title: dsRIP 6 hour

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

description:
dsRNA purified from BMDMs at 6 hours post LPS treatment using the J2 dsRNA antibody
Mouse_EER.bed

data_processing:
All reads were aligned to the mouse genome using GNUMAP-bs. GNUMAP-bs was run with arguments â--lib_type wt1 --read_type rna --num_threads 12 --mpi 0 -- 17  nt_conv a2i --top_k_hash 10 --map_quality sensitive.â
All alignments for a given biological sample were merged into one alignment file and filtered using the Useq application SamTranscriptomParser. For GNUMAP alignments, the following command options were used: -a 10000 -n 1000000 -p -r
Alignments were converted to pileup format using samtools (Version 0.1.19) mpileup with the command options "-A -B -Q 13".
Pileup files were parsed using the Useq (Version 8.7.9) application RNAEditingPileupParser with the comman options "-v M_musculus_Dec_2011 -t -m"
The USeq application RNAEditingScanSeqs with command options "-t -i" was used to detect editing enriched windows from RNAEditingPileupParser point data
The USeq application EnrichedRegionMaker with command options "-I 0 -s 3-g 2500" generated initial lists of editing-enriched regions. All regions with less than 2 editing-enriched windows were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: Mouse_EER.bed, BED format, Column 1 - Chromosome, Column 2 - Start Coordinate, Column 3 - Stop Coordinate, Column 4 - EER Name, Column 5 - arbitrary score, Column 6 - Strand
Supplementary_files_format_and_content: Mouse_sixRIP_Minus.bw, bigWig format, minus strand track displaying RNA editing sites
Supplementary_files_format_and_content: Mouse_sixRIP_Plus.bw, bigWig format, plus strand track displaying RNA editing sites

source_name: BMDM, dsRIP 6 hour

growth_protocol: BMDMs were differentiated from the bone marrow of 7-8 wk old male C57BL/6 mice using published protocols. BMDMs were differentiated in the presence of m-CSF derived from L929 fibroblast supernatent for 7 days before the stimulation with LPS. Experiments were performed in BMDM media. BMDM media consists of RPMI 1640, Life Technologies; 20% horse serum, Life Technologies; 2 mM L-glutamine, Life Technologies; 20 ug/ml Gentamicin; β-mercaptoethanol, Invitrogen; 30% L929 fibroblast supernatant containing macrophage-colony stimulating factor.

extract_protocol:
RNA was extracted using TRIzol reagent, depleted of DNA using TURBO-DNase, and extracted with phenol-chloroform followed by precipitation with ethanol. For dsRIP samples, dsRNA was then immunoprecipitated with the J2 dsRNA antibody from English and Scientific Consulting.
RNAs were fragmented to an average size of 150-200 nts prior to library preparation. cDNA libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to manufacturer's instructions, except for the inclusion of additional DMSO for the reverse transcription reaction.

treatment_protocol: When appropriate, macrophages were stimulated with 500 ng/ml of Ultrapure Lipopolysaccharide from Salmonella minnesota R595 (InvivoGen).

value: Bone marrow-derived macrophage

tag: timepoint

value: 6 hour

value: LPS

tag: rip antibody

value: J2 dsRNA antibody (English and Scientific Consulting,Catalog # 10010500, Lot # J2-1104)

tag: rna fraction

value: dsRIP


title: Total RNA 0 hour

status: Public on Apr 12 2016

type: SRA

description:
Total RNA from BMDMs at 0 hr post LPS treatment
Mouse_EER.bed

library_source: transcriptomic

data_processing:
All reads were aligned to the mouse genome using GNUMAP-bs. GNUMAP-bs was run with arguments â--lib_type wt1 --read_type rna --num_threads 12 --mpi 0 -- 17  nt_conv a2i --top_k_hash 10 --map_quality sensitive.â
All alignments for a given biological sample were merged into one alignment file and filtered using the Useq application SamTranscriptomParser. For GNUMAP alignments, the following command options were used: -a 10000 -n 1000000 -p -r
Alignments were converted to pileup format using samtools (Version 0.1.19) mpileup with the command options "-A -B -Q 13".
Pileup files were parsed using the Useq (Version 8.7.9) application RNAEditingPileupParser with the comman options "-v M_musculus_Dec_2011 -t -m"
The USeq application RNAEditingScanSeqs with command options "-t -i" was used to detect editing enriched windows from RNAEditingPileupParser point data
The USeq application EnrichedRegionMaker with command options "-I 0 -s 3-g 2500" generated initial lists of editing-enriched regions. All regions with less than 2 editing-enriched windows were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: Mouse_EER.bed, BED format, Column 1 - Chromosome, Column 2 - Start Coordinate, Column 3 - Stop Coordinate, Column 4 - EER Name, Column 5 - arbitrary score, Column 6 - Strand
Supplementary_files_format_and_content: Mouse_zero_Minus.bw, bigWig format, minus strand track displaying RNA editing sites
Supplementary_files_format_and_content: Mouse_zero_Plus.bw, bigWig format, plus strand track displaying RNA editing sites

molecule: total RNA

organism: Mus musculus

source_name: BMDM, Total RNA 0 hour

tag: cell type

value: 0 hour

tag: strain

tag: treatment

value: total RNA


title: dsRIP 12 hour

description:
dsRNA purified from BMDMs at 12 hours post LPS treatment using the J2 dsRNA antibody
Mouse_EER.bed

data_processing:
All reads were aligned to the mouse genome using GNUMAP-bs. GNUMAP-bs was run with arguments â--lib_type wt1 --read_type rna --num_threads 12 --mpi 0 -- 17  nt_conv a2i --top_k_hash 10 --map_quality sensitive.â
All alignments for a given biological sample were merged into one alignment file and filtered using the Useq application SamTranscriptomParser. For GNUMAP alignments, the following command options were used: -a 10000 -n 1000000 -p -r
Alignments were converted to pileup format using samtools (Version 0.1.19) mpileup with the command options "-A -B -Q 13".
Pileup files were parsed using the Useq (Version 8.7.9) application RNAEditingPileupParser with the comman options "-v M_musculus_Dec_2011 -t -m"
The USeq application RNAEditingScanSeqs with command options "-t -i" was used to detect editing enriched windows from RNAEditingPileupParser point data
The USeq application EnrichedRegionMaker with command options "-I 0 -s 3-g 2500" generated initial lists of editing-enriched regions. All regions with less than 2 editing-enriched windows were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: Mouse_EER.bed, BED format, Column 1 - Chromosome, Column 2 - Start Coordinate, Column 3 - Stop Coordinate, Column 4 - EER Name, Column 5 - arbitrary score, Column 6 - Strand
Supplementary_files_format_and_content: Mouse_twelveRIP_Minus.bw, bigWig format, minus strand track displaying RNA editing sites
Supplementary_files_format_and_content: Mouse_twelveRIP_Plus.bw, bigWig format, plus strand track displaying RNA editing sites

source_name: BMDM, dsRIP 12 hour

value: 12 hour


title: dsRIP 0 hour

description:
dsRNA purified from BMDMs at 0 hours post LPS treatment using the J2 dsRNA antibody
Mouse_EER.bed

data_processing:
All reads were aligned to the mouse genome using GNUMAP-bs. GNUMAP-bs was run with arguments â--lib_type wt1 --read_type rna --num_threads 12 --mpi 0 -- 17  nt_conv a2i --top_k_hash 10 --map_quality sensitive.â
All alignments for a given biological sample were merged into one alignment file and filtered using the Useq application SamTranscriptomParser. For GNUMAP alignments, the following command options were used: -a 10000 -n 1000000 -p -r
Alignments were converted to pileup format using samtools (Version 0.1.19) mpileup with the command options "-A -B -Q 13".
Pileup files were parsed using the Useq (Version 8.7.9) application RNAEditingPileupParser with the comman options "-v M_musculus_Dec_2011 -t -m"
The USeq application RNAEditingScanSeqs with command options "-t -i" was used to detect editing enriched windows from RNAEditingPileupParser point data
The USeq application EnrichedRegionMaker with command options "-I 0 -s 3-g 2500" generated initial lists of editing-enriched regions. All regions with less than 2 editing-enriched windows were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: Mouse_EER.bed, BED format, Column 1 - Chromosome, Column 2 - Start Coordinate, Column 3 - Stop Coordinate, Column 4 - EER Name, Column 5 - arbitrary score, Column 6 - Strand
Supplementary_files_format_and_content: Mouse_zeroRIP_Minus.bw, bigWig format, minus strand track displaying RNA editing sites
Supplementary_files_format_and_content: Mouse_zeroRIP_Plus.bw, bigWig format, plus strand track displaying RNA editing sites

source_name: BMDM, dsRIP 0 hour


title: Total RNA 12 hour

description:
Total RNA from BMDMs at 12 hr post LPS treatment
Mouse_EER.bed

data_processing:
All reads were aligned to the mouse genome using GNUMAP-bs. GNUMAP-bs was run with arguments â--lib_type wt1 --read_type rna --num_threads 12 --mpi 0 -- 17  nt_conv a2i --top_k_hash 10 --map_quality sensitive.â
All alignments for a given biological sample were merged into one alignment file and filtered using the Useq application SamTranscriptomParser. For GNUMAP alignments, the following command options were used: -a 10000 -n 1000000 -p -r
Alignments were converted to pileup format using samtools (Version 0.1.19) mpileup with the command options "-A -B -Q 13".
Pileup files were parsed using the Useq (Version 8.7.9) application RNAEditingPileupParser with the comman options "-v M_musculus_Dec_2011 -t -m"
The USeq application RNAEditingScanSeqs with command options "-t -i" was used to detect editing enriched windows from RNAEditingPileupParser point data
The USeq application EnrichedRegionMaker with command options "-I 0 -s 3-g 2500" generated initial lists of editing-enriched regions. All regions with less than 2 editing-enriched windows were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: Mouse_EER.bed, BED format, Column 1 - Chromosome, Column 2 - Start Coordinate, Column 3 - Stop Coordinate, Column 4 - EER Name, Column 5 - arbitrary score, Column 6 - Strand
Supplementary_files_format_and_content: Mouse_twelve_Minus.bw, bigWig format, minus strand track displaying RNA editing sites
Supplementary_files_format_and_content: Mouse_twelve_Plus.bw, bigWig format, plus strand track displaying RNA editing sites

source_name: BMDM, Total RNA 12 hour


title: Rag-/- pro-B H4K4me3 ChIP-seq Rep1

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina GAIIx or HiSeq1000 platforms using the default RTA analysis software.
ChIP-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse NCBIM37/mm9 genome assembly using Bowtie using default parameters. BAM files were imported to Seqmonk for quantitation
Nuclear RNA-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse NCBIM37/mm9 genome assembly using Bowtie using default parameters. BAM files were imported to Seqmonk for quantitation
VDJ-seq sequences were first demultiplexed based on Truseq barcodes and then adaptor- and low quality trimmed (Phred <20) using Trim Galore (Babraham Bioinformatics). Next, JH sequences were identified in read 2 (JH end). By analysing the sequence immediately downstream of each JH primer sequence in each JH read we determined that JH2 PCR primers significantly cross-amplified JH4 sequences, leading to chimaeric JH2-JH4 J reads. We concluded this mis-priming was unavoidable due to sequence similiarity between JH2 and JH4 and the requirement to use reverse JH primers at a set position 10bp distal to the start of the JH gene to ensure equal capture of all sequences including those that had undergone substantial exonuclease nibbling during DH-to-JH joining. To correct this we used the 4bp of bona fide JH2 sequence downstream of the JH2 primer sequence to reassign the chimaeric sequences to JH4 and replaced the incorrect JH2 sequence with the correct JH4 sequence before further processing. No significant mispriming was seen for the other JH genes (<5%). Following this, the low number of JH reads that extended less than 60bp beyond the JH primer sequence were discarded and for the remainder the 60bp of downstream sequence was scanned for duplicates. These could be either technical (PCR) or biological. In order to differentiate between these, the opposite end reads (read 1, VH or DH end) were mapped to the NCBIM37/mm9 mouse genome assembly using Bowtie allowing no mismatches (-n 0 -l 100) and discarding multimapping hits (-m 1 --strata --best) and then scanned for start position in the VH region. Read pairs that had identical read 2/JH end sequences (produced by combinatorial joining of VH, DH and JH) and the same start position at the read 1/VH or DH end (a product of the random sonication of the DNA) were considered duplicates and only one retained. The previously mapped read 1 (VH/DH) reads for these were then output as bowtie mapped BAM files.
Genome_build: NCBIM37/mm9
Supplementary_files_format_and_content: ChIP-seq: Quantitated ChIP-seq datafile is tab delimited and shows log2 RPM values for MACS peaks across the genome (p=1e-5). Replicate 2 was used for MACs peak determination, relative to input: (1) Chromosome; (2) Start; (3) End; (4-6) log2 RPM value
Supplementary_files_format_and_content: RNA-seq: Quantitated Nuclear RNA-seq datafile is tab delimited and shows log2 RPM values for 1kb windows spanning the genome: (1) Chromosome; (2) Start; (3) End; (4-5) log2 RPM value
Supplementary_files_format_and_content: VDJ-seq: Quantitated VDJ-seq datafile is tab delimited and contains the following columns: (1) Igh V gene name (from Johnson et al. 2006); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-7) Count of unique sense-oriented (relative to V gene) reads over the 1.1kb proximal to the V RSS encompassing the V exon, intron, leader exon and ~600bp of proximal sequence.

