title: batch4_chrom1_LoVo_HOXA6_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_HOXA6_PassedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab66689


title: batch3_chrom2_LoVo_NR2F6_Mouse_FailedQC

status: Public on Sep 25 2013

type: SRA

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: ChIP-seq experiment that failed automated QC; provided for control purposes

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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_NR2F6_FailedQC_peaks.txt: hg18

molecule: genomic DNA

organism: Homo sapiens

source_name: LoVo

growth_protocol: LoVo (ATCC CCL-229) 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

tag: cell type

value: colon adenocarcinoma

tag: hgn

tag: antibody

value: Santa Cruz Biotechnology, Inc. :sc-166941 X

tag: control sample

tag: qc successful

value: FailedQC

tag: number of peaks, fdr < 5%

tag: fraction of peaks close to tss

tag: lowest e-value for a high complexity de novo motif


title: batch3_chrom2_LoVo_NHLH1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_NHLH1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-66919 X


title: batch3_chrom2_LoVo_NFKB1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_NFKB1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-166588 X


title: batch3_chrom2_LoVo_NEUROD2_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_NEUROD2_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-98674 X


title: batch3_chrom2_LoVo_MYF6_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_MYF6_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-31952 X


title: batch3_chrom2_LoVo_MIXL1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_MIXL1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-98664 X


title: batch3_chrom2_LoVo_MAFG_Rabbit_PassedQC

description: ChIP-seq that passed automated QC; > 300 peaks, located close to TSS and/or enriched in high complexity motif(s)

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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_MAFG_PassedQC_peaks.txt: hg18

value: MAFG

value: Santa Cruz Biotechnology, Inc. :sc-22831 X

value: PassedQC


title: batch3_chrom2_LoVo_MAFB_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_MAFB_FailedQC_peaks.txt: hg18

value: MAFB

value: Santa Cruz Biotechnology, Inc. :sc-74521 X


title: batch3_chrom2_LoVo_NKX6-1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_NKX6-1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-15030 X


title: batch3_chrom2_LoVo_LHX6_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_LHX6_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-98607 X


title: batch3_chrom2_LoVo_LHX4_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_LHX4_FailedQC_peaks.txt: hg18

value: LoVo

value: Santa Cruz Biotechnology, Inc. :sc-22138 X


title: batch4_chrom1_LoVo_ARNT2_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_ARNT2_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Abcam :ab70122


title: batch3_chrom1_LoVo_MLLT7_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_MLLT7_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-34902 X

value: FailedQC


title: batch3_chrom2_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_CTCF_PassedQC_peaks.txt: hg18

value: CTCF

value: Santa Cruz Biotechnology, Inc. :sc-15914 X


title: batch3_chrom1_LoVo_RAD21_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_RAD21_PassedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-98784


title: batch4_chrom1_LoVo_NCOA1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_NCOA1_FailedQC_peaks.txt: hg18

value: Abcam :ab84


title: batch3_chrom1_LoVo_KLF13_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_KLF13_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-66819 X


title: batch4_chrom2_LoVo_ATF7_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_ATF7_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-19765 X


title: batch4_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_GLI2_PassedQC_peaks.txt: hg18

value: Abcam :ab26056

value: PassedQC


title: batch3_chrom2_LoVo_NKX2-8_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_NKX2-8_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-74691 X


title: batch3_chrom2_LoVo_LHX5_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_LHX5_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-19347 X


title: batch3_chrom1_LoVo_IRX5_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_IRX5_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-98397 X


title: batch3_chrom1_LoVo_IRF4_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_IRF4_FailedQC_peaks.txt: hg18

value: LoVo

value: Santa Cruz Biotechnology, Inc. :sc-48338 X


title: batch3_chrom1_LoVo_IRF3_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_IRF3_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Santa Cruz Biotechnology, Inc. :sc-33642 X


title: batch3_chrom1_LoVo_ISL2_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_ISL2_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-66457 X


title: batch3_chrom1_LoVo_ID4_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_ID4_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-13047 X

value: FailedQC


title: batch3_chrom1_LoVo_HOXD9_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HOXD9_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-137134 X


title: batch3_chrom2_LoVo_MTF1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_MTF1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-48775 X


title: batch3_chrom1_LoVo_IKZF5_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_IKZF5_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-131948 X


title: batch3_chrom2_LoVo_MSC_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_MSC_FailedQC_peaks.txt: hg18

value: MSC

value: Santa Cruz Biotechnology, Inc. :sc-9557 X


title: batch3_chrom1_LoVo_HOXD11_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HOXD11_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-68885 X


title: batch3_chrom1_LoVo_HOXD13_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HOXD13_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-66927 X


title: batch3_chrom1_LoVo_HOXB5_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HOXB5_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-82895 X


title: batch3_chrom1_LoVo_HOXB2_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HOXB2_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-28604 X


title: batch3_chrom1_LoVo_HOXB1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HOXB1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-28603 X


title: batch3_chrom1_LoVo_HNF1B_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HNF1B_PassedQC_peaks.txt: hg18

value: LoVo

value: Santa Cruz Biotechnology, Inc. :sc-22840 X

value: PassedQC


title: batch3_chrom1_LoVo_HOXA11_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HOXA11_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Santa Cruz Biotechnology, Inc. :sc-134584 X


title: p53R172H∆g/KrasG12D rep2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

library_source: transcriptomic

data_processing:
Each sample was sequenced twice, on separate lanes, in two different runs for a total of 4 paired-end read sets. All read sets were pooled together before the data processing
Alignment on mm9 transcriptome and splicing events detection performed using Tophat v2.0.4 with parameters -a 12 --solexa-quals --library-type fr-unstranded -r 200 coupled with Bowtie2 v2.0.6
Differential gene-level and exon-level expression between conditions performed using respectively DESeq v1.10.1 and DEXSeq v1.4.0 packages from Bioconductor project for the R statistical program. Significance threshold was set at 1 of log2 Fold Change and 10% of False Discovery Rate (FDR)
Molecule localization and pathway linkage was performed using Ingenuity
Chimera detection performed using ChimeraScan v0.4.5 with parameters -v --filter-unique-frags=1
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited files containing mean expression level, dispersion, FDR and fold change of exons (all_exons or significant_exons). Exon-level counts are also provided for each sample.

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Total RNA was isolated from lung specimens by using an IKA-Ultra-Turrax® T8 homogenizer (IKA-Werke) and TRIzol® reagent (Invitrogen), according to the manufacturer’s instructions. Genomic DNA contaminations were removed from total RNA by using DNA-free kit (Ambion) as per manufacturer's instructions.
TruSeq RNA kit (Illumina) was used for library construction. Briefly, cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments went through end repair process, addition of a single ‘A’ base, and ligation of adapters. The products were then purified and enriched with PCR to create the final cDNA library. Multiplexed DNA libraries were normalized to 10 nM and pooled in equal volumes.

tag: tissue

value: Lung

tag: age

value: post natal 30 weeks

tag: genotype/variation


title: p53R172H∆g/KrasG12D rep1


title: batch3_chrom1_LoVo_IRF8_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_IRF8_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-79536 X

value: FailedQC


title: batch5_chrom1_LoVo_NFE2L1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_NFE2L1_FailedQC_peaks.txt: hg18

value: Abcam :ab90524


title: batch3_chrom1_LoVo_HNF1A_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HNF1A_PassedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-10791 X


title: WT rep1

source_name: wild type

value: wild type


title: WT rep2


title: batch3_chrom1_LoVo_HIC2_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HIC2_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-86487 X


title: batch3_chrom1_LoVo_HIVEP3_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HIVEP3_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-161709 X


title: batch3_chrom1_LoVo_HES5_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HES5_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-25395 X


title: batch3_chrom1_LoVo_HESX1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HESX1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-15122 X


title: batch3_chrom1_LoVo_HOXD4_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HOXD4_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-82928 X


title: batch3_chrom1_LoVo_HES7_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HES7_FailedQC_peaks.txt: hg18

value: LoVo

value: Santa Cruz Biotechnology, Inc. :sc-69501 X


title: batch3_chrom1_LoVo_FOXP2_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_FOXP2_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-66897 X


title: batch3_chrom1_LoVo_FOXO1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_FOXO1_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Santa Cruz Biotechnology, Inc. :sc-67140 X


title: batch3_chrom1_LoVo_FOXK1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_FOXK1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-134550 X


title: 51B Homozygote

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

country: USA

institute: University of Colorado Anschutz Medical Campus

data_processing:
Align reads with Tophat
Calculate abundances with Cufflinks
Genome_build: dm3
Supplementary_files_format_and_content: fpmk

molecule: total RNA

organism: Drosophila melanogaster

source_name: 0-16 hr adult males

growth_protocol: All flies grown at 25C

extract_protocol:
Total RNA isolation with Trizol
Standard illumina library construction

tag: genotype

tag: gender

value: male


title: batch4_chrom1_LoVo_MITF_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_MITF_FailedQC_peaks.txt: hg18

value: MITF

value: Abcam :ab12039


title: 51B heterozygote

value: 51B / TM3, Ser, y+


title: batch3_chrom1_LoVo_FOXF1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_FOXF1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-47591 X

value: FailedQC


title: cwf10-ΔNTE _1_1

city: Nashville

first: Melanie

last: Ohi

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University Medical School

description: CWF10.2.127_1  (Name in expression table) Only this part of the read was used

data_processing:
The raw sequencing reads in BCL format were processed through CASAVA-1.8.2 for FASTQ conversion and demultiplexing. The RTA chastity filter was used and only the PF (passfilter) reads were retained for further analysis.
Paired-end reads of 76 base length (each end) originating from each sample were aligned using Bowtie 0.12.7 (Langmead B, et al., 2009 Genome Biol) to the S. pombe genome sequence (Ensembl S. pombe, Build EF1, version 13) (Kersey PJ, et al., 2010 Nucleic Acids Res) as well as to the corresponding exon-exon junctions database (only the first part of the paired-end reads was considered). Up to 3 base-pair mismatches were allowed. Reads that matched multiple loci were removed from further analysis, and the resultant alignment files were processed to generate ‘pile-ups’ against each chromosome. Bowtie commands --sam -p 8 -q -v 3 -m 1
Searches were performed against the genome sequence combined with a dataset of known exon-exon junctions as defined by Ensembl S. pombe release-13. To ensure that a 76 base read mapped to a splice junction, only the last 70 bases of the first exon and the first 70 bases of the second exon were considered (if the exon exceeded length 70). In this way, reads that overlapped a junction by less than 6 nucleotides were excluded. Reads that matched to more than one junction or elsewhere in the genome were also discarded
Genome_build: Ensembl S. pombe, Build EF1, version 58.1a
Supplementary_files_format_and_content: Expression table and RPKM summary for all samples tab-delimited

organism: Schizosaccharomyces pombe

source_name: S. pombe cells

growth_protocol: RNA was extracted from cwf10+ and cwf10-ΔNTE cells grown at 25°C. Yeast strains were grown in yeast extract (YE) media.

