title: Initial Screen RH-3 -250-+1 3 RHOX45

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


title: Initial Screen RH-3 -250-+1 2 RHOX44

status: Public on Sep 23 2013

type: SRA

city: Charlestown

first: Morgan

middle: Lee

last: Maeder

state: MA

country: USA

institute: Mass General Hospital

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa 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

tag: cell line

value: HeLa cells

tag: target loci

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


title: Initial Screen RH-2 -250-+1 3 RHOX42

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


title: Initial Screen RH-4 -250-+1 3 RHOX48

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


title: Initial Screen RH-2 -250-+1 2 RHOX41

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


title: Initial Screen RH-1 -250-+1 2 RHOX38

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


title: Initial Screen RH-3 -250-+1 1 RHOX43

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


title: Initial Screen -250-+1 GFP 3 RHOX60

value: Initial Screen -250-+1 GFP 3


title: Initial Screen RH-5 -250-+1 1 RHOX49

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


title: RH-4 mut 3 RHOX36

source_name: 293 cells

value: 293 cells

value: RH-4 mut 3


title: Initial Screen RH-2 -250-+1 1 RHOX40

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


title: RH-4 mut 2 RHOX35

value: RH-4 mut 2


title: RH-4 mut 1 RHOX34

value: RH-4 mut 1


title: RH-3 mut 3 RHOX33

value: RH-3 mut 3


title: RH-3 mut 2 RHOX32

value: RH-3 mut 2


title: A0572 embryo 1 extra-embryonic membranes

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

description: Illumina RNA-seq

library_source: transcriptomic

data_processing:
Illumina CASAVA 1.7 software was used for basecalling.
Adapter sequences were removed from the raw reads by custom scripts.
The short reads were aligned to the opossum reference genome (monDom5) using TopHat v1.4.1
The total expression level metric, FPKM (Fragments Per Kilobase-pair of exon Model), was calculated for all samples using Cufflinks v1.3.0 based on all mapped reads from the TopHat alignments. The multiple mapped reads were weighted using the “-u” parameter in Cufflinks. The expression level was normalized across the brain and extra-embryonic membrane samples using quartile normalization.
SNP positions were called in combined RNA-seq data from only uniquely mapped reads to the opossum reference genome with 40 of more coverage, using SAMtools software. Problematic SNPs with third allele, near  indel positions or on the exon-intron junctions were removed. In total, we called 68k SNPs in the transcriptome. The reference and alternative allele counts were summarized at high quality X-linked SNP positions. We then filtered out high-coverage SNPs with 8 or more coverage in at least one of two female F1 individuals in both reciprocal crosses. To quantify the allele-specific expression in the brain and extra-embyronic tissues of the reciprocal crosses, at each identified SNP position we calculated the ratio of the number of reference allele containing reads over the total coverage.
Genome_build: UCSC monDom5
Supplementary_files_format_and_content: gzipped tab-delimited text file includes the FPKM value for expressed Ensembl v64 genes.

molecule: total RNA

organism: Monodelphis domestica

source_name: embryonic day 13 extra-embryonic membranes

extract_protocol:
At 13 days post-copulation (d.p.c.), female opossums were anesthetized, the fetuses and respective extra-embryonic membranes (EEM) were collected and placed in either RNALater or PBS. Head/brain and EEM tissues were dissected for RNA extractions. After collection, the tissue was homogenized in TriReagent (Invirtogen) and total RNA was extracted using BCP (1-bromo-2 chloropropane), precipitated with isopropanol, and resuspended in RNase-free water. Potential gDNA contamination was removed by both DNase I treatment and the gDNA-removing column in Qiagen RNeasy Plus Mini kit (Qiagen, CA). RNA concentrations and A260nm/A280nm ratios were checked with a NanoDrop ND-1000 Spectrophotometer. The RNA quality was checked on both 1% agarose gel and Agilent 2100 Bioanalyzer.
The mRNA-seq libraries were made for brain and extra-embryonic membrane RNA samples with 1-3 µg total RNA input for four individuals in reciprocal F1 crosses and four individuals in the parental crosses, using Illumina TruSeq RNA Sample Prep Kit (Illumina Inc., CA).

tag: strain

value: LL2 mother (A0572) x LL2 father (A0573)

tag: developmental stage

value: embryonic day 13

tag: tissue

value: extra-embryonic membranes

tag: Sex

value: female


title: A0572 embryo 3 extra-embryonic membranes

description: Illumina RNA-seq

value: male


title: A0572 embryo 3 fetal brain

description: Illumina RNA-seq

source_name: embryonic day 13 fetal brain

value: fetal brain


title: A0580 embryo 1 fetal brain

description: Illumina RNA-seq

value: LL1 mother (A0580) x LL1 father (A0578)


title: A0572 embryo 1 fetal brain

description: Illumina RNA-seq


title: A0580 embryo 5 fetal brain

description: Illumina RNA-seq


title: RH-3 mut 1 RHOX31

value: RH-3 mut 1


title: Initial Screen RH-1 -250-+1 3 RHOX39

value: HeLa cells

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


title: A0579 embryo 4 fetal brain

description: Illumina RNA-seq

value: LL1 mother (A0579) x LL2 father (A0573)


title: GFP control 1 RHOX28

value: 293 cells

value: GFP control 1


title: GFP control 2 RHOX29

value: GFP control 2


title: A0580 embryo 1 extra-embryonic membranes

description: Illumina RNA-seq


title: A0579 embryo 3 fetal brain

description: Illumina RNA-seq


title: A0571 embryo 4 fetal brain

description: Illumina RNA-seq

value: LL2 mother (A0571) x LL1 father (A0578)


title: Off-target 2 RHOX26

value: Off-target 2


title: A0571 embryo 1 fetal brain

description: Illumina RNA-seq


title: Off-target 1 RHOX25

value: Off-target 1


title: RH-4 3 RHOX24


title: A0579 embryo 4 extra-embryonic membranes

description: Illumina RNA-seq


title: RH-4 2 RHOX23


title: RH-4 1 RHOX22


title: A0571 embryo 1 extra-embryonic membranes

description: Illumina RNA-seq


title: A0571 embryo 4 extra-embryonic membranes

description: Illumina RNA-seq


title: A0580 embryo 5 extra-embryonic membranes

description: Illumina RNA-seq


title: RH-3 3 RHOX21


title: RH-3 2 RHOX20


title: RH-3 1 RHOX19


title: RH-4 mut 3 RHOX18

value: RH-4 mut 3


title: RH-4 mut 2 RHOX17

value: RH-4 mut 2


title: 579_E11+E12_H3K9Ac_ChIP-seq

city: College Station

first: Kory

last: Douglas

state: TX

address: 4458 TAMU

institute: Texas A&M University

description:
pooled tissue from two sister fetuses
processed data file: Female_Fetal_Brain_H3K9Ac_MACS_Peaks.bed

data_processing:
Illumina CASAVA 1.7 software was used for basecalling.
Adapter sequences were removed from the raw reads by custom scripts.
The short reads were aligned to the opossum reference genome (monDom5) using Bowtie v. 1.1.2
Significant Peaks were called using MACS v. 1.0.1
Genome_build: UCSC monDom5 (http://www.ncbi.nlm.nih.gov/assembly/237648/)
Supplementary_files_format_and_content: BED files containing peaks, peak coordinates, and -10*log10(pvalue) of each peak

source_name: E13 fetal brain_H3K9Ac_ChIP-seq

extract_protocol:
Chromatin was extracted, digested with micrococcal nuclease, pooled (sisters only), and quantified using Qubit.  Chromatin was equally divided and ChIP was performed using the indicated antibodies.  Samples were purified using the Minelute PCR Purification Kit by Qiagen.  Enrichment was checked by qPCR.
ChIP-seq libraries were constructed using a modified version of the Illumina TruSeq RNA Sample Prep protocol.  All libraries were constructed at Global Biologics, Columbia, MO.

tag: gender

value: embryonic day 13

tag: chip antibody

tag: chip antibody vendor

value: Upstate-Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: 579_E11+E12_H3K9me3_ChIP-seq

description:
pooled tissue from two sister fetuses
processed data file: Female_Fetal_Brain_H3K9me3_MACS_Peaks.bed

source_name: E13 fetal brain_H3K9me3_ChIP-seq

value: female


title: 579_E11+E12_H3K27me3_ChIP-seq

description:
pooled tissue from two sister fetuses
processed data file: Female_Fetal_Brain_H3K27me3_MACS_Peaks.bed

source_name: E13 fetal brain_H3K27me3_ChIP-seq

value: fetal brain


title: GFP control 3 RHOX30

value: GFP control 3


title: 579_E11+E12_H3K4me3_ChIP-seq

description:
pooled tissue from two sister fetuses
processed data file: Female_Fetal_Brain_H3K4me3_MACS_Peaks.bed

source_name: E13 fetal brain_H3K4me3_ChIP-seq


title: RH-4 mut 1 RHOX16

value: RH-4 mut 1


title: 571_E10+E11_H3K27me3_ChIP-seq

value: LL2 Mother (A0571) X LL2 Father (A0578)


title: 571_E10+E11_H3K9Ac_ChIP-seq


title: 571_E10+E11_H3K9me3_ChIP-seq


title: A0579 embryo 3 extra-embryonic membranes

description: Illumina RNA-seq

value: extra-embryonic membranes


title: GFP control 3 RHOX12

value: HeLa cells


title: RH-3 mut 2 RHOX14

value: RH-3 mut 2


title: 571_E10+E11_H3K4me3_ChIP-seq


title: paTh2_StS6KO

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-polyA-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

molecule: polyA RNA

organism: Mus musculus

source_name: T helper 2 cells (Th2)

