title: ER_ChIP-Seq

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Alignment: Sequence reads were obtained and mapped to the February 2009 human reference sequence (GRCh37) using the Illumina Genome Analyzer Pipeline using Illumina’s ELAND software.
Peaks: High-quality aligned read data is converted to the BED format and analyzed for peaks using the FindPeaks and the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) Peaks showing altered pull-down patterns are mapped to the genome, and a list of candidate genes and other known features flanking each peak are generated.

source_name: MCF7 cell line

growth_protocol: MCF7 cells were grown in estrogen-depeleted media for three days prior to time=0 of estrogen treatment.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: The MCF7 cells were plated in 150 mm plates under normal growth conditions. When cell density reached 25% confluence, the media was changed to hormone free media for 96 h. The hormone deprived MCF7 cells were treated with ethanol or 20 nM estradiol (Sigma) for  6 h. For ChIP assays, the treated MCF7 cells were cross-linked with 1% formaldehyde for 15 min. The cross-linking reaction was stopped with 0.125 M glycine. The cross-linked cells were washed by PBS three times and stored at -80°C before use. The sonicated and fragmented, precleared chromatin lysate was incubated overnight with specific antibodies: ER (F-10, Santa Cruz), TRIM24 (Novus Biological), H3K4me2 (Active Motif) or normal sheep IgG (Upstate/Millipore).

tag: treatment (e=estrogen, n=control)

value: N

tag: chromatin ip antibody

value: ER

tag: chromatin ip antibody description

value: anti-estrogen receptor

tag: analysis batch


title: ER_ChIP-Seq - Estrogen treated

status: Public on Sep 17 2010

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

value: E


title: MCF7-input-DNA-Seq

value: total-DNA


title: H3K4me2_ChIP-Seq

value: anti-Histone H3, dimethyl lysine 4


title: H3K4me2_ChIP-Seq - Estrogen treated


title: T24_ChIP-Seq - Estrogen treated


title: H3K36me3_HeLa

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

description: Chromatin IP against H3K36me3

data_processing: Reads (36 bp) were aligned to the human (Homo Sapiens) reference genome. Sequences were aligned to the human HG18 reference genome using the Illumina Analysis Pipeline allowing one mismatch. Unless specified otherwise, only the tags uniquely aligning to the genome were considered for further analysis. The 36 bp sequence reads were directionally extended to 300 bp, corresponding to the length of the original fragments used for sequencing. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All ChIP-Seq sequence analyses were conducted based on the Human NCBI Built 36.1 genome assembly (HG18) accessed from the Ensembl (release 54; May 2009) or the UCSC (assembly March 2006) Genome Browsers.

source_name: Human cervical carcinoma cell line

growth_protocol: Transfected HeLa Kyoto cells were FACS sorted (Epics Altra flowcytometer, Beckman Coulter) for GFP positive cells, and cultured for 3-4 passages in DMEM with 10% FCS under 500 µg/ml G418 selection at 37˚C before usage for the ChIP and ChIP-Seq experiments. Generation of the BACs with GFP-fusion constructs within the endogenous genomic context of the target gene, and transfections of HeLa cells, were performed according to Poser et al (2008).

extract_protocol:
Stable Transfections with GFP-fusion constructs within the endogenous genomic context of the target gene
ChIP experiments were performed using 3.3x10^6 cells per ChIP according to standard protocols (Denissov et al, 2007), with two minor modifications. Crosslinking of the cells was performed on the culture plates for 20 minutes, while ChIP’ed DNA was purified by Qiaquick PCR purification Kit (Qiagen cat. no. 28106).

value: HeLa Kyoto cell line

tag: sample type

value: Antibody H3K36me3 from Diagenode (CS-058-100)

tag: antibody

tag: antibody manufacturer

value: Diagenode

tag: antibody catalog #


title: T24_ChIP-Seq


title: GATAD1-GFP_HeLa rep2

description: Chromatin IP against GFP

value: Antibody GFP (custom GFP antibody generously provided by Ina Poser); HeLa cells stably transfected with GATAD1-GFP BAC

value: anti-GFP

tag: transfection

value: GATAD1-GFP BAC


title: H3K9me3_HeLa

description: Chromatin IP against H3K9me3

value: Antibody H3K9me3 from Abcam (Ab8898-100)

value: Abcam


title: PHF8-GFP_HeLa rep2

description: Chromatin IP against GFP

value: Antibody GFP Abcam  (ab290-050); HeLa cells stably transfected with PHF8-GFP BAC

value: PHF8-GFP BAC


title: Sgf29-GFP_HeLa rep2

description: Chromatin IP against GFP

value: Antibody GFP Abcam  (ab290-050); HeLa cells stably transfected with Sgf29-GFP BAC

value: Sgf29-GFP BAC


title: H3K27me3_HeLa

description: Chromatin IP against H3K27me3

value: Antibody H3K27me3 from Upstate/Millipore (07-449)

value: Upstate/Millipore


title: BAP18-GFP_HeLa rep2

description: Chromatin IP against GFP

value: Antibody GFP Abcam  (ab290-050); HeLa cells stably transfected with BAP18-GFP BAC

value: BAP18-GFP BAC


title: wt_negative-control_HeLa

description: Chromatin IP against GFP

value: Antibody GFP Abcam  (ab290-050)


title: GM11831_RNAseq

status: Public on Sep 20 2010

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: polyA RNA_RNAseq

library_source: transcriptomic

data_processing: For alignment of the short reads sequences to the human reference sequence (HG18) and identification of SNPs, we used the program MAQ (version 0.6.8)26.  To minimize sequence errors, we used the first 40 of the 50 nucleotides in each sequence read for our analysis.  For the alignment, we used the default settings of MAQ: allowing up to 2 mismatches per read and requiring that the mismatch base qualities to be less than 70.  From the aligned reads with map quality scores of 30 or higher, we identified SNPs.  For this analysis, we used only known SNPs in (dbSNP 129).  To call a sample to be heterozygous at a SNP for our DAE analysis, we required that each allele to be represented in at least 5% of the total reads covering that locus.  To determine the expression level of a gene, we calculated RPKM as per Mortazavi et al17.

molecule: polyA RNA

source_name: lymphoblastoid cell line

growth_protocol: Immortalized B cells were grown at a density of 5 x 105 cells/mL in RPMI 1640 with 15 % fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin-streptomycin.

extract_protocol: mRNA-Seq was performed as recommended by the manufacturer (Illumina). Briefly, poly(A) mRNA was fragmented and first strand cDNA generated using random hexamers.  Following second strand cDNA synthesis, end repair, addition of a single A base, adaptor ligation, agarose gel isolation of ~200 bp cDNA and PCR amplification of the ~200 bp cDNA, the samples were sequenced using the Illumina Genome Analyzer.

tag: coriell cell line repository identifier


title: H3K4me3_HeLa

description: Chromatin IP against H3K4me3

value: HeLa Kyoto cell line

value: Antibody H3K4me3 Diagenode (pAb-MEHAHS-024)


title: N-PAC-GFP_HeLa rep2

description: Chromatin IP against GFP

value: Antibody GFP (custom GFP antibody generously provided by Ina Poser); HeLa cells stably transfected with N-PAC-GFP BAC

value: custom GFP from Ina Poser

value: N-PAC-GFP BAC


title: TRRAP-GFP_HeLa rep2

description: Chromatin IP against GFP

value: Antibody GFP Abcam  (ab290-050); HeLa cells stably transfected with TRRAP-GFP BAC

value: anti-GFP

value: TRRAP-GFP BAC


title: TRRAP-GFP_HeLa rep1

description: Chromatin IP against GFP

value: Abcam


title: Sgf29-GFP_HeLa rep1

description: Chromatin IP against GFP


title: PHF8-GFP_HeLa rep1

description: Chromatin IP against GFP

value: Antibody GFP Abcam  (ab290-050); HeLa cells stably transfected with PHF8-GFP BAC

value: PHF8-GFP BAC


title: BAP18-GFP_HeLa rep1

description: Chromatin IP against GFP


title: GATAD1-GFP_HeLa rep1

description: Chromatin IP against GFP

value: Antibody GFP Abcam  (ab290-050); HeLa cells stably transfected with GATAD1-GFP BAC

value: GATAD1-GFP BAC


title: N-PAC-GFP_HeLa rep1

description: Chromatin IP against GFP

value: Antibody GFP Abcam  (ab290-050); HeLa cells stably transfected with N-PAC-GFP BAC


title: NW-GFP-Goat[eve]_INPUT_2

status: Public on Sep 16 2010

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

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

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie version 0.12.5. Signal files were generated with the R package version 2.7.1 SPP 1.0. Peaks were called with MACS version 1.3.7.

organism: Drosophila melanogaster

growth_protocol: The iso1 (y; bw cn sp) flies or the transgenic 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.

treatment_protocol: No Treatment

tag: developmental stage


title: NW-GFP-Goat[eve]_E8-16h_INPUT_1


title: NW-GFP-Goat[eve]_INPUT_1


title: KW4-CG8478-D1_INPUT_1


title: LRWD1-GFP_HeLa

description: Chromatin IP against GFP

value: Antibody GFP Abcam  (ab290-050); HeLa cells stably transfected with LRWD1-GFP BAC

value: LRWD1-GFP BAC


title: NW-GFP-Goat[Dfd]_INPUT_2


title: NW-GFP-Goat[eve]_E8-16h_ChIPSeq_1 and 2

tag: antibody name

value: NW-GFP-Goat[eve]

value: White Lab

tag: lot/batch#

tag: catalog

value: Custom


title: NW-GFP-Goat[eve]_ChIPSeq_1 and 2


title: KW4-CG8478-D1_ChIPSeq_1 and 2


title: Orange_WT_170DAF

status: Public on Sep 22 2010

city: Ithaca

first: Qiang

last: Xu

state: NY

address: Tower Road, Cornell University

institute: Cornell University

description: small RNAs with 16-30 nt in length were isolated from the total RNA of WT and MT samples by size fractionation with 15% Tris-borate-EDTA urea polyacrylamide gel (TBU). After extraction from the gel, sRNA was dephosphorylatd by alkaline phosphatase (New England Biolabs Inc.). Then the small RNAs were ligated sequentially to 5? and 3? RNA/DNA chimeric oligonucleotide adaptors (Illumina). The ligation products were purified from 10% TBE urea polyacrylamide gel. Reverse transcription was performed with the ligated sRNAs as templates. The obtained cDNAs were sequenced using the Illumina 1 G Genome Analyzer by Beijing Genomics Institute (BGI) (Shenzhen, China).

data_processing: Sequences without adapters were discarded. The adapter-containing tags were used for further analysis after removement of  5' and 3' adapters.

