title: SA6_T

description:
Cytoplasmic RNA
H33389/DS189_Total_L1.D702_506

value: Total


title: R41-7

status: Public on Apr 11 2018

type: SRA

city: Avignon

first: Cédric

last: Alaux

address: Domaine Saint-Paul

department: UMR 406 Abeilles et Environnement

country: France

institute: INRA

description: pool of 10 varroa

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2).
The read quality of the RNA-seq libraries was evaluated using FastQC. Cleaned and filtered reads were de novo assembled using DRAP version 1.7 and filtered with at least one FPKM.
The resulting contigs were aligned with NCBI blast (blastx program, version 2.2.26) on Refseq protein, Swissprot and Ensembl protein reference files to retrieve the corresponding annotations. The contigs were also processed with rnammer (version 1.2) to find ribosomal genes, with repeatmasker (version open-4-0-3) to list the contained repeats and with interproscan (version 4.8) for gene ontology and structural annotation. Reads have been realigned back to contigs with bwa (version 0.7.12). The resulting sam files were compressed, sorted and indexed with samtools (version 1.1).
The contig expression counts have been generated from the bam files with samtools (idxstats program, version 1.1) and merged with unix commands. The alignment files have then been filtered for duplicates with samtools (rmdup program, version 1.1) before variant calling. The resulting bam files have been processed with GATK (version v3.0-0-g6bad1c6).
The assembly quality has been assessed in several ways. First, the read on contig re-alignment rate has been calculated for every sample using the bam files presented in the previous section. Second, the 308 Varroa destructor proteins found in NCBI protein database have been realigned using blat version  v. 35x1 on the contigs to retrieve their match coverage and similarity. Third, coverage and similarity have been calculated for the 12,035 NCBI Metaseiulus occidentalis proteins in the same way as for Varroa destructor proteins. Last, the contigs where processed with BUSCO (version 2) using the insecta_odb9 database.
Genome_build: de novo assembly contigs.fa
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample.

molecule: total RNA

organism: Varroa destructor

source_name: whole body

growth_protocol: Phoretic mites: capped brood frames of each colony were removed to prevent any mite being released from emerging brood cells. Four days later, one frame of bees was removed from the colony and phoretic mites were sampled directly on adult bees.  Phoretic mites artificially reared: An additional 20 mites were sampled together with the bees they were standing on and placed in a Pain cage, with 10 other non-infested bees. Cages were kept for 4 days in an incubator (28°C) before mites were sampled.   All subsequent stages were sampled from brood frames removed from the colonies and dissected in the laboratory.  Arresting mites: these mites were collected in unsealed L5 brood cells, as mites seen immobile at the bottom of the cells, immersed in larval food.  Pre-laying mites: these mites were collected from sealed brood cells containing moving larvae. These mites displayed an inflated ventral side due to activation of the ovaries.  Laying mites: these mites were collected from sealed brood cells containing pre-pupae and at least one mite egg (but no mite protonymph).  Post-laying mites: these mites were collected from capped brood cells containing purple-eye and white-body pupae (P5). Female mites were sampled if they were accompanied by at least one male and one female deutonymphs.  Non-reproducing mites: these mites were also collected from P5 brood cells, but identified as female mites with no offspring, i.e. in reproduction failure.  Emerging mites: these mites were collected from capped brood cells containing developing bees almost ready to emerge (but with an intact cell cap – P8 to P9).  Young mites: these mites were also collected from P8 to P9 cells, but identified thanks to their lighter body coloration as compared to founder females. These mites should have been just mated, but have yet to undergo their first phoretic and reproducing stages.  Male mites: these mites were also collected from P8 to P9 cells and identified thanks to their striking sexual dimorphism as compared to females. Males exhibit a yellow tan and a round-body shape.

extract_protocol:
Varroa were flash frozen in dry ice. RNA was extracted from pool of 10 varroas using Trizol reagent and the Qiagen RNeasy Mini Kit (QIagen)
Illumina TruSeq Stranded mRNA Sample Preparation kit was used with 200 ng of total RNA for the construction of sequencing libraries.

treatment_protocol: No treatment

tag: life cycle stage

value: males (collected from P8 to P9 brood cells)

tag: tissue

value: whole body

tag: age

value: adult

tag: colony


title: ESC (embryonic stem cells) biological rep3, 60 min

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

library_source: genomic

data_processing:
Although reads were paired-end, only the 1st reads (R1) were used for mapping due to low sequencing quality of the 2nd reads (R2).
Low quality sequences (Q < 30) were removed from the 3' end of the reads by trimGalore.
The trimed reads were mapped to the appropriately converted mouse (mm10) and lambda phage (internal control) genomic sequences by bismark.
Using these mapping results, methylation at individual C sites were determined by bismark-methylation-extractor.
The methylation levels at these cytosine sites were analyzed with discrimination of H and L strands.
Genome_build: mm10
Supplementary_files_format_and_content: The csv files contain methylation levels of individual C sites: position, strand, methylation level (%), the number of reads covering the cytosine site.

molecule: genomic DNA

organism: Mus musculus

source_name: bisulfite-treated mtDNA (and lambda DNA)

extract_protocol:
Mitochondrial nucleic acid containing mitochondrial DNA (mtDNA) was prepared from the purified mitochondria by protease K treatment, phenol extraction, chloroform/isoamyl-alcohol extraction and ethanol precipitation, followed by linearization of mtDNA by restriction enzyme digestion.
The mtDNA and spike-in lambda DNA were treated with 9.2M bisulfite, and used for PBAT library preparation as a template.

treatment_protocol: Highly purified mitochondrial fraction was prepared from cells/tissues by homogenization, washing, ultracentrifugation and benzonase treatment.

tag: strain

value: mitocondoria purified from embryonic stem cell line E14

tag: treatment

value: bisulfite-treated for 60 min


title: R41-8

description: pool of 10 varroa

value: phoretic mites (collected on adult bees)


title: ESC (embryonic stem cells) biological rep2, 60 min


title: R41-5

description: pool of 10 varroa

value: emerging mites (collected from P8 to P9 brood cells)


title: SA6_P

city: London

first: Rocio Teresa

last: Martinez-Nunez

state: Greater London

address: 5th Floor Tower Wing, Guy’s Campus

department: Infectious Diseases

country: United Kingdom

institute: King's College London

description:
Polyribosome-bound RNA
H33389/DS189_Poly_L1.D703_506

data_processing:
Base call files were converted into FASTQ files using Illumina Software (CASAVA)
Sequencing adapters and other low quality bases were clipped. Reads were aligned to External RNA Controls Consortium (ERCC) sequences to assess the success of library construction and sequencing. A subset (~1M reads) was aligned to other spiked-in control sequences (PhiX and other Illumina controls used during library preparation), residual sequences (globin and ribosomal RNA), and poly-A/T sequences that persisted after clipping. The reads were also aligned to a sampling of intergenic regions to assess the level of DNA contamination level
RSEM v1.2.0 was used to quantify and compute estimated counts by genes and transcripts (Li and Dewey 2011) using the UCSC knownGene. To determine the origin of all reads as a method of quality control, the unaligned reads were aligned to the full genome (not transcriptome) using BWA 0.6.2 (Li and Durbin 2009)
Upper Quartile normalization was used to normalize between different samples with different read depths for both aggregate gene expression and isoform analysis. Each sample was scaled to that the Upper Quartile of counts was equal to 1000. All 77k isoforms defined by UCSC hg19 were considered as initial candidates. 12,485 isoforms are associated with only one gene, and thus were not considered further. Over 12k isoforms had 0 or nearly 0 counts for all subjects. Only genes and isoforms with median counts of 10 or more on each group (Total or Polysome) were taken into account
PROC-GLM was used to perform preliminary statistical analysis
Genome_build: hg19
Supplementary_files_format_and_content: Text files containing non-normalized annotated gene counts and isoform counts for each sample

organism: Homo sapiens

source_name: Bronchial Epithelial Cells

growth_protocol: Epithelial brushings were collected using disposable, sheathed bronchial brushes (Olympus cytology brushes BC-202D-2010, KeyMed [Medical & Industrial Equipment] Ltd OLYMPUS Group Company), with 4 separate sets of brushings from the central airways. Brushings were placed in a sterile universal tube with 5 ml PBS and washed with 10mL of RPMI medium (PAA, GE Healthcare LifeSciences) supplemented with penicillin/streptomycin (Thermo Fisher Scientific). Brushings were spun at 1200 rpm for 10 minutes, medium was discarded and cells were resuspended in complete BEGM (Lonza). BECs were cultured in collagen (Thermo Fisher Scientific)-coated T25 flasks in BEGM complete medium and passaged onto 15cm2 collagen-coated dishes when 80% confluent. Polyribosome preparation and validations were performed in passage 1 cells

