title: P-14-08877-R

data_processing:
Data processing. Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple control metrics were obtained using FASTQC (v0.11.2), samtools (v0.1.19), BEDtools (v2.17.0) and custom scripts.
Gene expression analysis. The remaining clean set of reads were then aligned to the reference genome build hg19 (GRCh37) with STAR (v2.3.0e) using the default parameters. Multimapping reads (MAPQ>3) were discarded from downstream analyses. Gene expression levels were estimated by quantifying uniquely mapped reads falling into exonic regions defined by the ensGene annotation set from Ensembl (GRCh37; N=60234 genes) using featureCounts (v1.4.4). Normalization (mean-of-ratios), variance-stabilized transformations of the data, as well as differential expression analysis, were performed using DESeq2. Unless otherwise stated, all reported p-values have been adjusted for multiple testing using the Benjamini-Hochberg procedure.
Repeat element expression analysis. The clean set of rRNA-depleted RNA-seq reads were aligned to the human repeat genome, as previously described. The reference repeat sequences were downloaded from Repbase (v23.03) (http://www.girinst.org/repbase). We then combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus repeat element sequences. All subsequent steps closely mirror those detailed for gene expression analysis. Normalization (library size) factors derived from canonical genes (Ensembl ensGene annotation) using mean-of-ratios as described above were used to normalize repeat elements.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts

source_name: Tumor

tag: treatment


title: DIPGXIII-KO-C10P5_input

status: Public on May 13 2019

type: SRA

city: Montreal

first: Nada

last: Jabado

state: Québec

address: 1001 Décarie Boulevard

department: Department of Pediatrics

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (Bolger et al., 2014) (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple quality control metrics were obtained using FASTQC (v0.11.2), samtools (Li et al., 2009) (v0.1.19), BEDtools (Quinlan and Hall, 2010) (v2.17.0) and custom scripts.   Reads were processed as described for RNAseq, and then aligned using the human repeat genome as reference, as previously described (Solovyov et al., Cell Reports 2018). Repbase reference genome was used (Bao et al., 2015) (v23.03) (http://www.girinst.org/repbase). Since Repbase largely consists of family consensus sequences, reads are assigned to these sequences regardless of where and how many times they are present in the genome, mitigating mapping uncertainty. We combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus elements, and counted the number of reads mapping into each of these elements using featureCounts (MAPQ>3). Differential enrichment of H3K27ac at the consensus sequences were then calculated using DESeq2 (Love et al., 2014). The inverse of ChIP-Rx spike-in scaling factors (i.e. 1/rx) were supplied to DESeq2 as normalization factors (i.e. size factors).
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts

molecule: genomic DNA

organism: Homo sapiens

source_name: H3.3K27M-KO_Tumor-derived cell-line

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction ~5% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing (see below). ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads were washed and then incubated with 6ug of H3K27ac antibody (Diagenode, C15410196), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail (Life Technologies) at 65°C for 30 min followed by 2ul Proteinase K (Thermo Fisher Scientific) at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: genotype

tag: sample type

value: Tumor-derived cell-line

tag: chip antibody


title: Yng_11_H3K27ac

city: Miami

first: Maria

last: Figueroa

state: FL

address: 1501 NW 10th Avenue

department: Biochemistry

country: USA

institute: University of Miami

data_processing:
FastQC was run all samples. Samples with a sequencing duplication rate of >90% were discarded.
Adapters and reads of less than 25 basepairs were removed using cutadapt (version 1.12).
Reads were aligned to the hg19 genome using bowtie2 (version 2.0.5).
Reads were filtered to retain only those that were aligned and had one alignment (!XS:i:N) samtools (version 1.2)
Unique mapped reads for each IP type for each age group were pooled using samtools merge (version 1.2)
Peak calling using the pooled IP and its pooled corresponding Input was performed using macs2 (version 2.0.10.20131216) with the --nomodel option. For H3K4me1, H3K4me3, and H3K27ac, a q-value cutoff of 0.0001 with the narrow peak option was used. Broad peak calling with a q-value cutoff  of 0.1 was used for H3K27me3.
Bigwig files of the fold-enrichment(IP/Input) were generated using macs2 SPMR peak calling, followed by macs2 bdgcmp with the -m FE option.
Bigwig files of the log2(IP/Input) were generated using Deeptools2, with the following command: bamCompare --bamfile1 ip --bamfile2 input --outFileName name_log2.bw --ratio log2  -p 30 --verbose --outFileFormat bigwig --scaleFactorsMethod readCount.
Genome_build: hg19
Supplementary_files_format_and_content: One of the processed files is the bedgraph file containing the tag chromosome coordinates and score produced from macs2 peak calling on the pooled IPs and Inputs. For Input samples, the control_lamda.bdg file was uploaded, and for IPs, the treat_pileup.bdg was uploaded. If a donor was used for multiple IP types, then multiple bedgraph files (corresponding to each IP type) are included for the Input. The "_FE.bw" is a bigwig file that contains the fold-enrichment of the IP/Input. The "_log2.bw" is a bigwig file that contains the read-normalized log2(IP/Input) enrichment.

source_name: Bone marrow

extract_protocol:
Micro-ChIPseq was performed using the True MicroChIP (Diagenode, #C01010130) kit and antibodies that had been validated for specificity and reactivity using the MODified Histone Peptide Array (Active Motif, #13001). The following antibodies were used, 1 g H3K27me3 (Millipore, #07-449, Lot: 21494165), 1 g H3K4me3 (Abcam, #ab8580, Lot: GR164207-1), 0.5 g H3K4me1 (Diagenode, #C15410194, Lot: A1862D), or 0.5 g H3K27ac (Abcam, #ab4729, Lot: GR155970-2).
ChIP-seq libraries were prepared using the V1 MicroPlex Library Preparation kit (Diagenode, #C05010011). For the PCR amplification, a total of 16 amplification cycles was used. Libraries were purified using a 1:1 Ampure bead cleanup and eluted in 16 uL of Tris-HCl ph 8.0. Only libraries with enrichment at targeted sites by QPCR were used for sequencing. Libraries were multiplexed and sequenced using an Illumina Hi-Seq-2500 with 50bp single end sequencing.

treatment_protocol: Miltenyi MACS magnetic bead purification was used to enrich frozen bone marrow MNC for CD34+ cells. The CD34+ fraction was then stained with CD2-TC, CD3-TC, CD4-TC, CD7-TC, CD8-TC, CD10-TC, CD11b-TC, CD14-TC, CD19-TC, CD20-TC, CD56-TC, and Glycophorin A-TC followed by CD34-APC, CD38-PE-Cy7, CD123-PE,  CD45RA-FITC and DAPI. Using a BD FACSAria I, HSCe (DAPI-,Lin-, CD34+, CD38-) were FACS sorted. HSCe were sorted into 1mL IMDM 20% FBS. For H3K4me1, H3K4me3, and H3K27me3, 14,000-20,000 HSCe were used per immunoprecipitation; for H3K27ac, 15,000-35,000 cells were used per immunoprecipitation.

tag: cell type

value: HSCe (CD34+, CD38-,Lineage-)

tag: donor age

tag: donor sex

value: M


title: T7: chronic lymphocytic leukemia 7 (CytoScanHD_Array)

type: genomic

city: Brno

first: Karla

last: Plevova

address: Kamenice 5

department: Central European Institute of Technology

country: Czech Republic

institute: Masaryk University

hyb_protocol: CytoScan HD CytoScan HD/Cytogenetic Array 2.7M

data_processing: Chromosome Analysis Suite

label: biotin

source_name: peripheral blood

extract_protocol: DNA blood & tissue isolation kit, Qiagen

tag: gender

tag: tissue

value: peripheral blood

tag: diagnosis

value: chronic lymphocytic leukemia


title: HSJ-050

library_source: transcriptomic

molecule: total RNA

extract_protocol:
Total RNA was extracted from cell pellets using the RNeasy mini kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts. Paired-end sequencing was performed on the Illumina HiSeq 2000, 2500 and 4000 platforms.


title: KK29-RNA

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

data_processing:
Base calling was performed with RTA v1.18.61 software.
Sequence tags were aligned to the human reference genome hg19 and Ensembl transcript reference (H. Sapiens 75) using STAR aligner.
The numbers of read tags aligning to each region were extracted using featureCount producing a matrix of counts (tags per gene per sample)
Genes with less than 100 sequence reads across all samples were removed from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Gene Sequence tag counts

source_name: Resected brain sample

extract_protocol:
Direct-zol RNA Kit (Zymo Research Cat No. R2062)
NEBNext Ultra RNA Library Prep Kit for Illumina manual. Cat No. E7530

tag: disease

value: Non-epilepsy

value: brain


title: KK28-RNA


title: T1: chronic lymphocytic leukemia 1 (CytoScanHD_Array)

scan_protocol: CytoScan HD CytoScan HD/Cytogenetic Array 2.7M


title: KK27-RNA

value: HS - Epilepsy


title: KK24-RNA


title: PS14-0531


title: KK22-RNA


title: KK26-RNA


title: KK20-RNA


title: Old_24_H3K27me3

value: F


title: Yng_2_H3K27ac


title: Old_29_H3K27me3


title: KK21-RNA


title: HSJ-031


title: KK25-RNA


title: KK19-RNA


title: HSJ-030


title: Yng_8_H3K27ac


title: Old_16_H3K27me3


title: CCHMC_4968-HGG-04A


title: KK18-RNA


title: KK17-RNA


title: KK15-RNA

value: FCD

value: Ia  X  Y N


title: PH1233


title: HSJ-051


title: KK14-RNA


title: Yng_10_H3K27ac


title: Old_12_H3K27me3


title: Old_15_H3K27me3


title: KK13-RNA


title: P-13-06179


title: KK23-RNA


title: P-14-08877


title: Old_6_H3K27me3


title: KK11-RNA

value: IIa


title: KK12-RNA


title: KK10-RNA


title: HSJ-035


title: Yng_24_H3K27me3

value: Unknown


title: JN-695


title: KK8-RNA


title: Yng_23_H3K27me3


title: KK7-RNA


title: KK9-RNA


title: HSJ-020


title: KK5-RNA

value: IIb


title: KK6-RNA


title: KK3-RNA


title: JN-29T


title: Yng_17_H3K27me3


title: HSJ-019


title: Yng_18_H3K27me3


title: Yng_22_H3K27me3


title: Yng_12_H3K27me3


title: C-14-00110


title: KK29-INPUT

description: Total DNA

data_processing:
Sequenced tags were aligned to the human reference genome hg19 using BWA-ALN
Duplicate reads which aligned to the same location and strand in a given sample were removed using Samtools
Profiles of DNA methylation were compared between each sample and its respective input, using the MACS peak calling software
All peaks from all samples were overlapped. Regions which were covered by at least 2 peaks were used in downstream analysis.The numbers of read tags aligning to each region were extracted using featureCounts [25] producing a matrix of counts (tags per region per sample).
Genes with less than 100 sequence reads across all samples were removed from further analysis.
hg19
Genome_build: Sequence tag counts in regions of interest

extract_protocol:
DNeasy Blood & Tissue. Cat No. 69506
MethylMiner enrichment. Cat No.ME10025
NEBNext® Ultra™ DNA Library Prep Kit for Illumina. Cat No. E7645


