title: BCL5

description: 10x Genomics

source_name: peBC in engineered lung

value: differentiated cells

value: engineered lung


title: SC55-3.LB17026

status: Public on Feb 12 2020

type: SRA

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

country: USA

institute: The University of Texas MD Anderson Cancer Center

library_source: transcriptomic

data_processing:
Seqeuncing reads were processed using Cell Ranger v2.0 pipeline (10x Genomics)
Genome_build: hg38
Supplementary_files_format_and_content: UMI reads count were calculated by Cell Ranger v2.0

molecule: total RNA

organism: Homo sapiens

growth_protocol: Tumors were grown in mice to between 500-800 mm3

extract_protocol:
Tumors were collected and RNA extracted using Trizol reagent and purified with a Qiagen RNeasy kit
Sequencing library were constructed following 10x Genomics Chromiun v2 library preparation protocol.

treatment_protocol: Mice were untreated

tag: tissue

value: CTC

tag: patient diagnosis

value: small cell lung cancer (SCLC)

tag: treatment

value: cisplatin, relapsed


title: BCO1

status: Public on Feb 20 2020

city: New Haven

first: Allison

middle: M

last: Greaney

state: CT

address: 10 Amistad St

department: Biomedical Engineering

institute: Yale University

description: 10x Genomics

data_processing:
FASTQ read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 30 bp long were discarded.
Downstream processing was conducted with zUMIs v 0.4 (44) with the default parameters; the top 10,000 cell barcodes ranked by reads were output for each sample.
Genome_build: Ensembl Rnor6.0 release 92 was used to align the data to the rat transcriptome.
Supplementary_files_format_and_content: sparse matrix of raw counts
Supplementary_files_format_and_content: barcodes (column names for .mtx file)
Supplementary_files_format_and_content: genelist (rownames for .mtx file)

organism: Rattus norvegicus

source_name: peBC organoids

growth_protocol: Native rat tracheal epithelial scapings (TE1ep) were plated and peBC expanded on collagen-coated TCP using a pharmacologic expansion media (Propagenix)(BCP1, BCP3, BCP6).

extract_protocol:
Samples were rendered to a single cell suspension for sequencing enzymatically using platform-specific protocols (Greaney 2020).
Single-cell libraries were prepared using the standard 10x Genomics v2 processing workflow. Cell loadings were designed to yield 5000-10000 cells per library.
10x genomics standard library preparation. Sequencing on Illumina HiSeq 4000 sequencers, indexed to a depth of 160-220 million reads per library. Read 1 sequencing was 26 bp long, read 2 sequencing was 98 bp long.

treatment_protocol: peBC were differentiated on four in vitro culture platforms, including organoids in matrigel (BCO1), at air-liquid interface (BCALI), in engineered trachea (BCT1), and in engineered lung (BCL5). All differentiation was performed in Propagenix Airway Differentiation Medium (PADM).

tag: group

tag: protocol

value: organoids in matrigel


title: SC55-1.LB17001

value: untreated


title: SC4.LB17013

value: CDX flank


title: BCP1

description: 10x Genomics

source_name: peBC at P1

value: cultured cells

value: collagen-coated TCP using a pharmacologic expansion media (Propagenix)


title: SC49.LB17025


title: SC4.LB17014


title: SC55-2.LB17002

value: cisplatin


title: SC39.LB17020


title: SC4.LB17009


title: SC49.LB17023


title: D5_C

status: Public on Jan 11 2020

city: Ithaca

first: Andrea

middle: J

last: De Micheli

state: NY

address: 161 Weill Hall

institute: Cornell University

data_processing:
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to mm10 using Cell Ranger v2 pipeline (10X Genomics)
Gene expression data was processed with Seurat v2.3.4 (Satija lab) using R  v3.6.2 (2019-12-12)
Initial data filtering (minimum cells to express an included gene = 3, minium genes to be expressed in an included cell = 200)
Filtering by percent mitochondiral genes in included cells (maximum 0.2), number of UMIs in included cells (minimum 1000, maximum 60000), and number of mapped genes in included cells (maximum 8000)
Log-normalization of expression data
Cell annotations in metadata derived from unsupervised clustering in CCA space (CCA coefficients obtained by MultiCCA from Seurat (Satija Lab).
Genome_build: mm10
Supplementary_files_format_and_content: .txt tabulated files of metadata information, normalized gene expression matrix, and raw gene expression matrix

molecule: polyA RNA

organism: Mus musculus

source_name: Tibialis anterior muscle

extract_protocol:
The tibialis anterior muscle was digested into a single-cell suspension in Collagenase D and Dispase II for about 1h, then filtered to remove debris. Red blood cells were lyzed.
Single-cell RNA-sequencing libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v2 kit for all sample except D0_Cv3 with version 3) following the directions of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: age

value: 4 months

tag: Sex

value: M

tag: injury

value: Notexin, day 5 post-injury


title: D2_D

value: F

value: Notexin, day 2 post-injury


title: SC39.LB17018


title: SC39.LB17019


title: SC16.LB17029


title: SC4_LY2606368.LB17003

value: prexasertib, relapsed


title: shLUC-D5-RNA-rep3

status: Public on Jan 01 2020

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: RNA-seq was performed in shLUC condition at day 5 of macrophage differentiation

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (RNA-seq): STAR
alignment (ChIPseq, CUT&RUN, ATAC-seq): BWA
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: DIFFERENTIATING MACROPHAGE

growth_protocol: CD34 were cultured andf differentiated in IMDM, with heatinactivated FBS and  M-CSF. Primary Monocytes were cultured differentiated in IMDM with heat inactivated FBS and 25 ng/ul GM-CSF

extract_protocol: KAPA RNA HyperPrep Kit (Illumina Platforms) from KAPA BIOSYSTEMS

treatment_protocol: M-CSF  14 days (monocyte diff); GM-CSF 5 days (macrophages)

tag: cell type

value: DIFFERENTIATING MACROPHAGE


title: SC49.LB17024


title: SC4_Talazoparib.LB17004

value: talazoparib, relapsed


title: LUM0309: 7289502

status: Public on Jun 13 2020

city: Leiden

first: Pietro

last: Spitali

state: Zuid Holland

address: Postzone S4-P, Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: internal code: LUM0309

data_processing:
Data were aligned with STAR
Expression was quantified with cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: count table

source_name: tibialis anterior muscle

growth_protocol: Mice were fasted for 4-6 hours with access to water before collecing the blood sample. Blood was collected at 6, 12, 18, 24 and 30 weeks of age. About 100μl of blood were collected frmo the tail into RNA protecting tubes. Mice were anaesthetised during blood collection with 2% isoflurane in oxygen and a solution of lidocaine was applied on the tail after the procedure. Mice were sacrificed at 30 weeks of age when the tibialis anterior muscle was also collected.

extract_protocol:
Total RNA was purified from blood using the Rneasy Protect Animal blood kit and the globin mRNA content was reduced using the globin clear kit. Muscle RNA was purified with Tripure reagent.
Trueseq v2 paired end sequencing

tag: genotype/variation

value: WT

value: tibialis anterior muscle

tag: mouse id

tag: sample type

tag: origin

value: total RNA

tag: week

tag: weight before fasting (g)

tag: weight after fasting (g)

tag: time food removed

tag: time collection


title: SC16.LB17028

tag: tissue

tag: patient diagnosis

value: small cell lung cancer (SCLC)

tag: treatment


title: EGR1_M14_CUTRUN

description: EGR1 CUT&RUN was performed on differentiating CD34 into monocytes (day 14)

library_source: genomic

molecule: genomic DNA

source_name: DIFFERENTIATING MONOCYTES

extract_protocol: NEBNext ChIP-Seq ULTRAII DNA Sample Prep Kit (New England Biolabs, inc.)

value: DIFFERENTIATING MONOCYTES

tag: chip antibody

value: EGR1 BETHYL RABBIT POLICLONAL A303


title: EGR1_CD34_CUTRUN

description: EGR1 CUT&RUN was performed on CD34+ cells

source_name: CD34+ cells

value: CD34+ cells


title: shEGR1-D5-RNA-rep3

description: RNA-seq was performed in shEGR1 condition at day 5 of macrophage differentiation


title: EGR1_M5_CUTRUN

description: EGR1 CUT&RUN was performed on differentiating CD34 into monocytes (day 5)


title: 1295 LSK CTCF

status: Public on Jan 08 2020

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

data_processing:
Illumina's bcl2fastq2 to generate fastq files
Mapping to reference genome with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2  --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs)
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from Macs
Supplementary_files_format_and_content: broadpeak, peaks from Macs

source_name: bone marrow

extract_protocol:
Lysates were clarified from sonicated nuclei and CTCF-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying TruSeq ChIP-seq Sample Preparation Kit. (Part#  IP-202-1012). In brief, ChIP-enriched, fragmented DNA was subjected to end repair to generate blunt-end double stranded DNA, adenylation of 3’ ends, and adaptor ligation. Following ligation, SPRIselect (Beckman Coulter) beads were used at 0.9X and 0.6X for left and right side selection, respectively, to obtain an average library target size of ~300 bp. After size selection, fragments were amplified for 16 cycles, and PCR products were purified using Agencourt AMPureXP beads (Beckman Coulter).

tag: chip ab

tag: strain

tag: developmental stage

value: adult

tag: cell isolation markers

value: Lin-, Sca1+, cKit+


title: RNA-SEQ-MACROD5-shEGR1-rep1

description: RNA-seq was performed in shLUC condition in differentiated macrophages (day 5 of GM-CSF treatment)

data_processing:
Image analysis:: Firecrest (Illumina pipeline 1.9, default parameters)
base calling:: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (RNA-seq): STAR
alignment (ChIPseq, CUT&RUN, ATAC-seq): BWA
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

growth_protocol: Monocytes were cultured differentiated in IMDM with heat inactivated FPS and 25 ng/ul GM-CSF

treatment_protocol: GM-CSF 25 ng/ul 5 days

tag: cell type


title: 1296 LSK input


title: H3K27ac-MACROD5-shLUC

description: H3K27ac condition was performed in shLUC condition in differentiated macrophages (day 5 of GM-CSF treatment)

value: ABCAM Rabbit polyclonal AB4729


title: D5_B

tag: genotype

tag: age

value: 4 months

tag: Sex

tag: injury


title: WT_CTRL_RNA_D7-rep2

description: RNA-seq was performed in shLUC condition with no LPS treatment in differentiated macrophages


title: WT_LPS_RNA_D7-rep2

description: RNA-seq was performed in shLUC condition with LPS treatment in differentiated macrophages


title: WT_CTRL_RNA_D7-rep1

value: shLUC condition with no LPS treatment in differentiated macrophages


title: FLAG_EGR1_CTRL_RNA_D7-rep1

description: RNA-seq was performed in shEGR1 condition with no LPS treatment in differentiated macrophages

source_name: DIFFERENTIATED MACROPHAGE

value: DIFFERENTIATED MACROPHAGE


title: WT_LPS_RNA_D7-rep1

value: shLUC condition with LPS treatment in differentiated macrophages


title: RNA-SEQ-MACROD5-shLUC-rep1

description: RNA-seq was performed in shEGR1 condition in differentiated macrophages (day 5 of GM-CSF treatment)


