title: mule3713_day33_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
mule3713CG_SNP_counts.txt: UCSC equCab2


title: mule4107_day33_CG_RNAseq

status: Public on May 29 2012

type: SRA

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

country: USA

institute: Cornell University

library_source: transcriptomic

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
mule4107CG_SNP_counts.txt: UCSC equCab2

molecule: total RNA

organism: Equus asinus x Equus caballus

source_name: mule_embryonic day33_chorionic girdle

extract_protocol: The mRNA-seq libraries were made with 3 ug of starting total RNA samples using the mRNA-Seq 8-Sample Prep Kit (Illumina Inc., CA), following the Illumina protocol for mRNA sequencing sample preparation.

tag: tissue

value: invasive trophoblast tissue of the chorionic girdle

tag: developmental stage

value: embryonic day 33

tag: gender

value: female


title: MEF_H3K4me3

status: Public on May 30 2012

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

library_source: genomic

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_H3K4me3_peaks.bed: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse V19-OSKM Fibroblast

growth_protocol: Utx+/Y and Utx-/Y V6.5 Mouse ESCs were expaned in N2B27 2i/LIF conditions. MEFs were expanded in 2i/LIF condition with or without Doxycycline as indicated.

extract_protocol: 120ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 150ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer, 0.5 µl dNTP mix, 5 µl 10x Pfu Ultra Buffer, 1 µl Pfu Ultra-II Fusion, 1.5 µl Nuclease free water) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Approximately 5 picomoles of DNA library was then applied to each lane of the flow cell. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq2000 Analyzer following the manufacturer's protocols.

treatment_protocol: Approximately 60*10^6 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature (RT)), and then quenched with glycine (5 min at RT). Fixed cells were lysed in 50mM HEPES KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4°C (Roche, 04693159001), centrifuged at 950 x g for 10 min and re-suspended in 0.2% SDS, 10mM EDTA, 140mM NaCl and 10mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at -4°C to a size range between 200 and 800 bp, and precipitated by centrifugation. 10 ug of antibody were pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 hours at room temperature. Washed beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65°C. Eluate was incubated in 65°C for 4 hours, and then treated sequentially with RNaseA (Roche, 11119915001) for 30 min and Proteinase K (NEB, P8102S) for two hours. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881).

tag: chip antibody

value: H3K4me3; ChIP grade, ab8580, abcam

tag: strain

tag: doxycycline induction

tag: genotype/variation

value: WT Utx+/Y


title: mule3669_day33_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
mule3669CG_SNP_counts.txt: UCSC equCab2


title: Endogenous small RNAs from apple fruit

city: Guangzhou

first: Rui

last: Xia

state: Guangdong

address: 483 Wushan Rd, Tianhe

department: Horticulture

country: China

institute: South China Agricultural University

description: small RNA sequencing was conducted by BGI, using SOLid System 4.0 for apple flower and fruit and Illumina HiSeq 2000 for apple leaf and apple root

data_processing:
Adaptor were trimmed with CLC Genomic Workbench, and counted and merged with customized perl scripts.
Genome Build:
apple_fruit_proc.txt: apple genome V1 (GDR, www.rosaceae.org)

organism: Malus domestica

source_name: apple fruit

growth_protocol: Fruit tree are growing in normal field condition

extract_protocol: Libraries for apple flower and apple fruit were constructed according to the protocol of the SOLiD total RNA-seq kit. Libraries for apple leaf and root were constructed according to the standard protocol by the sequencing company BGI.

treatment_protocol: No treatment

tag: cultivar

value: Golden delicious

value: apple fruit

value: mixed stage


title: mule3561_day33_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
mule3561CG_SNP_counts.txt: UCSC equCab2


title: MEF_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_H3K27me3_peaks.bed: mm9

value: H3K27me3; ChIP grade, 07-449, Millipore


title: Endogenous small RNAs from apple flower

data_processing:
Adaptor were trimmed with CLC Genomic Workbench, and counted and merged with customized perl scripts.
Genome Build:
apple_flower_proc.txt: apple genome V1 (GDR, www.rosaceae.org)

source_name: apple flower

value: apple flower

value: whole flower


title: horse4105_day34_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
horse4105CG_SNP_counts.txt: UCSC equCab2

organism: Equus caballus

source_name: horse_embryonic day34_chorionic girdle

value: embryonic day 34


title: mule3710_day33_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
mule3710CG_SNP_counts.txt: UCSC equCab2

value: male


title: MEF_dox_H3K27me3

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files. We aligned reads to mm9 reference genome using bowtie version 0.12.5. We only considered reads that were uniquely aligned to the genome with up to a single mismatch, taking the single best match of each read.  We identified enriched intervals using MACS version 1.4.1, while using the sequencing of whole cell extract (WCE) as control in order to define a background model.
Genome Build:
MEF_dox_H3K27me3_peaks.bed: mm9

value: DOX


title: horse3654_day33_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
horse3654CG_SNP_counts.txt: UCSC equCab2

source_name: horse_embryonic day33_chorionic girdle


title: horse4061_day34_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
horse4061CG_SNP_counts.txt: UCSC equCab2


title: Introgression line IL8-2

city: Cambridge

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

data_processing: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline.  The 3 prime adaptor sequence was removed from the small RNA reads and the reads were aligned to the Tomato genome version bacs v340.  Only reads with 100% match to the genome were retained.

organism: Solanum lycopersicum x Solanum pennellii

source_name: young seedlings aerial tissue

growth_protocol: Tomato seedlings were grown in Conviron growth chambers at 23'C, 60% RH and 16/8 light cycle in high nutrient compost.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and small RNA fraction was separated by PAGE gel. Adapter sequences appropriate for Illumina sequencing were ligated.

treatment_protocol: Small RNAs were isolated from different lines of 2 week old Tomato seedlings.

tag: cell line

value: Introgression line IL8-2  lycopersicum background, penellii introgression

value: young seedlings aerial tissue

value: TCGTATGCCGTCTTCTGCTTGT


title: Solanum lycopersicum replicate 1

organism: Solanum lycopersicum


title: Introgression line IL8-2-1

value: Introgression line IL8-2-1  lycopersicum background, penellii introgression


title: Introgression line IL8-3

value: Introgression line IL8-3  lycopersicum background, penellii introgression


title: Introgression line IL8-3-1

value: Introgression line IL8-3-1  lycopersicum background, penellii introgression


title: Introgression line IL8-1-3

value: Introgression line IL8-1-3  lycopersicum background, penellii introgression


title: Introgression line IL8-1D

value: Introgression line IL8-1D  lycopersicum background, penellii introgression


title: Introgression line IL8-1-1

value: Introgression line IL8-1-1  lycopersicum background, penellii introgression


title: Solanum lycopersicum replicate 2


title: horse4119_day34_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
horse4119CG_SNP_counts.txt: UCSC equCab2

value: invasive trophoblast tissue of the chorionic girdle

value: female


title: F2 hybrid replicate 3


title: Introgression line IL1-1

value: Introgression line IL1-1,  lycopersicum background, penellii introgression


title: F2 hybrid replicate 2


title: F1 hybrid replicate 2


title: Solanum pennellii replicate 1

organism: Solanum pennellii


title: F1 hybrid replicate 1


title: 0-2hr Embryo ORC Chip-Seq extraction2_seq1 aliquote 1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: dORC2;target name: Drosophila ORC2p;host: Rabbit;antigen: purified full length protein;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Stephen P. Bell MIT;reference: Austin et al 1999;input DNA

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq analysis WIG Generation:DM:1 protocol. WIG Track Generation:    * Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.    * Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.    * Input subtracted ChIP density wiggle track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.    * To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.

organism: Drosophila melanogaster

source_name: 0-2hr Embryo ORC Chip-Seq

growth_protocol: A copy of Embryo collection protocol with more generic DB fieldsUsing newly eclosed females fattened on wet yeast paste, collect embryos for up to four hours on apple juice plates. To ensure that females have not been holding embryos, precollect embryos for one hour. Wash embryos off the four-hour collection dish with PBS; dechorionate in 50% bleach for 3 minutes, and collect dechorionated embryos with a fine nylon mesh screen.