title: KK16-RNA


title: KK28-INPUT

description: Total DNA


title: JN-26T


title: KK1-RNA


title: Old_5_H3K4me3


title: KK26-INPUT

description: Total DNA


title: KK25-INPUT

description: Total DNA


title: KK27-INPUT

description: Total DNA


title: JN-10T


title: KK4-RNA


title: KK24-INPUT

description: Total DNA


title: JN-7T


title: KK23-INPUT

description: Total DNA


title: KK22-INPUT

description: Total DNA


title: JN-35T


title: KK20-INPUT

description: Total DNA


title: Old_24_H3K4me3


title: KK21-INPUT

description: Total DNA


title: KK19-INPUT

description: Total DNA


title: PS113293


title: PL708


title: KK15-INPUT

description: Total DNA


title: KK16-INPUT

description: Total DNA


title: Old_7_H3K4me3


title: KK14-INPUT

description: Total DNA


title: KK13-INPUT

description: Total DNA


title: PL3948


title: Old_8_H3K4me3


title: Old_6_H3K4me3


title: PL150


title: KK11-INPUT

description: Total DNA


title: Old_29_H3K4me3


title: Yng_27_H3K4me3


title: PH1157


title: KK10-INPUT

description: Total DNA


title: KK8-INPUT

description: Total DNA


title: KK9-INPUT

description: Total DNA


title: KK7-INPUT

description: Total DNA


title: Yng_26_H3K4me3


title: Old_12_H3K4me3


title: BTTB-434


title: KK6-INPUT

description: Total DNA


title: KK12-INPUT

description: Total DNA


title: 2230


title: DIPGXIII

data_processing:
Data processing. Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple control metrics were obtained using FASTQC (v0.11.2), samtools (v0.1.19), BEDtools (v2.17.0) and custom scripts.
Gene expression analysis. The remaining clean set of reads were then aligned to the reference genome build hg19 (GRCh37) with STAR (v2.3.0e) using the default parameters. Multimapping reads (MAPQ<1) were discarded from downstream analyses. Gene expression levels were estimated by quantifying uniquely mapped reads falling into exonic regions defined by the ensGene annotation set from Ensembl (GRCh37; N=60234 genes) using featureCounts (v1.4.4). Normalization (mean-of-ratios), variance-stabilized transformations of the data, as well as differential expression analysis, were performed using DESeq2. Unless otherwise stated, all reported p-values have been adjusted for multiple testing using the Benjamini-Hochberg procedure.
Repeat element expression analysis. The clean set of rRNA-depleted RNA-seq reads were aligned to the human repeat genome, as previously described. The reference repeat sequences were downloaded from Repbase (v23.03) (http://www.girinst.org/repbase). We then combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus repeat element sequences. All subsequent steps closely mirror those detailed for gene expression analysis. Normalization (library size) factors derived from canonical genes (Ensembl ensGene annotation) using mean-of-ratios as described above were used to normalize repeat elements.
Genome_build: hg19
Supplementary_files_format_and_content: Raw abundance measurements of Ensembl genes
Supplementary_files_format_and_content: Raw abundance measurements of Repbase repeat elements

source_name: Tumor-derived cell-line

value: glioma tumor


title: Yng_18_H3K4me3


title: 1840


title: KK1-INPUT

description: Total DNA


title: HSJ-050-C5


title: Old_31_H3K4me1


title: KK28-MM

description: Methylated DNA


title: Old_29_H3K4me1


title: Yng_8_H3K4me3


title: Yng_17_H3K4me3


title: HSJ019-C7


title: KK5-INPUT

description: Total DNA


title: KK4-INPUT

description: Total DNA


title: KK27-MM

description: Methylated DNA


title: KK25-MM

description: Methylated DNA


title: KK24-MM

description: Methylated DNA


title: KK29-MM

description: Methylated DNA


title: Old_27_H3K4me1


title: KK26-MM

description: Methylated DNA


title: KK23-MM

description: Methylated DNA


title: Old_10_H3K4me1


title: DIPGXIII-C14


title: HSJ019-C4


title: KK22-MM

description: Methylated DNA


title: Old_7_H3K4me1


title: KK3-INPUT

description: Total DNA


title: KK2-INPUT

description: Total DNA


title: KK21-MM

description: Methylated DNA


title: DIPGVI-C30


title: Old_2_H3K4me1


title: KK19-MM

description: Methylated DNA


title: KK20-MM

description: Methylated DNA


title: BT245-C19


title: KK15-MM

description: Methylated DNA


title: SJG5-C23


title: KK16-MM

description: Methylated DNA


title: Yng_18_H3K4me1


title: Yng_17_H3K4me1


title: KK13-MM

description: Methylated DNA


title: KK14-MM

description: Methylated DNA


title: KK12-MM

description: Methylated DNA


title: huFib_3

city: Stanford

first: Thach

last: Mai

address: 269 Campus Dr

institute: Stanford University

data_processing:
Basecalls performed using Illunima HiSeq 2000 or Nextseq 500
RNA-seq reads were mapped to a concatenated genome sequence of human GRCh38/hg38 and mouse GRCm38/mm10 annotations using STAR/2.4.2a.
Following mapping, human and mouse transcript abundance were individually quantified using rsem/1.2.21.
Expression levels were normalized by transcripts per million (TPM).
Genome_build: mm10/hg19
Supplementary_files_format_and_content: text file with expected count, TPM and FPKM.

molecule: polyA RNA

source_name: human fibroblast

extract_protocol:
RNA was obtained using Rneasy purification kit
Libraries were prepared according to Illumina's instructions accompanying the Tru-Seq V2 kit (RS-122-2001). Briefly, Poly-A+ RNA was isolated from total RNA using oligo-dT magnetic beads (Illumina TruSeq V2). Following first (Superscript III, Life Technologies) and second strand synthesis, cDNA libraries were constructed according to standard Illumina protocols. RNA and DNA integrity and quality was measured using an Agilent Bioanalyzer 2100.

value: human lung fibroblast


title: KK11-MM

description: Methylated DNA


title: KK10-MM

description: Methylated DNA


title: huFib_2


title: Yng_14_H3K4me1


title: KK8-MM

description: Methylated DNA


title: Yng_10_H3K4me1


title: KK9-MM

description: Methylated DNA


title: huFib_1


title: Yng_2_H3K4me1


title: KK7-MM

description: Methylated DNA


title: KK6-MM

description: Methylated DNA


title: KK5-MM

description: Methylated DNA


title: KK4-MM

description: Methylated DNA


title: WX1_sRNAseq_run331

city: Bloomington

first: Malcolm

last: Winkler

state: IN

address: 1001 E. Third Street

department: Biology

institute: Indiana University

description: rRNA depleted, fragmented (sRNA-seq)

data_processing:
Adapters and low quality bases were trimmed using Trimmomatic (version 0.17)
Trimmed reads were mapped on the Streptococcus pneumoniae D39 using Bowtie2 version 2.0.0-beta7
Genome_build: Streptococcus pneumoniae D39 (RefSeq NC_008533) genome and D39 plasmid pDP1 sequence (RefSeq NC_005022)
Supplementary_files_format_and_content: tab-delimited counts file

organism: Streptococcus pneumoniae D39

source_name: cells

growth_protocol: Strains were grown in Difco Brain Heart Infusion Broth at 37oC in atmosphere of 5% CO2 to an OD620 of 0.15 to 0.2

extract_protocol:
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals)
For samples 1-6 and 8-9, the library was generated by removing DNA by DNase treatment, depleting rRNA with Ribo-Zero rRNA removal kit for gram-positive bacteria and subsequently utilizing the ScriptSeqTM v2 RNA-Seq Library Preparation kit (Epicenter).  For samples 7 and 10, the same protocol excpet for TruSeq® Stranded RNA kit (Illumina Inc.) was used to prepare sRNA libraries using 145 - 500 bp size selection.

tag: strain


title: WX2_sRNAseq_run335

description: rRNA depleted, fragmented (sRNA-seq)


title: WX2_mRNAseq_run333

description: rRNA depleted (mRNA-seq)


title: KK3-MM

description: Methylated DNA


title: KK1-MM

description: Methylated DNA


title: AML246 PU.1 ChIP d2 Dox technical rep2

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

institute: the university of Adelaide

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were mapped using the align function in the Rsubread package (version 1.16.1, Liao et al. Nucleic Acids Research, 2013) with default parameters.
ChIP-seq reads were aligned to the mm10 genome assembly using Rsubread
Data were filtered using the following specifications
Peaks were called using MACS version 2 with the following setting: callpeak (call peaks from alignment), qvalue 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bdg files were generated using macs2, bed files were generated using macs2, contains all peaks from macs2 peak calling under the specified q-value settings.

organism: Mus musculus

source_name: AML246  PU.1 ChIP-seq acute restoration

growth_protocol: Spleen cells were isolated from leukemic mice

extract_protocol:
ChIP-seq was performed using the PU.1 antibody T-21 from Santa Cruz
ChIP-seq libraries were prepared using Truseq ChIP seq DNA sample prep kit from Illumina.

treatment_protocol: Leukemic mice were untreated or treated with Dox for 2 resulting in shutdown of GFP-linked shRNA expression and acute restoration of endogenous PU.1 expression

tag: antibody

tag: immunophenotype

value: PU.1 High

value: Spleen cells of leukaemic recipient

value: 2 days Dox


title: AML246 PU.1 ChIP d2 Dox technical rep3


title: E14 mESCs CRISPR/Cas9 Site 7 replicate 1

city: Oxford

first: Dominic

last: Owens

address: John Radcliffe Hospital

department: MRC WIMM

country: United Kingdom

institute: University of Oxford

description: E14 mESCs targeted using CRISPR/Cas9 at Site 7 (Runx1, chr16)

data_processing:
Illumina MiSeq base calling
Adapter trimming using trim_galore 0.3.1
Mapping and allele reconstruction using CRISPResso 1.0.8
Genome_build: mm9
Supplementary_files_format_and_content: CRISPResso allele frequency file

source_name: Embryonic stem cells

growth_protocol: Feeder-free LIF conditioned mESC growth medium

extract_protocol:
Qiagen Dneasy Blood and Tissue Kit
PCR based addition of Illumina sequencing adapters

treatment_protocol: Lipofection of pX CRISPR plasmids with puromycin or GFP selection

tag: passages

tag: cell sex

value: M


title: E14 mESCs CRISPR/Cas9 Site 9 replicate 1

description: E14 mESCs targeted using CRISPR/Cas9 at Site 9 (Prickle2, chr6)


title: E14 mESCs CRISPR/Cas9 Site 7 replicate 2


title: FLHL-E105-Wt-Mm-Rep2-L7363

city: Berlin

first: Christina

last: Paliou

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Wildtype

data_processing:
50 bp paired-end reads were mapped to the mouse reference genome (mm9) using the STAR mapper version 2.4.2a with default settings besides the following options: outFilterMultimapNmax=5; outFilterMismatchNoverLmax=0.1; alignIntronMin=20; alignIntronMax=500000; chimSegmentMin=10. Reads per gene were counted based on the UCSC annotation tracks ‘known genes’ and ‘RefSeq’ combined via shared exon boundaries. The counting was implemented by applying the R function ‘summarizeOverlaps’ with 'mode=Union' and 'fragments=TRUE'. Finally, differential expression analysis was performed with the DEseq2.
Genome_build: mm9
Supplementary_files_format_and_content: bw

source_name: Limb

extract_protocol:
RNA was extracted from the limbs using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Limbs from 34-5 somite staged (E10.5) mouse embryos were dissected rapidly in PBS/DEPC water, snap frozen and stored at -80°C

value: Wildtype

tag: age

value: Embryonic day 10.5


title: AML246 PU.1 ChIP untreated technical rep1

value: PU.1 Low

tag: treatment

value: untreated


title: FLHL-E105-Wt-Mm-Rep1-L7362

description: Wildtype

tag: genotype


title: WW3_mRNAseq_run307

description: rRNA depleted (mRNA-seq)