extract_protocol:
Polyribosome profiling was done as described previously (Sterne-Weiler et al. 2013; Martinez-Nunez and Sanford 2016) with the addition of 500g/mL cycloheximide (Sigma-Aldrich UK) in the lysis buffer
TrueSeq Stranded mRNA Library Prep Kit

tag: seq name

tag: fraction

value: Polysome

tag: disease status

value: SA


title: R41-4

description: pool of 10 varroa

value: non-reproducing mites (collected from P5 brood cells, but without offspring)


title: ESC (embryonic stem cells) biological rep2, 40 min

value: bisulfite-treated for 40 min


title: R41-6

description: pool of 10 varroa

value: young mites (collected from P8  to P9 brood cells)


title: SA1_P

description:
Polyribosome-bound RNA
V10532/DS158_Poly_L3


title: R41-3

description: pool of 10 varroa

value: laying mites (collected from sealed brood cells containing pre-pupae)


title: SA5_T

description:
Cytoplasmic RNA
H33389/DS187_Total_L1.D712_505


title: R245-10

description: pool of 10 varroa

value: post-laying mites (collected from capped brood cells containing purple-eye and white-body pupae P5)


title: R41-2

description: pool of 10 varroa

value: pre-laying mites (collected from sealed brood cells containing moving larva)


title: R41-1

description: pool of 10 varroa

value: arresting mites (collected in unsealed L5 brood cells)


title: ESC (embryonic stem cells) biological rep2, 5 min

value: bisulfite-treated for 5 min


title: SA4_T

description:
Cytoplasmic RNA
H33389/DS159_Total_L1.D710_505

value: Total


title: R245-9

description: pool of 10 varroa

value: phoretic mites artificially reared in cages with adult bees

value: whole body


title: SA5_P

description:
Polyribosome-bound RNA
H33389/DS187_Poly_L1.D701_506


title: ESC (embryonic stem cells) biological rep2, 15 min

value: mitocondoria purified from embryonic stem cell line E14

value: bisulfite-treated for 15 min


title: ESC (embryonic stem cells) biological rep1, 60 min

value: bisulfite-treated for 60 min


title: R245-7

description: pool of 10 varroa

value: males (collected from P8 to P9 brood cells)

value: adult


title: R245-8

description: pool of 10 varroa

value: phoretic mites (collected on adult bees)


title: SA4_P

description:
Polyribosome-bound RNA
H33389/DS159_Poly_L1.D711_505

value: Polysome

value: SA


title: ESC (embryonic stem cells) biological rep1, 40 min

value: bisulfite-treated for 40 min


title: R245-4

description: pool of 10 varroa

value: non-reproducing mites (collected from P5 brood cells, but without offspring)


title: R245-5

description: pool of 10 varroa

value: emerging mites (collected from P8 to P9 brood cells)


title: R245-6

description: pool of 10 varroa

value: young mites (collected from P8  to P9 brood cells)


title: ESC (embryonic stem cells) biological rep1, 15 min


title: R245-2

description: pool of 10 varroa

value: pre-laying mites (collected from sealed brood cells containing moving larva)


title: HC3_T

description:
Cytoplasmic RNA
H33388/DS203_Total_L1.D706_505

value: HC


title: SA3_T

description:
Cytoplasmic RNA
H33388/DS205_Total_L1.D710_506

value: Total


title: R245-3

description: pool of 10 varroa

value: laying mites (collected from sealed brood cells containing pre-pupae)


title: ESC (embryonic stem cells) biological rep1, 5 min

value: bisulfite-treated for 5 min


title: R245-1

description: pool of 10 varroa

value: arresting mites (collected in unsealed L5 brood cells)

value: whole body


title: R204-10

description: pool of 10 varroa

value: post-laying mites (collected from capped brood cells containing purple-eye and white-body pupae P5)


title: liver biological rep2, 60 min

value: mitocondoria purified from liver

value: bisulfite-treated for 60 min


title: R204-8

description: pool of 10 varroa

value: phoretic mites (collected on adult bees)

value: adult


title: HC3_P

description:
Polyribosome-bound RNA
H33388/DS203_Poly_L1.D707_505

value: Polysome


title: liver biological rep1, 60 min


title: SA2_T

description:
Cytoplasmic RNA
H33388/DS200_Total_L1.D708_506

value: SA


title: liver biological rep1, 40 min

value: bisulfite-treated for 40 min


title: R204-6

description: pool of 10 varroa


title: R204-7

description: pool of 10 varroa

value: males (collected from P8 to P9 brood cells)


title: SA2_P

description:
Polyribosome-bound RNA
H33388/DS200_Poly_L1.D709_506


title: SA8_P

description:
Polyribosome-bound RNA
H33388/DS198_Poly_L1.D707_506


title: liver biological rep1, 15 min

value: bisulfite-treated for 15 min


title: R204-4

description: pool of 10 varroa

value: non-reproducing mites (collected from P5 brood cells, but without offspring)


title: HC2_T

description:
Cytoplasmic RNA
H33388/DS194_Total_L1.D704_505

value: HC


title: R204-3

description: pool of 10 varroa


title: brain biological rep1, 60 min

value: mitocondoria purified from brain


title: R204-2

description: pool of 10 varroa

value: pre-laying mites (collected from sealed brood cells containing moving larva)


title: HC1_T

description:
Cytoplasmic RNA
H33388/DS191_Total_L1.D702_505

value: Total


title: brain biological rep2, 60 min


title: HC2_P

description:
Polyribosome-bound RNA
H33388/DS194_Poly_L1.D705_505


title: brain biological rep1, 40 min


title: SA1_T

description:
Cytoplasmic RNA
H33388/DS158_Total_L1.D708_505


title: R204-9

description: pool of 10 varroa

value: phoretic mites artificially reared in cages with adult bees


title: brain biological rep1, 5 min

value: bisulfite-treated for 5 min


title: SET-2_STAT1-C1_input

city: Cambridge

first: Ioana

middle: Ilinca

last: Nitulescu

state: MA

address: 12 Oxford St

country: USA

institute: Harvard University

description: input for : SET2_STAT1-C1.fastq.gz

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC v.0.10.1 was used to check read quality metrics.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.1 with flags -n 1 -m 1 --best --strata
Duplicate reads were removed with MarkDuplicates (picard tools v.1.88)
SPP was used both for cross-correlation analysis and for peak finding using default parameters or FDR < 0.05. MACS2 was used either with default parameters or using --shiftsize to set the strand shift to match the SPP peak cross-correlation size. Regions on chrM or overlapping repeat elements (RepeatMasker bed file downloaded from UCSC 16 Nov. 2012) by > 70% were routinely excluded.
Genome_build: hg19
Supplementary_files_format_and_content: peak

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for Illumina sequencing were prepared using the KAPA Hyper Prep Kit for Illumina and ligated to unique Bioo Scientific NEXTflex barcode adaptors. Following ligation, libraries were amplified with 8-12 cycles of PCR and were then size-selected using a 2% gel cassette in the Pippin Prep System from Sage Science. DNA fragments of size 200-500bp were captured. Libraries were quantified by qPCR utilizing the KAPA Biosystems Illumina Library Quantification kit.

tag: cell type

value: essential thrombocythemia

tag: treatment protocol

value: CA 25 nM

tag: chip epitope

value: input

tag: chromatin prep#

tag: growth protocol

value: SET2 cells were grown in RPMI-1640 supplemented with 20% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.


title: brain biological rep1, 15 min


title: SET-2_STAT1-C2_input

description: input for : SET2_STAT1-C2.fastq.gz


title: R204-1

description: pool of 10 varroa

value: arresting mites (collected in unsealed L5 brood cells)

value: whole body

value: adult


title: SET-2_STAT1-D2_input

description: input for : SET2_STAT1-D2.fastq.gz

value: DMSO


title: SET-2_STAT1-D1_input

description: input for : SET2_STAT1-D1.fastq.gz


title: Mmar_RIF_24hrs_rep3

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description: Mmar.counts.txt

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
Quality trimmed read sequences were mapped to M. tuberculosis H37Rv and M. marinum MUSA reference genomes using BWA (Cole et al. 1998; Stinear et al. 2008; Li et al. 2009). Gene expression estimates were made as raw read counts using the Pyhton script ‘HTSeq- count’ (model type – union). Counts data were converted to counts per million (cpm) and genes were filtered if they failed to achieve a cpm value of 1 in at least 30% of libraries per conditions.
Normalization of raw read counts and differential expression analysis was performed using DeSeq2
Genome_build: M. marinum MUSA
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Mycobacterium marinum

source_name: M. marinum wild type MUSA

extract_protocol:
RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol.
The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer’s instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82.

value: rifampicin

tag: time point


title: Mmar_RIF_24hrs_rep2

description: Mmar.counts.txt


title: SET-2_STAT1-C2

description:
matched input: SET2_STAT1-C2.fastq.gz
SET-2_STAT1-CA_peaks.bed


title: SET-2_STAT1-C1

description:
matched input: SET2_STAT1-C1.fastq.gz
SET-2_STAT1-CA_peaks.bed


title: SET-2_STAT1-D2

description:
matched input: SET2_STAT1-D2.fastq.gz
SET-2_STAT1-DMSO_peaks.bed

value: DMSO 0.1%


title: Mmar_RIF_24hrs_rep1

description: Mmar.counts.txt


title: R204-5

description: pool of 10 varroa

value: emerging mites (collected from P8 to P9 brood cells)


title: liver biological rep1, 5 min

value: mitocondoria purified from liver


title: SET-2_STAT1-D1

description:
matched input: SET2_STAT1-D1.fastq.gz
SET-2_STAT1-DMSO_peaks.bed


title: Mmar_EMB_24hrs_rep2

description: Mmar.counts.txt

value: ethambutol


title: Mmar_STR_24hrs_rep1

description: Mmar.counts.txt

value: streptomycin


title: Mmar_EMB_24hrs_rep3

description: Mmar.counts.txt


title: Mmar_STR_24hrs_rep2

description: Mmar.counts.txt


title: Mmar_EMB_24hrs_rep1

description: Mmar.counts.txt


title: Mmar_INH_24hrs_rep2

description: Mmar.counts.txt

value: isoniazid


title: Mmar_INH_24hrs_rep3

description: Mmar.counts.txt


title: Mmar_CIP_24hrs_rep3

description: Mmar.counts.txt

value: ciprofloxacin


title: Mmar_CIP_24hrs_rep2

description: Mmar.counts.txt


title: mC_pYES2_DIRS1_A

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

institute: Queen Mary University of London

data_processing:
CASAVA v1.8.2
For methylC-seq, adapters were trimmed with BBduk with the options mink=3, qtrim=r, trimq=10 minlength=20, before alignment to the reference genome with Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.5.9 before methylation quantification with BSseeker2. For RNA-seq, reads were were aligned to the reference genome with HISAT2 --rna-strandness FR -N 1 --max-intronlen 20000 --dta, and a reference transcriptome was obtained using Stringtie default commands. Gene level expression quantification was obtained using Kallisto 0.42.3 using the annotation obtained from Stringtie and Augustus in intron-less mode (S_kawagutii_transcriptome.fasta.gz).
To build Symbiodinium minutum reference using BSseeker2, the scaffold names of the genome assembly were simplified using only the scaffold##### for each sequence entry, while the constant ".1|size####" were excluded.
Genome_build: Symbiodinium kawagutii assembly was downloaded from: http://web.malab.cn/symka_new/download.jsp, Symbiodinium minutum assembly was downloaded from http://marinegenomics.oist.jp/symb/viewer/download?project_id=21 ( symbB.v1.0.genome.fa.gz), Klebosrmidium nitens was downloaded from http://www.plantmorphogenesis.bio.titech.ac.jp/~algae_genome_project/klebsormidium/kf_download/120824_klebsormidium_Scaffolds_v1.0.fna (120824_klebsormidium_Scaffolds_v1.0.fna), Saccharomyces cerevisiae assembly was downloaded from NCBI (GCF_000146045.2_R64_genomic.fna.gz)
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here). Kallisto.tsv files contain target_id, length, effective length, estimated counts, tpm.

organism: Saccharomyces cerevisiae

source_name: gal-induced stationary phase culture

growth_protocol: Glycerol-lactate medium +2% galactose

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to 4 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).


title: mC_pYES2_DIRS2_A


title: mC_pYES2_DIRS2_B


title: mC_pYES2_DIRS1_B


title: mC_pYES2_LINE3_B


title: mC_pYES2_DNMT2_A


title: Mmar_Ctrl_24hrs_rep3

description: Mmar.counts.txt

value: control


title: mC_pYES2_DNMT2_B


title: Mmar_STR_24hrs_rep3

description: Mmar.counts.txt


title: Mmar_Ctrl_24hrs_rep1

description: Mmar.counts.txt


title: mC_pYES2_KnitDNMT3_B


title: mC_pYES2_LINE3_A


title: Mmar_RIF_4hrs_rep3

description: Mmar.counts.txt


title: mC_pYES2_DNMT3b_B


title: mC_pYES2_KnitDNMT3_A


title: Mmar_RIF_4hrs_rep1

description: Mmar.counts.txt


title: mC_pYES2_DNMT3b_A


title: Mmar_INH_24hrs_rep1

description: Mmar.counts.txt


title: Mmar_STR_4hrs_rep2

description: Mmar.counts.txt


title: mC_pYES2_DNMT3a_B


title: Mmar_STR_4hrs_rep1

description: Mmar.counts.txt


title: mC_pYES2_DNMT3a_A


title: mC_pYES2_empty_B


title: Mmar_EMB_4hrs_rep3

description: Mmar.counts.txt


title: Mmar_CIP_24hrs_rep1

description: Mmar.counts.txt


title: mC_pYES2_empty_A


title: Mmar_EMB_4hrs_rep2

description: Mmar.counts.txt


title: Mmar_Ctrl_24hrs_rep2

description: Mmar.counts.txt


title: mC_K_nitens

organism: Klebsormidium nitens

source_name: 2 weeks culture

growth_protocol: BCDAT medium, 23º, continuous light

extract_protocol:
DNeasy Plant Mini kit (Cat. No. 69104, Qiagen)
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to 4 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).


title: Mmar_INH_4hrs_rep2

description: Mmar.counts.txt


title: S_kawagutii_25_RNAseq

organism: Symbiodinium kawagutii

source_name: stationary stage culture 25ºC

growth_protocol: L1 medium (without silicate), 25˚, 14h/10h light/dark cycle

extract_protocol:
Trizol extraction
Illumina TruSeq Stranded Total RNA protocol with polyA selection


title: S_kawagutii_32_RNAseq

source_name: stationary stage culture 32ºC

growth_protocol: L1 medium (without silicate), 32˚, 14h/10h light/dark cycle


title: Mmar_CIP_4hrs_rep3

description: Mmar.counts.txt


title: Mmar_EMB_4hrs_rep1

description: Mmar.counts.txt


title: mC_S_kawagutii_25C

extract_protocol:
Phenol-chloroform extraction followed by bisulfite sequencing
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to 4 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).


title: Mmar_INH_4hrs_rep3

description: Mmar.counts.txt


title: mC_S_minutum_30C

organism: Symbiodinium sp. clade B

source_name: stationary stage culture 30ºC

growth_protocol: f/2 medium, 32˚, 12h/12h light/dark cycle

value: ITS2 type B2


title: Mmar_RIF_4hrs_rep2

description: Mmar.counts.txt


title: Mmar_STR_4hrs_rep3

description: Mmar.counts.txt


title: Mmar_Ctrl_4hrs_rep1

description: Mmar.counts.txt


title: Mmar_Ctrl_4hrs_rep2

description: Mmar.counts.txt


title: Mmar_Ctrl_4hrs_rep3

description: Mmar.counts.txt


title: Mmar_CIP_4hrs_rep1

description: Mmar.counts.txt


title: Mmar_CIP_4hrs_rep2

description: Mmar.counts.txt


title: mC_S_kawagutii_32C


title: mC_S_minutum_25C

growth_protocol: f/2 medium, 25˚, 12h/12h light/dark cycle


title: Mmar_INH_4hrs_rep1

description: Mmar.counts.txt


title: 1772122247_C12

status: Public on Apr 10 2018

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Processing was performed with the 10X Chromium cellranger pipline version 1.1 using default settings
The Unique Molecular Identifier and cellular barcode corresponding to each read have been appended to the read id separated by an underscore.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Excel file of mRNA molecule counts per gene per cell

source_name: spinal cord dorsal horn

extract_protocol:
Spinal cords of 3-4 week mice were collected in oxygenated artificial cerebral spinal fluid (ACSF) on ice. Grey matter dorsal horn was isolated and transferred into a dish with 37°C digestion solution  [300µl TrypLE™ Express (Life Technologies; cat#12605-010), 2 ml Papain solution (Worthington Biochemical; cat#LK003178; 25U/ml in ACSF), 100µl DNAse I (Worthington Biochemical; cat#LK003172; 1mM in ACSF) and 100µl ACSF].  The tissue was triturated using glass Pasteur pipettes with decreasing diameter until cells became visible at the bottom of the plastic dish. The solution was filtered using a 30µm cell strainer and diluted with 2.4ml ACSF and 0.6ml Neurobasal-A medium (Gibco; cat#10888) and centrifuged at 100g for 4min at 4°C. The supernatant was removed and the pellet resuspended in 0.5ml ASCF and 0.5ml Neurobasal-A medium, supplemented with L-Glutamine (Gibco; cat#25030-123), B27 (Gibco; cat#17504-044) and Penicillin/Streptomycin (Sigma 50x; cat#P4458). The cell suspension was transferred onto an Optiprep gradient [85µl of Optiprep Density Solution (Sigma; cat#D1556) mixed with 457.5µl ACSF and 457.5µl Neurobasal media including supplements], and centrifuged at 80g for 10min at 4°C. The supernatant was removed until only 100-200µl remained. 10µl of DNaseI was added to avoid cell clustering. The single cell density was evaluated and adjusted to 500 cells per µl using ACSF for dilution.
1000 cells/μl were resuspended in artificial cerebrospinal fluid and added to the Reverse transcription mix to aim for sampling of around 3500 cells. All downstream cDNA synthesis (13 PCR cycles), library preparation and sequencing were carried

tag: Sex

value: M

tag: total molecules

tag: cluster name

tag: celltype

value: vGat-Cre-tdTomato


title: 1772122247_A12

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title: 1772122248_H03


title: 1772122248_F01


title: 1772122248_E10


title: 1772122248_E11


title: 1772122248_E08


title: 1772122248_E05


title: 1772122248_E04


title: 1772122248_E03


title: 1772122248_D12


title: 1772122248_D09


title: 1772122248_D07


title: 1772122248_D10


title: 1772122248_D06


title: 1772122248_D05


title: 1772122248_F10


title: 1772122248_D04


title: 1772122248_D03


title: 1772122248_C12


title: 1772122248_C08


title: 1772122248_F03


title: 1772122248_C11


title: 1772122248_E12


title: 1772122248_B11


title: 1772122248_C04


title: 1772122248_B08


title: 1772122248_B05


title: 1772122248_B10


title: 1772122248_E07


title: 1772122248_B09


title: 1772122248_B03


title: 1772122248_A10


title: 1772122248_A09


title: 1772122248_A08


title: 1772122248_A06


title: 1772122248_B12


title: 1772122248_A04


title: 1772122248_B02


title: 1772122247_H07


title: 1772122247_H09


title: 1772122248_A01


title: 1772122247_F03


title: 1772122247_H08


title: 1772122248_A05


title: 1772122248_A02


title: 1772122247_F09


title: 1772122247_F01


title: 1772122247_E12


title: 1772122247_E11


title: 1772122247_E09


title: 1772122247_E08


title: 1772122247_E06


title: 1772122247_E02


title: 1772122248_B01


title: 1772122247_E01


title: 1772122247_D12


title: 1772122247_D11


title: Meg3int1KO_NPC_2

city: Montpellier

first: Ildem

last: Sanli

address: 1919 Route de Mende

institute: IGMM - CNRS

data_processing:
Base-calling was performed using Illumina Pipeline Casava (v1.8.2).
Adaptor trimming was performed using Cutadapt .
Reads were aligned using TopHat (v2.0.8b).
Normalized abundance measurements were obtained using quantification pipeline on SeqMonk (v0.32.1) with default parameters.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: tab-delimited bedgraph files include normalized abundance measurements. Processed data are provided for global RNA-seq reads and allele-specific data.  B6_ovSNPs represent the expression from the maternal chromosome, JF1_ovSNPs represent the expression from the paternal chromosome.

source_name: Neural Progenitor Cells

growth_protocol: Hybrid ESCs were derived from blastocysts obtained by crossing C57BL/6J and JF1 mice and maintained on gelatin-coated dishes in ESGRO-complete-plus medium containing GSK3β-inhibitor and LIF.

extract_protocol:
Total RNA was extracted from NPCs using miRNeasy Kit (Qiagen).
Libraries were generated from 200 ng of RNA by using the Illumina TruSeq Stranded mRNA Sample Prep Kit.

treatment_protocol: Cells were differentiated into NPCs (for 12 days) on matrigel-coated dishes using a previously published protocol (Gaspard et al., 2009), in DMEM medium supplemented with N2 (Life Technologies, 17502048) and B27, minus vitamin A (Life Technologies, 12587010). Cyclopamine (1 mM) was added to the medium during days 2-10 of differentiation.

value: C57BL6/J (Mus m. domesticus) x JF1 (Mus m. molossinus)

value: neural progenitor cells

tag: derived from

value: ES  BJ-WT3

tag: genotype

value: Meg3 delta intron 1


title: Meg3int1KO_NPC_1

tag: strain


title: Meg3promKO_NPC_1

value: Meg3 delta promoter


title: Meg3promKO_NPC_2


title: WT_NPC_1

value: wildtype


title: 1772122248_D01


title: 1772122247_H01


title: 1772122248_E01


title: TIG120_H3K27ac

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

description: TIG120 H3K27ac ChIP-seq

data_processing:
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Sequence reads were aligned to the human genome (hg19) using BWA software (v0.5.9rc1).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were created using deepTools2 (ver 2.4.0) with RPKM formula (--normalizeUsingRPKM).

source_name: Human dermal fibroblast

extract_protocol:
Cells were subjected to cross-linking. After fixation with 1% formamide, cells were sonicated to shear DNA. DNA-protein complexes were incubated with Protein G beads (GE Healthcare) and anti-histone modification polyclonal antibodies (H3K4me1/H3K4me3/H3K27ac/H3K36me3). After washing the beads, immunoprecipitants were eluted with 30 µL of Tris buffer.
Multiplexed ChIP-seq libraries were prepared from 10 ng of immunoprecipitated DNA fragments using NEBNext ChIP-seq Library Prep Master Mix (New England BioLabs). For sequencing using GAIIx (Illumina), cluster generation was performed using TruSeq SR Cluster Kit v2 (Illumina). Each lane of flow cells contained one sample. Sequencing was performed in single-read run mode with a total 76 cycles, including a 75-bp read and one cycle for phasing.

treatment_protocol: Human iPSCs were routinely maintained in Primate ESC medium (ReproCELL) supplemented with 4 ng/ml recombinant human basic fibroblast growth factor (bFGF, Wako) on mitomycin C-inactivated SNL feeder cells (McMahon and Bradley, 1990) or in StemFiT medium (Ajinomoto) on Laminin 511 E8 (Nippi)-coated plate. HDFs were maintained in Dulbecco’s modified eagle medium (DMEM, Life Technologies) containing 10% fetal bovine serum (FBS, Life Technologies) and 0.5% Penicillin/Streptomycin (Pen/Strep, Life Technologies).

value: Human dermal fibroblast

tag: antibody

value: Active Motif 39135 (Rabbit polyclonal anti-Histone H3 (acetyl K27))


title: 150127_I248_FCC6MHCACXX_L2_RDHUMbadpABMRABPEI-211

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

description: GC6 Cohort

data_processing:
Alignment STAR version STAR_2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using star STAR_2.3.1d
Junctions counts were calculated by using an in house script to count the number of reads mapped to all splice junctions in the genome
Gene counts were calculated by using HTSeq count
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including the raw junction counts for all the detected junctions in the genome and tab delimited gene counts table
Supplementary_files_format_and_content: rawCounts_GeneNames_AllSamples.csv: number of reads mapped to the genes in all samples
Supplementary_files_format_and_content: GC6_juncCounts_raw_Star.txt: number of reads mapped to the splice junctions in all samples

source_name: Blood

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

tag: tissue

value: blood

tag: code

tag: subjectid

tag: site

value: AHRI

tag: gender

tag: group

value: Control


title: 201B7_H3K36me3

description: 201B7 H3K36me3 ChIP-seq

source_name: Human induced Pluripotent Stem Cells

tag: cell type

value: Human induced Pluripotent Stem Cells

value: Active Motif 61101 (Rabbit polyclonal anti-Histone H3 (tri-methyl K36))


title: TIG120_H3K36me3

description: TIG120 H3K36me3 ChIP-seq


title: TIG120_H3K4me3

description: TIG120 H3K4me3 ChIP-seq

value: Abcam ab8580 (Rabbit polyclonal anti-Histone H3 (tri-methyl K4))


title: 201B7_H3K4me3

description: 201B7 H3K4me3 ChIP-seq


title: 150111_I270_FCC3515ACXX_L2_RDHUMbadpAAURAAPEI-218

description: GC6 Cohort


title: 201B7_H3K4me1

description: 201B7 H3K4me1 ChIP-seq

value: Abcam ab8895 (Rabbit polyclonal anti-Histone H3 (mono-methyl K4))


title: 150111_I270_FCC3515ACXX_L4_RDHUMbadpAAKRAAPEI-207

description: GC6 Cohort

value: M


title: 150127_I248_FCC6MHCACXX_L4_RDHUMbadpABJRABPEI-208

description: GC6 Cohort

value: F


title: STA14

city: Taipei

first: HSI-Wen

last: Yeh

state: TAIWAN

address: Academia Sinica, No. 128

department: Institute of biomedical  science

country: Taiwan

institute: Academia Sinica

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity/ low-quality sequence and mapped to human_Hg19 whole genome using  bowtie2 v2.2.6 and RSEM v1.2.2 by standard. Reads coverage per base is computed from reads alignment file (.bam file) and stored in .bedgraph format using genomeCoverageBed program in bedtoos v2.23.0procedures.Reads Per Kilobase of exon per Megabase of library size (RPKM) were then further calculated.
Genome_build: human_Hg19
Supplementary_files_format_and_content: bedgraph

growth_protocol: A549 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA isolated from A549 shLac control cells and shpspc1 cells was extracted by Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells were treated with or without 5ng/ml TGFb1 for 24 hours

tag: cell line

value: Non-small cell lung cancer cell line A549

tag: genotype/variation

value: control

tag: agent


title: 201B7_H3K27ac

description: 201B7 H3K27ac ChIP-seq


title: 150111_I270_FCC3515ACXX_L2_RDHUMbadpAAFRAAPEI-202

description: GC6 Cohort


title: STAi14

value: PSPC1 knockout


title: WT_NPC_2

value: C57BL6/J (Mus m. domesticus) x JF1 (Mus m. molossinus)

value: neural progenitor cells

value: ES  BJ-WT3


title: 150111_I270_FCC3515ACXX_L3_RDHUMbadpAAHRAAPEI-204

description: GC6 Cohort


title: 1772099115_C12

tag: Sex

tag: total molecules

tag: cluster name


title: 1772099115_C07

tag: age

tag: celltype


title: 1772099115_D06

tag: strain


title: 1772099115_A10


title: TIG120_H3K4me1

description: TIG120 H3K4me1 ChIP-seq

value: Human dermal fibroblast

tag: antibody


title: 150114_I248_FCC68DKACXX_L7_RDHUMbadpABDRABPEI-202

description: GC6 Cohort

tag: tissue


title: 150127_I248_FCC6MHCACXX_L4_RDHUMbadpABSRABPEI-218

description: GC6 Cohort

tag: code


title: 150111_I270_FCC3515ACXX_L6_RDHUMbadpAANRAAPEI-210

description: GC6 Cohort

tag: subjectid


title: 150127_I248_FCC6MHCACXX_L3_RDHUMbadpABTRABPEI-219

description: GC6 Cohort

tag: site

value: case (TB)


title: 150111_I270_FCC3515ACXX_L1_RDHUMbadpAABRAAPEI-202

description: GC6 Cohort

value: blood

tag: gender


title: 1772099114_H12


title: 1772099115_C04


title: 150127_I248_FCC6MHCACXX_L3_RDHUMbadpABQRABPEI-215

description: GC6 Cohort

value: AHRI

tag: group


title: 150127_I248_FCC6MHCACXX_L1_RDHUMbadpABIRABPEI-207

description: GC6 Cohort


title: 150114_I248_FCC68DKACXX_L8_RDHUMbadpABFRABPEI-204

description: GC6 Cohort


title: 1772099115_D03


title: 150127_I248_FCC6MHCACXX_L2_RDHUMbadpABNRABPEI-212

description: GC6 Cohort


title: 1772099115_B07


title: 1772099115_A06


title: 1772099114_G06


title: SA14


title: 1772099115_A03


title: 150111_I270_FCC3515ACXX_L3_RDHUMbadpAAGRAAPEI-203

description: GC6 Cohort


title: 150127_I248_FCC6MHCACXX_L3_RDHUMbadpABRRABPEI-216

description: GC6 Cohort


title: 1772099114_H02


title: 1772099114_G01


title: 150114_I248_FCC68DKACXX_L8_RDHUMbadpABGRABPEI-205

description: GC6 Cohort

value: Control


title: 150111_I270_FCC3515ACXX_L3_RDHUMbadpAAIRAAPEI-205

description: GC6 Cohort


title: 1772099114_G11


title: 1772099114_H10


title: 1772099114_E08


title: 150114_I248_FCC68DKACXX_L7_RDHUMbadpABCRABPEI-201

description: GC6 Cohort


title: 150111_I270_FCC3515ACXX_L8_RDHUMbadpAASRAAPEI-215

description: GC6 Cohort


title: 150111_I270_FCC3515ACXX_L8_RDHUMbadpAATRAAPEI-216

description: GC6 Cohort


title: 1772099114_E11


title: 150114_I248_FCC68DKACXX_L6_RDHUMbadpABARAAPEI-225

description: GC6 Cohort


title: 1772099114_E03


title: 150127_I248_FCC6MHCACXX_L2_RDHUMbadpABLRABPEI-210

description: GC6 Cohort


title: 1772099114_D11


title: 1772122248_A03

value: vGat-Cre-tdTomato


title: 1772122247_H02


title: 1772099114_F08


title: 1772099114_D08


title: 150127_I248_FCC6MHCACXX_L4_RDHUMbadpABZRABPEI-227

description: GC6 Cohort


title: 150111_I270_FCC3515ACXX_L8_RDHUMbadpAAVRAAPEI-219

description: GC6 Cohort


title: 1772099114_E12


title: 150111_I270_FCC3515ACXX_L4_RDHUMbadpAAJRAAPEI-206

description: GC6 Cohort


title: 150114_I248_FCC68DKACXX_L7_RDHUMbadpABERABPEI-203

description: GC6 Cohort


title: 1772099114_C03


title: 150114_I248_FCC68DKACXX_L4_RDHUMbadpAAWRAAPEI-220

description: GC6 Cohort


title: 1772099114_D01


title: 150111_I270_FCC3515ACXX_L7_RDHUMbadpAAPRAAPEI-212

description: GC6 Cohort


title: 1772099114_B09


title: 150111_I270_FCC3515ACXX_L1_RDHUMbadpAAARAAPEI-201

description: GC6 Cohort


title: 1772099114_A02


title: 150111_I270_FCC3515ACXX_L2_RDHUMbadpAAERAAPEI-201

description: GC6 Cohort


title: 1772099113_H12


title: 150127_I248_FCC6MHCACXX_L8_RDHUMbadpABORABPEI-213

description: GC6 Cohort


title: 1772099113_H10


title: 150114_I248_FCC68DKACXX_L6_RDHUMbadpAAZRAAPEI-223

description: GC6 Cohort


title: 150111_I270_FCC3515ACXX_L4_RDHUMbadpAALRAAPEI-208

description: GC6 Cohort


title: 1772099113_G10


title: 150114_I248_FCC68DKACXX_L8_RDHUMbadpABVRABPEI-221

description: GC6 Cohort


title: 1772099113_G06


title: 1772099114_B10


title: 1772099113_G01


title: 150127_I248_FCC6MHCACXX_L1_RDHUMbadpABHRABPEI-206

description: GC6 Cohort


title: 150114_I248_FCC68DKACXX_L6_RDHUMbadpAAXRAAPEI-221

description: GC6 Cohort


title: 1772099113_F11


title: 150114_I248_FCC68DKACXX_L4_RDHUMbadpAAYRAAPEI-222

description: GC6 Cohort


title: 150111_I270_FCC3515ACXX_L7_RDHUMbadpAAQRAAPEI-213

description: GC6 Cohort


title: 1772099113_F03


title: 1772099113_F07


title: 150127_I248_FCC6MHCACXX_L8_RDHUMbadpABPRABPEI-214

description: GC6 Cohort


title: 150111_I270_FCC3515ACXX_L6_RDHUMbadpAAMRAAPEI-209

description: GC6 Cohort


title: 1772099113_F09


title: 150127_I248_FCC6MHCACXX_L8_RDHUMbadpAADRAAPEI-204

description: GC6 Cohort


title: 1772099113_D09


title: SAi14


title: 150127_I248_FCC6MHCACXX_L7_RDHUMbadpABWRABPEI-222

description: GC6 Cohort


title: 1772099113_D04


title: 150127_I248_FCC6MHCACXX_L7_RDHUMbadpABYRABPEI-225

description: GC6 Cohort


title: 1772099113_D06


title: 1772099113_C10


title: 150111_I270_FCC3515ACXX_L1_RDHUMbadpAACRAAPEI-203

description: GC6 Cohort


title: 1772099113_C04


title: 150111_I270_FCC3515ACXX_L6_RDHUMbadpAAORAAPEI-211

description: GC6 Cohort


title: 150127_I248_FCC6MHCACXX_L7_RDHUMbadpABXRABPEI-223

description: GC6 Cohort


title: 150127_I248_FCC6MHCACXX_L1_RDHUMbadpABKRABPEI-209

description: GC6 Cohort


title: 1772099113_F10


title: 150111_I270_FCC3515ACXX_L7_RDHUMbadpAARRAAPEI-214

description: GC6 Cohort


title: 1772099113_B01


title: 140711_I266_FCC4M76ACXX_L8_RHUMdztTESRAAPEI-203

description: GC6 Cohort

value: SUN


title: 150114_I248_FCC68DKACXX_L4_RDHUMbadpABBRAAPEI-227

description: GC6 Cohort


title: 1772099112_H12


title: 1772099113_B02


title: 1772099112_H09


title: 140711_I266_FCC4M76ACXX_L8_RHUMdztTETRAAPEI-204

description: GC6 Cohort


title: 140711_I266_FCC4M76ACXX_L1_RHUMdztTBMRAAPEI-215

description: GC6 Cohort


title: 140711_I266_FCC4M76ACXX_L7_RHUMdztTEPRAAPEI-227

description: GC6 Cohort


title: 1772099113_D07


title: 140711_I266_FCC4M76ACXX_L7_RHUMdztTEQRAAPEI-201

description: GC6 Cohort


title: 1772099112_G03


title: 1772099112_D10


title: 140711_I266_FCC4M76ACXX_L6_RHUMdztTELRAAPEI-221

description: GC6 Cohort


title: 1772099112_D12


title: 1772099112_D03


title: 140711_I266_FCC4M76ACXX_L7_RHUMdztTEORAAPEI-225

description: GC6 Cohort


title: 140711_I266_FCC4M76ACXX_L3_RHUMdztTEFRAAPEI-214

description: GC6 Cohort


title: 140711_I266_FCC4M76ACXX_L4_RHUMdztTEJRAAPEI-219

description: GC6 Cohort


title: 1772099112_C07


title: 140711_I266_FCC4M76ACXX_L4_RHUMdztTEIRAAPEI-218

description: GC6 Cohort


title: 140711_I266_FCC4M76ACXX_L3_RHUMdztTEHRAAPEI-216

description: GC6 Cohort


title: 1772099112_C01


title: 140711_I266_FCC4M76ACXX_L3_RHUMdztTEGRAAPEI-215

description: GC6 Cohort


title: 1772099113_B04


title: 1772099112_B04


title: 140711_I266_FCC4M76ACXX_L6_RHUMdztTEMRAAPEI-222

description: GC6 Cohort


title: 140711_I266_FCC4M76ACXX_L4_RHUMdztTEKRAAPEI-220

description: GC6 Cohort


title: 1772099112_B12


title: 140711_I266_FCC4M76ACXX_L2_RHUMdztTECRAAPEI-211

description: GC6 Cohort


title: 140711_I266_FCC4M76ACXX_L2_RHUMdztTEBRAAPEI-210

description: GC6 Cohort


title: 1772099110_H12


title: 140711_I266_FCC4M76ACXX_L6_RHUMdztTENRAAPEI-223

description: GC6 Cohort


title: 1772099110_F11


title: 140711_I266_FCC4M76ACXX_L2_RHUMdztTEERAAPEI-213

description: GC6 Cohort


title: 1772099110_F01


title: 1772099110_H01


title: 1772099110_H06


title: 1772099110_F09


title: 1772099110_E04


title: 140711_I266_FCC4M76ACXX_L1_RHUMdztTBLRAAPEI-214

description: GC6 Cohort


title: 1772099112_A08


title: 1772099110_G10


title: 140711_I266_FCC4M76ACXX_L8_RHUMdztTERRAAPEI-202

description: GC6 Cohort


title: 1772099112_A03


title: 1772099110_E01


title: 140708_I232_FCC4MBMACXX_L1_RHUMdztTDGRAAPEI-213

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L1_RHUMdztTDERAAPEI-211

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L2_RHUMdztTDIRAAPEI-215

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L1_RHUMdztTDFRAAPEI-212

description: GC6 Cohort


title: 1772099110_D12


title: 1772099110_C12


title: 140708_I232_FCC4MBMACXX_L3_RHUMdztTDMRAAPEI-220

description: GC6 Cohort


title: 1772099110_D10


title: 140708_I232_FCC4MBMACXX_L2_RHUMdztTDJRAAPEI-216

description: GC6 Cohort


title: 1772099110_D05


title: 1772099110_B01


title: 1772099110_D03


title: 140711_I266_FCC4M76ACXX_L1_RHUMdztTBNRAAPEI-216

description: GC6 Cohort


title: 1772099110_B09


title: 140708_I232_FCC4MBMACXX_L3_RHUMdztTDKRAAPEI-218

description: GC6 Cohort


title: 1772099110_C11


title: 140708_I232_FCC4MBMACXX_L4_RHUMdztTDPRAAPEI-223

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L3_RHUMdztTDLRAAPEI-219

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L2_RHUMdztTDHRAAPEI-214

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L8_RHUMdztTDXRAAPEI-206

description: GC6 Cohort


title: 1772099110_B05


title: 1772099110_A06


title: 1772099110_A05


title: 140708_I232_FCC4MBMACXX_L8_RHUMdztTDWRAAPEI-205

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L8_RHUMdztTDYRAAPEI-207

description: GC6 Cohort


title: 1772099110_A04


title: 1772099109_H11


title: 140708_I232_FCC4MBMACXX_L7_RHUMdztTDTRAAPEI-202

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L7_RHUMdztTDVRAAPEI-204

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L6_RHUMdztTDQRAAPEI-225

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L7_RHUMdztTDURAAPEI-203

description: GC6 Cohort


title: 1772099110_A03


title: 1772099109_E11


title: 1772099109_F01


title: 140708_I232_FCC4MBMACXX_L6_RHUMdztTDRRAAPEI-227

description: GC6 Cohort


title: 1772099109_B08


title: 1772099109_A11


title: 1772099109_A03


title: 140708_I232_FCC4MBMACXX_L6_RHUMdztTDSRAAPEI-201

description: GC6 Cohort


