end reads to a collection of ribosomal RNA sequences using bowtie2 with standard parameters
Genome_build: The reads were mapped to the Sus scrofa genome assembly Ssc10.2/Ssr3 (http://hgdownload.cse.ucsc.edu/goldenPath/susScr3/bigZips/susScr3.fa.gz) using TopHat2 with default parameters
Supplementary_files_format_and_content: fold change data

molecule: total RNA

organism: Sus scrofa

source_name: F0 sperm

extract_protocol:
Trizol followed DNase treatment and chlorofom and penol extraction and RNA precipitation
Sperm RNA was directly used for library construction following illumina’s protocol TrueSeq RNA Sample Preparation v2 Guide

treatment_protocol: F0 boars received either a standard diet or a standard diet supplemented with methylating micronutrients from one to ten months of age. The supplemented diet contained additional methionine, choline, betaine, vitamin B6, B12 and folate.

tag: gender

value: male

tag: diet

tag: cell type

value: sperm cell


title: Input Rep10 ChIPSeq


title: 9599_RNA-seq

description: suppl_diet 3

value: standard diet supplemented with methylating micronutrients


title: 9600_RNA-seq

description: control_diet 3

value: standard diet


title: CAPG1 Rep2 ChIPSeq

description:
CAPG1_N2_Mxemb_average.wig
CAPG1_N2_MxEmb_peaks.bed

value: CAPG-1 SDQ3967 Rabbit polyclonal is against the antigen MPPKKRIRGPKLPALREEKSTGTDVASDESFNESADFLNNEELNNDQNDAENTVLSEGVSTLRINENMTKEDRACISAALFIKKRVVESIRTVFQSRDDI May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: HCP6 Rep4 ChIPSeq

description:
HCP6_N2_Mxemb_average.wig
HCP6_N2_MxEmb_peaks.bed


title: CAPG1 Rep3 ChIPSeq

value: CAPG-1 SDQ3990 Rabbit polyclonal is against the antigen MPPKKRIRGPKLPALREEKSTGTDVASDESFNESADFLNNEELNNDQNDAENTVLSEGVSTLRINENMTKEDRACISAALFIKKRVVESIRTVFQSRDDI May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: CAPG1 Rep1 ChIPSeq

value: embryo


title: PQN85 Rep3 ChIPSeq

description:
PQN85_N2_Mxemb_average.wig
PQN85_N2_Mxemb_peaks.bed


title: HCP6 Rep2 ChIPSeq


title: 9598_RNA-seq

description: control_diet 1


title: HCP6 Rep3 ChIPSeq


title: DPY28 Rep4 ChIPSeq

value: DPY-28 KH-DPY28 Rabbit Polyclonal to 1484-1499 aa sequence CKSAVADDDSDSDEFMLDD (PMID:19119011)


title: RAT_LVCP_Adult_3

city: Parkville

first: Shane

middle: A

last: Liddelow

state: Victoria

address: Level 8 Medical Building, Grattan Street

department: Pharmacology

country: Australia

institute: The University of Melbourne

data_processing:
Illumina 1.5 phred score encoding used for basecalls
Trimmed reads mapped with Bowtie (v. 0.12.7) and mappen to Ensembl rat genome (release 61)
Number of reads mapped to nuclear genes determined with HTSeq (v. 0.4.7p4)
Differential expression (between embryonic and adult samples) detected using Bioconductor edgeR package (v. 2.4.0), with common dispersion used to estimate vairance between samples.
Genome_build: Ensembl (Hubbard et al., 2009) rat genome, release 61
Supplementary_files_format_and_content: Tab-delimited text files including RPKM values for each sample

organism: Rattus norvegicus

source_name: Adult lateral ventricular choroid plexus

growth_protocol: Both left and right lateral ventricular choroid plexuses were carefully dissected out as previously described (Liddelow et al., 2012) and placed in fresh ice-cold RNase-free PBS. Plexuses were pooled (n = 10 animals) and centrifuged at 1000rpm for 30 seconds and excess PBS removed.

extract_protocol:
Total RNA was extracted from pools of E15 and adult lateral ventricular choroid plexus (n = 3 for both ages) using the RNeasy Mini Kit, Qiashredder columns and gDNA removal columns (Qiagen, Valencia, CA, USA) according to standard supplier protocol. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatments, control animals only were used in the study.

tag: age

value: Adult

value: Sprague-Dawley


title: DPY28 Rep3 ChIPSeq

value: DPY-28 SDQ4564 Rabbit polyclonal is against the antigen QQQPTRNNDGLSGFKSITEIIAEADNNIPSEQIDKDIDSFSSYSDISDWRGIPKFFPSLSSLSRRASTYENWENRFKVVDYLVSCSGALKDSVSDYVADY May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: RAT_LVCP_Adult_1


title: RAT_LVCP_Adult_2


title: DPY27 Rep4 ChIPSeq

value: DPY-27 SDQ3995 Rabbit polyclonal is against the antigen LSNGLSNVVIAPKRKQRRLEMLKLSDFGLDDDSDLPEFNRFPPATRRELSVEDSDEDDEPVRRRPRRQVEEEDEEDELIEEATPSPPPIVVQRRVRRSRH May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: RAT_LVCP_E15_3

source_name: Embryonic (E15) lateral ventricular choroid plexus

value: Embryonic day 15 (E15)


title: DPY26 Rep3 ChIPSeq


title: RAT_LVCP_E15_2


title: HCP6 TY1072 Rep1 ChIPSeq


title: DPY27 Rep2 ChIPSeq

value: DPY-27 JL00001 Rabbit polyclonal to 1-409 aa. (Ercan et al. Nat Genet. 2007) is against the antigen 1-409 aa


title: RAT_LVCP_E15_1


title: DPY26 TY1072 Rep2 ChIPSeq

description:
DPY26_TY1072_Mxemb_average.wig
DPY26_TY1072_MxEmb_peaks.bed

value: DPY-26 JL00003 Rabbit polyclonal to 40-1262 aa.  (PMID:19853451) is against the antigen 40-1262 aa


title: HCP6 Rep1 ChIPSeq


title: DPY26 TY1072 Rep1 ChIPSeq


title: AMA1 Rep1 ChIPSeq

description:
AMA1_N2_embryo_average.wig
AMA1_N2_MxEmb_peaks.bed

value: AMA1 Q2358 Rabbit polyclonal is against the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA  May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: CAPG2 Rep2 ChIPSeq

description:
CAPG2_N2_MxEmb_average.wig
CAPG2_N2_MxEmb_peaks.bed

value: CAPG-2 SDQ4484 Rabbit polyclonal to 808-907 aa is against the antigen IPKWMNKQCDLMEDDEENIFKNHREIVESLRQFHKRVSETDYWDEDSAKRMMHHFMLFSIVSASSKNDDEAYDDPRDEDYKPPHFISLALIKFILKEKSL May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: CAPG2 Rep4 ChIPSeq

value: CAPG-2 SDQ4567 Rabbit polyclonal to 808-907 aa is against the antigen IPKWMNKQCDLMEDDEENIFKNHREIVESLRQFHKRVSETDYWDEDSAKRMMHHFMLFSIVSASSKNDDEAYDDPRDEDYKPPHFISLALIKFILKEKSL May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: CAPG2 Rep3 ChIPSeq


title: DPY26 Rep1 ChIPSeq


title: CAPG2 Rep5 ChIPSeq


title: AMA1 Rep2 ChIPSeq

value: AMA1 Q2357  Rabbit polyclonal is against the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: CAPG2 Rep1 ChIPSeq


title: DPY27 Rep3 ChIPSeq


title: 3AB_Su(Hw)

status: Public on Sep 15 2013

city: Singapore

first: Chin-Tong

last: Ong

address: 1 Research Link

department: Developmental Biology

country: Singapore

institute: Temasek Life Sciences Lab

description: Chromatin IP against Su(Hw) in 3AB treated cells

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting. Same number of reads from control and 3AB treated samples were used for peak calling by MACS .
Genome Build:
AbSuHw.gff: DM3
AbSuHw_peaks.bed: DM3

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were maintained in Schneider's medium + 10 % HI FBS

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200–1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC.  Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC.  After washing and eluting from beads the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’  - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.
antibody reference: CP190, dCTCF and Su(Hw): Regulation of chromatin organization and inducible gene expression by a Drosophila insulator. Wood AM, Van Bortle K, Ramos E, Takenaka N, Rohrbaugh M, Jones BC, Jones KC, Corces VG. Mol Cell. 2011 Oct 7;44(1):29-38.
antibody reference: dCTCF, Su(Hw) and Mod(mdg4)2.2.: Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains. Van Bortle K, Ramos E, Takenaka N, Yang J, Wahi JE, Corces VG. Genome Res. 2012 Sep 20.

treatment_protocol: 10 million of S2 cells seeded in 4.5ml of media was incubated for 16 h after addition of 0.5 ml of water (Control) or 120mM of 3AB (3AB-12mM).

tag: chip antibody

value: Su(Hw) antibody 406 (rabbit)

tag: cell line

value: S2 DRSC:Schneider's line 2

tag: treatment

value: 3AB treated


title: 3AB_input

description: Input in 3AB treated S2 cells

data_processing: Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting. Same number of reads from control and 3AB treated samples were used for peak calling by MACS .


title: Ct_Mod

description: Chromatin IP against Mod(mdg4)2.2 in control S2 cells

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting. Same number of reads from control and 3AB treated samples were used for peak calling by MACS .
Genome Build:
CtMod.gff: DM3
CtMod_peaks.bed: DM3

value: Mod(mdg4)2.2 antibody (rabbit)

value: control


title: 3AB_Mod

description: Chromatin IP against Mod(mdg4)2.2 in 3AB treated cells

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting. Same number of reads from control and 3AB treated samples were used for peak calling by MACS .
Genome Build:
AbMod.gff: DM3
AbMod_peaks.bed: DM3


title: 3AB_dCTCF

description: Chromatin IP against dCTCF in 3AB treated cells

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting. Same number of reads from control and 3AB treated samples were used for peak calling by MACS .
Genome Build:
Ab-dCTCF.gff: DM3
Ab-CTCF_peaks.bed: DM3

value: dCTCF antibody 68 (rat)


title: Ct_dCTCF

description: Chromatin IP against dCTCF in control S2 cells

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting. Same number of reads from control and 3AB treated samples were used for peak calling by MACS .
Genome Build:
Ct-dCTCF.gff: DM3
Ct-CTCF_peaks.bed: DM3


title: DH5_N2_48

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: whole worm poly(A)-extracted mRNA library

data_processing:
Debarcoding of samples.
Sequencing reads for each sample and timepoint were seperately mapped to the transcriptome using bwa (version 0.5.9) with default parameters.
Reads were aggregated across all isoforms of a given gene.
Aggregated reads were converted to reads per million mapped reads per kilobase of transcript length (RPKM).
Genome_build: WS190
Supplementary_files_format_and_content: data_rpkm.txt: Tab separated data file listing all genes (rows) and expression data in RPKM for all samples and all time points. Column name indicates sample, strain and time point, separated by an underscore. The first two columns indicate the wormbase gene symbol and gene name, respectively.