title: AML246 PU.1 ChIP d2 Dox technical rep1


title: WW2_mRNAseq_run307

description: rRNA depleted (mRNA-seq)


title: E14 mESCs CRISPR/Cas9 Site 9 replicate 2


title: AML246 single cell clone 4 Wash

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were mapped using the align function in the Rsubread package (version 1.16.1, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.16.1) using the in-built mm10 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarise the values from replicates samples using functionality from the limma package (version 3.22.0, Smyth, 2005).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

growth_protocol: AML246 cells were grown in culture in IL3 supplemented media

extract_protocol:
FACS sorted cell pellets were lysed and RNA prepared on same day using QIAGEN RNeasy plus mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Single cell clones were sorted into 96 well plates grown for 3-4 weeks and either untreated, treated with Dox 14 days and treated with Dox for 14 days washed and left untreated for 14 day

value: GFPhigh

value: AML246 in vitro cultured single cell clones

value: 14 days Dox, wash, 14 days untreated


title: FLHL-E105-Lmbr1DelProm-Mm-Rep3-L7366


title: AML246 single cell clone 2 Wash


title: FLHL-E105-Lmbr1DelProm-Mm-Rep4-L7367


title: WX1_mRNAseq_run333

description: rRNA depleted (mRNA-seq)


title: AML246 single cell clone 2 untreated


title: AML246 PU.1 ChIP untreated technical rep2


title: AML246 single cell clone 4 untreated


title: WT3_mRNAseq_run307

description: rRNA depleted (mRNA-seq)


title: WT2_mRNAseq_run307

description: rRNA depleted (mRNA-seq)


title: FLHL-E105-Lmbr1DelProm-Mm-Rep2-L7365


title: AML246 single cell clone 1 untreated


title: AML246 single cell clone 1 Dox

value: GFPoff

value: 14 days Dox


title: H3K36me3-FLHL-E105-Wt-Mm-Rep2-L7329

description:
Wildtype
H3K36me3-FLHL-E105-Wt-Mm-Merge.bw

data_processing:
Single-end reads from ChIP-seq experiments were mapped with Bowtie-2.2.6 (Langmead and Salzberg, 2012) to reference genome mm9. Mapped reads were filtered for mapping quality ≥10, and duplicates were removed using samtools (https://github.com/samtools/samtools).
Reads were extended (chromatin modifications: 300bp, transcription factors: 200bp) and scaled (one million / total of unique reads) to produce coverage tracks. For figure display purposes, ChIP-seq BigWig files were merged using the bigWigMerge from UCSC tools. BigWig files were visualized in the UCSC browser.
Genome_build: mm9
Supplementary_files_format_and_content: bw

growth_protocol: Limb bud and midbrain were micro-dissected from 34-5 somite stage (E10.5) mouse embryos

extract_protocol:
Histone modifications were immunoprecipitated with the respective antibody (Lee et al., 2006, Jerkovic et al., 2017) and trascription factor ChIPs were performed with the  iDeal ChIP-seq kit for Transcription Factors (Cat. No. C01010055) according to guidelines.
We sheared chromatin using Bioruptor until reaching a fragment size of 200-500bp. 10-15μg of chromatin was then used for each replicate chromatin modification ChIP and 20μg for CTCF and RAD21 ChIP. ChIP for H3K27ac (Diagenode: C15410174), H3K36me3 K3K36me3 (Abcam:ab9050), CTCF (Diagenode:C15410210) and RAD21 (Abcam: ab992) was then performed as in Lee et al., 2006.
Libraries were prepared using the Nextera adaptors and sequenced 50 or 75bp reads.

treatment_protocol: Tissues were homogenized with Collagenase solution, fixed with 1% FA crosslinking for 10 minutes at room temperature,  cells were lysed in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 0.1mM EGTA, Protease Inhibitor) and upon PBS wash, snap frozen and stored in -80°C. Material was sonicated either in in buffer 3 for sonication (Lee et al.,) for chromatin modifications or sonication buffer included in the iDeal ChIP-seq kit for Transcription Factors (Cat. No. C01010055).

tag: embryonic stage

value: K3K36me3 (Abcam:ab9050)


title: FLHL-E105-Lmbr1DelProm-Mm-Rep1-L7364


title: AML410 untreated technical rep2

growth_protocol: Bone marrow cells were isolated from leukemic mice and GFP+ cells were isolated using FACS

treatment_protocol: Leukemic mice were untreated or treated with Dox for 2, 4 or 6 days, resulting in shutdown of GFP-linked shRNA expression and gradual restoration of endogenous PU.1 expression

value: bone marrow of leukaemic recipient


title: AML410 d4 Dox technical rep2

value: GFPmid

value: 4 days Dox


title: Arabidopsis_root_mRNA-seq_bulk

city: Berkeley

first: Benjamin

middle: Jeremy

last: Cole

state: CA

address: 1, Cyclotron Road

institute: DOE-Joint Genome Institute

data_processing:
Illumina CASAVA bcl2fastq v2.17 used for basecalling.
Sequenced reads were trimmed for adaptor sequence and polyA, then mapped to a combined GRCh38-TAIR10 or mm10-TAIR10 genome mega-reference using STAR v. 2.5.2b for Drop-seq data, or mapped to TAIR10 using HISAT for RNA-seq data.
Digital gene expression matrices were created by following the Drop-seq Core Computational Protocol version 1.0.1 (http://mccarrolllab.com/dropseq/) for Drop-seq data. For mRNA-seq data, library counts were generated use featureCounts.
Genome_build: GRCh38; mm10; TAIR10
Supplementary_files_format_and_content: digital gene expression matrices and library counts are provided as txt files

organism: Arabidopsis thaliana

source_name: whole root

growth_protocol: Seeds were sown at a density of ~125 seeds per row on sterile nylon mesh filters placed on top of plant growth media consisting of 1X Murashige and Skoog Basal Medium (Sigma-Aldrich, St. Louis, MO) supplemented with 1% sucrose (Sigma-Aldrich), 1% agar (Sigma-Aldrich), 2.6 mM 2-(N-Morpholino)ethanesulfonic acid (MES; Sigma-Aldrich), and adjusted to pH 5.7. Petri dishes were positioned vertically in an incubator (Percival Scientific, Perry, IA) under a long-day photoperiod (16 h of light) at 22°C.

extract_protocol:
Total RNA was isolated from flash frozen 5-day-old Arabidopsis root material using the Qiagen RNeasy kit (Carlsbad, CA).
An RNA library was prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) according to the manufacturer’s Low Sample (LS) Protocol.manufacturer’s Low Sample (LS) Protocol.

tag: ecotype

value: 5 day

value: WT

value: whole root


title: AML246 single cell clone 1 Wash


title: AML246 single cell clone 4 Dox


title: AML246 single cell clone 2 Dox


title: WW1_mRNAseq_run307

description: rRNA depleted (mRNA-seq)


title: AML410 d4 Dox technical rep1


title: H3K36me3-FLHL-E105-Wt-Mm-Rep1-L7328

tag: chip antibody


title: Arabidopsis_root_Drop-seq_replicate_B

extract_protocol:
Cells were used at their starting concentration after protoplasting. 2.5% human cells were added to each suspension. Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads as previously described (PMID: 26000488).
The library was prepared according to Drop-seq Laboratory Protocol version 3.1 (http://mccarrolllab.com/dropseq/) using Illumina's Nextera XT DNA Library Preparation Kit. The library was uniquely indexed and then pooled and sequenced on a single lane of a HiSeq 4000.

treatment_protocol: Protoplast suspensions were prepared from 5-day-old Arabidopsis seedlings using previously described methods (PMID: 16170893).


title: AML410 d6 Dox technical rep2

value: GFPlow

value: 6 days Dox


title: AML410 d2 Dox technical rep1

value: GFPhigh-mid

value: 2 days Dox


title: H3K36me3-FLHL-E105-delLmbr1-Mm-Rep1-L7330

description:
Lmbr1Δprom/Δprom
H3K36me3-FLHL-E105-delLmbr1-Mm-Merge.bw

value: Embryonic day 10.5


title: Arabidopsis_root_Drop-seq_replicate_A

extract_protocol:
Cells were diluted in Solution A (PMID: 16170893) to 96 cells/ul. 2.5% human cells were added to each suspension. Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads as previously described (PMID: 26000488).
The library was prepared according to Drop-seq Laboratory Protocol version 3.1 (http://mccarrolllab.com/dropseq/) using Illumina's Nextera XT DNA Library Preparation Kit. The library was uniquely indexed and then pooled and sequenced on a single lane of a HiSeq 4000.


title: AML410 d2 Dox technical rep2


title: AML410 untreated technical rep1

value: GFPhigh

value: untreated


title: AML246 d4 Dox technical rep 3

value: bone marrow of leukemic recipient


title: CTCF-MB-E105-WT-Mm-Rep1-L12245

description: Wildtype

value: Wildtype

value: CTCF (Diagenode:C15410210)


title: AML410 d6 Dox technical rep1


title: WT1_mRNAseq_run307

description: rRNA depleted (mRNA-seq)


title: AML246 d2 Dox technical rep3


title: AML246 d6 Dox technical rep3


title: AML246 untreated technical rep3


title: CTCF-FLHL-E105-WT-Rep2-L12248

description: Wildtype


title: H3K36me3-FLHL-E105-delLmbr1-Mm-Rep2-L7331

value: K3K36me3 (Abcam:ab9050)


title: AML246 d4 Dox technical rep2


title: CTCF-FLHL-E105-WT-Rep1-L12246

description: Wildtype


title: CTCF-FLHL-E105-i5-Mm-Rep1-L10937

description: ΔCTCF i5

value: deltaCTCF i5


title: Biofilm_environmental_DS3-Mar-B

city: Northfield

first: Heather

middle: Elizabeth

last: Driscoll

state: VT

address: 158 Harmon Drive

institute: Norwich University

description: Biofilm sampled on March 31, 2010 at site DS3, the most downstream biofilm sampling site on Wilson Park Creek.

hyb_protocol: Samples were injected into G2 PhyloChip arrays (Affymetrix) and placed in the Affymetrix Genechip® Hybridization Oven 640 at 48° C for 16-18 hours overnight. A full description of the G2 PhyloChip design is provided elsewhere (Brodie et al., 2006, 2007; DeSantis et al., 2007). Hybridized arrays were washed and stained with streptavidin-phycoerythrin followed by sequential incubations with biotin-couple polyclonal anti-streptavidin antibody and streptavidin-phycoerythrin as a fluorescent amplification step.

scan_protocol: Arrays were scanned with the 7G Affymetrix GeneChip® Scanner 3000.

data_processing: Raw image analysis was performed with Affymetrix® Expression ConsoleTM software. The raw data images produced from the scanner were processed into .CEL files, which contain measure intensities for each probe on the array. CEL files were analyzed by Second Genome (South San Francisco, CA, USA) using an empirical approach to define unique operational taxonomic units (eOTUs). The criteria for scoring the probe-level fluorescence intensity (FI) and the process by which individual probes are clustered into probesets, aka eOTUs, are described in detail elsewhere (Probst et al. 2014). Briefly, in the eOTU analysis taxonomically related probes were clustered into probesets when pairwise correlations between log2 transformed FI values were ≥0.85. Probesets were annotated with the 2012 GreenGenes taxonomy using Naive Bayesian scoring and a ≥80% bootstrapped confidence threshold (DeSantis et al. 2006; MacDonald et al. 2012). The mean log2 FI among the multiple probes for each eOTU, referred to as the hybridization score (HybScore), was calculated for each sample. A binary score (incidence) for each eOTU was assigned a 1 if 80% or more of the probes in that set were responsive in a given sample (present), otherwise a 0 was assigned (absent).  Eight hundred and fifty-eight eOTU abundances (HybScore multiplied by binary score) were included in downstream analyses.