extract_protocol:
Total RNA was prepared from cells by extraction with hot acidic phenol as described previously (Collart and Oliviero 2001 Curr Protoc Mol Biol).
Replicates were grown together and processed separately for all following steps. The Vanderbilt Technologies for Advanced Genomics Core Facility (VANTAGE, Nashville, TN) used the Illumina TruSeq Stranded mRNA Sample Preparation Kit to convert the mRNA in 100 ng of total RNA into a library of template molecules suitable for subsequent cluster generation and sequencing on the Illumina HiSeq 2500.  The input total RNA was quality-checked by running an aliquot on the Agilent Bioanalyzer to confirm integrity. The Qubit RNA fluorometry assay was used to measure concentration.  The input to library prep was 50 μl of 100 ng of DNase-treated total RNA (2 ng/μl). The total RNA underwent enrichment of the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads.  Following purification, the eluted poly(A) RNA was cleaved into small fragments of 120-210 bp using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using SuperScript II reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The cDNA fragments were then put through an end repair process, the addition of a single ‘A’ base, and ligation to the Illumina multiplexing adapters. The products were then purified and enriched with PCR to create the final cDNA sequencing library. The cDNA library underwent quality control by running on the Agilent Bioanalyzer HS DNA assay to confirm the final library size and on the Agilent Mx3005P qPCR machine using the KAPA Illumina library quantification kit to determine concentration. A 2 nM stock was created and samples pooled by molarity for multiplexing.  From the pool 12 pM was loaded into each well for the flow cell on the Illumina cBot for cluster generation. The flow cell was then loaded onto the Illumina HiSeq 2500 utilizing v3 chemistry and HTA 1.8. The raw sequencing reads in BCL format were processed through CASAVA-1.8.2 for FASTQ conversion and demultiplexing. The RTA chastity filter was used and only the PF (passfilter) reads were retained for further analysis.

tag: strain

value: h- cwf10 2-127-delta ade6-M21X leu1-32 ura4-D18

tag: variation


title: cwf10-ΔNTE _2_1

description: CWF10.2.127_2  (Name in expression table) Only this part of the read was used


title: V966M homozygote


title: cwf10-ΔNTE _2_2

description: CWF10.2.127_2  (this  part of the paired-end read was not used  in this study)


title: V966M heterozygote

value: V966M / TM3,twi-GFP,Sb,Ser


title: Wild-type_2_2

description: wtCWF10._2  (this  part of the paired-end read was not used  in this study)


title: Ago2 IP Rep2

data_processing:
Alignment using bowtie
Sam to wig using Bedtools
Genome_build: dm3
Supplementary_files_format_and_content: wig

source_name: S2 cells

growth_protocol: Dividing S2 cells

extract_protocol: Standard Illumina library construction

treatment_protocol: 2% formaldehyde for 1 min

tag: chip antibody

value: Mouse monoclonal to Ago2, gift from M. Siomi


title: batch3_chrom1_LoVo_FOS_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_FOS_FailedQC_peaks.txt: hg18

tag: cell line

value: FOSB

value: Santa Cruz Biotechnology, Inc. :sc-48869 X


title: Ago2 IP Rep 1


title: batch3_chrom1_LoVo_HEY1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_HEY1_FailedQC_peaks.txt: hg18

value: LoVo

tag: cell type

value: Santa Cruz Biotechnology, Inc. :sc-28746 X


title: Wild-type_1_2

description: wtCWF10._1 (this  part of the paired-end read was not used  in this study)


title: Wild-type_2_1

description: wtCWF10._2  (Name in expression table) Only this part of the read was used


title: batch3_chrom1_LoVo_FOXQ1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_FOXQ1_FailedQC_peaks.txt: hg18

tag: hgn

value: Santa Cruz Biotechnology, Inc. :sc-166266 X


title: Input


title: batch3_chrom1_LoVo_FOSB_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_FOSB_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: FOS

tag: antibody

value: Santa Cruz Biotechnology, Inc. :sc-166940 X


title: batch3_chrom1_LoVo_FERD3L_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_FERD3L_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-132748 X

tag: control sample


title: Bioreactor grown on methane 20%CH4: 20%O2: 60N2, biological replicate 2

city: Seattle

first: David

middle: A. C.

last: Beck

state: WA

address: Benjamin Hall IRB, Rm 440, UW Box 355014

department: ChemE & eScience Institute

institute: University of Washington

data_processing:
Reads were aligned to 20Z scaffold using BWA 0.6.1 with default parameters.
Samtools 0.1.17 was used to post-process the alignments from SAM to BAM format.
An in house tool 'bam2orf' was linked against the Samtools 0.1.17 libraries.  The tool processes the pileup to count the reads mapped at each base in a gene.  This number is summed across all bases in a given gene and divided by the read length.  This number is used as the input for the RPKM calculation.
Genome_build: The genome was downloaded from MaGE on 09-Dec-2011 (https://www.genoscope.cns.fr/agc/microscope/mage/ ).  The scaffold designation is MEALZv4.
Supplementary_files_format_and_content: Processed data files contain tab delimited tables with the locus tag and RPKM for all protein coding sequences.

organism: Methylotuvimicrobium alcaliphilum 20Z

growth_protocol: 50 ml culture in 250 ml vials, with shaking at 200rpm; Prior to incubation vials were flushed for 15 min with a gas mixture containing  20% CH4: 5% O2: 75% N2; Harvested at mid exponential phase

extract_protocol:
Cells were collected by centrifugation and lysed with bead beating. RNeasy Mini Kit was used for RNA isolation including the optional DNAse digestion step.
Libraries were prepared according to Illumina's instructions for 36 bp reads.

tag: culture type

value: Bioreactor culture


title: batch3_chrom1_LoVo_EVX1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_EVX1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-65095 X

tag: qc successful

tag: number of peaks, fdr < 5%


title: Bioreactor grown on methane 20%CH4:5%O2:75%N2, biological replicate 2


title: Bioreactor grown on methane 20%CH4:5%O2:75%N2, biological replicate 1


title: batch3_chrom1_LoVo_CREB3L1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_CREB3L1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-69367 X

tag: fraction of peaks close to tss

tag: lowest e-value for a high complexity de novo motif


title: Batch growth on methane, biological replicate 4

source_name: Batch growth on methane

value: Batch culture


title: batch3_chrom1_LoVo_CAMTA1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_CAMTA1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-74355 X

value: FailedQC


title: cwf10-ΔNTE _1_2

description: CWF10.2.127_1  (this  part of the paired-end read was not used  in this study)

value: h- cwf10 2-127-delta ade6-M21X leu1-32 ura4-D18


title: batch3_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_CTCF_PassedQC_peaks.txt: hg18

value: CTCF

value: Santa Cruz Biotechnology, Inc. :sc-15914 X

value: PassedQC


title: Wild-type_1_1

description: wtCWF10._1 (Name in expression table) Only this part of the read was used


title: batch3_chrom1_LoVo_FOXA2_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_FOXA2_PassedQC_peaks.txt: hg18

value: LoVo

value: Santa Cruz Biotechnology, Inc. :sc-271104 X


title: Batch growth on methane, biological replicate 3


title: batch3_chrom1_LoVo_BATF3_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_BATF3_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-162247 X


title: batch3_chrom1_LoVo_BHLHB3_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_BHLHB3_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Santa Cruz Biotechnology, Inc. :sc-32854 X


title: Batch growth on methane, biological replicate 1


title: batch3_chrom1_LoVo_BARX1_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_BARX1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-99053 X


title: Batch growth on methane, biological replicate 2


title: batch3_chrom1_LoVo_ARNTL_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_ARNTL_FailedQC_peaks.txt: hg18

value: ARNTL

value: Santa Cruz Biotechnology, Inc. :sc-48790 X


title: batch3_chrom1_LoVo_ATF7_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: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom1_LoVo_ATF7_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-19765 X


title: Radiation-induced_Sample

status: Public on Sep 24 2013

city: Hangzhou

first: Jiangfeng

last: Guo

state: Zhejiang

address: Xiasha No.2 Road

department: College of Life Science

country: China

institute: Zhengjiang Sci-Tech University

description: ATCC® BAA-149TM

data_processing:
Illumina Casava1.7 software used for basecalling.
The pre-process was used for the filtering of the adapter and the low-quality fragments. The rRNA was filtered next and most mRNA was left. The genome mapping made the most mRNA mapped to K. radiotolerans genome (NC_009664, NCBI) using TOPHAT (v0.1.0Beta, parameter: -m 2 -r 200)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks2.0.2 (-b -u -G)
Genome_build: ASM1730v1
Supplementary_files_format_and_content: table file (.xls) include RPKM values for each gene

organism: Kineococcus radiotolerans

source_name: Kineococcus radiotolerans

growth_protocol: The strain was cultured in PTYG nutrient solution (0.5% peptone, 0.5% tryptone, 0.5% yeast extract, 0.5% glucose, pH 5.3) at 30°C.

extract_protocol:
The total RNA was isolated from the strain using Trizol reagent according to manufacturer’s instructions (Invitrogen). The MICROBExpress Bacterial mRNA Enrichment Kit (Ambion, AM1905) was used for the rRNA filtering.
The cDNA library was constructed as the Illumina Hiseq2000 sequencing instructions.
The sequencing by synthesis was used in this experiment with double-direction pair-end sequencing by 2×100 nt.