extract_protocol:
Cross linking and chromatin extraction protocol for Drosophila ChIP experiments.
Chromatin IP of a chromatin extract with an antibody.
Generation of a genomic library suitable for Illumina sequencing, using the standard Illumina protocol.  This includes a 150-200bp size selection step.
Load sample onto flow cell at a (usually 2-8 pM, variable) concentration and run on an Illumina Genome Analyzer II for single-end sequencing for 36 or 76 nt. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald (or equivalents).

value: Embryo 0-2h


title: 0-2hr Embryo ORC Input extraction1_seq1 aliquote 1

description: input DNA

source_name: 0-2hr Embryo ORC Input


title: F2 hybrid replicate 1


title: horse4102_day34_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
horse4102CG_SNP_counts.txt: UCSC equCab2


title: donkey3694_day33_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
donkey3694CG_SNP_counts.txt: UCSC equCab2

organism: Equus asinus

source_name: donkey_embryonic day33_chorionic girdle

value: embryonic day 33


title: Introgression line IL2-5

value: Introgression line IL2-5 lycopersicum background, penellii introgression


title: hinny4108_day33_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
hinny4108CG_SNP_counts.txt: UCSC equCab2

organism: Equus caballus x Equus asinus

source_name: hinny_embryonic day33_chorionic girdle

value: male


title: 0-2hr Embryo ORC Chip-Seq extraction1_seq1 aliquote 1


title: 0-2hr Embryo PolII Input extraction1_seq1 aliquote 1

description: input DNA

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq_analysis:DM:1 protocol. *  WIG Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density wiggle track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

source_name: 0-2hr Embryo PolII Input


title: donkey3643_day33_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
donkey3643CG_SNP_counts.txt: UCSC equCab2


title: donkey3693_day33_CG_RNAseq

data_processing:
The reads were and aligned to the horse reference genome (UCSC version equCab2) using TopHat with a maximum of three mismatches. Genome-wide allelic expression ratios were quantified for each individual mule or hinny sample at informative SNP positions.
Genome Build:
donkey3693CG_SNP_counts.txt: UCSC equCab2


title: Endogenous small RNAs from apple root

description:
collected from young seedling
small RNA sequencing was conducted by BGI, using SOLid System 4.0 for apple flower and fruit and Illumina HiSeq 2000 for apple leaf and apple root

data_processing:
Adaptor were trimmed with CLC Genomic Workbench, and counted and merged with customized perl scripts.
Genome Build:
apple_root_proc.txt: apple genome V1 (GDR, www.rosaceae.org)

source_name: apple root

value: Golden delicious

value: apple root

value: young root


title: Apple degradome sequence

data_processing:
Adaptor were trimmed with CLC Genomic Workbench, and counted and merged with customized perl scripts.
Genome Build:
apple_deg_proc.txt: apple genome V1 (GDR, www.rosaceae.org)

source_name: Mixed tissue

value: Mixed tissue

value: mixed stage


title: input_unstim_3T3

status: Public on May 28 2012

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

country: France

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

description: 3T3 fibroblasts, unstimulated

data_processing:
Sequence reads were aligned to the mm9 reference genome using the bowtie program, allowing for up to 2 mismatches.
Fragment midpoints were summed in 200bp windows to generate wig files.
Summits (of peaks) were identified using MACS 1.4 with paramaters p=1e-4, nomodel, nolambda, shift=150, to generate bed files.

growth_protocol: 3T3 fibroblasts were cultured under standard conditions

extract_protocol: ChIP was performed using sonicated extracts from formaldehyde-fixed nuclei.  Immunoprecipitated or input DNA was re-sonicated to obtain a mean fragment size of around 300bp, ligated to adapters using the NEBNext kit (New England Biolabs), and amplified by PCR (18 cycles).  Sequencing was performed using single reads of 36bp.

treatment_protocol: unstimulated

tag: cell type

value: 3T3 fibroblasts


title: input_stim_3T3

description: 3T3 fibroblasts, 2h after stimulation with 10ng/ml TNF-alpha

treatment_protocol: stimulated for 2h with 10ng/ml TNF-alpha


title: H4ac_unstim_DC

description: dendritic cells, unstimulated

growth_protocol: Bone marrow-derived progenitor cells were cultured in 20ng/ml each of SCF, IL-3 and IL-6, retrovirally infected using the pSir-delta U6CHisD vector carrying a hairpin directed against the JmjD2d coding sequence, and selected using 2mM histidinol.  Dendritic cells were differentiated from progenitor cells in GM-CSF (4% X63-GMCSF supernatant) + 5ng/ml SCF for 4 days, followed by GM-CSF alone for 4 days.

value: dendritic cells

value: anti-H4ac (upstate cat# 06-866)


title: H4ac_stim_3T3


title: H4ac_unstim_3T3

description: 3T3 fibroblasts, unstimulated


title: H4ac_stim_DC

description: dendritic cells, 2h after stimulation with 100ng/ml LPS

treatment_protocol: stimulated for 2h with 100ng/ml LPS


title: 0-2hr Embryo PolII Chip-Seq extraction1_seq1 aliquote 1

description: ChIP DNA; Antibody information listed below: official name: Anti-RNA polymerase II clone CTD4H8;target name: RNA polymerase II;host: Mouse;antigen: unknown;clonal: Monoclonal;purified: Protein A/G;company: Upstate-Millipore;catalog: 05-623;short description: Anti-RNA polymerase II clone CTD4H8. Peptide containing 10 repeats of YSPT[pS]PS corresponding to the carboxyl-terminal domain of RNA polymerase II. Purified mouse IgG1 in buffer containing 0.02 M phosphate buffer pH 7.6 0.25 M NaCl and 0.1% Sodium Azide before the addition of glycerol to 30%.;input DNA

source_name: 0-2hr Embryo PolII Chip-Seq


title: H3K27ac_stim_3T3

value: anti-H3K27ac (abcam cat# 4729-100)


title: Solanum pennellii replicate 2

value: young seedlings aerial tissue

value: TCGTATGCCGTCTTCTGCTTGT


title: H3K27ac_unstim_DC

description: dendritic cells, unstimulated


title: input_unstim_DC

description: dendritic cells, unstimulated

data_processing:
Sequence reads were aligned to the mm9 reference genome using the bowtie program, allowing for up to 2 mismatches.
Fragment midpoints were summed in overlapping 2kb windows; the number of tags in ChIP samples was divided by the number of tags in the same window in the corresponding input sample (when this was greater than zero) to generate wig files.


title: H3K4me1_stim_3T3

value: anti-H3K4me1 (clone CMA302)


title: JmjD2_34_stim_DC

value: anti-JmjD2-family (clone 34)


title: input_stim_DC


title: H3K4me1_unstim_3T3

description: 3T3 fibroblasts, unstimulated


title: H3K27ac_unstim_3T3

description: 3T3 fibroblasts, unstimulated


title: H3K27ac_stim_DC


title: input_unstim_3T3

description: 3T3 fibroblasts, unstimulated

extract_protocol: ChIP was performed using sonicated extracts from formaldehyde-fixed nuclei.  Immunoprecipitated or input DNA was re-sonicated to obtain a mean fragment size of around 300bp, ligated to adapters using the NEBNext kit (New England Biolabs), and amplified by PCR (18 cycles).  Sequencing was performed using paired-end reads of 36bp each.  Average insert size was around 270bp (sd 100bp) based on the mapped distances between read-pairs.


title: JmjD2d_stim_DC

value: anti-JmjD2d (clone 1-7)


title: H3K9me3_stim_3T3

value: anti-H3K9me3 (clone 2F3)


title: H3K9me3_unstim_3T3

description: 3T3 fibroblasts, unstimulated


title: Endogenous small RNAs from apple leaf

data_processing:
Adaptor were trimmed with CLC Genomic Workbench, and counted and merged with customized perl scripts.
Genome Build:
apple_leaf_proc.txt: apple genome V1 (GDR, www.rosaceae.org)

source_name: apple leaf

value: apple leaf


title: JmjD2d_unstim_DC

description: dendritic cells, unstimulated


title: H3K4me1_stim_DC


title: input_stim_3T3


title: input_unstim_DC

description: dendritic cells, unstimulated


title: input_stim_DC


title: H3K9me3_stim_DC


title: H3K9me3_unstim_DC

description: dendritic cells, unstimulated


title: H3K4me1_unstim_DC

description: dendritic cells, unstimulated


title: Col_floral_mRNA

status: Public on May 26 2012

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Col

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR9) using Bowtie short read aligner. Alignments allowed for 2 mismatches and only uniquely mapping reads were retained for further analysis. The nrpe1, idn2, and idn2 idnl1 idnl2 libraries were compared to the Col library; the idnl1 idnl2 library, which was sequenced separately with the Col_2 library, was compared to the Col_2 library.
Processed data files: Distinct small RNAs with their raw abundance after removing the adapter sequences.
Genome_build: TAIR9

organism: Arabidopsis thaliana

source_name: WT (eco Columbia) flowers

growth_protocol: Constant light.