label: Biotin

organism: biofilm metagenome

source_name: Biofilm in water

label_protocol: Samples were then fragmented and labeled using DNase I (0.025 U/uL) and TdT (30 U/uL; Affymetrix GeneChip WT Terminal Labeling Kit: 900670).  Efficiency of the biotin labeling reaction was verified using NeutrAvidin (10 mg/mL) with a gel-shift assay.

extract_protocol: From each of 11 biofilm samples collected from four primary sites, DNA was polymerase chain reaction (PCR) amplified using universal 16S primers 27F (5’-AGAGTTTGATYMTGGCTCAG-3’) and 1492R (5’-GGYTACCTTGTTACGACTT-3’).  Samples were cleaned and concentrated using Pall Nanosep® 30K spin filters (Port Washington, NY, USA).

tag: distance upstream from d3-gage st st. luke's hospital (km)

tag: site name

tag: usgs station identification number

tag: sampling date

tag: sample notation

value: DS3 (Mar-B)


title: Biofilm_environmental_DS1-May

description: Biofilm sampled on May 25, 2010 at site DS1, the biofilm sampling site located immediately downstream of the airport on Wilson Park Creek.

value: DS1 (May)


title: Biofilm_environmental_US1-Mar-B

description: Biofilm sampled on March 30, 2010 at site US1, located on Edgerton Channel, upstream of the airport.

value: US1 (Mar-B)


title: CTCF-FLHL-E105-i4i5-Mm-Rep1-L10938

description: ΔCTCF i4i5

value: deltaCTCF i4i5


title: AML246 d6 Dox technical rep 2

tag: tissue


title: AML246 d6 Dox technical rep 1

tag: strain


title: AML246 d2 Dox technical rep1


title: Biofilm_environmental_DS2-Mar-B-riprap

description: Biofilm from riprapped stream edge sampled on March 31, 2010 at site DS2, a biofilm sampling site located downstream of the airport (downstream of site DS1 and upstream of site DS3) on Wilson Park Creek.

value: DS2 (Mar-B, riprap)


title: AML246 untreated technical rep2


title: CTCF-FLHL-E105-i4-Mm-Rep1-L10936

description: ΔCTCF i4

value: deltaCTCF i4


title: AML246 untreated technical rep1


title: Biofilm_environmental_DS2-Mar-B-sand

description: Biofilm from sandy midchannel sampled on March 31, 2010 at site DS2, a biofilm sampling site located downstream of the airport (downstream of site DS1 and upstream of site DS3) on Wilson Park Creek.

value: DS2 (Mar-B, sand)


title: Biofilm_environmental_DS1-gage-Mar-B

description: Biofilm sampled on March 30, 2010 at site DS1-gage, the USGS gaging station near site DS1 on Wilson Park Creek.

value: DS1-gage (Mar-B)


title: Biofilm_environmental_DS1-Mar-B

description: Biofilm sampled on March 30, 2010 at site DS1, the biofilm sampling site located immediately downstream of the airport on Wilson Park Creek.

value: DS1 (Mar-B)


title: MB-WT-Rep1_L12942

description:
wild type
MB-WT_L12942_L12943_merged_MAPQ30_KR_10kb.WashU.txt
vC_WT_MB_chr5_28789001_28799000_Shh_promoter.5kb_norm.bedgraph

data_processing:
Library strategy: Capture Hi-C
Raw sequencing reads were preprocessed with cutadapt v1.15 (Martin, 2011) to trim potential low quality bases (-q 20 -m 25) and Illumina sequencing adapters (-a and -A option with Illumina TruSeq adapter sequences according to the cutadapt documentation) at the 3’ end of reads. Next, sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v6.1.0 (Wingett et al., 2015) (no size selection, Nofill: 1, Format: Sanger). The pipeline was set up with Bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012) for short read mapping. The trimming of sequencing adapters in the first step would not have been necessary, because potentially remaining sequencing adapter in reads from valid ligation products should also be removed by the truncation after ligation sites implemented in the HiCUP pipeline. In case replicates were available, they were combined after the processing with the HiCUP pipeline. Juicer command line tools v1.7.6 (Durand et al., 2016) was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing (Durand et al., 2016; Knight and Ruiz, 2013; Rao et al., 2014). For binning and normalization, only the genomic region chr5:27,800,001- 30,600,000 enriched in the DNA-capturing step was considered. Therefore, only reads pairs mapping to this region were kept, shifted by the offset of 27,800,000 bp and imported with Juicer tools using a custom chrom.sizes file which contained only the length of the enriched region (2.8 Mb). Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb and 10kb resolution and coordinates were shifted back to their original values. Subtraction maps were generated from KR normalized maps, which were normalized in a pair-wise manner before subtraction. To account for differences between two maps in their distance-dependent signal decay, maps were scaled jointly across their sub-diagonals. Therefore, the values of each sub-diagonal of one map were divided by the sum of this sub-diagonal and multiplied by the average of these sums from both maps. Afterwards, the maps were scaled by 106 / total sum. cHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 97-th  percentile were truncated for visualization purposes.
In order to obtain more fine-grained interaction profiles for selected loci, we defined 10kb viewpoint regions and generated virtual Capture-C-like profiles based on the filtered, unique read-pairs that were also used for the cHiC maps. A read pair was considered in a profile, when it had a MAPQ≥30 and one read mapped to the defined viewpoint region, while the other read mapped outside of it. The reads outside of the viewpoint were counted per restriction fragment and read counts were binned afterwards to 1 kb bins. In case a fragment was overlapping more than one bin, the read count was distributed proportionally. Afterwards, the each binned profiles wasere smoothed by averaging over a running window of 5 bins and scaled by 103 / sum of all its counts in the enriched region on chr5. The viewpoint and a window ± 5kb around it were not considered for the computation of the scaling factor. The profiles were generated with custom Java code using htsjdk v2.12.0  (https://samtools.github.io/htsjdk/). Virtual Capture-C viepoint: Shh promoter (chr5:28,789,001-28,799,000)
Supplementary_files_format_and_content: bedgraph, txt

source_name: Embryonic Midbrain

growth_protocol: Limbs from 34-5 somite-stage (E10.5) mouse embryos were microdissected in PBS.

extract_protocol:
Tissues were homogenized in Collagenase solution, fixes with 2% FA at room temperature, 10 min and the cells were lysed in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 0.1mM EGTA, Protease Inhibitor). Upon PBS wash, samples were snap-frozen and stored at -80°C. Samples were then digested with DpnII, re-ligated, de-crosslinked and purified.
The 3C-library was then sheared using a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, time: 2 cycles of 60 s each, set mode: frequency sweeping, temperature: 4 to 7 °C). Adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions.

value: wild type


title: AML246 d2 Dox technical rep2

value: GFPhigh-mid

value: 2 days Dox


title: AML246 d4 Dox technical rep 1

value: GFPmid

value: bone marrow of leukemic recipient

value: 4 days Dox


title: Biofilm_environmental_DS1-Mar-A

description: Biofilm sampled on March 18, 2010 at site DS1, the biofilm sampling site located immediately downstream of the airport on Wilson Park Creek.

value: DS1 (Mar-A)


title: FLHL-i4i5_L12946-1

description:
ΔCTCF i4i5
FLHL-i4i5_L12946_L12946-2_merged_MAPQ30_KR_10kb.WashU.txt
vC_i4i5_FLHL_chr5_28789001_28799000_Shh_promoter.5kb_norm.bedgraph

source_name: Embryonic Limb Bud


title: Biofilm_environmental_DS1-Nov

description: Biofilm sampled on November 3, 2010 at site DS1, the biofilm sampling site located immediately downstream of the airport on Wilson Park Creek.

value: November 3, 2010

value: DS1 (Nov)


title: LC-8d-B

type: RNA

city: LUGO

first: Belen

middle: G

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

country: Spain

institute: University of Santiago de Compostela

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to turbot custom Oligo Microarrays (G2514F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Extended dynamic range implemented in the Agilent software was applied to avoid saturation in the highest intensity range. The Agilent feature extraction was used as raw data for further preprocessing. The processed signal (gProcessed-Signal) value was chosen for the statistical analysis.

organism: Ruditapes philippinarum

source_name: Haemocyte cells, laboratory challenge, 8 days, sample pool B

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA  of each strain and time using the Low Input Quick Amp Labeling Kit, One-Color (Cy3) (Agilent Technologies, USA)  according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: For WI study, 200 market-sized (≥ 40 mm in length, + 2 years old) adult Manila clams were collected from a P. olseni affected sea bed (Placeres, Ría de Pontevedra, NW Spain). In the case of the LC experiment, clams were collected from a P. olseni infection-free natural bed in Camariñas (Galicia, NW Spain) as confirmed by PCR (Casas et al., 2002a). These clams were kept at 14-17 oC in filtered (1 µm) seawater (35 ‰) with aeration for 1 week to adapt to indoor conditions.

extract_protocol: Haemolymph was collected from clam adductor muscle using a syringe with 25 mm gauge needle, and then transferred to a 1.5 mL tube and kept on crushed ice until haemocyte isolation. Haemolymph samples contaminated with bacteria or gametes were discarded after light microscope examination. Haemocytes were isolated from plasma by centrifuging haemolymph samples at 800 g for 10 min at 4 oC. The supernatant was then discarded and the pellet resuspended in 750 µL of RNAlater (Qiagen) solution and stored at -80 °C until RNA extraction. Total RNA was extracted using the Qiagen RNeasy mini kit with DNase following manufacturer’s instructions.

treatment_protocol: For LC experiment forty clams (40-45 mm shell length) were immersed individually in glasses containing 250 mL of filtered aerated seawater, either without parasite cells (control group) or with a suspension of 1 x 106 P.olseni zoospores (treatment group). The experiment lasted for 8 d and clams were not fed during this period.

value: haemocyte cells

tag: sample type

value: Perkinsus olseni laboratory challenge

tag: time point

value: 8 days

tag: pool

value: B


title: Biofilm_environmental_DS1-Jan

description: Biofilm sampled on January 28, 2010 at site DS1, the biofilm sampling site located immediately downstream of the airport on Wilson Park Creek.

value: January 28, 2010

value: DS1 (Jan)


title: ATAC-FLHL-E105-Wt-Mm-Rep1-L6684

description:
Wild type
ATAC-FLHL-E105-Wt-Mm-Rep1-L6684_R1_001.noDups_noChrM.Mapq30.bw
ATAC-FLHL-E105-Wt-Mm-L6684-L6685-Merge.bw

data_processing:
Paired-end reads were processed as described in the ENCODE (Encode Consortium, 2012) guidelines for mouse ATAC-seq samples. Firstly, ATAC-seq paired-end reads were trimmed to 30bp to allow fragments with closeby transposition events (<50bp) to map, i.e. increase read coverage at Nucleosome Free Regions. Secondly, trimmed reads were mapped with Bowtie2 (Langmead and Salzberg, 2012) and removed duplicated fragments with Picard RemoveDuplicates (https://broadinstitute.github.io/picard/). Lastly, bigWig files for display were generated with deepTools2 (Ramírez et al., 2016) for properly mapped read pairs (FLAG 0x2) with mapping quality ≥20.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig

extract_protocol:
50.000 cells were used for each reaction of tagmentation and protocol was performed as previously described (Buenrostro JD et al., 2015).
Libraries were prepared using the Nextera adaptors and sequenced

treatment_protocol: Limbs from 34-5 somite-staged (E10.5) mouse embryos were homohenized with Collagenase solution to achiev singe cell suspension.