treatment_protocol: The strain was treated with a 60Co radiation source at a dosage of 0.225 kGy/h for 20 h and then incubated for 3 h.

value: radiation induced


title: Bioreactor grown on methane 20%CH4: 20%O2: 60N2, biological replicate 1

value: Bioreactor culture


title: microRNA sequences in uninjured tissue

first: Jamie

middle: Ian

last: Morrison

address: Svante Arrheniusväg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

institute: Stockholm University

description: Small RNA

data_processing:
Base conversion was done using Illuminas OLB v1.9.
Reads from each of the pooled libraries were then separated based on their tagged-barcode sequence and aligned against miRNA data from miRBase release version 17.0 using Bowtie.
Rates per million (RPM) for each aligned microRNA was performed based on sequencing read counts.
Genome_build: miRBase version 17.0
Supplementary_files_format_and_content: Tab-delimited text file includes RPM values for each aligned microRNA.

organism: Notophthalmus viridescens

source_name: Uninjured tissue

extract_protocol:
Total RNA was isolated at indicated time-points (Uninj, 7dpi and 21dpi) and pooled from duplicate uninjured and regenerating hearts, using the mirVana™ miRNA Isolation Kit (Invitrogen).
The small RNA library construction was performed by ligating 5' and 3' adaptors to small RNAs. The small RNAs underwent RT-PCR, using the 3' adaptor sequence as the RT-primer, and small RNAs were enriched by PCR using primers designed against the 5' and 3' adaptors. Highly enriched adaptor ligated small RNAs purified from uninjured, 7dpi and 21dpi hearts were barcoded with 5’ adaptors tagged with ccc, ggg and aaa respectively.

treatment_protocol: Newts were anesthetized by placing them in an aqueous solution of 0.1% ethyl 3-aminobenzoate methanesulfonate salt (Sigma-Aldrich) for 15 min. Newts were positioned supine and an incision was made into the ventral body wall exposing the pericardium. The thoracic cavity was exposed fully with a single anchoring stitch, using a reverse cutting (3/8 circle 8 mm) needle with monofilament 8.0 non-absorbable suture, placed into both sides of the incised pericardium. Blunted 5.0 forceps were placed under the exposed aorta, and lifted, in order to expose the heart exteriorly. Starting just below where the atria enter the ventricle, a 27G needle (0.41 mm) was then used to make a diagonal left to right puncture of the ventricle wall. Using iridectomy scissors, the portion of the tissue pierced by the needle was removed from the ventricle. Haemorrhaging was stemmed via rapid clot formation, brought about by the application of local pressure with cotton swabs. The damaged hearts were manoeuvred back into the thoracic cavity and the pericardium and body wall were closed with interrupted stitches using sutures previously mentioned. Newts were left to recover for 24 hours in an aqueous solution of 0.5% sulfamerazine (Sigma-Aldrich) on ice, before being placed back into a 15-20°C water environment.

tag: developmental stage

value: adult

tag: tissue

value: heart

tag: condition

value: uninjured


title: Wild-type_Sample

description: ATCC® BAA-149TM

tag: genotype

value: wild type


title: microRNA sequences in 21-dpi regenerating tissue

description: Small RNA

source_name: Regenerating tissue, 21 dpi

value: 21 dpi


title: microRNA sequences in 7-dpi regenerating tissue

description: Small RNA

source_name: Regenerating tissue, 7 dpi

value: 7 dpi


title: Input for HSP70K71E

city: Bethesda

first: Jung

middle: S

last: Byun

state: MD

address: 37 convent drive, Bldg 37,  Rm 1042

institute: NCI/NIH

description:
T1_input
ChIP'd DNA

data_processing:
PhiX was used for sequencing control and illumina TruSeq V3 was used for sequencing chemistry.
The basic calling is analyzed by illumina RTA 1.8. 70.0 and allignment was used by illumina Casava 1.8.2
An unthresholded hotspot is determined as a contiguous union of 250 bp window whose z-scores are greater than 2.
Once a hotspot is called, the z-scoreof the hotspot is given by the maximum z-score of the constituent tags.
More detailed steps for ChIP-Seq data analysis were described in the manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files

growth_protocol: HEK293 cells and the cells expressing  HSP70K71E were proliferated with RPMI1640, 10% FBS, 25 mM HEPES, 1X PS

extract_protocol:
ChIP'd DNA was extracted accordingly in previous publication (Byun et al, ELL faciliates RNA polymerase II pause site entry and release. Nature Communications 3, 633 2012.
ChIP-Seq samples were sequenced on GAIIx with 36bp length using Illumina TruSeq v3 Chemistry, Allthe samples have good quality with over 93% of bases having Q30 or above. Library complexity is measured by uniquely aligned reads using picard's markduplicate utility.

value: Human Kidney Embryonic Cell line HEK293

tag: genotype/variation

value: none (input)


title: control1

city: Avignon

first: Cynthia

last: McDonnell

address: Site Agroparc, Domaine Saint-Paul

department: UR 406 Abeilles et Environnement

country: France

institute: INRA Avignon

description: DGE; Sample 5

data_processing:
Image analysis and base calling were performed using the Illumina pipeline.
Extraction of 16bp tags (reads were trimmed for adaptor sequence) and tag counting were performed using home-made perl script.
Supplementary_files_format_and_content: txt file containing reads and counts

organism: Apis mellifera

source_name: honey bee_brain_control

growth_protocol: One-day-old bees were held for 10 days in cages and in the dark at 28°C and 70% relative humidity. They were fed ad libitum with candy (30% honey, 70% powdered sugar) and water. Caged bees were also exposed to a Beeboost® (Pherotech, Delta, BC, Canada) releasing one queen-equivalent of queen mandibular pheromone per day.

extract_protocol:
Heads of the bees were separated from the body and the cuticle scratched with surgical tweezers before storing in RNAlater®-ICE solution (Ambion, Inc) at -20°C for 16-18 hours, according to manufacturer’s instructions. Brains were dissected on ice under a dissection microscope to remove all traces of the optic lobe and then re-stored at -80°C. Honey bee brains were pooled by 3 per tube, homogenized in 500 µL of TRIzol Reagent (Life Technologies Corp.), phase-separated with chloroform/TRIzol and the aqueous phase removed for precipitation with 70% ethanol. The resulting aqueous-ethanol solution was loaded onto a RNeasy mini spin column ofthe Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA). RNA isolation was performed according to the manufacturer’s instructions, starting with washing with Buffer RW1.
Sample preparation was performed using the DGE DpnII Sample preparation kit from Illumina (ref.FC-102-1007) according to the manufacturer's instruction. Briefly, 2µg of total RNA are incubated with magnetic oligo(dT) beads. Non poly-adenylated RNA are removed by several washes. Reverse transcription is performed on captured RNAs followed by the synthesis of the second strand of cDNA. Captured double stranded DNA is digested using DpnII. A ligation is performed with Illumina's GEX DpnII adapter 1 followed by a digestion using MmeI resulting in the release of tags. Those tags are ligated using Illumina's GEX Adapter 2 , amplified by PCR (15 cycles) and purified  on acrylamide gel. Libraries are validated using a DNA1000 BioAnalyzer chip, denatured using 0,1N NaOH, diluted to 8pM and sequenced following the manufacturer's instructions.

treatment_protocol: Before emergence, bees were collected and the presence or absence of varroa in the cells was checked. For the Nosema treatment, bees that were not parasitized by varroa at the pupae stage were then infected by feeding a sugar solution containing Nosema ceranae spores (2 µL at 50,000 spores/µl).

tag: parasite

tag: age

value: brain


title: control2

description: DGE; Sample 6


title: Input for control

description:
T2_input
ChIP'd DNA

tag: cell line

tag: chip antibody


title: CBP ChIP-Seq for control_n2

description:
T2CBP
ChIP'd DNA

value: anti-CBP [CBP/anti-KAT3A-chip grade, cat no. ab2832 ABCAM]


title: CBP ChIP-Seq for control_n1

description:
T2CBP
ChIP'd DNA


title: CBP ChIP-Seq for HSP70K71E_n2

description:
T1CBP
ChIP'd DNA


title: CBP ChIP-Seq for HSP70K71E_n1

description:
T1CBP
ChIP'd DNA


title: p300 ChIP-Seq for control_n2

description:
T2p300
ChIP'd DNA

value: anti-p300 [affinity purified p300 from our lab (ref, Byun et al, Nature Comm. 3, 633, 2012)]


title: Varroa2

description: DGE; Sample 2

source_name: honey bee_brain_Varroa

value: Varroa destructor


title: Nosema2

description: DGE; Sample 4

source_name: honey bee_brain_Nosema

value: Nosema ceranae


title: Nosema1

description: DGE; Sample 3


title: p300 ChIP-Seq for control_n1

description:
T2p300
ChIP'd DNA


title: p300 ChIP-Seq for HSP70K71E_n1

description:
T1p300
ChIP'd DNA


title: p300 ChIP-Seq for HSP70K71E_n2

description:
T1p300
ChIP'd DNA


title: Euploid_UMC6

city: Beijing

first: Ruosi

last: Zhang

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

data_processing:
Sequence data were generated using SOLiD3 system (Applied Biosystems) following the manufacturer’s instructions.
RNA-Seq reads were mapped onto the human reference genome (NCBI37/hg19) with Corona_lite_v4.2.2 software (Applied Biosystems), setting the parameters for full-length read mapping (50, 45, 40, 35 bp) with 5, 4, 4, and 3 mismatches. Only reads that uniquely mapped to the genome and reads for genes corresponding to mRNA were chosen for subsequent analysis.
Reads density for each gene (shown as RPKM value) was calculated by the number of uniquely mapped.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Gene ID, RPKM values and chromosome coordinates for each Sample

source_name: umbilical cord matrix cells induced pluripotent stem cell

extract_protocol:
Total RNA of each line was extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Poly(A)+ mRNA was isolated from total RNA using Oligotex (QIAGEN). RNA was fragmented with RNase III, preparing for constructing transcriptome libraries of each iPSC cell line.
Applied Biosystems SOLiD Whole Transcriptome Analysis Kit ( http://solid.appliedbiosystems.com) were applied to perform reversed transcription from 140–200 bp isolated RNA fragments into Single-strand cDNA.

tag: cell type

value: induced pluripotent stem cell

value: Euploid


title: Euploid_UMC1


title: Aneuploid_trisomy22

source_name: Trisomy 22 induced pluripotent stem cell

value: Partial Trisomy 11:22


title: Aneuploid_trisomy13

source_name: Trisomy 13 induced pluripotent stem cell

value: Trisomy 13


title: Aneuploid_XO

source_name: Monosomy X induced pluripotent stem cell

value: Monosomy X


title: Aneuploid_trisomy8

source_name: Trisomy 8 induced pluripotent stem cell

value: Trisomy 8


title: Th1_input DNA Th1

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

description: input DNA

data_processing:
Illumina Casava software used for basecalling and making Fastq files.
Short-read sequences were aligned to the mouse genome sequences (mm9 from University of California, Santa Cruz Genome Browser; http://genome.ucsc.edu/) using the Eland program. Sequences with two or more mismatches per sequence were excluded from the analysis.
Each aligned read sequence was extended to 120 bp in order to efficiently detect duplicate reads aligned to identical locations. These 120 bp tags were used for further analysis (Bed files)
Genome_build: mm9
Supplementary_files_format_and_content: Bed files

source_name: Naïve CD4 T cells from spleen cultured for 5 days in Th1 polarizing conditions

growth_protocol: Naïve (CD44lowCD62Lhigh) CD4+ T cells were purified from spleens of mice. For Th1, Th2 cell cultures, 7.5 × 10^5 naïve CD4 T cells were plated onto 48 well tissue culture plates (Costar) pre-coated with 10 μg/ml agonistic anti-TCRβ antibody (clone H57-597) with 1 μg/ml agonistic anti-CD28 antibody (clone 37.51, Biolegend) and 15 ng/ml IL-2. In addition, Th1 cultures contained 10 ng/ml recombinant mouse IL-12 (Wako) and anti-IL-4 antibody (clone 11B11), Th2 cultures contained 100 ng/ml recombinant mouse IL-4 (Peprotech) and anti-IFN-γ antibody (clone R4-6A2). After two days, the cells were recultured for an additional three days in the same culture medium with cytokines but without anti-TCRβ or anti-CD28 antibody stimulation.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
IP and input sample libraries were prepared using ChIP-Seq Sample Prep kit (Illumina). Adaptor-ligated DNA fragments were size fractionated by 12% acrylamide gel, and the 170- to 250-bp fraction was recovered. DNA thus obtained was amplified by 18 cycles of PCR. One nanogram of DNA was used for the sequencing reaction of the Illumina GAIIx, according to the manufacturer’s instructions. A total of 250,000–370,000 clusters was generated per tile, and 36 cycles of the sequencing reactions were performed.

tag: strain

value: spleen

value: Naive (CD44lowCD62Lhigh) CD4+ T cells

tag: cell subtype

value: Th1 cells


title: Varroa1

description: DGE; Sample 1


title: Th2_Ezh2_ChIPSeq

description: Chromatin IP against Ezh2

source_name: Naïve CD4 T cells from spleen cultured for 5 days in Th2 polarizing conditions

value: Th2 cells

value: anti-Ezh2 polyclonal

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat. #

tag: chip antibody lot #


title: Th1_control_Ab_ChIPSeq

description: Chromatin IP with control_Ab

value: Rabbit IgG polyclonal

value: Southern Biotech


title: Th1_Ezh2_ChIPSeq

description: Chromatin IP against Ezh2


title: ttDN_04_r2

status: Public on Sep 23 2013

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description:
RNA-Seq
Pooled-sicer-islands-from-total-RNASeq.txt
Pooled-cufflinks-transcripts-from-non-strand-sp-RNASeq.gtf

data_processing:
Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
Sequence reads were mapped to the mouse (mm9) genomes with bowtie (0.12.7). Uniquely mapped reads were kept for each lane. BEDGraph files were generated from bowtie outputs by using in-house scripts.
RNA-Seq tag enriched islands were determined by running SICER 1.03 (PMID: 19505939) for each individual sample (window size = 100bps, gap size = 200bps, E-value =100). Only islands from duplicates were kept. The islands are then merged together indepedently for samples from polyA RNA (non-strand specific) and from total RNA (non-strand specific). RNA-Seq islands within the same intergenic regions were clustered to form lincRNA clusters based on the similarity in expression profiles across all RNA-Seq libraries. Briefly, an island i joins a cluster C if 1) the Pearson Coefficient of gene expressions between i and at least one member from cluster C is greater than 0.8 and 2) i is the nearest island to cluster C; the 5'-most island is chosen as a seed to initiate the clustering and i constitutes a seed of a new cluster if it does not satisfy the two conditions. The nomenclature system for each lincRNA cluster follows LincR-RefGen-5'(or 3')S(or AS)-Dis, where RefGen is the neareast protein coding gene with a similar expression pattern to the lincRNA, 5'(or 3') defines the relative direction to the lincRNA, and Dis referres to the distance to the lincRNA.
Transcripts assembly was done for individual sample by using tophat v2.0.6 (--segment-length 18 --no-coverage-search and --keep-tmp; PMID 23618408) and cufflinks v2.1.1 (default paramters; PMID: 23222703) against mm9 genome sequence. Transcripts from all non-strand-specific-RNA-Seq samples were then merged by using cuffmerge v1.0.0 (default paramters). Spliced transcripts containing at least two exons were extracted and compiled in a seperate GTF file for downloading.
genome build: mm9
processed data files format and content: BEDGraph: plan text file. The first line include a track type decription, which is needed for this file to be upload to UCSC genome browser. The first three columns are chrom, starting and end position of a 100-bp window. The forth columns shows the number of tags within the window, normalized by total tag number (million) and by window size.
processed data files format and content: SICER: plan txt file from RNA-Seq tag enriched island from SICER 1.0.3. Columns from left to right denote chrom, starting position, ending position, and island score.
processed data files format and content: SICER-POOL: merged sicer island prediction from multiple samples. Columns from left to right denote chrom, starting position, ending position.
processed data files format and content: GTF: transcripts output from Cufflinks v2.1.1

source_name: DN4 cells (CD4-CD8-CD3-CD44-CD25-)

growth_protocol: For most of the experiments, CD4+ T cells were co-cultured with APCs at a 1:10 ratio in the presence of anti-CD3 (1μg/ml) and anti-CD28 (3μg/ml) for 3 days along with different combinations of antibodies and cytokines. For Th1 conditions: IL-12 (10ng/ml), IL-2 (50U/ml) and anti-IL-4 (10μg/ml); for Th2 conditions: IL-4 (5000U/ml), IL-2 (100U/ml), anti-IFNγ (10μg/ml) and anti-IL-12 (10μg/ml); for Th17 conditions: TGFβ1 (5ng/ml), IL-6 (10ng/ml), IL-1β (10ng/ml), IL-21 (10ng), anti-IL-4 (10μg/ml) anti-IFNγ (10μg/ml) and anti-IL-12 (10μg/ml); and for iTreg conditions: IL-2 (100U/ml), TGFβ1 (5ng/ml), anti-IL-4 (10μg/ml) anti-IFNγ (10μg/ml) and anti-IL-12 (10μg/ml) were added.  For short-term culture (≤72 hr) in the time-course experiments, naïve CD4+ T cells were cultured with anti-CD3/anti-CD28 beads (Invitrogen) along with the cocktail of cytokines and antibodies for the specific polarization condition. For STAT4 and STAT6 KO: CD4+ T cells were co-cultured with irradiated (3000 Rads) T cell-depleted splenocytes in the presence of 1 ug/ml of anti-CD3 (145-2C11) and 1ug/ml of anti-CD28 (37.51) for 4 days with various combinations of antibodies and cytokines: for Th1 conditions, 10 ng/ml of IL-12 and 10 ug/ml of anti-IL-4 (11B11); for Th2 conditions, 10ng/ml of IL-4, 10 ng/ml of IL-2, 10 ug/ml anti-IL-12 (C17.8) and anti-IFNg (XMG1.2).

extract_protocol:
For sequencing total RNA: the total RNAs were purified using Qiagen's miRNeasy micro kit (Qiagen cat# 217084) plus Qiagen’s DNase set (Qiagen cat# 79254) for on-column DNase digestion option. For sequencing PolyA RNA: PolyA-tailed RNAs were purified from pure total RNA using Dynabeads® mRNA DIRECT™ Kit (invitrogen cat# 610.12). Both were performed according to the kits' user manuals. For STAT4 and STAT6 KO: total RNAs were isolated using mirVana (Applied Biosystems) isolation kit. RNA concentration was determined using the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen) and RNA integrity was determined using Eukaryote Total RNA Nano Series II ChIP on a 2100 Bioanalyzer (Agilent). Three independent biological replicates were pooled for RNA-seq.
For total RNA-seq library prep: 10ng of purified total RNA was used for cDNA amplification using the Ovation RNA-Seq System V2 (NuGEN Technologies, Inc. cat# 7102-08). then 200ng of ds cDNA was sonicated in Diagenode's Bioruptor (level M, for a  total of 30 minutes of 20 seconds ON and 20 seconds OFF) to a size range of 100-400bp. For mRNA-seq library prep:  a random primer (invitrogen cat# 48190-011) was used to prime the purified PolyA tailed-RNA and the cDNA synthesis was performed using SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen cat# 11917-010)  according to the user’s manual. The ds cDNA was subject to sonication in Diagenode's Bioruptor (level M, total of 30 minutes of 20 seconds ON and 20 seconds OFF). Indexed library was prepared using Illumina’s multiplexing sample prep oligonucleotide kit (Ref# 1005709) with Epicentre's End-It DNA End-repair Kit (Epcentre, cat# ER81050) according to the user's manual and Illumina's multiplexing sample preparation guide. For STAT4 and STAT6 KO: RNA-seq libraries were prepared from 4 ug of total RNA using the TruSeq RNA sample prep kit following manufacturer’s protocol (Illumina). Briefly, oligo-dT purified mRNA was fragmented and subjected to first and second strand cDNA synthesis. cDNA fragments were blunt-ended, ligated to Illumina adaptors, and PCR amplified to enrich for the fragments ligated to adaptors.