extract_protocol: Illumina mRNA-seq preparation kit.

tag: ecotype/background

value: wild type

value: flowers


title: nrpe1_floral_mRNA

source_name: nrpe1-11 flowers

value: nrpe1-11 mutant


title: idnl1idnl2_floral_mRNA

source_name: idnl1-1 idnl2-1 double mutant flowers

value: idnl1-1 idnl2-1 mutant


title: idn2idnl1idnl2_floral_mRNA

source_name: idn2 idnl1-1 idnl2-1 triple mutant flowers

value: idn2-1 idnl1-1 idnl2-1 mutant


title: drm2_floral_mRNA

source_name: drm2-2 flowers

value: drm2-2 mutant


title: ChIP-Seq for SA2 in mES cells (rep 2)

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against SA2

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Embryonic 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 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number

value: V6.5 embryonic stem cells


title: BG03: Pol2 t=2

description: Chromatin IP against Smad3 in BG03 cells undergoing endodermal differentiation

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

organism: Homo sapiens

source_name: Endodermal Diff of BG03 cells t=2 Pol2

growth_protocol: hES cells were grown in mTESR media (Stem Cell Technologies) on plates coated with matrigel (BD Biosciences) in the absence of feeder cells. Once cells reached confluence they were rested for 24 hours in RPMI plus B27.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts in 20 second pulses for 3 min of sonication time. Half of the cell lysate was used for immunoprecipitation. 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: After 24 hours in RPMI plus B27, cells were treated with 50 ng/ml Activin for 2 hours prior to crosslinking with 1% formaldehyde

value: RNA Pol II (8WG16)

value: Covance MMS-126R

value: Embryonic stem cells

value: BGO3 (feeder free)


title: BGO3_t0_ChipSeq

description: Endodermal Diff of BG03 cells t=0 Pol2

treatment_protocol: Cells were crosslinked with 1% formaldehyde after 24 hours in RPMI plus B27


title: PR1 - Pol2 in mES cells + DMSO 18 hr_ChipSeq

description: Chromatin IP against PR1 - Pol2 in mES cells + DMSO 18 hr

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: 18 hour DMSO Treatment (Control for JQ1 Treatment)

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899


title: idn2idnl1idnl2_BSseq

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using BSseeker wrapper for the short read aligner. Alignments passing the conversion filter were filtered to eliminate sibling reads and then using to calculate methylation percentages for individual cytosines.
Processed data file *mincoverage5-CG.cytosine:
methylated/unmethylated cytosine counts for CG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHG.cytosine:
methylated/unmethylated cytosine counts for CHG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHH.cytosine:
methylated/unmethylated cytosine counts for CHH context cytosines with at least 5X coverage in all libraries
Genome Build:
idn2idnl1idnl2_nosibs_mincoverage5-CG_cytosine.txt: TAIR8
idn2idnl1idnl2_nosibs_mincoverage5-CHG_cytosine.txt: TAIR8
idn2idnl1idnl2_nosibs_mincoverage5-CHH_cytosine.txt: TAIR8

source_name: idn2-1 idnl1-1 idnl2-1 triple mutant leaves

growth_protocol: Constant light

extract_protocol: Illumina PE library construction

tag: ecotype

value: idn2-1 idnl1-1 idnl2-1 triple mutant

value: 3 week old leaves


title: idnl1idnl2_BSseq

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using BSseeker wrapper for the short read aligner. Alignments passing the conversion filter were filtered to eliminate sibling reads and then using to calculate methylation percentages for individual cytosines.
Processed data file *mincoverage5-CG.cytosine:
methylated/unmethylated cytosine counts for CG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHG.cytosine:
methylated/unmethylated cytosine counts for CHG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHH.cytosine:
methylated/unmethylated cytosine counts for CHH context cytosines with at least 5X coverage in all libraries
Genome Build:
idnl1idnl2_nosibs_mincoverage5-CG_cytosine.txt: TAIR8
idnl1idnl2_nosibs_mincoverage5-CHG_cytosine.txt: TAIR8
idnl1idnl2_nosibs_mincoverage5-CHH_cytosine.txt: TAIR8

source_name: idnl1-1 idnl2-1 double mutant leaves

value: idnl1-1 idnl2-1 double mutant


title: Brd4 ChIP-seq in mES cells

description: Chromatin IP against Brd4 in mES cells

value: Bethyl A301-985A


title: ChiP-Seq for SA1 in mES cells (rep 2)

description: Chromatin IP against SA1


title: drm2_BSseq

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using BSseeker wrapper for the short read aligner. Alignments passing the conversion filter were filtered to eliminate sibling reads and then using to calculate methylation percentages for individual cytosines.
Processed data file *mincoverage5-CG.cytosine:
methylated/unmethylated cytosine counts for CG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHG.cytosine:
methylated/unmethylated cytosine counts for CHG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHH.cytosine:
methylated/unmethylated cytosine counts for CHH context cytosines with at least 5X coverage in all libraries
Genome Build:
drm2_nosibs_mincoverage5-CG_cytosine.txt: TAIR8
drm2_nosibs_mincoverage5-CHG_cytosine.txt: TAIR8
drm2_nosibs_mincoverage5-CHH_cytosine.txt: TAIR8

source_name: drm2-2 mutant leaves


title: Small RNAs from B73xMo17 developing ear - high N

city: Urbana

first: Wesley

middle: T

last: Barber

state: IL

address: 1201 W. Gregory Drive

department: Department of Crop Sciences

institute: University of Illinois at Urbana-Champaign

data_processing:
PERL scripts were designed or scripts from the FASTX toolkit (version 0.0.12) were used to sort multiplexed libraries according to their barcode, to remove the 3' adapter and its artifacts, to filter the 5' adapter, to collapse reads into distinct sequences and to calculate abundance.
sRNAs were aligned to B73 and Mo17 genomic sequences using Novoalign (V2.07.11).

The processed data file 'high_N_developing_ear_abundance_file.txt' file is available as a supplementary file from the Series record.
Genome builds: B73 genome, maizesequence.org release 4a.53 (October, 2009); Mo17 whole genome shotgun clones.

organism: Zea mays

source_name: female inflorescence, B73xMo17

growth_protocol:
Developing ear samples were isolated from field-grown plants.
Tissue was collected from field-grown plots that were part of a larger yield-trial experiment where inbreds and hybrids were grown in separate blocks that were split by nitrogen fertilizer treatment (Summer, 2009, Urbana, IL). 40 seeds were sown per 3.6 m row, and rows were spaced 76 cm apart. 4 rows were sown per genotype. Plot was supplemented with recommended amounts of nitrogen for corn production in the Midwestern US (200 kg/ha).
The top developing ear was excised.

extract_protocol:
Total RNA was extracted using TRIzol according to the maufacturer's protocols (Invitrogen). Quantification and quality checks of total RNA was performed by A260/A280 spectrophotometry using a Nanodrop ND-1000, gel electrophoresis, and total RNA Bioanalzyer chips (Agilent).
sRNA library construction was performed according to the instructions of the Illumina Small RNA kit version 1.5. sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced as part of a multiplex of libraries (barcode=TCGA) on an Illumina Genome Analyzer. Sequences with an abundance of at least 1 read per million reads were retained in the dataset.

tag: genotype

value: developing ear

value: V12 growth stage


title: Small RNAs from B73 developing ear - low N

data_processing:
PERL scripts were designed or scripts from the FASTX toolkit (version 0.0.12) were used to sort multiplexed libraries according to their barcode, to remove the 3' adapter and its artifacts, to filter the 5' adapter, to collapse reads into distinct sequences and to calculate abundance.
sRNAs were aligned to B73 and Mo17 genomic sequences using Novoalign (V2.07.11).