molecule: total RNA

organism: Citrus sinensis

source_name: fruits

growth_protocol: The orange fruits were pick up from 3 different trees which cultivated at the Institute of Citrus Research located in Guilin, Guangxi Province, China

extract_protocol: small RNAs with 16-30 nt in length were isolated from the total RNA of WT and MT samples by size fractionation with 15% Tris-borate-EDTA urea polyacrylamide gel (TBU). After extraction from the gel, sRNA was dephosphorylatd by alkaline phosphatase (New England Biolabs Inc.). Then the small RNAs were ligated sequentially to 5’ and 3’ RNA/DNA chimeric oligonucleotide adaptors (Illumina). The ligation products were purified from 10% TBE urea polyacrylamide gel. Reverse transcription was performed with the ligated sRNAs as templates. The obtained cDNAs were sequenced using the Illumina 1 G Genome Analyzer by Beijing Genomics Institute (BGI) (Shenzhen, China).

tag: genotype

value: Anliu sweet orange, wildtype

tag: tissue

value: fruits, 170 DAF (days after flowering)


title: Orange_MT_170DAF

value: red-flesh mutant


title: NW-GFP-Goat[Dfd]_INPUT_1


title: NW-GFP-Goat[tll]_INPUT_1


title: NW-GFP-Goat[tll]_INPUT_2


title: NW-GFP-Goat[Dfd]_ChIPSeq_1 and 2

value: NW-GFP-Goat[Dfd]


title: NW-GFP-Goat[tll]_ChIPSeq_1 and 2

value: NW-GFP-Goat[tll]


title: p136_39_7

status: Public on Sep 13 2010

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing: SOLiD sequence tags were mapped to the full genome (Arabidopsis tair8 and rgsc3.4) with the  MAQ package 40 (V0.7.1, options: -c, n3, e180, C10)

organism: Rattus norvegicus

source_name: tail

extract_protocol:
One microgram of each individual genomic DNA sample was fragmented to ~ 100 nt double-stranded DNA fragments by sonication in 100 µl of 10 mM Tris buffer pH 8 using Covaris S2 sonicator (6 x 16 mm AFA fiber Tube, duty cycle: 20%, intensity: 5, cycles/burst: 200, frequency sweeping, 6 minutes). After fragmentation, fragments were blunt-ended and phosophorylated at 5'-prime end using End-it Kit (Epicentre) according to the manufacturer’s instructions. Double stranded adapters compatible with SOLiD sequencing (adapter 1: pre-annealed duplex of 5'-CTA TGG GCA GTC GGT GAT-3'  and 5'-ATC ACC GAC TGC CCA TAG TTT-3' and adapter 2 (sequence depends on multiplexing); adapter 2 for non- multiplex libraries: pre-annealed duplex of 5'- CCG GGT TCC TCA TTC TCT-3'  and 5'- AGA GAA TGA GGA ACC CGG TTT-3', adapter 2 for multiplexed libraries:  pre-annealed duplex of 5'-CGC CTT GGC CGT ACA GCA G-3' and 5'-GCT GTA CGG CCA AGG CG-3'; all oligo’s were acquired through Integrated DNA Technologies (Coralville, IA) and pre-annealing was done by mixing complementary oligonucleotides at 500 µM concentration and running on thermocycler with the following program: 95˚C for 3 min, 80˚C for 3 min, 70˚C for 3 min, 60˚C for 3 min, 50˚C for 3 min, 40˚C for 3 min and 4˚C hold), were ligated to the fragmented DNA (~ 1 µg) using Quick ligation kit (New England Biolabs) with 750 mM adaptor 1 and adaptor 2, 150 µl of 2x Quick ligation buffer, 5 µl Quick Ligase in a total volume of 300 µl. Samples were purified using Ampure beads (Agencourt) and amplified in 400 µl of Platinum PCR Supermix with 750 mM of both amplification PCR primers (P1_short:  5'-CTA TGG GCA GTC GGT GAT-3' with P2_short: 5’-CCG GGT TCC TCA TTC TCT -3’ for non-barcoded samples, with Bar_primer: 5’-GCT GTA CGG CCA AGG CG-3’ for multiplexed samples and with BC-primer: 5’-CTG CCC CGG GTT CCT CAT TCT CTN NNN NNN NNN CTG CTG TAC GGC CAA GGC G-3’ for barcoded samples multiplexed before enrichment, where N represent unique barcode sequence for each library), 2.5 U of Pfu DNA polymerase (Stratagene) and 5 U Taq DNA polymerase (Bioline). Before ligation-mediated amplification, the PCR sample was incubated at 72˚C for 5 minutes in PCR mix to perform nick translation on non-ligated 3'-ends. After 6 to 8 cycles of amplification, the library DNA was purified on Ampure beads and the quality was checked on a gel for the proper size range and the absence of adapter dimers and heterodimers.  Finally, single samples or equimolar pools of multiplexed barcoded samples were size selected on 4% agarose gel for 125-175bp fraction.
microarray hybridization: DNA was mixed with 31.7 μl of Nimblegen aCGH hybridization solution and denatured at 95˚C for 5 minutes. After denaturing the sample was hybridized for 72 hours at 42˚C on MAUI hybridization station. After hybridization, the array was washed using Nimblegen Wash Buffer Kit according the user’s guide for aCGH hybridization. Elution was performed using 800 μl of elution buffer (10 mM Tris pH 8.0) in an Agilent Microarray Hybridization Chamber at 95˚C for 30 minutes. After 30 minutes the chamber was quickly dissembled and elution buffer was collected. Eluted library DNA was concentrated by speedvac to a volume of 50 μl

value: F1 animals from mutant vs wildtype

tag: phenotype

value: unknown

tag: enrichment

value: yes

value: tail


title: grn_3


title: disc


title: elfd1


title: ppargama


title: trpm


title: bkr_b2


title: grin1


title: mr6r_d


title: vip


title: par1


title: orrk_2


title: qsnul


title: cyp2d1


title: gabr


title: piwi_l2


title: orrk_1


title: br53


title: Rn_enrich_11120


title: Rn_enrich_01233


title: Rn_enrich_01112


title: Rn_enrich_30222


title: Rn_enrich_02103


title: Rn_enrich_21011


title: gp146


title: Rn_enrich_13330


title: Rn_enrich_00313


title: Rn_enrich_23202


title: Rn_enrich_32031


title: pkr2_1


title: Myers_H1-hESC_cell_2x75_200_4

status: Public on Sep 11 2010

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCaltechRnaSeq

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/H1_ES_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCaltechRnaSeq

tag: cell organism

value: Human

tag: cell description

value: Human Embryonic Stem Cells

tag: cell karyotype

value: normal

tag: cell lineage

value: embryonic stem cells

tag: cell sex

value: M

tag: localization

value: cell

tag: readtype

tag: insertlength

tag: replicate


title: Myers_GM12878_cell_2x75_400_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/GM12878_protocol.pdf

tag: cell line

value: lymphoblastoid

value: relatively normal

value: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus

value: F


title: Myers_HepG2_cell_2x75_200_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/HepG2_protocol.pdf

value: liver carcinoma

value: cancer

value: endoderm


title: Myers_HepG2_cell_1x75D_ilNA_2

value: ilNA


title: Myers_H1-hESC_cell_1x75D_ilNA_2


title: Myers_H1-hESC_cell_2x75_200_3


title: Myers_K562_cell_1x75D_ilNA_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/K562_protocol.pdf

value: leukemia

value: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC


title: Myers_NHEK_cell_1x75D_ilNA_1

source_name: NHEK

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/Keratinocyte_protocol.pdf

value: NHEK

value: Normal Human Epidermal Keratinocytes

value: ectoderm


title: Myers_HeLa-S3_cell_2x75_200_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/HeLa-S3_protocol.pdf

value: Human

value: cervical carcinoma


title: Myers_HeLa-S3_cell_1x75D_ilNA_2


title: Myers_HUVEC_cell_1x75D_ilNA_2

source_name: HUVEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cell/human/HUVEC_protocol.pdf

value: HUVEC

value: Human Umbilical Vein Endothelial Cell

value: normal

value: mesoderm

value: U


title: Myers_HUVEC_cell_2x75_200_2

value: cell


title: Myers_GM12878_cell_1x75D_ilNA_2

value: lymphoblastoid

value: relatively normal

value: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus

value: F


title: Myers_HUVEC_cell_2x75_200_1


title: Myers_HepG2_cell_1x75D_ilNA_1

value: liver carcinoma

value: cancer

value: endoderm

value: M

value: ilNA


title: Myers_GM12878_cell_1x75D_ilNA_1

value: Human


title: Myers_HepG2_cell_1x32_ilNA_2


title: Myers_K562_cell_1x75D_ilNA_2

value: leukemia

value: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC


title: Myers_H1-hESC_cell_2x75_200_1

value: Human Embryonic Stem Cells

value: embryonic stem cells


title: Myers_HeLa-S3_cell_2x75_200_2

value: cervical carcinoma

value: ectoderm


title: Myers_HUVEC_cell_1x75D_ilNA_1

value: HUVEC

value: Human Umbilical Vein Endothelial Cell

value: normal

value: mesoderm

value: U

value: cell


title: Myers_HepG2_cell_1x32_ilNA_1

value: liver carcinoma

value: cancer


title: Myers_HepG2_cell_2x75_200_2

value: endoderm

value: M


title: Myers_H1-hESC_cell_2x75_200_2

value: Human


title: Normal tail tissue, specimen "G2_2-4"

status: Public on Sep 08 2010

city: Cambridge

first: Sebastian

last: Hoersch

state: MA

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

description:
raw file comprises 2 runs.
raw file run tags in fastq file: sp799 / sp809

data_processing:
Raw data generation: Sequencing was performed on an Illumina GAIIx Sequencer using Sequence Control Software v2.6.26. Sequences were processed with either Bustard.py (OLB 1.6.0) or GERALD.pl (CASAVA 1.6.0), downloaded from the Illumina website (http://www.illumina.com/software/genome_analyzer_software.ilmn), with a produced read length of 41 nucleotides. FASTQ sequence files were split into sample-specific subsets according to a barcode strategy and then barcodes were trimmed from the sequences using the applications fastx_barcode_splitter.pl and fastx_trimmer from the fastx_toolkit- 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/ ) package. Illumina sequence qualities were converted to Sanger sequence qualities using the MAQ application fq_all2std.pl (http://maq.sourceforge.net/qual.shtml ).
Processed data generation: Sequences were aligned to chromosomes in the zebrafish Zv8/danRer6 assembly using bwa0.5.7. Unassembled "scaffold" and "NA" fragments were not included in the alignment target. Alignments with quality scores of 10 or greater were extracted from the resulting SAM files, and counts were obtained for the number of reads aligning to consecutive, adjacent 100KB physical windows along the genome. Note that this data is not yet rescaled or normalized!
see readme.txt on the Series record for additional details

organism: Danio rerio

source_name: Tail from adult fish

growth_protocol: Fish were kept according to standard conditions described in: The Zebrafish Book: A Guide for the Laboratory use of Zebrafish (Danio rerio), Monte Westerfield - 1995 - Univ. of Oregon Press

extract_protocol: Samples for sequencing with the Illumina Genome Analyzer IIx system were prepared from the same batches of genomic DNA used for array-CGH, according to published methods (Quail MA, et al.(2008, PMID:19034268); Bentley DR, et al. (2008, PMID:18987734); Quail MA, etal. (2009, PMID: 19582764)). All the enzymes used in the preparation were from New England Biolabs, and the oligonucleotides were synthesized by Eurofins MWG Operon. Oligonucleotide sequences (ATTGGC; GATCTG; TCAAGT; CTGATC; AAGCTA; GTAGCC; TACAAG; CGTGAT; ACATCG; GCCTAA; TGGTCA; CACTGT) were added to the 3' end of the Illumina adaptors used for the paired-end library preparation in order to serve as barcodes so that multiple samples could be sequenced in the same reaction.