value: thymus

tag: development stage


title: ttTh2_2w_cyto_r1

description:
Total RNA from cytosol
Strand specific RNA-Seq

source_name: T helper 2 cells (Th2)

value: lymph nodes

value: 2 weeks under Th2 condition (in vitro)


title: ttTh2_2w_nucl_r1

description:
Total RNA from nuclei
Strand specific RNA-Seq


title: ttSP_nTreg_r2

source_name: tTreg (thymic-derived regulatory T cells)

value: tTreg


title: ttDN_03_r2

source_name: DN3 cells (CD4-CD8-CD3-CD44-CD25+)


title: ttTh2_2w_cyto_r2


title: ttTh2_2w_nucl_r2


title: ttDN_01_r2

source_name: DN1 cells (CD4-CD8-CD3-CD44+CD25-)


title: ttSP_CD4_r2

source_name: CD4 -SP cells (CD3+CD4+CD8-)

value: CD4 -SP


title: ttDP_02_r2

source_name: DP2 cells (CD4+CD8intermediateCD69+)


title: ttDP_01_r2

source_name: DP1 cells (CD4+CD8+CD3low)


title: ttDN_04_r1


title: ttSP_CD8_r2

source_name: CD8 -SP cells (CD3+CD4-CD8+)

value: CD8 -SP


title: ttDN_03_r1


title: ttDP_02_r1


title: ttSP_CD8_r1


title: ttDN_02_r2

source_name: DN2 cells (CD4-CD8-CD3-CD44+CD25+)


title: ttSP_CD4_r1


title: Th2_input DNA Th2

description: input DNA


title: ttDN_01_r1


title: ttSP_nTreg_r1


title: ttDN_02_r1


title: ttTh2_gata3KO_r1

value: C57BL/6 Gata3fl/fl, infected with  hCre-GFP-RV, GFP+


title: ttTh2_2w_linc-ctrl

value: 2 weeks under Th2 condition, control for lincR-Ccr2-5AS KD


title: Th2_control_Ab_ChIPSeq

description: Chromatin IP with control_Ab


title: ttITR_72h_r2

source_name: Induced regulatory T cells (iTreg)

value: 72 hrs under iTreg condition (in vitro)


title: ttTh2_2w_linc-sh40

value: 2 weeks under Th2 condition, lincR-Ccr2-5AS KD by sh40


title: ttTh17_72h_r2

source_name: T helper 17 cells (Th17)

value: 72 hrs under Th17 condition (in vitro)


title: ttTh2_72h_r2

value: 72 hrs under Th2 condition (in vitro)


title: ttITR_72h_r1


title: ttTh1_72h_r2

source_name: T helper 1 cells (Th1)

value: 72 hrs under Th1 condition (in vitro)


title: ttTh17_72h_r1


title: ttTh2_72h_r1


title: ttTh1_72h_r1


title: ttDP_01_r1


title: ttTh17_2w_r2

value: 2 weeks under Th17 condition (in vitro)


title: ttITR_2w_r1

value: 2 weeks under iTreg condition (in vitro)


title: ttITR_2w_r2


title: ttTh17_2w_r1


title: ttTh2_2w_r2


title: ttTh1_2w_r2

value: 2 weeks under Th1 condition (in vitro)


title: ttTh2_gata3WT_r1

value: C57BL/6 Gata3fl/fl, infected with  hCre-GFP-RV, GFP-


title: ttTh2_24h_r1

value: 24 hrs under Th2 condition (in vitro)


title: ttNIV_0h_r1

source_name: Naïve CD4+ T cells

value: lymph nodes

value: Naive CD4+ T cells


title: ttTh17_24h_r1

value: 24 hrs under Th17 condition (in vitro)


title: ttTh2_2w_r1

value: 2 weeks under Th2 condition (in vitro)


title: ttNIV_0h_r2


title: ttTh1_2w_r1


title: ttTh2_2w_linc-sh36

value: 2 weeks under Th2 condition, lincR-Ccr2-5AS KD by sh36


title: paTh17_2w_r2

description:
RNA-Seq
Pooled-sicer-islands-from-polyA-RNASeq.txt
Pooled-cufflinks-transcripts-from-non-strand-sp-RNASeq.gtf


title: ttTh1_24h_r1

value: 24 hrs under Th1 condition (in vitro)


title: paITR_1w_r2

value: 1 week under iTreg condition (in vitro)


title: paITR_1w_r1


title: paTh17_1w_r2

value: 1 week under Th17 condition (in vitro)


title: paTh17_2w_r1


title: ttTh1_tbetKO_r2

value: C57BL/6 T-bet deficient carrying T-bet-ZsGreen reporter


title: ttTh1_tbetWT_r2

value: C57BL/6 wild type carrying T-bet-ZsGreen reporter


title: ttTh1_tbetKO_r1


title: ttTh1_tbetWT_r1


title: paTh17_1w_r1


title: paTh2_2w_r2


title: paITR_72h_r2

value: 72 hrs under iTreg condition (in vitro)


title: paTh2_72h_r2

value: 72 hrs under Th2 condition (in vitro)


title: paITR_2w_r2


title: H2AZ-AP3 variant Day3

city: Cambridge

first: Laurie

last: Boyer

state: MA

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Sequence reads were mapped to mm9 whole genome using Tophat 1.14/ Bowtie 0.12.7 with the following parameters --min-anchor-length 6 --splice-mismatches 0 --min-intron-length 10 --max-intron-length 1000000 --min-isoform-fraction 0.0 --max-multihits 50 --no-novel-juncs --library-type fr-unstranded
Gene expression was calculated as Fragments per Kilobase of modeled exon per Million mapped reads (FPKM) using Cufflinks 1.3.0, and transcription start site (TSS)-specific gene expression were obtained from Cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file that includes RPKM values for each Sample, and log2(fold-changes) among samples at each time-point (with an added pseudo-count of 0.01 to each RPKM value).

source_name: ES cells

growth_protocol: V6.5 (129SvJae and C57BL/6; male) ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates.  Briefly, cells were grown in Knockout DMEM supplemented with 10% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006). ESCs used for the majority experiments, including ChIP-Seq, RNA-Seq and RT-qPCR, were plated without irradiated MEFs for the final passage.

extract_protocol: RNA was extracted using TRIzol. The purified RNA was the subjected to oligo (dT) selection, fragmentation and first and double strand synthesis with the Illumina Tru-Seq kit using manufacturer’s instructions. DNA fragments above 30bp was purified using SPRI-TE beads according to manufacturer’s instructions. The purified DNA was end repaired and single A bases were added for adaptor ligations. The adaptor-ligated DNA was then subjected to double SPRI-TE purification to select for ~200bp DNA fragments. These fragments were enriched and barcoded by PCR for multiplexing. A final SPRI-TE purification was performed to clean up the barcoded RNA-Seq libraries.

treatment_protocol: H2AZ-YFP, Acidic Patch (AP3)-YFP and H2A-YFP constructs were generated from the pAd-cDNA (Addgene). The AP3 H2AZ mutant is a triple point mutant of H2AZ in essential acidic patch region generated by replacing the H2AZ residues (G92N, D97N and S98K) in this region with the corresponding H2A residues, with the GFP in this vector being replaced by YFP, such that it is in frame C-terminal to the cDNA. EcoRI and XbaI digestion was performed to place H2AZ, AP3 and H2A cDNA in frame. This vector contains a CMV-promoter driven by an rtTA drug inducible system. The resulting lentiviral constructs were transfected into 293 cells using the protocol outlined by the RNAi consortium (BROAD Institute, http://www.broadinstitute.org/rnai/public/). The viral supernatant generated 48hrs after transfection was used to infect KH2 ESCs (Beard, 2006) to generate wildtype and mutant H2AZ transgenic ESC lines. The YFP transgenic ESCs were induced with 1µg/ml of doxycycline and FACS sorted for YFP positive cells. In order to study the selective impact of the H2AZ mutants, lentiviral constructs expressing short hairpins specifically directed at the 3’ UTR of endogenous H2AZ were introduced into the wild-type and mutant H2AZ transgenic KH2 ESC lines using RNA. Sequences of the different H2AZ 3’UTR-directed hairpin oligos are as follows: sh#2 5’- AACAGCTGTCCAGTGTTGGTG-3’; sh#5 5’- AATTAGCCTTCCAACCAACCA-3’. Hairpin oligos were annealed and cloned into pLKO.1 vector (Sigma) as detailed by the RNAi consortium, BROAD (http://www.broadinstitute.org/rnai/trc/lib). Blasticidin was used as a selection marker for the generation of endogenous H2AZ-depleted transgenic KH2 ESCs. The puromycin marker in the pLKO.1 vector was removed by digestion with BamHI and KpnI and replaced with blasticidin. The blasticidin cDNA was PCR amplified from pLenti6.2/V5-DEST Gateway® Vector (Invitrogen). V6.5 (129SvJae and C57BL/6) and the YFP transgenic ESCs were cultured as previously described (Boyer et al., 2006). The endogenous H2AZ-depleted transgenic KH2 ESCs were similarly cultured with the addition of blasticidin (5µg/ml) on blasticidin-resistant feeder cells (Iuchi, 2006).

value: Embryonic stem cells

value: H2AZ-AP3 variant

tag: time point


title: paITR_48h_r2

value: 48 hrs under iTreg condition (in vitro)


title: paITR_12h_r2

value: 12 hrs under iTreg condition (in vitro)


title: H2AZ KD Day3

value: H2AZ KD


title: H2AZ WT Day0

value: H2AZ WT


title: H2AZ WT Day3


title: H2AZ-AP3 variant Day0


title: paITR_24h_r2

value: lymph nodes

value: 24 hrs under iTreg condition (in vitro)


title: H2AZ KD Day0


title: stage 10 mRNA-seq

city: London

first: Caroline

last: Hill

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Cancer Research UK London Research Institute

description:
mRNA-seq
Sample 7

data_processing:
small RNA-seq reads were trimmed to remove sequencing adapters and aligned to the X. tropicalis genome allowing for zero mismatches using the bwa alignment program (Li and Durbin 2009).
Normalised abundance measurements were generated to allow comparison across the libraries using a linear scaling whereby the raw reads were multiplied by the greatest number of genomic alignments in any library divided by the number of genomic alignments in the library of interest.
mRNA-seq reads were aligned to the X. tropicalis genome using bowtie (Langmead et al. 2009) allowing up to 2 mismatches. mRNA-seq reads over splice junctions were aligned using TopHat (Trapnell et al. 2009).
mRNA-seq reads over splice junctions were aligned to the X. tropicalis genome using TopHat (Trapnell et al. 2009). Up to two sequence mismatches were permitted.
Normalised abundance measurements of mRNA reads were generated using the reads per kilobase per million of exon (RPKM) method for each gene annotated in RefSeq to normalize for transcript length and total read number (Mortazavi et al. 2008).
Genome_build: X. tropicalis genome, Joint Genome Institute assembly version 4.1 (Hellsten et al. 2010)
Supplementary_files_format_and_content: BED files were generated using bedtools software and contain alignments of trimmed small RNA reads to the X. tropicalis genome or alignments of trimmed mRNA-seq reads including reads spanning exon-exon junctions.

organism: Xenopus tropicalis

source_name: Whole embryos

growth_protocol: X. tropicalis embryos were obtained by in vitro fertilization, de-jellied in 2.2% cysteine and cultured in 1/20 x MMR + gentamycin until the indicated stage as described (Khokha et al. 2002).

extract_protocol: Total RNA was obtained by Trizol extraction from X. tropicalis embryos and the mRNA-seq sample prep kit (Illumina) was used to prepare the mRNA libraries. Briefly, polyadenylated RNA was selected, fragmented and cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen). Double-stranded cDNA was then synthesized using T4 DNA polymerase and used for Illumina sample preparation.

treatment_protocol: Embryos were not treated.

value: wild-type

tag: developmental stage

value: Embryonic stage 10

value: Whole embryos

tag: molecule subtype

value: Polyadenylated total RNA


title: stage 10 Vegetal Pole small RNA-seq

description:
small RNA-seq
Sample 5

source_name: Vegetal pole of embryo

extract_protocol: Total RNA was obtained by Trizol extraction from X. tropicalis embryos and treated with DNAse I (Worthington Biochemical Corporation). Small RNA libraries were prepared as described (Hafner 2008). Briefly, small RNAs of 18–30 nt were size-selected by gel purification and RNA adapters ligated on using T4 RNA ligase (Promega). cDNA was synthesized and used as a template to amplify the small RNA library by PCR. The PCR library was adjusted to 10 nM concentration and single-end sequenced using the small RNA sequencing primer (Illumina) on the Illumina platform on a Genome Analyzer IIx at the Cambridge Research Institute.

tag: tissue

value: Vegetal pole of embryo

value: small RNAs 18-30 nucleotides


title: paITR_2w_r1

value: 2 weeks under iTreg condition (in vitro)


title: HB ZF GFP +100 region 3 HBB198

city: Charlestown

first: Morgan

middle: Lee

last: Maeder

institute: Mass General Hospital

data_processing:
sequence reads were mapped using BSMAP v2.74 with default parameters
CPG counts determined by BSMAP were summarized and output to Excel files
Genome_build: hg19 or RHOXF2 reference sequence
Supplementary_files_format_and_content: processed data files are csv files summarizing the total number of methylated and unmethylated Cs in each sample

source_name: K562 cells

growth_protocol: K562, HeLa and 293 cells were grown under standard growth conditions

extract_protocol:
Genomic DNA was isolated using the Qiagen Blood Mini kit and bisulfite treated.  Bisulfite converted genomic DNA was PCR amplified with locus-specific primers.
Libraries were prepared using standard illumina multiplex library prep protocols.  Adapters were added either by PCR or by ligation

treatment_protocol: Cells were transfected (by nucleofection or lipofectamine) with plasmids encoding TALE-TET1 fusions