molecule: genomic DNA

source_name: Progenitor B cells

growth_protocol: All cells were flow sorted directly from bone marrow single cell suspensions

extract_protocol:
ChIP-seq: ChIP was performed as described (Schoenfelder et al., 2010), using an antibody against histone H3K4me3 (Ab8580, Abcam). Cross links were reversed with 200 mM NaCl, 12.5 mM EDTA, 50 mM NaHCO3, 0.5% SDS, 100 _g/ml proteinase K overnight at 65°C, and ChIP DNA was purified by PCI extraction and isopropanol precipitation.
RNA-seq: Nuclei were obtained from 2-5 x 10(6) flow-sorted Rag1-/- pro-B cells (B220+CD19+CD43+) by incubation in 5 ml 50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% NP40, 5 min on ice. RNA was isolated with a RNeasy mini kit (Qiagen) and treated with Turbo DNAse (Ambion).
VDJ-seq:  Genomic DNA was isolated using a Qiagen Dneasy blood and tissue kit
ChIP-seq: Paired end ChIP-seq libraries were prepared according to standard Illumina ChIP-seq library protocols.
RNA-seq: Paired-end strand-specific RNA-seq libraries for Illumina sequencing were generated as described (Parkhomchuk et al., 2009) except polyA+ RNA selection was omitted, first strand cDNA synthesis was performed with solely random hexamer primers, and double-stranded cDNA was fragmented with a Diagenode Bioruptor.
VDJ-seq: For each sample 10mg of DNA were sonicated to 500bp using a Covaris E220 sonicator using recommended settings then end-repaired and A-tailed using standard protocols and a short asymmetric adaptor ligated to both fragment ends. DNA was cleaned with a PCR cleanup kit (Qiagen) after end-repair, following A-tailing and following adaptor ligation. Biotinylated primers located in JH intergenic regions were then used in primer extension reactions (8 x 50_l) using Vent Exo- polymerase (2 units per tube; NEB) followed by purification with a PCR cleanup kit. Due to the placement of these primers and the fragment size of the sonicated DNA, primer extension of unrecombined JH segments would be favoured over that of DJH or VDJH recombined segments. Primer-extended sequences (enriched for unrecombined JH intergenic sequences) were then removed using streptavidin beads (My-one C1; Invitrogen) following the manufacturers protocol with incubation for 4 hours at room temperature (20 _l beads per sample). Following a further cleanup, a second primer extension (6 x 50 _l reactions, 2 units per tube) was performed using biotinylated reverse primers located immediately downstream of each JH gene. Streptavidin beads (20_l) were again used to isolate primer extended JH-specific products by incubation overnight with rotation. Illumina PE1 primers corresponding to the long strand of the asymmetric adaptor and JH-specific PE2 primers were then used to amplify the library off the beads in 15 cycle PCR reactions (4 x 25_l) using Pwo master mix (Roche). Following 1x size selection (to remove small products) and cleanup using AMPure XP beads (Beckman Coulter), a second round 5 cycle PCR was performed to add the remainder of the Illumina PE1 and PE2 adaptors, incorporating Truseq bar codes at the PE2 end, followed by a second 1x size selection/cleanup with AMpure XP beads. If necessary, a 'double-sided' Ampure XP size selection (0.5x followed by 1x) was used to remove a low quantity of library products >1kb as these are too large for efficient cluster generation in Illumina sequencing.

treatment_protocol: No treatments

tag: genotype/variation

tag: tissue

value: bone marrow

value: Rag1-/- ex vivo flow sorted pro-B cells

tag: markers


title: r04_391

first: Peter

middle: W

last: Reddien

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description: Expressed muscle markers by qPCR

data_processing:
Basecalls performed using CASAVA version 1.7.0
Reads were trimmed using cutadapt to remove Nextera transposon sequences and low quality 3′ base pairs
Reads were mapped to dd_Smed_v4 planarian transcriptome assembly [https://idisk.mpi-cbg.de/~brandl/planaria/dd_Smed_v4.nuc.fasta.zip] using bowtie 1 with --best. Reads for isotigs of contigs (all contig ids that vary only by the final number) were summed. Reads for significant mitochondrial and ribosomal RNA (dd_smedV4_0_0_1, dd_Smed_v4_7_0_1, and dd_Smed_v4_4_1_1) were discarded to generate readcount file.
Contigs with 2 or fewer reads total within all cells were discarded. Read counts were normalized to cpm and log transformed for visualizations.
True muscle cells were identified by principle component analysis on highly-expressed highly-varient genes. Troponin-expressing cells which fell within the clear muscle-like population of cells by PCA were used for further differential expression analyses.
SCDE analyses between cells from anterior regions and cells from posterior regions were performed to identify potential regionally expressed genes: anterior (regions 1, 2, 3; n=23 cells) versus posterior (regions 8, 9, 10; n=38 cells); head (region 1; 11 cells) versus post-pharyngeal (regions 7, 8, 9; n=35 cells); pre-pharyngeal (regions 2, 3, 4; n=22 cells) versus tail (region 10; n=12 cells)
Genome_build: dd_Smed_v4
Supplementary_files_format_and_content: [Read counts] Tab-delineated text file includes unnormalized read counts of contigs (summed isotigs) used for further analysis for all 177 cells. SCDE analyses: tab-delineated text file generated per Kharchenko et al, 2014 for each anterior-versus-posterior comparison between 115 muscle cells (anterior-enriched as positive values and posterior-enriched as negative values). Each file indicates the fold change as the maximum likelihood estimate (mle) with a lower (lb) and upper bound (ub) and a conservative estimate (ce, equal to lb (positive), ub (negative) or 0 (lb and ub have different signs)) and statistical significance as signed Z-score (Z) and conservative Z-score (cZ, Z score corrected for multiple hypothesis using Holm procedure).
Supplementary_files_format_and_content: [SCDE analyses] tab-delineated text file generated per Kharchenko et al, 2014 for each anterior-versus-posterior comparison between 115 muscle cells (anterior-enriched as positive values and posterior-enriched as negative values). Each file indicates the fold change as the maximum likelihood estimate (mle) with a lower (lb) and upper bound (ub) and a conservative estimate (ce, equal to lb (positive), ub (negative) or 0 (lb and ub have different signs)) and statistical significance as signed Z-score (Z) and conservative Z-score (cZ, Z score corrected for multiple hypothesis using Holm procedure).

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: Isolated planarian cell

growth_protocol: Asexual Schmidtea mediterranea strain (CIW4) animals starved 7-14 days before dissectioninto regions

extract_protocol:
Cells were lysed in total cell lysis buffer supplemented with 1% β-mercaptoethanol
cDNA libraries were constructed using SmartSeq2. Sequencing libraries were made using Nextera XT kit for cells expressing muscle markers.

treatment_protocol: Single cell suspensions for each region were stained with Hoechst, and non-dividing single cells were sorted by flow cytometry into 96 well plates

value: asexual CIW4

tag: ploidy

value: 2N (non-dividing)

tag: ap-region

value: non-muscle


title: r04_401

description: Expressed muscle markers by qPCR

value: muscle


title: r04_392

description: Expressed muscle markers by qPCR


title: r04_412

description: Expressed muscle markers by qPCR


title: r04_402

description: Expressed muscle markers by qPCR


title: r04_371

description: Expressed muscle markers by qPCR


title: r04_381

description: Expressed muscle markers by qPCR


title: r03_497

description: Expressed muscle markers by qPCR


title: r04_382

description: Expressed muscle markers by qPCR


title: r03_477

description: Expressed muscle markers by qPCR


title: r03_487

description: Expressed muscle markers by qPCR


title: r03_417

description: Expressed muscle markers by qPCR


title: r03_507

description: Expressed muscle markers by qPCR


title: r03_407

description: Expressed muscle markers by qPCR


title: r03_397

description: Expressed muscle markers by qPCR


title: Filo_TSAb_RNAseq_2

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

data_processing:
RNApolII ChIP-seq reads mapped using bowtie (- m1 -v1). bedGraphs generated using bedtools genomecov.
For RNA-seq of TSA-treated and control (DMSO-treated) cells, tpms were computed using kallisto.
Genome_build: Capsaspora genome v2 (Broad Institute)

organism: Capsaspora owczarzaki

source_name: Filopodial stage cells

extract_protocol: For ChIP-seq: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature (RT). Crosslinking was quenched with 0.125 M glycine for 5 min RT. Pelleted cells were lysed in Lysis buffer I (10 mM HEPES.KOH pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.2 % NP40, plus protease inhibitors and 0.5 mM DTT), incubated on ice for 10 minutes and centrifuged at 8000xg 10 min to pellet the nuclei. Nuclei were resuspended in Lysis buffer II (1%SDS, 10 mM EDTA, 50 mM tris ClH pH 8.1 plus protease inhibitors), incubated on ice for 10 min and sonicated for 15 min (15 cycles, each one 30sec “on”, 30 sec “off”) in a Bioruptor (Diagenode, Seraing, Belgium) in order to generate 200bp fragments.  For ChIP-seq: Libraries of immunoprecipitated and input DNA were prepared using the NEBNext DNA sample prep reagent Set 1 kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer's protocol.  For RNA-Seq: none provided by the submitter.