title: FLAG_EGR1_CTRL_RNA_D7-rep2

description: RNA-seq was performed in  shEGR1 condition with no LPS treatment in differentiated macrophages


title: EGR1-MACRO-D1

description: EGR1 CHIP-seq was performed in differentiating macrophages (day 1 of GM-CSF treatment)


title: EGR1-MACRO-D2

description: EGR1 CHIP-seq was performed in differentiating macrophages (day 2 of GM-CSF treatment)


title: EGR1-MONO

description: EGR1 CHIP-seq was performed in primary monocytes

source_name: PRIMARY-MONOCYTE

value: PRIMARY-MONOCYTE

value: primary monocytes


title: EGR1-MACRO-D4

description: EGR1 CHIP-seq was performed in differentiating macrophages (day 4 of GM-CSF treatment)

value: DIFFERENTIATING MACROPHAGE


title: EGR1_M3_CUTRUN

description: EGR1 CUT&RUN was performed on differentiating CD34 into monocytes (day 3)


title: FLAG_EGR1_LPS_RNA_D7-rep2

description: RNA-seq was performed in  shEGR1  condition with LPS treatment in differentiated macrophages


title: FLAG_EGR1_LPS_RNA_D7-rep1

description: RNA-seq was performed in  shEGR1 condition with LPS treatment in differentiated macrophages


title: EGR1-MACRO-D3

description: EGR1 CHIP-seq was performed in differentiating macrophages (day 3 of GM-CSF treatment)


title: 29-6T-AD-Input

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Reads were mapped to the reference human genome assembly GRCh37/hg19 using Bowtie v1.1.1 allowing up to two mismatches per sequencing tag (parameters -m 1 --best). Reads mapped to mitochondria or ENCODE blacklist regions were removed from downstream analysis.
Peaks were detected using MACS2 (broad peaks; FDR < 10e-2) for each histone mark and each individual patient, with treatment-matched input tags as control.
Tags pileup profiles (bedgraph files) were generated during MACS2 peak calling process to visualize signal per million reads (RPM). Treatment-matched input signal was subtracted from the pileup profiles using MACS2 (“bdgcmp”). Finally, bigwig files were generated using UCSC toolkit (“bedGraphToBigWig”).
Genome_build: hg19
Supplementary_files_format_and_content: enrichment regions in bed format and read pileup in bigwig format

source_name: Frozen postmortem brain tissue

extract_protocol:
Nuclei were isolated from 200 mg frozen brain tissue by dounce homogenization in nuclei isolation buffer followed by ultracentrifugation on a 1.8 M sucrose cushion. Nuclei pellets were resuspended and crosslinked in 1% formaldehyde for 10 min at RT, quenched with 125 mM glycine for 5 min and washed twice in cold PBS. 2 x 106 nuclei were lysed in nuclei lysis buffer and chromatin was sheared using a Covaris S220 sonicator to a final ~250 bp. Equal aliquots of sonicated chromatin were used per immunoprecipitation (IP) reaction with antibody (either H3K27ac, or H3K9ac or H3K122ac or H3K4em1) preconjugated to Protein G Dynabeads. 10% of each IP was used for the Inputs. ChIP reactions were incubated overnight at 4°C followed by ChIP washes and DNA was eluted in elution buffer (1% SDS, 50 mM Tris-HCl pH 8, 10 mM EDTA) at 65°C. Eluted DNA from ChIP and Input samples was reverse crosslinked and purified using PCR columns (Qiagen).
Sequencing libraries for ChIP experiments were prepared using NEBNext Ultra II reagents (New England Biolabs). All ChIP samples and Input were single-end sequenced on an Illumina NextSeq 500.

tag: disease state

value: AD

value: Lateral temporal lobe

value: input


title: ATAC-SEQ-MONO

description: ATAC-seq was performed in primary monocytes

extract_protocol: NextERA Illumina ATAC-seq kit


title: CHD4-MACRO-D4-rep2

description: CHD4 CHIP-seq was performed in differentiating macrophages (day 4 of GM-CSF treatment)

value: ABCAM Rabbit polyclonal AB72418


title: CHD4-MACRO-D4-rep1

value: differentiating macrophages (day 4 of GM-CSF treatment)


title: 25-5T-AD-Input


title: EGR1-MACRO-D4-CUTRUN

description: EGR1 CUT&RUN was performed in differentiating macrophages (day 4 of GM-CSF treatment)

data_processing:
Library strategy: CUT&RUN
Image analysis:: Firecrest (Illumina pipeline 1.9, default parameters)
base calling:: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (RNA-seq): STAR
alignment (ChIPseq, CUT&RUN, ATAC-seq): BWA
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

extract_protocol: Protocol as in Skene et al. 2018 (Nature Protocols)

value: EGR1 BETHYL RABBIT POLICLONAL A303


title: 31-7T-AD-Input


title: H3K27ac-MACROD5-shEGR1

description: H3K27ac condition was performed in shEGR1 condition in differentiated macrophages (day 5 of GM-CSF treatment)


title: 28-8T-AD-Input


title: 22-2T-AD-Input


title: ATAC-SEQ-MACRO

description: ATAC-seq was performed in  differentiating macrophages (day 4 of GM-CSF treatment)


title: 20-1T-AD-Input


title: 24-3T-AD-Input


title: 11-10T-Old-Input

value: Old


title: 13-11T-Old-Input


title: 27-5A-AD-H3K4me1

value: H3K4me1 - Abcam #8895


title: 15-13T-Old-Input


title: 28-8T-AD-H3K4me1


title: 26-3A-AD-H3K4me1


title: 1-15T-Young-Input

value: Young


title: 5-18T-Young-Input


title: 3-17T-Young-Input


title: 29-6T-AD-H3K4me1


title: 31-7T-AD-H3K4me1


title: 18-10A-Old-H3K4me1


title: 17-9A-Old-H3K4me1


title: 16-14T-Old-H3K4me1


title: 22-2T-AD-H3K4me1


title: 25-5T-AD-H3K4me1


title: 24-3T-AD-H3K4me1


title: 20-1T-AD-H3K4me1


title: 15-13T-Old-H3K4me1


title: 23-2A-AD-H3K4me1


title: 21-1A-AD-H3K4me1


title: 7-19T-Young-Input


title: 19-11A-Old-H3K4me1


title: 10-8A-Old-H3K4me1


title: 16-14T-Old-Input


title: 7-19T-Young-H3K4me1


title: 11-10T-Old-H3K4me1


title: 13-11T-Old-H3K4me1


title: 8-15A-Young-H3K4me1


title: 9-16A-Young-H3K4me1


title: 4-13A-Young-H3K4me1


title: 3-17T-Young-H3K4me1


title: 5-18T-Young-H3K4me1


title: 14-7A-Old-H3K4me1


title: 31-7T-AD-H3K122ac


title: 21-1A-AD-H3K122ac


title: 27-5A-AD-H3K122ac


title: 1-15T-Young-H3K4me1


title: 22-2T-AD-H3K122ac


title: 12-6A-Old-H3K4me1


title: 20-1T-AD-H3K122ac


title: 19-11A-Old-H3K122ac


title: 17-9A-Old-H3K122ac


title: 25-5T-AD-H3K122ac


title: 26-3A-AD-H3K122ac


title: 28-8T-AD-H3K122ac


title: 23-2A-AD-H3K122ac


title: 15-13T-Old-H3K122ac


title: 16-14T-Old-H3K122ac


title: 14-7A-Old-H3K122ac


title: 12-6A-Old-H3K122ac


title: 9-16A-Young-H3K122ac


title: 10-8A-Old-H3K122ac


title: 5-18T-Young-H3K122ac


title: 6-14A-Young-H3K122ac


title: 6-14A-Young-H3K4me1


title: 8-15A-Young-H3K122ac


title: 3-17T-Young-H3K122ac


title: 4-13A-Young-H3K122ac


title: 11-10T-Old-H3K122ac


title: 1-15T-Young-H3K122ac


title: 28-8T-AD-H3K27ac

value: H3K27ac - Abcam #4729


title: 26-3A-AD-H3K27ac


title: 24-3T-AD-H3K27ac


title: 27-5A-AD-H3K27ac


title: 22-2T-AD-H3K27ac


title: 18-10A-Old-H3K122ac


title: 13-11T-Old-H3K122ac


title: 31-7T-AD-H3K27ac


title: 25-5T-AD-H3K27ac


title: 21-1A-AD-H3K27ac


title: 16-14T-Old-H3K27ac


title: 20-1T-AD-H3K27ac


title: 29-6T-AD-H3K27ac


title: 14-7A-Old-H3K27ac


title: 13-11T-Old-H3K27ac


title: 19-11A-Old-H3K27ac


title: 7-19T-Young-H3K122ac


title: 18-10A-Old-H3K27ac


title: 12-6A-Old-H3K27ac


title: 11-10T-Old-H3K27ac


title: 17-9A-Old-H3K27ac


title: 7-19T-Young-H3K27ac


title: 15-13T-Old-H3K27ac


title: 6-14A-Young-H3K27ac


title: 9-16A-Young-H3K27ac


title: 23-2A-AD-H3K27ac


title: 5-18T-Young-H3K27ac


title: 10-8A-Old-H3K27ac


title: 8-15A-Young-H3K27ac


title: 28-8T-AD-H3K9ac

value: H3K9ac - Active Motif #39137


title: 4-13A-Young-H3K27ac


title: 31-7T-AD-H3K9ac


title: 1-15T-Young-H3K27ac


title: 2-12A-Young-H3K27ac


title: 23-2A-AD-H3K9ac


title: 25-5T-AD-H3K9ac


title: 27-5A-AD-H3K9ac


title: 15-13T-Old-H3K9ac


title: 19-11A-Old-H3K9ac


title: 29-6T-AD-H3K9ac


title: 26-3A-AD-H3K9ac


title: 12-6A-Old-H3K9ac


title: 24-3T-AD-H3K9ac


title: 22-2T-AD-H3K9ac


title: 3-17T-Young-H3K27ac


title: 8-15A-Young-H3K9ac


title: 13-11T-Old-H3K9ac


title: 17-9A-Old-H3K9ac


title: 16-14T-Old-H3K9ac


title: 18-10A-Old-H3K9ac


title: 20-1T-AD-H3K9ac


title: 14-7A-Old-H3K9ac


title: 10-8A-Old-H3K9ac


title: 11-10T-Old-H3K9ac


title: 9-16A-Young-H3K9ac


title: 4-13A-Young-H3K9ac


title: 3-17T-Young-H3K9ac


title: 2-12A-Young-H3K9ac


title: Dnmt3a_cKO_4122_bs

status: Public on Nov 26 2019

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

data_processing:
Raw FASTQ files were trimmed with Trim Galore, using a quality filter of 20, then rRNA sequences were filtered out using Bowtie, using rRNA sequences from Mus Musculus obtained from the NCBI sequence database (see Key Resources Table). The unaligned reads from this step were then aligned to mm9 using STAR (Dobin et al., 2013), using the default parameters. Reads mapping to multiple regions in the genome were then filtered out, and uniquely mapping reads were converted to BED files. Intronic and exonic reads were then separated. To do this, splice-site reads were first filtered out of the BED read files, then reads that mapped entirely within exons were added to the splice-site reads to make the exonic read file. All remaining reads that overlapped introns were considered intronic reads. Finally, reads were assigned to genes using bedtools coverage -counts.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file of all Cs in the genome covered at least once in the sample. 4th column gives the context of the methyl base, 5th column is the number of Cs mapping to C (indicating a methylated base) at that position, and the 6th column is the number of bases mapping to Cs or Ts (representing coverage).