The processed data file 'low_N_developing_ear_abundance_file.txt' file is available as a supplementary file from the Series record.
Genome builds: B73 genome, maizesequence.org release 4a.53 (October, 2009); Mo17 whole genome shotgun clones.

source_name: female inflorescence, B73

growth_protocol:
Developing ear samples were isolated from field-grown plants.
Tissue was collected from field-grown plots that were part of a larger yield-trial experiment where inbreds and hybrids were grown in separate blocks that were split by nitrogen fertilizer treatment (Summer, 2009, Urbana, IL). 40 seeds were sown per 3.6 m row, and rows were spaced 76 cm apart. 4 rows were sown per genotype. Plot was not supplemented with nitrogen.
The top developing ear was excised.

extract_protocol:
Total RNA was extracted using TRIzol according to the maufacturer's protocols (Invitrogen). Quantification and quality checks of total RNA was performed by A260/A280 spectrophotometry using a Nanodrop ND-1000, gel electrophoresis, and total RNA Bioanalzyer chips (Agilent).
sRNA library construction was performed according to the instructions of the Illumina Small RNA kit version 1.5. sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced as part of a multiplex of libraries (barcode=TGAC) on an Illumina Genome Analyzer. Sequences with an abundance of at least 1 read per million reads were retained in the dataset.


title: Small RNAs from Mo17 developing ear - low N

source_name: female inflorescence, Mo17

extract_protocol:
Total RNA was extracted using TRIzol according to the maufacturer's protocols (Invitrogen). Quantification and quality checks of total RNA was performed by A260/A280 spectrophotometry using a Nanodrop ND-1000, gel electrophoresis, and total RNA Bioanalzyer chips (Agilent).
sRNA library construction was performed according to the instructions of the Illumina Small RNA kit version 1.5. sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced as part of a multiplex of libraries (barcode=CTAG) on an Illumina Genome Analyzer. Sequences with an abundance of at least 1 read per million reads were retained in the dataset.


title: idn2_BSseq

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using BSseeker wrapper for the short read aligner. Alignments passing the conversion filter were filtered to eliminate sibling reads and then using to calculate methylation percentages for individual cytosines.
Processed data file *mincoverage5-CG.cytosine:
methylated/unmethylated cytosine counts for CG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHG.cytosine:
methylated/unmethylated cytosine counts for CHG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHH.cytosine:
methylated/unmethylated cytosine counts for CHH context cytosines with at least 5X coverage in all libraries
Genome Build:
idn2_nosibs_mincoverage5-CG_cytosine.txt: TAIR8
idn2_nosibs_mincoverage5-CHG_cytosine.txt: TAIR8
idn2_nosibs_mincoverage5-CHH_cytosine.txt: TAIR8

source_name: idn2-1 mutant leaves

value: idn2 mutant


title: idnl1idnl2_mRNA_leaves

description: idnl1idnl2 library

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using Bowtie short read aligner. Alignments allowed for 2 mismatches and only uniquely mapping reads were retained for further analysis. The nrpe1, idn2, and idn2 idnl1 idnl2 libraries were compared to the Col library, and the idnl1 idnl2 library, which was sequenced separately with the Col_2 library, was compared to the Col_2 libary.
Genome Build:
idnl1idnl2_leaves_RPKM_TAIR8_values.txt: TAIR8
Processed data files report RPKM values.

extract_protocol: Illumina TruSeq mRNA protocol


title: Small RNAs from B73 developing ear - high N

extract_protocol:
Total RNA was extracted using TRIzol according to the maufacturer's protocols (Invitrogen). Quantification and quality checks of total RNA was performed by A260/A280 spectrophotometry using a Nanodrop ND-1000, gel electrophoresis, and total RNA Bioanalzyer chips (Agilent).
sRNA library construction was performed according to the instructions of the Illumina Small RNA kit version 1.5. sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced as part of a multiplex of libraries (barcode=ATCG) on an Illumina Genome Analyzer. Sequences with an abundance of at least 1 read per million reads were retained in the dataset.


title: Small RNAs from B73xMo17 developing ear - low N

extract_protocol:
Total RNA was extracted using TRIzol according to the maufacturer's protocols (Invitrogen). Quantification and quality checks of total RNA was performed by A260/A280 spectrophotometry using a Nanodrop ND-1000, gel electrophoresis, and total RNA Bioanalzyer chips (Agilent).
sRNA library construction was performed according to the instructions of the Illumina Small RNA kit version 1.5. sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced as part of a multiplex of libraries (barcode=CGTA) on an Illumina Genome Analyzer. Sequences with an abundance of at least 1 read per million reads were retained in the dataset.


title: Col_BSseq

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using BSseeker wrapper for the short read aligner. Alignments passing the conversion filter were filtered to eliminate sibling reads and then using to calculate methylation percentages for individual cytosines.
Processed data file *mincoverage5-CG.cytosine:
methylated/unmethylated cytosine counts for CG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHG.cytosine:
methylated/unmethylated cytosine counts for CHG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHH.cytosine:
methylated/unmethylated cytosine counts for CHH context cytosines with at least 5X coverage in all libraries
Genome Build:
Col_nosibs_mincoverage5-CG_cytosine.txt: TAIR8
Col_nosibs_mincoverage5-CHG_cytosine.txt: TAIR8
Col_nosibs_mincoverage5-CHH_cytosine.txt: TAIR8

source_name: WT (eco Columbia) leaves

value: WT


title: Col_2_mRNA_leaves

description: Col_2 library

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using Bowtie short read aligner. Alignments allowed for 2 mismatches and only uniquely mapping reads were retained for further analysis. The nrpe1, idn2, and idn2 idnl1 idnl2 libraries were compared to the Col library, and the idnl1 idnl2 library, which was sequenced separately with the Col_2 library, was compared to the Col_2 libary.
Genome Build:
Col_2_leaves_RPKM_TAIR8_values.txt: TAIR8
Processed data files report RPKM values.


title: Small RNAs from Mo17 developing ear - high N

extract_protocol:
Total RNA was extracted using TRIzol according to the maufacturer's protocols (Invitrogen). Quantification and quality checks of total RNA was performed by A260/A280 spectrophotometry using a Nanodrop ND-1000, gel electrophoresis, and total RNA Bioanalzyer chips (Agilent).
sRNA library construction was performed according to the instructions of the Illumina Small RNA kit version 1.5. sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced as part of a multiplex of libraries (barcode=ACGT) on an Illumina Genome Analyzer. Sequences with an abundance of at least 1 read per million reads were retained in the dataset.


title: idn2idnl1idnl2_mRNA_leaves

description: idn2idnl1idnl2 library

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using Bowtie short read aligner. Alignments allowed for 2 mismatches and only uniquely mapping reads were retained for further analysis. The nrpe1, idn2, and idn2 idnl1 idnl2 libraries were compared to the Col library, and the idnl1 idnl2 library, which was sequenced separately with the Col_2 library, was compared to the Col_2 libary.
Genome Build:
idn2idnl1idnl2_leaves_RPKM_TAIR8_values.txt: TAIR8
Processed data files report RPKM values.


title: Small RNAs from Mo17xB73 shoot apex - 2007 expt

data_processing:
PERL scripts were designed or scripts from the FASTX toolkit (version 0.0.12) were used to sort multiplexed libraries according to their barcode, to remove the 3' adapter and its artifacts, to filter the 5' adapter, to collapse reads into distinct sequences and to calculate abundance.
sRNAs were aligned to B73 and Mo17 genomic sequences using Novoalign (V2.07.11).