tag: strain

value: Zebrafish TAB strain

tag: age

value: 8-24 month

value: Tail

tag: tumor type


title: MPNST tumor (p53 mutation), specimen "G2_2-4"

source_name: Tumor from adult fish

value: Peripheral nerve sheath

value: MPNST, from p53 mutation


title: MPNST tumor (rp gene mutation), specimen "G2_1-3"

description:
raw file comprises 3 runs.
raw file run tags in fastq file: sp733 / sp741 / sp746

value: MPNST, from rp gene mutation


title: MPNST tumor (rp gene mutation), specimen "G1_2-2"


title: Normal tail tissue, specimen "G1_2-2"


title: Myers_HeLa-S3_cell_1x75D_ilNA_1

value: cervical carcinoma

value: ectoderm

value: F

value: ilNA


title: spleen_RNAP-II_ChIP-Seq

status: Public on Sep 07 2010

first: Ravi

last: Gupta

address: 3601 Spruce Street

department: Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program

institute: The Wistar Institute

description: Chromatin IP against RNAP-II

data_processing:
Alignment: Alignment was performed using Bowtie and ELAND program
Peaks: Peak detection was performed using our three step procedure: (i) Identification of statistically significant sequence read enriched genomic regions (of length 1000bp). A region will be considered statistically significant if the number of reads within that region is higher than the number expected due to random background. We used Poisson distribution to estimate the background read count at a given significant level P (P <0.01). (ii) Creating the read overlapping profile for each identified region from step 1, by extending the sequence reads from the 5’ end to the 3’ end of the reads up to 400 bps (the average length of the ChIP-DNA fragment sequenced from the Solexa GA with Illumina standard ChIP-seq protocol). (iii) Peak identification – by counting the number of overlapped reads at each nucleotide position and defining the genomic position with the highest number as the peak position within the 1 kb significant region.

organism: Mus musculus

extract_protocol: About one gram of freshly dissected brain, kidney, liver, lung, or spleen tissue from FBV mice was minced finely and cross linked with 1% formaldehyde for 10 min at room temperature. To stop cross-linking glycine was added to a final concentration of 0.125 M. Next, the tissue sample was treated to isolate individual cells and cross-linked chromatin was fragmented to a size range of 0.2-0.8Kb. Chromatin immunoprecipitation was performed using 10µg of Pol-II antibody bound Dynal magnetic beads. The antibodies against Pol-II were purchased from Abcam Inc (ab5408). Following immunoprecipitation, the bound nucleoprotein complexes were extensively washed six times  with wash buffer 1 and once with wash buffer 2 (Wash buffer 1: 50mM HEPES-KOH (pH7.55), 500mM LiCl, 1mM EDTA, 1.0% NP-40 and 0.7% Na-deoxycholate; Wash buffer 2: TE containing 50mM NaCl)  and the ChIP enriched DNA was eluted and purified by phenol:chloroform:isoamyl alcohol extraction. This purified DNA (10ng) was further processed according to the Illumina Inc. instructions to prepare the library for sequencing ChIP enriched DNA.

tag: tissue type

value: spleen

value: FVB

tag: antibody

value: RNAP-II

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number


title: K562 cell_PMA treatment (10 ng/ml)_2 hours_EGR1_ChIPSeq

city: Nanjing

first: Xiaolong

last: Shi

state: Jiangsu

address: sipailou 2

department: State Key Laboratory of Bioelectronics

country: China

institute: Southeast University

description: Chromatin IP against EGR1

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (hg18) genomes using the standard SOLiD mapping pipeline, allowing up to 3 mismatches out of 35 bp. All mapping was performed in the SOLiD color space corresponding to dinucleotide encoding of the sequenced DNA. A SOLiD™ System matching pipeline's result file (.unique.csfasta.ma.) was generated in which only the reads that mapped at a unique position on the genome were retained. Then the SOLiD™ System matching pipeline's result file (.unique.csfasta.ma.) was converted into a BED format file named ‘Del_YM_SHI_2.unique.ma.35.3.cisgenome.bed’ using a perl script.
Peaks: Peak detection was performed with an integrated software system, CisGenome (http://www.biostat.jhsph.edu/~hji/cisgenome/). This software provides all basic function of ChIP-Seq data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. The reads with unique position in genome were used to find those genomic regions that were enriched in the EGR1 ChIP DNA fragments samples. The regions containing high quantities of sequencing reads are referred to as peaks. A peak file in COD format named ‘0919_W500_C6.cod’ was generated by CisGenome with the parameters of window width (W) = 500bp, and the cutoff value (C) = 6, the peaks with the reads from single direction less than 3 were filtered. The hg18 was used as the reference genome sequences.

source_name: human erythroleukemia cell line K562

growth_protocol: K562 cell was cultured in RMPI 1640 medium containing 10% fetal bovine serum (GIBCO) at 37°C with 5% CO2 incubator.

extract_protocol: PMA treated K562 cells were cross-linked with 1% formaldehyde for 12 min at room temperature. After nuclei lysis, the chromatin was fragmented by sonication. Then the EGR1-DNA complexes were isolated with anti-EGR1 antibody (H-588, Santa Cruz Biotechnology). The sequencing library was prepared according to SOLiD's instructions. Briefly, EGR1 ChIP DNA was sheared into 100-200 bp by sonication and then repaired by DNA end-repair kit (Epicentre). After that, the SOLiD adaptors were added and then the DNA was subjected to 19 cycles of PCR (2×enhancer (invitrogen) was added to increase the amplification for GC-rich sequences). PCR product of 180-250 bp size was incised from gel and then subjected to sequence with AB SOLiD System 2.0.

treatment_protocol: K562 cell was treated by PMA (10 ng/ml) for 2 hours.

tag: cell type

value: human erythroleukemia cell

tag: cell treatment

tag: chip antibody


title: liver_RNAP-II_ChIP-Seq

description: Chromatin IP against RNAP-II

value: liver


title: kidney_RNAP-II_ChIP-Seq

description: Chromatin IP against RNAP-II

value: kidney


title: YanHuang1_methy_rep74

status: Public on Sep 04 2010

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

department: Bioinformatics

institute: BGI-SHENZHEN

description: sample for paired-end library with insert size of 158 bp

data_processing: There are three parts in the methylation pipeline: pretreatment, alignment and caculation. Here are the steps: First, we pretreat both the solexa reads and the reference, transforming C to T or G to A. Then, we use SOAP to do the alignment  and choose the best reads if appearing in several alignment results. After that, we filter duplicate reads and get the infomation of former reads to judge the methylation profile.Finally, in order to caculate methylation rate and convertion rate, we gather the information of each site on each chromosome.

source_name: PBMC

growth_protocol: using fresh blood cells

extract_protocol: standard Illumina Genome Analyzer protocol

treatment_protocol: bisulphite treated

value: human peripheral blood mononuclear cells


title: YanHuang1_methy_rep73


title: YanHuang1_methy_rep75

description: sample for paired-end library with insert size of 99 bp


title: YanHuang1_methy_rep71


title: YanHuang1_methy_rep70


title: brain_RNAP-II_ChIP-Seq

description: Chromatin IP against RNAP-II

value: brain


title: YanHuang1_methy_rep77


title: YanHuang1_methy_rep76


title: Myers_NHEK_cell_2x75_200_1

value: NHEK

tag: cell organism

value: Human

tag: cell description

value: Normal Human Epidermal Keratinocytes

tag: cell karyotype

value: normal

tag: cell lineage

value: cell


title: YanHuang1_methy_rep67


title: YanHuang1_methy_rep66


title: YanHuang1_methy_rep68


title: YanHuang1_methy_rep69


title: YanHuang1_methy_rep65

description: sample for paired-end library with insert size of 143 bp


title: YanHuang1_methy_rep64


title: YanHuang1_methy_rep63


title: Normal tail tissue, specimen "G2_1-2"

value: Zebrafish TAB strain

value: 8-24 month

tag: tissue

value: Tail


title: lung_RNAP-II_ChIP-Seq

description: Chromatin IP against RNAP-II

value: lung


title: YanHuang1_methy_rep62


title: YanHuang1_methy_rep61


title: YanHuang1_methy_rep60


title: YanHuang1_methy_rep58


title: YanHuang1_methy_rep59


title: YanHuang1_methy_rep72


title: iHoxc9_Day5_ChIP-seq

city: University Park

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: Chromatin IP against V5-tagged Hoxc9

data_processing:
Alignment: Sequence reads were aligned to the mouse genome (version mm8) using Bowtie (Langmead et al Genome Biology 2009) version 0.9.9.2 with options -k 2 --best. Only uniquely mapping reads were analyzed further. Multiple hits aligning to the same nucleotide position are discarded above the level expected at a 10^-7 probability from a per-base Poisson model of the uniquely mappable portion of the mouse genome. In practice, this caps the number of hits that start at the same nucleotide to 3 in the RAR ChIP-seq experiments.
Peaks: Binding event detection is carried out using a customized methodology named SEEDS (Sequencing Experiment Event Detection Statistics) that uses statistical significance testing to find regions producing an over-abundance of sequenced reads in the signal experiments compared with the control. The algorithm is run twice across the data. The first pass estimates a scaling factor for control sequencing read depth and a model of the distribution of sequencing read alignment hits around binding events. The second pass applies these parameters to predict a final set of significant events. Before the first pass, the scaling factor is initialized to be the ratio of total hit counts between the signal and control channels. The binding distribution model is initialized to be an empirical distribution estimated around predicted binding events in Oct4 ChIP-seq data (Marson, et al. Cell 2008). All alignment hits are extended in both 3’ and 5’ directions, mirroring the observed distribution of hits around binding events. The extension magnitudes are set equal to the positions where the binding model distribution intersects a uniform distribution over the same area. Control channel hit counts are scaled using the signal-control scaling factor. A sliding window of bin width 50bp and offset 25bp is run over the genome. Overlapping extended hit counts are calculated for both the signal and (scaled) control channels. The background distribution of ChIP-seq hits is modeled as a non-homogenous Poisson process with parameters estimated from the scaled control hit counts. Specifically, the Poisson parameter is chosen as the maximum mean overlapping hit count in 50bp windows of those observed from i) the entire genome, ii) a 5Kbp window centered on the current location, and iii) a 10Kbp window centered on the current location. The use of this dynamic background model is motivated by the desire to correct local ChIP-seq enrichment biases that appear in the signal and control channels, and is similar to the model employed by MACS (Zhang, et al. Genome Biol 2008). A given bin is denoted as potentially enriched if the overlapping hit count exceeds that expected from the background model at a p-value of 10^-9. P-values for each potentially enriched bin’s over-representation in the signal channel over the control are calculated using the binomial distribution CDF (see Rozowsky, et al. Nature Biotech 2009). Neighboring regions in the set of potentially enriched regions are merged, and the maximal p-value observed for the constituent bins is attached to the resulting merged region. The p-values are corrected for multiple hypothesis testing using Benjamini & Hochberg’s method, and all regions with corrected p-values above 0.001 are discarded. False-discovery rates are estimated by repeating the event discovery procedures after swapping the scaled control channel and the signal channel. After the first pass, the scaling factor is estimated by carrying out linear regression on the hit counts observed in 10,000 bp windows that are devoid of potentially significant events in both the signal and control channels. The binding model is estimated from enriched regions with p-values < 10^-7 and signal/control hit count enrichment greater than 10. These regions are aligned around the 'peak' location, defined as the position of maximum probability when scanning the current binding model over the region's hit landscape.

