title: batch1_chrom1_LoVo_JUN_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_JUN_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_IRX3_Mouse_PassedQC

status: Public on Aug 15 2013

type: SRA

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: control sample: batch1_chrom1_LoVo_IgG_Mouse

library_source: genomic

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_IRX3_PassedQC_peaks.txt: hg18

molecule: genomic DNA

organism: Homo sapiens

source_name: LoVo

growth_protocol: LoVo (ATCC CCL-229) and GP5d (ECACC cat no. 95090715) colon adenocarcinoma cells were cultured in DMEM supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.

extract_protocol:
Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.
Libraries were constructed according to Illuminas standard protocol. The concentration of the library was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific Inc.) and 10 pmol of the DNA was applied for one flow-cell lane. Sequencing was performed using one lane of Illumina GAIIx, or alternatively, samples were indexed with DNA barcodes and four to six different samples were multiplexed in one library and sequenced using Illumina HiSeq 2000 (single 36 bp reads).

tag: cell line

value: LoVo

tag: cell type

value: colon adenocarcinoma

tag: enriched motif (p<0.001) with dbd sequence similarity > 65%.

tag: qc successful

value: PassedQC


title: batch1_chrom1_LoVo_HSF2_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HSF2_FailedQC_peaks.txt: hg18

value: FailedQC


title: batch1_chrom1_LoVo_HOXA7_Rabbit_PassedQC

description: control sample: batch1_chrom1_LoVo_IgG_Rabbit

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HOXA7_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_HOXA1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HOXA1_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_HOXB13_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HOXB13_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_HOXA10_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HOXA10_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_HNF4A_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HNF4A_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_HINFP_Goat_PassedQC

description: control sample: batch1_chrom1_LoVo_IgG_Goat

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HINFP_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_HES4_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HES4_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_HES2_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HES2_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_HES1_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HES1_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_GLIS3_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_GLIS3_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_GLIS2_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_GLIS2_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_HBP1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_HBP1_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_GMEB2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_GMEB2_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_GATA6_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_GATA6_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_GATA4_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_GATA4_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_GLI2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_GLI2_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_ETV4_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_ETV4_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_GATA2_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_GATA2_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_ELF2_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_ELF2_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_USF2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_USF2_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_ESRRA_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_ESRRA_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_ERF_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_ERF_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_EP300_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_EP300_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_ELF1_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_ELF1_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_E2F4_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_E2F4_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_E2F2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_E2F2_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_DBP_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_DBP_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CUX1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CUX1_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CTCF_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CTCF_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CREB3L2_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CREB3L2_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_GMEB1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_GMEB1_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CEBPG_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CEBPG_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CEBPZ_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CEBPZ_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_FOXM1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_FOXM1_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CEBPB_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CEBPB_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_FOXO3_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_FOXO3_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_BARX2_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_BARX2_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CASZ1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CASZ1_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_ATOH1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_ATOH1_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CASP8AP2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CASP8AP2_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_ASCL2_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_ASCL2_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_EHF_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_EHF_PassedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_ARNT_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_ARNT_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ZIC2_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ZIC2_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_VEZF1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_VEZF1_PassedQC_peaks.txt: hg18


title: FaireSeq_NT_2

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

description:
Faire NT #2.
Library strategy: FAIRE-Seq.

data_processing:
Basecalls performed using CASAVA v1.7.0
Sequence reads were mapped to the mm9 assembly of the mouse genome with Bowtie v0.12.9 (-q -m 1 -v 2 --best)
Duplicate reads were removed, and the remaining unique reads were normalized to a 10 million read count for peak calling analysis.
BedGraph files were generated by HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files show sequence density across mm9 genome. For FAIRseq, each bedgraph file contains sequence density of open chromatin fragment in the respective tissue type.

organism: Mus musculus

source_name: E12.5 Neural Tube

extract_protocol:
Tissue samples from E12.5 neural tube and E17.5 pancreas were dissected in cold PBS, homogenized, and crosslinked with 1% formaldehyde for 8 minutes at room temperature and fixation was terminated by adding glycine to a final concentration of 0.125 M. Samples were sonicated using a Diagenode bath Sonicator for 36 minutes, with 30 second on:off cycle times. Samples were centrifuged at 14,000 rpm to pellet debris. Two rounds of phenol:chloroform extraction were performed yielding 500 μl aqueous phase, to which 8.25 μl 5M NaCl solution was added. Samples were incubated overnight at 65 oC to reverse crosslinks. Samples were ethanol precipitated and resuspended in 50 μl 10mM Tris-HCl pH 7.5, digested for 4 hours using 5 μl 10 mg/ml Proteinase K. 1 μl of 10 mg/ml RNAse A was added, and incubated an additional 30 minutes at 37 oC. Samples were purified using a Qiagen PCR Cleanup kit.
All libraries were made according to NEBNext ChIP-Seq Library Prep Set Master Mix for Illumina protocol

tag: developmental stage

tag: strain

value: ICR

tag: tissue

value: Neural Tube


title: FaireSeq_Panc_1

description:
Faire Panc #1.
Library strategy: FAIRE-Seq.