title: 1772099108_H07


title: 140711_I269_FCC4MBUACXX_L1_RHUMdztTGMRAAPEI-201

description: GC6 Cohort


title: 140711_I269_FCC4MBUACXX_L1_RHUMdztTGNRAAPEI-202

description: GC6 Cohort


title: 1772099108_G08


title: 1772099108_C10


title: 140711_I269_FCC4MBUACXX_L3_RHUMdztTGRRAAPEI-206

description: GC6 Cohort


title: 1772099108_B11


title: 140711_I269_FCC4MBUACXX_L2_RHUMdztTGPRAAPEI-204

description: GC6 Cohort


title: 140711_I269_FCC4MBUACXX_L1_RHUMdztTGLRAAPEI-227

description: GC6 Cohort


title: 140711_I269_FCC4MBUACXX_L2_RHUMdztTGQRAAPEI-205

description: GC6 Cohort


title: 1772099106_F05


title: 140711_I269_FCC4MBUACXX_L2_RHUMdztTGORAAPEI-203

description: GC6 Cohort


title: 1772099109_D02


title: 140711_I269_FCC4MBUACXX_L3_RHUMdztTGTRAAPEI-208

description: GC6 Cohort


title: 140708_I232_FCC4MBMACXX_L4_RHUMdztTDNRAAPEI-221

description: GC6 Cohort


title: 1772099106_D01


title: 1772099105_F06


title: 1772099106_B04


title: 140708_I232_FCC4MBMACXX_L4_RHUMdztTDORAAPEI-222

description: GC6 Cohort


title: 1772099106_E06


title: 140708_I175_FCC4MEWACXX_L8_RHUMdztTCHRAAPEI-212

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L1_RHUMdztTBPRAAPEI-219

description: GC6 Cohort


title: 1772099105_G12


title: 140711_I269_FCC4MBUACXX_L3_RHUMdztTGSRAAPEI-207

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L7_RHUMdztTCDRAAPEI-208

description: GC6 Cohort


title: 1772099105_F03


title: 1772099105_D08


title: 1772099106_G03


title: 1772099105_B05


title: 140708_I175_FCC4MEWACXX_L7_RHUMdztTCERAAPEI-209

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L6_RHUMdztTCBRAAPEI-206

description: GC6 Cohort


title: 1772099105_C10


title: 140708_I175_FCC4MEWACXX_L6_RHUMdztTCARAAPEI-205

description: GC6 Cohort


title: 1772099105_A01


title: 140708_I175_FCC4MEWACXX_L6_RHUMdztTCCRAAPEI-207

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L7_RHUMdztTCFRAAPEI-210

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L4_RHUMdztTBXRAAPEI-202

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L4_RHUMdztTBYRAAPEI-203

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L4_RHUMdztTBZRAAPEI-204

description: GC6 Cohort


title: 1772099093_D10


title: 140708_I175_FCC4MEWACXX_L8_RHUMdztTCIRAAPEI-213

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L3_RHUMdztTBURAAPEI-225

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L3_RHUMdztTBVRAAPEI-227

description: GC6 Cohort


title: 1772099093_G10


title: 140708_I175_FCC4MEWACXX_L2_RHUMdztTBRRAAPEI-221

description: GC6 Cohort


title: 1772099093_C06


title: 1772099093_C01


title: 1772099093_C09


title: 140708_I175_FCC4MEWACXX_L3_RHUMdztTBWRAAPEI-201

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L2_RHUMdztTBTRAAPEI-223

description: GC6 Cohort


title: 1772099093_G11


title: 1772099093_A03


title: 1772099093_B11


title: 1772099092_F11


title: 1772099092_F10


title: 140708_I175_FCC4MEWACXX_L1_RHUMdztTBQRAAPEI-220

description: GC6 Cohort


title: 1772099092_H10


title: 140715_I272_FCC4MGCACXX_L1_RHUMdztTHORAAPEI-205

description: GC6 Cohort


title: 1772099093_H11


title: 140708_I175_FCC4MEWACXX_L1_RHUMdztTBORAAPEI-218

description: GC6 Cohort


title: 1772099092_E11


title: 1772099092_D05


title: 1772099093_D08


title: 140715_I272_FCC4MGCACXX_L7_RHUMdztTEDRAAPEI-212

description: GC6 Cohort


title: 140715_I272_FCC4MGCACXX_L8_RHUMdztTAAIDRAAPEI-221

description: GC6 Cohort

value: MRC


title: 1772099092_C11


title: 140715_I272_FCC4MGCACXX_L7_RHUMdztTEWRAAPEI-207

description: GC6 Cohort


title: 1772099092_C06


title: 1772099092_B08


title: 140715_I272_FCC4MGCACXX_L7_RHUMdztTHMRAAPEI-203

description: GC6 Cohort


title: 140715_I272_FCC4MGCACXX_L6_RHUMdztTHZRAAPEI-216

description: GC6 Cohort


title: 1772099091_C10


title: 140708_I175_FCC4MEWACXX_L2_RHUMdztTBSRAAPEI-222

description: GC6 Cohort


title: 140708_I175_FCC4MEWACXX_L8_RHUMdztTCGRAAPEI-211

description: GC6 Cohort


title: 1772099091_E10


title: 1772099105_C11


title: 140715_I272_FCC4MGCACXX_L6_RHUMdztTAAIBRAAPEI-219

description: GC6 Cohort


title: 1772099091_A05


title: 1772099090_H06


title: 140715_I272_FCC4MGCACXX_L6_RHUMdztTAAIARAAPEI-218

description: GC6 Cohort


title: 140715_I272_FCC4MGCACXX_L4_RHUMdztTHXRAAPEI-214

description: GC6 Cohort


title: 140715_I272_FCC4MGCACXX_L4_RHUMdztTHWRAAPEI-213

description: GC6 Cohort


title: 140715_I272_FCC4MGCACXX_L3_RHUMdztTHTRAAPEI-210

description: GC6 Cohort


title: 1772099092_A06


title: 140715_I272_FCC4MGCACXX_L3_RHUMdztTHURAAPEI-211

description: GC6 Cohort


title: 140715_I272_FCC4MGCACXX_L3_RHUMdztTHVRAAPEI-212

description: GC6 Cohort


title: 140715_I272_FCC4MGCACXX_L4_RHUMdztTHYRAAPEI-215

description: GC6 Cohort


title: 1772099090_E03


title: 1772099090_E05


title: 1772099090_C05


title: 140715_I272_FCC4MGCACXX_L2_RHUMdztTHRRAAPEI-208

description: GC6 Cohort


title: 140715_I272_FCC4MGCACXX_L8_RHUMdztTAAIERAAPEI-222

description: GC6 Cohort


title: 1772099090_C12


title: 140715_I272_FCC4MGCACXX_L2_RHUMdztTHSRAAPEI-209

description: GC6 Cohort


title: 1772099090_B11


title: 1772099090_A06


title: 140715_I272_FCC4MGCACXX_L1_RHUMdztTHNRAAPEI-204

description: GC6 Cohort


title: 1772099044_F09


title: 1772099044_E04


title: 140715_I272_FCC4MGCACXX_L1_RHUMdztTHPRAAPEI-206

description: GC6 Cohort


title: 1772099090_G01


title: 140715_I272_FCC4MGCACXX_L8_RHUMdztTAAICRAAPEI-220

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L1_RHUMdztTABRABPEI-202

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L8_RHUMdztTAVRAAPEI-223

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L8_RHUMdztTAKRABPEI-211

description: GC6 Cohort


title: 1772099044_C11


title: 1772099043_G11


title: 1772099043_B11


title: 140624_I266_FCC4MKDACXX_L8_RHUMdztTALRABPEI-212

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L7_RHUMdztTAJRABPEI-210

description: GC6 Cohort


title: 1772099042_B03


title: 1772099090_D01


title: 1772099042_A02


title: 1772099043_A01


title: 140624_I266_FCC4MKDACXX_L8_RHUMdztTAWRAAPEI-225

description: GC6 Cohort


title: 1772099041_D05


title: 140624_I266_FCC4MKDACXX_L7_RHUMdztTAVRAAPEI-223

description: GC6 Cohort


title: 1772099041_D03


title: 140624_I266_FCC4MKDACXX_L7_RHUMdztTAWRAAPEI-225

description: GC6 Cohort


title: 1772099041_B04


title: 140624_I266_FCC4MKDACXX_L7_RHUMdztTALRABPEI-212

description: GC6 Cohort


title: 1772099040_G06


title: 140715_I272_FCC4MGCACXX_L2_RHUMdztTHQRAAPEI-207

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L6_RHUMdztTATRAAPEI-221

description: GC6 Cohort


title: 1772099040_G04


title: 140624_I266_FCC4MKDACXX_L6_RHUMdztTAHRABPEI-208

description: GC6 Cohort


title: 1772099090_A03


title: 1772099041_A02


title: 1772099039_E08


title: 140624_I266_FCC4MKDACXX_L7_RHUMdztTAKRABPEI-211

description: GC6 Cohort


title: 1772099039_A09


title: 140624_I266_FCC4MKDACXX_L4_RHUMdztTATRAAPEI-221

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L6_RHUMdztTAURAAPEI-222

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L6_RHUMdztTAGRABPEI-207

description: GC6 Cohort


title: 1772099039_B04


title: 1772099015_H04


title: 1772099015_D12


title: 140624_I266_FCC4MKDACXX_L4_RHUMdztTAURAAPEI-222

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L4_RHUMdztTAGRABPEI-207

description: GC6 Cohort


title: 1772099015_H07


title: 140624_I266_FCC4MKDACXX_L4_RHUMdztTAHRABPEI-208

description: GC6 Cohort


title: 1772099015_A01


title: 1772099015_D07


title: 140624_I266_FCC4MKDACXX_L3_RHUMdztTAERABPEI-205

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L6_RHUMdztTAIRABPEI-209

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L3_RHUMdztTAFRABPEI-206

description: GC6 Cohort


title: 1772099014_H08


title: 140624_I266_FCC4MKDACXX_L2_RHUMdztTACRABPEI-203

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L2_RHUMdztTARRAAPEI-219

description: GC6 Cohort


title: 1772099014_F07


title: 1772099014_G05


title: 1772099014_G04


title: 140624_I266_FCC4MKDACXX_L1_RHUMdztTAARABPEI-201

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L2_RHUMdztTADRABPEI-204

description: GC6 Cohort


title: 1772099014_D05


title: 1772099014_D10


title: 140624_I266_FCC4MKDACXX_L1_RHUMdztTAQRAAPEI-218

description: GC6 Cohort


title: 1772099014_C04


title: 140624_I266_FCC4MKDACXX_L8_RHUMdztTAJRABPEI-210

description: GC6 Cohort


title: 1772099014_D09


title: 140624_I266_FCC4MKDACXX_L4_RHUMdztTAIRABPEI-209

description: GC6 Cohort


title: 1772099015_A03


title: 140715_I162_FCC4MRLACXX_L1_RHUMdztTAAJARAAPEI-220

description: GC6 Cohort


title: 1772072243_H01


title: 1772072243_F10


title: 1772099014_A10


title: 140715_I162_FCC4MRLACXX_L1_RHUMdztTAAJBRAAPEI-221

description: GC6 Cohort


title: 140715_I162_FCC4MRLACXX_L1_RHUMdztTAAJCRAAPEI-222

description: GC6 Cohort


title: 140624_I266_FCC4MKDACXX_L3_RHUMdztTASRAAPEI-220

description: GC6 Cohort


title: 1772072243_H07


title: 1772072243_D11


title: 1772072243_D10


title: 1772072243_D07


title: 140715_I162_FCC4MRLACXX_L2_RHUMdztTAAJDRAAPEI-223

description: GC6 Cohort


title: 140715_I162_FCC4MRLACXX_L2_RHUMdztTAAJERAAPEI-225

description: GC6 Cohort


title: 1772072243_D08


title: 140715_I162_FCC4MRLACXX_L3_RHUMdztTAAJIRAAPEI-203

description: GC6 Cohort


title: 140715_I162_FCC4MRLACXX_L4_RHUMdztTAAJLRAAPEI-206

description: GC6 Cohort


title: 1772072243_D02


title: 1772072243_B01


title: 1772072243_D06


title: 140715_I162_FCC4MRLACXX_L6_RHUMdztTAAJORAAPEI-209

description: GC6 Cohort


title: 140715_I162_FCC4MRLACXX_L7_RHUMdztTAAJQRAAPEI-211

description: GC6 Cohort


title: 140715_I162_FCC4MRLACXX_L4_RHUMdztTAAJJRAAPEI-204

description: GC6 Cohort


title: 140715_I162_FCC4MRLACXX_L4_RHUMdztTAAJKRAAPEI-205

description: GC6 Cohort


title: 1772072243_F05


title: 1772072243_C06


title: 140715_I162_FCC4MRLACXX_L6_RHUMdztTAAJNRAAPEI-208

description: GC6 Cohort


title: 140715_I162_FCC4MRLACXX_L3_RHUMdztTAAJGRAAPEI-201

description: GC6 Cohort


title: 1772072243_A09


title: 1772072243_A08


title: 1772072240_D04


title: 140715_I162_FCC4MRLACXX_L6_RHUMdztTAAJMRAAPEI-207

description: GC6 Cohort


title: 1772072242_A05


title: 1772072240_H12


title: 140715_I162_FCC4MRLACXX_L7_RHUMdztTAAJPRAAPEI-210

description: GC6 Cohort


title: 1772072243_B07


title: 140715_I162_FCC4MRLACXX_L8_RHUMdztTAAJURAAPEI-215

description: GC6 Cohort


title: 1772072240_E01


title: Hd2lox_Hd1

city: Manchester

first: Roshana

middle: S

last: Thambyrajah

address: Wilmslow Road

department: Stem Cell Biology

institute: CRUK Manchester

data_processing:
Basecall files generated from HiSeq sequencing run were converted to FASTQ format with Illumina’s bcl2fastq. Alignment was performed by bowtie2 (version 2.2.9) to mouse reference genome mm10 with default parameters. Generated SAM files from bowtie2 alignment were converted to BAM files by samtools 1.3.1 using htslib 1.3.2. Parameters for samtools SAM to BAM conversion: -bS -q 10 -F 260. Peaks were called using the program macs2 (version 2.1.1.20160309) with the settings "-q 0.01".
Genome_build: mm10
Supplementary_files_format_and_content: Peaks bed

source_name: haemogenic endothelium

growth_protocol: ES cell lines grown and differentiated as in Sroczynska et al, 2009

extract_protocol: ChIP performed with HighCell ChIP kit from Diagenode

treatment_protocol: no treatments

tag: cell type

value: ES-derived haemogenic endothelium

tag: passage

value: 25-30 passages

value: Hdac1 antibody, Diagenode (cat# C15410325-50)


title: 140715_I162_FCC4MRLACXX_L2_RHUMdztTAAJFRAAPEI-227

description: GC6 Cohort

value: M


title: 140715_I162_FCC4MRLACXX_L8_RHUMdztTAAJSRAAPEI-213

description: GC6 Cohort


title: 140715_I162_FCC4MRLACXX_L7_RHUMdztTAAJRRAAPEI-212

description: GC6 Cohort


title: Hd1_loxlox_Hd2

value: Hdac2 antibody, abcam (cat# ab7029)


title: Hd1_loxlox_Hd1


title: 1772072240_A12


title: Bry_Hdac1

value: 16-19 passages


title: 140718_I266_FCC4MRPACXX_L1_RHUMdztTEARAAPEI-209

description: GC6 Cohort

value: F


title: 140718_I266_FCC4MRPACXX_L8_RHUMdztTHLRAAPEI-202

description: GC6 Cohort


title: Hd2lox_Input


title: Hd1_loxlox_Input


title: Hd2lox_Hd2


title: Bry_Hdac2


title: 140718_I266_FCC4MRPACXX_L1_RHUMdztTDZRAAPEI-208

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L2_RHUMdztTGWRAAPEI-211

description: GC6 Cohort


title: 140715_I162_FCC4MRLACXX_L8_RHUMdztTAAJTRAAPEI-214

description: GC6 Cohort


title: ANPL_H3K27ac_ChIPSeq

city: Goyang-si

first: Junghyun

last: Jung

state: Gyeonggi-do

address: Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu

department: Life Science

country: South Korea

institute: Dongguk Uvi.

data_processing:
Sequencing was implemented on Illumina HiSeq2000. Trimmomatic v 0.33 (Bolger et al., 2014) was applied to remove Illumina adapter as well as trim and crop sequencing data. The reads were aligned to the mouse genome (mm10) using Bowtie v 1.1.2 (Langmead et al., 2009) and only uniquely mapped reads in the genome were used for downstream application. Heatmap and plot of average enrichments for chip-seq data were generated by Deeptools v 1.5 (Ramirez et al., 2014) applying k-means clustering (k=3). Bigwig files were also created by Deeptools and visualized by UCSC genome browser. Chip-Seq peaks were identified by MACS v 1.4.2 (Zhang et al., 2008) using broad peak calling analysis (--nomodel --shiftsize 73) and annotation of the called peaks were determined using ChIPseeker (Yu et al., 2015) r package.
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: fibroblast

extract_protocol: DNA libraries were made using KAPA library preparation kit (Illumina), according to the manufacturer’s instructions.

value: direct lineage reprogramming into induced dopamine neurons


title: ANPL+EMF+AuNPs_H3K27ac_ChIPSeq


title: 140718_I266_FCC4MRPACXX_L2_RHUMdztTGVRAAPEI-210

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L2_RHUMdztTGURAAPEI-209

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L3_RHUMdztTGYRAAPEI-213

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L3_RHUMdztTGXRAAPEI-212

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L4_RHUMdztTHCRAAPEI-218

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L4_RHUMdztTHBRAAPEI-216

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L4_RHUMdztTHARAAPEI-215

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L6_RHUMdztTHFRAAPEI-221

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L3_RHUMdztTGZRAAPEI-214

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L6_RHUMdztTHERAAPEI-220

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L7_RHUMdztTHGRAAPEI-222

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L8_RHUMdztTHJRAAPEI-227

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L8_RHUMdztTHKRAAPEI-201

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L8_RHUMdztTDCRAAPEI-209

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L1_RHUMdztTCKRAAPEI-215

description: GC6 Cohort


title: Bry_Input


title: 140709_I232_FCC4MUWACXX_L8_RHUMdztTDDRAAPEI-210

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L7_RHUMdztTHIRAAPEI-225

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L7_RHUMdztTCZRAAPEI-206

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L7_RHUMdztTDARAAPEI-207

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L4_RHUMdztTCTRAAPEI-227

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L6_RHUMdztTCXRAAPEI-204

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L6_RHUMdztTCWRAAPEI-203

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L4_RHUMdztTCSRAAPEI-225

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L3_RHUMdztTCPRAAPEI-221

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L3_RHUMdztTCQRAAPEI-222

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L4_RHUMdztTCURAAPEI-201

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L2_RHUMdztTCMRAAPEI-218

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L6_RHUMdztTHDRAAPEI-219

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L6_RHUMdztTCVRAAPEI-202

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L2_RHUMdztTCORAAPEI-220

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L2_RHUMdztTCNRAAPEI-219

description: GC6 Cohort


title: 140718_I266_FCC4MRPACXX_L7_RHUMdztTHHRAAPEI-223

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L1_RHUMdztTCJRABPEI-214

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L8_RHUMdztTAAMYRAAPEI-201

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L1_RHUMdztTCLRABPEI-216

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L8_RHUMdztTAAMZRAAPEI-202

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L8_RHUMdztTDBRAAPEI-208

description: GC6 Cohort


title: 140715_I162_FCC4MRLACXX_L3_RHUMdztTAAJHRAAPEI-202

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L7_RHUMdztTAAMTRAAPEI-221

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L6_RHUMdztTAAMVRAAPEI-223

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L7_RHUMdztTAAMXRAAPEI-227

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L6_RHUMdztTAAMSRAAPEI-220

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L4_RHUMdztTAAMPRAAPEI-216

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L7_RHUMdztTAAMWRAAPEI-225

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L6_RHUMdztTAAMURAAPEI-222

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L4_RHUMdztTAAMQRAAPEI-218

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L3_RHUMdztTAAMNRAAPEI-214

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L3_RHUMdztTCRRAAPEI-223

description: GC6 Cohort