source_name: wild-type (N2) at 20C: 48 hrs

growth_protocol: Embryos of wild-type (N2) and mutant nematodes were isolated by hypochlorite treatment and hatched larvae were synchronized by starvation. L1-arrested animals in starvation medium were spotted onto NGM plates with food (OP50 E. coli strain) and cultured at 20C or 25C, respectively.

extract_protocol:
Total RNA was isolated from synchronized larval populations using Trizol (Invitrogen). Each sample underwent 3 rounds of freeze-thaw cycles for enhanced efficiency.
Poly(A)+ RNA libraries were prepared from total RNA.

tag: temperature


title: Ct_CP190

description: Chromatin IP against CP190 in control S2 cells

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting. Same number of reads from control and 3AB treated samples were used for peak calling by MACS .
Genome Build:
CtCP190.gff: DM3
CtCP190_peaks.bed: DM3

value: CP190 antibody (rabbit)


title: Ct_Su(Hw)

description: Chromatin IP against Su(Hw) in control S2 cells

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting. Same number of reads from control and 3AB treated samples were used for peak calling by MACS .
Genome Build:
CtSuHw.gff: DM3
CtSuHw_peaks.bed: DM3


title: DH5_N2_46

source_name: wild-type (N2) at 20C: 46 hrs


title: DH5_N2_42

source_name: wild-type (N2) at 20C: 42 hrs


title: DH5_N2_40

source_name: wild-type (N2) at 20C: 40 hrs


title: DH5_N2_44

source_name: wild-type (N2) at 20C: 44 hrs


title: DH5_N2_38

source_name: wild-type (N2) at 20C: 38 hrs


title: DH4_lin4_48

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 48 hrs


title: DH4_lin4_46

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 46 hrs


title: Ct_input

description: Input in control S2 cells


title: DH4_lin4_44

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 44 hrs


title: DH4_lin4_40

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 40 hrs


title: DH4_lin4_42

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 42 hrs


title: DH4_lin4_36

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 36 hrs


title: DH4_lin4_38

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 38 hrs


title: DH4_lin4_32

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 32 hrs


title: DH4_lin4_34

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 34 hrs


title: DH4_lin4_30

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 30 hrs


title: 3AB_CP190

description: Chromatin IP against CP190 in 3AB treated cells

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting. Same number of reads from control and 3AB treated samples were used for peak calling by MACS .
Genome Build:
AbCP190.gff: DM3
AbCP190_peaks.bed: DM3

source_name: S2 cells


title: DH4_lin4_28

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 28 hrs


title: DH4_lin4_26

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 26 hrs


title: DH4_lin4_22

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 22 hrs


title: DH4_lin4_20

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 20 hrs


title: DH4_lin4_12

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 12 hrs


title: DH4_lin4_18

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 18 hrs


title: DH4_lin4_6

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 6 hrs


title: DH4_lin4_8

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 8 hrs


title: DH4_lin4_10

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 10 hrs


title: DH4_lin4_4

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 4 hrs


title: DH4_lin4_0

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 0 hrs


title: DH3_N2_28_5

source_name: wild-type (N2) at 25C: 28.5 hrs


title: Activated B-cells from individual B2

status: Public on Sep 17 2013

city: Baltimore

first: Kasper

middle: Daniel

last: Hansen

state: Maryland

address: 615 N Wolfe St. E3527

department: Biostatistics

institute: Johns Hopkins

data_processing:
Basecalls performed using CASAVA 1.8.1
Reads were aligned to bisulfite-treated genome with the Bsmooth pipeline, version 0.4.5-beta, with --bscpg option
The Bsmooth alignment pipeline used Bowtie 2.0.0-beta8 with --ignore-quals option
Only summarized data with a quality score greater than 20 was used. Data was processed using the Bsmooth function from the bsseq package from Bioconductor. Each sample was processed twice, one for small scale smoothing (used to find small DMRs, parameters were h = 1000, ns = 70) and once for large scale smoothing (used to find large hypomethylated blocks, parameters were h=20000,ns=500)
Only CpGs which had at least 2 samples with a coverage of 2 or more in each of the following 3 group (B1,B2,B3 activation), (B1,B2,B3 resting) and (B1,B2,B3 transformed)
Genome_build: human NCBI genome build 37, lambda phage (gi|9626243|ref|NC_001416.1|) and EBV virus (gi|86261677|emb|AJ507799.2|)
Supplementary_files_format_and_content: Rows are CpGs, columns are as follows: chr (chromosome) and pos (position) is genomic location. Cov is the number of reads covering the CpG and M is the number of reads covering the CpGs, supporting methylation. smallSmooth and largeSmooth are smoothed values for small and large scale smoothing.

organism: Homo sapiens

source_name: Activated B-cells

extract_protocol:
Epicentre Masterpure DNA isolation kit
Bisulfite converted Illumina TruSeq DNA library

treatment_protocol: Cells were either resting, CD40 activated or EBV transformed

tag: individual/donor id

tag: sample group

value: CD40 activation

tag: time point

value: day6 following CD40 activation


title: DH4_lin4_2

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 2 hrs


title: DH3_N2_25_5

source_name: wild-type (N2) at 25C: 25.5 hrs


title: DH3_N2_21

source_name: wild-type (N2) at 25C: 21 hrs


title: DH3_N2_19_5

source_name: wild-type (N2) at 25C: 19.5 hrs


title: DH3_N2_16_5

source_name: wild-type (N2) at 25C: 16.5 hrs


title: DH3_N2_22_5

source_name: wild-type (N2) at 25C: 22.5 hrs


title: DH3_N2_24

source_name: wild-type (N2) at 25C: 24 hrs


title: DH3_N2_15

source_name: wild-type (N2) at 25C: 15 hrs


title: DH3_N2_18

source_name: wild-type (N2) at 25C: 18 hrs


title: DH3_N2_13_5

source_name: wild-type (N2) at 25C: 13.5 hrs


title: DH4_lin4_24

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 24 hrs


title: DH4_lin4_16

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 16 hrs


title: DH3_N2_10_5

source_name: wild-type (N2) at 25C: 10.5 hrs


title: DH3_N2_7_5

source_name: wild-type (N2) at 25C: 7.5 hrs


title: DH4_lin4_14

source_name: lin-4 knockout mutant (lin4(e912)) at 20C: 14 hrs


title: DH3_N2_9

source_name: wild-type (N2) at 25C: 9 hrs


title: A37G Ribo-Seq 0 ppm Se

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

description: Ribosome protected mRNA

data_processing:
base calling was done with the standard Illumina  pipeline
Sequence reads were trimmed for adaptor sequences, and aligned using bowtie (alignment parameters -m1 -v2 -a --best --strata) to a mm9 RefSeq mRNA database in which each transcript with multiple isoforms was reduced to a single entry corresponding to the longest isoform. For Selenoprotein analysis, a data base of selenoprotein mRNAs was created from RefSeq entries and ribosome protected or mRNA sequences were aligned individually using the same bowtie parameters.
Reads per kilobase per million mapped reads (RPKM for total RNA RPFKM for ribosome protected fragments) in each experiment were determined for entire mRNAs, for coding sequences (excluding the first 15 and last 3 codons). For selenoproteins, coding sequences upstream of the UGA-Sec codon and downstream of the UGA-Sec codon were also examined and assigned RPKM values.
Genome_build: RefSeq July 2008 release
Supplementary_files_format_and_content: RPKM

organism: Mus musculus

source_name: Liver

extract_protocol:
Livers were excised, flash frozen in liquid nitrogen, and homogenized in the presence of cycloheximide using a bead mill. Ribo-Seq samples were treated with Rnase 1 and monosomes isolated by ultracentrifugation. Ribosome protected fragments and total mRNA were isolated using Trizol reagent.
TruSeq small RNA Sample Kit

tag: transgene

value: Contains 20 copies TrspA37G

value: 3 weeks

value: 6 week diet 0 ppm selenium


title: DH3_N2_6

source_name: wild-type (N2) at 25C: 6 hrs


title: DH2_N2_38

source_name: wild-type (N2) at 20C: 38 hrs


title: DH3_N2_4_5

source_name: wild-type (N2) at 25C: 4.5 hrs


title: DH3_N2_1_5

source_name: wild-type (N2) at 25C: 1.5 hrs


title: DH3_N2_0

source_name: wild-type (N2) at 25C: 0 hrs


title: DH3_N2_3

source_name: wild-type (N2) at 25C: 3 hrs


title: DH2_N2_36

source_name: wild-type (N2) at 20C: 36 hrs


title: DH3_N2_27

source_name: wild-type (N2) at 25C: 27 hrs


title: DH2_N2_34

source_name: wild-type (N2) at 20C: 34 hrs


title: DH2_N2_32

source_name: wild-type (N2) at 20C: 32 hrs


title: DH2_N2_30

source_name: wild-type (N2) at 20C: 30 hrs


title: DH2_N2_28

source_name: wild-type (N2) at 20C: 28 hrs


title: DH2_N2_26

source_name: wild-type (N2) at 20C: 26 hrs


title: DH2_N2_24

source_name: wild-type (N2) at 20C: 24 hrs


title: DH2_N2_22

source_name: wild-type (N2) at 20C: 22 hrs


title: DH3_N2_12

source_name: wild-type (N2) at 25C: 12 hrs


title: DH2_N2_16

source_name: wild-type (N2) at 20C: 16 hrs


title: DH2_N2_8

source_name: wild-type (N2) at 20C: 8 hrs


title: DH2_N2_12

source_name: wild-type (N2) at 20C: 12 hrs


title: DH2_N2_14

source_name: wild-type (N2) at 20C: 14 hrs


title: DH2_N2_18

source_name: wild-type (N2) at 20C: 18 hrs


title: DH2_N2_2

source_name: wild-type (N2) at 20C: 2 hrs


title: DH2_N2_0

source_name: wild-type (N2) at 20C: 0 hrs


title: DH2_N2_4

source_name: wild-type (N2) at 20C: 4 hrs


title: DH2_N2_6

source_name: wild-type (N2) at 20C: 6 hrs


title: DH2_N2_10

source_name: wild-type (N2) at 20C: 10 hrs


title: pHAN_GFP_RNAseq

city: Bethesda

first: Hossein

last: Zare

address: 5o South Dr #1347

institute: NIH

description:
PolyA RNA sequencing
Processed data file 'PhanDRR1.2_PhanGFP_cds_exp.diff.txt' is linked as a supplementary file on the Series record.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using illumina pipline (Eland) , and TopHat(Trapnell C, et.al 2009) for RNA-Seq
MyoD and MyoG Peaks were called using MACS ( Zhang et al, 2008), with pvalue of 10^-6, --gsize mm, and the rest were default setting. H3k4me1 peaks were called using SICER Algorithm ( Zang et al, 2009) with the following setting: window size (200bp), window pvalue (0.2), gap size(600bp) and the FDR of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: peak files in bed formats and wig files were generated using filtered reads residing in enriched regions
Supplementary_files_format_and_content: RNA-Seq: txt files represent FPKM(RPKM) and differential expression analysis