source_name: E17.5 Pancreas

value: Pancreas


title: RnaSeq_E15.5_Pancreas_WT

description:
mRNA
E15.5 Pancreas WT #1, E15.5 Pancreas WT #2

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA (NT samples v1.30, Pancreas v1.7.0)
Sequence reads were aligned to the mm9 build of the mouse genome using TopHat v2.0.4 . Default settings were used with the following exceptions: -G option (instructs TopHat to initially map reads onto a supplied reference transcriptome) and –no-novel-junc
Biological replicate were specified and used to build an expression level model determined by the FPKM method of Cuffdiff v2.0.2 . Upper quartile normalization (-N option) was performed to more accurately estimate levels of low-abundance transcripts, and multiple read correction (-u option) was selected to better distribute reads mapping to multiple genomic locations. To correct any sequence-specific bias introduced during the library preparation option  b was used. All other settings were left at default values.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file showing FPKM values for each tissue sample (linked as supplementary file on the Series record).

molecule: total RNA

source_name: E15.5 Pancreas

extract_protocol:
Mouse neural tubes were dissected from E12.5 2.3Ptf1a-GFP embryos into DMEM/F12 on ice and dissociated in 0.25% trypsin for 15 minutes at 37°C. Trypsin activity was quenched with 2% fetal bovine serum, and GFP positive cells were purified from the resulting single cell suspension by fluorescence activated cell sorting. Total RNA from the sorted cells was extracted and purified with Zymo’s Mini RNA Isolation Kit.For the whole E15.5 pancreas, total RNA was isolated using Trizol(Invitrogen).
Neural tube and pancreata libraries were made according to Illumina’s mRNA-seq sample prep protocol. Pancreas libraries were made according to Illumina’s Tru-seq mRNA sample prep protocol

tag: genotype/variation

value: WT


title: batch2_chrom1_LoVo_TP73_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_TP73_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_TRPS1_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_TRPS1_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CSDA_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CSDA_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_TOX4_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_TOX4_FailedQC_peaks.txt: hg18


title: IgG_MT_control

city: Shenzhen

first: Kun

last: Sun

address: Rm B505, No. 9 Duxue Road, Nanshan District

department: Cancer Research

country: China

institute: Shenzhen Bay Laboratory

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using SOAP2 with parameters: -v 2 -r 0 -m 0 -p 20
Peaks were called using MACS2 version 2.0.9, for YY1, q-value=10-5 is used as the cutoff; for Ezh2, H3K4me3 and H3K27me3, q-value=10-2 is used
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation
Overlaping analysis was performed using in-house programs and the maximum distance limitation is set to 1000bp
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS2, scores represent q value

source_name: C2C12 myotubes

growth_protocol: C2C12 myoblasts were growed in gowth medium containing DMEM, 10% FBS and 1% pen/srep.

extract_protocol:
Chromatins from myoblasts and myotubes were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies
ChIP-seq libraries were constructed closely according to the standard illumina pair-end ChIP-seq procedure

treatment_protocol: C2C12 myoblasts were induced to differentiate by culturing in differentiation medium (DMEM, 2% horse serum and 1% pen/strep)

value: C2C12 cell-line

value: Myotube (MT)

tag: chip antibody

value: IgG

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #


title: batch2_chrom1_LoVo_TEL_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_TEL_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_TEAD2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_TEAD2_PassedQC_peaks.txt: hg18


title: IgG_MB_control

source_name: C2C12 myoblasts

value: Myoblast (MB)


title: YY1_MT_ChIP-seq


title: batch2_chrom1_LoVo_T_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_T_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_STAT3_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_STAT3_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CDX2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CDX2_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_TCF3_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_TCF3_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_SREBF1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_SREBF1_FailedQC_peaks.txt: hg18


title: batch1_chrom1_LoVo_CAMTA2_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_CAMTA2_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_SOX3_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_SOX3_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_SP2_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_SP2_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_SPIB_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_SPIB_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_SOX2_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_SOX2_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_RORA_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_RORA_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_SMAD1_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_SMAD1_FailedQC_peaks.txt: hg18


title: FaireSeq_NT_1

description:
Faire NT #1.
Library strategy: FAIRE-Seq.

data_processing:
Basecalls performed using CASAVA v1.7.0
Sequence reads were mapped to the mm9 assembly of the mouse genome with Bowtie v0.12.9 (-q -m 1 -v 2 --best)
Duplicate reads were removed, and the remaining unique reads were normalized to a 10 million read count for peak calling analysis.
BedGraph files were generated by HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files show sequence density across mm9 genome. For FAIRseq, each bedgraph file contains sequence density of open chromatin fragment in the respective tissue type.