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: BALB/c STAT6 deficient

value: lymph nodes

tag: development stage

value: 4 days under Th2 condition (in vitro)


title: paTh2_StS6CT

value: BALB/c


title: GFP control 2 RHOX11

value: GFP control 2


title: Initial Screen RH-6 -250-+1 1 RHOX52

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


title: GFP control 1 RHOX10

value: GFP control 1


title: paTh1_StS4KO

source_name: T helper 1 cells (Th1)

value: BALB/c STAT4 deficient

value: 4 days under Th1 condition (in vitro)


title: Off-target 3 RHOX9

value: Off-target 3


title: paTh1_StS4CT


title: paTh2_2w_r1

value: 2 weeks under Th2 condition (in vitro)


title: Off-target 2 RHOX8

value: Off-target 2


title: RH-3 mut 3 RHOX15

value: RH-3 mut 3


title: Off-target 1 RHOX7

value: Off-target 1


title: RH-4 2 RHOX5


title: RH-3 mut 1 RHOX13

value: RH-3 mut 1


title: RH-4 1 RHOX4

value: HeLa cells


title: RH-3 3 RHOX3


title: RH-4 3 RHOX6


title: paTh2_1w_r1

value: 1 week under Th2 condition (in vitro)


title: paTh1_1w_r2

value: 1 week under Th1 condition (in vitro)


title: RH-3 2 RHOX2


title: paTh1_2w_r1

value: lymph nodes

value: 2 weeks under Th1 condition (in vitro)


title: paTh1_1w_r1


title: paNIV_0h_r1

source_name: Naïve CD4+ T cells

value: Naive CD4+ T cells


title: KL ZF GFP 3 KLF96

source_name: K562 cells

value: K562 cells

value: KL ZF GFP 3


title: paTh1_12h_r1

value: 12 hrs under Th1 condition (in vitro)


title: paTh1_24h_r1

value: 24 hrs under Th1 condition (in vitro)


title: paNIV_0h_r2


title: Initial Screen RH-1 -250-+1 1 RHOX37

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


title: KL ZF GFP 2 KLF95

value: KL ZF GFP 2


title: KL ZF off target 3 KLF93

value: KL ZF off target 3


title: paTh2_1w_r2


title: paTh1_72h_r2

value: 72 hrs under Th1 condition (in vitro)


title: paTh1_2w_r2


title: KL ZF off target 1 KLF91

value: KL ZF off target 1


title: KL ZF off target 2 KLF92

value: KL ZF off target 2


title: paTh17_48h_r2

source_name: T helper 17 cells (Th17)

value: 48 hrs under Th17 condition (in vitro)


title: KL ZF GFP 1 KLF94

value: KL ZF GFP 1


title: paTh2_48h_r2

value: 48 hrs under Th2 condition (in vitro)


title: KL ZF-2 2 KLF89

value: KL ZF-2 2


title: KL ZF-1 3 KLF87

value: KL ZF-1 3


title: RH-3 1 RHOX1

value: HeLa cells


title: KL ZF-2 1 KLF88

value: KL ZF-2 1


title: KL ZF-2 3 KLF90

value: K562 cells

value: KL ZF-2 3


title: paTh1_48h_r2

value: lymph nodes

value: 48 hrs under Th1 condition (in vitro)


title: paTh2_24h_r2

value: 24 hrs under Th2 condition (in vitro)


title: paTh17_24h_r2

value: 24 hrs under Th17 condition (in vitro)


title: paTh1_24h_r2

value: 24 hrs under Th1 condition (in vitro)


title: KL ZF-1 2 KLF86

value: KL ZF-1 2


title: KL ZF-1 1 KLF85

value: KL ZF-1 1


title: paTh2_12h_r2

value: 12 hrs under Th2 condition (in vitro)


title: KL-1 CD 50ug off target 3 KLF84

value: KL-1 CD 50ug off target 3


title: paTh17_12h_r2

value: 12 hrs under Th17 condition (in vitro)


title: paTh1_12h_r2

value: 12 hrs under Th1 condition (in vitro)


title: KL-1 CD 50ug off target 2 KLF83

value: KL-1 CD 50ug off target 2


title: paITR_8h_r2

source_name: Induced regulatory T cells (iTreg)

value: 8 hrs under iTreg condition (in vitro)


title: paTh17_72h_r2

value: 72 hrs under Th17 condition (in vitro)


title: paTh2_8h_r2

value: 8 hrs under Th2 condition (in vitro)


title: paTh17_8h_r2

value: 8 hrs under Th17 condition (in vitro)


title: paTh17_4h_r2

value: 4 hrs under Th17 condition (in vitro)


title: paITR_4h_r2

value: lymph nodes

value: 4 hrs under iTreg condition (in vitro)


title: paTh1_4h_r2

value: 4 hrs under Th1 condition (in vitro)


title: paTh1_8h_r2

value: 8 hrs under Th1 condition (in vitro)


title: KL-1 CD 50ug off target 1 KLF82

value: K562 cells

value: KL-1 CD 50ug off target 1


title: KL-1 CD 20ug off target 3 KLF81

value: KL-1 CD 20ug off target 3


title: KL-1 CD 20ug off target 1 KLF79

value: KL-1 CD 20ug off target 1


title: KL-1 CD 5ug off target 3 KLF78

value: KL-1 CD 5ug off target 3


title: paTh17_48h_r1

value: 48 hrs under Th17 condition (in vitro)


title: paITR_72h_r1

value: 72 hrs under iTreg condition (in vitro)


title: paTh2_72h_r1

value: 72 hrs under Th2 condition (in vitro)


title: paTh17_72h_r1


title: paTh1_72h_r1

value: 72 hrs under Th1 condition (in vitro)


title: paTh2_4h_r2

value: 4 hrs under Th2 condition (in vitro)


title: paTh2_48h_r1

value: 48 hrs under Th2 condition (in vitro)


title: KL-1 CD 5ug off target 2 KLF77

value: KL-1 CD 5ug off target 2


title: KL-1 CD 2ug off target 3 KLF75

value: KL-1 CD 2ug off target 3


title: paTh17_24h_r1

value: lymph nodes

value: 24 hrs under Th17 condition (in vitro)


title: KL-1 CD 5ug off target 1 KLF76

value: KL-1 CD 5ug off target 1


title: paITR_24h_r1

value: 24 hrs under iTreg condition (in vitro)


title: KL-1 CD 20ug off target 2 KLF80

value: K562 cells

value: KL-1 CD 20ug off target 2


title: paITR_12h_r1

value: 12 hrs under iTreg condition (in vitro)


title: Off-target 3 RHOX27

value: 293 cells

value: Off-target 3


title: paTh17_12h_r1

value: 12 hrs under Th17 condition (in vitro)


title: KL-1 CD 2ug off target 1 KLF73

value: KL-1 CD 2ug off target 1


title: paTh17_8h_r1

value: 8 hrs under Th17 condition (in vitro)


title: KL-1 CD 50ug 3 KLF72

value: KL-1 CD 50ug 3


title: paTh2_8h_r1

value: 8 hrs under Th2 condition (in vitro)


title: paITR_48h_r1

value: 48 hrs under iTreg condition (in vitro)


title: paITR_8h_r1

value: 8 hrs under iTreg condition (in vitro)


title: KL-1 CD 50ug 2 KLF71

value: KL-1 CD 50ug 2


title: paTh2_24h_r1

value: lymph nodes

value: 24 hrs under Th2 condition (in vitro)


title: KL-1 CD 20ug 3 KLF69

value: KL-1 CD 20ug 3


title: paTh1_48h_r1

value: 48 hrs under Th1 condition (in vitro)


title: KL-1 CD 20ug 2 KLF68

value: K562 cells

value: KL-1 CD 20ug 2


title: paITR_4h_r1

value: 4 hrs under iTreg condition (in vitro)


title: paTh1_8h_r1

value: 8 hrs under Th1 condition (in vitro)


title: paTh2_12h_r1

value: 12 hrs under Th2 condition (in vitro)


title: KL-1 CD 20ug 1 KLF67

value: KL-1 CD 20ug 1


title: paTh17_4h_r1

value: 4 hrs under Th17 condition (in vitro)


title: KL-1 CD 5ug 2 KLF65

value: KL-1 CD 5ug 2


title: KL-1 CD 5ug 3 KLF66

value: KL-1 CD 5ug 3


title: KL-1 CD 2ug off target 2 KLF74

value: KL-1 CD 2ug off target 2


title: paTh1_4h_r1

value: 4 hrs under Th1 condition (in vitro)


title: KL-1 CD 2ug 3 KLF63

value: KL-1 CD 2ug 3


title: H2AZ WT ChIP-Seq

city: Cambridge

first: Laurie

middle: A

last: Boyer

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 0.12.3, with the following parameters --solexa1.3-quals --best --strata -m 1 -n 2 -p 8 -S.
Sequences were extended +200 bp for histone marks and allocated in 25-bp bins.
A Poissonian model was used to determine statistically enriched bins with a P-value threshold set at 1x10-9 as described previously (Marson et al., 2008).  Additionally, we required that genomic bins were at least 5 fold over input to be considered enriched peaks.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using an in-house perl script interacting with Bedtools (as described in Wamstadt et al. Cell 2012).

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: The ChIP protocol has been adapted from previous studies (Lee et al., 2006; Boyer et al., 2006, Creyghton et al., 2008) with the following modification. Diagenode Bioruptor was used to sonicate with 30 cycles of 30 sec on, 30 sec off. The samples were sonicated in 15ml polystyrene tubes at 4°C while samples were immersed in ice cold water. Antibodies used for ChIP include:  ~200 ng of DNA was submitted to SPRI-works Fragment Library System I (Beckman Coulter) for each library prepared. Briefly, the DNA is subjected to size selection (200-400bp) with magnetic beads, end repaired, then a single adenine nucleotide is added to allow for directional ligation of adaptors. For this study, a 1:100 dilution of Single End read adapters (Illumina) was used in the ligation reaction. Each sample was then amplified for 19 cycles, using the Illumina protocol, adding additional bases from the PCR primers that aid sequences to anneal to the Illumina Genome Analyzer flow cell. The samples were then purified on a Qiagen MinElute column, and libraries were quantified by Quant-it DNA Assay (Invitrogen, Q-33120), and examined for proper size and structure by Bioanalyzer (Agilent) and qPCR.

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).

tag: cell type

value: Embryonic stem cells

tag: genotype/variation

value: Anti-GFP (Abcam:Ab290)


title: H2AZ-AP3-modified ChIP-Seq


title: H3K27me3 ChIP-Seq

value: WT

value: H3K27me3 (Millipore:07-449)


title: Linker test GFP 3 KLF60

value: Linker test GFP 3


title: KL-1 CD 2ug 1 KLF61

value: K562 cells

value: KL-1 CD 2ug 1


title: Linker test GFP 2 KLF59

value: Linker test GFP 2


title: KL-1 CD 2ug 2 KLF62

value: KL-1 CD 2ug 2


title: Linker test GFP 1 KLF58

value: Linker test GFP 1


title: KL-1 CD 5X G4S linker 2 KLF56

value: KL-1 CD 5X G4S linker 2


title: KL-1 CD 5X G4S linker 3 KLF57

value: KL-1 CD 5X G4S linker 3


title: KL-1 CD 4X G4S linker 1 KLF52

value: KL-1 CD 4X G4S linker 1


title: KL-1 CD 4X G4S linker 2 KLF53

value: KL-1 CD 4X G4S linker 2


title: KL-1 CD 5X G4S linker 1 KLF55

value: KL-1 CD 5X G4S linker 1


title: KL-1 CD 3X G4S linker 2 KLF50

value: KL-1 CD 3X G4S linker 2


title: KL-1 CD 3X G4S linker 3 KLF51

value: KL-1 CD 3X G4S linker 3


title: paTh2_4h_r1

value: lymph nodes

value: 4 hrs under Th2 condition (in vitro)


title: KL-1 CD 2X G4S linker 3 KLF48

value: KL-1 CD 2X G4S linker 3


title: KL-1 CD 2X G4S linker 2 KLF47

value: KL-1 CD 2X G4S linker 2


title: KL-1 CD 1X G4S linker 2 KLF44

value: KL-1 CD 1X G4S linker 2


title: KL-1 CD 1X G4S linker 3 KLF45

value: K562 cells

value: KL-1 CD 1X G4S linker 3


title: KL-1 CD 3X G4S linker 1 KLF49

value: KL-1 CD 3X G4S linker 1


title: KL-1 CD G3S linker 3 KLF42

value: KL-1 CD G3S linker 3


title: KL-1 CD 5ug 1 KLF64

value: KL-1 CD 5ug 1


title: KL-1 CD 2X G4S linker 1 KLF46

value: KL-1 CD 2X G4S linker 1


title: KL-1 CD G3S linker 2 KLF41

value: KL-1 CD G3S linker 2


title: KL-1 GFP opposite strand 3/HB-4 PCR#2-3 KLF39/HBB48

value: KL-1 GFP opposite strand 3/HB-4 PCR#2-3


title: KL-1 GFP opposite strand 1/HB-4 PCR#2-1 KLF37/HBB46

value: KL-1 GFP opposite strand 1/HB-4 PCR#2-1


title: KL-1 CD off target opposite strand 3/HB-2 PCR#2-3 KLF36/HBB42


title: KL-1 CD off target opposite strand 2/HB-2 PCR#2-2 KLF35/HBB41


title: KL-1 CD opposite strand 2/HB-1 PCR#2-2 KLF32/HBB38

value: KL-1 CD opposite strand 2/HB-1 PCR#2-2


title: KL-1 CD opposite strand 3/HB-1 PCR#2-3 KLF33/HBB39

value: KL-1 CD opposite strand 3/HB-1 PCR#2-3


title: KL-1 CD 4X G4S linker 3 KLF54

value: KL-1 CD 4X G4S linker 3


title: KL-2 GFP 3 KLF30

value: KL-2 GFP 3


title: KL-1 GFP opposite strand 2/HB-4 PCR#2-2 KLF38/HBB47

value: KL-1 GFP opposite strand 2/HB-4 PCR#2-2


title: KL-2 GFP 2 KLF29

value: KL-2 GFP 2


title: KL-1 CD opposite strand 1/HB-1 PCR#2-1 KLF31/HBB37

value: KL-1 CD opposite strand 1/HB-1 PCR#2-1


title: KL-1 CD off target opposite strand 1/HB-2 PCR#2-1 KLF34/HBB40


title: KL-2 GFP 1 KLF28

value: KL-2 GFP 1


title: KL-2 FL 3 KLF24

value: K562 cells

value: KL-2 FL 3


title: KL-2 FL off target 1 KLF25

value: KL-2 FL off target 1


title: KL-2 FL off target 3 KLF27

value: KL-2 FL off target 3


title: KL-1 CD 1X G4S linker 1 KLF43

value: KL-1 CD 1X G4S linker 1


title: KL-2 FL 1 KLF22

value: KL-2 FL 1


title: KL-2 FL 2 KLF23

value: KL-2 FL 2


title: KL-2 CD off target 3 KLF21

value: KL-2 CD off target 3


title: KL-1 CD G3S linker 1 KLF40

value: KL-1 CD G3S linker 1


title: KL-2 CD 2 KLF17

value: KL-2 CD 2


title: KL-2 CD 3 KLF18

value: KL-2 CD 3


title: KL-2 CD 1 KLF16

value: KL-2 CD 1


title: KL-2 CD off target 1 KLF19

value: KL-2 CD off target 1


title: KL-2 CD off target 2 KLF20

value: KL-2 CD off target 2


title: KL-1 GFP 3 KLF15

value: KL-1 GFP 3


title: KL-1 GFP 2 KLF14

value: KL-1 GFP 2


title: KL-1 GFP 1 KLF13

value: KL-1 GFP 1


title: KL-1 FL off target 1 KLF10

value: K562 cells

value: KL-1 FL off target 1


title: KL-1 FL 1 KLF7

value: KL-1 FL 1


title: KL-1 FL off target 2 KLF11

value: KL-1 FL off target 2


title: KL-1 CD off target 3 KLF6

value: KL-1 CD off target 3


title: KL-1 CD off target 2 KLF5

value: KL-1 CD off target 2


title: KL-1 CD off target 1 KLF4

value: KL-1 CD off target 1


title: KL-2 FL off target 2 KLF26

value: KL-2 FL off target 2


title: KL-1 CD 2 KLF2

value: KL-1 CD 2


title: KL-1 CD 1 KLF1

value: KL-1 CD 1


title: WT 8hpf poly(A)+ mRNA

status: Public on Sep 22 2013

city: New Haven

first: Antonio

middle: J.

last: Giraldez

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: processed data file: mRNA_exon_rpkm.txt

data_processing:
Base calling was performed using CASAVA-1.8.2.
For mRNA-Seq, raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded, using Bowtie v0.12.9 with switches --seedlen 25 -n 3 -k 1 -y -e 10000. Unaligned reads were then aligned strand-specific to the zebrafish Zv9 (UCSC danRer7) genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes (with names in the form GeneX.GeneY) are constructed for reads that do not align uniquely to either gene separately, but align to both genes and nowhere else in the genome. The microRNA miR-430 polycistronic precursor is also listed as a meta gene, called ‘mir-430_hairpin’. RPKMs for gene introns (total RNA samples only) are similarly calculated, normalizing against the non-repetitive sum length of a gene’s introns, and the total number of aligned exonic reads in the sample.
For Ribosome Profiling,  reads were trimmed of 3’ adapter sequence, and reads in the trimmed length range 28-29nts were retained for ribosome protected fragments, >=18nts for input mRNA. Reads were aligned as above, retaining only uniquely aligned reads to the sense CDS sequences of protein-coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe, and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations.
Genome_build: Ensembl Zv9 / UCSC danRer7
Supplementary_files_format_and_content: RPKM tables for exons and introns for mRNA-Seq; and RPKM tables for CDS regions for ribosome profiling, generated as described above.

organism: Danio rerio

source_name: WT 8hpf poly(A)+ mRNA

extract_protocol:
For mRNA-Seq, total RNA from five embryos was extracted using Trizol (Invitrogen) for each experimental condition. RNA was treated with TURBO DNase (Ambion) for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling, 50 wild type embryos for each condition were collected at 64-cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction (ARTseq Ribosome Profiling Kit, RPHMR12126, Epicentre). For nuclease treatment, 3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28-29nt fragments were gel purified as previously described in (Bazzini et al., 2012) and cloned according to the manufacturers protocol (ARTseq Ribosome Profiling Kit, RPHMR12126, Epicentre).
TruSeq strand-specific libraries were constructed according to standard protocols. For total mRNA-Seq, sequencing libraries were treated with Epicentre Ribo-Zero Gold kits according to the published protocol, in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in (Bazzini et al., Science 2012).

treatment_protocol: Treated embryos were injected at 1-cell stage for all treatements except cycloheximide, which was applied by bathing 32-cell embryos and incubating at 27degreesC.

value: TUAB

tag: Stage

value: Whole embryos

tag: treatment


title: WT 6hpf poly(A)+ mRNA

description: processed data file: mRNA_exon_rpkm.txt

source_name: WT 6hpf poly(A)+ mRNA


title: KL-1 CD 3 KLF3

value: KL-1 CD 3


title: Cycloheximide 4hpf Total mRNA

description:
processed data file: mRNA_exon_rpkm.txt
processed data file: total_RNA_intron_rpkm.txt

source_name: Cycloheximide 4hpf Total mRNA

value: cycloheximide


title: MZpou5f1 Nanog + SoxB1 MO + rescue mRNA 8hpf poly(A)+ mRNA

description: processed data file: mRNA_exon_rpkm.txt

value: MZpou5f1 {hi349Tg/hi349Tg}

value: Nanog MO, SoxB1 MO, rescue mRNA


title: MZpou5f1 Nanog + SoxB1 MO + rescue mRNA 6hpf poly(A)+ mRNA

description: processed data file: mRNA_exon_rpkm.txt


title: MZpou5f1 Nanog + SoxB1 MO 6hpf poly(A)+ mRNA

description: processed data file: mRNA_exon_rpkm.txt

value: Nanog MO, SoxB1 MO


title: KL-1 FL off target 3 KLF12

value: K562 cells

value: KL-1 FL off target 3


title: MZpou5f1 Nanog + SoxB1 MO + rescue mRNA 4hpf Total mRNA


title: KL-1 FL 2 KLF8

value: KL-1 FL 2


title: KL-1 FL 3 KLF9

value: KL-1 FL 3


title: Nanog + SoxB1 MO Total mRNA rep2

description: processed data file: mRNA_exon_rpkm.txt, total_RNA_intron_rpkm.txt

source_name: Nanog + SoxB1 MO Total mRNA

tag: rna subtype

value: total RNA


title: Nanog MO 6hpf Total mRNA

source_name: Nanog MO 6hpf Total mRNA

value: Nanog MO


title: Alpha-amanitin 6hpf Total mRNA

source_name: Alpha-amanitin 6hpf Total mRNA

value: alpha-amanitin


title: MZpou5f1 SoxB1 MO 6hpf Total mRNA

source_name: MZpou5f1 SoxB1 MO 6hpf Total mRNA

value: SoxB1 MO


title: Nanog + SoxB1 MO Total mRNA rep1


title: Cycloheximide 6hpf Total mRNA

source_name: Cycloheximide 6hpf Total mRNA


title: MZpou5f1 6hpf Total mRNA

source_name: MZpou5f1 6hpf Total mRNA


title: WT 6hpf Total mRNA rep3

source_name: WT 6hpf Total mRNA


title: WT 6hpf Total mRNA rep2


title: WT 6hpf Total mRNA rep1


title: MZpou5f1 SoxB1 MO 4hpf Total mRNA

source_name: MZpou5f1 SoxB1 MO 4hpf Total mRNA


title: MZpou5f1 Nanog + SoxB1 MO 4hpf Total mRNA


title: MZpou5f1 Nanog MO 4hpf Total mRNA

source_name: MZpou5f1 Nanog MO 4hpf Total mRNA


title: MZpou5f1 4hpf Total mRNA

source_name: MZpou5f1 4hpf Total mRNA


title: Nanog + SoxB1 MO 4hpf Total mRNA

source_name: Nanog + SoxB1 MO 4hpf Total mRNA


title: MZpou5f1 Nanog + SoxB1 MO 8hpf poly(A)+ mRNA

description: processed data file: mRNA_exon_rpkm.txt


title: MZpou5f1 Nanog + SoxB1 MO 6hpf Total mRNA


title: Nanog MO 4hpf Total mRNA

source_name: Nanog MO 4hpf Total mRNA


title: U1U2 MO 4hpf Total mRNA

source_name: U1U2 MO 4hpf Total mRNA

value: U1 MO, U2 MO


title: Alpha-amanitin 4hpf Total mRNA

source_name: Alpha-amanitin 4hpf Total mRNA


title: WT 4hpf Total mRNA

source_name: WT 4hpf Total mRNA


title: WT 4hpf poly(A)+ mRNA

description: processed data file: mRNA_exon_rpkm.txt

source_name: WT 4hpf poly(A)+ mRNA

value: polyA RNA


title: WT 2hpf Total mRNA

source_name: WT 2hpf Total mRNA

value: TUAB


title: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling

description: processed data file: ribosome_profiling_rpkm.txt

data_processing:
Library strategy: Ribosome Profiling
Base calling was performed using CASAVA-1.8.2.
For mRNA-Seq, raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded, using Bowtie v0.12.9 with switches --seedlen 25 -n 3 -k 1 -y -e 10000. Unaligned reads were then aligned strand-specific to the zebrafish Zv9 (UCSC danRer7) genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes (with names in the form GeneX.GeneY) are constructed for reads that do not align uniquely to either gene separately, but align to both genes and nowhere else in the genome. The microRNA miR-430 polycistronic precursor is also listed as a meta gene, called ‘mir-430_hairpin’. RPKMs for gene introns (total RNA samples only) are similarly calculated, normalizing against the non-repetitive sum length of a gene’s introns, and the total number of aligned exonic reads in the sample.
For Ribosome Profiling,  reads were trimmed of 3’ adapter sequence, and reads in the trimmed length range 28-29nts were retained for ribosome protected fragments, >=18nts for input mRNA. Reads were aligned as above, retaining only uniquely aligned reads to the sense CDS sequences of protein-coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe, and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations.
Genome_build: Ensembl Zv9 / UCSC danRer7
Supplementary_files_format_and_content: RPKM tables for exons and introns for mRNA-Seq; and RPKM tables for CDS regions for ribosome profiling, generated as described above.

value: Whole embryos


title: Nanog + SoxB1 MO input mRNA for Ribosome Profiling


title: WT ribosome protected fragments for Ribosome Profiling


title: WT input mRNA for Ribosome Profiling

source_name: WT input mRNA for Ribosome Profiling


title: Hela TFAM 20G2C12 12228

status: Public on Sep 21 2013

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

institute: STANFORD UNIVERSITY

data_processing:
base calling: Casava1.8
read alignment: Bowtie 0.12.7, separate alignments against the nuclear and mitochondrial genomes
bedgraph track generation: custom-written python script
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million); separate tracks for the nuclear and mitochondrial genomes

growth_protocol: HeLaS3 cells were cultured in Dulbeco's modified Eagle's medium (DMEM, Invitrogen #11955) containing 10% bovine serum (Invitrogen #16170), penicillin and streptomycin, and L-glutamine (2mM). Cells were fed 24 hours before harvest for ChIP-seq, which was performed at 80-90% confluency.

extract_protocol:
Cells were fixed for 10min at RT in 1% formaldehyde, harvested using a cell scraper, washed once in ice-cold PBS, and resuspended in RIPA buffer with protease inhibitor. The sample was then sonicated using an 3.2mm microtip (QSonica Sonicator 4000) at 30s on 30s off intervals and 40% amplitude for 180min while in a -30C 3:1 isopropanol and water bath containing dry ice. Subsequent steps were performed as per the standard protocol. DNA was size-selected during library building to an average fragment size of 200bp. Libraries were sequenced using Illumina HiSeq 2000.
Libraries were generated following Illumina's DNA Sample Prep Kit protocol

tag: cell line

value: HeLa

value: custom antibody, 20G2C12


title: Hela Input 20G2C12 12278


title: KL-1 CD 50ug 1 KLF70

source_name: K562 cells

tag: target loci

value: KL-1 CD 50ug 1


title: Heat Stress Sample 4 (2170)

status: Public on Sep 20 2013

city: Ames

first: Derrick

middle: Jamaal

last: Coble

state: IA

address: 2254 Kildee Hall

department: Animal Science

institute: Iowa State University

data_processing:
Basecalls performed using CASAVA version 1.8
Read quality was controlled using the FastQC suite version 0.10.1. (https://preview.iplantcollaborative.org/de/#workspace). A Phred score of 28 was used to control for read quality.
RNA-seq reads were aligned to the Gallus gallus genome assembly using the Genomic Short-Read Nucleotide Alignment Program. The data were run using “32 worker threads” to optimize computational efficiency. The output was set to “split” and put into a SAM format for convenient downstream analysis. During the alignment, the “-m” setting for mismatches was set at default to allow GSNAP to auto set the number of allowed mismatches based on read length, which allowed for the best alignment across intron-exon boundaries.
Raw reads were calculated and annotated using the HT-seq package (version 4.7) in Python (http://www-huber.embl.de/users/anders/HTSeq/), which is an open source program that allows the input of raw counts from aligned reads to be annotated with gene names based on genomic features. The parameters “m<mode>”, and “-- mode=<mode>=” were set to “intersection non-empty”. The stringency of these settings allows HT-seq to identify as many genes as possible based on overlap resolution. The parameter “-stranded” was set to “no” because the cDNA library preparation was not strand specific. The parameter “–a <minaqual” was set to “default (0)” because the read quality threshold was cutoff at PHRED 28. The feature type was set at “-- type=exon” so that the reads would be counted based on exons. The GFF attribute used as the feature ID (“--idattr=<id attribute>”) was set to “gene_id”, allowing the NCBI GFF file to output gene names. For unmapped reads, special categories were provided that explained why the reads were not mapped back to the reference genome.
Genome_build: Gallus gallus Build 4.0
Supplementary_files_format_and_content: The txt files were generated using the HT-seq program and report gene names and counts.

organism: Gallus gallus

source_name: heat stressed liver

extract_protocol:
Liver samples of  25 mg were homogenized in 0.6mL of TRI Reagent Solution (Ambion) and total mRNA was isolated using the Ambion MagMax-96 kit protocol. To ensure high-quality RNA for microarray hybridization,  samples were ethanol precipitated as follows. Samples were combined with 50 microliters of RNAse free water to 100  microliters. Ten microliters of 3M sodium acetate, 300 microliters of 100% ethanol, and 20 micrograms of glycogen were added to the water-RNA mixture. These samples were incubated at -80 degrees celsius overnight  and centrifuged at 48 celsius for 25 min at 14,000 rpm. The supernatant was aspirated and the pellets were washed with 500 microliters of 70% ethanol. This mixture was centrifuged again at 7,600g for 5 min at 48 celsius. The supernatant was removed and the pellet was redissolved in RNAse free water. The samples were stored at -80 degrees celsius until usage.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hi-Seq 2000 platform following the manufacturer's protocols.

treatment_protocol: From 22 to 28 days of age, heat-stressed broilers were exposed to daily 7-hour cycles  of 35 degrees Celsius, while a control group was kept at 25 degrees Celsius throughout this time.

value: hepatic

tag: age

value: 28 days of age

tag: stress

value: heat (35 degrees Celsius)


title: Hela Input 20F8A9 12333


title: Hela Input 20G2C12 12527


title: Hela Input 20G2C12 12229


title: Heat Stress Sample 3 (2162)

tag: tissue


title: Control Sample 1 (2145)

source_name: control liver

value: control


title: Control Sample 2 (2154)


title: Heat Stress Sample 2 (2153)


title: Control Sample 3 (2163)


title: SoxB1 MO 4hpf Total mRNA

source_name: SoxB1 MO 4hpf Total mRNA

tag: strain


title: Hela TFAM 20G2C12 12277


title: Heat Stress Sample 1 (2146)


title: Hela TFAM 20G2C12 12526


title: Hela TFAM 20F8A9 12332

value: custom antibody, 20F8A9


title: nmt1-hsf1_Thi-

city: Lausanne

first: Aleksandar

last: Vjestica

state: Vaud

address: Genopode Building, University of Lausanne

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: Sample 6

data_processing:
Galaxy:FastQC_Remove sequencing artifacts
Galaxy:Tophat Select a reference genome  Schizosaccharomyces_pombe_1.1    Is this library mate-paired?  single    TopHat settings to use  full    Library Type  FR Unstranded    Anchor length (at least 3)  8    Maximum number of mismatches that can appear in the anchor region of spliced alignment  0    The minimum intron length  70    The maximum intron length  500000    Allow indel search  Yes    Max insertion length.  3    Max deletion length.  3    Maximum number of alignments to be allowed  20    Minimum intron length that may be found during split-segment (default) search  50    Maximum intron length that may be found during split-segment (default) search  500000    Number of mismatches allowed in the initial read mapping  2    Number of mismatches allowed in each segment alignment for reads mapped independently  2    Minimum length of read segments  25    Use Own Junctions  Yes    Use Gene Annotation Model  Yes    Gene Model Annotations  49: Spombe_chrAll.gtf    Use Raw Junctions  No    Only look for supplied junctions  No    Use Closure Search  No    Use Coverage Search  Yes    Minimum intron length that may be found during coverage search  50    Maximum intron length that may be found during coverage search  20000    Use Microexon Search  No
Galaxy:Cuffdiff Transcripts  49: Spombe_chrAll.gtf  *from ENSEMBL)  Perform replicate analysis  No    SAM or BAM file of aligned RNA-Seq reads  85: Tophat for Illumina on data 49 and data 31: accepted_hits    SAM or BAM file of aligned RNA-Seq reads  77: Tophat for Illumina on data 49 and data 29: accepted_hits    Library normalization method  geometric    Dispersion estimation method  pooled    False Discovery Rate  0.05    Min Alignment Count  10    Perform quartile normalization  No    Use multi-read correct  Yes    Perform Bias Correction  Yes    Reference sequence data  cached    Set Additional Parameters? (not recommended)  No
Genome_build: Schizosaccharomyces pombe genome build 1.1., for details see Wood V et al. Nature 415(6874):871-880, 2002
Supplementary_files_format_and_content: tabular txt, cuffdiff output, gene expression comparison to control cells

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown at temperatures and in media that are indicated for each sample. For details see Gould KL (2004) Protocols for experimentation with Schizosaccharomyces pombe. Methods 33: 187-188.

extract_protocol:
Qiagen RNeasy Mini Kit was used to extract total RNA.
1. Poly-A RNA is purified from total RNA (100 ng to 4000 ng) using poly-T oligo-attached magnetic beads.   2. Purified poly-A RNA is eluted from the magnetic beads and is simultaneously fragmented.  Cleaved RNA fragments are primed with random hexamers.  3. Randomly primed RNA fragments are used to generate first strand cDNA using reverse transcriptase.  4. The RNA template strand is removed from the first strand cDNA and the second strand cDNA is synthesized.  5. Ampure XP beads are used to purify the ds cDNA from the second strand reaction mix.  6.   Overhangs on the double-stranded cDNA are removed using an End Repair mix which results in the generation of blunt ends.  A 3' to 5' exonuclease activity in this mix removes the 3' overhangs and a polymerase activity fills in the 5' overhangs.  7. The blunt-ended cDNA fragments are purified using Ampure XP Beads.  8. A single  %22A%22 nucleotide is added to the 3' ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation reaction.    9. Indexed adapters are ligated to the ends of the ds cDNA. A corresponding  %22T%22 residue on the 3' end of the adapter provides a complimentary overhang for ligating the adapter to the %22A%22 overhang on the cDNA fragment.  These adapters include all sequences needed for hybridization to a sequencing flowcell .   10. Adapter-ligated cDNA molecules are purified with Ampure XP Beads.  11. PCR is performed to enrich those DNA fragments that have adapter molecules ligated to both ends.  The PCR reaction is performed using primers that anneal to the ends of the adapters.  A total of 15 cycles of PCR is performed.  12. PCR amplified library molecules are purified using Ampure XP beads.  13. The concentration of the amplified library is measured on a NanoDrop spectrophotometer.  14. An aliquot of the amplified library is run on a DNA1000 bioanalyzer chip to validate the approximate size range of the library.  15. The concentration of cluster forming units in the library is defined by qPCR using the Kapbiosystems KAPA Library Quant Kit.

treatment_protocol: The indicated sample was shifted from 24oC to 36oC for 15 minutes

tag: media

value: MM Thi-

tag: stress conditions

value: unstressed, grown at 24C


title: WT_MMThi-

description: Sample 5

value: wild type


title: mas5D

description: Sample 3

value: YES


title: IPC_input_2

city: Providence

first: Hua

last: Bai

state: RI

address: 34 Olive St, BMC502

department: EEB

institute: Brown University

data_processing:
Basecalls performed using CASAVA version 1.6
ChIP-seq reads were aligned to the Drosophila reference genome (dmel5.22) using Bowtie
Reads from two replicates were pulled together before peak calling
Peaks were called using PeakSeq with the following setting:
min_threshold = 30  max_threshold = 100  max_gap = 100  number_of_sims = 5   FDR_required = 0.01   bin_size = 10000   max_count = 3   Pf=1   pval_threshold=0.01
Genome_build: dmel5.22
Supplementary_files_format_and_content: candi_final_with_gene.txt files were generated to show the nearest gene next to the candidate peaks

organism: Drosophila melanogaster

source_name: female adult flies

extract_protocol:
About 200-250 adult females (~200 mg) at the age of 15-day-old were pooled for each ChIP sample. Flies were homogenized and cross-linked in 1 X PBS containing 1 % formaldehyde. The fly lysate were sonicated using Branson 450 sonicator to break down the chromatin into a pool of DNA fragment with average size of 500 bp. Immunoprecipitation was performed using Dynal protean A beads (Invitrogen) and affinity purified anti-dFOXO antibody made in our laboratory . Following the wash with LiCl and TE buffer, the DNA-protein complex was eluted from the Dynal beads, reverse-crosslinked and purified.
About 20 ng of ChIP DNA (dFOXO-bound DNA) and input DNA (DNA sample before the immunoprecipitation) were used in library preparation following the methods described in Quail, M.A., et al., Nat Methods. 2008 (5). 1005-1010. Briefly, DNA was end-repaired using an End-It DNA End Repair Kit from Epicentre (# ER0720). The blunt, phosphorylated ends were treated with Klenow (3’->5’ exo-) from NEB (# M0212s) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 150~350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel.

value: IPC ablation mutants

tag: chip antibody

tag: gender

value: female

tag: genotype

value: whole organism


title: WT_24oC

description: Sample 1


title: IPC_chip_1

value: dFOXO


title: IPC_input_1


title: Control Sample 4 (2169)


title: chico_chip_2

value: chico heterozygous mutants


title: chico_input_1


title: chico_input_2


title: chico_chip_1


title: H3K27ac_Input

city: New York

first: Lionel

last: Ivashkiv

state: NY

address: 535 East 70th Street

institute: Hospital for Special Surgery

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg19 genome assembly using BOWTIE with default configurations.
peaks were called using ChIPSeeqer with the following setting: STAT1 -t_15  -t_fold 2; H3K27Ac  -t_20 -t_fold 3 ; IRF1 -t_15 -t_fold 2;
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using ChIPSeeqer

The headers for peak *txt files are as follows (from the left):

Chromosome  : chromosome name
Start_Position  : the first (genomic) coordinate of the peak
End_Position  : the second (genomic) coordinate of the peak
Avg_p-value  : average log p-value of the nucleotides in the normalized peak region
Score   : score estimated as the average ChIP reads/length of peak (minus the average INPUT reads/length of peak - if INPUT is available)
Posmaxpeakheight    : the position of the maximum height of the peak
Maxpeakheight  : the maximum peak height (in reads)
RelPosMaxPeakHeight(%) : the relative position of the maximum height of the peak, e.g., 50% means the highest point is at the middle of the peak
Peak_Size  : the size of the peak (in bp)
Mid_point  : the middle position of the peak
Summit_dist_from_mid  : the distance of the maximum height from the middle of the peak

source_name: Peripheral blood cells

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).

extract_protocol:
Sonicated cell lysates of nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was purified using MinElute PCR Purification kit and PCR amplified with Illumina primers for 15 cycles. Library fragments of 200-300 bp were band isolated from an 1.5% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina HiSeq 2000 Sequencer following the manufacturer's protocols.

treatment_protocol: Cells were treated with or without IFN-g (100U/ml) for 24 hours, and then stimulated with LPS (50ng/ml) for 3 or 6 hours as indicated.

value: CD14+ monocytes

value: none, input

tag: experimental condition

value: Combination of the 4 conditions


title: IRF1_Input

tag: cell type


title: STAT1_Input


title: H3K27Ac_ChIPSeq_rep2_C

value: H3K27ac (Abcam ab-4729)

value: Cultured with MCSF (10ng/ml) and stimulated with LPS (50ng/ml) for 3 hours.


title: H3K27Ac_ChIPSeq_rep2_D

value: Cultured with MCSF (10ng/ml) and IFN-gamma (100U/ml) for 24 hours, stimulated with LPS (50ng/ml) for 3 hours.


title: IRF1_ChIPSeq_B

value: IRF1 (Santa Cruz sc-497)

value: Cultured with MCSF (10ng/ml) and IFN-gamma (100U/ml) for 24 hours.


title: IRF1_ChIPSeq_E

value: Cultured with MCSF (10ng/ml) and stimulated with LPS (50ng/ml) for 6 hours.


title: H3K27Ac_ChIPSeq_rep2_B


title: ssa2D

description: Sample 4

tag: genotype/variation

value: unstressed, grown at 24C


title: IRF1_ChIPSeq_A

value: Cultured with MCSF (10ng/ml)


title: STAT1_ChIPSeq_rep2_B

value: STAT1 (Santa Cruz sc-345)


title: H3K27Ac_ChIPSeq_rep1_C


title: H3K27Ac_ChIPSeq_rep1_A


title: H3K27Ac_ChIPSeq_rep1_B


title: H3K27Ac_ChIPSeq_rep2_A


title: WT_36oC_15min

description: Sample 2

value: wild type

value: YES

value: heat-stress, shifted from 24C to 36C for 15 minutes


title: IPC_chip_2

value: IPC ablation mutants

value: dFOXO

value: female

value: whole organism


title: H3K27Ac_ChIPSeq_rep1_D

value: CD14+ monocytes


title: IRF1_ChIPSeq_F

value: Cultured with MCSF (10ng/ml) and IFN-gamma (100U/ml) for 24 hours, stimulated with LPS (50ng/ml) for 6 hours.


title: STAT1_ChIPSeq_rep1_B


title: STAT1_ChIPSeq_rep1_A


title: STAT1_ChIPSeq_rep2_D


title: STAT1_ChIPSeq_rep1_C

value: Cultured with MCSF (10ng/ml) and stimulated with LPS (50ng/ml) for 3 hours.


title: STAT1_ChIPSeq_rep1_D

value: Cultured with MCSF (10ng/ml) and IFN-gamma (100U/ml) for 24 hours, stimulated with LPS (50ng/ml) for 3 hours.


title: Sample_RNA-IP_IgG_GM12750

city: Ann Arbor

first: Isabel

middle: Xiaorong

last: Wang

state: Michigan

address: 210 washtenaw ave

department: Pediatrics&Genetics

institute: HHMI/University of Michigan

data_processing:
We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.
Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches ≤[(read length+2)/12-2]; Mapping score ≥20;  Soft-clipping on (-trim-mismatch-score=-3);  Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted.  SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments.  Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.
Expression levels of RNA transcripts were analyzed using Cufflinks.
Genome_build: HG18

source_name: cultured B-cells

growth_protocol: Cultured B-cell lines from two CEPH individuals (Centre d'Etude du Polymorphisme Humain), GM12004 and GM12750, were obtained from Coriell (Camden, NJ, USA).  The B-cells were grown to a density of 5x105 cells/mL in RPMI 1640 supplemented with 15% fetal bovine serum, 100 units/mL penicillin and 100 μg/mL streptomycin, and 2 mmol/L L-glutamine.  For downstream experiments, cells were harvested 24 hours after addition of fresh medium.

extract_protocol: RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen).  For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen).  RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively.  The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated.

treatment_protocol: 5X105 cultured B cells were transfected with 2.5 nmol Accell siRNAs (Thermo Scientific) against ADAR1 and ADAR2 according to the manufacturer’s protocols.  2.5nmol of non-targeting control siRNA (NTC-siRNA) was transfected as negative controls.  The transfected cells with siRNAs were incubated at 37°C in Accell transfection media for 96 hours.  In time course experiment, cells were treated with another 2.5nmol of siRNAs 24 hours following the first treatment.  Accell media was then replaced with regular growth media.  Cells were allowed to recover for 24 hours before being harvested.  For protein immunoprecipitation, Cells were lysed in Lysis buffer (20 mM Tris HCl (pH 8), 137 mM NaCl, 10% glycerol, 1% Nonidet P-40 (NP-40) and 2 mM EDTA) supplemented with 1XComplete protease inhibitors (Roche) and 1Xphosphatase inhibitors II and III (Sigma). Cell lysates containing 150 mg of total protein were incubated with 1 µg of anti-ADAR1 (#HPA003890, Sigma), or negative control rabbit IgG (ab46540, ABCAM) at 4°C overnight.  Immuno-complex was pulled down using Protein A agarose (Roche), and washed 4 times with lysis buffer.  Immunoprecipitate was eluted in 20 mM Tris/7.5, 150 mM NaCl, 2.5 mM MgCl2, 0.2% SDS at 30°C for 1 hour.  Protein samples were analyzed by Western Blot using anti-ADAR antibody (1:1000) or anti-tubulin (1:2000, Millipore).  For RNA-immunoprecipitation, anti-ADAR1 RNA-immunoprecipitation was carried out using Magna RNA-Binding Protein Immunoprecipitation Kit (Millipore) following manufacturer’s protocol.  Briefly, for each immunoprecipitation reaction, 2X107 cultured B-cells were harvested and lysed in 100 µl of Lysis Buffer with protease and RNase inhibitors.  1 µg of anti-ADAR antibody (#HPA003890, Sigma) or negative control rabbit IgG (ab46540, ABCAM) were conjugated to magnetic Protein A/G beads.  100 µl of cell lysate was added into 900µl Immunoprecipitation Buffer with RNase inhibitor and incubated with cRNase inhibitor, and incubated with protease K in presence of 1%SDS at 55°C for 30 minutes.  RNA was then extracted from supernatants using phenol:chloroform:isoamyl alcohol and precipitated using ethanol.

value: B-cells

tag: directional rnaseq

value: Non-directional

tag: experiment

value: RNAIP-IgG

value: RNA-IP using control IgG

tag: antibody vendor/catalog#

value: ABCAM, ab46540


title: Sample_GM12750_ADARkd_BTime

tag: cell line

tag: treatment

value: siRNA knockdown of ADAR1, 48 hour time point


title: Sample_GM12750_nt_Dtime

value: NTC- D-Time

value: non-targeting control siRNA, 96 hour time point


title: Sample_RNA-IP_ADAR_GM12750

value: RNA-IP using ADAR1 antibody

value: Sigma, #HPA003890


title: Sample_RNA-IP_ADAR_GM12004


title: Sample_GM12750_ADARkd_CTime

value: siRNA knockdown of ADAR1, 72 hour time point


title: Sample_GM12750_ADARkd_ATime

value: Adar1-KD-A Time24h

value: siRNA knockdown of ADAR1, 24 hour time point


title: Sample_GM12750_ADARkd_DTime

value: siRNA knockdown of ADAR1, 96 hour time point


title: Sample_GM12004_ADARkd

value: siRNA knockdown of ADAR1


title: Sample_GM12004_ADAR2_kd

value: siRNA knockdown of ADAR2


title: Sample_GM12004_NT

value: cDNA-NTC-siRNA

value: non-targeting control siRNA


title: Sample_GM12750_Directional_NT

value: B-cells

value: Directional

value: cDNAdirectional


title: Sample_GM12750_ADAR_KD

value: Non-directional


title: Pcon_vegmix_1

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

country: Germany

institute: Ruhr-University Bochum

data_processing:
Illumina Casava 1.8 used for base calling
reads were trimmed for low quality bases, and reads with undefined bases ("N") were removed as described in Teichert et al. 2012, BMC Genomics 13: 511
read counts and expression ratios for annotated gene models were determined as described in Teichert et al. 2012, BMC Genomics 13:511
Genome_build: P. confluens genome version 01 (genome project ID #65573, BioProject acc. PRJNA65573)
Supplementary_files_format_and_content: tab-delimited text file on Series record includes normalized read counts and expression ratios for all annotated genes as well as additional information (e.g. best blastp hit, predicted localization etc.)

organism: Pyronema omphalodes

source_name: vegetative mycelium (pool)

growth_protocol: Growth for samples Pcon_sex was in surface cultures in constant light (pool of RNAs from 3, 4, and 5d) in WPC medium, for Pcon_veg samples in surface cultures in WPC in constant darkness (pool of RNAs from 3, 4, and 5d), and for Pcon_vegmix samples, pooled RNA from the following conditions was used: growth in WPC in submerged culture in constant light and constant darkness, and growth in BMM in surface culture in constant darkness, all for 3d

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy lipid tissue mini kit with some modifications as described in Nowrousian and Kück 2006, FEMS Microbiol Lett 257: 328-335
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: vegetative mycelium (pool)


title: Pcon_veg_2

source_name: vegetative mycelium

value: vegetative mycelium


title: Pcon_vegmix_2


title: Sample_GM12004_Directional

value: no


title: Sample_GM12750_Directional


title: Sample_GM12750_Directional_ADAR_KD


title: Pcon_veg_1


title: Sample_RNA-IP_IgG_GM12004

value: RNAIP-IgG

value: RNA-IP using control IgG

value: ABCAM, ab46540


title: Sample_GM12004_baseline

value: cDNAbaseline


title: Pcon_sex_1

source_name: sexually developing mycelium

value: sexually developing mycelium


title: XT32_ctrl_polyA-RNA_2nd

status: Public on Sep 19 2013

city: London

first: George

middle: E.

last: Gentsch

state: Greater London

address: 1 Midland Road

department: Developmental Biology Laboratory

country: United Kingdom

institute: The Francis Crick Institute

description: Control embryos (2nd biological replicate)

data_processing:
Basecalls were performed using Casava version 1.8.
Bowtie 0.12.7 (Langmead, 2010) was used with the parameters -a --best -v 3 -y -I 0 -X 10000 to align the reads to the ensembl JGI4.1 transcriptome. Any read pair that aligned to multiple transcripts of different genes was discarded, and any read pair that mapped to one or many transcripts of the same gene was counted once. This set of valid read alignments was used to estimate the fragment size distribution. The counting process was repeated to discard outlying fragment sizes.
Quantitative readouts from RNA-Seq experiments were analysed by means of the R package called DESeq (Anders and Huber, 2010) to identify differentially expressed genes.
Genome_build: X. tropicalis JGI v4.1
Supplementary_files_format_and_content: Tab-delimited text file includes raw read counts for each sample.

organism: Xenopus tropicalis

source_name: embryo

growth_protocol: Embryos were grown to the indicated developmental stage in 0.05x MMR at 25ºC.

extract_protocol:
Embryos were flash-frozen on dry ice, and total RNA was extracted using Trizol (Invitrogen) and subjected to two precipitations with ethanol and LiCl.
Total RNA to the amount of two X. tropicalis embryos (~3 µg) was processed according to the Illumina TruSeq protocol (November 2010). The quality was controlled on the Bioanalyser 2100 (Agilent) using the DNA-specific chip DNA 1000 (Agilent).
Libraries were read paired-end along 55 bases on the Illumina HiSeq 2000 machine.

treatment_protocol: Embryos were injected as indicated at 1-cell stage with 20ng morpholino antisense oligonucleotide to block Brachyury protein expression.

value: Nigerian (Cam4), wild-type

value: early tadpole (st. 32)

value: injection of 20ng control morpholino at 1-cell stage


title: XT20_polyA-RNA

description: Uninjected embryos

value: early tailbud (st. 20)

value: no treatment


title: XT32_ctrl_polyA-RNA_3rd

description: Control embryos (3rd biological replicate)


title: Pcon_sex_2


title: XT32_BB3KD_polyA-RNA_2nd

description: Double knock-down of Xbra and Xbra3 (2nd biological replicate)

value: injection of Xbra/Xbra3 splicing- and translation-blocking morpholino (20ng total) at 1-cell stage


title: XT32_ctrl_polyA-RNA_1st

description: Control embryos (1st biological replicate)


title: XT32_BB3KD_polyA-RNA_1st

description: Double knock-down of Xbra and Xbra3 (1st biological replicate)


title: pvu_ehb

city: Montréal

first: Pablo

last: Cingolani

state: Quebec

address: 701 Avenue du Docteur-Penfield

country: Canada

institute: McGill University

description: Pvu restriction enzyme (Rubicon)

data_processing:
Library strategy: Pvu-Seq
Image analysis, base calling and sequence extraction was performed using standard Illumina Pipeline v1.6 software
Read mapping was performed using BWA, except for RNA-Seq which was done by Bowtie (TopHat)
For BS-Seq analysis we used our analysis pipeline (BS-Miner)
RNA-Seq primary analysis was performed using Tophat-Cufflinks suite
For mDip analysis, peak detection was performed using MACS
Pvu-Seq reads: Peak detection using MACS v1.4 (forcing zero length shift)
Genome_build: Amel2
Supplementary_files_format_and_content: Standard VCF (methylation calls), BED files (peaks), FPKM (RNA-seq)
Image analysis, base calling and sequence extraction was performed using standard Illumina Pipeline v1.6 software
Read mapping was performed using BWA, except for RNA-Seq which was done by Bowtie (TopHat)
For BS-Seq analysis we used our analysis pipeline (BS-Miner)
RNA-Seq primary analysis was performed using Tophat-Cufflinks suite
For mDip analysis, peak detection was performed using MACS
Genome_build: Amel_2.0
Supplementary_files_format_and_content: Standard VCF (methylation calls), BED files (peaks), FPKM (RNA-seq)

organism: Apis mellifera

source_name: honey bee

extract_protocol: Pvu: Using ThruPLEX-FD Prep Kit (Rubicon Genomics), following library preparations from Manual:R40048-08 (QAM-094-001).  Template Preparation: 10 µL of each DNA sample ; add 3µL of pre-mix of Template Preparation Buffer and Template Preparation Enzyme; centrifuge; incubate.  Library Synthesis: Add 2µL of pre-mix of Library Synthesis Buffer and Library Synthesis Enzyme to each sample; centrifuge; incubate.  Amplification: pre-mix of Library Amplification Buffer and Library Amplification Enzyme; add 58 µL to each library; add 2 µL of one Indexing Reagen and mix; centrifuge. Library purification by AMPure

value: head


title: Sample_GM12750_NT

value: B-cells

value: cDNA-NTC-siRNA

value: non-targeting control siRNA


title: mDip_hmc

description: IP hmC antibody

data_processing:
Image analysis, base calling and sequence extraction was performed using standard Illumina Pipeline v1.6 software
Read mapping was performed using BWA, except for RNA-Seq which was done by Bowtie (TopHat)
For BS-Seq analysis we used our analysis pipeline (BS-Miner)
RNA-Seq primary analysis was performed using Tophat-Cufflinks suite
For mDip analysis, peak detection was performed using MACS
Pvu-Seq reads: Peak detection using MACS v1.4 (forcing zero length shift)
Genome_build: Amel2
Supplementary_files_format_and_content: Standard VCF (methylation calls), BED files (peaks), FPKM (RNA-seq)
Image analysis, base calling and sequence extraction was performed using standard Illumina Pipeline v1.6 software
Read mapping was performed using BWA, except for RNA-Seq which was done by Bowtie (TopHat)
For BS-Seq analysis we used our analysis pipeline (BS-Miner)
RNA-Seq primary analysis was performed using Tophat-Cufflinks suite
For mDip analysis, peak detection was performed using MACS
Genome_build: Amel_2.0
Supplementary_files_format_and_content: Standard VCF (methylation calls), BED files (peaks), FPKM (RNA-seq)

extract_protocol: meDIP: Shear DNA to ~600bp fragments:  3µg DNA + TE to 130µl in microTUBE. Denature DNA, 125µl (3µg) sheared DNA + 330µl TE. IP and wash: add 51µl 10x IP buffer + 3µl (1µg/µl) antibody; incubate > 2hours at 4C; add 25µl protein G beads; incubate > 2hours; collect beads with a magnetic rack; wash beads with 700µl 1xIP buffer, incubating 10 minutes x RT x 900rpm (or RT rotator); repeat wash 2 more times. The mC antibodies were mouse monoclonal (Active Motif, Inc.) and the hmC antibodies were rabbit polyclonal (Active Motif, Inc.). Immunoprecipitation was with protein G beads (Active Motif, Inc.) following the manufacturer’s protocol.

tag: medip antibody

value: Rabbit polyclonal hmC antibody(Active Motif, Inc.)


title: rna_ehb

extract_protocol: mRNA libraries were constructed from 4 biological replicates per group using the Illumina (San Diego, CA) mRNA-seq protocol (June, 2010 version) with multiplex adapters. Each replicate contained pooled RNA from 4 individual bees. We synthesized 75 nt mRNA sequences using an Illumina Genome Analyzer Iix, with 4 indexed libraries in each lane, to a read depth of ca. 4–9 million reads/library.

tag: tissue


title: m_ehb

description: Bisulfite converted

extract_protocol: Bisulfite: Using guidelines from Illumina (Whole‐genome Bisulfite Sequencing for Methylation Analysis, Part # 15021861 Rev. B). Fragment the gDNA to 250 bp peak size; convert overhangs resulting from fragmentation into blunt ends using T4 DNA polymerase and Klenow enzyme; add a single ‘A’ nucleotide to the 3’ end; ligates adapters to the ends of the DNA fragments; remove unligated adapters, and select a 275–350 bp size‐range of DNA fragments for bisulfite treatment; treat with bisulfite to convert any un‐methylated Cytosine to Thymidine (EpiTect Bisulfite Kit); PCR to selectively enrich those DNA fragments that have methylated adapter molecules on both ends


title: TP_kidney

city: Bei Jing

first: Shilin

last: Tian

address: Xueqing Road

department: genome research

country: China

institute: Novogene Bioinformatics Technology CO.ltd

description: Sample 4

data_processing:
Illumina Casava1.82 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Tibetan pig whole genome using Tophat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Tibetan pig whole genome de novo (PRJNA186497 available on Jan 1, 2014)
Supplementary_files_format_and_content: tab-delimited text files containing RPKM values for each Sample

organism: Sus scrofa

extract_protocol:
total RNA was extracted with Trizol.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Tibetan

tag: local origin

value: Ganzi Tibetan autonomous prefecture, Sichuan province, China

value: Kidney


title: XT32_BB3KD_polyA-RNA_3rd

description: Double knock-down of Xbra and Xbra3 (3rd biological replicate)

tag: strain


title: mDip_mc

description: IP mC antibody

value: Mouse monoclonal mC antibody (Active Motif, Inc.)


title: iMN-ESCs with Dox treatment 1

city: Brockport

first: Rongkun

last: Shen

state: New York

address: 350 New Campus Dr

institute: SUNY Brockport

data_processing:
Basecalls performed using GAPipeline
ChIP-seq reads were aligned to the mm9 genome assembly using BWA v0.5.8a with default parameters.
To exclude the multiple-hit reads and low-mapping-quality reads, only the reads with mapping quality>25 were kept for further analysis. If several reads had the exact same sequence and direction, only one copy was kept for the analysis to minimize the artifacts introduced by PCR amplification during sample preparation.
The samples trea-ted with Dox were regarded as Isl1-Lhx3-ChIP, whereas the samples without Dox were regarded as control. To achieve more robust analysis, the sequencing data from two biological repli-cates were pooled for each dataset.
The peak calling was con-ducted with QuEST v2.4 software (10) using the“transcription factor”option (bandwidth 30 bp, region size 300 bp) and the recommended peak-calling parameters (30-fold Isl1-Lhx3-ChIP to control enrichment for seeding the regions, threefold Isl1-Lhx3-ChIP enrichment for extending the regions, and threefold Isl1-Lhx3-ChIP to control fold enrichment).
Genome_build: mm9
Supplementary_files_format_and_content: peaks, tab-delimited text: Peak_id Locus ChIP_score Background_Score Region_start Region_end Max_position ChIP_tags

source_name: iMN-ESCs

growth_protocol: Generation of inducible motor neuron ES cells (iMN-ESCs) was described previously (6). The A172LoxP ESC line (7) was maintained in an undifferentiated state on 0.1% gelatin-coated dishes in the ESC growth media that consisted of Knockout DMEM, 10% (vol/vol) FBS, 0.1 mM nonessential amino acids, 2 mML-glutamine, 0.1 mM β-mercaptoethanol, and recombinant leukemia in-hibitory factor (LIF, 1000 units/mL, Chemicon). A gene encoding FLAG-tagged Isl1-Lhx3 fusion construct was inserted into Tet-inducible plasmid p2Lox and were cotransfected with pSALK-Cre into ESC lines by electroporation. Stable transfectants were isolated by selection with neomycin (G418, 400 μg/mL) for 7 d. Doxycycline (Dox)-dependent induction of FLAG-Isl1-Lhx3 was confirmed by RT-PCR and Western blotting and immunohisto-chemical analyses usingα-Isl1,α-Lhx3, andα-FLAG antibodies. The differentiation of iMN-ESCs into MNs was done as previously described (6). Briefly, embryoid bodies of iMN-ESCs were treated with 0.5μM RA alone for 2 d and then were cultured without or with Dox (2μg/mL) in the presence of RA for 4 d. The cells were treated with LIF (1,000μ/mL) for 16 h before harvest.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's ChIP-Seq Sample Preparation protocol.

value: inducible motor neuron ES cells

tag: chip antibody

value: anti-Flag antibody

value: Dox treatment


title: TP_lung

description: Sample 3

value: Lung


title: Sample_GM12750_baseline

value: Non-directional

value: cDNAbaseline

value: no


title: TP_heart

description: Sample 1

value: Heart


title: TP_liver

description: Sample 2

value: Liver


title: INPUT_XBRA20.1

description: Input for Xbra ChIP-Seq (early tailbud)

data_processing:
Basecalls were performed using Casava version 1.8.
ChIP-seq reads were aligned to the X. tropicalis genome assembly 4.1 using CLC Bio Genomics Workbench 5.5 default settings. Non-specific and ambiguous matches were ignored.
ChIP-Seq peaks were identified using MACS 2.0.4 (Zhang et al., 2008, PMID:18798982). Settings were as follows: effective genome size, 1,700,000,000bp; band width, 300bp; Model fold, 3-30; Range for calculating regional lambda, 1,000-10,000bp; FDR, 0.01.
Genome_build: X. tropicalis JGI v4.1 (August 2005, JGI4.1/xenTro2, available on the UCSC Genomic Browser)
Supplementary_files_format_and_content: BigWig files with -log(peak p-value)

source_name: Input for Xbra ChIP-Seq (early tailbud)

growth_protocol: Approximately 3000 dejellied embryos were grown for each ChIP-Seq experiment to the indicated developmental stage in 0.05x MMR at 22C.

extract_protocol:
Cross-linked chromatin was extracted with E1, E2 and E3 (Lee et al., 2006 , PMID:17406303). Chromatin was solubilised and sheared to fragments of 100-500bp peaking around 200 bp. ChIP was performed with ChIP-grade antibodies coupled to Dynabeads M-280. Beads were extensively washed with 10 times pre-chilled RIPA buffer (50 mM Hepes-KOH pH7.5, 500 mM LiCl, 1mM EDTA, 1% Igepal CA-630, 0.7% (w/v) Na-deoxycholate) and twice in pre-chilled TEN (10 mM Tris pH8.0, 1 mM EDTA, 150 NaCl). Bound chromatin was eluted from the beads with elution buffer (50 mM Tris pH8.0, 1 mM EDTA pH8.0, 1% SDS) at 65C for 30 min. ChIP and input samples were supplemented with 1/20 volume of 5 M NaCl before incubating them for 6-15 h at 65C to reverse cross-links. One volume of TE pH 8.0 and 200 µg/ml of CONCERT RNase A (Invitrogen) was added to the samples for a 1-h incubation at 37C. The samples were further treated with 200 µg/ml of proteinase K (Ambion) for 2-4 h at 55C. Eventually, the DNA fragments were purified with phenol:chloroform:isoamylalcohol and precipitated in ethanol for sequencing. The air-dried DNA pellet was dissolved in 32 µl of molecular-grade water. The amount of DNA was quantified using a Qubit fluorometer (Invitrogen) following the manufacturer’s instructions. The yield of co-immunoprecipitated DNA was about 10 ng, which created robust libraries.
The single-end library was generated based on the manufacturer’s instructions (Illumina) with minor modifications. DNA fragments were end-repaired, ligated to adaptors at a final dilution of 1:480, size-selected to 200-300 bp by E-gel (Invitrogen) and PCR (18 cycles) amplified. The DNA Clean & Concentrator-5 kit (Zymo Research) was used to clean up reactions. DNA was eluted from the column at 50C. Upon solid phase reversible immobilisation (SPRI) purification, the integrity of the library was checked on the Agilent 2100 Bioanalyzer using an Agilent DNA 1000 chip.
ChIP-Seq libraries were sequenced for 40 cycles on the Illumina Genome Analyser IIx.

treatment_protocol: Embryos were washed in 0.01x MMR and fixed at room temperature with fresh formaldehyde (molecular biology grade; Sigma F-8775) at a final concentration of 1% (v/v). The fixation time was determined empirically according to the developmental stage of the embryo to achieve efficient chromatin shearing and ChIP enrichment. Early developmental stages were fixed over a longer time period than later stages: X. tropicalis gastrula (stage 11-12.5) for 20-25 min and early tailbud (stage 19-20) for 15 min. Fixative solution was aspirated and embryos quickly washed 3-4 times with cold 0.01x MMR. Batches of approximately 250 embryos were equilibrated in ice-cold HEG solution (50 mM HEPES-KOH pH7.5, 1 mM EDTA pH8.0, 20% glycerol). Once the embryos settled, excess HEG was removed. Embryo batches were snap-frozen in liquid nitrogen and stored at -80C for future use.