source_name: Cortex nucleus

growth_protocol: Brain tissue was taken from MeCP2 knockout, overexpression, and wild-type mice maintained under standard housing conditions.

extract_protocol:
Cerebral cortex 7-10 weeks of age was dissected on ice in phosphate buffer saline. The tissue was flash-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from 1/16th of a whole cortex using RLT buffer following RNeasy Micro Kit (Qiagen). Nuclear RNA was isolated following a modified version of the protocol described by Mo et al., 2015. Briefly, half of a cortex was homogenized in 0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH using a glass dounce homogenizer. Nuclei were isolated via centrifugation at 10,000g for 18 minutes at 4°C (Sorvall HB-4) by pelleting through a 30% iodixanol density gradient (Sigma D1556). RNA was isolated from nuclei by resuspending pellet in RLT buffer following the RNeasy Micro Kit (Qiagen).
RNA libraries were generated from 250ng total and nuclear RNA with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) using a modified amplification protocol (37°C, 15 minutes; 98°C, 30 seconds; (98°C, 10 seconds; 65°C, 30 seconds; 72°C, 30 seconds)x13; 72°C, 5 minutes; 4°C hold. RNA libraries were pooled at a final concentration of 8-10nM
RNA was sequenced using Illumina HiSeq 2500 or 3000 with the Genome Technology Access Center (GTAC) at Washington University in St. Louis, typically yielding 20-30 million single-end reads per sample.

value: Baf53B Conditional knock-out

value: Male

value: 7-8 weeks


title: Dnmt3a_cKO_9_bs

value: Female


title: 21-1A-AD-H3K9ac


title: Dnmt3a_cKO_4755_bs


title: 1-15T-Young-H3K9ac


title: 5-18T-Young-H3K9ac


title: siNT_HCMV_1

status: Public on Oct 02 2019

city: Princeton

first: Thomas

last: Shenk

state: New Jersey

address: 119 Lewis Thomas Laboratory, Washington Road

department: Molecular Biology

institute: Princeton University

data_processing:
Illumina Casava1.8+ software used for basecalling.
Barcode-split data was analyzed using Galaxy. RNA STAR aligner was used to map reads to the genome.
Counts for genes were obtained using featureCounts application from subread package
Differential expression was computed using the DESeq2 package.
Genome_build: Human and HCMV fasta and annotation (.gtf) files were created for mapping by combining sequences and annotations from Ensembl annotation, build 38 and TB40 (KF297339).
Supplementary_files_format_and_content: tab-delimited text files include raw counts and expression for each sample

source_name: CMV infected fibroblasts

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were transfected with siRNAs 24h before infection. Cells were infected at MOI of 3.

tag: transfection

value: siNT

value: human lung fibroblasts

tag: cell line

value: HFF

tag: passage

tag: infection

value: CMV/TB40 strain

tag: virus accession number


title: siP2Y2_mock_2

source_name: mock infected fibroblasts

value: mock


title: Dnmt3a_cKO_4965_bs


title: siP2Y2_HCMV_2


title: Dnmt3a_cKO_4757_bs


title: siP2Y2_mock_1


title: siP2Y2_HCMV_1


title: siNT_mock_2


title: 6-14A-Young-H3K9ac

tag: tissue

value: Lateral temporal lobe


title: 7-19T-Young-H3K9ac

tag: chip antibody


title: LuCaP_173_2_s2_ET292

status: Public on Jul 17 2019

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LuCaP 173.2 PDX tumor

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X. For PDX samples, sequences aligning to the mm10 mouse genome deriving from potential contamination with mouse tissue were removed from the analysis as previously described (PMID: 24278200.)
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 173.2 PDX tumor

growth_protocol: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice (PMID: 28156002).

extract_protocol:
Total RNA was isolated from 98 CRPC metastases frozen in Optimal Cutting Temperature compound (OCT; Tissue-Tek) from 55 patients with RNA STAT-60 (Tel-Test). Using an H&E stained slide for each metastatic site for orientation, one millimeter core punches of tumor were obtained, or where appropriate multiple sections enriched for tumor were cut using a Leica CM3050S cryostat. Total RNA was isolated from flash frozen LuCaP xenograft tissue or cell lines with RNA STAT-60 (Tel-Test) followed by purification with RNeasy Mini Kit (Qiagen) utilizing the manufacturer’s recommended in solution DNase digestion (Qiagen).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol. Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

tag: gender

value: male

value: prostate cancer

tag: molecular phenotype


title: LuCaP_173_1_s6_ET289

description: LuCaP 173.1 PDX tumor

source_name: LuCaP 173.1 PDX tumor


title: LuCaP_173_2_s2_ET223

description: LuCaP 173.2 PDX tumor


title: siNT_HCMV_2


title: LuCaP_147CR_s3

description: LuCaP 147CR PDX tumor

source_name: LuCaP 147CR PDX tumor


title: siNT_mock_1


title: LuCaP_173_1_s6_ET222

description: LuCaP 173.1 PDX tumor


title: LuCaP_147CR_s23n2_ET2390

description: LuCaP 147CR PDX tumor


title: LuCaP_145_2_p9s26n3

description: LuCaP 145.2 PDX tumor

source_name: LuCaP 145.2 PDX tumor


title: LuCaP_145_2_p9s25n3

description: LuCaP 145.2 PDX tumor


title: LuCaP_145_1_p2s18n5

description: LuCaP 145.1 PDX tumor

source_name: LuCaP 145.1 PDX tumor


title: LuCaP_145_1_p25s19n5

description: LuCaP 145.1 PDX tumor


title: Dnmt3a_cKO_6_bs

tag: strain


title: LuCaP_136CR_s4_2

description: LuCaP 136CR PDX tumor

source_name: LuCaP 136CR PDX tumor


title: LuCaP_105CR_s7

description: LuCaP 105CR PDX tumor

source_name: LuCaP 105CR PDX tumor


title: LuCaP_93_p39s31n6

description: LuCaP 93 PDX tumor

source_name: LuCaP 93 PDX tumor


title: LuCaP_93_p39s22n6

description: LuCaP 93 PDX tumor


title: LuCaP_96CR_s40n1_ET1784

description: LuCaP 96CR PDX tumor

source_name: LuCaP 96CR PDX tumor


title: LuCaP_136CR_s4_1

description: LuCaP 136CR PDX tumor


title: LuCaP_105CR_s11_ET78

description: LuCaP 105CR PDX tumor


title: LuCaP_70CR_s3

description: LuCaP 70CR PDX tumor

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X.  For PDX samples, sequences aligning to the mm10 mouse genome deriving from potential contamination with mouse tissue were removed from the analysis as previously described (PMID: 24278200.)
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 70CR PDX tumor


title: LuCaP_96CR_s41n1_ET2411

description: LuCaP 96CR PDX tumor


title: LuCaP_73CR_s4n1_020713

description: LuCaP 73CR PDX tumor

source_name: LuCaP 73CR PDX tumor


title: LuCaP_73CR_s9n1_ET2068

description: LuCaP 73CR PDX tumor


title: LuCaP_96CR_s39n1_ET1173

description: LuCaP 96CR PDX tumor


title: LuCaP_78CR_s2

description: LuCaP 78CR PDX tumor

source_name: LuCaP 78CR PDX tumor


title: LuCaP_81CR_s5

description: LuCaP 81CR PDX tumor

source_name: LuCaP 81CR PDX tumor


title: LuCaP_77CR_s18n2_ET414

description: LuCaP 77CR PDX tumor

source_name: LuCaP 77CR PDX tumor


title: LuCaP_77CR_s18n2_ET232

description: LuCaP 77CR PDX tumor


title: LuCaP_70CR_s6

description: LuCaP 70CR PDX tumor


title: LuCaP_23.1CR3_s7_ET1838

description: LuCaP 23.1CR3 PDX tumor

source_name: LuCaP 23.1CR3 PDX tumor


title: LuCaP_35CR_s54

description: LuCaP 35CR PDX tumor

source_name: LuCaP 35CR PDX tumor


title: LuCaP_35CR_s59n1

description: LuCaP 35CR PDX tumor


title: Liver_control_110d_female_5

status: Public on Jun 25 2019

city: Mexico

first: CONSUELO

last: LOMAS

state: MEXICO

address: Vasco de Quiroga 15, Belisario Domínguez Sección XVI,

department: REPRODUCTIVE BIOLOGY

country: Mexico

institute: INCMNSZ

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_49
Control 5 female

data_processing:
Libraries were normalized to 10 nM and were diluted/denatured to 20 pM before loading on the cBot 2X100 Paired end sequencing was performed on the Illumina HiSeq 2500 sequencer.
Output demultiplexed reads were exported to Partek Flow for analysis.
Read FASTQ files were quality trimmed to Phred 30 at each end.
Trimmed reads were aligned to the Rattus norvegicus genomic reference (RGSC 5.0/rn5) with STAR aligner v2.3.1j.
Gene and transcript abundance were quantified against rn5 RefSeq annotation and normalized for transcript abundance for all samples as a dataset using RPKM.
Genome_build: RGSC 5.0/rn5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

extract_protocol:
F1 liver tissue samples (10-20 mg) were homogenized with the BioSpec BeadBeater and RNA was extracted using the QIagen miRNeasy mini kit (Qiagen), according to the manufacturer’s instructions for n= 6 controls and n= 5 MO for each sex. RNA isolated quantity and quality were determined by using a Nanodrop spectrophotometer (Nanodrop Technologies, DE, USA) and stored at -80°C until use.
cDNA libraries were prepared from 1 μg total RNA using an Illumina TruSeq RNA LS Sample Preparation kit v2 according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). Final individual cDNA libraries were assessed for quality and fragment size using the Agilent DNA 1000. Sequencing libraries were quantified with KAPA Library Quantification kit for Illumina platforms.

value: Wistar

tag: maternal diet

value: control (C) diet

value: post natal day 110

value: female

value: liver


title: LuCaP_23.1CR3_s10_ET2785

description: LuCaP 23.1CR3 PDX tumor

tag: cell type


title: Liver_control_110d_female_6

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_50
Control 6 female


title: LuCaP_78CR_s5

description: LuCaP 78CR PDX tumor


title: LuCaP_81CR_s9_ET1092

description: LuCaP 81CR PDX tumor


title: LuCaP_23.1CR3_s9_ET2651

description: LuCaP 23.1CR3 PDX tumor


title: Liver_control_110d_female_1

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_44
Control 1 female


title: Liver_control_110d_female_2

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_46
Control 2 female


title: Liver_control_110d_female_4

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_48
Control 4 female


title: Liver_control_110d_male_6

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_56
Control 6 male


title: Liver_control_110d_female_3

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_47
Control 3 female


title: Liver_control_110d_male_5

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_45
Control 5 male


title: Liver_control_110d_male_4

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_34
Control 4 male


title: Liver_control_110d_male_2

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_12
Control 2 male


title: Liver_control_110d_male_3

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_23
Control 3 male


title: Liver_control_110d_male_1

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_1
Control 1 male


title: LuCaP_35CR_s37

description: LuCaP 35CR PDX tumor


title: Dropseq_1

status: Public on Apr 23 2019

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

description: Drop-seq

data_processing:
The Drop-seq core computational pipeline was used for processing next generation sequencing reads of the scRNA-seq data, as previously described (Pubmed ID: 26000488).
Genome_build: hg19
Supplementary_files_format_and_content: Raw count matrix from Drop-seq experiments with 16327 genes and 10360 cells in R data object (sparse matrix) and csv format.

source_name: Parenchymal lung tissue

extract_protocol:
For each sample, 1-1.5 g of tissue was homogenized by mincing with scissors into smaller pieces (~0.5 mm2/piece). Prior to tissue digestion, lung homogenates were cleared from excessive blood by addition of 35 ml of ice-cold PBS, followed by gentle shaking and tissue collection using a 40μm strainer. The bloody filtrate was discarded. The tissue was transferred into 8 ml of enzyme mix consisting of dispase (50 caseinolytic U/ml), collagenase (2 mg/ml), elastase (1 mg/ml), and DNase (30 µg/ml) for mild enzymatic digestion for 1 hour at 37°C while shaking. Enzyme activity was inhibited by adding 5 ml of PBS supplemented with 10% FCS. Dissociated cells in suspension were passed through a 70μm strainer and centrifuged at 300g for 5 minutes at 4°C. The cell pellet was resuspended in 3 ml of red blood cell lysis buffer and incubated at room temperature for 2 minutes to lyse remaining red blood cells. After incubation, 10 ml of PBS supplemented with 10% FCS was added to the suspension and the mix was centrifuged at 300g for 5 minutes at 4°C. The cells were taken up in 1 ml of PBS supplemented with 10% FCS, counted using a Neubauer chamber and critically assessed for single cell separation. Dead cells were counted to calculate the overall cell viability, which needed to be above 85% to continue with Drop-Seq. 250,000 cells were aliquoted in 2.5 ml of PBS supplemented with 0.04% of bovine serum albumin and loaded for Drop-Seq at a final concentration of 100 cells/μl.
Drop-seq experiments were performed largely as described previously (Pubmed ID: 26000488) with few adaptations during the single cell library preparation. Briefly, using a microfluidic polydimethylsiloxane (PDMS) device (Nanoshift), single cells (100/µl) from the lung cell suspension were co-encapsulated in droplets with barcoded beads (120/µl, purchased from ChemGenes Corporation, Wilmington, MA) at rates of 4000 µl/hr. Droplet emulsions were collected for 15 min/each prior to droplet breakage by perfluorooctanol (Sigma-Aldrich). After breakage, beads were harvested and the hybridized mRNA transcripts reverse transcribed (Maxima RT, Thermo Fisher). Unused primers were removed by the addition of exonuclease I (New England Biolabs), following which beads were washed, counted, and aliquoted for pre-amplification (2000 beads/reaction, equals ~100 cells/reaction) with 12 PCR cycles (primers, chemistry, and cycle conditions identical to those previously described. PCR products were pooled and purified twice by 0.6x clean-up beads (CleanNA). Prior to tagmentation, cDNA samples were loaded on a DNA High Sensitivity Chip on the 2100 Bioanalyzer (Agilent) to ensure transcript integrity, purity, and amount. For each sample, 1 ng of pre-amplified cDNA from an estimated 1000 cells was tagmented by Nextera XT (Illumina) with a custom P5 primer (Integrated DNA Technologies). Single cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq4000 using 0.2 nM denatured sample and 5% PhiX spike-in. For priming of read 1, 0.5 µM Read1CustSeqB (primer sequence: GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC) was used.

value: Parenchymal lung tissue

tag: smoker

value: yes, >100py

tag: segment

value: lower lobe, left

tag: number of cells


title: Dropseq_4

description: Drop-seq

value: Male

tag: age

value: yes, >60py

value: upper lobe, left


title: Dropseq_3

description: Drop-seq

value: no

value: main bronchus


title: Dropseq_2

description: Drop-seq

value: yes, 45py


title: 192_ET: ECFC1_etop_induced

status: Public on Mar 27 2019

type: RNA

city: Belfast

first: Kiran

middle: John

last: Mcloughlin

address: Jubilee Road

department: Centre for Experimental Medicine

institute: Queen's University Belfast

hyb_protocol: The labeled cRNAs were hybridised onto the Human LncRNA Array v4.0 (8 x 60K, Arraystar).

scan_protocol: After washing the slides, the arrays were scanned by the Agilent Scanner G2505C. Agilent Feature Extraction software (version 11.0.1.1) was used to analyse the acquired array images.

data_processing: Quantile normalisation and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalisation of the raw data, mRNAs that at least 3 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: ECFC exposed to etoposide

label_protocol: The sample preparation and microarray hybridisation were performed based on the manufacturer’s standard protocols with minor modifications. Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

growth_protocol: ECFCs were grown in EGM-2 (Lonza) supplemented with 10% FBS (Invitrogen) and allowed to reach confluency before treatment. Cells were passaged following defined treatment protocols to allow senescence induction to take hold, before cells were lysed and homogenised using 700uL of Qiazol (Qiagen)

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (Qiagen) following manufacturers protocol. Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis and Agilent 2100 Bioanalyzer. For microarray analysis, Agilent Array platform was employed.

treatment_protocol: Confluent ECFCs were exposed to one of the following treatments: A. 10gy X-ray, four days recovery, passaging, RNA extraction 4 days post-passage. B. 1uM Etoposide for four days, four days recovery, passaging, RNA extraction 4 days post-passage. C. ECFCs were passaged until Hayflick limit was reached/cells exhausted their replicative potential. RNA was then extracted.

value: Umbilical Cord Blood

tag: treatment

value: 1uM Etoposide

value: ECFCs


title: 193F_LP: ECFC2_late_passage

source_name: ECFC in late passage

value: Late/Serial Passaging


title: SKOV3ip1_DKC1_KD_s2_n2

status: Public on Feb 21 2019

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: Quebec

address: 3201 Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

description:
cDNA library produced with TGIRT
TPM_matrix_all_datasets.csv

data_processing:
Fastq files were checked for quality using FastQC and trimmed using Trimmomatic (Bolger et al. 2014) (parameters: TRAILING:30, LEADING:30, MINLEN:20) to remove Illumina sequencing adapters and portions of reads of low quality.
Reads were aligned using STAR with parameters optimized for the alignment of multi-mapped reads (parameters: --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --outFilterMultimapNmax 100, --winAnchorMultimapNmax 100, --alignEndsProtrude 5, ConcordantPair). The reference genome used was hg38 and the reference annotation to build the STAR alignment index was taken from Ensembl (v87).
Gene expression estimation in CPM and TPM was produced with CoCo (v 0.2.1p4) to optimize the quantification of small non-coding RNAs (parameters: -c both). The annotation provided to CoCo was the Ensembl (v87) annotation bonified with the 115 new sncRNA gene entries as well as the tRNAs from GtRNAdb (PMID: 26673694) and modified through the use of the CoCo correct annotation module (default parameters).
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated-value (csv) file holding the name of every gene and their abundance value (TPM) for each dataset

source_name: SKOV3ip1 cell line

extract_protocol:
Total RNA was extracted using Qiagen’s RNEasy minikit according to their protocol with on-column DNAse 1 digestion then evaluated on an Agilent Bioanalyser.
5 µg of the RNA sample, to which a 1ul spike-in of ERCC EXfold mix 1 was added (Thermofisher Scientific) were ribo-depleted by using a RiboZero Gold (Human/Mouse/Rat) kit (Illumina). 50ng of the resulting sample were then fragmented using an NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) at 94°C for 2 or 3min (depending on RIN) and treated with T4 polynucleotide kinase (Epicentre) to remove 3′ phosphates and 2′, 3′ cyclic monophosphates, which impede TGIRT template switching (Mohr et al. 2013). RNAs were purified after ribo-depletion, fragmentation, and dephosphorylation by using a modified version of the Zymo RNA Clean & Concentrator protocol (addition of eight sample volumes of ethanol to increase retention of very small RNA species). The recovered RNA was used for cDNA synthesis via TGIRT template switching with 1 μM TGIRT-III RT (InGex, LLC) for 15 min at 60°C, as previously described (Qin et al. 2016). The template-switching reaction seamlessly links the complement of an Illumina Read 2 sequencing primer-binding site (R2R DNA) to the 5′ end of the cDNA during cDNA synthesis, after which a DNA oligonucleotide containing the complement of an Illumina Read 1 sequencing primer-binding site (R1R DNA) is ligated to the cDNA 3′ end by using Thermostable 5′ AppDNA/RNA Ligase (New England Biolabs). Ligated cDNAs with R1R and R2R sequencing adapters on either end were then amplified for 12 cycles of PCR (Qin et al. 2016; initial denaturation at 98°C for 5 sec, followed by cycles of 98°C for 5 sec, 65°C for 10 sec, 72°C for 10 sec), during which Illumina capture and index sequences were added. Libraries were size-selected by using Ampure XP beads (Beckman-Coulter), evaluated on an Agilent 2100 Bioanalyzer, and quantified using Qubit 2.0 fluorometer (Invitrogen) as was the final equimolar pool of the TGIRT-seq libraries. They were then sequenced using the Illumina NextSeq 500 instrument (75-nt paired-end reads) with the Illumina NextSeq 500/550 High Output Kit v2 (150 Cycles).

value: Ovarian serous cystadenocarcinoma

tag: growth protocol

value: grown in DMEM/F12 (50/50) medium (Wisent), supplemented with 10 % fetal bovine serum and 2 mM L-glutamine. Cell propagation and passaging were as recommended by ATCC (American Type Culture Collection). Cells were trypsinized and collected in 5X106 pellets resuspended in 700ul TRIzol (Ambion) and kept at -80°C until RNA extraction

value: 10nM DKC1 targeting siRNA 2 using Lipofectamine 2000 (Invitrogen)


title: SKOV3ip1_DKC1_KD_s2_n1


title: SKOV3ip1_DKC1_KD_s1_n2

value: 10nM DKC1 targeting siRNA 1 using Lipofectamine 2000 (Invitrogen)


title: Ovary_n1

source_name: Ovary tissue

value: Ovary tissue


title: Ovary_n2


title: Prostate_n2

source_name: Prostate tissue

value: Prostate tissue


title: Prostate_n3


title: SKOV3ip1_DKC1_KD_s1_n1


title: Ovary_n3


title: B2_ET: ECFC3_etop_induced


title: SKOV3ip1_Lipofectamin_n1

value: Lipofectamine 2000 (Invitrogen)


title: Prostate_n1


title: B2_LP: ECFC3_late_passage


title: Sample_4h_0nM_pos

status: Public on Feb 07 2019

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street

institute: University of Toronto

description: Sample 14

data_processing:
RNA-Seq reads were mapped to GRCh37 with Gencode v24lift37 annotation using STAR (v2.5.3a), the GeneCounts parameter was set to quantMode to get raw counts on genes
RNA-Seq reads were mapped to GRCh37 using Tophat v2.1.0 with Gencode v24lift37 annotations. Unaligned reads were converted to fastq format with bamToFastq function from the Bedtools suite and used to call fusion with TopHat-Fusion v2.1.0, with anchor length set as 20 bp. The resulting fusion reads were annotated with CIRCexplorer v1.1.10.
edgeR(v3.12.1) was used to obtain FPKM
Genome_build: GRCh37
Supplementary_files_format_and_content: txt files for gene raw counts and reads encompassing back-splicing site for circRNAs
Supplementary_files_format_and_content: circRNA_RPKM_CPC.csv: comma-separated text file; circRNA RPKM for CPCGENE dataset.
Supplementary_files_format_and_content: circRNA_RPKM_NGS.csv: comma-separated text file; circRNA RPKM for NGS-ProToCol dataset.
Supplementary_files_format_and_content: circRNA_annotation.csv: comma-separated text file; circRNA annotation.
Supplementary_files_format_and_content: circRNA_RPKM_circRNA_RPKM_cpc144_patient.csv: comma-separated text file; RPKM for all circRNAs detected in CPCGENE cohort.
Supplementary_files_format_and_content: circRNA_annotation_76311.csv: comma-separated text file; circRNA annotation.

source_name: LNCaP

growth_protocol: The four PCa cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin. LNCaP cells were serum starved for 48 hours before stimulation with 10 nM double hydrogen testosterone (DHT) for 4 or 16 hours.

extract_protocol:
For the preparation of the RNA-Seq libraries for the four cell lines, 10 µg of total RNA was subjected to RiboMinus for the removal of the ribosomal RNA by using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K155001). After RiboMinus treatment, the samples (~1 µg left) were divided into two equal portions, one treated with RNase R and the other incubated only with the digestion buffer. Samples were cleaned-up by phenol-chloroform before resuspension in a small volume of RNase-free H2O.
he library preparation commenced directly with the fragmentation step by mixing the sample and the Fragment, Prime, Finish Mix in the TruSeq Stranded mRNA Library Prep Kit at a 1:1 ratio, followed by the manufacturer’s protocol for the remainder of the procedure. RNA-Seq libraries were sequenced as single-end reads in duplicates at ~50 million reads per library using HiSeq 2000 platforms.

tag: rnase r treatment

value: yes

value: 0 nM double hydrogen testosterone 4h

tag: cell line

value: LNCaP

value: prostate cancer cell line


title: Sample_4h_0nM_neg

description: Sample 13

value: no


title: Sample_4h_10nM_pos

description: Sample 16

value: 10 nM double hydrogen testosterone 4h


title: 193F_X: ECFC2_xray_induced

source_name: ECFC exposed to X-ray

value: Umbilical Cord Blood

value: 10gy X-ray


title: 192_LP: ECFC1_late_passage

value: ECFCs


title: B2_EP: ECFC3_early_passage

source_name: ECFC in early passage

value: Control


title: B2_X: ECFC3_xray_induced


title: Sample_4h_10nM_neg

description: Sample 15


title: SKOV3ip1_Lipofectamin_n2

value: Ovarian serous cystadenocarcinoma


title: Breast_n1

source_name: Breast tissue

value: Breast tissue


title: Breast_n2


title: Sample_16h_0nM_neg

description: Sample 9

value: 0 nM double hydrogen testosterone 16h


title: 193F_EP: ECFC2_early_passage


title: Sample_42D-

description: Sample 3


title: Sample_22Rv1-

description: Sample 1


title: Sample_V16Aplus

description: Sample 7


title: 192_X: ECFC1_xray_induced


title: Wild-Type CHXTIG profiling 4

status: Public on Jan 27 2019

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (NNNNNNCACTCGGGCACCAAGGA) removed with Skewer
4 random nucleotides included in RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed from the 5’ end of reads. Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Genome_build: SacCer3 R64-1-1
Supplementary_files_format_and_content: Count tables for relative codon occupancies or fixed-step WIG density files for mapped reads

organism: Saccharomyces cerevisiae

source_name: Wild-Type CHXTIG profiling

growth_protocol: Yeast cells were grown to OD ~0.5.

extract_protocol:
Lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 15-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold treatment. Upon dephosphorylation of sample RNA, linker was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Yeast cells were harvested by vacuum filtration and flash frozen. Samples were homogenized and lysed with lysis buffer using a freezer mill.

value: Wild-Type

tag: plasmid(s)

tag: molecule subtype

value: Ribosome Protected mRNA (15-34 nt)


title: Sample_16h_10nM_neg

description: Sample 11

value: 10 nM double hydrogen testosterone 16h


title: 192_EP: ECFC1_early_passage

tag: tissue


title: Sample_PC3plus

description: Sample 6


title: Sample_V16A-

description: Sample 8


title: Wild-Type CHXANS profiling 1

description:
processed data file:
CHXANS_21ntRPF_occupancy.csv
wtCHXANS1

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (NNNNNNCACTCGGGCACCAAGGA) removed with Skewer
4 random nucleotides included in RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed from the 5’ end of reads. Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Genome_build: SacCer3 R64-1-1, Ce10, hg19
Supplementary_files_format_and_content: Count tables for relative codon occupancies or fixed-step WIG density files for mapped reads

source_name: Wild-Type CHXANS profiling

growth_protocol: Yeast cells were grown to OD ~0.5; mammalian cells were grown to ~75% confluence; Synchronized L1 worms were plated on HT115 bacteria transformed with pL4440 vector and cultured at 25˚C for ~48 hours.

tag: genotype/variation


title: Wild-Type CHXANS profiling 2

description:
processed data file:
CHXANS_21ntRPF_occupancy.csv
wtCHXANS2


title: Sample_16h_0nM_pos

description: Sample 10


title: Sample_22Rv1plus

description: Sample 2


title: Sample_42Dplus

description: Sample 4


title: Sample_16h_10nM_pos

description: Sample 12


title: S. sclerotiorum 1980 grown in Potato Dextrose Broth rep2

status: Public on Jan 24 2019

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

description:
Sample 2
HDX14

data_processing:
HiSeq control software 2.2.38 or 2.2.58, RTA 1.18.61.0 or RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function of the CLC genomics software with default settings.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the RNA-seq analysis function of the CLC genomics software with default settings.
Genome_build: S. sclerotiorum version 2.0: https://www.ncbi.nlm.nih.gov/genome/487?genome_assembly_id=290987
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Sclerotinia sclerotiorum

source_name: 4-days old culture

growth_protocol: Samples1-6: S. sclerotiorum was grown in liquid potato dextrose medium (P6685 - Sigma) for 4 days at 24°C under shaking at 180 rpm. Cultures were filtered using vacuum and a fritted glass column protected with a doubled miracloth membrane and ground in liquid nitrogen.

extract_protocol:
The edge and center of developed mycelial colonies (15 to 30 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed at the center of a Petri dish or on the adaxial surface of leaves and plants. The border (ring of ~5mm wide) and center of colonies were collected with a scalpel and frozen in liquid nitrogen.

value: control

tag: culture medium

value: Potato Dextrose Broth


title: Border of S. sclerotiorum 1980 colony grown on Potato Dextrose Agar rep2

description:
Sample 9
HDX57

source_name: 15 to 30mm wide colony (about 2 days old)

value: border

value: Potato Dextrose Agar


title: Center of S. sclerotiorum 1980 colony grown on Arabidopsis thaliana rep1

description:
Sample 13
HDX31

value: center

value: Arabidopsis thaliana


title: S. sclerotiorum 1980 grown in Potato Dextrose Broth rep1

description:
Sample 1
HDX13


title: Center of S. sclerotiorum 1980 colony grown on Potato Dextrose Agar rep1

description:
Sample 8
HDX56


title: Center of S. sclerotiorum 1980 colony grown on Arabidopsis thaliana rep2

description:
Sample 14
HDX32


title: Center of S. sclerotiorum 1980 colony grown on Arabidopsis thaliana rep3

description:
Sample 15
HDX33


title: Border of S. sclerotiorum 1980 colony grown on Potato Dextrose Agar rep1

description:
Sample 7
HDX55


title: Center of S. sclerotiorum 1980 colony grown on Potato Dextrose Agar rep3

description:
Sample 12
HDX60


title: Border of S. sclerotiorum 1980 colony grown on Potato Dextrose Agar rep3

description:
Sample 11
HDX59


title: Center of S. sclerotiorum 1980 colony grown on Potato Dextrose Agar rep2

description:
Sample 10
HDX58


title: S. sclerotiorum 1980 grown in Potato Dextrose Broth rep3

description:
Sample 3
HDX15


title: WT vs crz2_Hyp37C_rep1

status: Public on Nov 20 2018

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

institute: Institut Pasteur

description: Sample 10

hyb_protocol: Gene Expression Hybridization Kit (Cat# 5188-5242) from Agilent Technologies was used to prepare 50 µl of purified labeled samples as recommended by the manufacturer, followed by hybridization to the Agilent-026869 array.

scan_protocol: Images of Cy5 and Cy3 fluorescence were generated by scanning the expression arrays using an Axon Autoloader 4200AL scanner (Molecular Devices, Downington, PA). Images were analyzed with the GenePix Pro 6.1.0.2 software (Molecular Devices, Downington, PA).

data_processing: GenePix Results (GPR) files were imported into the Arraypipe 2.0 for spot filtering, background subtraction (limma normexp BG correction) and Lowess global normalization of signal intensities.

organism: Candida albicans

source_name: Wild-type lab strain, grown under Hyp37C

label_protocol: First-strand cDNA synthesis and Cy5/Cy3 labeling from 20 µg total RNA was performed using the Superscript III indirect cDNA labeling system (Invitrogen).

growth_protocol: For the CRZ2_2h, CRZ2_4h and TETp microarray experiments (Samples 1-6 and 19-22), total RNA was extracted from 3 independently-generated crz2Δ/crz2Δ strains carrying the PTET-CRZ2 fusion (samples 1-6) or the PTET empty vector (samples 19-22), pre-grown overnight in 10 ml YPD at 30ºC then diluted in fresh YPD medium supplemented or not with 40 µg.mL−1 doxycycline to an OD600 nm of 0.3 and re-grown for 2 (samples 1-3) and 4 (samples 4-6 and 19-22) hours. For the WT vs. crz2Δ/Δ and the Norm > Hyp shift microarray experiments (samples 7-12 and 13-18, respectively), strains CEC369 (wild-type) and C90 (crz2Δ/Δ) were grown overnight in 10 ml YPD at 30ºC, then diluted to an OD600 nm of 0.16 in 250-ml flasks containing 50 ml of YPD medium. The flasks were incubated in a BBL GasPak anaerobic jar at 37°C for 24 h without shaking (Hypoxia 37ºC) or in a 30ºC-incubator for 24h under vigorous shaking (Normoxia, 30ºC).

extract_protocol: Total RNA was extracted using the hot phenol method as described in Znaidi et al. (2013) PLoS Pathogens 9: e1003519.

treatment_protocol: See growth protocol.

tag: strain/background

value: wild-type

tag: growth condition

value: hypoxia (37C)

source_name: crz2-/- homozygous mutant strain, grown under Hyp37C

value: homozygous crz2-/- deletion


title: WT vs crz2_Hyp37C_rep2

description: Sample 11


title: nKO3

status: Public on Sep 21 2018

city: Santiago

first: Dolores

last: Busso

address: Alameda 340 Edificio CIM-Patio 4 piso

department: Nutrition, Diabetes and Metabolism

country: Chile

institute: Pontificia Universidad Católica de Chile

data_processing:
Grooming of de-multiplexed reads was performed with FASTQ groomer 1.04.
Mapping was done using TopHat2 0.7.
Transcript abundance estimation and differential expression significance testing were computed with Cufflinks 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Cufflinks output for all the comparisons are contained in the processed data spreadsheet (.xlsx). Output consists of gene identifiers, chromosome location, mean FPKM for each condition, log2 fold change, and raw and adjusted significance levels.

source_name: Whole E9.5 embryo

extract_protocol:
Total RNA was extracted with the PureLink RNA Micro Kit (Invitrogen, CA) and DNA was eliminated by incubation with DNAse I (Sigma, MO), following manufacturers´ instructions.
Strand-specific RNA-seq libraries were generated for each sample from 500 ng of total RNA using the Kapa Stranded mRNA-seq kit (Kapa Biosystems, South Africa) after poly-A enrichment according to the instructions of the manufacturer.  The consistent fragment lengths of the sequencing libraries were ascertained using a Bioanalyzer 2100 micro-capillary gel electrophoresis instrument (Agilent, CA).  The barcoded libraries were quantified by fluorometry on a Qubit instrument (Life Technologies, CA), and pooled in equimolar ratios. The pool was quantified by qPCR with a Kapa Library Quant kit (Kapa Biosystems, South Africa).

tag: strain

value: Whole embryo

tag: developmental stage

tag: Sex

value: Female

tag: genotype

value: SR-B1 KO normal


title: WT3


title: KO-NTD2

value: SR-B1 KO NTD


title: Untagged_100u_Mnase_HA_IP

status: Public on Sep 26 2018

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

institute: UBC

data_processing:
Fastq files were aligned to saccer3 using BWA
Samtools was used to filter for mapped reads with a mapping quality score of at least 10
Bedtools and AWK were used to convert the BAM files into bed files of mapped DNA fragments
Fragments smaller than 1000 bp were selected for using AWK
Coverage per million fragments was calculated and converted to wig file format
Genome_build: saccer3
Supplementary_files_format_and_content: wig files, coverage in 1bp intervals

source_name: Yeast

growth_protocol:
Yeast strains were arrested in G1 with alpha factor, and crosslinked with 1% formaldehyde for 15 minutes
Cells were grown in YPD

extract_protocol:
MNase ChIP-seq: cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in 1000 μl of NP-S buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP-40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) and digested with 100u microccocal nuclease at 37°C for 10 minutes to obtain predominantly mono-nucleosomal DNA. Reactions were stopped with the addition of 10 mM EDTA and digested lysates were clarified by centrifugation at 9000g for 10 minutes. To extract insoluble chromatin, pellets were re-suspended in 300 μl of lysis buffer with 0.2% SDS, and sonicated in a Diagenode Bioruptor at high output for 30 seconds on/30 seconds off four cycles. Extracts were then re-clarified by centrifugation at 9000g for 10 minutes, and the supernatant pooled with the pre-existing extract. The buffer composition of the lysate was adjusted to that of the original lysate buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF), and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE.
Sequencing libraries were prepared as described previously (Maltby et al. 2012; Martin et al. 2017). Briefly, 2 ng of ChIP or input material was end-repaired, A-tailed, and adapters ligated, before PCR amplification with indexed primers. We performed 10 and 11 rounds of PCR amplification for MNase and sonication ChIP-seq experiments, respectively. All DNA purification steps used SPRI (Solid Phase Reversible Immobilization) magnetic beads. Samples were pooled, gel-purified (50 bp - 600 bp region) and sequenced on an Illumina HiSeq 2500.

treatment_protocol: 1% formaldehyde crosslinking

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 SPT16-HA6::HIS3

tag: chip antibody

tag: growth stage


title: WT Norm_Hyp shift_rep2

description: Sample 14

source_name: Wild-type lab strain, grown under Norm30C

value: normoxia (30C)

source_name: Wild-type strain, grown under Hyp37C


title: KO-NTD1


title: WT Norm_Hyp shift_rep3

description: Sample 15


title: crz2 Norm_Hyp shift_rep3

description: Sample 18

source_name: crz2-/- homozygous mutant strain, grown under Norm30C


title: nKO2


title: Untagged_100u_Mnase_Input


title: CRZ2_2h_rep3

description: Sample 3

source_name: Untreated control, grown in YPD medium during 2h

value: homozygous crz2-/- deletion and CIp-PTET-CRZ4

tag: treatment

tag: time point

source_name: Dox-treated at a concentration of 40 µg/mL in YPD medium for 2h

value: doxycycline


title: WT Norm_Hyp shift_rep1

description: Sample 13


title: crz2 Norm_Hyp shift_rep1

description: Sample 16


title: WT vs crz2_Hyp37C_rep3

description: Sample 12


title: CRZ2_2h_rep2

description: Sample 2

value: homozygous crz2-/- deletion and CIp-PTET-CRZ3


title: CRZ2_4h_rep2

description: Sample 5

source_name: Untreated control, grown in YPD medium during 4h

value: homozygous crz2-/- deletion and CIp-PTET-CRZ6

source_name: Dox-treated at a concentration of 40 µg/mL in YPD medium for 4h


title: CRZ2_4h_rep3

description: Sample 6

value: homozygous crz2-/- deletion and CIp-PTET-CRZ7


title: crz2 Norm_Hyp shift_rep2

description: Sample 17


title: CRZ2_2h_rep1

description: Sample 1

value: homozygous crz2-/- deletion and CIp-PTET-CRZ2


title: CRZ2_4h_rep1

description: Sample 4

value: homozygous crz2-/- deletion and CIp-PTET-CRZ5


title: WT vs crz2_Norm30C_rep1

description: Sample 7


title: WT vs crz2_Norm30C_rep2

description: Sample 8


title: WT vs crz2_Norm30C_rep3

description: Sample 9


title: nKO1


title: WT2


title: KO-NTD3


title: 3O_mRNA-seq

status: Public on Feb 20 2018

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

address: 910 Light Street, Apartment 2

department: Biology

institute: The Johns Hopkins Univeristy

description: total RNA-seq

data_processing:
The program trim galore was used with base settings to trim adapter sequences from reads and to filter out low phred score reads (<20).
The reference-based alignments were assembled into transcriptomes using the program stringtie in order to build full-length transcripts, calculate coverage and expression values (TPM). The assembly was guided by a gene annotation file from the H. volcanii DS2 (NCBI refseq taxid 2246) genome to build transcripts and annotate them either as a gene or novel transcript.
gffcompare under default options was used to compare the assembled transcriptomes against the gene annotation file from H. volcanii DS2 (NCBI refseq taxid 2246) to annotate transcripts as genes or non-coding RNA (antisense or intergenic).
The program featureCounts was used to rapidly count reads and was run with strand-specific options on, paired-end mode on, multi-mapping off.
The read counts were then used in the R differential expression software package DESeq2 to calculate differential expression of sRNAs and mRNAs.
Genome_build: ASM2568v1 GCF_000025685.1

organism: Haloferax volcanii DS2

source_name: Replicate 3 Oxidative Stress mRNA-sq

growth_protocol: H. volcanii auxotrophic strain H53 (Δpyre2, ΔtrpA) was used for all experiments. Culturing in liquid and solid media was done in rich medium (Hv-YPC), at 42°C and with shaking at 220 rpm (Amerix Gyromax 737).[31] Uracil and tryptophan were added to a final concentration of 50 µg/mL, each.

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Miniprep kit with the following modifications: after addition of RNA lysis buffer to the frozen cell pellets, cells were processed with a 23 G needle and syringe to insure complete cell lysis. H. volcanii liquid culture is slimy and viscous thus to increase cellular lysis a 23 G needle and syringe was used to suck up and break down the cell pellet. Total RNA was then extracted following the standard kit protocol.
Total RNA, for each biological replicate and condition, was size-selected using denaturing polyacrylamide gel electrophoresis. 20 µg of total RNA was loaded onto a 7% denaturing urea polyacrylamide gel (SequaGel, National Diagnostics) in 0.5 x TBE buffer and ran at constant power of 30 W until bromophenol blue bands reached the bottom of the gel. The gel was stained with SYBR Gold, visualized on a blue light box, and bands in the 50-500 nucleotide range, as indicated by the RNA Century Marker plus ladder (ThermoFisher), were excised. Small RNAs (sRNA) were eluted by rotating overnight in 1.2 mL 0.3 M NaCl, ethanol precipitated, and DNase I (NEB) treated (37 °C for 2 hours) as previously described. Strand-specific libraries were prepared using the SMART-seq Ultralow RNA input kit (Takara), insert sizes checked with the Bioanalyzer RNA pico kit (Agilent), and paired-end sequencing (2 x 150 bp) was carried out on the Illumina HiSeq 2500 platform at the Johns Hopkins University Genetic Resources Core Facility (GRCF). Library preparation and sequencing was as described above, omitting the size-selection by denaturing gel electrophoresis.

treatment_protocol: We exposed 5 biological replicates of H. volcanii strain H53 liquid cultures to the oxidative stress agent H2O2. Initially, cultures were grown in 80 mL of Hv-YPC under optimal conditions to an OD of 0.4 (mid exponential phase). To ensure homogeneity, each replicate was subsequently split into two 40 mL cultures, one used for the non-challenged (control) condition and the other for the oxidative stress condition. For the latter condition, 2 mM H2O2  (80% survival rate, previously determined) was directly added to the cultures followed by an hour incubation at 42 °C with shaking at 220 rpm. Cultures were then rapidly cooled down, centrifuged at 8000 rpm  for 5 minutes and the pellets resuspended in 18% sea water. The cell suspensions were then transferred to a 1 mL tube and centrifuged at 8000 rpm  for 3 minutes, the pellets were flash frozen and stored at -80 °C until ready for RNA extraction. Control non-challenged culture replicates were processed in the same manner without the addition of H2O2.

value: 2 mM H2O2

tag: target molecule

value: Total RNA


title: B6_M_T_4 [Bisulfite-Seq OX]

status: Public on Dec 15 2017

city: Cambridge

first: Nicolas

last: Walker

address: Downing Street

department: Genetics

institute: University of Cambridge

data_processing:
We first used trimgalore (Kreuger, 2012) to trim for low quality sequence and adaptors, with the following parameters: --fastqc --trim1 --paired. We then aligned reads to male and female genomes using bismark v0.13.1(Kreuger, 2011) with the parameters --nonbsmm. We then further ran the deduplicatebismark program with options --outputfile --outputreportfile --paired. From these outputs we used the bismarkmethylationextractor program with the following options --buffersize 25G --zerobased --ignore 3 --ignorer2 3 --nooverlap --report --gzip --bedGraph --cytosinereport --CX. We extracted counts for the CpG sites from the deduplicated CXreport file. We merged the counts at CpG positions by sex to form one female and one male CpGenome for both the cell types
Genome_build: mm10
Supplementary_files_format_and_content: cpg.meth

source_name: from CD4+CD62L+ T cells

growth_protocol: C57BL/6 mice at 6-8 weeks of age were used for spleen collection purposes.

extract_protocol:
Naïve CD4+ T lymphocytes were purified from single-cell suspensions by MACS depletion of non-CD4+ T cells as well as regulatory T cells and TCRγ/δ+ T cells, using a cocktail of specific biotin conjugated antibodies against CD8a (Ly-2), CD45R (B220), CD49b (DX5), CD11b (Mac-1), Ter-119, CD25 and TCRγ/δ+ using the CD4+ CD62L+ T Cell Isolation Kit II (Miltenyi) to obtain an unlabeled pre-enriched CD4+ T cell fraction. Collected cells were suspended in PBS containing 2% FBS and Fc receptors were blocked with FcR blocking reagent for 10 minutes at 4°C (Miltenyi). Cells were further fluorescently stained with a combination of CD4-FITC (Miltenyi), CD44-APC clone IM7 (eBioscience), CD62L clone MEL-14 (BD Pharmingen), eFluor® 450 CD25 clone PC61.5 (eBioscience), for 10 minutes at 4°C, washed and then stained with DAPI (Life Technologies) to cell sort the live population of naïve CD4+, CD62Lhi, CD44lo, CD25- T lymphocytes using the MoFlo XDP system (Beckman Coulter). Samples were gated on single cells for doublet discrimination and non-viable cells were excluded using the viability dye 4’, 6 – diamidine – 2 – phenylindole (DAPI). AllPrep DNA/RNA Mini Kit (Qiagen) was used to perform simultaneous isolation of RNA and DNA from 10^6 sorted naïve CD4+ T cells and resting B cells.
triplicate 1µg samples of genomic DNA isolated from either naive CD4+ T cells or resting B cells were fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, the DNA samples were spiked with synthetic fragments of DNA pre-labelled by PCR with 5mC and 5hmC used in the analysis step to determine the bisulfite conversion efficiency of cytosine forms (unmodified, 5mC and 5hmC). Libraries were prepared using the TruSeq DNA library preparation kit v2 (Illumina, FC-121-2001) according to manufacturer’s instructions with some modifications. After ligation of TruSeq methylated adapters (ME-100-0010, Illumina) and AMPure® XP (Beckman) bead purification half of the sample was oxidized by treatment with KRuO4 (15 mM in 0.05 M NaOH) for 1 hr, performed as previously described

value: male


title: 1O_mRNA-seq

description: total RNA-seq

source_name: Replicate 1 Oxidative Stress mRNA-sq


title: WT1

value: wild-type


title: 2O_mRNA-seq

description: total RNA-seq

source_name: Replicate 2 Oxidative Stress mRNA-sq


title: B6_M_T_3 [Bisulfite-Seq OX]


title: B6_M_B_1 [Bisulfite-Seq OX]

source_name: from CD43- B cells


title: B6_F_B_5 [Bisulfite-Seq OX]

value: female


title: B6_M_B_2 [Bisulfite-Seq OX]


title: 1C_mRNA-seq

description: total RNA-seq

source_name: Replicate 1 Control No challenge mRNA-sq

value: No challenge


title: B6_F_T_7 [Bisulfite-Seq OX]


title: 3C_mRNA-seq

description: total RNA-seq

source_name: Replicate 3 Control No challenge mRNA-sq


title: B6_M_B_2 [Bisulfite-Seq]

description:
from CD43- B cells
B6_M_B_BS_A1-cpg.meth

tag: cell type

value: CD43- B cells


title: B6_M_T_3 [Bisulfite-Seq]

description:
from CD4+CD62L+ T cells
B6_M_T_BS_A3-cpg.meth

value: CD4+CD62L+ T cells


title: B6_M_B_1 [Bisulfite-Seq]


title: 2C_mRNA-seq

description: total RNA-seq

source_name: Replicate 2 Control No challenge mRNA-sq


title: B6_F_B_6 [Bisulfite-Seq]

description:
from CD43- B cells
B6_F_B_BS_A6-cpg.meth


title: B6_M_T_4 [Bisulfite-Seq]


title: B6_F_B_5 [Bisulfite-Seq]


title: B6_F_T_7 [Bisulfite-Seq]

description:
from CD4+CD62L+ T cells
B6_F_T_BS_A7-cpg.meth


title: B6_F_T_8 [Bisulfite-Seq]


title: YFP control B cells, biological rep 2

status: Public on Feb 14 2018

city: Boston

first: Baochun

last: Zhang

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from YFP-expressing control B cells

hyb_protocol: Fragmented, biotinylated cDNA was hybridized to Mouse Gene 2.0 ST arrays for 16 hours at 45oC and 60rpm in a Affymetrix GeneChip™ Hybridization Oven 645. Mouse GeneChip ST arrays were washed/stained using the Affymetrix FS450 automated fluidics station.

scan_protocol: GeneChips were scanned in an Affymetrix GCS3000 7G scanner with autoloader.

data_processing: The microarray data were normalized using RMA method from the R package "oligo".

source_name: YFP-expressing B cells

label_protocol: Total RNA was processed using the Affymetrix GeneChip™ WT PLUS Reagent Kit.  The kit generates amplified and biotinylated sense-stranded DNA targets for hybridization.

growth_protocol: B cells were isolated from the spleens of YFPflSTOP/+ and LMP1flSTOP/YFPflSTOP mice, by CD43 depletion using magnetic-activated cell sorting (Miltenyi Biotec); the cells were treated with TAT-Cre; two days posttreatment, reporter (YFP)+ cells were purified by FACS sorting for RNA extraction.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) according to manufacturer’s instructions.

tag: background strain

value: (C57BL6XBALBc) F1

value: YFPflSTOP/+

tag: gender

value: Female

value: Spleen


title: LMP1-B cells, biological rep 2

description: Gene expression data from LMP1-expressing B cells

source_name: LMP1-expressing B cells

tag: tissue


title: YFP control B cells, biological rep 1

tag: genotype/variation


title: tomato inoculated by S. sclerotiorum rep 3

status: Public on Dec 12 2017

data_processing:
HiSeq control software 2.2.38, RTA 1.18.61.0, Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function of the CLC genomics software with default settings.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the RNA-seq analysis function of the CLC genomics software with default settings.
Genome_build: TAIR10 (A. thaliana) - version 3 (S. lycopersicum)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Solanum lycopersicum

source_name: 4-week old plants mature leaves

growth_protocol: Plants were grown in Jiffy pots under controlled conditions at 22°C, with a 9 hour light period and a light intensity of 120 µmol/m2/s 4 weeks prior to infection

extract_protocol:
The edge of developed necrotic lesions (15 to 30 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mature leaves of 4 week-old Arabidopsis thaliana and Solanum lycopersicum (Heinz genotype) were inoculated or not with the S. sclerotiorum strain 1980. An agar plug (5mm in diameter) containing actively growing S. sclerotiorum mycelium was placed on the adaxial surface of leaves and plants were maintained at 80% humidity

value: cv Heinz

value: infected


title: B6_F_B_6 [Bisulfite-Seq OX]


title: LMP1-B cells, biological rep 1


title: B6_F_T_8 [Bisulfite-Seq OX]


title: Sample_PC3-

description: Sample 5

tag: rnase r treatment

value: no

tag: cell line

value: prostate cancer cell line


title: A. thaliana inoculated by S. sclerotiorum rep 3

organism: Arabidopsis thaliana

value: Col-0 ecotype


title: tomato inoculated by S. sclerotiorum rep 2


title: 193F_ET: ECFC2_etop_induced

source_name: ECFC exposed to etoposide

value: Umbilical Cord Blood

value: 1uM Etoposide

value: ECFCs


title: A. thaliana inoculated by S. sclerotiorum rep 2


title: A. thaliana inoculated by S. sclerotiorum rep 1


title: tomato inoculated by S. sclerotiorum rep 1


title: control-110 whole blood Control genomic DNA

status: Public on May 03 2017

type: genomic

first: Rosanna

last: Weksberg

address: 555 University Ave.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Using an Illumina HiScan

data_processing: Background subtraction and normalization to internal array controls were performed on raw intensity data using Illumina GenomeStudio v2011.1 Methylation Module 1.9 software. Probes containing single nucleotide polymorphisms (SNPs), cross-reactive probes with sequences aligned to multiple positions with ≥ 90% identity, and non-specific chromosome probes were removed.

label: Cy5 and Cy3

source_name: whole blood genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: All genomic DNA were extracted from whole blood using standard procedures. One microgram of genomic DNA was sodium bisulfite modified using the Qiagen EZ DNA Methylation kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Modified genomic DNA was then processed and analyzed on the Infinium HumanMethylation450 BeadChip from Illumina according to the manufacturer’s protocol.

value: male

tag: age (years)

tag: sample type

value: Control for validation cohort

tag: disease state

value: Control

value: whole blood


title: control-119 whole blood Control genomic DNA


title: control-122 whole blood Control genomic DNA


title: control-103 whole blood Control genomic DNA

value: female


title: control-121 whole blood Control genomic DNA


title: control-115 whole blood Control genomic DNA


title: control-124 whole blood Control genomic DNA


title: control-116 whole blood Control genomic DNA


title: control-118 whole blood Control genomic DNA


title: control-111 whole blood Control genomic DNA


title: control-125 whole blood Control genomic DNA


title: control-108 whole blood Control genomic DNA


title: control-123 whole blood Control genomic DNA


title: control-112 whole blood Control genomic DNA


title: control-106 whole blood Control genomic DNA


title: control-114 whole blood Control genomic DNA


title: control-120 whole blood Control genomic DNA


title: control-101 whole blood Control genomic DNA


title: control-99 whole blood Control genomic DNA


title: control-107 whole blood Control genomic DNA


title: control-97 whole blood Control genomic DNA


title: control-109 whole blood Control genomic DNA


title: control-105 whole blood Control genomic DNA


title: control-113 whole blood Control genomic DNA


title: control-98 whole blood Control genomic DNA


title: control-102 whole blood Control genomic DNA


title: control-100 whole blood Control genomic DNA


title: control-117 whole blood Control genomic DNA


title: control-96 whole blood Control genomic DNA


title: control-104 whole blood Control genomic DNA


title: control-93 whole blood Control genomic DNA


title: control-95 whole blood Control genomic DNA


title: control-94 whole blood Control genomic DNA


title: control-91 whole blood Control genomic DNA


title: control-88 whole blood Control genomic DNA


title: control-92 whole blood Control genomic DNA


title: control-82 whole blood Control genomic DNA


title: control-89 whole blood Control genomic DNA


title: control-84 whole blood Control genomic DNA


title: control-85 whole blood Control genomic DNA


title: control-87 whole blood Control genomic DNA


title: control-83 whole blood Control genomic DNA


title: control-86 whole blood Control genomic DNA


title: control-73 whole blood Control genomic DNA


title: control-76 whole blood Control genomic DNA


title: control-78 whole blood Control genomic DNA


title: control-81 whole blood Control genomic DNA


title: control-77 whole blood Control genomic DNA


title: control-71 whole blood Control genomic DNA


title: control-70 whole blood Control genomic DNA


title: control-68 whole blood Control genomic DNA


title: control-69 whole blood Control genomic DNA


title: control-72 whole blood Control genomic DNA


title: control-67 whole blood Control genomic DNA


title: control-62 whole blood Control genomic DNA


title: control-64 whole blood Control genomic DNA


title: control-79 whole blood Control genomic DNA


title: control-61 whole blood Control genomic DNA


title: control-66 whole blood Control genomic DNA


title: control-63 whole blood Control genomic DNA


title: control-58 whole blood Control genomic DNA


title: control-59 whole blood Control genomic DNA


title: control-90 whole blood Control genomic DNA


title: control-51 whole blood Control genomic DNA


title: control-54 whole blood Control genomic DNA


title: control-65 whole blood Control genomic DNA


title: control-57 whole blood Control genomic DNA


title: control-80 whole blood Control genomic DNA


title: control-50 whole blood Control genomic DNA


title: control-49 whole blood Control genomic DNA


title: control-60 whole blood Control genomic DNA


title: control-45 whole blood Control genomic DNA


title: control-75 whole blood Control genomic DNA


title: control-47 whole blood Control genomic DNA


title: control-44 whole blood Control genomic DNA


title: control-42 whole blood Control genomic DNA


title: control-46 whole blood Control genomic DNA


title: control-55 whole blood Control genomic DNA


title: control-56 whole blood Control genomic DNA


title: control-43 whole blood Control genomic DNA


title: control-48 whole blood Control genomic DNA


title: control-52 whole blood Control genomic DNA


title: control-53 whole blood Control genomic DNA


title: control-31 whole blood Control genomic DNA

value: Control for KMT2D LOF discovery cohort


title: control-40 whole blood Control genomic DNA


title: control-27 whole blood Control genomic DNA

value: Control for CHD7 LOF discovery cohort


title: control-30 whole blood Control genomic DNA


title: control-26 whole blood Control genomic DNA


title: control-35 whole blood Control genomic DNA


title: control-34 whole blood Control genomic DNA


title: control-24 whole blood Control genomic DNA


title: control-36 whole blood Control genomic DNA


title: control-29 whole blood Control genomic DNA


title: control-22 whole blood Control genomic DNA


title: control-41 whole blood Control genomic DNA


title: control-25 whole blood Control genomic DNA


title: control-38 whole blood Control genomic DNA


title: control-21 whole blood Control genomic DNA


title: control-33 whole blood Control genomic DNA


title: control-20 whole blood Control genomic DNA


title: control-32 whole blood Control genomic DNA


title: control-37 whole blood Control genomic DNA


title: control-23 whole blood Control genomic DNA


title: control-18 whole blood Control genomic DNA


title: control-39 whole blood Control genomic DNA


title: control-19 whole blood Control genomic DNA


title: control-16 whole blood Control genomic DNA


title: control-17 whole blood Control genomic DNA


title: control-74 whole blood Control genomic DNA


title: control-13 whole blood Control genomic DNA


title: control-6 whole blood Control genomic DNA


title: control-14 whole blood Control genomic DNA


title: control-7 whole blood Control genomic DNA


title: control-28 whole blood Control genomic DNA


title: control-3 whole blood Control genomic DNA


title: control-11 whole blood Control genomic DNA


title: control-10 whole blood Control genomic DNA


title: control-2 whole blood Control genomic DNA


title: KDM6A-1 whole blood KDM6A pathogenic genomic DNA

value: Validation cohort

value: KDM6A variant


title: control-5 whole blood Control genomic DNA


title: control-8 whole blood Control genomic DNA


title: control-4 whole blood Control genomic DNA


title: KMT2D-36 whole blood KMT2D pathogenic genomic DNA

value: KMT2D variant


title: KMT2D-37 whole blood KMT2D VUS genomic DNA


title: KMT2D-32 whole blood KMT2D pathogenic genomic DNA


title: KMT2D-28 whole blood KMT2D VUS genomic DNA


title: KMT2D-26 whole blood KMT2D likely pathogenic genomic DNA


title: KMT2D-33 whole blood KMT2D likely pathogenic genomic DNA


title: KMT2D-29 whole blood KMT2D pathogenic genomic DNA


title: KMT2D-30 whole blood KMT2D likely pathogenic genomic DNA


title: KMT2D-25 whole blood KMT2D likely pathogenic genomic DNA


title: KMT2D-27 whole blood KMT2D VUS genomic DNA


title: control-1 whole blood Control genomic DNA


title: KMT2D-23 whole blood KMT2D VUS genomic DNA


title: control-15 whole blood Control genomic DNA


title: control-12 whole blood Control genomic DNA


title: KMT2D-19 whole blood KMT2D VUS genomic DNA

value: KMT2D sequence variant


title: KMT2D-31 whole blood KMT2D VUS genomic DNA


title: KMT2D-18 whole blood KMT2D VUS genomic DNA


title: KMT2D-22 whole blood KMT2D likely pathogenic genomic DNA


title: KMT2D-17 whole blood KMT2D VUS genomic DNA


title: KMT2D-35 whole blood KMT2D VUS genomic DNA


title: KMT2D-21 whole blood KMT2D VUS genomic DNA


title: KMT2D-20 whole blood KMT2D VUS genomic DNA


title: control-9 whole blood Control genomic DNA


title: KMT2D-15 whole blood KMT2D VUS genomic DNA


title: KMT2D-10 whole blood KMT2D LOF genomic DNA

value: KMT2D LOF discovery cohort

value: Kabuki


title: KMT2D-11 whole blood KMT2D LOF genomic DNA


title: KMT2D-12 whole blood KMT2D VUS genomic DNA


title: KMT2D-9 whole blood KMT2D LOF genomic DNA


title: KMT2D-13 whole blood KMT2D VUS genomic DNA


title: KMT2D-5 whole blood KMT2D LOF genomic DNA


title: KMT2D-34 whole blood KMT2D VUS genomic DNA


title: CHD7-72 whole blood CHD7 pathogenic genomic DNA

value: CHD7 variant


title: KMT2D-1 whole blood KMT2D LOF genomic DNA


title: KMT2D-14 whole blood KMT2D VUS genomic DNA


title: KMT2D-3 whole blood KMT2D LOF genomic DNA


title: KMT2D-4 whole blood KMT2D LOF genomic DNA


title: KMT2D-7 whole blood KMT2D LOF genomic DNA


title: CHD7-68 whole blood CHD7 likely pathogenic genomic DNA


title: CHD7-70 whole blood CHD7 VUS genomic DNA


title: KMT2D-16 whole blood KMT2D VUS genomic DNA


title: KMT2D-2 whole blood KMT2D LOF genomic DNA


title: KMT2D-6 whole blood KMT2D LOF genomic DNA


title: CHD7-69 whole blood CHD7 pathogenic genomic DNA


title: KMT2D-8 whole blood KMT2D LOF genomic DNA


title: CHD7-65 whole blood CHD7 VUS genomic DNA


title: CHD7-62 whole blood CHD7 VUS genomic DNA


title: CHD7-66 whole blood CHD7 VUS genomic DNA


title: CHD7-58 whole blood CHD7 pathogenic genomic DNA


title: CHD7-61 whole blood CHD7 pathogenic genomic DNA


title: CHD7-56 whole blood CHD7 pathogenic genomic DNA


title: CHD7-59 whole blood CHD7 VUS genomic DNA


title: CHD7-54 whole blood CHD7 VUS genomic DNA


title: CHD7-71 whole blood CHD7 likely pathogenic genomic DNA


title: CHD7-63 whole blood CHD7 likely pathogenic genomic DNA


title: CHD7-57 whole blood CHD7 VUS genomic DNA


title: CHD7-45 whole blood CHD7 VUS genomic DNA


title: CHD7-67 whole blood CHD7 VUS genomic DNA


title: CHD7-53 whole blood CHD7 pathogenic genomic DNA


title: CHD7-52 whole blood CHD7 pathogenic genomic DNA


title: CHD7-48 whole blood CHD7 VUS genomic DNA


title: KMT2D-24 whole blood KMT2D VUS genomic DNA


title: CHD7-64 whole blood CHD7 pathogenic genomic DNA


title: CHD7-55 whole blood CHD7 pathogenic genomic DNA


title: CHD7-50 whole blood CHD7 VUS genomic DNA


title: CHD7-39 whole blood CHD7 VUS genomic DNA


title: CHD7-60 whole blood CHD7 pathogenic genomic DNA


title: CHD7-47 whole blood CHD7 pathogenic genomic DNA


title: CHD7-43 whole blood CHD7 VUS genomic DNA


title: CHD7-46 whole blood CHD7 pathogenic genomic DNA


title: CHD7-42 whole blood CHD7 VUS genomic DNA


title: CHD7-41 whole blood CHD7 pathogenic genomic DNA


title: CHD7-40 whole blood CHD7 pathogenic genomic DNA


title: CHD7-44 whole blood CHD7 VUS genomic DNA


title: CHD7-36 whole blood CHD7 pathogenic genomic DNA


title: CHD7-37 whole blood CHD7 VUS genomic DNA


title: CHD7-38 whole blood CHD7 VUS genomic DNA


title: CHD7-34 whole blood CHD7 pathogenic genomic DNA


title: CHD7-33 whole blood CHD7 VUS genomic DNA


title: CHD7-49 whole blood CHD7 VUS genomic DNA


title: CHD7-35 whole blood CHD7 VUS genomic DNA


title: CHD7-28 whole blood CHD7 VUS genomic DNA

value: CHD7 sequence variant


title: CHD7-21 whole blood CHD7 VUS genomic DNA


title: CHD7-23 whole blood CHD7 VUS genomic DNA


title: CHD7-18 whole blood CHD7 LOF genomic DNA

value: CHD7 LOF discovery cohort

value: CHARGE


title: CHD7-27 whole blood CHD7 VUS genomic DNA

value: male


title: CHD7-20 whole blood CHD7 VUS genomic DNA


title: CHD7-24 whole blood CHD7 VUS genomic DNA


title: CHD7-19 whole blood CHD7 LOF genomic DNA


title: CHD7-32 whole blood CHD7 VUS genomic DNA


title: CHD7-29 whole blood CHD7 VUS genomic DNA


title: CHD7-51 whole blood CHD7 pathogenic genomic DNA


title: CHD7-22 whole blood CHD7 VUS genomic DNA


title: CHD7-30 whole blood CHD7 VUS genomic DNA


title: CHD7-25 whole blood CHD7 VUS genomic DNA


title: CHD7-31 whole blood CHD7 VUS genomic DNA