title: batch2_chrom1_LoVo_REST_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_REST_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_RBCK1_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_RBCK1_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_RARA_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_RARA_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_RARG_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_RARG_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_SATB1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_SATB1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_PDX1_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_PDX1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_PHF20_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_PHF20_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_PATZ1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_PATZ1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_OTX1_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_OTX1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_PAX2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_PAX2_FailedQC_peaks.txt: hg18


title: YY1_MB_SC1703_ChIP-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using SOAP2 with parameters: -v 2 -r 0 -m 0 -p 20
Peaks were called using MACS2 version 2.0.9, for YY1, q-value=10-5 is used as the cutoff; for Ezh2, H3K4me3 and H3K27me3, q-value=10-2 is used
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation
Overlaping analysis was performed using in-house programs and the maximum distance limitation is set to 1000bp
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS2, scores represent q value


title: batch2_chrom1_LoVo_NKX2-5_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_NKX2-5_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_NKX2.2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_NKX2.2_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_NKX2-1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_NKX2-1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_NFYA_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_NFYA_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_NFKB2_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_NFKB2_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_NKX3-1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_NKX3-1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_NFATC1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_NFATC1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_MXD1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_MXD1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_MSX1_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_MSX1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_NFATC4_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_NFATC4_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_MEIS3_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_MEIS3_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_MNT_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_MNT_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_MAZ_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_MAZ_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_LYL1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_LYL1_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_LMX1B_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_LMX1B_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_MEF2D_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_MEF2D_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_LIN9_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_LIN9_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_JUND_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_JUND_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_LHX3_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_LHX3_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_JDP2_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_JDP2_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ISL1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ISL1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_HOXA2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_HOXA2_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_HSF1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_HSF1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_HOXC6_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_HOXC6_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_HIF1A_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_HIF1A_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_HMGA1_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_HMGA1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_GLI3_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_GLI3_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_GLIS1_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_GLIS1_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_HOXA13_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_HOXA13_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_HIVEP1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_HIVEP1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_GATA1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_GATA1_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_FOXG1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_FOXG1_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_GLI1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_GLI1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_FOXK2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_FOXK2_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ZFHX3_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ZFHX3_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_FOXP3_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_FOXP3_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_FOXD2_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_FOXD2_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_FEV_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_FEV_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_EVI1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_EVI1_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_HSF4_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_HSF4_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ETV7_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ETV7_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_EZH2_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_EZH2_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ESR1_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ESR1_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_FOXA1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_FOXA1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_EOMES_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_EOMES_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ERG_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ERG_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ELF3_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ELF3_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_E2F8_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_E2F8_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_EMX1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_EMX1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ERM_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ERM_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_E2F7_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_E2F7_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_E2F3_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_E2F3_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_E2F1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_E2F1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_DLX6_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_DLX6_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_DMRT1_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_DMRT1_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_DLX2_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_DLX2_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_DLX4_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_DLX4_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_CREM_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_CREM_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_CREB3L4_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_CREB3L4_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_DLX1_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_DLX1_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_CREB3_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_CREB3_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_CLOCK_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_CLOCK_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_CIC_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_CIC_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_BTF3_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_BTF3_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_BARHL1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_BARHL1_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ATF5_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ATF5_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ATF1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ATF1_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_AR_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_AR_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ALX4_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ALX4_FailedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_AEBP2_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_AEBP2_PassedQC_peaks.txt: hg18


title: batch2_chrom1_LoVo_ZFAT_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_ZFAT_FailedQC_peaks.txt: hg18


title: plusDHT_ASO_CTL_hs15l7_2

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

state: CA

address: 9500 Gilman Drive

institute: HHMI/UCSD

description: GRO-seq

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to hg18 using Bowtie2, and we kept only 1 aligned read/ genome position for downstream analyses.
The bedgraph files were generated by using HOMER.
The sequencing reads were counted by using BEDTools.
The differential gene expression was assessed by edgeR.
Genome_build: hg18
Supplementary_files_format_and_content: BedGraph files display of continuous-valued data in track format, and were generated by using the HOMER suite ("makeUCSCfile" command).
Supplementary_files_format_and_content: BED file after aligning the reads to hg18 by using Bowtie2, keeping only 1 mapped read / genome position

source_name: LNCaP cells

growth_protocol: We maintain LNCaP cells in RPMI 1640 + 10% FBS media. We typically grow LNCaP cells in 150 or 100 mm polystyrene tissue culture dishes depending on number of cells required. Media is changed at minimum twice per week, or before media becomes orange. Cells are split soon after reach 80% confluence.

extract_protocol:
Nuclei were isolated from LNCaP cells with appropriate transfection and -/+ DHT treatment. GRO-seq libraries were prepared from 10 million cells based on previously published protocols (Wang et al., 2011). Libraries were sequenced on Illumina Hi-Seq 2000.
After harvesting the cells, RNA polymerases were allowed to run-on for 5 minutes at 30C (~100bp) in the presence of sarkosyl and BrUTP. The RNA was then base hydrolyzed and purified. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads. Run-on RNA was then polyadenylated to generate primer sites for first strand cDNA synthesis. Complementary poly-T primers contain two adaptor sequences separated by an Ape1 restriction site, which after circularization and Ape1 digestion, will terminate both ends, thus permitting cDNA generation, PCR-amplification, and library generation for deep sequencing.

treatment_protocol: Prior to androgen treatment, we grow the cells in UltraCULTURE (Phenol red free) + 5% Charcoal Dextran Stripped (CDS) serum for 48 hours. For androgen induction, we treat cells with DHT from a 100 uM stock in 70% ethanol to a final concentration of 100 nM.

value: LNCaP cells

tag: transfected with

value: siCTL

tag: treated with

value: 100 nM DHT


title: minusDHT_ASO_CTL_hs15l7_1

description: GRO-seq


title: minusDHT_ASO_PCGEM1_hs15l4_3

description: GRO-seq


title: siPYGO2_plusDHT_hs26l2_4

description: GRO-seq

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to hg18 using Bowtie2, and we kept only 1 aligned read/ genome position for downstream analyses.
The bedgraph files were generated by using HOMER.
The sequencing reads were counted by using BEDTools.
The differential gene expression was assessed by edgeR.
Genome_build: hg18
Supplementary_files_format_and_content: BED aligned files after aligning the reads to hg18 by using Bowtie2, keeping only 1 mapped read / genome position
Supplementary_files_format_and_content: BedGraph files display of continuous-valued data in track format, and were generated by using the HOMER suite ("makeUCSCfile" command).

growth_protocol: We maintain LNCaP cells in RPMI 1640 + 10% FBS medium. We typically grow LNCaP cells in 150 or 100 mm polystyrene tissue culture dishes depending on number of cells required. Media is changed at minimum twice per week, or before media becomes orange. Cells are split soon after they reach 80% confluence.

extract_protocol:
Nuclei were isolated from LNCaP cells with appropriate transfection and -/+ DHT treatment. GRO-seq libraries were prepared from 5 million cells based on previously published protocols (Wang et al., 2011). Libraries were sequenced on Illumina Hi-Seq 2000.
After harvesting the cells, RNA polymerases were allowed to run-on for 5 minutes at 30C (~100bp) in the presence of sarkosyl and BrUTP. The RNA was then base hydrolyzed and purified. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads. Run-on RNA was then polyadenylated to generate primer sites for first strand cDNA synthesis. Complementary poly-T primers contain two adaptor sequences separated by an Ape1 restriction site, which after circularization and Ape1 digestion, will terminate both ends, thus permitting cDNA generation, PCR-amplification, and library generation for deep sequencing.

treatment_protocol: Prior to androgen treatment, we grow the cells in UltraCULTURE (Phenol red free) + 5% Charcoal Dextran Stripped (CDS) serum for 48 hours. For androgen induction, we treat cells with DHT from a 100 uM stock in 70% ethanol to a final concentration of 100 nM


title: plusDHT_ASO_PCGEM1_hs15l4_4

description: GRO-seq


title: minusDHT_ASO_PRNCR1_hs15l7_3

description: GRO-seq


title: siPYGO2_minusDHT_hs26l2_3

description: GRO-seq


title: plusDHT_ASO_PRNCR1_hs15l7_4

description: GRO-seq


title: siCTL_plusDHT_hs26l2_2

description: GRO-seq


title: Panc_Input_control

description: Panc Input control

data_processing:
Basecalls performed using CASAVA (NT Ptf1a v1.6.0,Pancreas Ptf1a v1.3.0,All other samples v1.7.0)
Sequence reads were mapped to the mm9 assembly of the mouse genome with Bowtie v0.12.9 (-q -m 1 -v 2 --best)
Duplicate reads were removed, and the remaining unique reads were normalized to a 10 million read count for peak calling analysis.
Peak calling was performed by HOMER using an FDR cutoff of 0.001. Putative peaks were required to have 4-fold enrichment over the control/input sample and a cumulative Poisson p-value of <0.0001
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files show sequence density across mm9 genome. Each ChIPseq bedgraph file name describes the transcription factor used for ChIP in the respective tissue type.

extract_protocol:
Neural tube (caudel to midbrain), telencephalon, or limb tissues from E12.5 mouse embryos, or pancreata from E17.5 embryos were dissected and placed in Buffer A (15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 0.2 mM EDTA, 0.5 mM EGTA, 0.34 M sucrose) on ice. Nuclei were liberat
All libraries were made according to Illumina’s ChIP-seq DNA sample prep protocol

tag: antibody


title: plusDHT_PCGEM1_hs17l4_4

description: ChIRP-seq

data_processing:
library strategy: ChIRP-seq
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to hg18 using Bowtie2, and we kept only 1 aligned read/ genome position for downstream analyses.
The bedgraph files were generated by using HOMER.
The peak finding was carried by using HOMER.
The motif enrichment analysis was carried by using HOMER.
Genome_build: hg18
Supplementary_files_format_and_content: BedGraph files display of continuous-valued data in track format, and were generated by using the HOMER suite ("makeUCSCfile" command).
Supplementary_files_format_and_content: BED file after aligning the reads to hg18 by using Bowtie2, keeping only 1 mapped read / genome position
Supplementary_files_format_and_content: HOMERpeak files display the coordinates of the peaks, as these were predicted by the HOMER suite ("findPeaks" command).

growth_protocol: We maintain LNCaP cells in RPMI 1640 + 10% FBS medium. We typically grow LNCaP cells in 150 or 100 mm polystyrene tissue culture dishes depending on number of cells required. Cells are split soon after reach 80% confluence.

extract_protocol:
ChIRP was performed as described (Chu et al 2011) with minor modifications. Briefly, 60-mer antisense DNA probes targeting PRNCR1 and PCGEM1 full-length sequences were designed by http://www.singlemoleculefish.com/designer.html. A set of probes targeting LacZ RNA was also designed as the negative control. All probes were biotinylated using Label IT® Nucleic Acid Biotin Labeling Kit from Mirus Biotechnology. LNCaP cells were fixed with 1% formaldehyde for 10 min at room temperature. Crosslinking was then quenched with 125mM glycine for 5 min. The chromatin preparation, hybridization/elution, deep sequencing steps were essentially performed as described (Chu et al 2011) except that washing was conducted at 50 °C and 65°C.
ChIRP complexes were washed and the DNA was extracted and purified by QIAquick Spin columns (Qiagen). For ChIRP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing.

treatment_protocol: Prior to androgen treatment, we grow the cells in UltraCULTURE (Phenol red free) + 5% Charcoal Dextran Stripped (CDS) serum for 48 hours. We treat cells with DHT from a 100 uM stock in 70% ethanol to a final concentration of 100 nM.


title: minusDHT_PCGEM1_hs17l4_3

description: ChIRP-seq


title: siCTL_minusDHT_hs26l2_1

description: GRO-seq


title: ChIPseq_Ptf1a_Tel_1_control

description: Ptf1a Tel #1

source_name: E12.5 Telencephalon

value: Lab generated rabbit anti-Ptf1a (AN255/256)

value: Telencephalon


title: ChIPseq_Foxa2_Panc_2

description: Foxa2 Panc #1

value: Goat anti-Foxa2 (Santa cruz;Hnf3b M-20 #6554)


title: ChIPseq_Rbpjl_Panc_2

description: Rbpjl Panc #2

value: Lab generated rabbit anti-Rbpjl (AN2165/2166)

tag: antibody ref

value: Beres TM, Masui T, Swift GH, Shi L, Henke RM, MacDonald RJ. 2006. PTF1 is an organ-specific and Notch-independent basic helix-loop-helix complex containing the mammalian Suppressor of Hairless (RBP-J) or its paralogue, RBP-L. Mol Cell Biol 26:117-130.


title: ChIPseq_Foxa2_Panc _1

description: Foxa2 Panc #1

value: ICR


title: batch2_chrom1_LoVo_CBFB_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_CBFB_FailedQC_peaks.txt: hg18

value: LoVo

value: colon adenocarcinoma

value: FailedQC


title: batch2_chrom1_LoVo_CEBPE_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch2_chrom1_LoVo_CEBPE_FailedQC_peaks.txt: hg18


title: NT_Input_control

description: NT Input control

value: Neural Tube


title: ChIPseq_Rbpj_NT_1

description: Rbpj NT #1

value: Lab generated rabbit anti-Rbpj(Tx857)


title: ChIPseq_Ptf1a_Panc_1

description: Ptf1a Panc #1

value: Rose SD, Swift GH, Peyton MJ, Hammer RE, MacDonald RJ. 2001. The role of PTF1-P48 in pancreatic acinar gene expression. J Biol Chem 276:44018-44026.

value: Pancreas


title: ChIPseq_Rbpj_NT_2

description: Rbpj NT #2


title: ChIPseq_Ptf1a_NT_2

description: Ptf1a NT #2


title: ChIPseq_Ptf1a_NT_1

description: Ptf1a NT #1


title: RnaSeq_2.3Ptf1aGFP_NT

description:
2.3Ptf1a::GFP transgene contains the Ptf1a 2.3 kb autoregulatory enhancer region (chr2:19351717-19354014 from mm9)  cloned upstream of the beta-globin basal promoter driving  GFP followed by a bovine growth hormone polyA signal sequence. MEREDITH, D. M., MASUI, T., SWIFT, G. H., MACDONALD, R. J. & JOHNSON, J. E. 2009. Multiple transcriptional mechanisms control Ptf1a levels during neural development including autoregulation by the PTF1-J complex. J Neurosci, 29, 11139-48.
mRNA
2.3Ptf1a-GFP+ NT #1, 2.3Ptf1a-GFP+ NT #2

data_processing:
Basecalls performed using CASAVA (NT samples v1.30, Pancreas v1.7.0)
Sequence reads were aligned to the mm9 build of the mouse genome using TopHat v2.0.4 . Default settings were used with the following exceptions: -G option (instructs TopHat to initially map reads onto a supplied reference transcriptome) and –no-novel-junc
Biological replicate were specified and used to build an expression level model determined by the FPKM method of Cuffdiff v2.0.2 . Upper quartile normalization (-N option) was performed to more accurately estimate levels of low-abundance transcripts, and multiple read correction (-u option) was selected to better distribute reads mapping to multiple genomic locations. To correct any sequence-specific bias introduced during the library preparation option  b was used. All other settings were left at default values.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file showing FPKM values for each tissue sample (linked as supplementary file on the Series record).

value: WT


title: ChIPseq_Rbpjl_Panc_1

description: Rbpjl Panc #1


title: H3K4me3_MB_ChIP-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using SOAP2 with parameters: -v 2 -r 0 -m 0 -p 20
Peaks were called using MACS2 version 2.0.9, for YY1, q-value=10-5 is used as the cutoff; for Ezh2, H3K4me3 and H3K27me3, q-value=10-2 is used
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation
Overlaping analysis was performed using in-house programs and the maximum distance limitation is set to 1000bp
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS2, scores represent q value

value: C2C12 cell-line

value: Myoblast (MB)

value: Millipore


title: Input_Abrupt

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: Input DNA

data_processing:
Alignment: Sequence reads were mapped to Drosophila melanogaster (dm3, April 2006) using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml). All reads mapping with two or fewer mismatches were retained.PeakSeq was used to create the signal maps as wig files.
Peak-calling: Peak detection was performed with the PeakSeq program (http://www.gersteinlab.org/proj/PeakSeq/), using each respective Input as a control. The final peak files are provided in BED format.
Genome_build: dm3
Supplementary_files_format_and_content: WIG file represents genome wide ChIP profile
Supplementary_files_format_and_content: BED file represents signal enriched regions

organism: Drosophila melanogaster

source_name: Eye/antennal imaginal discs [input]

extract_protocol:
Eye-antennal discs were dissected and samples cross-linked in a 1.8% formaldehyde solution on a rotating wheel for 5 mins, prior to DNA being sheared by sonication (15 cycles of 20 seconds, 35% amplitude) to produce fragments of ~500bp (Perez-Lluch et al. 2011). 100ml of extract (corresponding to ~100 discs) was used for each immunoprecipitation. 35ml of 50% Protein A-Sepharose CL4B was added to each sample, and cleared after 1.5 hours incubation. 2ml of anti-Abrupt antibody was then added per sample (or, for the input DNA controls, no antibody was added), and incubated overnight with rotation. Immunocomplexes were recovered by adding 35ml Protein A-Sepharose to each sample, incubating for 3 hours at 4oC, and then harvesting by centrifugation. Chromatin was decrosslinked by RNase and Proteinase K incubations, and the DNA column purified (Qiagen). For each sequencing sample, 3 to 6 IPs were pooled.
Libraries were prepared according to Illumina instructions.

value: Eye/antennal imaginal discs

value: none (input)

value: UAS-ab55 (Cook et al. 2004)


title: Abrupt

description: chromatin IP against Abrupt overexpressing ab alone

source_name: Eye/antennal imaginal discs [ChIP]

value: anti-Abrupt (a polyclonal rabbit antibody from Steven Crews)


title: Ezh2_MB_ChIP-seq

value: Cell Signaling


title: Smg6 deficient mouse ES cells rep1

status: Public on Aug 14 2013

city: Beijing

first: Bao-Fa

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description: replicate 1

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.0.9
For each sample, RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene.
Differentially expressed genes between control and  Smg6 deficient ES cells  samples were determined using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: mm10

source_name: ES cells

extract_protocol:
RNA was isolated from control and Smg6 deficient ES cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 50 bp.

value: ES cells

value: Smg6 deficient

value: Embryo


title: NAC_ChIPSeq

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
Standard Illumina pipeline including CASSAVA
ChIP-Seq reads were aligned to soybean reference genome (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches per read.
MACS sofware was used to call peaks
Peaks were called using bandwidth 300 bp; mfold, 30; P-value of 1.00e-05
Genome_build: Glyma1
Supplementary_files_format_and_content: tab-delimited text files

organism: Glycine max

source_name: Germinating Cotyledons

growth_protocol: Plants were grown in optimal greenhouse conditions. Tissues were harvested 3-4 days after plant. Fresh cotyledons from developmental stage 4 and stage 5 were used to construct ChIP-Seq libraries.