tag: stage/cell type

value: Filopodial

tag: chip antibody


title: Total RNA 6 hour

description:
Total RNA from BMDMs at 6 hr post LPS treatment
Mouse_EER.bed

data_processing:
All reads were aligned to the mouse genome using GNUMAP-bs. GNUMAP-bs was run with arguments â--lib_type wt1 --read_type rna --num_threads 12 --mpi 0 -- 17  nt_conv a2i --top_k_hash 10 --map_quality sensitive.â
All alignments for a given biological sample were merged into one alignment file and filtered using the Useq application SamTranscriptomParser. For GNUMAP alignments, the following command options were used: -a 10000 -n 1000000 -p -r
Alignments were converted to pileup format using samtools (Version 0.1.19) mpileup with the command options "-A -B -Q 13".
Pileup files were parsed using the Useq (Version 8.7.9) application RNAEditingPileupParser with the comman options "-v M_musculus_Dec_2011 -t -m"
The USeq application RNAEditingScanSeqs with command options "-t -i" was used to detect editing enriched windows from RNAEditingPileupParser point data
The USeq application EnrichedRegionMaker with command options "-I 0 -s 3-g 2500" generated initial lists of editing-enriched regions. All regions with less than 2 editing-enriched windows were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: Mouse_EER.bed, BED format, Column 1 - Chromosome, Column 2 - Start Coordinate, Column 3 - Stop Coordinate, Column 4 - EER Name, Column 5 - arbitrary score, Column 6 - Strand
Supplementary_files_format_and_content: Mouse_six_Minus.bw, bigWig format, minus strand track displaying RNA editing sites
Supplementary_files_format_and_content: Mouse_six_Plus.bw, bigWig format, plus strand track displaying RNA editing sites

source_name: BMDM, Total RNA 6 hour


title: r03_387

description: Expressed muscle markers by qPCR


title: r03_377

description: Expressed muscle markers by qPCR


title: Filo_DMSOb_RNAseq_2


title: r02_447

description: Expressed muscle markers by qPCR


title: Cys_RNApolI_S2_ChIPSeq

source_name: Cystic stage cells

value: Cystic

value: anti-RNApolII PhosphoS2 (#ab5095, Abcam)


title: r02_437

description: Expressed muscle markers by qPCR


title: Cys_RNApolI_4H8_ChIPSeq

value: anti-RNApolII CTD4H8 (#904001, Biolgened/Covance)


title: Cys_RNApolI_8WG16_ChIPSeq

value: anti-RNApolII 8WG16 (#ab817, Abcam)


title: r02_427

description: Expressed muscle markers by qPCR


title: Rag-/- pro-B nuclear RNA-seq Rep1

molecule: nuclear RNA


title: Agg_RNApolI_S2_ChIPSeq

source_name: Aggregative stage cells

value: Aggregative


title: r02_426

description: Expressed muscle markers by qPCR


title: r02_396

description: Expressed muscle markers by qPCR


title: r02_386

description: Expressed muscle markers by qPCR


title: r01_525

description: Expressed muscle markers by qPCR


title: Agg_RNApolI_8WG16_ChIPSeq


title: Filo_RNApolI_S2_ChIPSeq


title: Agg_RNApolI_4H8_ChIPSeq


title: r01_515

description: Expressed muscle markers by qPCR


title: r01_514

description: Expressed muscle markers by qPCR


title: r01_504

description: Expressed muscle markers by qPCR


title: Filo_RNApolI_8WG16_ChIPSeq


title: Cys_input_DNA

data_processing:
Genome mapping using Bowtie v1.1.1 with -v 1 -m 1 parameters.
Remove duplicates using samtools v1.1
For ChIP-seq: Peak calling using MACS2 with parameters --nomodel, --shiftsize 100 and a q-value threshold of 0.01; except for H3K36me3 samples, for which additionally used --broad parameter and a q-value threshold of 0.05. Corrected by genome mappability.
For ATAC-seq:  Peak calling using MACS2 with parameters -q 0.001 --extsize 40 --call-summits --nomodel
Genome_build: Capsaspora genome v2 (Broad Institute)
Supplementary_files_format_and_content: Peak BED files from MACS2 peak calling

growth_protocol: Capsaspora strain ATCC30864 cells were grown axenically in 5 ml flasks with ATCC medium 1034 (modified PYNFH medium) in an incubator at 23¼C

extract_protocol:
For ChIP-seq: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature (RT). Crosslinking was quenched with 0.125 M glycine for 5 min RT. Pelleted cells were lysed in Lysis buffer I (10 mM HEPES.KOH pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.2 % NP40, plus protease inhibitors and 0.5 mM DTT), incubated on ice for 10 minutes and centrifuged at 8000xg 10 min to pellet the nuclei. Nuclei were resuspended in Lysis buffer II (1%SDS, 10 mM EDTA, 50 mM tris ClH pH 8.1 plus protease inhibitors),  incubated on ice for 10 min and sonicated for 15 min (15 cycles, each one 30sec “on”, 30 sec “off”) in a Bioruptor (Diagenode, Seraing, Belgium) in order to generate 200bp fragments.
For ChIP-seq: Libraries of immunoprecipitated and input DNA were prepared using the NEBNext DNA sample prep reagent Set 1 kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer's protocol.
For ATAC-seq: Fresh nuclei were obtained using Lysis Buffer I (10 mM HEPES.KOH pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.2 % NP40)
For ATAC: Fresh nuclei incubated 30min at 37ºC with Tn5 transposases from the Nextera DNA Library Prep Kit (Illumina, San Diego, CA)

value: none (input)


title: Cys_H3K36me3_ChIPSeq

value: anti-H3K36me3 (#ab9050, Abcam)


title: r01_474

description: Expressed muscle markers by qPCR


title: Filo_TSAa_RNAseq_1


title: r01_473

description: Expressed muscle markers by qPCR


title: Cys_H3K27ac_ChIPSeq

value: anti-H3K27Ac (#07-360, Millipore)


title: r01_464

description: Expressed muscle markers by qPCR


title: Filo_DMSOa_RNAseq_1


title: Cys_H3K4me1_ChIPSeq

value: anti-H3K4me1 (#ab8895, Abcam)


title: r01_441

description: Expressed muscle markers by qPCR


title: r01_454

description: Expressed muscle markers by qPCR


title: Filo_RNApolI_4H8_ChIPSeq


title: r01_453

description: Expressed muscle markers by qPCR


title: Agg_ATAC_1

description: processed data file: ATAC _nucleosome_free_peaks_MERGED.bed

data_processing:
Library strategy: ATAC-Seq
Genome mapping using Bowtie v1.1.1 with -v 1 -m 1 parameters.
Remove duplicates using samtools v1.1
For ChIP-seq: Peak calling using MACS2 with parameters --nomodel, --shiftsize 100 and a q-value threshold of 0.01; except for H3K36me3 samples, for which additionally used --broad parameter and a q-value threshold of 0.05. Corrected by genome mappability.
For ATAC-seq:  Peak calling using MACS2 with parameters -q 0.001 --extsize 40 --call-summits --nomodel
Genome_build: Capsaspora genome v2 (Broad Institute)
Supplementary_files_format_and_content: Peak BED files from MACS2 peak calling


title: r01_463

description: Expressed muscle markers by qPCR


title: Agg_input_DNA


title: r01_440

description: Expressed muscle markers by qPCR


title: Cys_H3K4me3_ChIPSeq

value: anti-H3K4me3 (#pAb-003-050, Diagenode)


title: r01_494

description: Expressed muscle markers by qPCR


title: Agg_H3K27ac_ChIPSeq


title: Agg_H3K4me1_ChIPSeq


title: r01_430

description: Expressed muscle markers by qPCR


title: r01_421

description: Expressed muscle markers by qPCR


title: Agg_H3K36me3_ChIPSeq


title: r01_431

description: Expressed muscle markers by qPCR


title: Cys_ATAC_1


title: r01_420

description: Expressed muscle markers by qPCR


title: r01_410

description: Expressed muscle markers by qPCR


title: Agg_H3K4me3_ChIPSeq


title: Filo_input_DNA


title: Filo_ATAC_1


title: r01_390

description: Expressed muscle markers by qPCR


title: Filo_H3K36me3_ChIPSeq


title: r01_400

description: Expressed muscle markers by qPCR


title: r01_380

description: Expressed muscle markers by qPCR


title: Filo_H3K27ac_ChIPSeq


title: Agg_ATAC_2


title: Filo_ATAC_2


title: Filo_H3K4me3_ChIPSeq


title: Chlamy-DpnI-0.5h

city: Chicago

first: Guan-Zheng

last: Luo

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

data_processing:
Library strategy: DA-6mA-seq
After adaptor trimming and quality control, reads were aligned to reference genome (Cre4 for Chlamydomonas, PlasmoDB-24 for Plasmodium and Pench1 for Penicillium) by Bowtie V1.0.1
The positions of 5' ends were summed in the genome-wide as the potential DpnI cleavage sites (assigned as x).
For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1
A binominal distribution model was assumed that each read could be randomly sheared and mapped with a probability p = 1/gs (gs = genome size) or cleaved by DpnI. The total reads number was assigned as n. The P-value of each genomic locus with 5' reads ends was calculated as C_n^x p^x 〖(1-p)〗^(n-x).
The P-values were further corrected by Bonferroni correction and FDR<0.01 was set as the cutoff to determine a real DpnI cleavage site.
Genome_build: Cre4 for Chlamydomonas, PlasmoDB-24 for Plasmodium and Pench1 for Penicillium
Supplementary_files_format_and_content: bedGraph files are generated by in-house script representing the reads ends count at genomic loci

organism: Chlamydomonas reinhardtii

source_name: Algae cultured in constant light

growth_protocol: Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+)  was grown in standard Tris-Acetate-Phosphate (TAP) medium in  at 25 ºC with 220 rpm shaking and constant light.

extract_protocol:
Genomic DNA is extracted by DNeasy Plant Mini Kit (Qiagen, Cat. no. 69104).
Standard Illumina DNA library construction

tag: culture media

value: Tris-Acetate-Phosphate (TAP)

tag: reaction time

value: 0.5 hours


title: Plasm-DpnI-12h

organism: Plasmodium falciparum

source_name: Plasmodium gDNA from ATCC

value: Standard culture (ATCC)

value: 12 hours


title: PBMC_mergedReplicates_sample19

status: Public on Apr 11 2016

city: Stanford

first: Stephen

last: Montgomery

address: 300 Pasteur Lane

institute: Stanford University

description: Read counts per peak from ATAC-seq

data_processing:
ATAC-seq libraries were prepared as described in Buenrostro et al 2013
Sequencing reads were mapped to the reference genome (hg19) and reads passing QC (MAQ>30) were used for peak calling.
Peak calling was performed by pooling by all samples (N=20) together and calling peaks using MACS2
Peaks were defined as the 250 upstream and downstream of the midpoint of each peak called by MACS2
Read counts over each peak was called per sample using HT-Seq
Genome_build: hg19
Supplementary_files_format_and_content: Bed files with read counts per peak for specific sample

organism: Homo sapiens

source_name: PBMC

extract_protocol:
PBMCs were isolated from buffy coats using a Ficoll gradient. 50,000 cells were used for each transposition reaction.
ATAC-seq libraries were prepared as described in Buenrostro et al 2013

tag: Sex

value: F


title: PBMC_mergedReplicates_sample14

description: Read counts per peak from ATAC-seq


title: PBMC_mergedReplicates_sample18

description: Read counts per peak from ATAC-seq


title: Chlamy-DpnI-12h


title: PBMC_mergedReplicates_sample17

description: Read counts per peak from ATAC-seq


title: Pen-DpnI-12h

data_processing:
Library strategy: DAMA-seq
After adaptor trimming and quality control, reads were aligned to reference genome (Cre4 for Chlamydomonas, PlasmoDB-24 for Plasmodium and Pench1 for Penicillium) by Bowtie V1.0.1
The positions of 5' ends were summed in the genome-wide as the potential DpnI cleavage sites (assigned as x).
For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1
A binominal distribution model was assumed that each read could be randomly sheared and mapped with a probability p = 1/gs (gs = genome size) or cleaved by DpnI. The total reads number was assigned as n. The P-value of each genomic locus with 5' reads ends was calculated as C_n^x p^x 〖(1-p)〗^(n-x).
The P-values were further corrected by Bonferroni correction and FDR<0.01 was set as the cutoff to determine a real DpnI cleavage site.
Genome_build: Cre4 for Chlamydomonas, PlasmoDB-24 for Plasmodium and Pench1 for Penicillium
Supplementary_files_format_and_content: bedGraph files are generated by in-house script representing the reads ends count at genomic loci

organism: Penicillium chrysogenum

source_name: Penicillium from ATCC


title: PBMC_mergedReplicates_sample20

description: Read counts per peak from ATAC-seq


title: PBMC_mergedReplicates_sample16

description: Read counts per peak from ATAC-seq

value: M


title: PBMC_mergedReplicates_sample12

description: Read counts per peak from ATAC-seq


title: PBMC_mergedReplicates_sample15

description: Read counts per peak from ATAC-seq


title: PBMC_mergedReplicates_sample11

description: Read counts per peak from ATAC-seq


title: Input ChIP-seq WT

city: Shanghai

first: Gang

last: Wei

state: Shanghai

address: 320 Yue Yang Road

country: China

institute: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Basecalling was performed using CASAVA version 1.4
ChIP-seq reads were mapped to dm3 using bowtie version 1.0.0 with at most 2-mismatches allowed. Only uniquely mapped reads were kept for further analysis.
H4K20me1 peaks were called using SICER with window size 200bp, gap size 200bp, E value 0.01, fragment length 150bp, redundant reads level 3.
Mapped redundant-removed reads were extended to 200bp and then converted into total reads number normalized bigWig format.
RNA-seq reads were first mapped to dm3 refSeq transcriptome and then unmapped reads were mapped to dm3 reference using TopHat version 2.0.11 with at most 2-mismatches allowed and multiple mapped cutoff 5.
Genes expression level were quantified using cufflinks. Differentially expressed genes were identified using DEGseq with P value 0.001.
Genome_build: dm3
Supplementary_files_format_and_content: Peak files in BED format. BigWig files for ChIP-seq datasets were generated using UCSC genome browser tools. Genes expression level for each sample in table file.