value: Wild type

value: Embryonic day 10.5


title: LC-24h-B

source_name: Haemocyte cells, laboratory challenge, 24 hours, sample pool B


title: MB-WT-Rep2_L12943

value: wild type


title: LC-8d-C

source_name: Haemocyte cells, laboratory challenge, 8 days, sample pool C

value: C


title: ATAC-FLHL-E105-Wt-Mm-Rep2-L6685

description:
Wild type
ATAC-FLHL-E105-Wt-Mm-Rep2-L6685_R1_001.noDups_noChrM.Mapq30.bw
ATAC-FLHL-E105-Wt-Mm-L6684-L6685-Merge.bw


title: ATAC-FLHL-E105-delLmbr1-Mm-Rep2-L7249

description:
Lmbr1Δprom/Δprom
ATAC-FLHL-E105-delLmbr1-Mm-Rep2-L7249_R1_001.noDups_noChrM.Mapq30.bw
ATAC-FLHL-E105-delLmbr1-Mm-L7248-L7249-Merge.bw


title: JN-57T_input

data_processing:
Adaptor sequences and the first four nucleotides of each read were removed from the read sets using Trimmomatic (Bolger et al., 2014) (v0.32).  Reads were scanned from start to end and truncated if and when the average quality of a 4-nucleotide sliding window fell too low (phred33<30). Short reads (<30 bp) were subsequently discarded. Multiple quality control metrics were obtained using FASTQC (v0.11.2), samtools (Li et al., 2009) (v0.1.19), BEDtools (Quinlan and Hall, 2010) (v2.17.0) and custom scripts.   Reads were processed as described for RNAseq, and then aligned using the human repeat genome as reference, as previously described (Solovyov et al., Cell Reports 2018). Repbase reference genome was used (Bao et al., 2015) (v23.03) (http://www.girinst.org/repbase). Since Repbase largely consists of family consensus sequences, reads are assigned to these sequences regardless of where and how many times they are present in the genome, mitigating mapping uncertainty. We combined humrep.ref and humsub.ref into a single reference of repeat sequences for the human genome, covering a total of 1132 consensus elements, and counted the number of reads mapping into each of these elements using featureCounts (MAPQ>3). Differential enrichment of H3K27ac at the consensus sequences were then calculated using DESeq2 (Love et al., 2014). The inverse of ChIP-Rx spike-in scaling factors (i.e. 1/rx) were supplied to DESeq2 as normalization factors (i.e. size factors).
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction ~5% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing (see below). ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads were washed and then incubated with 6ug of H3K27ac antibody (Diagenode, C15410196), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail (Life Technologies) at 65°C for 30 min followed by 2ul Proteinase K (Thermo Fisher Scientific) at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

value: Tumor


title: LC-24h-C

source_name: Haemocyte cells, laboratory challenge, 24 hours, sample pool C


title: ATAC-FLHL-E105-delLmbr1-Mm-Rep1-L7248

description:
Lmbr1Δprom/Δprom
ATAC-FLHL-E105-delLmbr1-Mm-Rep1-L7248_R1_001.noDups_noChrM.Mapq30.bw
ATAC-FLHL-E105-delLmbr1-Mm-L7248-L7249-Merge.bw


title: JN-29T_input


title: Biofilm_environmental_DS1-Feb

description: Biofilm sampled on February 24, 2010 at site DS1, the biofilm sampling site located immediately downstream of the airport on Wilson Park Creek.

value: February 24, 2010

value: DS1 (Feb)


title: 749_Lmbr1Dprom_Shh TSS_Rep2

description:
Lmbr1Δprom/Δprom
Lmbr1_Dprom_Shh TSS_Merge.bedgraph
Lmbr1_Dprom_vs_Wildtype_chr5_28000000_30000000_subtract_RPM.bedgraph

data_processing:
Library strategy: 4C-seq
We merged biological replicates on the raw read level. 4C-seq reads were filtered for the primer  sequence including the first restriction enzyme dpnII.  After preprocessing clipped reads were mapped to the reference NCBI37/mm9 genome using BWA-MEM (v0.7.12-r1044) with default settings.
4C-seq contacts were analyzed in the murine region chr5:28000000-30000000
To calculate read count profiles, the viewpoint and adjacent fragments 2 kb up- and downstream were removed. A sliding window of 5 fragments was chosen to smooth the data and data was normalized to reads per million mapped reads (RPM).
To compare interaction profiles of different samples, we subtracted them for each window of normalized reads.
Genome_build: mm9
Supplementary_files_format_and_content: RPM.bedgraph

extract_protocol:
4C-seq libraries were prepared following the published protocol (van de Werken et al., 2012). DpnII was used for the first digestion, and Csp6I was used in the second digestion. For each viewpoint, a total of 1.6 mg of each library was amplified by PCR with the following primers: 4C_Shh_D/C_Read: CCATCCCCAGATGTGAGTGT,4C_Shh_D/C_Rev: CCATCGCAGCCCCAGTCT
Samples were sequenced with Ilumina Hi-Seq technology according to standard procedures.

treatment_protocol: Limbs from homozygous E10.5 embryos were microdissected in 1% PBS and homogenized in 500µl Collagenase solution. 2% FA solution was used for fixation.

tag: viewpoint

value: Shh TSS


title: AR012

data_processing:
Using Cutadapt (version 1.12), all reads were trimmed to 72 basepairs and adapters were removed.
Reads were aligned to the hg19 gencode v19 reference genome using the STAR aligner (version 2.5.2b), specifying the following parameters: outFilterType= BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1 , outFilterMismatchNmax=999, alignIntronMin=20, alignIntronMax=1000000, alignMatesGapMax=1000000, alignEndsType=EndToEnd.
Gene counts were calculated using QoRTs. QoRTs was run in stranded mode using the hg19 gencode annotation file that included ERCC spike-in information, but did not include entries for ribosomal RNA, mitochondrial RNA, or tRNA.
Genome_build: hg19
Supplementary_files_format_and_content: The processed file is a text file that contains the raw counts generated by QoRTs.

source_name: PB CD34+ cells_sgCTRL

growth_protocol: Frozen PB CD34+ cells (n=4 replicates) were thawed and cultured in IMDM + 20% Human Serum AB + hTPO (100 ng/ml), hSCF (100 ng/ml), hIL-6 (20 ng/ml), hFLT-3 (10 ng/ml) and non-essential amino acids for 72 hrs under low oxygen conditions.

extract_protocol:
RNA was extracted using the Qiagen Allprep Micro kit (Qiagen, #80204), following the manufacturer’s instructions.
Stranded ribodepelted libraries were prepared by the University of Miami Sequencing Core using the Illuminia TruSeq Stranded Total RNA kit (Illumina, #20020596). ERCC spike-ins were included for library preparation. Libraries were sequenced on the HiSeq-3000 with 75 bp paired-end sequencing.

treatment_protocol: Cells were transfected with equimolar amounts of Cas9 protein (PNA Bio, 1 μg/μL in PBS) and sgRNAs using the Neon Transfection System (Thermo Fisher). Electroporation conditions used were 1600 volts, 10 milliseconds, and 3 pulses. For controls, CD34+ cells were transfected with equimolar amounts of Cas9 protein (PNA Bio, 1 μg/μL in PBS) and a non-targeting sgRNA. Following transfection, cells were cultured in cytokine supplemented medium (IMDM + 20% Human Serum AB + hTPO (100 ng/ml), hSCF (100 ng/ml), hIL-6 (20 ng/ml), hFLT-3 (10 ng/ml) and non-essential amino acids for 72 hrs under low oxygen conditions. CD34+ cells were then FACS isolated and cultured using the above media and low oxygen conditions. After 72 hrs in culture, cells were used for RNA extraction.

tag: donorid

value: BB

tag: age

value: ND

tag: Sex

value: F

value: Peripheral blood (PB)

tag: cell type

value: sgCTRL

tag: sample


title: 2230_input

tag: genotype

tag: chip antibody


title: AR011

source_name: PB CD34+ cells_sgKLF6

tag: treatment


title: 748_Lmbr1Dprom_Shh TSS_Rep1

tag: embryonic stage


title: 1840_input


title: KO.2 RNAseq

city: Ann Arbor

first: Robert

middle: J

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

data_processing:
Basecalls were performed using CASAVA v1.8.2
FastQ files were bases were trimmed using cutadapt, removing the universal Illumina adapter base sequence, while hard-clipping the first 13 bp from the 5' end of the reads. Reads shorter than 26 bp were discarded (cutadapt -a AGATCGGAAGAGC -u 13 -m 26)
Reads were aligned and gene-level counts were obtained using RSEM, with the bowtie aligner option, with a seed-length of 26 and allowing for 2 bp mismatches. (rsem-calculate-expression -p 8 --seed-length 26 -bowtie-n 2)
TMM normalization of gene-level counts was performed using the abundance_estimates_to_matrix.pl script from Trinity v2.2.0. (abundance_estimates_to_matrix.pl --est_method RSEM)
Counts data was imported into limma, lowly expressed genes removed (kept if > 1 count per million mapped reads in all replicates of at least one group), data was voom transformed, and differential expression comparisons were performed.
Genome_build: X. tropicalis genome (v4.1)
Supplementary_files_format_and_content: Processed data files inclued gene-level counts matrix, as well as RSEM output for each sample showing the length, effective length, expected count, transcripts per million reads mapped (TPM), and fragments per kilobase per million reads mapped (FPKM) for each gene.

organism: Xenopus tropicalis

source_name: Brain (POA/hypothalamus/thalamus)

growth_protocol: We obtained wildtype (WT) Xenopus tropicalis frogs from NASCO and reared them in dechlorinated tap water at 25C under a 13L:11D photoperiod, and fed them frog brittle (NASCO, Fort Atkinson, WI) or Sera Micron plankton food (tadpoles only). We obtained the heterozygous thra mutant frog line (TRαM5) from Dr. Yun-Bo Shi.

extract_protocol:
We isolated total RNA from tadpole brain using Tri Reagent (Sigma-Aldrich, St. Louis, MO) and the Direct-zol RNA kit (Zymogen) following the manufacturers’ instructions. The quality of the RNA was analyzed using a Bioanalyzer
Total RNA libraries were prepared by the University of Michigan DNA Sequencing Core.

treatment_protocol: For treatment of tadpoles with 3,5,3’-triiodothyronine (T3; sodium salt, Sigma-Aldrich, St. Louis, MO), we dissolved the hormone in 0.01N NaOH to make a 500 μM stock solution, then we added the stock to the aquarium water to a final concentration of 5 nM T3 for all experiments; controls received an equivalent amount of 0.01N NaOH. We treated Nieuwkoop-Faber stage 54 tadpoles with vehicle or T3 added to the aquarium water for 16 hr before harvesting tissues for RNA isolation.

value: Mutant (thra KO)

value: Brain

value: Vehicle (NaOH) 16 hr


title: KO.3 RNAseq


title: KO.1_T3 RNAseq


title: KO.1 RNAseq


title: KO.2_T3 RNAseq


title: AR010


title: BTTB-434_input


title: 746_WT_Shh_TSS_Rep1

description:
WT_Shh_TSS_Merge.bedgraph
Lmbr1_Dprom_vs_Wildtype_chr5_28000000_30000000_subtract_RPM.bedgraph


title: KO.3_T3 RNAseq


title: LC-10h-B

source_name: Haemocyte cells, laboratory challenge, 10 hours, sample pool B

value: haemocyte cells

value: Perkinsus olseni laboratory challenge

value: B


title: AR009


title: JN-57T_H3K27ac

value: H3K27ac antibody (Diagenode, C15410196)


title: LC-10h-C

source_name: Haemocyte cells, laboratory challenge, 10 hours, sample pool C

value: C


title: WT.2_T3 RNAseq

value: Wild type


title: LC-10h-A

source_name: Haemocyte cells, laboratory challenge, 10 hours, sample pool A

value: A


title: AR008


title: JN-29T_H3K27ac

value: Tumor


title: LC-8d-A

source_name: Haemocyte cells, laboratory challenge, 8 days, sample pool A

value: 8 days


title: LC-24h-A

source_name: Haemocyte cells, laboratory challenge, 24 hours, sample pool A


title: LC-C-24h

source_name: Haemocyte cells, Control 24 hours

value: control


title: WT.1_T3 RNAseq


title: WI-B

source_name: Haemocyte cells, wild infection, sample pool B

value: Perkinsus olseni wild infection


title: 747_WT_Shh_TSS_Rep2

source_name: Limb

value: Embryonic day 10.5

value: Shh TSS


title: AR007

value: F

value: Peripheral blood (PB)


title: LC-C-8d

source_name: Haemocyte cells, Control 8 days


title: AR006

value: sgCTRL


title: WT.2 RNAseq

value: Brain

value: Vehicle (NaOH) 16 hr


title: WT.3 RNAseq


title: 1840_H3K27ac


title: BTTB-434_H3K27ac


title: WI-A

source_name: Haemocyte cells, wild infection, sample pool A

value: haemocyte cells


title: LC-C-10h

source_name: Haemocyte cells, Control 10 hours


title: LZy24-3

status: Public on May 12 2019

city: Wuhan

first: Peng

last: Zhao

address: Luojia Hill

department: College of Life Sciences

country: China

institute: Wuhan University

description: Amplified with SMART-Seq Ultra Low Input RNA Kit

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to arabidopsis genome TAIR10 using Tophat2.
Expression level are quantified by a software package: RSEM (RNASeq by Expectation Maximization v1.3.0).
Genome_build: Arabidopsis thaliana genome TAIR10

source_name: Hybrid zygote at 24 HAP from the cross between Ler and Col

growth_protocol: In greenhouse under long-day conditions (16 h light/8 h dark) at 22 °C

extract_protocol:
mRNA was extracted with Dynabeads® mRNA DIRECT™ Micro Kit. And SMART-Seq v4 Ultra Low Input RNA Kit was used to generate cDNA library for sequencing
Libraries were constructed using NEBNext Ultra DNA Library Prep Kit for Illumina.

tag: ecotype background

value: Ler (♀)× Col (♂)

tag: developmental stage

value: 24 HAP

value: Zygote


title: CZy24-2

source_name: Hybrid zygote at 24 HAP from the cross between Col and Ler

value: Col (♀)× Ler (♂)


title: WT.1 RNAseq

value: Wild type

tag: tissue


title: WT.3_T3 RNAseq


title: 2230_H3K27ac

value: Tumor

value: H3K27ac antibody (Diagenode, C15410196)


title: WI-C

source_name: Haemocyte cells, wild infection, sample pool C

value: C


title: LZy24-1


title: WI-Control

source_name: Haemocyte cells, wild control

value: wild type


title: CZy14-3

source_name: Hybrid zygote at 14 HAP from the cross between Col and Ler

value: 14 HAP


title: CZy14-2


title: CZy14-1


title: LZy24-2


title: LZy14-3

source_name: Hybrid zygote at 14 HAP from the cross between Ler and Col


title: CZy24-3


title: LZy14-2


title: pdxJ_11plus_vs_pdxJ_11minus_II_csw

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

description: Ratio (pdxJ(11+) / pdxJ(11-))

hyb_protocol: Purified cDNA samples to be compared were pooled and prepared using Agilent’s Gene Expression Hybridization Kit. The two-color samples were hybridized at 65°C while rotating for 17 hours using Agilent's hybridization chamber and hybridization oven. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Escherichia coli BW25113

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described (Kranz et al., 2018, BMC Genomics 19(1):753; doi: 10.1186/s12864-018-5111-1).

growth_protocol: Strains were grown in M9-glucose minimal medium (1x M9-salts, 2 mM MgSO4, 0.1 mM CaCl2, 0.4 % Glucose). When the culture reached an optical density of 0.5 cells were harvested by centrifugation(3 min, 5000 x g) mixed with crushed ice to ensure rapid cooling. The pelleted cells were shock-frozen in liquid nitrogen and stored at -80° C until RNA preparation.

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Kranz et al., 2018, BMC Genomics 19(1):753; doi: 10.1186/s12864-018-5111-1).

tag: genotype/variation

value: control

value: sample


title: CZy24-1


title: pdxJ_X3plus_vs_pdxJ_WTplus_I

description: Ratio (pdxJ(X3+) / pdxJ(WT+))

tag: sample type

source_name: pdxJ(WT+)

value: pdxJ(WT+)


title: RBPJ_ChIP-seq in RD1 cells, rep1

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

data_processing:
Quality control of FASTQ files was done using FastQC.
Reads were aligned to the Ensembl  GRCm38 version 92  (mus musculus) genome using Bowtie ( options -k 1 -m 3) 1.1.2
Duplicate reads were removed with Picard's MarkDuplicates function.
Samtools was used to convert aligned reads to BAM format.
For Browser visualization bigwig files with coverage information were generated using deeptools bamCoverage function
Genome_build: GRCm38 version 92 (mus musculus)
Supplementary_files_format_and_content: bigwig files (of coverage) at 25 bp resolution

source_name: RD1 cells

growth_protocol: Mouse RD1 cells were grown at 37°C with 5% CO2 in Pericyte Medium (Sciencell Catalog #1201) using collagen I-coated dishes.

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907)
Library-prep kit: Diagenode MicropPlex Library Preparation kit v2 (C05010012)

treatment_protocol: None.

value: Brain pericytes

value: Anti-RBPJ (Cell Signaling, #5313)


title: RBPJ_ChIP-seq in RD1 cells, rep2


title: H3K4me3_ChIP-seq in RD1 cells, rep2

value: Anti-H3K4me3 (Diagenode, pAb-003-050)


title: LZy14-1


title: H3K4me3_ChIP-seq in RD1 cells, rep1


title: AR005

source_name: PB CD34+ cells_sgKLF6

value: F

value: Peripheral blood (PB)


title: pdxJ_X3plus_vs_pdxJ_WTplus_II_csw

description: Ratio (pdxJ(X3+) / pdxJ(WT+))


title: H3K4me1_ChIP-seq in RD1 cells, rep2

value: Anti-H3K4me1 (Abcam, ab8895)


title: 32C-3

source_name: 32-cell embryo

value: Col

value: 32-cell embryo


title: 32C-2


title: H3K4me1_ChIP-seq in RD1 cells, rep1


title: pdxJ_11plus_vs_pdxJ_11minus_I

description: Ratio (pdxJ(11+) / pdxJ(11-))


title: H3_ChIP-seq in RD1 cells, rep2

value: Anti-histone H3 (Abcam, ab1791)


title: 1C-3

source_name: 1-cell embryo

value: 1-cell embryo


title: H3_ChIP-seq in RD1 cells, rep1


title: 1C-2


title: 32C-1


title: 1C-1


title: Input_ChIP-seq in RD1 cells, rep1


title: Input_ChIP-seq in RD1 cells, rep2


title: CtIP_KO

city: New York

first: Xiaobin

middle: Summer

last: Wang

state: NEW YORK

address: 1130 Siant Nicholas Ave, Room 501

department: Institute for Cancer Genetics

institute: Columbia University Medical Center

data_processing:
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 genome (mm9). The best-path searching algorithm (related to YAHA; ref. 50) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads are then filtered to exclude mispriming events, germ-line (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. To plot all of the S-region junctions, including those in the repeats but unequivocally mapped to an individual switch region, we combined the ones filtered by a mappability filter but unequivocally mapped to S regions with “good” reads passing both the mappability (both deduplicated) filters (please see ref. 28 for simulation and details on plotting). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait and prey-break site. Blunt junctions are considered to have no MHs or insertions.
Mutation rate was calculated by custom Excel integrated VBA script. Mutations were determined by comparing the actual bait sequence of each IgH junction with the germ-line bait sequence based on the IgH sequence from 129/Sv strain (NCBI gene accession no. AJ851868.3). Only true mismatches (no insertion or deletion within 7 nt) were counted as a mutation.
Genome_build: mm9
Supplementary_files_format_and_content: .xlsx files generated from tab-delimited text files after analysis for reads distribution and mutation rates.

source_name: B cells

growth_protocol: Purified splenic B (CD43-) cells from mice carrying preassembled IgH and IgK loci (129Sv background) were cultured in RPMI mediume with cytokines (anti-CD40 (1 ng/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)).

extract_protocol:
Genomic DNA was extracted from day 4 cultured B cells with standard DNA extraction protocol. Basically cells were washed with PBS before lysed overnight with rapid lysis buffer containing 10mM tris PH 7.5, 10mM EDTA PH8.0, 10mM NaCl, 0.5% SDS and 1mg/ml Proteinase K at 56 °C. DNA was precipated from lysed cells with 100% EtOH and washed with 70% EtOH before air dry and re-dissolving by 10mM tris/ 0.1mM EDTA TE buffer.
Libraries were prepared according to protocol in (Hu J, et al. Nat Protoc 11:853–871.(2016)) Linear amplifications were performed using Sμ-specific biotin primer  5′/5BiosG/CAGACCTGGGAATGTATGGT3′) and followed by nesting PCR with (5′CACACAAAGACTCTGGACCTC3′)  AflII is used to remove germ-line sequence.
high-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v

treatment_protocol: Cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

value: anti-CD40 and Il4 activated B cells

value: CD21Cre+ CtIP C/- XRCC4 +/C

tag: strain


title: Zy24-2

source_name: Zygote at 24 HAP

value: 24 HAP

value: Zygote


title: XRCC4_KO

value: CD21Cre+ CtIP +/- XRCC4 C/-


title: CtIP_AA

value: CtIP T855A/T855A


title: Wildtype

value: CD21Cre+ CtIP +/C XRCC4 +/C


title: Zy14-3

source_name: Zygote at 14 HAP

value: 14 HAP


title: Zy14-1

source_name: Zygote at 14 hours after pollination (HAP)


title: DNMT1_siRNA_BS_rep3

city: Gainesville

first: Xiefan

last: Fang

state: Florida

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

data_processing:
The fastq files generated from MiSeq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. A reference genome with the amplicon sequences was built and bisulfite converted in silico with Bismark Bisulfite Mapper. The high quality sequence reads were aligned to the reference genome using Bowtie 2. Cytosine methylation counting was performed with the Bismark methylation extractor.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include percent methylation for each cytosine in the target gene promoters.

source_name: Embryonic cardiomyocyte

growth_protocol: Primary cardiomyocytes were isolated from mouse E13.5 embryonic ventricles. Briefly, hearts were dissected from embryos, and the ventricular tissue from each litter of embryos was pooled and digested with papain solution that contained 4 mg/ml papain, 1.1 mM EDTA, 5.5 mM L-cystein, and 67 mM b-mercaptoethanol dissolved in the Earle’s Balanced Salt Solution. Digestion was terminated with 1 mg/ml soybean trypsin inhibitor solution. Cells were suspended in DMEM supplemented with 10% inactivated fetal bovine serum, 2 mM L-glutamine, and antibiotic/antimycotic solution. Cells were placed in non-coated flasks for 1 h to allow differential attachment to occur. The non-attached cells, which are predominantly cardiomyocytes, were transferred to new flasks coated with 2% gelatin.

extract_protocol:
At 72 h after transfection, cells were released with Accutase (Innovative Cell Technologies, San Diego, CA) and dissociated with Accumax (Innovative Cell Technologies). To sort cardiomyocytes, dissociated cells were stained with anti-VCAM1 antibody conjugated with allophycocyanin (APC; BioLegend, San Diego, CA), followed by magnetic sorting using anti-APC microbeads and magnetic assisted cell sorting (MACS) columns (Miltenyi Biotec, Bergisch Gladbach, Germany). DNA was extracted with the Quick-gDNA™ MicroPrep kit (Zymo Research, Irvine, CA). Genomic DNA was treated with sodium metabisulfite for bisulfite conversion. Bisulfite specific PCR primers for fifteen target genes (two promoter regions per gene) were designed with Methyl Primer Express V1.0 (Thermo Fisher Scientific, Waltham, MA). Target gene regions were PCR-amplified from the bisulfite-converted DNA with ZymoTaq™ PreMix (Hot start DNA taq polymerase, ZYMO Research). The fifteen genes include Myh6, Myh7, Myh7b, Nppa, Nppb, Tnnc1, Tnni3, Tnnt2, Camta1, Camta2, Cdkn1A, Cdkn1B, Cdkn1C, Mef2c, and Mef2d. PCR products were cleaned with the ZR-96 DNA Clean & Concentrator™-5 kit (ZYMO Research). PCR products from the same genomic DNA sample were pooled at equal concentration ratio.
PCR products from the same genomic DNA were made into an indexed sequencing library with the Nextera XT DNA Library Preparation kit and the Nextera XT Index Kit (Illumina). Briefly, amplicon pools were tagmented, PCR-amplified with index primers, and cleaned with AMPure XP beads. The libraries were validated with an Agilent 2200 TapeStation high sensitivity DNA assay and quantitated by a KAPA Library Quantification kit (Illumina platforms; Kapa Biosystems) on a GeneAmp 7300 Real Time PCR (Thermo Fisher Scientific).

treatment_protocol: Cardiomyocytes were cultured for 48 h at 37°C to reach 70-80% confluency. Cells were transfected with either Qiagen FlexiTube GeneSolution (with 4 siRNAs) DNMT1 siRNA (#GS13433) or AllStars negative control siRNA (#1027281) at 12 nM using lipofectamine RNAiMAX (n=3 per treatment).

value: cardiomyocyte

value: embrynoic day 13.5

value: DNMT1 siRNA


title: Zy14-2


title: Zy24-1


title: DNMT1_siRNA_BS_rep2


title: DNMT1_siRNA_BS_rep1


title: 1613_B1_M_28 [CNLX17]

city: saint-genes-champanelle

first: Pierre-Alexis

last: Billa

address: route de theix

department: UMRH

country: France

institute: INRA

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Data were processed using miRDeep2 package (2.0.0.8). The raw reads were firstly trimmed against Illumina adapters, then mapped to the Btau_5.0.1 genome assembly as miRBase v22.1 with the Mapper module.
Precursors and mature miRNAs were identified using the miRDeep2 core module, miRDeep2.pl. Potential miRNAs were annotated accordingly against ortholog miRNAs in goat, sheep and humans (miRBase release 22.1). We used a miRDeep2 score ≥5 as a cut-off threshold.
The normalization and differential expression analysis of the known and predicted miRNAs were conducted with the DESeq2 R package v1.18.1.
Genome_build: Btau_5.0.1
Supplementary_files_format_and_content: tab-delimited text files include raw expression values, normalized values, DESeq2 result for each sample

organism: Bos taurus

source_name: Montbeliarde_mammary gland biopsy

extract_protocol:
total RNA extraction from 30 to 66 g of mammary glande using miRvana kit
Small RNA-Seq librairies were generated from 2000 ng of total RNA using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer's instructions. The protocol takes advantage of the natural structure common to most microRNA molecules that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3' RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5' RNA adapter. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 15 sec at 72oC] x 13 cycles; 10 min at 72oC) to create cDNA constructs. Amplified cDNA constructs of 140 to 160 nt were selectively isolated by acrylamide gel purification followed by ethanol precipitation.  The final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: breed

value: Montbeliarde

value: mammary gland biopsy


title: 1640_B1_M_2 [CNLX19]


title: 9615_B1_M_35 [CNLX15]


title: EC-3

source_name: Egg Cell

value: Col

value: Mature egg cell

value: Egg Cell


title: negative_siRNA_BS_rep3 (2)

value: negative siRNA


title: 2614_B1_M_33 [CNLX23]


title: 2182_B1_H_20 [CNLX9]

source_name: Holstein_mammary gland biopsy

value: Holstein


title: EC-2


title: 5663_B1_M_25 [CNLX13]


title: negative_siRNA_BS_rep2 (2)


title: negative_siRNA_BS_rep1 (2)


title: EC-1


title: 8200_B1_H_26 [CNLX3]


title: 1652_B1_M_15 [CNLX21]


title: 1165_B1_H_1 [CNLX1]


title: 1155_B1_H_27 [CNLX7]


title: 9195_B1_H_3 [CNLX5]


title: sample 78 [Pancreatic cancer]

status: Public on May 11 2019

city: København Ø

first: Mathias

middle: Husted

last: Torp

address: Blegdamsvej 9

department: Genomic Medicine

country: Denmark

institute: Rigshospitalet

hyb_protocol: affymetrix manufactures procedure

scan_protocol: affymetrix manufactures procedure

data_processing: RMA normalization

source_name: tumor biopsy

label_protocol: affymetrix manufactures procedure

extract_protocol: Qiagen manufactures procedure automatized on QiaCube for DNA and RNA isolation. RNA quality and quantity was controled by BioAnalyzer and Nanodrop.

value: tumor biopsy

tag: cancer

value: Pancreatic cancer

tag: mutated gene

value: FANCM

tag: predicted

tag: parp predicted

value: kmeans-2:PARP insensitive


title: sample 77 [Renal cell carcinoma]

value: Renal cell carcinoma


title: sample 92 [Colorectal cancer]

value: Colorectal cancer


title: sample 84 [Ovarian cancer]

value: Ovarian cancer


title: sample 88 [Bile duct cancer]

value: Bile duct cancer


title: sample 72 [Breast cancer]

value: Breast cancer


title: sample 91 [Colorectal cancer]


title: sample 73 [Mesothelioma]

value: Mesothelioma

value: FANCC


title: sample 82 [Neuroendocrine cancer]

value: Neuroendocrine cancer

value: kmeans-2:PARP sensitive


title: sample 74 [Gastric cancer]

value: Gastric cancer


title: sample 87 [Colorectal cancer]

value: ATM


title: sample 79 [Colorectal cancer]

value: FANCA


title: sample 69 [Breast cancer]


title: sample 75 [CUP]

value: CUP


title: sample 85 [Mesothelioma]

value: tumor biopsy

value: XPC


title: sample 80 [Cervical cancer]

value: Cervical cancer


title: sample 81 [NSCLC]

value: NSCLC

value: BLM

value: kmeans-2:PARP insensitive


title: sample 68 [Colorectal cancer]

value: Colorectal cancer


title: sample 86 [vulvovaginal]

value: vulvovaginal


title: sample 71 [Colorectal cancer]


title: sample 67 [Colorectal cancer]


title: sample 64 [Breast cancer]

value: Breast cancer


title: sample 90 [Colorectal cancer]


title: sample 89 [Prostate cancer]

value: Prostate cancer

value: NBN


title: sample 83 [Prostate cancer]


title: sample 66 [Breast cancer]


title: sample 65 [Breast cancer]


title: sample 70 [Renal cell carcinoma]

value: Renal cell carcinoma


title: sample 76 [Colorectal cancer]

value: kmeans-2:PARP sensitive


title: sample 59 [Colorectal cancer]


title: sample 61 [NSCLC]


title: sample 60 [Sarcoma]

value: Sarcoma


title: sample 54 [Mesothelioma]

value: Mesothelioma

value: FANCM


title: sample 56 [Ovarian cancer]

value: Ovarian cancer

value: ATR


title: sample 53 [Pancreatic cancer]

value: tumor biopsy

value: Pancreatic cancer


title: sample 57 [Melanoma]

value: Melanoma


title: sample 48 [Breast cancer]


title: sample 62 [Cervical cancer]

value: Cervical cancer

value: XPC


title: sample 58 [Bile duct cancer]

value: Bile duct cancer

value: kmeans-2:PARP insensitive


title: sample 47 [Others]

value: Others

value: IPMK


title: sample 50 [Breast cancer]

value: Breast cancer


title: sample 45 [Bile duct cancer]

value: ATM


title: sample 40 [Oesophageal cancer]

value: Oesophageal cancer


title: sample 63 [Urothelial cancer]

value: Urothelial cancer


title: sample 49 [Urothelial cancer]

value: kmeans-2:PARP sensitive


title: sample 55 [Colorectal cancer]

value: Colorectal cancer

value: BLM


title: sample 36 [Ovarian cancer]

value: Ovarian cancer


title: sample 52 [Breast cancer]

value: tumor biopsy


title: sample 42 [Colorectal cancer]


title: sample 38 [Colorectal cancer]


title: sample 44 [Thymoma]

value: Thymoma


title: sample 46 [Breast cancer]


title: sample 51 [CUP]

value: CUP

value: RECQL


title: sample 39 [NSCLC]

value: NSCLC


title: sample 41 [Breast cancer]


title: sample 37 [Bile duct cancer]

value: Bile duct cancer


title: sample 43 [Breast cancer]

value: kmeans-2:PARP insensitive


title: sample 35 [NSCLC]


title: sample 34 [Ovarian cancer]


title: sample 32 [Mesothelioma]

value: Mesothelioma

value: FANCA


title: sample 27 [Colorectal cancer]


title: sample 26 [Prostate cancer]

value: Prostate cancer


title: sample 29 [Head and Neck cancer]

value: Head and Neck cancer


title: sample 30 [Sarcoma]

value: Sarcoma


title: sample 31 [Ovarian cancer]


title: sample 28 [Adenoid cystic carcinoma]

value: Adenoid cystic carcinoma


title: sample 23 [Colorectal cancer]


title: sample 22 [Colorectal cancer]


title: sample 25 [Pancreatic cancer]

value: Pancreatic cancer


title: sample 20 [Colorectal cancer]

value: Colorectal cancer


title: sample 21 [Sarcoma]

value: WRN

value: kmeans-2:PARP sensitive


title: sample 18 [Head and Neck cancer]

value: tumor biopsy


title: sample 15 [Cervical cancer]

value: Cervical cancer

value: XPC


title: sample 14 [Mesothelioma]


title: sample 09 [Colorectal cancer]


title: sample 12 [Hepatocellular carcinoma]

value: Hepatocellular carcinoma


title: sample 33 [Pancreatic cancer]


title: sample 19 [Colorectal cancer]


title: sample 17 [Pancreatic cancer]


title: sample 11 [Colorectal cancer]


title: sample 13 [Ovarian cancer]

value: Ovarian cancer


title: sample 07 [Pancreatic cancer]


title: sample 16 [Mesothelioma]


title: sample 24 [Cervical cancer]

value: NBN


title: sample 08 [Melanoma]

value: Melanoma

value: ATM

value: kmeans-2:PARP insensitive


title: Oleic Acid + SPE/PAPE [OS_2]

city: Urbana

first: Zeynep

last: Madak-Erdogan

state: Illinois

address: 1201 W. Gregory Dr, 359 ERML Hall

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Illinois

description:
OS_2
processed data file: deg_OA.txt

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v1.8.4 Conversion Software (Illumina).
FASTQ files were trimmed using FASTQ Trimmer (version 1.0.0). TopHat2 (version 0.5) was employed to map paired RNA-Seq reads to version hg19 of the Homo sapiens reference genome in the UCSC genome browser in conjunction with the RefSeq genome reference annotation. Gene expression values (raw read counts) from BAM files were calculated using the StrandNGS (version 2.1) Quantification tool. Partial reads were considered and the option of detecting novel genes and exons was selected. Default parameters for finding novel exons and genes were specified. The DESeq normalization algorithm using default values was selected. Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene, for each treatment relative to the vehicle control. We considered genes with fold-change >2 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: GRCh37
Supplementary_files_format_and_content: deg_OA.txt: Tab-delimited text file includes gene expressions.