extract_protocol:
Cell lysates were clarified from sonicated nuclei and transcription factor-DNA complexes were isolated with polyclonal antibodies developed against the YABBY or NAC transcription factors. Separate controls which were not treated with antibody were used for each experiment. Then DNA-antibody complexes were precipitated following standard protocol and DNA was recovered by dissociating the complexes. ChIP-Seq library construction and high-throughput sequencing was carried out by the Illumina HiSeq2000 at the Keck Center, University of Illinois at Urbana-Champaign.
libraries were prepared for sequencing using standard Illumina protocols
We used custom made rabbit polyclonal antibodies produced by GenScript Corporation.  Antibodies were developed against synthetic peptides representing plant specific, NAC and YABBY transcription factors. Gene models annotated as NAC transcription factor, Glyma12g04380.1 and Glyma11g12170.1, were used to design synthetic peptide (VRTGGKGTMRRKKK) for the production of antibody against NAC transcription factor. Similarly gene models annotated as YABBY transcription factor, Glyma13g22620.1 and Glyma17g12200.1 were used to design synthetic peptide (TEERVVNRPPEKRQ) for the production of antibody against YABBY transcription factor.

tag: cultivar

value: Williams

tag: Stage

value: 3-4 days after planting

tag: purification

value: NAC


title: YY1_MB_AB58066_ChIP-seq

tag: cell line

tag: cell type

value: Abcam


title: Smg6 deficient mouse ES cells rep2

description: replicate 2


title: CHIK_28_rep1

status: Public on Aug 13 2013

city: Blacksburg

first: Kevin

last: Myles

state: VA

address: Fralin Biotechnology Center

department: Fralin Life Science Institute

institute: Virginia Tech

data_processing:
Basecalls performed using CASAVA version 1.4.
Randomly 25 million sequences were selected for analysis from each library using an in-house perl script.
VectorBase Aedes aegypti genome AaegL1.2 was used for both Ae. aegypti and Ae. albopictus alignments.
Mosquito ncRNAs were taken out using bowtie v12.7 (-q -t -p 8 -v 3 -k 1 -m 1).
CHIK viral small RNAs were removed using bowtie v12.7 (-q -t -p 8 -v 1 -k 1 -B 1 --best).
Mosquito miRNAs, transposable elements, and endosiRNAs were removed using bowtie v12.7 (-q -t -p 8 -v 1 -k 1 -B 1 --best).
Individual counts for each small RNA class was totaled using in-house perl scripts.
Libraries were normalized using edgeR, using counts from viRNAs, miRNAs, TE, and endosiRNAs.
Genome_build: AaegL1
Supplementary_files_format_and_content: Processed counts were pasted into excel spreadsheet

organism: Aedes albopictus

source_name: whole body, 28C, CHIKV infected

growth_protocol: All mosquito strains [Ae. aegypti Liverpool, khw (white eye) and all transgenic strains, Ae. albopictus Wise County strain] were reared in environmental chambers with a light cycle of 14:10 (day:night) and humidity of 80%. For all experiments, mosquitoes were hatched under vacuum for ~30 minutes, counted, and dispensed (n=~400) into 4 L of water pre-chilled at 18oC or pre-warmed at 28oC.

extract_protocol:
Small RNA libraries derived from whole female Ae. albopictus infected with CHIKV (three biological replicates per temperature) were barcoded and constructed with Illumina's TruSeq small RNA prep kit and sequenced on an Illumina HiSeq.
RNA from pools of 5 females was extracted using TRIreagent following manufacturer's instructions.

treatment_protocol: Mosquitoes reared at 18oC or 28oC were injected with equivalent amounts of virus, transferred to 28oC, and processed 8 hours later.

value: Wise County

tag: gender

value: female

value: whole body

tag: growth temperature

tag: treatment

value: Chikungunya virus (CHIKV) strain 37797 infection


title: CHIK_28_rep2

tag: strain

tag: tissue


title: CHIK_18_rep2

source_name: whole body, 18C, CHIKV infected


title: CHIK_18_rep3


title: CHIK_28_rep3


title: YABBY_ChIPSeq

tag: chip antibody

value: YABBY


title: Abrupt_scrib

description: chromatin IP against Abrupt overexpressing ab in scrib mutant clones

source_name: Eye/antennal imaginal discs, scrib mutant [ChIP]

value: Eye/antennal imaginal discs

value: FRT82B,scrib1 (Bilder and Perrimon 2000)


title: H3K27me3_MB_ChIP-seq

value: C2C12 cell-line

value: Myoblast (MB)

tag: chip antibody manufacturer

value: Millipore


title: ChIPseq_Ptf1a_Panc_2

description: Ptf1a Panc #2

tag: developmental stage

value: ICR

value: Lab generated rabbit anti-Ptf1a (AN255/256)

value: Rose SD, Swift GH, Peyton MJ, Hammer RE, MacDonald RJ. 2001. The role of PTF1-P48 in pancreatic acinar gene expression. J Biol Chem 276:44018-44026.