organism: Drosophila melanogaster

source_name: 3rd instar larvae wing discs

growth_protocol: Drosophila larvae are grown under standard conditions at 25 degrees.

extract_protocol:
For RNA-seq, drosophila third instar larvae wing discs from indicated genetypes were dissected into Trizol, and total RNA was extracted for the construction of sequencing libraries. For ChIP-seq, drosophila third instar larvae wing discs from Act5c-Gal4 were cross-linked, sonicated and subjected for ChIP assay with anti-H4K20me1 antibody. After reverse cross-link and protein digestion with proteinase K, the immunoprecipitated genomic DNA was extracted with DNA purification kit (QIAGEN) and for construction of sequencing libraries.
ChIP-seq and unstrand RNA-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Act5c-Gal4 virgins are crossed with Act5c-Gal4 or indicated RNAi (yw; UAS-dsRNA Polycomb, PR-Set7 or E(z)) males under standard conditions at 25 degrees

value: Act5c-Gal4 (WT)

value: y1 w*; P{Act5C-GAL4}25FO1/CyO, y+

value: 3rd instar larvae wing discs


title: H4K20me1 ChIP-seq WT

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: RNA-seq Polycomb RNAi

description: processed data file: all.genes.expression.in.FPKM.txt

value: Act5c-Gal4 X Polycomb RNAi

value: y1 w*; P{Act5C-GAL4}25FO1,UAS-dsRNA Polycomb


title: RNA-seq WT


title: PBMC_mergedReplicates_sample9

description: Read counts per peak from ATAC-seq


title: PBMC_mergedReplicates_sample10

description: Read counts per peak from ATAC-seq


title: PBMC_mergedReplicates_sample8

description: Read counts per peak from ATAC-seq


title: r01_370

description: Expressed muscle markers by qPCR

value: asexual CIW4

value: 2N (non-dividing)

value: muscle


title: PBMC_mergedReplicates_sample4

description: Read counts per peak from ATAC-seq


title: PBMC_mergedReplicates_sample6

description: Read counts per peak from ATAC-seq


title: PBMC_mergedReplicates_sample13

description: Read counts per peak from ATAC-seq


title: PBMC_mergedReplicates_sample5

description: Read counts per peak from ATAC-seq


title: PBMC_mergedReplicates_sample3

description: Read counts per peak from ATAC-seq


title: Filo_H3K4me1_ChIPSeq

value: Filopodial

value: anti-H3K4me1 (#ab8895, Abcam)


title: PBMC_mergedReplicates_sample2

description: Read counts per peak from ATAC-seq


title: Gfi1_KO_Th_Gfi1_ChIP

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie (Galaxy Tool Version 1.0.1)
peaks were called using MACS (Galaxy Tool Version 1.1.2)
All ChIP-seq analysis was performed on Galaxy
Genome_build: mm9
Supplementary_files_format_and_content: peak file

source_name: Gfi1-KO CD4 Thn cell

growth_protocol: Naïve CD4 T (CD44lowCD62LhighCD25negative) cells were prepared using a CD4+CD62L+ T cell isolation kit II (cat#130-093-227; Miltenyi Biotec).  Naïve CD4 T cells were stimulated with an immobilized anti-TCR-β mAb (3 μg/ml, H57-597; BioLegend) and an anti-CD28 mAb (1 μg/ml, 37.5; BioLegend), and IL-2 (10 ng/ml, Cat.21-8021:Tonbo biosciences) for two days. Next, the cells were transferred to a new plate and further cultured in the presence of  IL-2 (10 ng/ml).

extract_protocol:
Lysates were clarified from sonicated nuclei and transcription factor-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext ChIP-Seq Library prep regent (E6200)

tag: strain background

value: spleen

value: Naive CD4 T (CD44lowCD62LhighCD25negative) cells

value: Gfi

value: Santa Cruz

tag: chip antibody lot#


title: Gfi1_WT_Th_Gfi1_ChIP

source_name: Gfi1-WT CD4 Thn cell

value: wild type

tag: cell type


title: 03C6-2 rep1

city: Hangzhou

first: Jianping

last: Lu

state: Zhejiang

address: 866 Yuhantang Road

department: College of Life Sciences

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Magnaporthe oryzae 70-15 (MG8) whole genome using tophat 2.0.8b with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1
Genome_build: MG8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Pyricularia oryzae

source_name: Mycelium

growth_protocol: The strains were cultured in liquid CM medium at 25˚C with shaking at 180 rpm for 2 d

extract_protocol:
Total RNA was extracted from ground mycelia in liquid nitrogen with RNeasy Plant mini kit (QIAGEN)
RNA libraries were prepared for sequencing using NEBNext RNA sample preparation kit (NEB) with standard Illumina protocols

treatment_protocol: The mycelia were collected and incubated in H2O at 25˚C for 4 h

tag: strain

tag: developmental stage

value: Mycelia under starvation

tag: genotype


title: WT_70-15_rep2


title: 03C6-2 rep2


title: 03E4-1 rep2


title: 03E4-1 rep1


title: 03C6-2 rep3


title: 03E4-1 rep3


title: WT_70-15_rep1


title: PBMC_mergedReplicates_sample7

description: Read counts per peak from ATAC-seq

value: M


title: PBMC_mergedReplicates_sample1

description: Read counts per peak from ATAC-seq

value: F


title: ATAC-Seq_Sample09_Fibroblast_Rep3

city: Kyoto

first: Koji

last: Kitazawa

state: Kyoto

address: 465 Kajiicho Kamigyoku

department: Ophthalmology

institute: Kyoto Prefectural University of Medicine

description: Protocol: ATAC-Seq

data_processing:
Library strategy: ATAC-Seq
Basecalls performed using BCL2FASTQ version 1.8.4.
Mapping was performed by BWA (version 0.6.2) , allowing up to 2 mismatches, using the reference human genome, NCBI build 37 (hg19) .
PCR duplicated reads and multi-mapped reads were discarded using Samtools (version 0.1.19).
Peak detection was performed using Hotspot (version 4.1.0)  with a false discovery rate (FDR) cut-off of 0.01
Genome_build: hg19
Supplementary_files_format_and_content: bed files which contain peak information were generated using Hotspot version 4.1.0.

source_name: Fibroblasts

extract_protocol:
Sorted cells were lysed in 5 to 10 μl ice-cold ATAC lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1 % IGEPAL CA-630) for 10 minutes. Without nuclear extraction step, samples were processed using transposase reaction mix of Nextera DNA sample preparation kit (Illumina), with incubation for 30 minutes at 37 ˚C. Indices were incorporated using Nextera Index Kit (Illumina) in amplification step.
ATAC-seq libraries were purified using Ampure XP beads (Beckman Coulter Genomics) to remove remaining adapters. Libraries were assessed for the quality and quantity using Agilent Bioanalyzer 2000 and the KAPA library quantification kit for Illumina (KAPA Biosystems).

value: fibroblast


title: ATAC-Seq_Sample09_Fibroblast_Rep2

description: Protocol: ATAC-Seq


title: ATAC-Seq_Sample09_Fibroblast_Rep1

description: Protocol: ATAC-Seq


title: ATAC-Seq_Sample07_CEC_Rep3

description: Protocol: ATAC-Seq

source_name: CEC, Donor B, passage 2

value: corneal epithelium


title: ATAC-Seq_Sample06_CEC_Rep2

description: Protocol: ATAC-Seq


title: ATAC-Seq_Sample05_CEC_Rep1

description: Protocol: ATAC-Seq


title: ATAC-Seq_Sample01_6TFs_Rep3

description: Protocol: ATAC-Seq

source_name: 6TFs transduced-fibroblasts


title: ATAC-Seq_Sample01_6TFs_Rep1

description: Protocol: ATAC-Seq


title: ATAC-Seq_Sample01_6TFs_Rep2

description: Protocol: ATAC-Seq


title: Input_H3K27Ac-ChIP-seq-Rep1

city: Naples

first: Antonio

last: Baldini

address: Via Pietro Castellino 111

country: Italy

institute: CNR Institute of Genetics and Biophysics Adriano Buzzati Traverso

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using Bioscope (version 1.3.1) for SOLiD data and Bowtie (version 0.12.9) for Illumina data.
To identify enriched regions, MACS (version 1.4.2) with Tbx1 ChIP data, and SICER4 (version 1.1) for H3K4me1 data were used and Bedtools30 to identify sub-regions consistently enriched in biological replicates.
For each potential region of Tbx1 enrichment, we computed an enrichment score as follows: the number of reads in each region was calculated, this value was divided by the total number of non-duplicated mapped reads and by the peak’s length, and multiplied by the scale factor of 109 to normalize counts across samples and regions. The resulting value, called enrichment score, was used to filter out the potential peaks. A peak was considered golden if its enrichment score was greater or equal to 0.7 in both ChIP replicates and at least 4 reads were observed in the Input.
The differentially enriched regions between NT SiRNA and Tbx1 SiRNA, Tbx1 SiRNA and Tbx1 SiRNA+TCP conditions were identified using SICER-df.
RNA-Seq data: In order to compare differentially expressed polyadenylated genes, 6 RNA samples were used for libraries preparation with the Illumina's strand specific RNA seq protocol, barcoded and pooled in one lane. The raw data for the high-throughput sequencing of cDNA were generated with Illumina platform for strand specific single-end reads of length 50 bp. Two biological replicates were sequenced for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, logFC or posterior probability for differentially expressed genes, chromosome coordinates, annotated genes using ChIPpeakAnno (R package).

growth_protocol: P19CL6 cells were grown in Dulbecco-Modified Minimal Essential Medium supplemented with 10% fetal bovine serum.

extract_protocol:
For ChIP analysis, P19Cl6 cells and mouse embryos were cross-linked in 1% formaldehyde and chromatin was extracted and sonicated in microtubes using the Covaris® S2 instrument. Soluble chromatin was incubated with TBX1 antibody, H3K4me1 and H3K27Ac antibodies. For expression analysis, RNA was extracted from E9.5 embyos and P19Cl6 cells at day 1 during differentiation.
For ChIP analysis, ChIP DNA or input samples were prepared for Solexa and Solid sequencing using Chip-Seq Sample Preparation kit and TruSeq SBS kit v3 HS  or NEB Next DNA Simple Prep Master Mix set 3. For RNA-seq libraries preparation we used the Illumina's strand specific RNA seq protocol.