value: K562 cells

tag: target loci

value: HB ZF GFP +100 region 3


title: stage 8 small RNA-seq

description:
small RNA-seq
Sample 1

tag: genotype/variation

value: Embryonic stage 8


title: stage 10 small RNA-seq

description:
small RNA-seq
Sample 2


title: stage 18 small RNA-seq

description:
small RNA-seq
Sample 3

value: Embryonic stage 18


title: stage 10 Animal Pole small RNA-seq

description:
small RNA-seq
Sample 4

source_name: Animal pole of embryo

value: Animal pole of embryo


title: HB ZF GFP +100 region 2 HBB197

value: HB ZF GFP +100 region 2


title: HB ZF GFP +100 region 1 HBB196

value: HB ZF GFP +100 region 1


title: HB ZF-6 3 HBB192

value: HB ZF-6 3


title: HB ZF off-target +100 region 1 HBB193

value: HB ZF off-target +100 region 1


title: HB ZF off-target +100 region 2 HBB194

value: HB ZF off-target +100 region 2


title: HB ZF-6 2 HBB191

value: HB ZF-6 2


title: HB ZF off-target +100 region 3 HBB195

value: HB ZF off-target +100 region 3


title: HB ZF-5 3 HBB189

value: HB ZF-5 3


title: HB ZF-5 2 HBB188

value: HB ZF-5 2


title: stage 18 mRNA-seq

description:
mRNA-seq
Sample 8

value: wild-type

value: Whole embryos

value: Polyadenylated total RNA


title: HB ZF-5 1 HBB187

value: K562 cells

value: HB ZF-5 1


title: stage 8 mRNA-seq

description:
mRNA-seq
Sample 6

value: Embryonic stage 8


title: HB ZF-3 3 HBB183

value: HB ZF-3 3


title: HB ZF-3 2 HBB182

value: HB ZF-3 2


title: HB ZF-4 3 HBB186

value: HB ZF-4 3


title: HB ZF-3 1 HBB181

value: HB ZF-3 1


title: HB ZF-4 2 HBB185

value: HB ZF-4 2


title: HB ZF-2 3 HBB180

value: HB ZF-2 3


title: HB ZF-2 2 HBB179

value: HB ZF-2 2


title: HB ZF-2 1 HBB178

value: HB ZF-2 1


title: HB ZF GFP -300 region 2 HBB176

value: HB ZF GFP -300 region 2


title: HB ZF off-target -300 region 3 HBB174

value: HB ZF off-target -300 region 3


title: HB ZF GFP -300 region 3 HBB177

value: HB ZF GFP -300 region 3


title: HB ZF GFP -300 region 1 HBB175

value: HB ZF GFP -300 region 1


title: HB ZF off-target -300 region 1 HBB172

value: HB ZF off-target -300 region 1


title: HB ZF-1 3 HBB171

value: HB ZF-1 3


title: HB ZF-1 2 HBB170

value: K562 cells

value: HB ZF-1 2


title: HB ZF-1 1 HBB169

value: HB ZF-1 1


title: Time Course GFP Day 30 3 HBB168

value: Time Course GFP Day 30 3


title: HB ZF-6 1 HBB190

value: HB ZF-6 1


title: Time Course Off-target Day 30 3 HBB165

value: Time Course Off-target Day 30 3


title: Time Course Off-target Day 30 2 HBB164

value: Time Course Off-target Day 30 2


title: Time Course Off-target Day 30 1 HBB163

value: Time Course Off-target Day 30 1


title: Time Course GFP Day 30 1 HBB166

value: Time Course GFP Day 30 1


title: Time Course GFP Day 30 2 HBB167

value: Time Course GFP Day 30 2


title: Time Course HB-6 Day 30 1 HBB160

value: Time Course HB-6 Day 30 1


title: HB ZF-4 1 HBB184

value: HB ZF-4 1


title: Time Course HB-6 Day 30 2 HBB161

value: Time Course HB-6 Day 30 2


title: Time Course HB-5 Day 30 2 HBB158

value: Time Course HB-5 Day 30 2


title: Time Course HB-5 Day 30 1 HBB157

value: Time Course HB-5 Day 30 1


title: Time Course HB-4 Day 30 1 HBB154

value: Time Course HB-4 Day 30 1


title: Time Course HB-5 Day 30 3 HBB159

value: Time Course HB-5 Day 30 3


title: HB ZF off-target -300 region 2 HBB173

value: K562 cells

value: HB ZF off-target -300 region 2


title: Time Course GFP Day 14 1 HBB151

value: Time Course GFP Day 14 1


title: Time Course Off-target Day 14 3 HBB150

value: Time Course Off-target Day 14 3


title: Time Course Off-target Day 14 1 HBB148

value: Time Course Off-target Day 14 1


title: Time Course Off-target Day 14 2 HBB149

value: Time Course Off-target Day 14 2


title: Time Course HB-5 Day 14 3 HBB144

value: Time Course HB-5 Day 14 3


title: Time Course GFP Day 14 3 HBB153

value: Time Course GFP Day 14 3


title: Time Course HB-5 Day 14 2 HBB143

value: Time Course HB-5 Day 14 2


title: Time Course HB-6 Day 14 1 HBB145

value: Time Course HB-6 Day 14 1


title: Time Course HB-5 Day 14 1 HBB142

value: Time Course HB-5 Day 14 1


title: Time Course HB-4 Day 14 3 HBB141

value: Time Course HB-4 Day 14 3


title: Time Course GFP Day 14 2 HBB152

value: Time Course GFP Day 14 2


title: Time Course HB-4 Day 14 2 HBB140

value: Time Course HB-4 Day 14 2


title: Time Course HB-6 Day 30 3 HBB162

value: Time Course HB-6 Day 30 3


title: Time Course HB-6 Day 14 3 HBB147

value: Time Course HB-6 Day 14 3


title: Time Course HB-6 Day 14 2 HBB146

value: Time Course HB-6 Day 14 2


title: Time Course GFP Day 7 2 HBB137

value: K562 cells

value: Time Course GFP Day 7 2


title: Time Course Off-target Day 7 3 HBB135

value: Time Course Off-target Day 7 3


title: Time Course HB-4 Day 14 1 HBB139

value: Time Course HB-4 Day 14 1


title: Time Course HB-6 Day 7 3 HBB132

value: Time Course HB-6 Day 7 3


title: Time Course GFP Day 7 1 HBB136

value: Time Course GFP Day 7 1


title: Time Course Off-target Day 7 2 HBB134

value: Time Course Off-target Day 7 2


title: Time Course Off-target Day 7 1 HBB133

value: Time Course Off-target Day 7 1


title: Time Course HB-4 Day 30 3 HBB156

value: Time Course HB-4 Day 30 3


title: Time Course HB-4 Day 30 2 HBB155

value: Time Course HB-4 Day 30 2


title: Time Course HB-6 Day 7 2 HBB131

value: Time Course HB-6 Day 7 2


title: Time Course HB-6 Day 7 1 HBB130

value: Time Course HB-6 Day 7 1


title: Time Course GFP Day 7 3 HBB138

value: Time Course GFP Day 7 3


title: Time Course HB-5 Day 7 2 HBB128

value: Time Course HB-5 Day 7 2


title: Time Course HB-5 Day 7 1 HBB127

value: Time Course HB-5 Day 7 1


title: Time Course HB-5 Day 7 3 HBB129

value: Time Course HB-5 Day 7 3


title: Time Course GFP Day 4 1 HBB121

value: Time Course GFP Day 4 1


title: Time Course HB-4 Day 7 2 HBB125

value: K562 cells

value: Time Course HB-4 Day 7 2


title: Time Course GFP Day 4 3 HBB123

value: Time Course GFP Day 4 3


title: Time Course HB-4 Day 7 1 HBB124

value: Time Course HB-4 Day 7 1


title: Time Course GFP Day 4 2 HBB122

value: Time Course GFP Day 4 2


title: Time Course Off-target Day 4 3 HBB120

value: Time Course Off-target Day 4 3


title: Time Course HB-6 Day 4 2 HBB116

value: Time Course HB-6 Day 4 2


title: Time Course Off-target Day 4 1 HBB118

value: Time Course Off-target Day 4 1


title: Time Course HB-6 Day 4 3 HBB117

value: Time Course HB-6 Day 4 3


title: Time Course HB-6 Day 4 1 HBB115

value: Time Course HB-6 Day 4 1


title: Time Course HB-5 Day 4 3 HBB114

value: Time Course HB-5 Day 4 3


title: Time Course Off-target Day 4 2 HBB119

value: Time Course Off-target Day 4 2


title: Time Course HB-5 Day 4 1 HBB112

value: Time Course HB-5 Day 4 1


title: Time Course HB-5 Day 4 2 HBB113

value: Time Course HB-5 Day 4 2


title: Time Course HB-4 Day 4 3 HBB111

value: Time Course HB-4 Day 4 3


title: Time Course HB-4 Day 7 3 HBB126

value: Time Course HB-4 Day 7 3


title: Western Blot samples HB-5mut 1 HBB103

value: Western Blot samples HB-5mut 1


title: Time Course HB-4 Day 4 2 HBB110

value: K562 cells

value: Time Course HB-4 Day 4 2


title: Western Blot samples HB-5mut 2 HBB104

value: Western Blot samples HB-5mut 2


title: Time Course HB-4 Day 4 1 HBB109

value: Time Course HB-4 Day 4 1


title: Western Blot samples GFP 3 HBB108

value: Western Blot samples GFP 3


title: Western Blot samples HB-5 1 HBB100

value: Western Blot samples HB-5 1


title: Western Blot samples GFP 2 HBB107

value: Western Blot samples GFP 2


title: Western Blot samples GFP 1 HBB106

value: Western Blot samples GFP 1


title: Western Blot samples HB-5mut 3 HBB105

value: Western Blot samples HB-5mut 3


title: Western Blot samples HB-5 3 HBB102

value: Western Blot samples HB-5 3


title: Western Blot samples HB-4mut 1 HBB97

value: Western Blot samples HB-4mut 1


title: Western Blot samples HB-4mut 2 HBB98

value: Western Blot samples HB-4mut 2


title: Western Blot samples HB-4mut 3 HBB99

value: Western Blot samples HB-4mut 3


title: Western Blot samples HB-4 2 HBB95

value: Western Blot samples HB-4 2


title: HB-6mut PCR#3-2 HBB89

value: HB-6mut PCR#3-2


title: HB-6mut PCR#3-1 HBB88

value: HB-6mut PCR#3-1


title: Western Blot samples HB-4 1 HBB94

value: Western Blot samples HB-4 1


title: HB-6mut PCR#3-3 HBB90

value: K562 cells

value: HB-6mut PCR#3-3


title: GFP PCR#3-3 HBB93

value: GFP PCR#3-3


title: HB-6 PCR#3-1 HBB85


title: GFP PCR#3-2 HBB92

value: GFP PCR#3-2


title: GFP PCR#3-1 HBB91

value: GFP PCR#3-1


title: HB-5mut PCR#3-3 HBB84

value: HB-5mut PCR#3-3


title: HB-6 PCR#3-2 HBB86


title: HB-6 PCR#3-3 HBB87


title: HB-5mut PCR#3-2 HBB83

value: HB-5mut PCR#3-2


title: Western Blot samples HB-5 2 HBB101

value: Western Blot samples HB-5 2


title: HB-5 PCR#3-2 HBB80


title: HB-4mut PCR#3-1 HBB76

value: HB-4mut PCR#3-1


title: HB-4mut PCR#3-3 HBB78

value: HB-4mut PCR#3-3


title: HB-5 PCR#3-3 HBB81


title: HB-4 PCR#3-1 HBB73


title: GFP PCR#2-2 HBB71

value: GFP PCR#2-2


title: GFP PCR#2-3 HBB72

value: GFP PCR#2-3


title: HB-4 PCR#3-2 HBB74


title: off-target PCR#2-3 HBB69

value: off-target PCR#2-3


title: HB-5mut PCR#3-1 HBB82

value: HB-5mut PCR#3-1


title: off-target PCR#2-2 HBB68

value: off-target PCR#2-2


title: off-target PCR#2-1 HBB67

value: off-target PCR#2-1


title: GFP PCR#2-1 HBB70

value: GFP PCR#2-1


title: HB-10 PCR#2-3 HBB66

value: K562 cells


title: Western Blot samples HB-4 3 HBB96

value: Western Blot samples HB-4 3


title: HB-4 PCR#3-3 HBB75


title: HB-10 PCR#2-2 HBB65


title: HB-9 PCR#2-2 HBB62


title: HB-9 PCR#2-3 HBB63


title: HB-8 PCR#2-3 HBB60