source_name: Day5 motor neurons

growth_protocol: ES cells were differentiated as previously described (Wichterle, et al. Cell 2002).  Briefly, ES cells were trypsinized and seeded at 5x10e5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 1, Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x10e7 cells on Day 0. An inducible Hoxc9-V5 tagged line was made by inserting the appropriate coding sequence followed by a his-V5 tag peptide in the LoxP of the Ainv15 cell line (ATCC SCRC-1029). Induction of the transgenes was done by adding 2ug/ml of Doxycycline for ~30 hours.

extract_protocol: ChIP protocols were adapted from http://jura.wi.mit.edu/young_public/hESregulation/ChIP.html.  Descriptions of these protocol modifications have been previously published (Guenther, et al., Genes Dev 2008). Briefly, approximately 6x10e7 cells taken from each developmental time point were cross-linked using formaldehyde and snap-frozen in liquid nitrogen.  Cells were thawed on ice, resuspended in 5ml lysis buffer 1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and mixed on a rotating platform at 4°C for 5 minutes.  Samples were spun down for 3 minutes at 3000rpm, resuspended in 5ml lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and mixed on a rotating platform for 5 minutes at room temperature.  Samples were spun down once more, resuspended in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp.  Triton X-100 was added to the lysate after sonication to final concentrations of 1% and the lysate spun down to pellet cell debris.  The resulting whole-cell extract supernatant was incubated on a rotating mixer overnight at 4°C with 100 µL of Dynal Protein G magnetic beads that had been preincubated for 24 hours with 10 µg of the appropriate antibody in a PBS/BSA solution. Anti-V5 (Abcam, ab15828) antibody was used for the ChIP experiment. After approximately 16 hours of bead-lysate incubation, beads were collected with a Dynal magnet.  ChIP samples probing for transcription factor binding were washed with the following regimen, mixing on a rotating mixer at 4°C for 5 minutes per buffer: low-salt buffer (20 mM Tris at pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high-salt buffer (20 mM Tris at pH 8.1, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10 mM Tris at pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% deoxycholate, 1% NP-40), and TE containing 50 mM NaCl.  ChIP samples probing for histone and chromatin marks were washed 4 times with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and then once with TE containing 50 mM NaCl, again mixing on a rotating mixer at 4°C for 5 minutes per buffer.  After the final bead wash, samples were spun down to collect and discard excess wash solution, and bound antibody-protein-DNA fragment complexes were eluted from the beads by incubation in elution buffer at 65°C with occasional vortexing.  Cross-links were reversed by overnight incubation at 65°C.  Samples were digested with RNase A and Proteinase K to remove proteins and contaminating nucleic acids, and the DNA fragments precipitated with cold EtOH. Purified DNA fragments were processed according to a modified version of the Illumina/Solexa sequencing protocol (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Ectopic exposure to retinoic acid and hedgehog agonist at day 2 during the differentiation protocol.

value: Ainv15 (ATCC SCRC-1029)

tag: cell stage

value: Day 5

tag: chip-antibody

value: anti-V5 (Abcam, ab15828)


title: YanHuang1_methy_rep56


title: YanHuang1_methy_rep57


title: YanHuang1_methy_rep55


title: YanHuang1_methy_rep54


title: YanHuang1_methy_rep53


title: YanHuang1_methy_rep52


title: YanHuang1_methy_rep48


title: YanHuang1_methy_rep46


title: YanHuang1_methy_rep49


title: YanHuang1_methy_rep47


title: YanHuang1_methy_rep51


title: YanHuang1_methy_rep42

description: sample for paired-end library with insert size of 128 bp


title: YanHuang1_methy_rep44


title: YanHuang1_methy_rep40


title: YanHuang1_methy_rep39


title: YanHuang1_methy_rep38


title: YanHuang1_methy_rep41


title: YanHuang1_methy_rep36


title: YanHuang1_methy_rep37


title: YanHuang1_methy_rep35


title: YanHuang1_methy_rep33


title: YanHuang1_methy_rep32


title: YanHuang1_methy_rep34


title: YanHuang1_methy_rep31


title: YanHuang1_methy_rep29


title: YanHuang1_methy_rep28


title: YanHuang1_methy_rep50


title: YanHuang1_methy_rep25


title: YanHuang1_methy_rep27


title: YanHuang1_methy_rep26


title: YanHuang1_methy_rep45


title: YanHuang1_methy_rep43


title: YanHuang1_methy_rep21

description: sample for paired-end library with insert size of 200 bp


title: YanHuang1_methy_rep23


title: YanHuang1_methy_rep19


title: YanHuang1_methy_rep22


title: YanHuang1_methy_rep24


title: YanHuang1_methy_rep18


title: YanHuang1_methy_rep12


title: YanHuang1_methy_rep17


title: YanHuang1_methy_rep11


title: YanHuang1_methy_rep13


title: YanHuang1_methy_rep15


title: YanHuang1_methy_rep16


title: YanHuang1_methy_rep14


title: YanHuang1_methy_rep9


title: YanHuang1_methy_rep8


title: YanHuang1_methy_rep30


title: YanHuang1_methy_rep10


title: YanHuang1_methy_rep3


title: YanHuang1_methy_rep4


title: YanHuang1_methy_rep5


title: YanHuang1_methy_rep6


title: YanHuang1_methy_rep2


title: YanHuang1_methy_rep1


title: YanHuang1_methy_rep20


title: XOherm_L3_mononuc_seq

status: Public on Sep 02 2010

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 408 Fordham Hall, CB# 3280

department: Biology

institute: University of North Carolina at Chapel Hill

description: sequencing of mononucleosomal DNA

data_processing: Raw coverage tracks: The sequencing was done using Illumina paired end reads technology. All lanes of each replicate were combined and mapped together. The two single reads of each pair were mapped independently to WS170 genome, using a proprietary software (SeqHit) allowing a single mismatch and no gaps. The hits of the non unique reads were extended to a nucleosomes length and their union defined the non unique regions. The pairs of mapped reads that define a valid (up to 200 basepairs length) and unique regions are collected. The raw coverage of a basepair is caluclated by summing up the number of unique reads covering it. Zero value is assigned to unique basepairs that were covered by none.

organism: Caenorhabditis elegans

source_name: L3 XO hermaphrodites

growth_protocol: Worms were grown in standard S-basal media liquid culture. TY2205 (her-1(e1520) sdc-3(y126) V; xol-1(y9) X) were grown at 20C and bleached for embryos. Embryos were starved to L1, and filtered through 20uM Nitex memberane to remove dead embryos. L1s were fed and grown in 20C liquid culture until most were L3. Worms were collected and washed with M9 and PBS. Worms were resuspended in 1 pellet volume of PBS+ protease inhibitors (Calbiochem) and frozen as “popcorn” in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: Frozen worms (popcorn) were broken into smaller pieces with biopulverizer and ground to a powder with mortar and pestle. The frozen powder was briefly crosslinked 1 minute at room temperature with 1% formaldehyde. Sample was dounced and chromatin was obtained by centrifugation at 4000g. Chromatin was digested with increasing amounts of MNase. Mononucleosomal DNA was purified with Qiagen Gel Extraction kit. For a detailed protocol see http://www.modencode.org/ protocol: Worm adult nucleosome preparation:JL:SE1.    Solexa_Library_Prep DNA was incubated with End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3’ ends. The DNA fragments were ligated with single-end adaptor (Illumina) and then amplified by PCR with single end primers. The amplicon was loaded into an agarose gel, and mononucleosome length DNA was recovered from the gel. For a detailed protocol see http://www.modencode.org/ protocol:Solexa Library Preparation:JL:SE1

treatment_protocol: Crosslink frozen worm powder 1 minute at room temperature with PBS containing 1% formaldehyde.

tag: strain

tag: developmental stage

value: L3 larval stage


title: germlinecontaining_mononuc_seq

description: sequencing of mononucleosomal DNA

source_name: young germ line containing (feminized- no embryos) adults

growth_protocol: Worms were grown in standard S-basal media liquid culture. DH245 (fem-2 (b245)) were grown at 15C and bleached for embryos. Embryos were starved to L1 and then fed and shifted to 23C. Adults were collected over 35uM Nitex membrane, and washed with M9 and PBS. Adults were resuspended in 1 pellet volume of PBS+ protease inhibitors (Calbiochem) and frozen as “popcorn” in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/. protocol:Worm adult growth and harvest:JL:HP2

extract_protocol: Frozen adults (popcorn) were broken into smaller pieces with biopulverizer and ground to a powder with mortar and pestle. The frozen powder was briefly crosslinked 1 minute at room temperature with 1% formaldehyde. Sample was dounced and chromatin was obtained by centrifugation at 4000g. Chromatin was digested with increasing amounts of MNase. Mononucleosomal DNA was purified with Qiagen Gel Extraction kit. For a detailed protocol see http://www.modencode.org/ protocol: Worm adult nucleosome preparation:JL:SE1.    Solexa_Library_Prep DNA was incubated with End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3’ ends. The DNA fragments were ligated with single-end adaptor (Illumina) and then amplified by PCR with single end primers. The amplicon was loaded into an agarose gel, and mononucleosome length DNA was recovered from the gel. For a detailed protocol see http://www.modencode.org/ protocol:Solexa Library Preparation:JL:SE1

value: adult


title: nakedDNA_MNase_seq

description: sequencing of naked DNA digested with Mnase

source_name: naked DNA digested with Mnase

growth_protocol: Genomic DNA from N2 was prepared. DNA was cut with MNase to fragments less than 500 bp.

extract_protocol: MNase digested 50 ng DNA was incubated with End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3’ ends. The DNA fragments were ligated with single-end adaptor (Illumina) and then amplified by PCR with single end primers. The amplicon was loaded into an agarose gel, and mononucleosome length DNA was recovered from the gel. For a detailed protocol see http://www.modencode.org/ protocol:Solexa Library Preparation:JL:SE1

treatment_protocol: No treatment


title: YanHuang1_methy_rep7


title: S2_20HS_PREIMMUNE

city: Farmington

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description: ChIP with Preimmune serum

data_processing: Alignment:  Sequence tags were aligned to the Drosophila melanogaster April 2006 release of the reference genome using MAQ, http://maq.sourceforge.net/maq-man.shtml.  We tolerated up to 3 mismatches and only considered those tags that mapped uniquely.