treatment_protocol: For cardiomyocytes differentiation and transient transfection the cells were plated on a tissue culture dish with Non-targeting SiRNA or Tbx1 SiRNA. 20 hours later the medium was replaced with a growth medium containing 10 μM 5-Aza and 1mM TCP or saline solution for 24 h. After 24 hours the cells were collected and processed for further analysis. For mice drug treatment, Intraperitoneal injections of 10 mg/kg body weight of Tranylcypromine were administered at E7.5, E8.5 and E9.5 to pregnant mice. Control animals were injected with an equal volume of  carrier (sterile 0.9% NaCl).WT and Tbx1Lacz/+ E9.5 mouse embryos were dissected and processed for further analysis.

value: P19Cl6 during cardiomyocytes differentiation


title: Input_H3K27Ac-ChIP-seq-Rep2


title: ATAC-Seq_Sample09_Fibroblast_Rep4

description: Protocol: ATAC-Seq


title: H3K27Ac_ChIP-seq-Rep2


title: WT_RNA-seq-Rep2

description:
Expressed_Genes_in_embryos.txt
Differentially_expressed_Genes_Tbx1_HET_vs_WT.txt

source_name: Mouse embryos

tag: treatment

value: No treatment


title: H3K27Ac_ChIP-seq-Rep1


title: WT_70-15_rep3


title: Tbx1_HET_+TCP_RNA-seq-Rep2

value: TCP


title: ATAC-Seq_Sample08_CEC_Rep4

description: Protocol: ATAC-Seq


title: WT_RNA-seq-Rep1


title: H3K4me1_WT_ChIP-seq-Rep2

description: Changed_Genes_Mixture_Model_Tbx1_HET_vs_WT.txt


title: Tbx1_HET_RNA-seq-Rep1

description: Differentially_expressed_Genes_Tbx1_HET_vs_WT.txt


title: H3K4me1_WT_ChIP-seq-Rep1


title: Tbx1_HET_+TCP_RNA-seq-Rep1


title: Tbx1_HET_RNA-seq-Rep2


title: H3K4me1_Tbx1_HET_+TCP_ChIP-seq-Rep2


title: ATAC-Seq_Sample01_6TFs_Rep4

description: Protocol: ATAC-Seq


title: H3K4me1_Tbx1_HET_+TCP_ChIP-seq-Rep1


title: H3K4me1_Tbx1_HET_ChIP-seq-Rep2


title: H3K4me1_Tbx1_HET_ChIP-seq-Rep1


title: Input_WT_rep1


title: Input_Tbx1_HET_rep2


title: Input_Tbx1_HET_+TCP_rep1


title: Input_Tbx1_HET_rep1


title: Input_Tbx1_HET_+TCP_rep2


title: H3K4me1_Tbx1_SiRNA+TCP-ChIP-seq-Rep2

description: Differentially_methylated_regions_Tbx1-SiRNA+TCP_vs_Tbx1-SiRNA.txt

value: Tbx1-SiRNA + TCP


title: H3K4me1_Tbx1_SiRNA-ChIP-seq-Rep2

description:
Differentially_methylated_regions_Tbx1-SiRNA_vs_NT-SiRNA.txt
Differentially_methylated_regions_Tbx1-SiRNA+TCP_vs_Tbx1-SiRNA.txt


title: H3K4me1_Tbx1_SiRNA+TCP-ChIP-seq-Rep1


title: H3K4me1_Tbx1_SiRNA-ChIP-seq-Rep1


title: Input_WT_rep2


title: Input_Tbx1_SiRNA+TCP-ChIP-seq-Rep1


title: Input_Tbx1_SiRNA+TCP-ChIP-seq-Rep2


title: 03C6-2 rep3

organism: Pyricularia oryzae 70-15

growth_protocol: The conidia were cultured on plasitc membranes in H2O at 28˚C for 5 h

extract_protocol:
Total RNA was extracted from appressoria with RNeasy Plant mini kit (QIAGEN). Purified RNA was analyzed on a ND-8000 spectrophotometer (Nanodrop, Technologies, Wilmington, DE), agarose electrophoresis or a 2100-Bioanalyzer (Agilent Technologies, Santa Clara, CA), to determine the quantity. RNA samples were used if there was no smear on the agarose. RNA samples were also used if the 260/280 ratio was above 2.0 and the RIN (RNA integrity number) was greater than 7.0.
RNA libraries were prepared for sequencing using NEBNext RNA sample preparation kit (NEB) with standard Illumina protocols

tag: tissue

value: Appressorium

value: Appressorium at 5 hpi


title: 03C6-2 rep1


title: Input_Tbx1_SiRNA-ChIP-seq-Rep1


title: H3K4me1_NT_SiRNA-ChIP-seq-Rep1

description: Differentially_methylated_regions_Tbx1-SiRNA_vs_NT-SiRNA.txt

value: NT-SiRNA


title: H3K4me1_NT_SiRNA-ChIP-seq-Rep2


title: 03C6-2 rep2


title: Input_Tbx1_SiRNA_ChIP-seq-Rep2


title: WT rep2


title: Input_NT_SiRNA-ChIP-seq-Rep2


title: Input_NT_SiRNA-ChIP-seq-Rep1


title: Input (A-beta)

city: London

first: Sandeep

middle: K

last: Gill

state: Ontario

address: 100 Perth Drive

department: Molecular Medicine

country: Canada

institute: Robarts Research Institute

data_processing:
Samples were demulitplexed and basecalling was done in Basespace by the Donnelly Sequencing Centre
Sequenced reads were masked for low-complexity or low-quality sequences, and then aligned to the hg38 genome using BWA in Galaxy with standard parameters
Peaks were called using MACS in Galaxy with with p-value <0.00001 and standard parameters, and filtered out significant peaks found in the corresponding input sample.
Genome_build: hg38
Supplementary_files_format_and_content: .bed files containing MACS derived peaks; scores represent peak value

source_name: SH-SY5Y cells

growth_protocol: Human neural SH-SY5Y cells were maintained in DMEM in T-75 flasks prior to plating on 100cm dishes (4.0 x 10^5 cells) and differentiated for 3 d with retinoic acid (final 10.0 x 10^6 cells) with 3 plates per treatment

extract_protocol:
Cells were cross-linked with paraformaldehyde, lysed and sonicated prior to extraction of DNA-protein complexes with antibody
ChIP-seq samples were individually barcoded with Illumina TruSeq® adapter sequences for library construction at the Donnelly Sequencing Centre (Toronto, ON) according to the manufacturer's instructions

treatment_protocol: Cells were treated with either vehicle (Ham's F-12 media) or 100 nM amyloid-beta1-42 oligomers for 4 h

tag: cell line

value: neural cells

tag: passages

tag: treated with


title: SATB1 (A-beta)

value: 100 nM amyloid-beta1-42 oligomers for 4 h

tag: chip antibody

value: anti-SATB1 (sc-5990)


title: hCEC-OVOL2

data_processing:
Sequence reads were mapped to the human genome HG38 by BWA aligner.
Genome_build: HG38
Supplementary_files_format_and_content: bigwig files were generated using bam_to_wiggle.py script (http://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py).

source_name: primary corneal epithelium cell

growth_protocol: Human CEC cell line (Araki-Sasaki et al., 1995) was cultured in Dulbecco’s modified Eagle’s medium and Ham’s F12 (1:1 mixture) and included 10% fetal bovine serum, 5μg/mL insulin, 0.1 nmol/L cholera toxin, 10 ng/mL EGF.

extract_protocol: 10 ng of immunoprecipitated DNA was ligated with adaptors of Illumina GAIIx using illumina TruSeq ChIP Sample Prep Kit (illumina).

treatment_protocol: Approximately 10^7 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature), and then quenched with glycine (5 min at room temperature). Fixed cells were lysed in 50 mM HEPES KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4 °C (Roche, 04693159001), centrifuged at 950g for 10 min and re-suspended in 0.2% SDS, 10 mM EDTA, 140 mM NaCl and 10 mM Tris-HCl. Cells were then fragmented with a Covaris Sonicater (model E210) at 8 °C to a size range between 200–500 bp, and precipitated by centrifugation. Ten micrograms of each antibody were pre-bound by incubating with Protein-G Dynabeads (Invitrogen, 100-03D) in IP dilution buffer (16.7 mM Tris-HCl, pH 8.0, 1.2 mM EDTA, 1.1% Trion X-100, 167 mM NaCl, and 0.01% SDS). Washed beads were added to the chromatin lysate, and then incubated overnight at 4 °C. Samples were washed 2 times with IP dilution buffer, twice with Low NaCl buffer (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, and 0.1% SDS), twice with High NaCl buffer (20 mM Tris-HCl, pH8.0, 2 mM EDTA, 1% Trion X-100, 500 mM NaCl, and 0.1% SDS) twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), twice with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA), and then eluted in 0.5% SDS, 5 mM EDTA, 25 mM Tris-HCl pH 8.0 with Pronase (Roche, 165921) at 42 °C for 2 h and at 65 °C overnight. And then DNA was purified with the MinElute Reaction Cleanup kit (Qiagen, 28204). Human-OVOL2 antibodies (SantaCruz Biotechnology, sc-85804) was used for chromatin immunoprecipitation experiments.

value: corneal epithelium cell

tag: vendor

value: SantaCruz Biotech

tag: cat. #


title: Input (Vehicle)

value: vehicle (Ham's F-12 media)


title: Dclk1+ sample ZT002

city: New York

first: Timothy

middle: Cragin

last: Wang

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with bowtie version 0.12.7 and Tophat HTSeq-0.6.1 .
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: Xlsx file with raw counts for each gene

source_name: Pancreatic Dclk1+  cells  from Dclk1-CreERT;tdtomato mice

extract_protocol:
RNA was extracted from each group using RNAqueous®-Micro Total RNA Isolation Kit (Thermo Sci,catalog no. AM1931) and the quality of purified RNA samples was determined using a Bioanalyzer 2100 (Agilent) with an RNA Pico kit. RNAs with RNA Integrity Number (RIN) values greater than 8.0 were used to generate sequencing libraries. Extracted RNA samples were amplified by Ovation® RNA-Seq System V2 (NuGEN) Kit. Amplified cDNA was labeled with Encore biotin module Kit (NuGEN) for RNA-Seq applications.
Illumina Truseq RNA Sample Prep v2 using the LT protocol.

value: CBA x C57BL/6J

value: pancreas

value: Dclk1 positive


title: 82-kDa ChAT (A-beta)

value: In-house C-terminal anti-ChAT antibody


title: Dclk1+ sample ZT003


title: Dclk1+ sample ZT004


title: WT rep3

value: wild type


title: SATB1 (Vehicle)


title: HCE-T-OVOL2

data_processing:
Sequence reads were mapped to the human genome HG38 by BWA aligner.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: CEC cell line, HCE-T

treatment_protocol: Approximately 10^7 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature), and then quenched with glycine (5 min at room temperature). Fixed cells were lysed in 50 mM HEPES KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4 °C (Roche, 04693159001), centrifuged at 950g for 10 min and re-suspended in 0.2% SDS, 10 mM EDTA, 140 mM NaCl and 10 mM Tris-HCl. Cells were then fragmented with a Covaris Sonicater (model E210) at 8 °C to a size range between 200–500 bp, and precipitated by centrifugation. Ten micrograms of each antibody were pre-bound by incubating with Protein-G Dynabeads (Invitrogen, 100-03D) in IP dilution buffer (16.7 mM Tris-HCl, pH 8.0, 1.2 mM EDTA, 1.1% Trion X-100, 167 mM NaCl, and 0.01% SDS). Washed beads were added to the chromatin lysate, and then incubated overnight at 4 °C. Samples were washed 2 times with IP dilution buffer, twice with Low NaCl buffer (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, and 0.1% SDS), twice with High NaCl buffer (20 mM Tris-HCl, pH8.0, 2 mM EDTA, 1% Trion X-100, 500 mM NaCl, and 0.1% SDS) twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), twice with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA), and then eluted in 0.5% SDS, 5 mM EDTA, 25 mM Tris-HCl pH 8.0 with Pronase (Roche, 165921) at 42 °C for 2 h and at 65 °C overnight. And then DNA was purified with the MinElute Reaction Cleanup kit (Qiagen, 28204). Human-OVOL2 antibodies (SantaCruz Biotechnoligiy, sc-85804) was used for chromatin immunoprecipitation experiments.