The processed data file '2007_shoot_apex_abundance_file.txt' is available as a supplementary file from the Series record.
Genome builds: B73 genome, maizesequence.org release 4a.53 (October, 2009); Mo17 whole genome shotgun clones.

source_name: seedling shoot apex, Mo17xB73

growth_protocol:
Shoot apex samples were isolated from greenhouse-grown plants.
40 seeds were sown in a flat consisting of 1:1:1 soil, peat, perlite mix and grown in a greenhouse under 16 hours of light and 8 hours of dark during the fall of 2007.
Maize seedlings were cut at their root nodes. Coleoptiles and all tissue from fully emerged leaves were removed using a dissecting needle. Tissue enriched for leaf primordia and the shoot apex was isolated by cutting 1 cm above the base of the shoot.

extract_protocol:
Total RNA was extracted using TRIzol according to the maufacturer's protocols (Invitrogen). Quantification and quality checks of total RNA was performed by A260/A280 spectrophotometry using a Nanodrop ND-1000, gel electrophoresis, and total RNA Bioanalzyer chips (Agilent).
sRNA library construction was performed by the Michael Smith Genome Sciences Centre following the protocol of Lu et al. (2007) (PMID 17889797). sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced with Illumina SBS technology on an Illumina Genome Analyzer.

value: shoot apex

value: 11 days after sowing (3-4 leaf stage)


title: idn2_floral_mRNA

source_name: idn2-1 flowers

value: idn2-1 mutant

value: flowers


title: ago4_floral_mRNA

source_name: ago4-4 flowers

value: ago4-4 mutant


title: idn2_mRNA_leaves

description: idn2 library

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using Bowtie short read aligner. Alignments allowed for 2 mismatches and only uniquely mapping reads were retained for further analysis. The nrpe1, idn2, and idn2 idnl1 idnl2 libraries were compared to the Col library, and the idnl1 idnl2 library, which was sequenced separately with the Col_2 library, was compared to the Col_2 libary.
Genome Build:
idn2_leaves_RPKM_TAIR8_values.txt: TAIR8
Processed data files report RPKM values.


title: PR2 - Pol2 in mES cells + JQ1 18 hr_ChipSeq

description: Chromatin IP against PR2 - Pol2 in mES cells + JQ1 18 hr

treatment_protocol: 18 Hour JQ1 Treatment

value: V6.5 embryonic stem cells


title: Small RNAs from Mo17 shoot apex - 2007 expt

source_name: seedling shoot apex, Mo17

extract_protocol:
Total RNA was extracted using TRIzol according to the maufacturer's protocols (Invitrogen). Quantification and quality checks of total RNA was performed by A260/A280 spectrophotometry using a Nanodrop ND-1000, gel electrophoresis, and total RNA Bioanalzyer chips (Agilent).
sRNA library construction was performed by the Michael Smith Genome Sciences Centre following the protocol of Lu et al. (2007) (PMID 17889797). sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced with Illumina SBS technology on an Illumina Genome Analyzer. Sequences with at least 5 reads were retained in the dataset.


title: Small RNAs from Mo17 shoot apex - 2011 expt

data_processing:
PERL scripts were designed or scripts from the FASTX toolkit (version 0.0.12) were used to sort multiplexed libraries according to their barcode, to remove the 3' adapter and its artifacts, to filter the 5' adapter, to collapse reads into distinct sequences and to calculate abundance.
sRNAs were aligned to B73 and Mo17 genomic sequences using Novoalign (V2.07.11).

The processed data file '2011_shoot_apex_abundance_file.txt' is available as a supplementary file from the Series record.
Genome builds: B73 genome, maizesequence.org release 4a.53 (October, 2009); Mo17 whole genome shotgun clones.

growth_protocol:
Shoot apex samples were isolated from greenhouse-grown plants.
24 seeds were sown in a flat consisting of 1:1:1 soil, peat, perlite mix and grown in a greenhouse under 16 hours of light and 8 hours of dark during the winter of 2011.
Maize seedlings were cut at their root nodes. Coleoptiles and all tissue from fully emerged leaves were removed using a dissecting needle. Tissue enriched for leaf primordia and the shoot apex was isolated by cutting 1 cm above the base of the shoot.

extract_protocol:
Total RNA was extracted using TRIzol according to the maufacturer's protocols (Invitrogen). Quantification and quality checks of total RNA was performed by A260/A280 spectrophotometry using a Nanodrop ND-1000, gel electrophoresis, and total RNA Bioanalzyer chips (Agilent).
sRNA library construction was performed according to the instructions of the Illumina TruSeq Small RNA preparation kit. sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced as part of a multiplex (barcode=ATCACG) of libraries on an Illumina HiSeq 2000 system. Sequences with an abundance of at least 1 read per million reads were retained in the dataset.

value: 14 days after sowing (3-4 leaf stage)


title: nrpe1_mRNA_leaves

description: nrpe1 library

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using Bowtie short read aligner. Alignments allowed for 2 mismatches and only uniquely mapping reads were retained for further analysis. The nrpe1, idn2, and idn2 idnl1 idnl2 libraries were compared to the Col library, and the idnl1 idnl2 library, which was sequenced separately with the Col_2 library, was compared to the Col_2 libary.
Genome Build:
nrpe1_leaves_RPKM_TAIR8_values.txt: TAIR8
Processed data files report RPKM values.

source_name: nrpe1-11 mutant leaves

value: nrpe1-11 mutant


title: Small RNAs from B73 shoot apex - 2011 expt

source_name: seedling shoot apex, B73


title: Small RNAs from B73xMo17 shoot apex - 2007 expt

source_name: seedling shoot apex, B73xMo17


title: Col_mRNA_leaves

description: Col library

data_processing:
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using Bowtie short read aligner. Alignments allowed for 2 mismatches and only uniquely mapping reads were retained for further analysis. The nrpe1, idn2, and idn2 idnl1 idnl2 libraries were compared to the Col library, and the idnl1 idnl2 library, which was sequenced separately with the Col_2 library, was compared to the Col_2 libary.
Genome Build:
Col_leaves_RPKM_TAIR8_values.txt: TAIR8
Processed data files report RPKM values.


title: Small RNAs from B73 shoot apex - 2007 expt


title: RNA Pol2 (8WG16) ChIPseq in mES cells treated with retinoic acid for 8 hours

description: Chromatin IP against RNA Pol2 (8WG16) in mES cells treated with retinoic acid for 8 hours

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Embryonic 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 one passage off of MEFs, on gelatinized tissue-culture plates.  Cells were treated with retinoic acid for 8 hours prior to crosslinking and ChIP analysis.

treatment_protocol: This work was done in collaboration with Scott McCuine, who got the cells from Esteban Mazzoni (Columbia).  Esteban treated the cells with retinoic acid for 8 hours prior to crosslinking.

value: RNA Pol II (8WG16)

value: Covance MMS-126R

tag: drug

value: retinoic acid

tag: duration of treatment

value: 8 hr


title: Al-free_targets

status: Public on May 25 2012

first: Hai

last: Nian

address: College of Agriculture, South China Agricultural University

department: College of Agriculture

data_processing:
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011).
Genome_build: ftp://ftp.jgi-psf.org/pub/ JGI_data/phytozome/v7.0/Gmax/annotation/Gmax_109_transcript.fa.gz

organism: Glycine soja

source_name: roots of wild soybean

growth_protocol: Germinated seedlings were transferred into nutrient solution and grown in chamber with 70% relative humidity, 28 / 25 °C and a light regime of 14 h light / 10 h dark

extract_protocol: Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions. Small RNA libraries were generated from the two samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.

treatment_protocol: Two days after transplant, seedlings were transferred into nutrient solution with 0 (Al-free), 50 (Al-treated) μmol/L AlCl3 (pH 4.5). Roots from 10 cm root apex were harvested after 1, 3, 6, 12, 24, 48 and 96 h after the initiation of stress. Samples from different treatment were then pooled for RNA extraction.

tag: sample type

value: targets

value: roots

tag: treatment

value: Al-free


title: Al-free_miRNA

value: miRNA

tag: tissue


title: Al-treated_targets

value: Al-treated


title: Al-treated_miRNA


title: Tagmented single-cell level cDNA with Tn5 transposase #1

city: London

first: Kenta

last: Yashiro

address: Charterhouse Square

department: Willaim Harvey research Institute

institute: Barts and The London School of Medicine and Dentistry, Queen Mary University of London

description:
ES_SC_Nextera_1
Technical replicate 1 of 3.
Single cell lysate (total RNA).

data_processing:
Illumina Pipeline RTA 1.8.70.0 / BCL Converter 1.7.1 / CASAVA 1.7.0 was used for image analysis and base calling.
Reads were aligned to the mouse mm9 genome and RefSeq transcripts using Partek Flow. Up to 2 mismatches in 28 bases in the seed was allowed.
Aligned reads were mapped to RefSeq gene definitions and annotated by Partek Genomics Suite.
RPKMs were calculated by Partek Genomics Suite.
Reads mapped to multiple sites were allocated according to the relative distribution of reads mapped to unique locations.
Genome_build: mm9

source_name: E14tg2a ES cell line, tagmentation

growth_protocol: Cells were grown in GMEM/10% FBS of ES cell grade supplemented with NEAA, Glutamax, Pyruvate, beta-mercaptoethanol, and LIF.

extract_protocol:
Single-cell cDNA preparation: Total RNA was prepared from E14tg2a ES cells with the QIAGEN RNeasy Mini Kit. 10 pg of total RNA equivalent to the single cell level was used for 1st strand cDNA synthesis with Oligo (dT) tagged by V1 primer. After the addition of poly (A) tail to the 3'-end of the 1st strand, the 2nd strand was synthesized with Oligo (dT) tagged by V3 primer. The single-cell level cDNA was amplified by 20 cycles of PCR with V1 and V3 primers.

Library preparation with Sonication: A single cell cDNA was fragmented by a Covaris E210 AFA Ultrasonicator. Libraries were prepared with the Illumina mRNA-seq kit (RS-100-0801). The obtained product (single cell cDNA) was subjected to fragmentation by a sonicator, end-repair, adaptor ligation, and library preparation with PCR.

Library preparation with hyperactive Tn5 transposase: The libraries were prepared with the Nextera DNA preparation kit (Illumina compatible) (Epicentre, an Illumina company) with some modification. 100 ng of single cell cDNA was suspended in HMW buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (hyperactive Tn5 transposase), incubating at 55C for 5 min. Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research), and then the libraries were prepared by PCR with Nextera PCR enzyme, Nextera primer cocktail, and Nextera adaptor 2 according to the following program: one cycle of 72C for 3 min and 95 C for 30 s (one cycle), 13 cycles of 95C for 10s, 62C for 30s, 72C for 3min.

value: embryonic stem cell

tag: library preparation method

value: tagmentation with hyperactive Tn5 transposase


title: Tagmented single-cell level cDNA with Tn5 transposase #2

description:
ES_SC_Nextera_2
Technical replicate 2 of 3.
Single cell lysate (total RNA).


title: Sonicated single-cell level cDNA #3

description:
ES_SC_Sonicate_3
Technical replicate 3 of 3.
Single cell lysate (total RNA).

source_name: E14tg2a ES cell line, sonication

value: sonication


title: Tagmented single-cell level cDNA with Tn5 transposase #3

description:
ES_SC_Nextera_3
Technical replicate 3 of 3.
Single cell lysate (total RNA).


title: Sonicated single-cell level cDNA #2

description:
ES_SC_Sonicate_2
Technical replicate 2 of 3.
Single cell lysate (total RNA).


title: Input_HCT116-WT_no-treatment_rep2

status: Public on May 24 2012

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
ChIP-Seq reads were mapped by the Eland to hg18, keeping only uniquely mapping genes and discarding all but one of clonal reads.  BEDGRAPH files were generated using bed files as the input files.  Only chromosome positions with at least 5 monoclonal reads are retained.
Genome_build: hg18
Supplementary_files_format_and_content: bed files, BEDGRAPH files:  standard UCSC genome browser format

source_name: human colorectal carcinoma cell line HCT116

growth_protocol: HCT116 cells were grown in McCoys media, supplemented with 10% FBS and 1% pen-strep.

treatment_protocol: Cells were treated with 10 ng/ml TNF-alpha for 30-60 mins.

tag: celll line

value: Wild type

tag: stimulation

tag: chip antibody

tag: data processing (alignment) algorithm

value: ELAND


title: HP1-gamma_HCT116-WT_no-treatment_rep2

tag: genotype/variation

value: HP1 gamma

tag: chip antibody vendor

value: Millipore

tag: chip antibody catalog number

tag: chip antibody lot numbers


title: RNA-Seq_HCT116-KD_TNF-treatment_rep2

data_processing:
Reads were mapped by bowtie to hg18, keeping only uniquely mapping genes and discarding all but one of clonal reads. RPKM was calculated as the number of reads per kilo base of exon model per million reads mapped. BEDGRAPH files were generated using bed files as the input files.  Only chromosome positions with at least 5 monoclonal reads are retained
Genome_build: hg18
Supplementary_files_format_and_content: bed files, BEDGRAPH files:  standard UCSC genome browser format

value: HP1 gamma knock down

value: TNF

value: Bowtie


title: RNA-Seq_HCT116-WT_no-treatment_rep2


title: RNA-Seq_HCT116-KD_no-treatment_rep2


title: RNA-Seq_HCT116-WT_TNF-treatment_rep2


title: HP1-gamma_HCT116-WT_TNF-treatment_rep2


title: Input_HCT116-WT_TNF-treatment_rep2


title: Input_HCT116-WT_no-treatment_rep2

data_processing: ChIP-Seq reads were mapped by bowtie to hg18, keeping only uniquely mapping reads and discarding all but one of clonal reads.  Bedgraph files were generated using bed files as the input files.  Only chromosome positions with at least 5 monoclonal reads are retained.

tag: cell line

tag: alignment program


title: HP1-gamma_HCT116-WT_no-treatment_rep1

data_processing: ChIP-Seq reads were mapped by the Eland to hg18, keeping only uniquely mapping genes and discarding all but one of clonal reads.  Bedgraph files were generated using bed files as the input files.  Only chromosome positions with at least 5 monoclonal reads are retained.

tag: antibody vendor

tag: antibody catalog number

tag: antibody lot numbers


title: Input_HCT116-WT_TNFa-treatment_rep1

value: TNF-alpha


title: RNA-Seq_HCT116-WT_no-treatment

data_processing: Reads were mapped by bowtie to hg18, keeping only uniquely mapping genes and discarding all but one of clonal reads. RPKM was calculated as the number of reads per kilo base of exon model per million reads mapped. Bedgraph files were generated using bed files as the input files.  Only chromosome positions with at least 5 monoclonal reads are retained


title: Input_HCT116-WT_rep1


title: HP1-gamma_HCT116-WT_rep2


title: RNA-Seq_HCT116-KD_no-treatment


title: Input_HCT116-WT_no-treatment_rep1


title: RNA-Seq_HCT116-KD_TNFa-treatment


title: HP1-gamma_HCT116-WT_TNFa-treatment_rep1


title: HP1-gamma_HCT116-WT_rep1


title: RNA-Seq_HCT116-WT_TNFa-treatment


title: Sonicated single-cell level cDNA #1

description:
ES_SC_Sonicate_1
Technical replicate 1 of 3.
Single cell lysate (total RNA).

tag: cell type


title: Broad_Combined_HepG2

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHmm

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

value: Combined

tag: datatype description

value: Multi-assay Synthesis

tag: cell

tag: cell organism

value: human

tag: cell description

value: hepatocellular carcinoma

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: softwareversion


title: Broad_Combined_HUVEC

source_name: HUVEC

value: HUVEC

value: umbilical vein endothelial cells

value: normal

value: mesoderm

value: U


title: Broad_Combined_NHLF

source_name: NHLF

value: NHLF

value: lung fibroblasts


title: Broad_Combined_H1-hESC

value: embryonic stem cells

value: inner cell mass


title: Broad_Combined_HMEC

source_name: HMEC

value: Broad

value: Bernstein - Broad Institute

value: HMEC

value: mammary epithelial cells

value: ectoderm


title: Broad_Combined_NHEK

source_name: NHEK

value: Combined

value: Multi-assay Synthesis

value: NHEK

value: human

value: epidermal keratinocytes


title: Broad_Combined_GM12878

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal

value: F


title: RWPE1-ERG HiC (library 2, rep 3)

status: Public on May 23 2012

city: New York

first: David

last: Soong

state: NY

address: 1305 York Avenue

department: Institute for Computational Biomedicine

institute: Weill Cornell Medical College

description: RWPE1 cell line stably over-expressing truncated ERG encoded by the most common TMPRSS2-ERG isoform.

data_processing:
Library strategy: HiC
HiC: Base-calling was done using the standard Illumina pipeline. We aligned the two ends of the 54bp paired reads separately to the reference human genome hg18 using the BWA aligner. Reads mapped ambiguously to multiple locations on the genome were discarded. We further used an in-house pipeline and filtered out clonal reads caused by PCR artifacts based on the 5' and 3' read positions, removed non-ligated DNA fragments, and retained interactions with consistent expected placement relative to HindIII enzyme digestion sites.
Genome_build: hg18
Supplementary_files_format_and_content: BED: Intra-chromosomal interactions in UCSC BED format (http://genome.ucsc.edu/FAQ/FAQformat#format1). Interactions are merged from all replicates.
Supplementary_files_format_and_content: SIF: Inter-chromosomal interactions; each row consists of the start and end coordinates of each paired-end read. Interactions are merged from all replicates.

Processed data files are linked to the Series record as supplementary files.

source_name: RWPE1-ERG prostate epithelial cell line

growth_protocol: All cells were grown in medium following ATCC recommended conditions. Briefly, the base medium for this cell line is provided by Invitrogen (GIBCO) as part of a kit: Keratinocyte Serum Free Medium (K-SFM), Kit Catalog Number 17005-042. This kit is supplied with each of the two additives required to grow this cell line (bovine pituitary extract (BPE) and human recombinant epidermal growth factor (EGF) at the following concentrations: 0.05 mg/ml BPE - provided with the K-SFM kit. 5 ng/ml EGF - provided with the K-SFM kit.

extract_protocol: DNA was extracted using phenol/chloroform and Qiagen MinElute extraction. All library constructions were generated following recommended protocols and reagents from Illumina.

tag: cell line

value: benign prostate epithelial cells

tag: overexpressing

value: truncated ERG

tag: passages

tag: library


title: RWPE1-GFP HiC (library 2, rep 2)

description: RWPE1 cell line stably over-expressing empty vector containing GFP.

source_name: RWPE1-GFP prostate epithelial cell line

value: empty vector containing GFP


title: RWPE1-GFP HiC (library 2, rep 3)


title: RWPE1-ERG HiC (library 2, rep 1)


title: RWPE1-ERG HiC (library 2, rep 4)


title: RWPE1-GFP HiC (library 1)


title: RWPE1-GFP HiC (library 2, rep 1)


title: RWPE1-GFP HiC (library 2, rep 4)


title: RWPE1-ERG RNA-seq

data_processing:
RNA-seq: Base-calling was done using the standard Illumina pipeline. We aligned the paired-end RNA-seq reads to the RefSeq transcriptome database (version 11/25/2009) using BWA, removed clonal reads caused by PCR artifacts, and quantified expression levels in RPKM (reads per kilobase of exon model per million mapped reads) units using an in-house program.
Genome_build: hg18
Supplementary_files_format_and_content: RPKM: Tab-delimited text file containing the RPKM for each gene/transcript.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen). All library constructions were generated following recommended protocols and reagents from Illumina.


title: RWPE1-GFP RNA-seq


title: RWPE1-ERG HiC (library 2, rep 2)


title: RWPE1-ERG ChIP-seq (Input)

data_processing:
ChIP-seq: Base-calling was done using the standard Illumina pipeline. We aligned the ChIP-seq reads to the hg18 human genome using BWA and identified ERG-binding sites using ChIPseeqer.
Genome_build: hg18
Supplementary_files_format_and_content: ChIPseeqer: Each row corresponds to a peak. For details, please go to: http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_use

Processed data files are linked to the Series record as supplementary files.

source_name: RWPE1-ERG prostate epithelial cell line, input

tag: chip antibody


title: RWPE1-ERG HiC (library 1)

tag: cell type


title: Anti-H3K4me3 Prdm9-/- Testis

status: Public on May 22 2012

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description: Sample 15

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file (available on Series records) represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
PRDM9_H3K4me3_Testis_peaks.bedGraph: mm9
PRDM9_H3K4Me3_Sample1_Testis.bed: mm9

source_name: Anti-H3K4me3 Prdm9-/-_testis_ChIP-Seq

growth_protocol: Cells were extracted from testis of euthanized mice and subjected to immunoprecipitation.

extract_protocol: Lysates from mouse testis cells were crosslinked, sonicated and immunoprecipitated with anti-DMC1 or anti-RAD51 antibodies. Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation.

tag: strain

tag: genotype/variation

tag: tissue

value: testis

value: Anti-H3K4me3 Millipore (#07-473)

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: sequencing technique

value: ChIP-Seq


title: Anti-H3K4me3 Prdm9-/- Liver

description: Sample 16

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file (available on Series records) represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
PRDM9_H3K4me3_Liver_peaks.bedGraph: mm9
PRDM9_H3K4Me3_Sample1_Liver.bed: mm9

source_name: Anti-H3K4me3 Prdm9-/-_liver_ChIP-Seq

value: liver


title: Broad_Combined_K562

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: leukemia, "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

value: cancer

value: mesoderm


title: Stanford_ChipSeq_HepG2_Nrf1_IgG-rab

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSydhTfbs

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: human

value: hepatocellular carcinoma

tag: cell karyotype

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Mouse monoclonal, Immunogen corresponding to amino acids 201-286 of Human NRF1. Antibody Target:NRF1

tag: antibody targetdescription

value: NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: control

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid

tag: replicate


title: Stanford_ChipSeq_HepG2_JunD_IgG-rab

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: cell

value: JunD

value: rabbit polyclonal IgG. Antibody Target:JunD

value: The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq)

value: Santa Cruz Biotech


title: Stanford_ChipSeq_GM12878_TBLR1_(ab24550)_IgG-mus

value: Stanford

value: Snyder - Stanford University

tag: cell organism

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

value: Rabbit polyclonal, immunogen:Recombinant full length protein (Human). Antibody Target:TBLR1

value: F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation

value: IgG-mus

value: Input signal from Normal Mouse IgG ChIP-seq.


title: Stanford_ChipSeq_GM12878_NF-E2_(SC-22827)_std

value: ChipSeq

value: Chromatin IP Sequencing

value: human

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Rabbit Polyclonal, epitope:1-230 mapping at the N-terminus of NF-E2 of human origin. Antibody Target:NF-E2

tag: antibody targetdescription

value: Transcription factor NF-E2 45 kDa subunit is a component of the NF-E2 complex and essential for regulating erythroid and megakaryocytic maturation and differentiation. Binds to the hypersensitive site 2 (HS2) of the beta-globin control region (LCR). This subunit (NFE2)recognizes the TCAT/C sequence of the AP-1-like core palindrome present in a number of erythroid and megakaryocytic gene promoters. Requires MAFK or other small MAF proteins for binding to the NF-E2 motif. May play a role in all aspects of hemoglobin production from globin and heme synthesis to procurement of iron. NFE2 has been shown to interact with CREB binding protein.

value: std

value: Standard input signal for most experiments.


title: Stanford_ChipSeq_GM12878_IRF3_IgG-mus

value: Stanford

value: Snyder - Stanford University

value: Rabbit polyclonal; epitope corresponding to amino acids 1-425 of IRF-3 of human origin. Antibody Target:IRF3

value: Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

tag: control description

tag: controlid


title: Stanford_ChipSeq_HepG2_IRF3_IgG-rab

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: hepatocellular carcinoma

value: cancer

value: endoderm

value: M

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: replicate


title: Stanford_ChipSeq_HepG2_USF2_IgG-rab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

tag: cell karyotype

tag: cell lineage

value: Mouse monoclonal. Immunogen corresponds to amino acids 1-101 of Human USF2. Antibody Target:USF2

value: Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3').

value: abcam


title: Stanford_ChipSeq_K562_Pol2(phosphoS2)_std

value: Stanford

value: leukemia, "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

value: mesoderm

tag: cell sex

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal against peptide conjugated to KLH derived from within residues 1600 - 1700 of S. cerevisiae RNA polymerase II CTD repeat YSPTSPS, phosphorylated at S2. Antibody Target:POL2S2

value: RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain.

value: Abcam

value: std

value: Standard input signal for most experiments.


title: Anti-DMC1 F1 Sample 2

description:
Sample 8
processed data file: F1_DSB_hotspots.bedGraph (available on Series records)

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
F1_SSDS_Sample2_Testis_ssDNA_type1.bed: mm9

source_name: Anti-DMC1 F1_testis_SSDS

tag: strain

tag: genotype/variation

value: wild type

tag: tissue

value: testis

tag: chip antibody

value: Anti-DMC1 (C-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: sequencing technique

value: Single Stranded DNA Sequencing (SSDS)


title: Stanford_ChipSeq_HepG2_Rad21_IgG-rab

tag: lab

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: human

value: hepatocellular carcinoma

value: cancer

value: endoderm

value: M

value: Rabbit polyclonal. Antibody Target:RAD21

tag: antibody targetdescription

value: Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14

tag: antibody vendorname

tag: antibody vendorid

tag: control

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid

tag: replicate


title: RWPE1-ERG ChIP-seq (ERG)

source_name: RWPE1-ERG prostate epithelial cell line, ERG ChIP

tag: cell line

tag: cell type

value: benign prostate epithelial cells

tag: overexpressing

value: truncated ERG

tag: passages

value: ERG

tag: antibody vendor

value: Epitomics

tag: antibody catalog #

tag: antibody lot#


title: Stanford_ChipSeq_NB4_Max_std

tag: lab

value: Stanford

tag: lab description

tag: datatype

tag: cell organism

tag: cell description

value: acute promyelocytic leukemia cell line. (PMID:1995093)

tag: cell karyotype

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Max

tag: antibody antibodydescription

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Max of human origin. Antibody Target:Max

value: The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq).