source_name: S2 cells-DRSC (lot 181A1)

growth_protocol: The ChIP protocol has been previously described in Ni et al. MCB, Feb. 2008, p. 1161–1170  with the following changes:  S2-DRSC (lot 181A1) cells were grown in Schneider’s media with 10% FBS (lot ASD29137).

extract_protocol: The sample preparation was previously described in Quail,M.A. et al. Nature Methods 5, 1005 - 1010 (2008) with some modifications.  Only one size selection, after adapter ligation, was performed.  Quant-iT Pico Green (Invitrogen) staining was used to quantify the DNA sample.

treatment_protocol: For the HS sample, cells were instantaneously heat shocked at 36.5°C by the addition of 48°C media to the 25°C culture.  Cells were cross-linked at room-temperature with a final concentration of 2% paraformaldhyde and extract was sonicated as in the same manner as Ni et al. MCB, Feb. 2008, p. 1161–1170, but thrice the duration.

tag: passages


title: S2_20HS_HSF_IP

description: ChIP with anti-HSF serum


title: S2_NHS_HSF_IP

description: ChIP with anti-HSF serum


title: S2_20HS_HSF_KD-IP

description: ChIP with anti-HSF serum


title: deartorry_bighead_carp_sRNAs

status: Public on Sep 01 2010

city: Wuhan

first: Wei

last: Chi

address: 7# Donghu South road

institute: Insititute of Hydrobiology

data_processing: We first filtered low quality reads, no 3'adaptor reads, 5′adaptor contaminants and sequences shorter than 18 nucleotides. The remained sequences were mapped to zebrafish genome by SOAP (http://soap.genomics.org.cn) with a tolerance of one mismatch. The matched sequences were blasted against Rfam database and NCBI genbank database to separate out rRNA, tRNA, snRNA and snoRNA. After being classified into different categories based on the sequence similarity, the remnant reads of our datasets were compared to currently released miRNAs in miRBase to identify conserved miRNAs.

organism: Hypophthalmichthys nobilis

source_name: juvenie bighead carp tissue

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen). Small RNAs, of 16–30 nt in length, were first isolated from the total RNA by size fractionation with 15% TBE urea polyacrylamide gel (TBU) and were ligated to an activated 5'adaptor. After the purification of the small RNA/5'adaptor products, a 3'adaptor (Illumina) was ligated, then purified. The 5' small RNA adapter is necessary for amplification of the small RNA fragment. This adapter also contains the DNA sequencing primer binding site. The 3' small RNA adapter is necessary for reverse transcription and corresponds to the surface bound amplification primer on the flow cell used on the Cluster Station. Afterwards, reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with 5' and 3' adapters. The amplified cDNA constructs were purified on 6% Novex TBE PAGE gel and then used for sequencing.

value: mix of heart, liver, spleen, kidney, brain

value: juvenile

tag: average insert size

tag: standard deviation


title: S2_NHS_HSF_KD-IP

description: ChIP with anti-HSF serum


title: h3_mesc_ChipSeq

status: Public on Aug 31 2010

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against h3_mesc

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using Bowtie.

source_name: Embyonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

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

treatment_protocol: Cells were grown under normal culture conditions.

tag: treatment

value: normal culture condition

tag: antibody manufacturer

value: Abcam

value: V6.5 embryonic stem cells

tag: genetic background

tag: antibody lot number


title: h3_mesc_sb_ChipSeq

description: Chromatin IP against h3_mesc_sb

treatment_protocol: Cells were grown under normal culture conditions and treated with SB431542 at 10uM for 24 hours prior to crosslinking

value: TGF-beta inhibitor SB431542 for 24 h

tag: chip antibody

tag: antibody catalog number

tag: cell type


title: H3K4me2_HeLa_ChIPSeq

city: La Jolla

last: Rosenfeld

address: 9500 Gilman Drive

department: School of Medicine

institute: HHMI/UCSD

description: ChIP against H3K4me2

data_processing: The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline. The sequencing reads were aligned to the human genome UCSC build hg18 by using BOWTIE alignment. Both uniquely aligned reads and the sequencing reads that align to repetitive regions were kept for downstream analysis (if a read aligns to multiple genome locations, only one location is arbitrarily chosen).

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM medium with 10% FBS.

extract_protocol: the libraries were constructed following Illumina's Chip-Seq. Sample prep kit. Briefly, Chip DNA was end-blunted and added with an "A" base so the adaptors from Illumina with a “T” can ligate on the ends. Then 200-400 bp fragments are gel isolated and then purified.  18 cycles of PCR was done to amplify the library.

treatment_protocol: HeLa cells were either unsynchronized or synchronized by double thymidine block protocol to obtain G1 and G1/S phases cells or by colcemid to obtain M phase cells

tag: cell line

value: HeLa cells

tag: antibody

tag: antibody catalog


title: SMC4_HeLa_M_ChIPSeq

description: ChIP against SMC4

value: Abcam; Bethyl Laboratories, Inc.


title: PHF8_HeLa_unsyn_ChIPSeq

description: ChIP against PHF8


title: H4K20me1_HeLa_M_ChIPSeq

description: ChIP against H4K20me1


title: E2F1_HeLa_ChIPSeq

description: ChIP against E2F1

value: Santa Cruz Biotechnology, Inc.


title: h3_c2c12_ChipSeq

description: Chromatin IP against h3_c2c12

source_name: myotubes

growth_protocol: C2C12 myoblasts were grown under typical C2C12 myoblast conditions.  Myotube formation was induced for 48 hours in 2% horse serum and 1x selenium, transferrin and insulin.

value: myotubes differentiated for 48 h

value: C2C12 cells


title: h3_38b9_ChipSeq

description: Chromatin IP against h3_38b9

source_name: pro-B cell

growth_protocol: 38B9 (pro-B) cells were grown under typical conditions in RPMI media with 10% FCS.

value: 38B9 cells


title: H3Ac_ChIPSeq

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

description: Chromatin IP against H3Ac

data_processing: Sequenced reads of 25 bp were obtained using the Illumina Analysis Pipeline (all Illumina, CA). All reads were mapped to the mouse genome (mm9) and only uniquely matching reads were retained. Those unique tags were mapped into non-overlapping 200 bps windows of genome for STAT3 binding sample. Significant peaks (islands) were identified based on window tag-count threshold determined from a P-value of 0.05 (defined by Poisson background model).

source_name: CD4+ T cells

growth_protocol: CD4+ T cells were activated with irradiated APC and TCR stimulation and polarized with IL-6 and IL-23 for 3 days. Before harvesting, cells were restimulated with anti-CD3, anti-CD28 and IL-23 for 2 h.

extract_protocol: Cross-linked T cells were treated with MNase to generate approximately 80% mononucleosomes and 20% dinucleosomes. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 100 ng of DNA. Antibodies against histone H3K4me3 (ab8580, Abcam, MA), acetyl-histone H3 (Millipore, 06-599), and STAT3 (14-6727, ebiosciences, CA) were used. The ChIP DNA fragments were blunt-ended, ligated to the Illumina adaptors, and sequenced using the Illumina 1G Genome Analyzer.

value: CD4+ T cells stimulated by IL-6 and IL23

value: pan-H3Ac (Millipore, 06-599)


title: hsal_larva [small RNA]

status: Public on Aug 27 2010

city: shenzhen

first: zhiyong

last: huang

institute: BGI-Shenzhen, Shenzhen 518083, China

description:
small RNA reads
Sequenced reads were generated from larva of Hsal

data_processing:
Processed data file build: CamFlo_v1.0 or HarSal_v1.0

Adaptor sequences in reads were removed based on the sequence identity, by our in-house perl script, using a overlapping alignment algorithm. we remove sequence in the ends of a read which overlaps with the adaptor sequence with minimal length of 5bp and sequence identity >= 90%.

The *smRNA_*.clean.fa.gz processed files contain clean tags and filtered, 18-30 nt, unique sequence reads of smallRNA with counts in fasta format.
Format:
>clean_tags     reads_count
reads_sequence
Data Filter:
1. Remove low qulity reads strictly
2. Trim 3' adaptor (TCGTATGCCGTCTTCTGCTTG) sequence
3. Remove 5' adaptor (GTTCAGAGTTCTACAGTCCGACGATC)  contaminants
4. Remove too small and polyA
5. Remove reads not in 18-30 nt

organism: Harpegnathos saltator

source_name: larva

extract_protocol: We gel-purified 18-30 nts RNAs from total RNA sample, Illumina 5’ and 3’ RNA adapter were sequentially ligated to the RNA fragments and the ligated products were size-selected on denaturing polyacrylamide gels. The adapter-linked RNA was reverse transcribed with small RNA RT primers and amplified with 15 cycles of PCR using small RNA PCR primer 1 and 2 (Illumina). The libraries were sequenced with the Illumina Genome Analyzer.

value: larva

tag: colony


title: silvercarp_sRNAs

organism: Hypophthalmichthys molitrix

source_name: juvenie silver carp tissue

tag: tissue


title: hsal_worker [small RNA]

description:
small RNA reads
Sequenced reads were generated from worker of Hsal

source_name: worker

value: worker


title: Stat3_ChIPSeq

description: Chromatin IP against Stat3

tag: strain

value: phospho-Stat3 (14-6727, ebiosciences, CA)


title: hsal_gammergate [mRNA]

description: Sequenced reads were generated from gammergate of Hsal

data_processing:
Sequenced reads were aligned onto the corresponding reference (CamFlo_v1.0 or HarSal_v1.0) using TopHat v1.0.11 with default parameters except  -r 200 --mate-std-dev 20 -I 10000

Processed data file build: CamFlo_v1.0 or HarSal_v1.0

source_name: gammergate

extract_protocol:
Poly-A+ RNA was isolated from each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using a 1G Illumina Genome Analyzer and the paired-end sequencing module.
The raw reads of Transcriptome study are pair-end data, the insert size is 200bp with a sd of 11.

tag: developmental stage

value: gammergate


title: hsal_male [small RNA]

description:
small RNA reads
Sequenced reads were generated from male of Hsal

source_name: male

tag: gender

value: male


title: H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

value: H3K4me3 (ab8580, Abcam, MA)


title: hsal_egg [small RNA]

description:
small RNA reads
Sequenced reads were generated from egg of Hsal

source_name: egg

value: egg


title: hsal_male [mRNA]

description: Sequenced reads were generated from male of Hsal


title: hsal_worker [mRNA]

description: Sequenced reads were generated from worker of Hsal


title: miRNA_Clonorchis sinensis

status: Public on Sep 03 2010

city: Guangzhou

first: Zhu

last: Xingquan

state: Guangdong Province

address: 483 Wushan Street, Tianhe District

department: College of Veterinary Medicine

institute: South China Agricultural University

description: miRNA of fluke worm, parasite

data_processing: After masking of adaptor sequences and removal of redundancy and reads smaller than 18 nt as well, the cleans reads were screened against GenBank and Rfam database (version 9.0) (http://www.sanger.ac.uk/ software/Rfam/mirna) to remove non-coding RNA, such as rRNA, tRNA, snRNA, snoRNA, and other ncRNA. The sequences of candidate precursors were analyzed using RepeatMasker (http://www.repeatmasker.org) to eliminate the repetitive sequences and then the left reads were searched against the Sanger miRBase (version 13.0) to identify the conserved miRNAs. The family distribution of conserved miRNA and the nucleotide bias were gathered statistically to analysis the expression and coding characters of miRNAs. Reads that cannot match any database above were marked as unannotation. Cleans reads were then mapped onto the genome of Schistosoma japonicum (http://lifecenter.sgst.cn/schistosoma/cn) using the program of Short Oligo nucleotide Analysis Package (SOAP). The perfectly matched unannotation reads were predicted with software of Mfold (http://www.bioinfo.rpi.edu/applications/mfold) and then evaluated by MirCheck. Thereafter, the precursors (hairpin) of miRNAs were inspected manually in order to remove false predictions. Predicted precursors that miRNAs and miRNA* can be found in its both arms were deemed as high probability and stem-loop hairpins were considered typical when the mature miRNAs present in one arm instead of loop of hairpin precursors and with free energy hybridization lower than -18 kcal/mol.