source_name: mammary cells

extract_protocol:
Total RNA was extracted using Trizol reagent and further cleaned using the RNeasy kit (QIAGEN).
The stranded RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'.
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane for 101 cycles on a HiSeq2500 using a TruSeq SBS sequencing kit version 4.

treatment_protocol: MCF-7 cells were treated with Veh (0.1% EtOH), 100 nM oleic acid (OA) in presence or absence of 1 μM PaPE-1 for 24 h.

tag: cell line

tag: cell type

value: breast cancer cell line

value: Oleic Acid + SPE/PaPE


title: sample 06 [Urothelial cancer]

value: Urothelial cancer


title: Oleic Acid/Vehicle [OV_1]

description:
OV_1
processed data file: deg_OA.txt

value: Oleic Acid


title: sample 10 [Breast cancer]

value: Breast cancer


title: sample 03 [Colorectal cancer]

value: Colorectal cancer


title: sample 05 [Mesothelioma]

value: Mesothelioma


title: Oleic Acid/Vehicle [OV_3]

description:
OV_3
processed data file: deg_OA.txt


title: Oleic Acid + SPE/PAPE [OS_3]

description:
OS_3
processed data file: deg_OA.txt


title: Control/Vehicle [CV_1]

description:
CV_1
processed data file: deg_OA.txt

value: Vehicle (ethanol)


title: sample 04 [Bile duct cancer]

value: tumor biopsy

value: Bile duct cancer

value: kmeans-2:PARP sensitive


title: Control/Vehicle [CV_2]

description:
CV_2
processed data file: deg_OA.txt


title: 37Y Female HSCe 38

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: run1407_lane12_read1_indexN707-S507=Jan11_Cell_7

data_processing:
FASTQ sequence files were aligned to the human genome version 19 (hg19) using RSEM.
Single-cell were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using an empirical Bayes moderated t-test p<0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values

source_name: Bone Marrow

extract_protocol:
Single cell CD34+CD38- HSCe were prepared using the C1™ Single-Cell Auto Prep System (Fluidigm, San Fransisco, CA), according to the manufacturer’s instructions. Flow-sorted cells were counted and resuspended at a concentration of 350 cells per mL PBS then loaded onto a primed C1 Single-Cell Auto Prep Integrated Fluidic Chip for mRNA-Seq (5-10 mm).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

treatment_protocol: Miltenyi Automacs Pro separator (Miltenyi, San Diego, CA) was used to enrich bone marrow MNC for CD34+ cells. The CD34+ fraction was then stained with lineage antibodies conjugated to PerCP-Cy™5.5: CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD19, CD20, CD24, CD56, CD66b, Glycophorin A, and CD90-biotin, followed by Streptavidin APC-Cy7, CD123-PE, CD34-APC, CD38-PE-Cy7, and CD45RA-FITC. Cell sorting was performed on a BD FACSAria II with a 100 um nozzle.

value: Lin - CD34+ CD38- Hematopoietic Stem Cell Enriched

tag: donor sex

value: F

tag: donor age


title: 37Y Female HSCe 40

description: run1407_lane12_read1_indexN708-S507=Jan11_Cell_15


title: 37Y Female HSCe 44

description: run1407_lane12_read1_indexN710-S508=Jan11_Cell_24


title: 37Y Female HSCe 43

description: run1407_lane12_read1_indexN709-S508=Jan11_Cell_16


title: 37Y Female HSCe 35

description: run1407_lane12_read1_indexN706-S506=Jan11_Cell_6


title: 37Y Female HSCe 41

description: run1407_lane12_read1_indexN708-S508=Jan11_Cell_8


title: 37Y Female HSCe 29

description: run1407_lane12_read1_indexN705-S502=Jan11_Cell_26


title: 37Y Female HSCe 31

description: run1407_lane12_read1_indexN705-S504=Jan11_Cell_12


title: 37Y Female HSCe 36

description: run1407_lane12_read1_indexN707-S505=Jan11_Cell_21


title: 37Y Female HSCe 37

description: run1407_lane12_read1_indexN707-S506=Jan11_Cell_14


title: 37Y Female HSCe 42

description: run1407_lane12_read1_indexN709-S507=Jan11_Cell_23


title: 37Y Female HSCe 28

description: run1407_lane12_read1_indexN704-S517=Jan11_Cell_25


title: 37Y Female HSCe 39

description: run1407_lane12_read1_indexN708-S506=Jan11_Cell_22


title: 37Y Female HSCe 30

description: run1407_lane12_read1_indexN705-S503=Jan11_Cell_19


title: 37Y Female HSCe 33

description: run1407_lane12_read1_indexN706-S504=Jan11_Cell_20


title: 37Y Female HSCe 32

description: run1407_lane12_read1_indexN705-S505=Jan11_Cell_5


title: 37Y Female HSCe 24

description: run1407_lane12_read1_indexN703-S517=Jan11_Cell_17


title: 37Y Female HSCe 27

description: run1407_lane12_read1_indexN704-S504=Jan11_Cell_4


title: 37Y Female HSCe 26

description: run1407_lane12_read1_indexN704-S503=Jan11_Cell_11


title: 37Y Female HSCe 23

description: run1407_lane12_read1_indexN703-S503=Jan11_Cell_3


title: sample 02 [Colorectal cancer]


title: 37Y Female HSCe 34

description: run1407_lane12_read1_indexN706-S505=Jan11_Cell_13


title: 37Y Female HSCe 20

description: run1407_lane12_read1_indexN702-S502=Jan11_Cell_2


title: 37Y Female HSCe 22

description: run1407_lane12_read1_indexN703-S502=Jan11_Cell_10


title: 37Y Female HSCe 25

description: run1407_lane12_read1_indexN704-S502=Jan11_Cell_18


title: 37Y Female HSCe 18

description: run1405_lane12_read1_indexN712-S504=Grimes_Jan_11_Cell_76


title: 37Y Female HSCe 14

description: run1405_lane12_read1_indexN711-S503=Grimes_Jan_11_Cell_75


title: 37Y Female HSCe 19

description: run1407_lane12_read1_indexN701-S517=Jan11_Cell_1


title: 37Y Female HSCe 17

description: run1405_lane12_read1_indexN712-S503=Grimes_Jan_11_Cell_83


title: 37Y Female HSCe 16

description: run1405_lane12_read1_indexN712-S502=Grimes_Jan_11_Cell_90


title: 37Y Female HSCe 13

description: run1405_lane12_read1_indexN711-S502=Grimes_Jan_11_Cell_82


title: 37Y Female HSCe 10

description: run1405_lane12_read1_indexN709-S517=Grimes_Jan_11_Cell_73


title: sample 01 [Breast cancer]

value: ATR


title: 36Y Female HSCe 86

description: run1907_lane12_read1_indexN712-S507=Oct26_Cell_47


title: 37Y Female HSCe 4

description: run1405_lane12_read1_indexN702-S506=Grimes_Jan_11_Cell_78


title: 37Y Female HSCe 8

description: run1405_lane12_read1_indexN704-S508=Grimes_Jan_11_Cell_80


title: 37Y Female HSCe 3

description: run1405_lane12_read1_indexN702-S505=Grimes_Jan_11_Cell_85


title: 37Y Female HSCe 7

description: run1405_lane12_read1_indexN704-S507=Grimes_Jan_11_Cell_87


title: 37Y Female HSCe 11

description: run1405_lane12_read1_indexN710-S502=Grimes_Jan_11_Cell_74


title: 37Y Female HSCe 6

description: run1405_lane12_read1_indexN703-S507=Grimes_Jan_11_Cell_79


title: 37Y Female HSCe 9

description: run1405_lane12_read1_indexN705-S508=Grimes_Jan_11_Cell_88


title: 37Y Female HSCe 5

description: run1405_lane12_read1_indexN703-S506=Grimes_Jan_11_Cell_86


title: 37Y Female HSCe 12

description: run1405_lane12_read1_indexN710-S517=Grimes_Jan_11_Cell_81


title: 37Y Female HSCe 1

description: run1405_lane12_read1_indexN701-S504=Grimes_Jan_11_Cell_84


title: 37Y Female HSCe 2

description: run1405_lane12_read1_indexN701-S505=Grimes_Jan_11_Cell_77


title: 37Y Female HSCe 21

description: run1407_lane12_read1_indexN702-S517=Jan11_Cell_9


title: 36Y Female HSCe 84

description: run1907_lane12_read1_indexN712-S505=Oct26_Cell_61


title: 36Y Female HSCe 87

description: run1907_lane12_read1_indexN712-S508=Oct26_Cell_40


title: 36Y Female HSCe 80

description: run1907_lane12_read1_indexN711-S505=Oct26_Cell_53


title: 37Y Female HSCe 15

description: run1405_lane12_read1_indexN711-S517=Grimes_Jan_11_Cell_89


title: 36Y Female HSCe 83

description: run1907_lane12_read1_indexN711-S508=Oct26_Cell_32


title: 36Y Female HSCe 85

description: run1907_lane12_read1_indexN712-S506=Oct26_Cell_54


title: 36Y Female HSCe 77

description: run1907_lane12_read1_indexN710-S507=Oct26_Cell_31


title: 36Y Female HSCe 79

description: run1907_lane12_read1_indexN711-S504=Oct26_Cell_60


title: 36Y Female HSCe 78

description: run1907_lane12_read1_indexN710-S508=Oct26_Cell_24


title: 36Y Female HSCe 76

description: run1907_lane12_read1_indexN710-S506=Oct26_Cell_38


title: 36Y Female HSCe 71

description: run1907_lane12_read1_indexN709-S507=Oct26_Cell_23


title: 36Y Female HSCe 70

description: run1907_lane12_read1_indexN709-S506=Oct26_Cell_30


title: 36Y Female HSCe 69

description: run1907_lane12_read1_indexN709-S505=Oct26_Cell_37


title: 36Y Female HSCe 74

description: run1907_lane12_read1_indexN710-S504=Oct26_Cell_52


title: 36Y Female HSCe 82

description: run1907_lane12_read1_indexN711-S507=Oct26_Cell_39


title: 36Y Female HSCe 73

description: run1907_lane12_read1_indexN710-S503=Oct26_Cell_59


title: 36Y Female HSCe 64

description: run1907_lane12_read1_indexN708-S508=Oct26_Cell_8


title: 36Y Female HSCe 68

description: run1907_lane12_read1_indexN709-S504=Oct26_Cell_44


title: 36Y Female HSCe 67

description: run1907_lane12_read1_indexN709-S503=Oct26_Cell_51


title: 36Y Female HSCe 81

description: run1907_lane12_read1_indexN711-S506=Oct26_Cell_46


title: 36Y Female HSCe 75

description: run1907_lane12_read1_indexN710-S505=Oct26_Cell_45


title: 36Y Female HSCe 66

description: run1907_lane12_read1_indexN709-S502=Oct26_Cell_58


title: 36Y Female HSCe 63

description: run1907_lane12_read1_indexN708-S507=Oct26_Cell_15