value: Pancreas


title: H3K4me3_Basal

city: Stanford

first: Anne

last: Brunet

state: California

address: 300 Pasteur Drive,

department: Genetics

institute: Stanford University

data_processing:
Reads with low quality scores (sequences that have phred <15 on 85% seq) were filtered using the fastx toolbox (fastq_quality_filter -v -Q 33 -q 15 -p 85)
Reads were aligned to mm9 using bowtie-0.12.7 (bowtie -p 4 -S -q -v 2 -m 3 --best --strata)
For chromatin marks, peaks were generated using Macs (version 2) software with "broad option" and with default settings (macs2 --broad)
For transcription factor, peaks were generated using QuEST 2.1 using the highest stringency peak calling parameters (Fold enrichment > 50, bandwidth=30)
Genome_build: mm9
Supplementary_files_format_and_content: H3K27me3, H3K4me1 and H3K4me1 peak files were generated using MACS 2, Ascl1 and FoxO3 peak bed files were generated using QuEST 2.1

source_name: Neural progenitor cells

growth_protocol: Adult (12-week-old) mouse NPCs were isolated as previously described (Renault et al., Cell Stem Cell 2009). Briefly, whole mouse forebrains were homogenized and incubated for 30 min in HBSS (Invitrogen) with 1 U/ml DispaseII (Roche), 250 U/ml DNaseI (Sigma) and 2.5 U/ml Papain (Worthington) at 37oC. After mechanical dissociation, cells were purified by sequential 25% and 65% Percoll (Amersham) gradients. Cells were cultured in high growth factor signaling conditions: Neurobasal A (Invitrogen) medium supplemented with penicillin/streptomycin/glutamine (Invitrogen), 2% B27 (Invitrogen) and 20 ng/ml each of FGF2 (Peprotec) and EGF (Peprotec).

extract_protocol:
Chromatin was cross-linked with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. Cells were washed and incubated in swelling buffer (10 mM HEPES pH 7.8, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT, 0.5 mM PMSF) for 15 min on ice, followed by nuclei isolation by dounce homogenization. Nuclei were pelleted and resuspended in RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 1% SDS in PBS pH 7.4), and chromatin was sheared with a Vibra-Cell Sonicator VC130 (Sonics) six times for 30 sec at 60% amplitude.
Single end libraries were generated according to the manufacturer’s instructions (Illumina).

treatment_protocol: To induce FOXO3 nuclear accumulation, cells were incubated in low growth factor signaling conditions: Neurobasal A medium supplemented with penicillin/streptomycin/glutamine and 2% B27 for 4 hours, followed by a 1.5 hour incubation with 20 mM LY294002 (LY, Calbiochem-Novabiochem Corp.), a specific PI3K inhibitor, to inhibit residual growth factor signaling.

value: FVB/N

value: Primary adult neural progenitor cell

tag: passages

value: H3K4me3:Active Motif 39159, lot# 0169004


title: H3K4me1_Basal


title: Ascl1_Basal


title: FoxO3_Plus_LY

value: Foxo3-NFL:Brunet Lab (Greer et al., 2007 PMID 17900900)


title: H3K27me3_Basal

value: H3K27me3:Millipore 07-449 lot# DAM1588246


title: Rag1KO DN rep1

first: Eugene

middle: M

last: Oltz

state: MO

address: 660 S Euclid Avenue

department: Pathology and Immunology

institute: Washington Univeristy in St.Louis

description: DNtranscripts.GTF

data_processing:
Raw data was demultiplexed and aligned to the reference genome (mm9) using TopHat. Transcript abundances are then estimated from the alignment files using Cufflinks.
Genome_build: mm9

source_name: Rag1KO Thymocytes

extract_protocol:
RNAfrom thymuses (4 week old mice) was harvested using ambion Ribopure kit. 1 ug of total RNA for the construction of sequencing libraries.
Ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (EpiCentre). mRNA was then fragmented and reverse transcribed to yield double stranded cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-2000 using paired end reads extending 101 bases.

value: thymus

tag: age

value: 3-4 weeks

tag: genotype/variation


title: normal ES cells rep2

description: replicate 2

value: ES cells

value: wild type

value: Embryo


title: Input_Abrupt_scrib

description: Input DNA

source_name: Eye/antennal imaginal discs, scrib mutant [input]

value: Eye/antennal imaginal discs

tag: antibody

value: none (input)

value: FRT82B,scrib1 (Bilder and Perrimon 2000)


title: CHIK_18_rep1

value: Wise County

value: female

value: whole body

value: Chikungunya virus (CHIKV) strain 37797 infection


title: batch1_chrom1_LoVo_EGR1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings:
Genome_build: hg18
Supplementary_files_format_and_content: Peak files generated using MACS 1.4
Genome Build:
batch1_chrom1_LoVo_EGR1_PassedQC_peaks.txt: hg18

source_name: LoVo

value: LoVo

value: colon adenocarcinoma

tag: enriched motif (p<0.001) with dbd sequence similarity > 65%.

tag: qc successful

value: PassedQC


title: Background_Basal

value: FVB/N

value: Primary adult neural progenitor cell

value: No Antibody


title: normal ES cells rep1

description: replicate 1