value: Santa Cruz Biotech

value: std

value: Standard input signal for most experiments.


title: Broad_Combined_HSMM

source_name: HSMM

value: Broad

value: Bernstein - Broad Institute

value: Combined

tag: datatype description

value: Multi-assay Synthesis

tag: cell

value: HSMM

value: human

value: skeletal muscle myoblasts

value: normal

tag: softwareversion


title: Stanford_ChipSeq_GM10847_Input_IgG-mus

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: lymphoblastoid, International HapMap Project, CEPH/Utah, treatment:Epstein-Barr Virus transformed

value: mesoderm

value: F

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control

value: IgG-mus

tag: control description

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: controlid

tag: labversion

value: Illumina 2.0, low confidence sequences excluded

tag: replicate


title: Stanford_ChipSeq_K562_UBTF_(SAB1404509)_IgG-mus

tag: lab

tag: lab description

tag: datatype

tag: cell organism

tag: cell description

value: leukemia, "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

value: cancer

value: No special treatment or protocol applies

value: Mouse monoclonal, immunogen:UBTF (NP_055048, 551 a.a. ~ 651 a.a) partial recombinant protein with GST tag. Antibody Target:UBTF

tag: antibody targetdescription

value: Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes

tag: antibody vendorname

value: Sigma-Aldrich

tag: antibody vendorid


title: Anti-DMC1 13R Sample 2

description:
Sample 4
processed data file: 13R_DSB_hotspots.bedGraph (available on Series records)

data_processing:
For SSDS samples, reads were mapped to the mm9 genome using the modified bwa algorithm (bwa_ra), described in Khil et al., Genome Research 2012. Read pairs originating from type 1 single-stranded DNA were then selected.
Peak calling was performed on pooled SSDS samples for each genetic background.  Potential peak centres were identified using SISSRs. Adjacent (within 100 nt) putative centres were merged. True peak centres were identified as the midpoint between the median of the forward and reverse tag distributions in the 2 Kb region around each putative centre. Final peaks were defined as the 2 Kb region around the centre.
For ChIP-Seq samples, reads were mapped to the mm9 genome using the Illumina Genome Analyzer Pipeline.  Reads with less than two mismatches were not aligned.  MACS was used to define peaks.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome Build:
13R_SSDS_Sample2_Testis_ssDNA_type1.bed: mm9

source_name: Anti-DMC1 13R_testis_SSDS

tag: strain

tag: genotype/variation

value: wild type

tag: tissue

value: testis

tag: chip antibody

value: Anti-DMC1 (C-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: sequencing technique

value: Single Stranded DNA Sequencing (SSDS)


title: Stanford_ChipSeq_GM12892_Pol2_IgG-mus

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: treatment

tag: treatment description

tag: antibody

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: control

tag: control description

tag: controlid

tag: labversion

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded. Data paired with GM12892_IgG_Control.


title: Stanford_ChipSeq_HeLa-S3_BAF170_IgG-mus

tag: lab

tag: lab description

tag: datatype

tag: cell organism

tag: cell description

value: cervical carcinoma

value: cancer

value: ectoderm

value: No special treatment or protocol applies

value: BAF170 (H-116) is a rabbit polyclonal antibody raised against amino acids 1093-1208 of BAF170 of human origin. Antibody Target:BAF170

tag: antibody targetdescription

value: BAF170 (Brg1-Associated Factor, 170 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: IgG-mus

value: Input signal from Normal Mouse IgG ChIP-seq.

value: remapped from hg18, Data paired with IgG_Control.

tag: replicate


title: Stanford_ChipSeq_K562_Brg1_IgG-mus

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: human

value: leukemia, "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

tag: cell karyotype

tag: cell lineage

tag: cell sex

tag: treatment

value: Brg-1 (G-7) is a mouse monoclonal antibody raised against amino acids 209-296 mapping near the N-terminus of Brg-1 of human origin. Antibody Target:BRG1

value: Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex.

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded. Data paired with IgG_Control.


title: Harvard_ChipSeq_MCF10A-Er-Src_Input_std

value: Harvard

value: Struhl - Harvard University

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: normal

value: ectoderm

value: F

tag: treatment description

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid


title: Stanford_ChipSeq_HeLa-S3_Nrf1_IgG-mus

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: cell organism

tag: cell description

value: cervical carcinoma

value: cancer

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Mouse monoclonal, Immunogen corresponding to amino acids 201-286 of Human NRF1. Antibody Target:NRF1

value: NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding.

value: Abcam

value: IgG-mus

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: labversion

value: remapped from hg18, Data set paired with HeLa-S3_MouseIgG_Control.


title: Stanford_ChipSeq_NB4_c-Myc_std

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: human

value: acute promyelocytic leukemia cell line. (PMID:1995093)

tag: cell karyotype

value: mesoderm

value: U

value: c-Myc

value: rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target:c-Myc

tag: antibody targetdescription

value: transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: replicate


title: Stanford_ChipSeq_K562_Ini1_IgG-mus

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: leukemia, "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

value: cancer

tag: cell lineage

tag: cell sex

value: F

tag: treatment

tag: treatment description

tag: antibody

value: Ini1 (C-20) is an affinity purified goat polyclonal antibody raised against a peptide mapping near the C-terminus of Ini1 of human origin. Antibody Target:INI1

value: Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex.

tag: control

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded. Data paired with IgG_Control.


title: Stanford_ChipSeq_HeLa-S3_Ini1_IgG-mus

tag: lab

tag: lab description

tag: datatype

value: Chromatin IP Sequencing

tag: cell organism

value: human

value: cervical carcinoma

value: ectoderm

value: No special treatment or protocol applies

value: IgG-mus

tag: control description

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: controlid


title: Stanford_ChipSeq_K562_Input_IgG-mus

tag: datatype description

tag: cell

tag: cell description

tag: cell karyotype

value: mesoderm

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: labversion

value: Illumina 2.0, low confidence sequences excluded


title: Stanford_ChipSeq_A549_CEBPB_IgG-rab

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

tag: cell lineage

value: endoderm

tag: cell sex

value: M

value: CEBPB

tag: antibody antibodydescription

value: Rabbit polyclonal IgG. Antibody Target:CEBPB

tag: antibody targetdescription

value: epitope mapping at the C-terminus of C/EBP-beta of rat origin

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: replicate


title: Stanford_ChipSeq_HepG2_forskolin_Pol2_std

treatment_protocol: forskolin

tag: lab

tag: lab description

tag: datatype

value: Chromatin IP Sequencing

value: human

value: hepatocellular carcinoma

value: cancer

tag: treatment

value: forskolin

tag: treatment description

value: low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder)

tag: antibody

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: control

value: std

value: Standard input signal for most experiments.

value: Illumina 2.0, low confidence sequences excluded.  Data paired with HepG2_Forskolin_Control.


title: Stanford_ChipSeq_K562_Pol2_IgG-mus

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: leukemia, "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

tag: cell karyotype

value: mesoderm

value: F

value: No special treatment or protocol applies

value: IgG-mus

tag: control description

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: controlid

value: remapped from hg18, Data paired with IgG_Control.


title: Stanford_ChipSeq_HepG2_insulin_SREBP1_std

treatment_protocol: insulin

value: Chromatin IP Sequencing

value: human

value: hepatocellular carcinoma

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

value: insulin

value: DMEM with 0.5% BSA supplemented with 100 nM insulin and 10 uM 22-hydroxycholesterol for 6 h. (Snyder)

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:SREBP1

tag: antibody targetdescription

value: Sterol regulatory element binding transcription factor 1

tag: antibody vendorname

value: Santa Cruz Biotech

tag: labversion

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded.  Data paired with HepG2_Insulin_Control.