value: Nigerian (Cam4)

value: wild type

value: embryo

value: early tailbud (st.19-20)


title: iMN-ESCs without Dox treatment 1

value: without Dox treatment


title: INPUT_XBRA12.2

description: Input for Xbra ChIP-Seq (gastrula), biological replicate

source_name: Input for Xbra ChIP-Seq (gastrula)

value: gastrula (st. 11-12.5)


title: XBRA12.2

description: Xbra ChIP-Seq (gastrula), biological replicate

source_name: Xbra ChIP-Seq (gastrula)

value: Xbra

tag: chip antibody reference


title: INPUT_VEGT12.1

description: Input for VegT ChIP-Seq (gastrula)

source_name: Input for VegT ChIP-Seq (gastrula)


title: XBRA20.1

description: Xbra ChIP-Seq (early tailbud)

source_name: Xbra ChIP-Seq (early tailbud)


title: INPUT_XBRA12.1

description: Input for Xbra ChIP-Seq (gastrula)


title: XEOMES12.1

description: Eomes ChIP-Seq (gastrula)

source_name: Eomes ChIP-Seq (gastrula)

value: Eomes


title: XBRA12.1

description: Xbra ChIP-Seq (gastrula)


title: XVEGT12.1

description: VegT ChIP-Seq (gastrula)

source_name: VegT ChIP-Seq (gastrula)

value: VegT


title: INPUT_XEOMES12.1

description: Input for Eomes ChIP-Seq (gastrula)

source_name: Input for Eomes ChIP-Seq (gastrula)


title: iMN-ESCs with Dox treatment 2

value: inducible motor neuron ES cells

value: anti-Flag antibody


title: [E-MTAB-1585] 7sk_5c [re-analysis]

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221950

data_processing:
Alignment information was extracted from E-MTAB-1585 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585/). Only sequences that mapped uniquely to the genome were directionally extended and the reads were counted across the genome to generate wig files. Further, reads were normalized using reads per millions. Normalized control tracks were subtracted from knockdown ones to illustrate the RNA expression pattern caused by 7SK knockdown.
Genome_build: mm9

source_name: 7sk KO_ESCs_RNA-seq

extract_protocol: Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using  the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37 degrees C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37 degrees C. The resulting RNA (5' mono-phosphorylated and 3' OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3' and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for library construction. Sequencing was performed in a HiSeq 2000 instrument (Illumina) to produce 50nt single-end reads. Sequence reads were trimmed to remove any trailing 3'-adapter sequence using Reaper version 12-048 (http://www.ebi.ac.uk/research/enright/software/kraken) with options: -3p-global 12/1/0/2 -3p-prefix 12/1/0/2 -3p-head-to-tail

treatment_protocol: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 10^6 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1uM PD0325901 (AxonMedChem), 3uM CHIR99021 (AxonMedChem) and 10^6 units/L LIF (ESGRO, Millipore)). 1ug/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Cells were transfected with 1000 pmol antisense oligonucleotides (Integrated DNA Technologies) using the Mouse ES Cell Nuclefector Kit (Lonza).

tag: strain background

value: embryonic stem cells

tag: transfected with

value: 5' antisense oligo

value: 7SK knockdown


title: [E-MTAB-1585] 7sk_6c [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221953

tag: cell type

value: 3' antisense oligo


title: iMN-ESCs without Dox treatment 2


title: [E-MTAB-1585] 7sk_4a [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221948

value: scrambled oligo control

tag: genotype/variation


title: [E-MTAB-1585] 7sk_5a [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221946


title: [E-MTAB-1585] 7sk_2c [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221951


title: [E-MTAB-1585] 7sk_3c [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221954


title: [E-MTAB-1585] 7sk_3a [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221944


title: [E-MTAB-1585] 7sk_2a [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221955


title: [E-MTAB-1585] 7sk_2b [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221957


title: [E-MTAB-1585] 7sk_1c [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221945


title: Epididymis4_DNase-Seq

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Avenue

institute: Case Western Reserve University Medical School

description: Genome-wide DNase-I hypersensitive sites in HEE cells; pool of two individual samples

data_processing:
Data processing is described in detail at http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=346639599&c=chr21&g=wgEncodeOpenChromDnase, and is summarized here.
Sequences from each experiment were aligned to the genome using BWA (Li et al., 2008) for the GRCh37 (hg19) assembly. The command used for these alignments was: [ > bwa aln -t 8 genome.fa s_1.sequence.txt.bfq > s_1.sequence.txt.sai ] where genome.fa is the whole genome sequence and s_1.sequence.txt.bfq is one lane of sequences converted into the required bfq format.
Using F-seq, the resulting digital signal was converted to a continuous wiggle track that employs a Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). The exact command used for this step was: [ > fseq -l 600 -v -f 0 -b <bff files> -p <iff files> aligments.bed ] where the bff files are the background files based on alignability, the iff files are the background files based on the Input experiments, and alignments.bed is a bed file of filtered sequence alignments.
Discrete DNaseI HS sites (peaks) were identified from DNase-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant.
Genome_build: hg19
Supplementary_files_format_and_content: epid_combined_finalPeaks.narrowPeak contains combined peak calls (as described above) from Epididymis3_DNase-Seq and Epididymis4_DNase-Seq in ENCODE narrowPeak format (BED6+4).

source_name: Human epididymal epithelial cells (pool of two individual samples)

growth_protocol: Growth conditions as described in Harris, A., and Coleman, L. (1989) Ductal epithelial cells cultured from human fetal epididymis and vas deferens: relevance to sterility in Cystic Fibrosis. J.Cell Sci., 92: 687-690.

extract_protocol:
Extraction was performed according to the protocol at http://genome.ucsc.edu/ENCODE/protocols/general/Duke_DNase_protocol.pdf
Library construction was performed according to the protocol at http://genome.ucsc.edu/ENCODE/protocols/general/Duke_DNase_protocol.pdf

treatment_protocol: No treatment.

value: immature

value: epididymis

value: epithelia


title: Epididymis3_DNase-Seq

description: Genome-wide DNase-I hypersensitive sites in HEE cells

source_name: Human epididymal epithelial cells


title: [E-MTAB-1585] 7sk_1b [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221956

value: wild type


title: [E-MTAB-1585] 7sk_1a [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221952


title: DP103-3 (iFLMbeta-GFP)

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

institute: Max Planck Institute for Developmental Biology

data_processing:
Base calling: Illumina SCS/RTA version 2.8
Read filtering and trimming: SHORE import version 0.8 (shore.sf.net). Filtering parameters: “-n 10% -c -k 32”
Read mapping: SHORE mapflowcell version 0.8 (shore.sf.net) utilizing GenomeMapper version 0.4.4 (http://1001genomes.org/software/genomemapper.html). mapflowcell alignment parameters “-n 4 --select=10,11,12,13 --restrict=on”
Peak calling: SHORE peak version 0.8 (shore.sf.net). Peak calling on each set of replicates using default peak calling parameters, TAIR10 genome annotation file provided via “-a”.
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak region lists generated by SHORE peak, see README.txt

organism: Arabidopsis thaliana

source_name: DP103-3 (iFLMbeta-GFP)

growth_protocol: 15 days LD 16ºC (gFLM) and 10 days LD 23ºC (iFLMbeta and iFLMdelta)

extract_protocol:
Material collection: ZT8. ChIP protocol using anti-GFP Ab (Abcam #ab290)
Libraries were prepared according to manufacture's instructions of the ChIP-seq sample prep kit from Illumina. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA from 150-400 bp was band isolated from an agarose gel. The purified DNA was PCR amplified with Illumina primers for 18 cycles and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

tag: ecotype

value: Seedlings

tag: antibody

value: anti-GFP Ab (Abcam #ab290)


title: DP96-4  (iFLMbeta control)

source_name: DP96-4  (iFLMbeta control)

value: IP with untagged FLM protein


title: DP97-1  (iFLMdelta control)

source_name: DP97-1  (iFLMdelta control)


title: DP104-1 (iFLMdelta-GFP)

source_name: DP104-1 (iFLMdelta-GFP)


title: DP104-4 (iFLMdelta-GFP)

source_name: DP104-4 (iFLMdelta-GFP)


title: DP97-4  (iFLMdelta control)

source_name: DP97-4  (iFLMdelta control)


title: [E-MTAB-1585] 7sk_6a [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221947


title: DP103-1 (iFLMbeta-GFP)

source_name: DP103-1 (iFLMbeta-GFP)


title: [E-MTAB-1585] 7sk_4c [re-analysis]

description:
Derived from ArrayExpress E-MTAB-1585 [Dr. Paul Bertone]
ERX221949


title: DP96-1  (iFLMbeta control)

source_name: DP96-1  (iFLMbeta control)


title: rna_ahb

organism: Apis mellifera scutellata

source_name: Africanized honey bee

value: head


title: FliRas 3df

city: Eggesteing Leopolshafen

first: marina

last: mione

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genomics

institute: Karlsruhe Institute of Technology

data_processing:
Base-calls and demultiplexing using Illumina Casava 1.8.
Low-quality base-calls were removed using the 'quality_trim' application in the CLC bio Assembly Cell 3.2 software package. Settings: minimum remaining read length 30, minimum quality 20, at least 50% of the read must be good quality.
Reads were aligned to Ensembl predicted cDNAs (Danio_rerio.Zv9.63.cdna.all.fa) using the 'clc_ref_assemble_short' application in the CLC bio Assembly Cell 3.2 software package. Settings: mismatch cost 2, gap cost 3, deletion cost 3, score limit 8; random placement of repeats, up to 50 alignments per read.
Alignment files were translated into counts per transcript using the 'assembly_table' application, and summarized into genes based on Ensembl transcript/gene annotations using a custom script. Non-unique alignments were divided amongst target genes by ratio of unique reads, yielding a corrected total reads count per gene. This count was divided by the total length of constituent transcripts and by the total number of aligned read, and multiplied by a billion, to arrive at a RPKM-like expression value.
Genome_build: Zv9 (Ensembl release 63)
Supplementary_files_format_and_content: Tab-delimited text files with read counts and RPKM-normalized values for every gene.

source_name: Whole zebrafish larvae

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Larvae for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ug of total RNA for the construction of sequencing libraries.

tag: Stage

value: 3 days post fertilization

value: whole larvae

tag: genetic background

value: AB

tag: genotype


title: pvu_ahb

description: Pvu restriction enzyme (Rubicon)


title: CTRL 3dpf


title: m_ahb

description: Bisulfite converted