title: HB-8 PCR#2-2 HBB59


title: HB-7 PCR#2-3 HBB57


title: HB-8 PCR#2-1 HBB58


title: HB-4mut PCR#3-2 HBB77

value: HB-4mut PCR#3-2


title: HB-7 PCR#2-2 HBB56


title: HB-5 PCR#3-1 HBB79


title: HB-7 PCR#2-1 HBB55


title: HB-6 PCR#2-3 HBB54


title: HB-6 PCR#2-2 HBB53


title: HB-6 PCR#2-1 HBB52


title: HB-5 PCR#2-3 HBB51


title: HB-5 PCR#2-2 HBB50


title: HB-5 PCR#2-1 HBB49


title: HB-3 PCR#2-3 HBB45


title: HB-3 PCR#2-2 HBB44


title: GFP PCR#1-3 HBB36

value: GFP PCR#1-3


title: GFP PCR#1-2 HBB35

value: GFP PCR#1-2


title: GFP PCR#1-1 HBB34

value: GFP PCR#1-1


title: HB-10 PCR#2-1 HBB64


title: HB-9 PCR#2-1 HBB61


title: off-target PCR#1-3 HBB33

value: off-target PCR#1-3


title: off-target PCR#1-2 HBB32

value: off-target PCR#1-2


title: HB-10 PCR#1-1 HBB28


title: HB-10 PCR#1-3 HBB30


title: HB-9 PCR#1-2 HBB26


title: HB-9 PCR#1-3 HBB27


title: HB-9 PCR#1-1 HBB25


title: HB-8 PCR#1-3 HBB24


title: HB-8 PCR#1-2 HBB23


title: HB-7 PCR#1-3 HBB21


title: HB-8 PCR#1-1 HBB22


title: HB-7 PCR#1-1 HBB19


title: HB-7 PCR#1-2 HBB20


title: HB-3 PCR#2-1 HBB43


title: HB-6 PCR#1-2 HBB17


title: HB-6 PCR#1-3 HBB18


title: HB-5 PCR#1-2 HBB14


title: HB-4 PCR#1-3 HBB12


title: HB-6 PCR#1-1 HBB16


title: HB-5 PCR#1-3 HBB15


title: HB-4 PCR#1-1 HBB10


title: HB-5 PCR#1-1 HBB13


title: HB-3 PCR#1-3 HBB9


title: HB-4 PCR#1-2 HBB11


title: off-target PCR#1-1 HBB31

value: off-target PCR#1-1


title: HB-10 PCR#1-2 HBB29


title: HB-2 PCR#1-3 HBB6


title: HB-2 PCR#1-1 HBB4


title: HB-2 PCR#1-2 HBB5


title: HB-1 PCR#1-1 HBB1


title: Western Blot samples GFP -250 to +1 2 RHOX149

source_name: 293 cells

value: 293 cells

value: Western Blot samples GFP -250 to +1 2


title: Western Blot samples GFP -250 to +1 3 RHOX150

value: Western Blot samples GFP -250 to +1 3


title: Western Blot samples RH-4mut -250 to +1 3 RHOX147


title: Western Blot samples GFP -250 to +1 1 RHOX148

value: Western Blot samples GFP -250 to +1 1


title: Western Blot samples RH-4mut -250 to +1 2 RHOX146


title: Western Blot samples RH-4 -250 to +1 3 RHOX144

value: Western Blot samples RH-4 -250 to +1 3


title: Western Blot samples RH-4 -250 to +1 2 RHOX143

value: Western Blot samples RH-4 -250 to +1 2


title: Western Blot samples RH-4mut -250 to +1 1 RHOX145


title: Western Blot samples RH-4 -250 to +1 1 RHOX142

value: Western Blot samples RH-4 -250 to +1 1


title: Western Blot samples RH-3mut -250 to +1 3 RHOX141


title: Western Blot samples RH-3 -250 to +1 3 RHOX138

value: Western Blot samples RH-3 -250 to +1 3


title: HB-3 PCR#1-2 HBB8

value: K562 cells


title: Western Blot samples RH-3 -250 to +1 1 RHOX136

value: Western Blot samples RH-3 -250 to +1 1


title: Western Blot samples RH-3mut -250 to +1 2 RHOX140


title: Western Blot samples GFP -650 to -850 3 RHOX135

value: Western Blot samples GFP -650 to -850 3


title: Western Blot samples RH-3 -250 to +1 2 RHOX137

value: Western Blot samples RH-3 -250 to +1 2


title: Western Blot samples GFP -650 to -850 2 RHOX134

value: Western Blot samples GFP -650 to -850 2


title: Western Blot samples GFP -650 to -850 1 RHOX133

value: Western Blot samples GFP -650 to -850 1


title: HB-1 PCR#1-3 HBB3


title: Western Blot samples RH-3mut -650 to -850 1 RHOX130


title: Western Blot samples RH-3mut -650 to -850 2 RHOX131


title: Western Blot samples RH-3mut -650 to -850 3 RHOX132


title: HB-1 PCR#1-2 HBB2


title: Western Blot samples RH-3 -650 to -850 3 RHOX129


title: Western Blot samples RH-3 -650 to -850 2 RHOX128


title: Western Blot samples RH-3 -650 to -850 1 RHOX127


title: RH-3 + RH-4 3 RHOX126


title: RH-3 + RH-4 2 RHOX125


title: HB-3 PCR#1-1 HBB7


title: RH-3 + RH-4 3 RHOX123

source_name: HeLa cells

value: HeLa cells


title: RH-3 + RH-4 2 RHOX122


title: RH-3 + RH-4 1 RHOX121


title: GFP -650 to -850 3 RHOX120


title: GFP -650 to -850 2 RHOX119


title: GFP -650 to -850 1 RHOX118


title: Off target -650 to -850 3 RHOX117

value: Off target -650 to -850 3


title: Western Blot samples RH-3mut -250 to +1 1 RHOX139


title: Off target -650 to -850 2 RHOX116

value: Off target -650 to -850 2


title: RH-3mut -650 to -850 3 RHOX114

value: 293 cells


title: Off target -650 to -850 1 RHOX115

value: Off target -650 to -850 1


title: RH-3mut -650 to -850 2 RHOX113


title: RH-3mut -650 to -850 1 RHOX112


title: RH-3 -650 to -850 2 RHOX110


title: Initial Screen  -650 to -850 GFP 3 RHOX108

value: Initial Screen  -650 to -850 GFP 3


title: RH-3 -650 to -850 1 RHOX109


title: Initial Screen  -650 to -850 off target 3 RHOX105


title: Initial Screen  -650 to -850 GFP 2 RHOX107

value: Initial Screen  -650 to -850 GFP 2


title: RH-3 -650 to -850 3 RHOX111


title: Initial Screen  -650 to -850 off target 1 RHOX103


title: Initial Screen  -650 to -850 off target 2 RHOX104


title: Initial Screen  -650 to -850 GFP 1 RHOX106

value: Initial Screen  -650 to -850 GFP 1


title: Initial Screen RH-10 -650 to -850 2 RHOX98

value: Initial Screen RH-10 -650 to -850 2


title: Initial Screen RH-10 -650 to -850 1 RHOX97

value: Initial Screen RH-10 -650 to -850 1


title: Initial Screen RH-11 -650 to -850 2 RHOX101

value: Initial Screen RH-11 -650 to -850 2


title: Initial Screen RH-9 -650 to -850 2 RHOX95

value: Initial Screen RH-9 -650 to -850 2


title: RH-3 + RH-4 1 RHOX124


title: Initial Screen RH-9 -650 to -850 3 RHOX96

value: Initial Screen RH-9 -650 to -850 3


title: Initial Screen RH-11 -650 to -850 1 RHOX100

value: Initial Screen RH-11 -650 to -850 1


title: Initial Screen RH-11 -650 to -850 3 RHOX102

value: Initial Screen RH-11 -650 to -850 3


title: Initial Screen RH-8 -650 to -850 1 RHOX91

value: Initial Screen RH-8 -650 to -850 1


title: Initial Screen RH-8 -650 to -850 2 RHOX92

value: Initial Screen RH-8 -650 to -850 2


title: Initial Screen RH-7 -650 to -850 2 RHOX89

value: Initial Screen RH-7 -650 to -850 2


title: Initial Screen RH-7 -650 to -850 3 RHOX90

value: Initial Screen RH-7 -650 to -850 3


title: Initial Screen RH-3 -650 to -850 3 RHOX87

value: Initial Screen RH-3 -650 to -850 3


title: Initial Screen RH-9 -650 to -850 1 RHOX94

value: 293 cells

value: Initial Screen RH-9 -650 to -850 1


title: Initial Screen RH-7 -650 to -850 1 RHOX88

value: Initial Screen RH-7 -650 to -850 1


title: Initial Screen RH-3 -650 to -850 2 RHOX86

value: Initial Screen RH-3 -650 to -850 2


title: Initial Screen RH-6 -250-+1 3 RHOX78

value: Initial Screen RH-6 -250-+1 3


title: Initial Screen RH-3 -650 to -850 1 RHOX85

value: Initial Screen RH-3 -650 to -850 1


title: Initial Screen -250-+1 offtarget 2 RHOX80

value: Initial Screen -250-+1 offtarget 2


title: Initial Screen RH-10 -650 to -850 3 RHOX99

value: Initial Screen RH-10 -650 to -850 3


title: Initial Screen -250-+1 offtarget 1 RHOX79

value: Initial Screen -250-+1 offtarget 1


title: Initial Screen -250-+1 offtarget 3 RHOX81

value: Initial Screen -250-+1 offtarget 3


title: Initial Screen RH-6 -250-+1 1 RHOX76

value: Initial Screen RH-6 -250-+1 1


title: Initial Screen RH-5 -250-+1 3 RHOX75

value: Initial Screen RH-5 -250-+1 3


title: Initial Screen -250-+1 GFP 2 RHOX83

value: Initial Screen -250-+1 GFP 2


title: Initial Screen RH-4 -250-+1 3 RHOX72

value: Initial Screen RH-4 -250-+1 3


title: Initial Screen RH-6 -250-+1 2 RHOX77

value: Initial Screen RH-6 -250-+1 2


title: Initial Screen RH-5 -250-+1 1 RHOX73

value: Initial Screen RH-5 -250-+1 1


title: Initial Screen RH-4 -250-+1 2 RHOX71

value: Initial Screen RH-4 -250-+1 2


title: Initial Screen RH-5 -250-+1 2 RHOX74

value: 293 cells

value: Initial Screen RH-5 -250-+1 2


title: Initial Screen RH-2 -250-+1 3 RHOX66

value: Initial Screen RH-2 -250-+1 3


title: Initial Screen RH-3 -250-+1 2 RHOX68

value: Initial Screen RH-3 -250-+1 2


title: Initial Screen RH-3 -250-+1 3 RHOX69

value: Initial Screen RH-3 -250-+1 3


title: Initial Screen RH-3 -250-+1 1 RHOX67

value: Initial Screen RH-3 -250-+1 1


title: Initial Screen RH-2 -250-+1 2 RHOX65

value: Initial Screen RH-2 -250-+1 2


title: Initial Screen RH-2 -250-+1 1 RHOX64

value: Initial Screen RH-2 -250-+1 1


title: Initial Screen RH-1 -250-+1 3 RHOX63

value: Initial Screen RH-1 -250-+1 3


title: Initial Screen RH-1 -250-+1 2 RHOX62

value: Initial Screen RH-1 -250-+1 2


title: Initial Screen RH-1 -250-+1 1 RHOX61

value: Initial Screen RH-1 -250-+1 1


title: Initial Screen RH-8 -650 to -850 3 RHOX93

value: Initial Screen RH-8 -650 to -850 3


title: Initial Screen -250-+1 GFP 2 RHOX59

value: HeLa cells

value: Initial Screen -250-+1 GFP 2


title: Initial Screen -250-+1 GFP 1 RHOX82

value: Initial Screen -250-+1 GFP 1


title: Initial Screen -250-+1 GFP 3 RHOX84

value: Initial Screen -250-+1 GFP 3


title: Initial Screen -250-+1 GFP 1 RHOX58


title: Initial Screen -250-+1 offtarget 3 RHOX57

value: Initial Screen -250-+1 offtarget 3


title: Initial Screen RH-6 -250-+1 3 RHOX54

value: Initial Screen RH-6 -250-+1 3


title: Initial Screen RH-4 -250-+1 1 RHOX70

value: 293 cells

value: Initial Screen RH-4 -250-+1 1


title: Initial Screen -250-+1 offtarget 2 RHOX56

value: Initial Screen -250-+1 offtarget 2


title: Initial Screen RH-6 -250-+1 2 RHOX53

value: Initial Screen RH-6 -250-+1 2


title: Initial Screen -250-+1 offtarget 1 RHOX55

value: Initial Screen -250-+1 offtarget 1


title: Initial Screen RH-5 -250-+1 2 RHOX50

value: Initial Screen RH-5 -250-+1 2


title: Initial Screen RH-5 -250-+1 3 RHOX51

value: Initial Screen RH-5 -250-+1 3


title: Initial Screen RH-4 -250-+1 2 RHOX47

value: Initial Screen RH-4 -250-+1 2


title: Initial Screen RH-4 -250-+1 1 RHOX46