value: HCE-T

value: corneal epithelium cell (CEC) line

tag: chip antibody vendor


title: 82-kDa ChAT (Vehicle)


title: Dclk1- sample ZT008

source_name: Pancreatic Dclk1- cells  from Dclk1-CreERT;tdtomato mice

value: Dclk1 negative


title: Dclk1+ sample ZT001


title: HCE-T-input

value: none (input)


title: H3K4me1-ChIP-seq-Rep1

value: P19Cl6 during cardiomyocytes differentiation


title: H3K4me1-ChIP-seq-Rep2

value: Tbx1-SiRNA + TCP


title: Dclk1- sample ZT006


title: Dclk1- sample ZT005

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq version 1.8.4.
Reads were mapped to the genome with Bowtie2 2.0.0-beta7, Tophat2 2.0.4, and HTSeq-0.6.1 .
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: Xlsx file with raw counts for each gene


title: Dclk1- sample ZT007


title: ChIP-seq-Input-Rep3

value: No treatment


title: Tbx1-ChIP-seq-Rep2

value: NT-SiRNA


title: Tbx1-ChIP-seq-Rep1


title: WT rep1

value: Appressorium

value: Appressorium at 5 hpi


title: 1145F60_WSBEiJ

city: Bar Harbor

first: Steven

middle: C

last: Munger

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Lane: L001

data_processing:
Basecalls were performed with CASAVA version 1.8.0
Fragmented fastq files from CASAVA were concatenated together, and then reads that did not pass quality filtering were removed with fastq_illumina_filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/)
Single-End Read Alignment - Only the R1 forward read file for each sample was used in this analysis following the methods described in Munger et al. (GENETICS 2014, doi: 10.1534). Individualized transcriptomes (isoform sequences) derived from the genome fasta file and corresponding gene annotation gtf files were used to construct Bowtie-compatible indexes with the rsem-prepare-reference command in RSEM software (Li and Dewey, 2010; RSEM version 1.2.1). The Bowtie aligner (version 0.12.8) was used to align reads to transcript sequences. Alignments with up to three mismatches (-v 3) across the 100bp read were considered valid, but only the best “strata” of alignments were reported. For a given read, the best stratum is the alignment(s) with the fewest mismatches.
Transcript Abundance Quantitation - Estimates of isoform and gene-level abundance were obtained with RSEM (Li and Dewey 2010). Bowtie alignment files in .bam format were input into the rsem-calculate-expression command. Based on the library fragment size distributions observed on the Agilent Bioanalyzer, fragment length mean was specified as 280bp with a standard deviation of 50bp (RSEM parameters --fragment-length-mean 280 –fragment-length-sd 50). For reads with multiple valid isoform alignments, RSEM implements an expectation-maximization (EM) algorithm that assigns all or a proportion of each multimapping read to one or more isoforms based on the number of uniquely-aligning reads to those transcripts. RSEM estimates isoform expression (counts), and gene-level counts are calculated as the sum of the corresponding isoforms.
Normalization - For each sample, RSEM count estimates were normalized to the upper quartile value (after trimming zeros).
Genome_build: Mouse NCBIM37/mm9. Individualized strain genomes were based on NCBIM37 coordinates.
Supplementary_files_format_and_content: All processed data files are tab-delimited txt files. Each file contains a data matrix with rows representing Ensembl gene identifiers and columns representing samples.

source_name: Subcutaneous Fat

growth_protocol: Female mice from C57BL/6J, NZO/HiLtJ, CAST/EiJ, and WSB/EiJ (n= 6 for each strain, n= 24 total) were obtained from The Jackson Laboratory (JAX). Mice were received at ~3 weeks of age, housed at JAX, and beginning at 4 weeks of age given free access to either a control diet containing 17% kcal fat (TD.8010, Harlan Laboratories, Madison, W) or a high-fat, high-sucrose diet containing 45% kcal from fat and 34% (by weight) sucrose (TD.08811)) from wean age throughout the study. Animals were sacrificed at 26 weeks of age, and subcutaneous inguinal fat pads were collected, stored in RNAlater at -80C, and profiled by RNA-seq analysis.

extract_protocol:
Inguinal fat pads were dissected and stored in RNAlater at -80C). Total RNA was isolated using the Trizol Plus RNA extraction kit (Life Technologies) with on-column DNase digestion.
Following the Illumina TruSeq standard protocol, indexed mRNA-seq libraries were generated from 1μg total RNA followed by QC and quantitation on the Agilent Bioanalyzer and the Kapa Biosystems qPCR library quantitation method.

tag: sample

value: WSB/EiJ

value: Subcutaneous Fat

tag: age (weeks)

tag: genotyped sex

value: Female

tag: diet

value: High Fat

tag: barcode

value: GTGAAA


title: ChIP-seq-Input-Rep1

tag: cell type


title: 1145F59_WSBEiJ

description: Lane: L001

tag: strain

value: GTCCGC


title: 1145F57_WSBEiJ

description: Lane: L001

value: CCGTCC


title: 1145F48_WSBEiJ

description: Lane: L001

value: Standard

value: ATGTCA


title: 0928F58_CASTEiJ

description: Lane: L001

value: CAST/EiJ

value: GCCAAT


title: 1145F46_WSBEiJ

description: Lane: L001

value: AGTCAA


title: 0928F57_CASTEiJ

description: Lane: L001

value: ACAGTG


title: RBF rep2

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

data_processing:
After filtering out low quality reads that contained more than 5 ‘N’s and over 50% of the sequence with low quality value (Phred score < 5), the MeDIP-seq data were aligned to pig reference genome (Sscrofa 10.2),allowing up to four mismatches using SOAP2 software (Version 2.21)
The reads mapping to multiple genomic location were regarded as duplicates and just chose one read. To avoid stochastic sampling drift, we filtered out CpG sites that were covered by less than a 10 read depth.
The DMRs identification method was used our previous description, the normality and equal variance of the read depth at each CpG in LBF and RBF were tested using Bartlett's test (passing if P > 0.05, failed for p < 0.05).
Subsequently, a parametric (passing Bartlett's test) or non-parametric test (failing Bartlett's test) was used to select highly variable CpGs (P < 0.01) as seed sites for candidate DMRs. Then a 3’ downstream adjacent the CpG wes incorporated into the seed CpGs (up to 200 bp), and the new seed CpGs would repeatedly adjacent the next CpG until appearing a low-variance CpG (P > 0.01), which was allowed to be up to 2 kb from the seed CpG.
If five or more CpGs in a genomic region demonstrated significant different (P < 0.01) read depths between LBF and RBF, then taken this as a DMR. The P values for the DMRs were also corrected using the Benjamini-Hochberg method (FDR < 0.01, 1,000 permutations).
Genome_build: Sus_scrofa.Sscrofa10.2
Supplementary_files_format_and_content: excel file with DMR peaks.

organism: Sus scrofa

source_name: Backfat adipose

extract_protocol:
Genomic DNA extracted using the DNeasy Blood & Tissue Kit (Qiagen) according as the manufacturer’s instructions.
Genomic DNA sonicated to approximately 100-500 bp fragments with a Bioruptor sonicator (Diagenode, NJ, USA). Then, libraries were constructed using a Paired-End DNA Sample Prep kit (Illumina, CA, USA) according as the manufacturer’s instructions. The fragments were ligated with adaptor and immunoprecipitated by monoclonal anti-methylcytidine antibody (Diagenode, NJ, USA). The enriched fragments with methylation and 10% input DNA were purified (DNA Clean & Concentrator-5 columns) and amplified by adaptor-mediated PCR. Then the MeDIP libraries were subjected to paired-end sequencing using Illumina HiSeq 2000 and a 50 bp read length.

value: adipose

tag: breed

value: Rongchang pig

tag: Sex

value: female

tag: age

value: post natal day 210


title: 0928F52_CASTEiJ

description: Lane: L001

tag: tissue

value: TTAGGC


title: 0928F49_CASTEiJ

description: Lane: L001

value: Subcutaneous Fat

value: ATCACG


title: 2105F32_NZOHiLtJ

description: Lane: L001

value: NZO/HILtJ

value: Female

value: High Fat

value: ATTCCT


title: 0928F51_CASTEiJ

description: Lane: L001

value: Standard

value: CGATGT


title: 0928F56_CASTEiJ

description: Lane: L001

value: CAST/EiJ

value: TGACCA


title: 2105F31_NZOHiLtJ

description: Lane: L001

value: ACTGAT


title: LBF rep3

value: Landrace pig


title: LBF rep2

value: adipose


title: RBF rep1

value: Rongchang pig


title: LBF rep1

value: female


title: ChIP-seq-Input-Rep2

value: P19Cl6 during cardiomyocytes differentiation

tag: treatment

value: No treatment


title: 2105F22_NZOHiLtJ

description: Lane: L001

value: Subcutaneous Fat

value: GTTTCG


title: dRcsA_2

city: Blacksburg

first: Alison

middle: Kernell

last: Burke

state: VA

address: 970 Washington St SW

department: Biological Sciences

institute: Virgina Tech

data_processing:
Fastq files uploaded to Geneious version 8
Geneious used to align all fastq files to the P. stewartii genome contigs
Geneious determined number of sequences aligning to each gene and data exported to Microsoft Excel
Number of sequences was converted to expression by multiplying by 1000000 and dividing by the total number of sequences aligning to the genome.
Microsoft Excel used to aligned all mutant data to obtain average expression for each gene and then align the mutant averages to the wild type averages to determine changes in expression
Genome_build: AHIE00000000
Supplementary_files_format_and_content: .xlsx files containing sequence counts, normalized expression, wild-type comparision for changes in expression, gene names and identifiers

organism: Pantoea stewartii subsp. stewartii

source_name: bacterium

growth_protocol: Culture grown overnight inRM plus nalidixic acid (20 ug/ml)  broth and subcultured the following day into 5 ml of RM media with nalidixic acid.  Cultures were grown to mid-log phase before harvest of cell pellet

extract_protocol:
RNA isolation with Qiagen miRNeasy kit with on column Dnase I digestions.  rRNA was delepted using Epicentre Gram negative rRNA depeletion kit.
RNA libraries were prepared for sequencing using standard Illumina protocols at Virginia Bioinformatic Institute

treatment_protocol: Qiagen RNAprotect  was added to the cell culture

tag: genotype

value: deletion of rcsA


title: dLrhA_1

value: deletion of lrhA


title: 2105F21_NZOHiLtJ

description: Lane: L001

value: NZO/HILtJ

value: Female

value: GTGGCC


title: 2105F30_NZOHiLtJ

description: Lane: L001

value: High Fat

value: GAGTGG


title: 0664F69_C57BL6J

description: Lane: L001

value: CTTGTA


title: dLrhA_2


title: RBF rep3

value: post natal day 210


title: 1145F47_WSBEiJ

description: Lane: L001

value: WSB/EiJ

value: Standard

value: AGTTCC


title: dRcsA_1


title: 0664F66_C57BL6J

description: Lane: L001

value: TAGCTT


title: Tbx1_SiRNA+TCP-RNA-seq-Rep2

description: Differentially_expressed_Genes_Tbx1-SiRNA+TCP_vs_Tbx1-SiRNA.txt

value: P19Cl6 during cardiomyocytes differentiation

value: Tbx1-SiRNA + TCP


title: Tbx1_SiRNA+TCP-RNA-seq-Rep1


title: Tbx1_SiRNA-RNA-seq-Rep2

description:
Differentially_expressed_Genes_Tbx1-SiRNA_vs_NT-SiRNA.txt
Differentially_expressed_Genes_Tbx1-SiRNA+TCP_vs_Tbx1-SiRNA.txt


title: WT_0.5_1

value: Wild-Type


title: Tbx1_SiRNA-RNA-seq-Rep1


title: 2105F23_NZOHiLtJ

description: Lane: L001

value: Subcutaneous Fat

value: CGTACG


title: NT_SiRNA-RNA-seq-Rep2

description:
Expressed_Genes_in_P19Cl6d1.txt
Differentially_expressed_Genes_Tbx1-SiRNA_vs_NT-SiRNA.txt

value: NT-SiRNA


title: 0664F58_C57BL6J

description: Lane: L001

value: ACTTGA


title: NT_SiRNA-RNA-seq-Rep1


title: K562 NaBut PU.1 ChIP-seq Rep 1

status: Public on Apr 10 2016

city: Durham

first: Christopher

middle: L

last: Frank

state: NC

address: 101 Science Dr.