organism: Clonorchis sinensis

source_name: total RNA from clonorchis sinensis parasite in wild cats

extract_protocol: RNA fragments of 20-30 bases long were isolated and purified from 10 μg total RNA by Novex 15% TBE-Urea gel. The 5´ and 3´ adaptors (Illumina) were added to the ends of fragments. Reverse transcription PCR (RT-PCR) was preformed using a RT-PCR kit (Invitrogen). The fragments were purified using 6% TBE PAGE gel and used for high-throughput sequencing with Solexa sequencer.

value: adult

tag: source

value: wild cat

tag: location

value: Guangzhou, China

value: whole worm


title: cflo_major [small RNA]

description:
small RNA reads
Sequenced reads were generated from major of Cflo

organism: Camponotus floridanus

source_name: major

value: major


title: cflo_egg [small RNA]

description:
small RNA reads
Sequenced reads were generated from egg of Cflo


title: cflo_minor [small RNA]

description:
small RNA reads
Sequenced reads were generated from minor of Cflo

source_name: minor

value: minor


title: cflo_major [mRNA]

description: Sequenced reads were generated from major of Cflo


title: hsal_egg [mRNA]

description: Sequenced reads were generated from egg of Hsal


title: cflo_larva [small RNA]

description:
small RNA reads
Sequenced reads were generated from larva of Cflo


title: cflo_male [mRNA]

description: Sequenced reads were generated from male of Cflo


title: cflo_egg [mRNA]

description: Sequenced reads were generated from egg of Cflo


title: hsal_gammergate [small RNA]

description:
small RNA reads
Sequenced reads were generated from gammergate of Hsal


title: cflo_male [small RNA]

description:
small RNA reads
Sequenced reads were generated from male of Cflo


title: cflo_minor [mRNA]

description: Sequenced reads were generated from minor of Cflo


title: New ZFNs DD/RR 20pg normal stage_2_off_target_seq_barcode_GC

status: Public on Aug 25 2010

city: Worcester

first: Scot

last: Wolfe

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

description:
94 off-target sites and the target site were PCR amplified using the genomic DNA from the ZFN  treated embryos. The different ZFN treatments were barcoded and sequences belonging to different sites can be binned using 9 bp unique prefix
n/a

data_processing: Sequences were categorized into different treatments using the 2bp barcode. Sequences belonging to different off-target sites and the target site were binned using a unique 9 bp nonamer

source_name: New ZFNs DD/RR 20pg Normals

extract_protocol: The off-target sites were amplified from genomic DNA from  ZFNs treated embryos and pooled together. PCR products from different treatments of ZFNs were barcoed and the pools were amplified using Illumina 1.1 and 2.1 geomic primers.

treatment_protocol: zebrafish embryos at single cell stage were injected with ZFN mRNAs at different doses

value: 24 h old embryos

tag: genotype

value: Wild Type

tag: treatment

value: New ZFNs DD/RR 20 pg

tag: phenotype

value: normal


title: Original ZFNs DD/RR 10pg normal stage_2_off_target_seq_barcode_GA

source_name: Original ZFNs DD/RR 10pg Normals

value: Original ZFNs DD/RR 10 pg


title: Original ZFNs DD/RR 20pg monster stage_2_off_target_seq_barcode_TA

source_name: Original ZFNs DD/RR 20pg Monsters

value: Original ZFNs DD/RR 20 pg

value: monster


title: Original ZFNs DD/RR 20pg monster stage_2_off_target_seq_barcode_CG

source_name: Original ZFNs DD/RR 20pg Monsters (Replicate)


title: Original ZFNs EL/KK 50pg normal stage_2_off_target_seq_barcode_GG

source_name: Original ZFNs EL/KK 50pg Normals

value: Original ZFNs EL/KK 50 pg


title: Original ZFNs EL/KK 100pg monster  stage_2_off_target_seq_barcode_CT

source_name: Original ZFNs EL/KK 100pg Monsters

value: Original ZFNs EL/KK 100 pg


title: New ZFNs DD/RR 20pg monster stage_2_off_target_seq_barcode_CC

source_name: New ZFNs DD/RR 20pg Monsters


title: Original ZFNs DD/RR 10pg monster stage_2_off_target_seq_barcode_CA

source_name: original ZFNs DD/RR 10pg Monsters

value: original ZFNs DD/RR 10 pg


title: Original ZFNs El/KK 100pg normal stage_2_off_target_seq_barcode_AT

source_name: Original ZFNs El/KK 100pg Normals

value: Original ZFNs El/KK 100 pg


title: Original ZFNs DD/RR 10pg monster stage_2_off_target_seq_barcode_AG

source_name: Original ZFNs DD/RR 10pg Monsters (duplicate)


title: hsal_larva [mRNA]

description: Sequenced reads were generated from larva of Hsal

source_name: larva

value: larva


title: New ZFNs DD/RR 10pg normal stage_2_off_target_seq_barcode_AC

source_name: New ZFNs DD/RR 10pg Normals

value: New ZFNs DD/RR 10 pg


title: MIP5FU_RNA-Seq

city: Vancouver

first: Malachi

last: Griffith

state: BC

address: 675 West 10th Avenue

department: Genome Sciences Centre

country: Canada

institute: British Columbia Cancer Agency

description:
HS04401
RNA-Seq of polyA RNA from 5-FU resistant colorectal cancer cell line

data_processing:
Data were processed by the Alternative Expression Analysis (ALEXA)-Seq approach (see Nature Methods publication or www.AlexaPlatform.org for details)
processed data file build: hg18
processed data file type: ALEXA-Seq

source_name: Colorectal cancer cell line, FU-resistant

growth_protocol: Cell lines were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 10% new born calf serum (Invitrogen), 1% kanamycin (Invitrogen) and 1% penicillin/streptomycin (Invitrogen) at 37ºC in a humidified environment of 5% CO2. The media for MIP/5FU cultures were supplemented with the chemotherapy drug 5-fluorouracil (5-FU) to a final concentration of 5 µM to maintain resistance. Cultures used for RNA isolation were seeded at a density of 10-30% and grown in media without drug or antibiotics for ~48 hours.

extract_protocol:
Total RNA was isolated using an ‘RNeasy’ kit (Qiagen). Total RNA was DNAseI (Qiagen) treated during RNA isolation according to Qiagen’s instructions. RNA was quantified and assessed for degradation using an RNA 6000 Nano assay (Agilent) and was not used for library construction if it had an RNA integrity score less than nine out of ten. For each sample, polyadenylated RNA was purified from 16.8 µg of DNAseI treated total RNA using the MACS™ mRNA Isolation Kit (Miltenyi Biotec).  The resulting polyA+ RNA was used for cDNA synthesis followed by fragmentation into 190-210 bp fragments and generation of RNA-Seq libraries as follows. Double-stranded cDNA was synthesized from purified polyA+ RNA using a Superscript™ Double-Stranded cDNA Synthesis kit (Invitrogen) and random hexamer primers (Invitrogen) at a concentration of 5 µM. The resulting cDNA was sheared using a Sonic Dismembrator 550 for 5 minutes at amplitude setting ‘7’ (Fisher  Scientific) and size separated by PAGE (8%). The 190-210bp DNA fraction was excised, eluted overnight at 4°C in 300 μl of elution buffer (5:1, LoTE buffer (3 mM Tris- Cl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate) and purified using a QIAquick purification kit (Qiagen). The sequencing library was prepared following the Illumina Genome Analyzer paired end library protocol (Illumina) with 10 cycles of PCR amplification. PCR products were purified on QIAquick MinElute columns (Qiagen) and assessed and quantified using an DNA 1000 series II assay (Agilent) and Qubit fluorometer (Invitrogen) respectively.

Size of fragments selected by PAGE during library construction was 190-210.
Fragment size inferred by mapping read pairs to known transcripts was: 227 with a standard deviation of 35.2

treatment_protocol: A cell line sensitive to 5-FU (MIP101) was passaged in the presence of increasing concentrations of 5-FU resulting in selection of a clone resistant to the drug (MIP/5FU)25. The resulting cells were profiled to test the utility of our method in detecting alternative expression events. The resistant cell line exhibited a 10-fold increase in the IC50 for 5-FU and as a clonal derivative of the sensitive cell line was expected to be highly related except for polymorphisms arising during exposure to 5-FU.

value: colorectal cancer cell line MIP/5FU

value: Colorectal cancer cells derived from a liver metastasis

tag: drug

value: Fluorouracil (5-FU)

tag: drug sensitivity

value: 5-FU resistant


title: Uninjected stage_2_off_target_seq_barcode_AA

source_name: Uninjected

value: 24 h old embryos

value: uninjected


title: MIP101_RNA-Seq

description:
HS04391
RNA-Seq of polyA RNA from 5-FU sensitive colorectal cancer cell line

source_name: Colorectal cancer cell line, FU-sensitive

value: colorectal cancer cell line MIP101

value: 5-FU sensitive


title: Original ZFNs DD/RR 10pg normal stage_2_off_target_seq_barcode_TC

source_name: Original ZFNs DD/RR 10pg normals (duplicate)

value: Wild Type

value: Original ZFNs DD/RR 10 pg

value: normal


title: Original ZFNs EL/KK 50pg monster stage_2_off_target_seq_barcode_TG

source_name: Original ZFNs EL/KK 50pg monsters

value: Original ZFNs EL/KK 50 pg

value: monster


title: cflo_larva [mRNA]

description: Sequenced reads were generated from larva of Cflo


title: mm9-Bcell-WT-LPS-dex-rabbit_IgG

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

description:
Chromatin IP

All experiments were performed with mice generated by crossing Cd19-cre mice (as described in Rickert et al. B lymphocyte-specific, Cre-mediated mutagenesis in mice. Nucleic Acids Res. 1997 Mar 15;25(6):1317-8.) with Paxip flox/flox mice (as described in Kim et al. Pax transactivation-domain interacting protein is required for urine concentration and osmotolerance in collecting duct epithelia. J Am Soc Nephrol. 2007 May;18(5):1458-65.).

data_processing: Sequence reads were obtained and aligned to the mouse genome (mm9) using the standard Illumina Genome Analyzer Pipeline. Only uniquely mapped reads were retained. BedGraph data files were built by summing sequence read numbers into 200bp (or 400bp for PolII) non-overlapping windows, with read position shifted 75bp (or 150bp for PolII) to represent the DNA fragment center. More details as described in Daniel et al., 2010.

source_name: mouse B cells

growth_protocol: B cells were isolated from spleens of 6- to 14-week-old mice by immunomagnetic depletion with α-CD43 beads (Miltenyi Biotech).

extract_protocol: Resting or 2 day stimulated B cells were harvested for chromatin preparation, and ChIP and Illumina sequencing was performed.  Briefly, for histone modification ChIPs, cells were washed and digested with MNase to generate native mononuclesomal chromatin fragments. For Pol II and PTIP ChIPs, cells were treated with 1% formaldehyde for 10min at room temperature to generate cross-linked chromatin. Chromatin from 10^7 cells was used for each ChIP experiment. DNA was quantified using PicoGreen (Invitrogen) prior to library preparation.  Libraries were prepared by making blunt-end DNA with End-It end repair kit (Epicentre #ER81050) according the manufacturer's instructions.  The blunt, phosphorylated ends were treated with Taq DNA polymerase (5U/ul, Invitrogen #18038-042) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~220 bp were band isolated from an agarose gel. The purified DNA quantified using PicoGreen (Invitrogen) was captured on an Illumina flow cell for cluster generation using Single-Read Cluster Generation Kit v2. Libraries were sequenced on the Genome Analyzer following the SBS Sequencing 36 Cycle Kit v3 protocol.

treatment_protocol: B cells were stimulated with LPS (25 μg/ml; Sigma), and either α-IgD-dextran (2.5ng/ml; FinaBio) or IL4 (5 ng/ml; Sigma) for 2 days as indicated.

value: Cd19-cre X Paxip flox/flox

tag: age

value: 6-14 weeks

value: spleen

value: B cells

tag: genome/variation

value: wild type

value: rabbit IgG

tag: antibody vendor, cat#, lot#

tag: treatment group

value: dextran

tag: sample type

value: negative control


title: mm9-Bcell-KO-LPS-IL4-H3K4me3

tag: cell type

value: PTIP-knockout

tag: antibody

value: interleukin-4 (IL4)


title: mm9-Bcell-KO-unstim-PTIP

description:
Chromatin IP
The anti-PTIP antibody was provided by the Kai Ge laboratory, NIDDK/NIH.

All experiments were performed with mice generated by crossing Cd19-cre mice (as described in Rickert et al. B lymphocyte-specific, Cre-mediated mutagenesis in mice. Nucleic Acids Res. 1997 Mar 15;25(6):1317-8.) with Paxip flox/flox mice (as described in Kim et al. Pax transactivation-domain interacting protein is required for urine concentration and osmotolerance in collecting duct epithelia. J Am Soc Nephrol. 2007 May;18(5):1458-65.).

tag: strain

tag: tissue

value: PTIP

value: unstimulated


title: mm9-Bcell-WT-unstim-PTIP


title: mm9-Bcell-KO-LPS-dex-H4K8ac


title: mm9-Bcell-WT-LPS-dex-H4K8ac


title: mm9-Bcell-WT-LPS-dex-H2BK5ac


title: mm9-Bcell-WT-LPS-dex-ASH2


title: mm9-Bcell-KO-LPS-dex-H3K9ac


title: mm9-Bcell-WT-LPS-IL4-H3K4me3


title: mm9-Bcell-KO-LPS-dex-H2BK5ac


title: mm9-Bcell-KO-LPS-dex-H3K27ac


title: mm9-Bcell-WT-LPS-dex-H3K9ac


title: mm9-Bcell-KO-LPS-dex-PTIP


title: mm9-Bcell-WT-LPS-dex-Pol_II

value: Pol II (4H8)


title: mm9-Bcell-KO-LPS-dex-Pol_II


title: mm9-Bcell-KO-LPS-dex3-H3K4me3


title: mm9-Bcell-WT-LPS-dex3-H3K4me3


title: mm9-Bcell-WT-LPS-dex-H3K36me3


title: mm9-Bcell-WT-LPS-dex-H3K27ac


title: mm8-Bcell-KO-dex-H3K4me2

data_processing: Sequence reads were obtained and aligned to the mouse genome (mm8) using the standard Illumina Genome Analyzer Pipeline. Only uniquely mapped reads were retained. BedGraph data files were built by summing sequence read numbers into 200bp (or 400bp for PolII) non-overlapping windows, with read position shifted 75bp (or 150bp for PolII) to represent the DNA fragment center. More details as described in Daniel et al., 2010.

extract_protocol: Resting or 2 day stimulated B cells were harvested for chromatin preparation, and ChIP and Illumina sequencing was performed.  Briefly, for histone modification ChIPs, cells were washed and digested with MNase to generate native mononuclesomal chromatin fragments. For Pol II and PTIP ChIPs, cells were treated with 1% formaldehyde for 10min at room temperature to generate cross-linked chromatin. Chromatin from 10^7 cells was used for each ChIP experiment. DNA was quantified using PicoGreen (Invitrogen) prior to library preparation.  Libraries were prepared by making blut-end DNA with End-It end repair kit (Epicentre #ER81050) according the manufacturer's instructions.  The blunt, phosphorylated ends were treated with Taq DNA polymerase (5U/ul, Invitrogen #18038-042) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~220 bp were band isolated from an agarose gel. The purified DNA quantified using PicoGreen (Invitrogen) and was captured on an Illumina flow cell for cluster generation using Single-Read Cluster Generation Kit v2. Libraries were sequenced on the Genome Analyzer following the SBS Sequencing 36 Cycle Kit v3 protocol.

tag: antibody vendor, cat#

value: Abcam, ab11946


title: mm8-Bcell-WT-dex-H3K4me2


title: mm8-Bcell-KO-dex1-H3K4me3

value: Abcam, ab8580


title: mm8-Bcell-KO-dex2-H3K4me3


title: mm8-Bcell-KO-dex-H3K4me1

value: Abcam, ab8895


title: mm9-Bcell-WT-LPS-dex-PTIP


title: mm8-Bcell-WT-dex1-H3K4me3


title: mm8-Bcell-WT-dex2-H3K4me3


title: mm8-Bcell-WT-dex-H3K4me1


title: mm8-Bcell-unstim-H3K4me3


title: Total RNA from yeast, treated with RNase S1, replicate 3

status: Public on Aug 24 2010

first: Michael

last: Kertesz

address: 318 Campus Dr.

institute: Stanford University

description:
S1 rep. 3
PolyA transcripts from log-phase growing yeast, treated with structure-specific enzyme.

data_processing:
Obtained sequences were truncated to 35bp before mapping, and required to map uniquely to either the yeast genome or transcriptome, allowing up to one mismatch and no insertions or deletions. Mapping of the short reads to the yeast transcriptome was done using version 1.1.0 of SHRiMP, which supports direct "color space" mapping, downloaded from http://compbio.cs.toronto.edu/shrimp/. We required the alignment to start from the first base of the read, as PARS relies on the first base to recover a valid enzyme cleavage point. Reads that were not uniquely mapped were discarded and all genomic locations to which those reads mapped were marked as 'unmappable' due to ambiguity.
Processed data file linked as supplementary file to Series GSE22393 record.

organism: Saccharomyces cerevisiae

source_name: Yeast polyA RNA, RNase S1-treated

growth_protocol: S cerevisiae is grown to log phase at 23C, 200rpm.

extract_protocol: Total RNA is extracted from log phase yeast using hot acid phenol, chlorofom and ethanol precipitation.  The RNA is then double polyA selected and folded in vitro in structure buffer(10mM Tris pH7, 10mM Mg2+, 100mM KCl).  The folded RNA is cleaved using RNase V1 or S1 nuclease for 15min at room temperature.  The enzymes are inactivated by phenol chloroform extraction.  The RNA is then fragmented to a size of around 200 bases using alkaline hydrolysis (50mM Sodium Carbonate [NaHCO3/Na2Co3] pH 9.2, 1 mM EDTA) at 95C for 3min.  The RNA is ran onto a 6% PAGE gel and fragments between 50-200 bases are cut out and eluted out of the gel.  The RNA fragments are then ligated to 5' and 3' adapters and reverse transcribed.  This is followed by PCR (18-20cycles) and another PAGE to size select for a library size of 150-250 bases.

tag: protocol

value: RNase S1


title: Total RNA from yeast, treated with RNase S1, replicate 2

description:
S1 rep. 2
PolyA transcripts from log-phase growing yeast, treated with structure-specific enzyme.


title: mm9-Bcell-KO-LPS-dex-H3K36me3

value: Cd19-cre X Paxip flox/flox


title: Total RNA from yeast, treated with RNase V1, replicate 4

description:
V1 rep. 4
PolyA transcripts from log-phase growing yeast, treated with structure-specific enzyme.

source_name: Yeast polyA RNA, RNase V1-treated

value: RNase V1


title: Total RNA from yeast, treated with RNase S1, replicate 1

description:
S1 rep. 1
PolyA transcripts from log-phase growing yeast, treated with structure-specific enzyme.


title: Total RNA from yeast, treated with RNase V1, replicate 1

description:
V1 rep. 1
PolyA transcripts from log-phase growing yeast, treated with structure-specific enzyme.


title: Total RNA from yeast, treated with RNase V1, replicate 2

description:
V1 rep. 2
PolyA transcripts from log-phase growing yeast, treated with structure-specific enzyme.


title: MEF_Drosha

status: Public on Aug 18 2010

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

description: Adaptor sequences clipped then mapped to miRNA loci

data_processing: Sequences were first clipped of 3' adaptor sequencess (5'-CTGTAGGCACCATCAAT) as small RNAs are shorter than the 36bp read lengths. These were then mapped to the mouse genome.

source_name: MEF

extract_protocol: 19-30nt small RNAs fractionated by gel electrophoresis. Adaptors were ligated only to species with 5' phosphate and 3' hydroxyl

tag: genetic background

value: C57BL/6 backcrossed

value: Derived from E14.5 Drosha  Rosa26-CreER emybryos

value: 6-7 weeks

value: MEF


title: CD4_Drosha

source_name: CD4+ T cell

value: FACS-sorted from spleen and lymph nodes of Drosha CD4-cre mice

value: CD4+ T cell


title: CD4_Dicer

value: FACS-sorted from spleen and lymph nodes of Dicer CD4-cre mice


title: MEF_control

value: Derived from E14.5 Rosa26-CreER emybryos


title: MEF_Dicer

value: Derived from E14.5 Dicer Rosa26-CreER emybryos


title: CD4_control

value: FACS-sorted from spleen and lymph nodes of CD4-cre mice


title: H3K27me3 levels of wild-type M-BMM

status: Public on Aug 22 2010

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

country: Japan

institute: Kyoto University

data_processing: For each ChIP-Seq dataset, uniquely mapped ChIP-Seq tags with at most 4 mismatches were considered for further analysis. Locations of tags were shifted by +100 bps from their 5' ends, in order to reflect the center of the original DNA fragment corresponding to each tag. To obtain an overall picture of the H3K27me3 distribution, we collected the tags mapped to transcribed regions (based on the genomic-wide July 2007 mm9 RefSeq mouse gene annotations in the UCSC database 44, http://genome.ucsc.edu/), and their upstream and downstream regions (30kb each). Upstream and downstream regions were separated into 30 bins of 1kb each, and transcribed regions were separated into 50 bins of equal size. ChIP-Seq tags mapped to each bin were counted for both wild-type and Jmjd3–/– M-BMM.

source_name: mouse macrophages, WT

growth_protocol: Wild-type and Jmjd3-/- bone marrow cells were cultured with 20 ng/ml M-CSF for 5 days.

extract_protocol: Cells were washed twice using ice cold PBS containing complete mini and then lysis buffer (1%SDS, 10mM EDTA, 50mM Tris-HCl (pH=8.1)) was added. After harvesting cells into a conical tube, sonication (TOMY UR-20P) was performed to obtain the DNA fragments. Fragment lengths peaked between 150 and 300 bps. An antibody against histone H3K27me3 (Millipore 07-449) was pre-bound overnight to 80l of Dynabeads (VERITAS) in PBS/BSA 0.5%. Beads were then added to lysates and incubation was allowed to proceed overnight. Beads were washed once with High salt immune complex wash buffer (Millipore) and Low salt immune complex wash buffer (Millipore), seven times using LiCl immune complex wash buffer (Millipore) and once in TE containing 50mM NaCl. DNA was eluted in elution buffer (1%SDS 10mM EDTA, 50mM Tris-HCl (pH=8.1)) and cross links reversed by incubation overnight at 65℃. After RNase A and Proteinase K treatment, DNA was then purified via ethanol precipitation using Etachinmate (Nippongene). Yields were ~100 ng/5×106 macrophages. Two hundred ng of DNA was used for the fragment library. P1 and P2 adaptor ligation and all subsequent steps were performed on all samples according to the SOLiD 3 Plus System Fragment Library Preparation protocol.

value: macrophages

tag: antibody manufacturer

value: Millipore

tag: antibody catalog #

tag: genotype/variation

value: wild-type


title: Treg_Drosha

source_name: CD4+CD25+ Treg

value: CD4+CD25+ Treg


title: Treg_Dicer


title: Treg_control


title: DN3_Dicer

source_name: DN3 thymocytes

value: FACS-sorted from thymus of Dicer Lck-cre mice

value: DN3 thymocytes


title: DN3_Drosha

value: FACS-sorted from thymus of Drosha Lck-cre mice


title: DN3_control

value: C57BL/6 backcrossed

value: FACS-sorted from thymus of Lck-cre mice


title: IGF1R_CHiPseq

city: Montreal

first: Ali

last: Tofigh

state: Quebec

address: McGill Centre for Bioinformatics , Life Sciences Complex, Bellini Building, room 435, 3649 Promenade Sir-William-Osler

institute: McGill University

data_processing:
processed data file build: hg19
Alignment: The software MAQ was used to align the reads to the genome (hg19)
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: DFB cells

growth_protocol: DFB cells were cultured under standard conditions in RPMI medium containing 10% fetal bovine serum (FBS)

extract_protocol: A sequencing library was prepared from 10 ng of ChIP-DNA according to the manufacturer’s manual (“Preparing samples for ChIP sequencing of DNA,” part#11257047 revA, Illumina). Briefly, the ChIP-DNA was end-repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase (PNK), followed by purification on a QIAquick PCR purification column (Qiagen). An A-base was ligated to the blunt ends of the DNA fragments with Klenow DNA polymerase and the sample was purified on a MinElute PCR purification column (Qiagen). Adapters for sequencing were ligated to the DNA fragments and the library was sizeselected on an agarose gel. A 150- to 300-bp fragment was excised from the gel, purified on a Qiagen gel-extraction column, and amplified for 18 cycles of PCR, followed by purification with a MinElute PCR purification kit. The quality and quantity of the library was evaluated by the Agilent Technologies 2100 Bioanalyzer and a DNA 1000 kit. A 3 pM solution of the purified library was used in the cluster generation on the Cluster Station (Illumina Inc.). Sequencing was performed for 36 cycles with the Genome Analyzer I according to the manufacturer’s protocols. Image analysis and base calling was performed with the analysis pipeline that was supplied with the Genome Analyzer instrument.

value: DFB malignant melanoma cell line

tag: chip antibody

value: IGF-I Receptor beta Antibody

tag: chip antibody vendor

value: Cell Signaling Technology

tag: chip antibody catalog #


title: Total RNA from yeast, treated with RNase V1, replicate 3

city: Stanford

description:
V1 rep. 3
PolyA transcripts from log-phase growing yeast, treated with structure-specific enzyme.

value: RNase V1


title: Rh4, input DNA

status: Public on Aug 17 2010

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: RH4, input DNA

data_processing: Alignment: Sequence reads were obtained and mapped to the human hg18 (March, 2006) genomes using ELAND from the Illumina Genome Analyzer Pipeline.

source_name: Rh4, input

growth_protocol: RPMI with 10% fetal bovine serum.

extract_protocol: ChIP-seq

tag: cell line

value: rhabdomyosarcoma

tag: pax3-fkhr status

value: positive


title: Rh4, input DNA lane 2

description: Input Control (8/4/08)_L082008


title: RD, pFM2 IP lane 1

description: RD, pFM2 IP

source_name: RD, pFM2 IP

value: RD

value: negative


title: Rh4 pFM2 IP lane 2

description: pFM2 (8/4/08)_L082008

source_name: Rh4, pFM2 IP


title: H3K27me3 levels of Jmjd3-/- M-BMM

value: macrophages


title: RD, input DNA

description: RD, input DNA

source_name: RD, input


title: RD, pFM2 IP lane 2

description: RD, pFM2 IP


title: Control oligo(dT)

status: Public on Aug 15 2010

city: Cambridge

first: Joshua

middle: Z

last: Levin

address: 320 Charles Street

institute: Broad Institute of MIT & Harvard

data_processing: We used Arachne to map the reads to the genome. Reads in single end libraries were mapped uniquely, allowing up to 4 mismatches.  Reads in paired-end libraries were first mapped non-uniquely allowing up to 4 mismatches, and then we searched for unique pairing of the non unique read mappings.  A unique pairing is defined as a single pair of mappings on the same chromosome, up to 500 bp apart, with reads on opposite strands.

source_name: Yeast grown in liquid culture

growth_protocol: Cells were grown at 30 C in a shaking water bath (New Brunswick Scientific) in the following medium:  1.5% yeast extract,  1% peptone, 2% dextrose, 0.2% SC amino acid mix  (Sunrise Science).  Cells were then harvested by freezing in liquid nitrogen, spun 5 minutes ,  3700 x g  in a Sorvall Legend RT to pellet the cells, and resuspended in 2 ml RNAlater (Ambion).

extract_protocol:
Library construction: Standard (fragmented mRNA, not strand-specific); random hexamer & oligo(dT) primed cDNA
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).

tag: growth stage

value: Mid-log


title: Control

extract_protocol:
Library construction: Standard (fragmented mRNA, not strand-specific); random hexamer primed cDNA
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).


title: BiSulfite "H"

extract_protocol:
Library construction: BiSulfite (see He et al. (2008) Science)
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).


title: dUTP

extract_protocol:
Library construction: dUTP 2nd strand marking (see Parkhomchuk et al. (2009) Nucleic Acids Res.); random hexamer primed cDNA
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).


title: Heart_p300_ChIP-seq

city: Berkeley

first: Matthew

middle: James

last: Blow

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

description: Tissue pooled from ~150 embryos Chromatin IP against p300

data_processing:
Bed: Sequence reads were  mapped to the mouse (mm9) genome using BLAT. Reads mapping to multiple sites in the genome with an equivalent score, and duplicate reads with identical start sites were discarded.
Wig: Aligned read coordinates were extended to 300bp in the direction of the alignment. Coverage depth was calculated from extended reads at 25bp intervals throughout the genome.
peaks: Peak detection was performed using QuEST (Valouev et al, Nat Methods, 2009), using a regional q-value cutoff of ≥ 2. Peaks overlapping repeats, or duplicated regions of the genome were removed as likely mapping artifacts.

source_name: Mouse embryonic day 11.5 (e11.5) heart

extract_protocol: Embryonic forebrain, midbrain and limb tissue was isolated from CD-1 mouse embryos at e11.5.  Tissue samples were cross linked and cells were dissociated and subject to  chromatin isolation, sonication and immunoprecipitation using an anti-p300 antibody (Santa Cruz Biotechnology, SC-585, Lot L2704).  ChIP DNA was sheared by sonication, end-repaired, ligated to solexa sequencing adapters and amplified by emulsion PCR.  Gel purified amplified ChIP DNA between 300 and 500bp was sequenced on the Solexa / Illumina Genome Analyzer to generate 36 bp reads.

tag: gender

value: Mixed male / female

tag: developmental stage

value: embryonic day 11.5 (e11.5)

value: heart


title: Midbrain_p300_ChIP-seq_2

source_name: Mouse embryonic day 11.5 (e11.5) midbrain

value: midbrain


title: dUTP oligo(dT)

extract_protocol:
Library construction: dUTP 2nd strand marking (see Parkhomchuk et al. (2009) Nucleic Acids Res.); random hexamer & oligo(dT) primed cDNA
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).


title: SMART

extract_protocol:
Library construction: SMART™ (Switching Mechanism at 5’ end of RNA Template)
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).

value: Late Mid-log


title: Illumina RNA Ligation - SPRI

extract_protocol:
Library construction: Illumina RNA Ligation - SPRI beads
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).


title: Hybrid

extract_protocol:
Library construction: SMART - RNA Ligation
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).

value: Diauxic Shift


title: Illumina RNA Ligation

extract_protocol:
Library construction: Illumina RNA Ligation
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).


title: NNSR

extract_protocol:
Library construction: “Not-Not-So-Random” primer protocol (‘NNSR’), where we modified the original Not-So-Random (NSR) method (Armour et al. 2009 Nature Methods) by replacing the “not so random” primers for cDNA synthesis with random (or “not not so random”) primers
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).


title: Rh4, pFM2 IP

description: Rh4, pFM2 IP

tag: cell type

tag: antibody


title: RNA Ligation

extract_protocol:
Library construction: RNA Ligation (see Lister et al. (2008) Cell)
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion).  Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).

tag: strain


title: p63_1_ChIPSeq

city: Nijmegen

first: Jo

middle: Huiqing

last: Zhou

address: Geert Grooteplein 26-28

department: Human Genetics

institute: NCMLS

description: Chromatin IP against p63

data_processing: Reads were aligned to the human genome (hg18) using ELAND. Peaks were called using MACS with default settings and p-value threshold of 1e-9.

source_name: primary keratinocyte

growth_protocol: The human primary keratinocytes were maintained in KGM medium.

extract_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature, quenched with 0.125 M glycine and washed at 4C with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl in HEG buffer (1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES pH 7.6). Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, HEG) and sonicated using a Bioruptor Sonicator.

treatment_protocol: undifferentiation condition

tag: tissue

value: epidermis

value: 4A4 against p63

value: primary cells

value: keratinocytes