molecule: polyA RNA

growth_protocol: C2C12 myoblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol:
For ChIP-Seq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNA-Seq, RNA was extracted according to TRIzol protocol (invitrogen).
For ChIPSeq, cells were cross-linked in 1% formaldehyde and processed according to Mousavi et al. 2012. Purified DNA was processed according to manufacturer's protocol. For polyA RNA-Seq, Illumina protocol was followed. For ribosomal depletion, ribo-zero was used (epicenter).

treatment_protocol: For differentiation, cells were placed in media containing Dulbecco's Modified Eagle Medium (DMEM) supplemented with 2% horse serum, penicillin/streptomycin and insulin-Transferrin-selenium-A.

value: 4hrs differentiating Myocytes


title: MT_MyoD_ChIPseq

description:
Chromatin IP against MyoD
MT_MyoD_ChIPseq1
MT_MyoD_ChIPseq2

value: 48hrs differentiating Myotubes

value: MyoD (C-20, Santa Cruz)


title: MB_H3K4me1_ChIPseq

description: Chromatin IP against H3K4me1

value: Proliferating Myoblasts

value: H3K4me1 (ab8895, Abcam)


title: GFPi_RNAseq

description:
PolyA RNA sequencing
Processed data file 'DRRi_GFPi_cds_exp.diff.txt' is linked as a supplementary file on the Series record.


title: Activated_SatCells_RNAseq

description: Ribosome minus total RNA sequencing

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using illumina pipline (Eland) , and TopHat(Trapnell C, et.al 2009) for RNA-Seq
MyoD and MyoG Peaks were called using MACS ( Zhang et al, 2008), with pvalue of 10^-6, --gsize mm, and the rest were default setting. H3k4me1 peaks were called using SICER Algorithm ( Zang et al, 2009) with the following setting: window size (200bp), window pvalue (0.2), gap size(600bp) and the FDR of 0.05
Bigwig files were generated using BedTools (Quinlan AR and Hall IM, 2010) and wigToBigWig(UCSC genome browser website) programs
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: peak files in bed formats and wig files were generated using filtered reads residing in enriched regions
Supplementary_files_format_and_content: RNA-Seq: txt files represent FPKM(RPKM) and differential expression analysis; bigwig files

source_name: Satellite Cells

value: satellite cells 72hrs in GM


title: MT_RNA_RNAseq

description: Ribosome minus total RNA sequencing


title: A/WSN/33 infected

city: Evanston

first: William

last: Buggele

state: IL

address: 2200 Campus Dr.

institute: Northwestern University

data_processing:
Sequence tags were processed and analyzed using BioScope software package (Applied Biosystems)
MicroRNA sequence tags were normalized by thousand mappable tags
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file of microRNA sequence tags per thousand mappable tags

source_name: Alveolar epithelial cell line, A549

growth_protocol: A549 cells were cultured in F12K media (Gibco) supplemented with 10% cosmic calf serum (Hyclone) and penicillin and streptomycin

extract_protocol:
RNA was purified and size fractionated using miRNEASY RNA isolation kit and Rneasy MinElute Clean up kit (Qiagen)
Libraries were constructed using 1 microgram of small RNA and the Small RNA Expression Kit (Applied Biosystems)

treatment_protocol: Cells were either mock infected or infected with either A/Udorn/72 or A/WSN/33 (5 pfu/cell) for 10 hours

tag: infection


title: MB_MyoD_ChIPseq

description:
Chromatin IP against MyoD
MB_MyoD_ChIPseq1
MB_MyoD_ChIPseq2

tag: strain


title: A/Udorn/72 infected


title: MT_H3K4me1_ChIPseq

description: Chromatin IP against H3K4me1

tag: developmental stage


title: DRRi_RNAseq


title: DH2_N2_20

source_name: wild-type (N2) at 20C: 20 hrs


title: genomic DNA from nonneuronal cells_subj5

status: Public on Sep 14 2013

city: Bronx

first: Stella

last: Dracheva

state: New York

address: James J. Peters VA Medical Center,130 W Kingsbridge Rd

department: Dept. of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

data_processing:
library strategy: Extended Reduced Representation Bisulfite Sequencing (ERRBS)
Image capture, analysis, and base calling were performed using Illumina’s CASAVA 1.8.2 pipeline.
Raw data were processed at Epigenomics Core Facility of Weill Cornell Medical College, New York, NY, using in-house pipeline with the Bismark aligner.
The average bisulfite conversion rate was 98.4±1.4% (Mean±SD).
Differential methylation analysis was performed using the methylKit R package.
Genome_build: hg19
Supplementary_files_format_and_content: ERRBS processed methylation data; tab-delimited text files (separate files for sites within CG, CHG and CHH sequence context) include chromosome position of the site, strand, coverage, detected frequency of C, detected frequency of T
*CpG.NEUR.mincov10.txt files are for CpG sites, coverage above 10 reads and *CHG.NEUR.mincov10.txt for non-CpG sites, CHG sequence context, coverage above 10 reads (minimal coverage reads = 10)
The file names indicate 'subject#', 'sequence coontext (CHG, CHH, or CpG)', cell type (NEUR for neuronal, GLIA for glial)

source_name: FACS-sorted nuclei from human postmortem brain

extract_protocol:
nuclei isolation: neuronal and nonneuronal nuclei from human postmortem brain material were isolated by fluorescence-activated sorting, as described in Kozlenkov et.al., (2013), Nucleic Acids Research (accepted for publication)
DNA extraction: genomic DNA was isolated by proteinase K treatment, phenol extraction and ethanol precipitation
ERRBS protocol: Extended Reduced Representation Bisulfite Sequencing (ERRBS) was performed as described in: Akalin et.al. (2012),PLoS. Genet., and Kozlenkov et.al (2013), Nucleic Acids Research (2013, accepted for publication).
sequencing: The amplified libraries were sequenced on an Illumina HiSeq2000 per manufacturer’s protocol for 50 bp single end read runs.

tag: subject id

value: male

value: adult

tag: disease state

value: normal

tag: tissue

value: orbitofrontal cortex

value: nonneuronal cells


title: genomic DNA from neuronal cells_subj6

tag: gender

value: neuronal cells


title: genomic DNA from nonneuronal cells_subj6

tag: cell type


title: genomic DNA from nonneuronal cells_subj4

tag: age


title: MEF_ko_rep3

status: Public on Sep 13 2013

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

institute: A*Star Singapore

data_processing:
Illumina Casava v1.8 used for basecalling.
Sequences were mapped to mm9 using TopHat v2.03 and Bowtie 2.0.0.6 with parameters -m 1 -n 2 --no-coverage-search --library-type fr-unstranded --solexa-quals
FPKM values were computed using cuffdiff 2.02 with parameters -u --total-hits-norm -N
To determine differential splicing events, MATS 3.0.6 beta was used counting junction reads and reads falling into the tested region within ENSEMBL v65 gene definitions. Matching embryos were analysed individually and only significant events occurring in at least two replicates were considered. Splicing events were labelled significant if the sum of the reads supporting a specific event exceeded 10 reads, the p-value was lower than 0.05 and the minimum inclusion level difference as determined by MATS was higher than 0.2. All other parameters were left at the default value.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and differential splicing results for each sample

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Neurosphere cultures were established as previously described. Briefly, E14.5 embryos were harvested and cortices carefully dissected in ice-cold PBS and incubated in trypsinfor 10 min at 37°C. The tissue was then mechanically dissociated into single cell suspension and passed through a 40 μm cell strainer into complete NSC medium, 1% penicillin-streptomycin, 20 ng/ml recombinant human epidermal growth factor and 20 ng/ml recombinant human fibroblast growth factor-basic.  Mouse Embryonic Fibroblasts (MEFs). Primary MEFs were prepared from E14.5 embryos as previously described 48 and maintained in a humidified 5% CO2 atmosphere at 37°C in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. To induce PRMT5 knockout, MEFs (passage 1) were grown to confluence in 15 cm-dishes.

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit v2(Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: PRMT5F/F ER day 4 NPCs and MEFs were treated with either 50nM 4-OHT or the equivalent volume of ethanol for 24 hours before splitting to induce PRMT5 knockout.

value: MEF

value: Prmt5 depletion

tag: genotype

value: Prmt5 F/FER

value: mixed C57BL/6 X 129S1/SvlmJ


title: MEF_wt_rep3

value: control

value: EtOH


title: MEF_ko_rep2


title: MEF_ko_rep1


title: pHAN_DRR1.2_RNAseq

value: 4hrs differentiating Myocytes

tag: chip antibody


title: NPC_ko_rep3

source_name: Neural progenitor cells

value: NPC

tag: treatment


title: NPC_ko_rep1


title: NPC_wt_rep3


title: MEF_wt_rep1


title: genomic DNA from neuronal cells_subj4


title: NPC_ko_rep2


title: MT_MyoG_ChIPseq

description:
Chromatin IP against MyoG
MT_MyoG_ChIPseq1
MT_MyoG_ChIPseq2

value: 48hrs differentiating Myotubes

value: MyoG (M-225, Santa Cruz)


title: EBNA 3 ChIP-seq

city: Liverpool

first: Aditi

last: Kanhere

address: Institute of Systems, Molecular and Integrative Biology

country: United Kingdom

institute: University of Liverpool

data_processing:
Image analysis and base calling were performed using the solexa pipeline. Reads were aligned to the human genome build hg19 using Eland, background corrected using whole cell extract data, and converted to tags per million total reads. Significant peaks were identified with MACS.
Genome_build: hg19
Supplementary_files_format_and_content: EBNA2_peaks.txt: peak file, MACS output (pval = 10-7)
Supplementary_files_format_and_content: EBNA3_peaks.txt: peak file, MACS output (pval = 10-7)

source_name: Mutu III Burkitt's Lymphoma cell-line

growth_protocol: Cells were cultured in RPMI 1640, 10% foetal bovine serum and antibiotics and passaged twice weekly.

extract_protocol:
Following cross-linking, glycine was added to a final concentration of 1.25 M and cells were washed in PBS and lysed in 300 ul of cell lysis buffer (85 mM KCl, 0.5% NP-40, 5 mM PIPES pH 8.0, 1 mM PMSF and EDTA-free protease inhibitor cocktail (Roche)) per 10 7 cells. Following a 10 minute incubation on ice, cell nuclei were pelleted by centrifugation at 8000 rpm for 5 minutes at 4 oC in a bench-top Microfuge. The nuclei were then resuspended in 200 µl of SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.0 plus protease inhibitors) per 10 7 cells and sonicated to reduce DNA length to between 200 and 600 bp. ChIP was carried out using 600 µl of chromatin from 30 x 10 6 cross-linked cells diluted 10-fold in IP dilution buffer and pre-cleared with protein A sepharose beads. An input control sample was removed and EBNA 3 proteins precipitated overnight with rotation at 4ºC using 60 µl sheep polyclonal anti-EBNA 3 antibodies (Abcam, ab16128). EBNA 2 was precipitated using 48 µg EBNA 2-specific mouse monoclonal antibody (PE2) followed by an additional 2 hr incubation with 80 µg rabbit anti-mouse antibodies (Dako). BSA-coated protein A sepharose beads were then added and immune complexes collected by rotation at 4ºC for 3 hrs. Beads were washed for 10 minutes at 4 ºC with rotation using a series of different wash buffers. Complexes were washed once in low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 150 mM NaCl), once in high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 500 mM NaCl), once in LiCl wash buffer (250 mM LiCl, 1% NP40, 1% Na deoxycholate, 1 mM EDTA, 10 mM Tris pH 8.0) and twice in TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Immune complexes were eluted in TE elution buffer (10 mM Tris pH 8.0, 5 mM EDTA, 1% SDS) at 65 ºC for 15 minutes. TE elution buffer was added to the input control sample and all samples were then incubated at 65 ºC overnight to reverse the crosslinks and samples were treated with 0.2 µg/ml RNAse A for 1 hr at 37 ºC to remove RNA. DNA was purified using QIAquick gel extraction (Qiagen).
ChIP and input DNA (10 ng) was used to generate sequencing libraries with a ChIP-seq sample prep kit (Illumina). DNA fragments were end repaired, phosphorylated, 3’-dA overhangs added and adapters ligated according to the manufacturer’s instructions. PCR-amplified samples (16-cycles) were separated on a 2% agarose gel in TAE buffer, visualized using SYBR-safe stain and a Dark Reader transilluminator (Clare Chemical Research). The region of the gel containing 150-350 bp DNA fragments was excised and DNA purified using a gel extraction kit (Qiagen). The library was quantified using an Agilent bioanalzer and subjected to 35bp single-end read sequencing with an Illumina Genome Analyzer IIx.

treatment_protocol: Mutu III cells were diluted to 5x10 5 cells/ml 24 hrs prior to chromatin preparation. Cells were then resuspended at 1x10 7 cells/ml and formaldehyde was added to a final concentration of 1% (v/v) for 15 minutes at room temperature with rocking to cross-link proteins and DNA.

tag: cell line

value: Mutu III

tag: cell line origin

value: B-cell line derived from a tumour biopsy

tag: clone number

value: clone 48

value: EBNA 3

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: input DNA


title: EBNA 2 ChIP-seq

value: EBNA 2(PE2)


title: Input ChIP-Seq

city: MARSEILLE

first: Nathalie

last: AUPHAN-ANEZIN

address: Parc Scientifique de Luminy

country: France

institute: CIML

data_processing:
Pre-processing  Sequence reads of 50 and 75 bp were produced respectively with a SOLiDTM V4.0 or hq5500xl sequencers, according to standard Life Technologies protocols. Sequence read mapping to version 9 build 37 (mm9) of the mouse genome was achieved with Bfast (v0.7.0), only reads with a unique best scoring alignment and mapping once to the genome were retained for subsequent analyses, to prevent spurious calls in repetitive regions. To reduce the risk of potential bias, we discarded all tags with exactly the same coordinates.     Generation of Wigged files  Reads were elongated to 204 bp and 189 bp for replicates 1 and 2, respectively. The values were summed up in non-overlapping 50 bp bins along each chromosome to generate Wigged files using a R custom script.     Peak calling  Significant STAT5 bound regions were retrieved using the HOMER peak-calling tool (http://biowhat.ucsd.edu/homer/) with a FDR of 0.001, and a local input fold enrichment of 4.
genome build: MM9

source_name: purified memory TCRP1A eTC-STAT5CA

growth_protocol: TCRP1A CD8 T lymphocytes were activated by their cognate P1A Ag. After 24h, an active form of Stat5 (STAT5CA) was introduced in activated cells. Culture was continued for another 48h to induce their differentiation in effector T cells. These 72h activated T cells were injected in congeneic hosts and recovered 70 days later from hosts’ spleen and lymph nodes: TCRP1A eTC-STAT5CA.

extract_protocol: Chromatin Preparation (ChIP):  EDTA-free protease inhibitors (Roche, France) were added to all washing buffers to a finalconcentration of 1X. Aliquots of 5x107 cells were lysed after resuspension in 2 ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at 4°C. Chromatin was collected by centrifugation for 5 minutes at 4°C and 1.350g in a tabletop centrifuge, and washed in 2 ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8,10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was collected,resuspended in 2 ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mMNaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000(Misonix Inc, USA) sonicator for 16 cycles (30 seconds on, 30 seconds off, amplitude 40) with the tubessubmerged in ice-cold sonication solution (500mM NaCl, 20% ethanol). After the addition ofTriton X-100 to a final concentration of 1%, particulates were collected through centrifugation at20.000g and 4°C for 20 minutes. For batch processing, supernatants were combined, mixedthoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at-80°C until use and 50μl aliquots were taken to serve as input controls.  Inputs were combined with an equal volume of 2x elution buffer (100mM Tris pH 8, 20mM EDTA pH 8, 2% SDS) and incubated overnight in a water bath at 65°C for 13-15 hours. SDS was then diluted by the addition of an equal volume of TE (10mM Tris pH 8, 1mM EDTA pH 8) and RNA was digested by RNase A at a final concentration of 0.2μg/ml at 37°C for 2 hours. Samples were subsequently Proteinase K treated at 55°C for two hours at a final concentration of0.2μg/ml. DNA was purified by two subsequent phenol:chloroform:isoamylalcohol (25:24:1, pH8) extractions and followed by a Qiaquick purification (PCR purification columns, Qiagen,Germany). To ensure greater DNA purity, columns were washed twice with PE buffer and elutedin 50μl H2O. DNA concentration was measured using a Nanodrop 1000 (Thermo Scientific,France) and 1 ul was used to verify sonication efficiencies using High Sensitivity DNA chips on a 2100 Bioanalyzer. ChIP experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G. Beads were washed 3x with 1ml and subsequently resuspended in 250μl of blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody (anti-Stat5a; PA-ST5A from R&D Sysytems), the beads were incubated at 4°C overnight on a rotating wheel. Unbound antibodies were removed through three further washes with 1ml of blocking solution. Beads were resuspended in 100μl of blocking solution, extracts were added and the mix was incubated overnight at 4°C on a rotating wheel. EDTA-free protease inhibitors (Roche) were added to all washing buffers to a final concentration of 1x. Beads were washed 8 times in RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE+ (10mM Tris pH 8, 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps at 65°C for 15 and 10 minutes in 60μl and 40μl of elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65°C overnight (13-15 hours) for crosslink reversal. DNA was purified as described for the input.    Sequencing  10 ng of Input and 90 µl of STAT5a ChIP were used for high throughput sequencing. Standard Applied Biosystems Life Technologies protocols were followed for the creation of short-insert bar-coded libraries (insert length ~150 bp) according to the ChIP-seq Kit Guide from the manufacturer (cms_079323.pdf) and library preparation guide (cms_081748.pdf). The library was PCR amplified with 15 cycles. The amplified fragments were verified on a 2100 Bioanalyzer (Agilent, USA) before sequencing on an AB SOLiDTM V4.0 or hq5500XL (Life Technologies) according to the manufacturer’s protocol.

treatment_protocol: CD8 T cells were prepared from LN or spleen according to the standard procedures. Cell suspensions were passed over Ficoll-PaqueTM solution (Amersham Biosciences AB).

value: purified memory TCRP1A eTC-STAT5CA

value: Blood

value: memory CD8+ T cells


title: genomic DNA from neuronal cells_subj5

value: male

value: adult

value: normal

value: orbitofrontal cortex

value: neuronal cells


title: input DNA

city: Chicago

first: Aly

middle: Azeem

last: Khan

address: 6045 S. Kenwood Ave.

institute: University of Chicago

data_processing:
Base calling was performed using Illumina software pipeline (Genome Analyzer)
Align to the mouse genome (mm10) using bowtie (version 0.12.8) allowing 1 mismatch and reporting only uniquely aligning hits.
Peak calling was perfomed using (QuEST) v2.4 with input chromatin as control.
Genome_build: mm10
Supplementary_files_format_and_content: Peaks listed with genomic coordinates and QuEST score

source_name: Innate type-2 lymphocytes

extract_protocol:
~3 x 10^7 cells were harvested, crosslinked with formaldehyde, sonicated, IPed with appropriate antibodies and reverse-crosslinked to obtain 300-500 bp DNA fragments.
Standard Illumina kit was used for library construction.

tag: cell type/growth condition

value: ILC2s were sorted from the MLN of IL-25-treated mice

tag: antibody


title: Stat5a ChIP-Seq

tag: strain

tag: developmental stage

value: R&D Systems


title: ILC2_Gfi1_ChIP

value: anti-Gfi1 (a custom rabbit polyclonal antibody raised against N- and C-terminal peptides)


title: NPC_wt_rep1

value: NPC

value: control

value: Prmt5 F/FER

value: EtOH

value: mixed C57BL/6 X 129S1/SvlmJ


title: Campylobacter jejuni wildtype dRNA-seq, noTEX

city: Norfolk

first: Arnoud

last: van Vliet

address: Colney Lane

department: Gut Health and Food Safety Programme

institute: Institute of Food Research

description: half of RNA sample treated with terminator exonuclease, other half not, used for separate cDNA libraries

data_processing:
Sequences were obtained from SFF files, processed by the sfotware provided by the 454 FLX2 sequencing service at the University of Liverpool, UK
Sequencing reads were grouped based on the barcode tag, the 5' adapter was clipped, and reads of >70% A were removed.
The remaining reads were aligned against the C. jejuni genome NCTC 11168 genome sequence (NC_002163.1) using Segemehl version 0.0.9.3 (Hoffmann et al., 2009), and converted into number of reads per nucleotide position, for the plus and minus strand of the genome
Graphs representing the number of mapped reads per nucleotide were loaded in the Integrated Genome Browser software from Affymetrix (Nicol et al., 2009).
Genome_build: ASM908v1
Supplementary_files_format_and_content: Histogram files (.gr) for use in the Integrated Genome Browser software from Affymetrix (Nicol et al., 2009). Scores represent the number of reads per nucleotide position.  Files represent plus strand of genome or minus strand of genome.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Campylobacter jejuni

growth_protocol: The motile Campylobacter jejuni strain NCTC 11168  was grown to late log phase (OD600=0.21)

extract_protocol:
Total RNA was purified omitting size selection, to avoid the loss of small RNA molecules. The exclusion of rRNA and tRNA was also omitted, to avoid the potential loss of other RNA species. RNA was isolated using hot phenol (Mattatall & Sanderson, 1996), to ensure that small RNAs would not be removed by the extraction procedure. The RNA was treated with DNase I to remove residual genomic DNA.
The RNA sample was split in two equal fractions, and one of the two fractions was treated with Terminator Exonuclease (TEX, Peicentre Biotechnology) for enrichment of primary RNAs (Sharma et al., 2010). Both samples were treated with Tobacco Acid Phosphatase (TAP, Cambio, UK) to generate 5'-P ends for downstream ligation of 454 adapters. After ligation of an RNA oligonucleotide to the phosphorylated 5’-ends of RNA, and polyadenylation of RNA, first strand cDNA was generated using an oligo-dT containing 454-B primer. The cDNA fragments were barcoded and amplified, and used for generation of cDNA libraries for the 454 FLX system at Vertis Biotech, Germany. These libraries were subsequently analysed using a Roche FLX/Titanium sequencer using standard protocols from the manufacturer.

tag: description

value: wildtype strain, motile

tag: growth protocol

value: late log growth phase

tag: rna sample treatment

value: not treated with terminator exonuclease


title: ChIP Stat5a replicate

description: ChIP

tag: cell type

value: purified memory TCRP1A eTC-STAT5CA

tag: tissue

value: Blood

tag: passages

value: memory CD8+ T cells


title: D. yakuba input

first: Kevin

middle: P.

last: White

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

data_processing:
Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5.
Signal files were generated with the R 2.7.1 package SPP 2.7.1.
Peaks were called with MACS 1.3.7.
Genome_build: droYak2 (D. yakuba)

organism: Drosophila yakuba

growth_protocol: 1. the iso1 (y; bw cn sp) flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol:
After chromatin immuno-precipitation, the DNA is purified in 30ul of water. 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 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
ChIP and input libraries were prepared for sequencing using standard Illumina protocols

value: White prepupa

tag: chip antibody


title: MEF_wt_rep2

value: MEF

tag: treatment

tag: genotype


title: yak_pse_vir_pool

status: Public on Sep 12 2013

city: Lyon

first: Mathilde

last: PARIS

address: 32-34 avenue Tony Garnier

department: Institut de Genomique Fonctionnelle de Lyon

institute: CNRS

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were mapped to the genomes using tophat {Trapnell:2009dp}. Refined annotations of D. yakuba, D. pseudoobscura and D. virilis were based on the reference annotations (Flybase releases 1.3, 2.22 and 1.2 respectively) and mRNA-seq data obtained from pools of embryos. The reference annotations and mapped reads were given as inputs to cufflinks (version 1.0.3) {Roberts:2011hw} with the options –g and ‘--3-overhang-tolerance 300’. Statistics on the new annotations are given in Table S4.
mRNA measurements were obtained as follows: reads from single-embryo mRNA-seq were mapped to the genome sequence using tophat and mRNA levels were estimated using cufflinks {Trapnell:2010kd} and refined annotations (except D. melanogaster samples for which the reference annotation was used).
Genome_build: Apr. 2006 assembly (Flybase Release 5) of the D. melanogaster genome, the February 2006 assembly (Flybase release 2) of the D.pseudoobscura genome and the February 2006 assembly (Flybase release 1) of the D.virilis genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism:
Drosophila pseudoobscura
Drosophila virilis
Drosophila yakuba

source_name: Blastoderm embryo

growth_protocol: Blastoderm embryos

extract_protocol:
total RNA was extracted using Trizol, according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild type

value: whole embryo

value: Blastoderm

value: wild type


title: D. yakuba ChIP-seq rep 1


title: Dpse_mHB

description:
ChIP_metatable_HB.txt
HB: Inter species comparison of peak location, alignment quality, peak height, peak height based on motif content.

data_processing:
Basecalls performed using CASAVA version 1.4
We used the Apr. 2006 assembly (Flybase Release 5) of the D. melanogaster genome, the February 2006 assembly (Flybase release 2) of the D.pseudoobscura genome and the February 2006 assembly (Flybase release 1) of the D.virilis genome.  We trimmed all sequenced tags so that their average quality was above 30 and mapped the tags to the genomes using Bowtie v0.12.7 {Langmead:2009fv} with command-line options ‘-v 1 -m 1’ for small reads (length below 35bp) and ‘-v 1 –m 3 for long reads (length above 70bp), thereby keeping only tags that mapped uniquely to the genome with at most one or three mismatch. ChIP data was parsed independently for each experiment using two separate peak callers. First, we used MACS (version 1.4) {Zhang:2008gm}, with the following parameter “-g dm --off-auto --nomodel --pvalue=1e-2” and “--shiftsize=110 --mfold=10,10000 --slocal=2000 --llocal=20000"" or ” --shiftsize=60 --mfold=4,10000"" depending on the length distribution for DNA fragment sizes prior to sequencing. We also called peaks using Grizzly Peak fitting program (Capaldi et al., 2008, Harrison et al., 2011) with estimated DNA fragment length of 150 or 250.
We then intersected the two sets of peaks, and filtered out all peaks not supported by both methods. To account for low complexity peaks and possible PCR artifacts, we further removed peaks with negative correlation (<-0.1) among the Forward and Reverse reads, peaks where 60% of the reads mapped to less than 1% of the positions, and peaks whose height was less than three times the height of Input reads in the same locus.
ChIP data was parsed independently for each experiment using two separate peak callers. First, we used MACS (version 1.4) {Zhang:2008gm}, with the following parameter “-g dm --off-auto --nomodel --pvalue=1e-2” and “--shiftsize=110 --mfold=10,10000 --slocal=2000 --llocal=20000" or ” --shiftsize=60 --mfold=4,10000" depending on the length distribution for DNA fragment sizes prior to sequencing. We also called peaks using Grizzly Peak fitting program {Capaldi:2008ff, Harrison:2011iy} with estimated DNA fragment length of 150 or 250.
We then intersected the two sets of peaks, and filtered out all peaks not supported by both methods. To account for low complexity peaks and possible PCR artifacts, we further removed peaks with negative correlation (<-0.1) among the Forward and Reverse reads, peaks where 60% of the reads mapped to less than 1% of the positions, and peaks whose height was less than three times the height of Input reads in the same locus.
We took as an initial dataset the union of all bound regions in the different replicates
Genome_build: Apr. 2006 assembly (Flybase Release 5) of the D. melanogaster genome, the February 2006 assembly (Flybase release 2) of the D.pseudoobscura genome and the February 2006 assembly (Flybase release 1) of the D.virilis genome
Supplementary_files_format_and_content: bwt files were generated using bowtie. They indicate the coordinates of mapped reads.

source_name: Blastoderm embryos

growth_protocol: Embryos collected from large population cages for 1 hour, aged to appropriate stage, fixed in formaldehyde.

extract_protocol:
Chromatin was isolated by CsCl gradient ultracentrifugation, fragmented and immunoprecipitated with affnity-purified antibody
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly DNA fragments were converted to phosphorylated blunt ends using T4 DNA polymerase, Klenow DNA polymerase, and T4 polymerase kinase, a 3' A base overhang was added using Klenow DNA polymerase exo- (3' to 5' exo minus), and Illumina adapters were ligated to the fragments. We carried out the PCR step for enrichment of adapter-modified DNA prior to the library size selection, and limited the amplification to 15 cycles. After the amplification step, we size-selected DNA fragments of 150-250 bp.

tag: strains

value: HB (Li et al., 2008)


title: Dpse_mBCD

description:
ChIP_metatable_BCD.txt
BCD: Inter species comparison of peak location, alignment quality, peak height, peak height based on motif content.

value: Bicoid (Li et al. 2008)


title: Dpse_mGT

description:
ChIP_metatable_GT.txt
GT: Inter species comparison of peak location, alignment quality, peak height, peak height based on motif content.

value: GT  (Li et al. 2008)


title: Dpse_Input_1


title: NPC_wt_rep2

value: NPC

value: control

value: Prmt5 F/FER

value: EtOH


title: D. yakuba ChIP-seq rep 2


title: Dpse_mKR

description:
ChIP_metatable_KR.txt
KR: Inter species comparison of peak location, alignment quality, peak height, peak height based on motif content.

value: KR (Li et al., 2008)


title: Dmel_mGT_1

value: Oregon R


title: Dmel_mHB


title: Dmel_mKR


title: Dmel_vBCD

description:
Similar quantities of chromatin from the three species D. melanogaster, D. pseudoobscura and D. virilis were pooled after sonication and before ChIP. ChIP product was sequenced and reads were mapped to each species separately and reads that ambiguously mapped to several genomes were tossed. A very small quantity of mapped reads (less than 1%) were discarded, and the pooling had virtually no effect on read mapping.
ChIP_metatable_BCD.txt
BCD: Inter species comparison of peak location, alignment quality, peak height, peak height based on motif content.

organism:
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila virilis

value: Oregon R, MV2-25, V46

value: Bicoid, counter-purified agians D. virilis protein (Li et al. 2008)


title: mel_6


title: Dmel_Input_2


title: Campylobacter jejuni wildtype dRNA-seq, +TEX

value: wildtype strain, motile

value: late log growth phase

value: treated with terminator exonuclease


title: mel_5

value: Wild type

value: whole embryo


title: mel_3

value: Blastoderm

value: wild type


title: mel_4


title: mel_1


title: vir_4

organism: Drosophila virilis


title: Dmel_vKR

description:
Similar quantities of chromatin from the three species D. melanogaster, D. pseudoobscura and D. virilis were pooled after sonication and before ChIP. ChIP product was sequenced and reads were mapped to each species separately and reads that ambiguously mapped to several genomes were tossed. A very small quantity of mapped reads (less than 1%) were discarded, and the pooling had virtually no effect on read mapping.
ChIP_metatable_KR.txt
KR: Inter species comparison of peak location, alignment quality, peak height, peak height based on motif content.

value: KR, counter-purified agians D. virilis protein (Li et al., 2008)


title: yak_5


title: vir_6


title: yak_6


title: vir_3


title: vir_1


title: Dmel_Input_4

description: Similar quantities of chromatin from the three species D. melanogaster, D. pseudoobscura and D. virilis were pooled after sonication and before ChIP. ChIP product was sequenced and reads were mapped to each species separately and reads that ambiguously mapped to several genomes were tossed. A very small quantity of mapped reads (less than 1%) were discarded, and the pooling had virtually no effect on read mapping.


title: yak_4


title: yak_3


title: yak_1


title: yak_2


title: panH3-a549-3d-control

city: Charlottesville

first: Marcin

middle: Piotr

last: Cieslik

state: VA

address: 400 Stribling Ave Ext

institute: University of Virginia

description: processed data file: panH3-a549-3d-differential.tdf

data_processing:
Images generated by the Illumina sequencer were initially processed using the the Illumina pipeline.
read alignment: BWA 0.5.9-r16 using the HG19 reference with all default options, matches with smallest edit distance, ties resolved by picking a random.
Sequences that fully or partially overlapped regions with mappability issues, e.g. repetitive sequences, were discarded. These included regions with high false positive rates of enrichments, as identified by Pickrell et al [PMID: 21690102]
Mapped reads were extended to 200bp in the 3’ direction. The the genome was segmented into 200bp bins, and extended tags were assigned to each genomic bin they overlapped giving the per-window tag count (enrichment profile).
The raw enrichment profiles were normalized between the treated (3D) and control (3D) samples using an implementation of the normalization procedure used in the DESeq algorithm [pmid:20979621]. Next, we calculate a differential profile by subtracting the normalized control signal from the treated signal at each genomic window.
To locate putative enhancer sites using epigenetic data: initial putative loci was derived from the enrichment profiles H3K27ac and H3K4me1. The SICER software was used to call peaks of both marks in the epithelial and mesenchymal states, using corresponding panH3 samples as a control Peak calls with gaps less than or equal to 600bp were merged. The final calls were based on a FDR corrected p-value with a cutoff of 0.01. These peaks were subsequently used to delineate enhancer regions. Putative enhancers, for either of the two histone modifications, were centered (“anchored”) on the window that had the highest enrichment within a SICER peak. Sites were filtered to exclude those that overlapped H3K4me3 SICER peaks. H3K4me1 peaks within 1kb of  H3K27ac peaks were collapsed to the H3K27ac-based site. The resulting set of 200bp putative enhancer sites were expanded to include the flanking 1kb, to produce a set of 75,937 potential enhancer sites, each 2200bp in length. The initial set of 75,937 putative enhancers was further filtered to enrich for regions with significant epigenetic changes during EMT, yielding a final set of 30,681 differential enhancers.
Genome_build: HG19
Supplementary_files_format_and_content: files ending with "BED" are the results of aligning the "FASTQ" to the reference genome and are in the UCSC BED file format (the 'enhancer-sites.bed' file resulted from computing over all samples in this dataset), files ending with "TDF" (linked to Series records) are the differential enrichment profiles in the IGV "tiled" format suitable for viewing in IGV.

source_name: a549 3D culture

growth_protocol: NSCLC lines A549 were obtained from ATCC and maintained as 2D cultures in DMEM (CellGro), 10% FBS (Invitrogen) and penicillin/streptomycin (Invitrogen). For 3D cultures, cells were grown to approximately 80% confluency, trypsinized, resuspended in DMEM/10% FBS and pipeted onto the underside of a sterile 10 cm tissue-culture plate lid and incubated for 48 hours to facilitate cellular aggregation and spheroid formation.

extract_protocol:
Control and EMT-induced cells were cross-linked in 1% formaldehyde. The cross-linking reaction was quenched using 125 mM glycine, and the samples were collected for ChIP-Seq analysis according to the Myers lab protocol as described (Johnson et al.)  Approximately 1.2 x 10^7 cells were used per IP, and the DNA was sheared to approximately 400 bp fragments by sonication with a bioruptor.
After DNA recovery, we used standard Illumina protocols and reagents to prepare the ChIP-seq library (Illumina 11257047 rev A).

treatment_protocol: 3D cultures were subject to two treatment rounds of 10 ng/mL TNF and 2 ng/mL TGF treatment and incubation for 48 hours each.

tag: cell line

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #


title: H4K8ac-a549-3d-treated

description: processed data file: H4K8ac-a549-3d-differential.tdf

tag: treated twice with

value: 10 ng/mL TNF and 2 ng/mL TGF for 48hr each

value: Millipore


title: H4R3me2sym-a549-3d-treated

description: processed data file: H4R3me2sym-a549-3d-differential.tdf

value: Abcam


title: H4K20me1-a549-3d-treated

description: processed data file: H4K20me1-a549-3d-differential.tdf


title: H4R3me2sym-a549-3d-control


title: H4K8ac-a549-3d-control


title: panH3-a549-3d-treated


title: Dmel_mBCD

value: Bicoid (Li et al. 2008)


title: H4K20me1-a549-3d-control


title: mel_2


title: H3K9me3-a549-3d-treated

description: processed data file: H3K9me3-a549-3d-differential.tdf


title: vir_5


title: H3R17me2asym-a549-3d-treated


title: H3R17me2asym-a549-3d-control


title: vir_2


title: H3K9me3-a549-3d-control


title: H3K9me1-a549-3d-treated

description: processed data file: H3K9me1-a549-3d-differential.tdf


title: H3K9me1-a549-3d-control


title: H3K79me3-a549-3d-treated

description: processed data file: H3K79me3-a549-3d-differential.tdf


title: H3K9ac-a549-3d-treated

description: processed data file: H3K9ac-a549-3d-differential.tdf


title: H3K79me3-a549-3d-control


title: H3K9ac-a549-3d-control


title: H3K4me3-a549-3d-control

description: processed data file: H3K4me3-a549-3d-differential.tdf


title: H3K4me3-a549-3d-treated


title: H3K36me3-a549-3d-control

description: processed data file: H3K36me3-a549-3d-differential.tdf


title: H3K4me2-a549-3d-treated

description: processed data file: H3K4me2-a549-3d-differential.tdf


title: H3K4me2-a549-3d-control


title: H3K4me1-a549-3d-control

description: processed data file: H3K4me1-a549-3d-differential.tdf


title: H3K4me1-a549-3d-treated


title: H3K27me3-a549-3d-treated

description: processed data file: H3K27me3-a549-3d-differential.tdf


title: H3K27me3-a549-3d-control


title: H3K27ac-a549-3d-treated

description: processed data file: H3K27ac-a549-3d-differential.tdf


title: H3K27me2-a549-3d-control

description: processed data file: H3K27me2-a549-3d-differential.tdf


title: H3K27me2-a549-3d-treated


title: H3K27ac-a549-3d-control


title: H3K14ac-a549-3d-control

description: processed data file: H3K14ac-a549-3d-differential.tdf


title: pre-iPSC Ugcg replicate 1 read counts

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: UCLA

description: partially induced pluripotent stem cells derived from MEFs by retorviral over-expression of Oct4, SOx2, Klf4 and c-Myc

data_processing:
Two to seven 4C libraries were multiplexed and sequenced using the Illumina Genome Analyzer II to obtain 76 base pair (bp) reads or Illumina HIseq-2000 to obtain 100 bp reads.
The resultant reads were mapped to the mouse genome using Bowtie software (Langmead et al., 2009). Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis.
Reads that were successfully aligned to the genome were then remapped to the 736,199 unique HindIII sites along the genome (with respect to the 50bp upstream and downstream of the site) by matching their respective loci.
Genome_build: MM9
Supplementary_files_format_and_content: bedGraph-formatted files contain unqiue HindIII loci and associated 4C-seq read counts

source_name: cell culture

growth_protocol: standard cell culture

extract_protocol:
submitter has not supplied any information
submitter has not supplied any information

value: pre-iPSCs


title: H2AZ-a549-3d-treated

description: processed data file: H2AZ-a549-3d-differential.tdf

value: abcam


title: H2AZ-a549-3d-control


title: pre-iPSC Stk35 replicate 2 read counts


title: pre-iPSC Tbx5 replicate 1 read counts


title: pre-iPSC Tbx5 replicate 2 read counts


title: H3K36me3-a549-3d-treated


title: pre-iPSC Rhbdd1 replicate 1 read counts


title: pre-iPSC Stk35 replicate 1 read counts


title: pre-iPSC Rhbdd1 replicate 2 read counts


title: pre-iPSC Prss22 replicate 1 read counts


title: pre-iPSC Pcdhb19 replicate 3 read counts


title: pre-iPSC Pcdhb19 replicate 4 read counts


title: pre-iPSC Prss22 replicate 2 read counts


title: pre-iPSC Nfia replicate 2 read counts


title: pre-iPSC Pcdhb19 replicate 2 read counts


title: pre-iPSC Nfia replicate 1 read counts


title: pre-iPSC Krt131 replicate 2 read counts


title: pre-iPSC Pou5f1 replicate 6 read counts


title: pre-iPSC Hoxa10 replicate 2 read counts


title: pre-iPSC Pcdhb19 replicate 1 read counts


title: pre-iPSC Krt131 replicate 1 read counts


title: pre-iPSC Nfia replicate 3 read counts


title: pre-iPSC Dppa3 replicate 4 read counts


title: pre-iPSC Hoxa10 replicate 1 read counts


title: pre-iPSC Ugcg replicate 2 read counts


title: pre-iPSC Dppa3 replicate 3 read counts


title: pre-iPSC Dppa3 replicate 2 read counts


title: pre-iPSC Dppa3 replicate 1 read counts


title: pre-iPSC Dppa2 replicate 3 read counts


title: pre-iPSC Dppa2 replicate 4 read counts


title: pre-iPSC 1700067P10Rik replicate 4 read counts


title: pre-iPSC Dppa2 replicate 2 read counts


title: pre-iPSC 1700067P10Rik replicate 2 read counts


title: pre-iPSC 1700067P10Rik replicate 1 read counts


title: pre-iPSC Pou5f1 replicate 8 read counts


title: pre-iPSC 1700067P10Rik replicate 3 read counts


title: pre-iPSC Krt131 replicate 3 read counts


title: MEF Stk35 replicate 5 read counts

description: mouse embryonic fibroblast cells

value: MEFs


title: MEF Stk35 replicate 3 read counts

description: mouse embryonic fibroblast cells


title: MEF Stk35 replicate 2 read counts

description: mouse embryonic fibroblast cells


title: MEF Stk35 replicate 4 read counts

description: mouse embryonic fibroblast cells


title: MEF Stk35 replicate 1 read counts

description: mouse embryonic fibroblast cells


title: MEF Rhbdd1 replicate 3 read counts

description: mouse embryonic fibroblast cells


title: MEF Rhbdd1 replicate 4 read counts

description: mouse embryonic fibroblast cells


title: MEF Rhbdd1 replicate 1 read counts

description: mouse embryonic fibroblast cells


title: MEF Prss22 replicate 3 read counts

description: mouse embryonic fibroblast cells


title: MEF Pou5f1 replicate 7 read counts

description: mouse embryonic fibroblast cells


title: MEF Prss22 replicate 1 read counts

description: mouse embryonic fibroblast cells


title: MEF Prss22 replicate 2 read counts

description: mouse embryonic fibroblast cells


title: MEF Pou5f1 replicate 5 read counts

description: mouse embryonic fibroblast cells


title: MEF Pou5f1 replicate 4 read counts

description: mouse embryonic fibroblast cells


title: MEF Pou5f1 replicate 6 read counts

description: mouse embryonic fibroblast cells


title: MEF Nfia replicate 5 read counts

description: mouse embryonic fibroblast cells


title: MEF Nfia replicate 1 read counts

description: mouse embryonic fibroblast cells


title: H3K14ac-a549-3d-treated


title: MEF Nfia replicate 3 read counts

description: mouse embryonic fibroblast cells


title: MEF Krt131 replicate 2 read counts

description: mouse embryonic fibroblast cells


title: MEF Hoxa10 replicate 5 read counts

description: mouse embryonic fibroblast cells


title: MEF Krt131 replicate 1 read counts

description: mouse embryonic fibroblast cells


title: MEF Hoxa10 replicate 4 read counts

description: mouse embryonic fibroblast cells


title: MEF Hoxa10 replicate 3 read counts

description: mouse embryonic fibroblast cells


title: MEF Dppa3 replicate 5 read counts

description: mouse embryonic fibroblast cells


title: MEF Dppa2 replicate 7 read counts

description: mouse embryonic fibroblast cells


title: MEF Dppa3 replicate 6 read counts

description: mouse embryonic fibroblast cells


title: MEF Dppa3 replicate 4 read counts

description: mouse embryonic fibroblast cells


title: MEF Dppa2 replicate 3 read counts

description: mouse embryonic fibroblast cells


title: MEF Dppa2 replicate 6 read counts

description: mouse embryonic fibroblast cells


title: MEF 1700067P10Rik replicate 3 read counts

description: mouse embryonic fibroblast cells


title: MEF 1700067P10Rik replicate 2 read counts

description: mouse embryonic fibroblast cells


title: MEF 1700067P10Rik replicate 1 read counts

description: mouse embryonic fibroblast cells


title: iPSC Ugcg replicate 2 read counts

description: induced pluripotent stem cells derived from MEFs by retorviral over-expression of Oct4, SOx2 and Klf4

value: iPSCs


title: iPSC Tbx5 replicate 3 read counts


title: iPSC Ugcg replicate 1 read counts


title: iPSC Tbx5 replicate 2 read counts


title: iPSC Stk35 replicate 2 read counts


title: iPSC Tbx5 replicate 4 read counts


title: iPSC Tbx5 replicate 1 read counts


title: iPSC Rhbdd1 replicate 2 read counts


title: iPSC Pou5f1 replicate 4 read counts


title: iPSC Pou5f1 replicate 3 read counts


title: iPSC Stk35 replicate 1 read counts


title: iPSC Pou5f1 replicate 2 read counts


title: iPSC Pcdhb19 replicate 5 read counts


title: iPSC Pcdhb19 replicate 4 read counts


title: iPSC Pou5f1 replicate 5 read counts


title: MEF Dppa2 replicate 5 read counts

description: mouse embryonic fibroblast cells


title: iPSC Hoxa10 replicate 6 read counts


title: MEF Dppa2 replicate 4 read counts

description: mouse embryonic fibroblast cells


title: iPSC Nfia replicate 2 read counts


title: iPSC Pcdhb19 replicate 2 read counts


title: iPSC Hoxa10 replicate 4 read counts


title: iPSC Pcdhb19 replicate 1 read counts


title: iPSC Hoxa10 replicate 5 read counts


title: iPSC Dppa3 replicate 2 read counts


title: iPSC Hoxa10 replicate 2 read counts


title: iPSC Dppa3 replicate 1 read counts


title: iPSC 1700067P10Rik replicate 2 read counts


title: iPSC Rhbdd1 replicate 1 read counts


title: ESC Zfp42 replicate 2 read counts

description: mouse embryonic stem cells

value: ESCs


title: iPSC 1700067P10Rik replicate 1 read counts


title: ESC Zfp42 replicate 1 read counts

description: mouse embryonic stem cells


title: iPSC Dppa2 replicate 2 read counts


title: iPSC Dppa2 replicate 1 read counts


title: iPSC Pcdhb19 replicate 3 read counts


title: ESC Vegfc replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Ugcg replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Tbx5 replicate 3 read counts

description: mouse embryonic stem cells


title: iPSC Nfia replicate 1 read counts


title: ESC Vegfc replicate 1 read counts

description: mouse embryonic stem cells


title: ESC Ugcg replicate 1 read counts

description: mouse embryonic stem cells


title: ESC Tbx5 replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Rhbdd1 replicate 3 read counts

description: mouse embryonic stem cells


title: ESC Stk35 replicate 1 read counts

description: mouse embryonic stem cells


title: ESC Tbx5 replicate 1 read counts

description: mouse embryonic stem cells


title: ESC Stk35 replicate 2 read counts

description: mouse embryonic stem cells


title: iPSC Hoxa10 replicate 1 read counts


title: ESC Rhbdd1 replicate 1 read counts

description: mouse embryonic stem cells


title: iPSC Hoxa10 replicate 3 read counts


title: ESC Rhbdd1 replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Prss22 replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Prss22 replicate 1b read counts

description: mouse embryonic stem cells


title: ESC Krt131 replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Maoa replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Hoxa10 replicate 1 read counts

description: mouse embryonic stem cells


title: ESC Pou5f1 replicate 8 read counts

description: mouse embryonic stem cells


title: ESC Nfia replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Pcdhb19 replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Hoxa10 replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Nfia replicate 1 read counts

description: mouse embryonic stem cells


title: ESC Dppa3 replicate 1 read counts

description: mouse embryonic stem cells


title: ESC Dppa2 replicate 3 read counts

description: mouse embryonic stem cells


title: ESC 1700067P10Rik replicate 1 read counts

description: mouse embryonic stem cells


title: EED+/+ ESC Tbx5 replicate 5 read counts

description: sibling wild-type to Eed mutant ESC line

value: EED+/+ ESCs

value: EED+/+


title: ESC Maoa replicate 1 read counts

description: mouse embryonic stem cells


title: ESC 1700067P10Rik replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Dppa2 replicate 2 read counts

description: mouse embryonic stem cells


title: EED+/+ ESC Tbx5 replicate 2 read counts


title: ESC Pcdhb19 replicate 1 read counts

description: mouse embryonic stem cells


title: EED+/+ ESC Ptprg replicate 5 read counts


title: ESC Pcdhb19 replicate 3 read counts

description: mouse embryonic stem cells


title: EED+/+ ESC Tbx5 replicate 3 read counts


title: MEF Nfia replicate 4 read counts

description: mouse embryonic fibroblast cells


title: EED+/+ ESC Tbx5 replicate 1 read counts


title: EED+/+ ESC Ptprg replicate 4 read counts


title: ESC Prss22 replicate 1a read counts

description: mouse embryonic stem cells


title: small DNA associated with RsAgo expressed in E. coli BL21(DE3)

city: Pasadena

first: Ivan

last: Olovnikov

state: CA

address: 1200 E California Blvd

department: Division of Biology

institute: California Institute of Technology

description: small DNA

data_processing:
raw data file SRX335028 contains two libraries: ~15-19nt and ~45nt. They can be split by clipping 3` adapter: reads that can be clipped belong to ~15-19nt library, reads that cannot be clipped belong to ~45nt library.
small RNA- and small DNA-seq libraries: fastq to fasta conversion, clipping 3' adapter (TGGAATTCTCGGGTGCCAAGGC), min. length 13nt (non-clipped reads discarded), collapse
long RNA: fastq to fasta conversion, collapse
Supplementary_files_format_and_content: Supplementary_files_format_and_content: fasta files containing clipped (min13nt) and collapsed reads (number of reads is shown in sequence name)

organism: Escherichia coli BL21(DE3)

source_name: 6xHis-tag RsAgo protein expressed in E. coli

growth_protocol: R. sphaeroides cells were grown in Sistrom's minimal medium A at 30C; E. coli cells were grown in LB medium at 37C

extract_protocol: small DNA libraries were prepared according to Olovnikov et al., 2013 using adapters and primers compatible with Illumina TruSeq Small RNA Sample Preparation Kit. Protein was isolated from cells induced for ~5 hours with 1mM IPTG. Talon beads (Clontech) were used for affinity purification.

treatment_protocol: induction of protein was done with 1mM IPTG for 5-10 hours

tag: genotype/variation

tag: induced to express

value: 6xHis-tag RsAgo

tag: affinity purification using

value: Talon beads (Clontech)


title: EED+/+ ESC Tbx5 replicate 4 read counts

tag: strain


title: ESC Dppa3 replicate 2 read counts

description: mouse embryonic stem cells


title: ESC Krt131 replicate 1 read counts

description: mouse embryonic stem cells


title: total small RNA (13-30nt) from strain 29 with pSRKKm-RsAgo plasmid

description: small RNA

organism: Cereibacter sphaeroides ATCC 17029

source_name: total small RNA

extract_protocol: small RNA libraries were prepared according to Brennecke et al., 2007 using adapters and primers from Illumina TruSeq Small RNA Sample Preparation Kit. Small RNA from cells induced for 8 hours with 1mM IPTG was isolated using Amresco Phenol-Free Total RNA Purification Kit.

tag: containing plasmid

value: pSRKKm-RsAgo plasmid


title: total small RNA (13-30nt) from strain 29 with empty pSRKKm plasmid

description: small RNA

value: wild type

value: empty pSRKKm plasmid


title: small RNA associated with RsAgo expressed in E. coli BL21(DE3)

description: small RNA

extract_protocol: small RNA libraries were prepared according to Brennecke et al., 2007 using adapters and primers from Illumina TruSeq Small RNA Sample Preparation Kit. Protein was isolated from cells induced for ~5 hours with 1mM IPTG. Talon beads (Clontech) were used for affinity purification.


title: EED+/+ ESC Ptprg replicate 3 read counts


title: EED+/+ ESC Pou5f1 replicate 7 read counts


title: EED+/+ ESC Ptprg replicate 2 read counts


title: ribosomal RNA-depleted total RNA from strain 25 RsAgo mutant (replica 1)

description: ribosomal RNA-depleted total RNA

organism: Cereibacter sphaeroides ATCC 17025

source_name: ribosomal RNA-depleted total RNA

extract_protocol: library built from rRNA-depleted total RNA. RNA was extracted from cells at early stationary phase using Amresco Phenol-Free Total RNA Purification Kit. For rRNA depletion EpiBio Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria was used. Illumina TrueSeq RNA Sample Preparation Kit v2 was used for library preparation.

value: RsAgo mutant


title: EED+/+ ESC Pou5f1 replicate 5 read counts


title: ribosomal RNA-depleted total RNA from strain 25 RsAgo mutant (replica 2)

description: ribosomal RNA-depleted total RNA


title: EED+/+ ESC Pou5f1 replicate 2 read counts


title: EED+/+ ESC Pcdhb19 replicate 5 read counts


title: EED+/+ ESC Pcdhb19 replicate 4 read counts


title: EED+/+ ESC Pcdhb19 replicate 1 read counts


title: EED+/+ ESC Pcdhb19 replicate 2 read counts


title: EED+/+ ESC Hoxd replicate 2 read counts


title: EED+/+ ESC Hoxd replicate 1 read counts


title: total RNA from wild type strain 25

description: total RNA

source_name: total RNA

extract_protocol: library built from total RNA using Illumina TrueSeq RNA Sample Preparation Kit v2. RNA was extracted from cells at early stationary phase using Amresco Phenol-Free Total RNA Purification Kit.


title: EED+/+ ESC Hoxc replicate 2 read counts


title: total small RNA (13-30nt) from wild type strain 25 (replica 2)

description: small RNA


title: total small RNA (13-30nt) from strain 25 RsAgo mutant

description: small RNA


title: ribosomal RNA-depleted total RNA from strain 25 wt (replica 2)

description: ribosomal RNA-depleted total RNA


title: EED+/+ ESC Hoxc replicate 1 read counts


title: EED+/+ ESC Hoxb replicate 2 read counts


title: EED+/+ ESC Hoxb replicate 1 read counts


title: total small RNA (13-30nt) from strain 25 with pSRKKm-RsAgo plasmid

description: small RNA


title: total small RNA (13-30nt) from strain 25 with empty pSRKKm plasmid

description: small RNA


title: EED+/+ ESC Ptprg replicate 1 read counts


title: EED+/+ ESC Hoxa10 replicate 3 read counts


title: EED+/+ ESC Hoxa10 replicate 4 read counts


title: EED+/+ ESC Hoxa10 replicate 5 read counts


title: ribosomal RNA-depleted total RNA from strain 25 wt (replica 1)

description: ribosomal RNA-depleted total RNA


title: EED-/- ESC Tbx5 replicate 3 read counts

description: Eed mutant mouse embryonic stem cells

value: EED-/- ESCs

value: EED-/-


title: small DNA (~20-25nt) associated with RsAgo expressed in strain 25

description: small DNA

source_name: 6xHis-tag RsAgo protein expressed in wild-type strain 25

extract_protocol: small DNA libraries were prepared according to Olovnikov et al., 2013 using adapters and primers compatible with Illumina TruSeq Small RNA Sample Preparation Kit. Protein was isolated from cells induced for ~10 hours with 1mM IPTG. Talon beads (Clontech) were used for affinity purification.


title: EED+/+ ESC Pcdhb19 replicate 3 read counts


title: total small RNA (13-30nt) from wild type strain 25

description: small RNA


title: EED-/- ESC Tbx5 replicate 2 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Tbx5 replicate 1 read counts

description: Eed mutant mouse embryonic stem cells


title: EED+/+ ESC Hoxa10 replicate 1 read counts


title: EED-/- ESC Ptprg replicate 1 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Pou5f1 replicate 2 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Pou5f1 replicate 4 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Ptprg replicate 2 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Ptprg replicate 3 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Pcdhb19 replicate 3 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Pou5f1 replicate 1 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Pcdhb19 replicate 1 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Hoxd replicate 2 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Pcdhb19 replicate 2 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Hoxd replicate 1 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Hoxc replicate 2 read counts

description: Eed mutant mouse embryonic stem cells


title: EED-/- ESC Hoxc replicate 1 read counts

description: Eed mutant mouse embryonic stem cells


title: EED+/+ ESC Hoxa10 replicate 2 read counts


title: Dmel_vHB

description:
Similar quantities of chromatin from the three species D. melanogaster, D. pseudoobscura and D. virilis were pooled after sonication and before ChIP. ChIP product was sequenced and reads were mapped to each species separately and reads that ambiguously mapped to several genomes were tossed. A very small quantity of mapped reads (less than 1%) were discarded, and the pooling had virtually no effect on read mapping.
ChIP_metatable_HB.txt
HB: Inter species comparison of peak location, alignment quality, peak height, peak height based on motif content.

tag: developmental stage

value: Blastoderm

value: Oregon R, MV2-25, V46

value: HB, counter-purified agians D. virilis protein (Li et al., 2008)


title: EED-/- ESC Hoxb replicate 1 read counts

description: Eed mutant mouse embryonic stem cells

tag: cell type


title: EED-/- ESC Hoxb replicate 2 read counts

description: Eed mutant mouse embryonic stem cells


title: Dmel_mGT_2

description:
ChIP_metatable_GT.txt
GT: Inter species comparison of peak location, alignment quality, peak height, peak height based on motif content.

value: GT  (Li et al. 2008)


title: EED-/- ESC Hoxa10 replicate 3 read counts

description: Eed mutant mouse embryonic stem cells


title: small RNA (~15-19nt and ~45nt) associated with RsAgo expressed in strain 25

description: small RNA

extract_protocol: small RNA libraries were prepared according to Brennecke et al., 2007 using adapters and primers from Illumina TruSeq Small RNA Sample Preparation Kit. Protein was isolated from cells induced for ~10 hours with 1mM IPTG. Talon beads (Clontech) were used for affinity purification.


title: H2-2

city: Chongqing

first: Ling

last: Jia

address: Tiansheng Road 1

country: China

institute: State key laboratory of silkworm genome biology

data_processing:
RTA and OLB-1.9.4 were used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence and less than 18nt sequence to obtain the clean data. then mapped to silkoworm genome using
The clean data were mapped to silkworm genome using soap software with the parameters -v 0 -r 2 -M 0.
Genome_build: silkworm genome http://silkworm.swu.edu.cn/silkdb/doc/download.html
Supplementary_files_format_and_content: fasta files including the unique sequences and the corresponding reads

organism: Bombyx mori

source_name: hemolymph

extract_protocol:
Silkworm hemolymph was collected by cutting the first and second pairs of prolegs from the fifth instar day-5 larvae, using the sterile tubes containing a few crystals of phenylthiourea. Hemolymph samples were centrifuged (4000 x g, 10 min, 4℃) and the supernatants were stored at -80℃ until use. The silkworm hemolymph was extracted using mirVana™ PARIS™ Kit (AM1556, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: DAZAO

value: the fifth instar day-5 of larvae

value: wide type


title: Dmel_Input_3

description: Similar quantities of chromatin from the three species D. melanogaster, D. pseudoobscura and D. virilis were pooled after sonication and before ChIP. ChIP product was sequenced and reads were mapped to each species separately and reads that ambiguously mapped to several genomes were tossed. A very small quantity of mapped reads (less than 1%) were discarded, and the pooling had virtually no effect on read mapping.


title: H2-1


title: EED-/- ESC Hoxa10 replicate 2 read counts

description: Eed mutant mouse embryonic stem cells


title: mel_pse_vir_pool

value: Wild type

tag: tissue

value: whole embryo


title: pre-iPSC Dppa2 replicate 1 read counts

value: pre-iPSCs


title: pre-iPSC Pou5f1 replicate 2 read counts


title: pre-iPSC Pou5f1 replicate 1 read counts


title: ESC Pou5f1 replicate control_2 read counts

description: mouse embryonic stem cells

value: ESCs


title: ESC Pou5f1 replicate control_3 read counts

description: mouse embryonic stem cells


title: ESC Pou5f1 replicate 5a read counts

description: mouse embryonic stem cells