institute: Duke University

data_processing:
Basecalls performed using CASAVA v1.8
DNase-seq (first 20 bp) and ChIP-seq reads mapped to UCSC hg19 with Bowtie v1.1.0 allowing only unique alignments with up to 1 mismatch, RNA-seq reads mapped to UCSC knownGenes reference with Tophat v2.0 allowing up to 2 mismatches
Putative PCR artifacts (pileup of identical reads) filtered from mapped DNase-seq and ChIP-seq prior to peak calls
DNase-seq and ChIP-seq peak calls made with MACS2 v2.1.0, FPKM expression values estimated by Cufflinks v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: DNase-seq and ChIP-seq .bed files of peak calls contain chromosome, start, stop, name, score, fold-change, -log10 p-value, -log10 q-value, summit position; RNA-seq Cufflinks text files contain gene-level FPKM abundances with gene name and locus

source_name: K562 NaBut PU.1 ChIP-seq

growth_protocol: K562 cells were obtained from ATCC (CCL-243) and maintained in 1x RPMI1640 media (with L-glutamine) supplemented with 10% FBS and 1x penicillin/streptomycin (Life Technologies). GM12878 lymphoblasts obtained from Coriell and maintained in 1x RPMI 1640 media (with L-glutamine) supplemented with 15% FBS and 1x penicillin/streptomycin (Life Technologies). CRC119 cells maintained in 1x RPMI 1640 media (with L-glutamine) supplemented with 10% FBS, 1x NaPyruvate, 0.02 M HEPES, and 1x penicillin/streptomycin (Life Technologies).

extract_protocol:
Perfomed as described in PMID:17540862. Chromatin sonicated with Bioruptor (Diagenode) for 45 min.( 30 sec. on/off, High) in 1x RIPA buffer. DNA fragments resuspended in 1% Triton X-100, 2mM EDTA, 20mM TrisCl, 150 mM NaCl buffer, pre-cleared with Protein A Dynabeads for 2 hr. at 4°C, and 6 μg of rabbit anti-PU.1 Santa Cruz Biotech sc-22805 (Life Tech.) incubated with the sonicated chromatin overnight at 4°C. Protein A beads were bound to antibody-chromatin mixture for 3 hours at 4°C and then washed 5 times with LiCl wash buffer (500 mM LiCl, 100 mM TrisCl, 1% NP40, 1% sodium deoxycholate) and once with 1x TE . Crosslinking was reversed with overnight 65°C incubation in 1% SDS, 0.1M sodium bicarbonate buffer and DNA was eluted with a PCR cleanup kit (Qiagen). Following TruSeq adapter ligations, DNA fragments were separated from free adapters by AmpureXL bead size selection steps and PCR amplification was performed for 18 cycles.
~20 million cells crosslinked with 1% formaldehyde for 10 min. at RT, quenched with glycine, and lysed with 1x RIPA buffer.

tag: cell line

value: myelogenous leukemia cell line

tag: treated with

value: 0.5 mM NaBut

tag: duration of treatment

value: 72 hours

tag: chip antibody

value: rabbit anti-PU.1

value: Santa Cruz Biotech

tag: chip antibody cat. #


title: Gata2-IP_vehicle

city: Boston

first: Jeff

last: Shearstone

address: 70 Fargo Street

department: Biology

institute: Acetylon Pharmaceuticals

description: Sample immunoprecipitated with antibodies against Gata-2 (20 ul, sc-9008, Santa Cruz, Dallas, TX)

data_processing:
The 50-nt sequence reads were mapped to the human genome, build Hg19, using the BWA algorithm with default settings. For the analysis, all data files were normalized to the same number of unique alignments without duplicate reads (24 million). Sequence tags were extended in silico (using Active Motif software) at their 3'-ends to a length of 150 bp. To identify the density of fragments (extended tags) along the genome, the genome was divided into 32-nt bins and the number of fragments in each bin was determined.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Erythroid progenitors

growth_protocol: CD34+ cells isolated from human bone marrow of healthy normal donors were cultured in a 2-phase system. This system has been described previously (Sankaran, Menne et al. 2008).  Cells were expanded for 7 days in StemSpan SFEM (StemCell, Vancouver, Canada) supplemented with CC100 (StemCell), 100 U/ml penicillin and 100 ug/ml streptomycin. CC100 is a mix of Flt-3 ligand, stem cell factor (SCF), interleukin-3 (IL3), and interleukin-6 (IL6). Cells were then cultured for an additional 7 days in erythroid differentiation media, composed of StemSpan SFEM supplemented with 1 U/ml erythropoietin (EPO), 5 ng/ml (IL3), 20 ng/ml (SCF), 2 uM dexamethasone, 1 uM beta-estradiol, 100 U/ml penicillin and 100 ug/ml streptomycin.

extract_protocol:
Cells were fixed in 1% formaldehyde for 15 min at room temperature. Crosslinking reaction was extinguished by adding glycine to 125 mM. Cells were washed three times in PBS, 0.5% lgepal CA-630, 1 mM phenylmethanesulfonyl fluoride (PMSF). Cell pellets were snap frozen on dry ice and stored at -80°C
ChIP-Seq was performed by Active Motif (Carlsbad, CA). Chromatin (30 ug) from vehicle or ACY-957 treated cells was immunoprecipitated with antibodies against Gata-2 (20 ul, sc-9008, Santa Cruz, Dallas, TX), HDAC1 (20 ug, ab7028, Abcam, Cambridge, MA), or HDAC2 (4 ug, ab12169, Abcam). ChIP DNA, as well as a control sample composed of equal amounts of input DNA from each treatment group, was processed into Illumina libraries using standard procedures, and libraries were sequenced on HiSeq 2000.

treatment_protocol: Cells were treated with vehicle (DMSO) or the HDAC1/2-selective inhibitor ACY-957 at 1 micromolar for 7 days in erythroid differentiation media.

value: Erythroid progenitors derived from human CD34+ bone marrow cells

tag: antibody

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog number


title: HDAC1-IP_vehicle

description: Sample immunoprecipitated with antibodies against HDAC1 (20 ug, ab7028, Abcam, Cambridge, MA)

value: Abcam


title: Input

description: Input is a control sample composed of equal amounts of input DNA from each treatment group

value: none (control sample composed -Input)


title: Gata2-IP_ACY-957


title: K562 SAHA PU.1 ChIP-seq Rep 1

source_name: K562 SAHA PU.1 ChIP-seq

value: 1 μM SAHA

tag: chip antibody vendor


title: HDAC2-IP_vehicle

description: Sample immunoprecipitated with antibodies against HDAC2 (4 ug, ab12169, Abcam)

tag: cell type


title: WT_0.5_2


title: K562 SAHA PU.1 ChIP-seq Rep 2


title: K562 SAHA PU.1 ChIP-seq Rep 3


title: K562 DMSO Vehicle Control PU.1 ChIP-seq Rep 1

source_name: K562 DMSO Vehicle Control PU.1 ChIP-seq

value: 0.01% DMSO vehicle


title: K562 DMSO Vehicle Control PU.1 ChIP-seq Rep 3


title: K562 PBS Vehicle Control PU.1 ChIP-seq Rep 1

source_name: K562 PBS Vehicle Control PU.1 ChIP-seq

value: 0.5% 1xPBS vehicle


title: K562 Input Control Treated ChIP-seq Rep 1

source_name: K562 Input Control Treated ChIP-seq

extract_protocol:
Chromatin sonicated with Bioruptor (Diagenode) for 45 min.( 30 sec. on/off, High) in 1x RIPA buffer and aliquot was reserved for input control. Crosslinking was reversed with overnight 65°C incubation in 1% SDS, 0.1M sodium bicarbonate buffer and DNA was eluted with a PCR cleanup kit (Qiagen). Following TruSeq adapter ligations, DNA fragments were separated from free adapters by AmpureXL bead size selection steps and PCR amplification was performed for 18 cycles.
~20 million cells crosslinked with 1% formaldehyde for 10 min. at RT, quenched with glycine, and lysed with 1x RIPA buffer.


title: 0664F57_C57BL6J

description: Lane: L001

tag: sample

tag: strain

tag: age (weeks)

tag: genotyped sex

value: Female

tag: diet

value: Standard

tag: barcode

value: CAGATC


title: K562 Input Control ChIP-seq Rep 1

source_name: K562 Input Control ChIP-seq


title: K562 KD Vector Control SAHA RNA-seq Rep 2

source_name: K562 KD Vector Control SAHA RNA-seq

extract_protocol:
2 μg total RNA was used for Illumina Stranded mRNA-seq Library Prep Kit with polyA selection
Cell pellets were washed with 1xPBS and total RNA extracted with RNAeasy kit (Qiagen)

tag: genotype/variation

value: vector control (for PU.1 depletion)


title: K562 KD Vector Control DMSO RNA-seq Rep 2

source_name: K562 KD Vector Control DMSO RNA-seq

tag: cell line


title: K562 Input Control Treated ChIP-seq Rep 2

tag: treated with


title: K562 KD Vector Control SAHA RNA-seq Rep 1

tag: duration of treatment


title: K562 KD Vector Control DMSO RNA-seq Rep 1


title: K562 Input Control ChIP-seq Rep 2


title: 0664F67_C57BL6J

description: Lane: L001

tag: tissue

value: Subcutaneous Fat

value: High Fat

value: GGCTAC


title: K562 PU.1 shRNA2 DMSO RNA-seq Rep 1

source_name: K562 PU.1 shRNA2 DMSO RNA-seq

value: myelogenous leukemia cell line

value: PU.1 shRNA; PU.1 depletion

value: 72 hours


title: K562 PU.1 shRNA2 DMSO RNA-seq Rep 2


title: K562 PU.1 shRNA1 SAHA RNA-seq Rep 1

source_name: K562 PU.1 shRNA1 SAHA RNA-seq


title: K562 PU.1 shRNA1 SAHA RNA-seq Rep 2


title: K562 PU.1 shRNA1 DMSO RNA-seq Rep 1

source_name: K562 PU.1 shRNA1 DMSO RNA-seq


title: K562 OE Vector Control RNA-seq Rep 2

source_name: K562 OE Vector Control RNA-seq

value: vector control (for PU.1 overexpression)

value: none (untreated)


title: Drug_b2_27_RNA-seq

city: chapel hill

first: Yunjung

last: Kim

state: North Carolina

address: 120 Mason farm road

institute: UNC at Chapel Hill

description: strand-specific

data_processing:
We mapped lane-level reads to mm9 using Tophat v2.0.6 using default parameters and --library-type fr-firststrand option for strand-specific libraries
We removed reads with low quality score, potential PCR duplicates
The aligned lane-levl bam files were merged into one bam file for each sample
Mapped reads were summarized into gene-level expression estimates using Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: GTF files include RPKM values for each Sample generated from Cufflinks

source_name: C57BL/6J, striatum, RNAseq

extract_protocol:
Total RNA was extracted from striatum using Total RNA Purification 96-well Kit
Barcode libraries were created using Illumina TruSeq RNA sample preparation Kit v2

treatment_protocol: All animals were bred at UNC from mice that were less than six generations removed from founders acquired from the Jackson Laboratory (Bar Harbor, ME).

tag: treatment

value: Drug

value: striatum

tag: batch

tag: rna integrity number


title: Drug_b2_33_RNA-seq

description: strand-specific


title: placebo_b2_32_RNA-seq

description: strand-specific

value: placebo


title: placebo_b2_26_RNA-seq

description: strand-specific


title: K562 PU.1 Overexpression RNA-seq Rep 1

source_name: K562 PU.1 Overexpression RNA-seq

value: PU.1 overexpression


title: K562 OE Vector Control RNA-seq Rep 1


title: K562 PU.1 Overexpression RNA-seq Rep 2


title: placebo_b2_28_RNA-seq

description: strand-specific


title: K562 NaBut 72hr RNA-seq Rep 2

source_name: K562 NaBut 72hr RNA-seq

extract_protocol:
2 μg total RNA was used for Illumina mRNA-seq Library Prep Kit with polyA selection
Cell pellets were washed with 1xPBS and total RNA extracted with RNAeasy kit (Qiagen)

value: 0.5 mM NaBut


title: Drug_b2_35_RNA-seq

description: strand-specific


title: Drug_b2_29_RNA-seq

description: strand-specific


title: K562 NaBut 72hr RNA-seq Rep 3


title: K562 PU.1 shRNA1 DMSO RNA-seq Rep 2

value: 0.01% DMSO vehicle


title: placebo_b2_22_RNA-seq

description: strand-specific


title: Drug_b2_23_RNA-seq

description: strand-specific


title: Drug_b2_21_RNA-seq

description: strand-specific


title: K562 PU.1 shRNA2 SAHA RNA-seq Rep 1

source_name: K562 PU.1 shRNA2 SAHA RNA-seq

value: 1 μM SAHA


title: Drug_b1_9_RNA-seq

description: strand-specific


title: Drug_b2_25_RNA-seq

description: strand-specific


title: Drug_b2_31_RNA-seq

description: strand-specific


title: placebo_b1_8_RNA-seq

description: strand-specific


title: Drug_b1_7_RNA-seq

description: strand-specific


title: K562 PBS Vehicle Control RNA-seq Rep 2

source_name: K562 PBS Vehicle Control RNA-seq

value: 0.5% 1xPBS vehicle


title: K562 SAHA 72hr RNA-seq Rep 1

source_name: K562 SAHA 72hr RNA-seq


title: Drug_b1_5_RNA-seq

description: strand-specific


title: placebo_b1_6_RNA-seq

description: strand-specific


title: K562 NaBut 72hr RNA-seq Rep 1


title: K562 SAHA 72hr RNA-seq Rep 2


title: placebo_b1_20_RNA-seq

description: strand-specific


title: placebo_b1_2_RNA-seq

description: strand-specific


title: K562 DMSO Vehicle Control RNA-seq Rep 2

source_name: K562 DMSO Vehicle Control RNA-seq


title: K562 DMSO Vehicle Control PU.1 ChIP-seq Rep 2

source_name: K562 DMSO Vehicle Control PU.1 ChIP-seq

tag: chip antibody

value: rabbit anti-PU.1

value: Santa Cruz Biotech

tag: chip antibody cat. #


title: Drug_b1_3_RNA-seq

description: strand-specific


title: CRC119 SAHA Vehicle Control DNase-seq Rep 2

source_name: CRC119 SAHA Vehicle Control DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150184
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

tag: cell type

value: colorectal cancer cell line

value: 0.5 μM SAHA


title: K562 DMSO Vehicle Control RNA-seq Rep 1

value: myelogenous leukemia cell line


title: placebo_b1_4_RNA-seq

description: strand-specific


title: Drug_b1_19_RNA-seq

description: strand-specific


title: CRC119 SAHA Vehicle Control DNase-seq Rep 1

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150183
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: K562 PBS Vehicle Control RNA-seq Rep 1


title: K562 PU.1 shRNA2 SAHA RNA-seq Rep 2

value: PU.1 shRNA; PU.1 depletion


title: CRC119 DMSO Vehicle Control DNase-seq Rep 2

source_name: CRC119 DMSO Vehicle Control DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150182
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: 72 hours


title: Drug_b1_17_RNA-seq

description: strand-specific


title: Drug_b1_15_RNA-seq

description: strand-specific


title: CRC119 DMSO Vehicle Control DNase-seq Rep 1

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150181
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: placebo_b1_16_RNA-seq

description: strand-specific


title: GM12878 DMSO Vehicle Control DNase-seq Rep 2

source_name: GM12878 DMSO Vehicle Control DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150178
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: lymphoblasts


title: GM12878 SAHA Vehicle Control DNase-seq Rep 2

source_name: GM12878 SAHA Vehicle Control DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150180
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: GM12878 SAHA Vehicle Control DNase-seq Rep 1

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150179
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: K562 PBS Vehicle Control RNA-seq Rep 3


title: placebo_b1_12_RNA-seq

description: strand-specific


title: GM12878 DMSO Vehicle Control DNase-seq Rep 1

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150177
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: Drug_b1_13_RNA-seq

description: strand-specific


title: K562 KD Vector Control SAHA DNase-seq Rep 2

source_name: K562 KD Vector Control SAHA DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150176
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: vector control (for PU.1 depletion)


title: K562 KD Vector Control DMSO DNase-seq Rep 1

source_name: K562 KD Vector Control DMSO DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150173
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: placebo_rh12_DNase-seq

data_processing:
read sequences were aligned to mm9 using bowtie with parameters (-m 1 --best --strata)
we filtered to remove quality score < 10, PCR duplicates.
We used F-seq for estimation of enriched peaks to identify potential open chromatin regions
Genome_build: mm9
Supplementary_files_format_and_content: bed files for DNase I cut peak regions

source_name: C57BL/6J, right hemisphere, DNase-seq

extract_protocol:
Genomic DNA was extracted from mouse brain samples
The extracted nuclei were digested with different amounts of DNase I for 16 min at 37° C. The reactions were terminated by the addition of 50 mM EDTA. Libraries were constructed from pooled digests and sequenced.

value: right hemisphere

tag: lane


title: placebo_b1_10_RNA-seq

description: strand-specific

tag: strain

value: striatum


title: K562 PU.1 shRNA2 SAHA DNase-seq Rep 2

source_name: K562 PU.1 shRNA2 SAHA DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150172
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: 0664F60_C57BL6J

description: Lane: L001

source_name: Subcutaneous Fat

extract_protocol:
Inguinal fat pads were dissected and stored in RNAlater at -80C). Total RNA was isolated using the Trizol Plus RNA extraction kit (Life Technologies) with on-column DNase digestion.
Following the Illumina TruSeq standard protocol, indexed mRNA-seq libraries were generated from 1μg total RNA followed by QC and quantitation on the Agilent Bioanalyzer and the Kapa Biosystems qPCR library quantitation method.

tag: sample

value: Subcutaneous Fat

tag: age (weeks)

value: Female

value: Standard

value: GATCAG


title: K562 KD Vector Control DMSO DNase-seq Rep 2

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150174
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: 0.01% DMSO vehicle


title: placebo_rh6_DNase-seq

value: placebo


title: K562 KD Vector Control SAHA DNase-seq Rep 1

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150175
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: 1 μM SAHA


title: drug_rh21_DNase-seq

value: drug


title: K562 PU.1 shRNA2 DMSO DNase-seq Rep 1

source_name: K562 PU.1 shRNA2 DMSO DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150169
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: drug_rh7_DNase-seq


title: Transgenic3

city: Salt Lake City

first: Santhosh

last: Karanth

state: UT

address: 15 North 2030 East, Rm No. 3460

department: Molecular Medicine Program

institute: University of Utah School of Medicine

data_processing:
Reads were aligned to the genome using novoalign
Annotated splice junctions generated by the MakeTranscriptome command in the USeq
Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq
Differential gene expression analysis was performed on the resulting count table using DESeq2
Genome_build: Zv9 genome build
Supplementary_files_format_and_content: excel file with read counts, FPKM and statistical analysis

organism: Danio rerio

extract_protocol:
Total RNA  extracted using a DirectZol RNA miniprep kit (Zymo Research)
Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild-type and single-end 50-bp reads were generated on a Hiseq 2500 machine

value: Liver

tag: transgene

tag: developmental stage

value: 7 dpf larvae


title: K562 PU.1 shRNA2 DMSO DNase-seq Rep 2

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150170
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: myelogenous leukemia cell line

tag: genotype/variation


title: K562 PU.1 shRNA1 SAHA DNase-seq Rep 2

source_name: K562 PU.1 shRNA1 SAHA DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150168
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

tag: cell line

value: PU.1 shRNA; PU.1 depletion


title: Transgenic1


title: WT3


title: placebo_rh14_DNase-seq


title: K562 PU.1 shRNA2 SAHA DNase-seq Rep 1

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150171
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

tag: treated with

value: 72 hours


title: K562 PU.1 shRNA1SAHA DNase-seq Rep 1

source_name: K562 PU.1 shRNA1SAHA DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150167
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

tag: duration of treatment


title: WT2

tag: tissue


title: placebo_st1_DNase-seq

source_name: C57BL/6J, striatum, DNase-seq

tag: treatment


title: WT1


title: drug_G877_ATACseq

data_processing:
library strategy: ATAC-seq
read sequences were aligned to mm9 using bowtie with parameters (-m 1 --bset --strata)
we filtered to remove quality score < 10, PCR duplicates.
We used F-seq for estimation of enriched peaks to identify potential open chromatin regions
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using F-seq and converted to bigwig format

source_name: C57BL/6J, striatum, ATACseq

extract_protocol:
Genomic DNA was extracted from mouse brain samples
Libraries were amplified for a total of 10–12 cycles, purified using 1.2X Ampure beads and eluted in 20ul H2O. Following purification, library fragments were amplified using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers. To reduce GC and size bias in our PCR we monitored the PCR reaction using qPCR in order to stop amplification prior to saturation. The libraries were amplified for 5 cycles, a 5ul aliquot was run in a qPCR side reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were purified using 1.2X Ampure beads and eluted in 20ul H2O. Libraries were amplified for a total of 10–12 cycles.


title: Transgenic2


title: K562 OE Vector Control DNase-seq Rep 1

source_name: K562 OE Vector Control DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150163
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: vector control (for PU.1 overexpression)

value: none (untreated)


title: K562 OE Vector Control DNase-seq Rep 2

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150164
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: K562 PU.1 shRNA1 DMSO DNase-seq Rep 1

source_name: K562 PU.1 shRNA1 DMSO DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150165
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: K562 High NaBut 72hr DNase-seq Rep 2

source_name: K562 High NaBut 72hr DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150160
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: 2 mM NaBut


title: placebo_G875_ATACseq

value: striatum


title: K562 PU.1 Overexpression DNase-seq Rep 1

source_name: K562 PU.1 Overexpression DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150161
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: PU.1 overexpression


title: K562 PU.1 Overexpression DNase-seq Rep 2

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150162
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis