title: Donor 2 - ChIPseq using H3K27Ac antibody - D4 (AT1-like) cells


title: Donor 2 - ChIPseq using H3K27Ac antibody - D0 (AT2) cells

status: Public on Oct 27 2021

type: SRA

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

state: CA

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

country: USA

institute: City of Hope

library_source: genomic

data_processing:
For DNA, Fastq files were aligned to the bisulfite hg19 genome by the USC Epigenome Center core. For RNA and ChIPseq, Reads were aligned to the canonical Hg19 genome using Bowtie 2.
For DNA, Bis-SNP was used for methylation and SNPtype calling (Liu et al., Genome Biology, 2012). For RNA, TopHat2 was used to assemble transcripts using Gencode. For ChIPseq, peaks were called using SICER with gap spacing of 600 for H3K27me3 and H3K79me2, gap spacing of 200 for other marks. MACS2 was also used to call enhancer regions for ROADMAP/ENCODE comparisons.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNA and ChIPseq have aligned bigwig files.
Supplementary_files_format_and_content: DNA files have peak domains in R files for processed UMR, LMR, and PMR regions.
Supplementary_files_format_and_content: UMRsLMRs.gr.D0.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: UMRsLMRs.gr.D4.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: UMRsLMRs.gr.D6.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: PMDs.D0dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: PMDs.D4dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: PMDs.D6dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: UMRsLMRs.D0.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: UMRsLMRs.D4.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: UMRsLMRs.D6.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D0dna.tab: partially methylated domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D4dna.tab: partially methylated domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D6dna.tab: partially methylated domains tab-delimited file.

molecule: genomic DNA

organism: Homo sapiens

source_name: purified primary AT2 cells

growth_protocol: Primary AT2 cells were extracted as described previously and differentiated in vitro for six days (Marconett et al., PLoS Genetics, 2013).

extract_protocol:
DNA, RNA, and ChIP material were prepared as previously published (Zuber et al., JNCI, 2016).
Library construction was performed at the USC Epigenome Center core, as previously described (Zuber et al., JNCI, 2016).
WGBS Indexes were included on Donor 1 samples. Donor 1 D0 Index : TGACCA, Donor 1 D2 Index: CAGTG, Donor 1 D4 Index: GCCAAT, Donor 1 D6 Index: CAGATC. ChIPseq samples were multiplexed on Illumina HiSeq2000 lanes, the indicated adapters on FASTQ files were used to de-multiplex.

treatment_protocol: Purified DNA underwent bisulfite treatment as described previously (Zuber et al., JNCI, 2016). RNA underwent polyA selection and library preparation as previously described (Zuber at al., 2016). ChIP material underwent adapter ligation, library preparation, and multiplexed sequencing as previously described (Zuber et al., 2016).

tag: cell type

value: purified primary AT2 cells

tag: time point

tag: chip antbody

tag: donor

tag: material type

value: ChIP DNA


title: sample 39, PPMS 11

status: Public on Dec 14 2021

type: RNA

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description: Gene expression data for a patient with PPMS

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Thermo Fisher Scientific.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.2 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.
Exon-level processed data are available on the series record.

label: Biotin

molecule: total RNA

source_name: B cells from the peripheral blood

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Twenty ml of peripheral blood were taken from MS patients during regular clinical visits as well as from healthy donors at the Rostock University Medical Center.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll density gradient separation (Histopaque-1077, Sigma-Aldrich). Untouched B cells were then enriched from the PBMC by negative selection using the Pan B Cell Isolation Kit (Miltenyi Biotec). Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) in combination with the RNase-free DNase set (Qiagen).

treatment_protocol: The patients were treated with different therapies according to the approved labels and the guidelines and recommendations of the German Society of Neurology.

tag: subject identifier

tag: group

value: PPMS patient

tag: therapy

value: glucocorticosteroids

tag: Sex

value: male

tag: age (years)

tag: disease duration (years)

tag: edss score

tag: relapses in previous year


title: Donor 2 - ChIPseq using H3K4me1 antibody - D4 (AT1-like) cells

source_name: In vitro differentiated AT1-like cells

value: In vitro differentiated AT1-like cells


title: sample 36, PPMS 8


title: Donor 2 - ChIPseq using H3K4me1 antibody - D6 (AT1-like) cells


title: sample 38, PPMS 10


title: sample 27, healthy control 27

description: Gene expression data for a healthy individual

value: healthy control


title: Donor 2 - ChIPseq using H3K4me1 antibody - D0 (AT2) cells


title: sample 28, healthy control 28

value: female


title: Donor 2 - ChIPseq input DNA for normalization - D4 (AT1-like) cells

value: ChIP INPUT DNA


title: sample 31, PPMS 3


title: sample 24, healthy control 24


title: sample 32, PPMS 4


title: sample 23, healthy control 23


title: sample 25, healthy control 25


title: sample 22, healthy control 22


title: Donor 2 - ChIPseq input DNA for normalization - D0 (AT2) cells


title: sample 29, PPMS 1


title: Donor 1 - ChIPseq using CTCF antibody - D0 (AT2) cells

value: CTCF


title: Donor 1 - FAIRE library - D6 (AT1-like) cells

data_processing:
Library strategy: FAIRE
For DNA, Fastq files were aligned to the bisulfite hg19 genome by the USC Epigenome Center core. For RNA and ChIPseq, Reads were aligned to the canonical Hg19 genome using Bowtie 2.
For DNA, Bis-SNP was used for methylation and SNPtype calling (Liu et al., Genome Biology, 2012). For RNA, TopHat2 was used to assemble transcripts using Gencode. For ChIPseq, peaks were called using SICER with gap spacing of 600 for H3K27me3 and H3K79me2, gap spacing of 200 for other marks. MACS2 was also used to call enhancer regions for ROADMAP/ENCODE comparisons.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNA and ChIPseq have aligned bigwig files.
Supplementary_files_format_and_content: DNA files have peak domains in R files for processed UMR, LMR, and PMR regions.
Supplementary_files_format_and_content: UMRsLMRs.gr.D0.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: UMRsLMRs.gr.D4.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: UMRsLMRs.gr.D6.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: PMDs.D0dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: PMDs.D4dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: PMDs.D6dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: UMRsLMRs.D0.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: UMRsLMRs.D4.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: UMRsLMRs.D6.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D0dna.tab: partially methylated domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D4dna.tab: partially methylated domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D6dna.tab: partially methylated domains tab-delimited file.

value: FAIRE DNA


title: sample 30, PPMS 2


title: Donor 2 - ChIPseq input DNA for normalization - D6 (AT1-like) cells


title: Donor 1 - FAIRE library - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using CTCF antibody - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K79me2 antibody - D6 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K27me3 antibody - D0 (AT2) cells


title: Donor 1 - ChIPseq using H3K27Ac antibody - D6 (AT1-like) cells


title: Donor 1 - FAIRE library - D0 (AT2) cells


title: Donor 1 - ChIPseq using H3K9Ac antibody - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K27Ac antibody - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K79me2 antibody - D0 (AT2) cells


title: Donor 1 - ChIPseq using H3K27me3 antibody - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K9Ac antibody - D6 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K27Ac antibody - D0 (AT2) cells


title: Donor 1 - ChIPseq using H3K9Ac antibody - D0 (AT2) cells


title: Donor 1 - ChIPseq using CTCF antibody - D6 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K4me1 antibody - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K4me1 antibody - D0 (AT2) cells


title: Donor 1 - ChIPseq input DNA for normalization - D6 (AT1-like) cells


title: Donor 1 - ChIPseq input DNA for normalization - D0 (AT2) cells


title: Donor 1 - ChIPseq using H3K79me2 antibody - D4 (AT1-like) cells


title: Donor 1 - ChIPseq input DNA for normalization - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K27me3 antibody - D6 (AT1-like) cells


title: SLL006: genomic DNA from CLL/SLL (FFPE)

status: Public on Sep 02 2021

type: genomic

city: Toronto

first: Daniel

last: Xia

address: 200 Elizabeth Street

country: Canada

institute: University Health Network

description: CLL/SLL

hyb_protocol: Labeled DNA was incubated at 48°C for 16–24 hours

scan_protocol: Arrays were imaged using an Illumina iScan instrument

data_processing:
Methylation data were extracted and normalized using the Bioconductor package minfi v1.30
Average Beta or normalized (Illumina method) Average Beta (beta_TGL51_illumina_annot_geo.csv)

label: Cy3 and Cy5

source_name: chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL)

label_protocol: 250ng of DNA were subjected to bisulphite conversion using the Zymo EZ DNA Methylation kit, followed by amplification, fragmentation and fluorophore-labeled

extract_protocol: Genomic DNA was extracted and purified from FFPE samples using Qiagen QIAamp DNA FFPE Tissue Kit and processed with the FFPE DNA Restoration Kit (Illumina)

tag: disease state

value: Lymphoma

tag: disease subtype

value: CLL/SLL


title: AAV-SYN nfected 2

status: Public on Jun 20 2021

city: Birmingham

first: David

last: Figge

state: AL

address: 1719 6th Ave. S, CIRC 520

department: Neurology

institute: University of Alabama-Birmingham

library_source: transcriptomic

data_processing:
Sequencing files were processed, mapped to mm10, and count matrices were extracted using the Cell Ranger 308 Single Cell Software (v 3.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: barcodes, features, and matrix files are tsv, mtx, and gunzipped

organism: Mus musculus

source_name: ventral midbrain

extract_protocol:
Sorted cells were loaded onto the 10X Chromium 303 platform (10X genomics), and libraries were constructed using the Single Cell 3′ 304 Reagent Kit V2 according to the manufacturer’s instructions.
10x Genomics Single Cell 3' Reagent Kit V2. Samples were sequenced to an average   depth of 20,000 reads per cell on an Illumina NovaSeq

tag: tissue

value: Pooled Ventral Midbrain from AAV-SYN infected animal

tag: strain


title: AAV-SYN infected 1


title: SLL004: genomic DNA from CLL/SLL (FFPE)

description: CLL/SLL


title: Patient sample BACI217

status: Public on Jun 08 2021

city: Chapel Hill

first: Kim Lab

last: UNC

state: NC

address: 450 West Drive, Room 21-209

institute: UNC-CH LCCC

data_processing:
Reads were aligned with STAR aligner to (GrCH38 version 22) human assembly using the STAR/Salmon pipeline (Dobin et al, 2013).
Expression was quantified using the RSEM package (Li & Dewey, 2011) and the GrCH38 human transcriptome reference
Genes were filtered for a minimum expression count (at least 10 reads in at least 5 samples), and for a protein coding annotation by Ensemble (final set of genes = 16,901).
Differential expression was assessed using the DESeq2 package (Love et al, 2014) on this filtered set of genes.
For all other analyses, all expression values were log2(1+x) transformed, median centered and upper quartile scaled.
Genome_build: GrCH38 v.22
Supplementary_files_format_and_content: BACI_log_trans_normalized_RNAseq.csv = Log transformed and filtered read count output in comma separated values format.
Supplementary_files_format_and_content: salmon_tpm_gene.matrix.tsv = TPM values in tab-delimited text format.

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2093

extract_protocol:
DNA and RNA were extracted from macrodissected FFPE sections using the truXTRAC FFPE total nucleic acid kit (Covaris).
DNA was sequenced far a targeted mutation panel comprising 144 genes using the OmniSeq Comprehensive® assay (OmniSeq®) Buffalo New York.  Sequencing was performed using the ION CHEF and Ion S5XL 540 NGS chip using 30ng DNA input.  A no template control (NTC), CNV negative (NA12878 FFPE DNA), SNV/Indel positive, CNV gain positive and CNV loss positive control sample was included in each run
RNA was used to generate sequencing libraries using the SureSelect XT RNA direct prep kit (Agilent Technologies).  Libraries were individually captured, reviewed for appropriate size using an Agilent Bioanalyzer or TapeStation trace, and quantitated using the KAPA library quantitation kit (Roche) prior to equal molar pooling.

tag: gender

value: F

tag: race

value: White

tag: ethnicity

value: Not Hispanic or Latino

tag: age

tag: smoking status

value: Former

tag: histology

value: Transitional cell carcinoma

tag: overall survival

tag: alive

value: Yes

tag: primary tumor location

value: Bladder

tag: ecog

value: N

value: Pembrolizumab

tag: pfs

tag: progressed

tag: tmb

value: Intermediate


title: AAV-GFP infected 1

value: Pooled Ventral Midbrain from AAV-GFP infected animal


title: Patient sample BACI211

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2091

value: TCC with other histologies mixed

value: Small cell neuroendocrine w/ TCC components

value: No

value: Y

value: Atezolizumab

value: PD

value: High


title: Patient sample BACI210

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2090

value: M

value: Unknown


title: Patient sample BACI212

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2119

value: Not Hispanic or Latino

value: Former

value: Low


title: Patient sample BACI219

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2121

value: White

value: Transitional cell carcinoma

value: Yes

value: Bladder


title: Donor 1 - ChIPseq using H3K4me1 antibody - D6 (AT1-like) cells

tag: cell type

value: In vitro differentiated AT1-like cells

tag: time point

tag: chip antbody

tag: donor

tag: material type

value: ChIP DNA


title: Patient sample BACI207

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2088

tag: gender

tag: race

value: Black or African American

value: Ureter/renal pelvis

value: N

value: Pembrolizumab

value: PR

value: Intermediate


title: Patient sample BACI208

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2103

value: F

tag: ethnicity

tag: age

value: Y

value: CR

value: No


title: Patient sample BACI205

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2118

value: M

value: Not Hispanic or Latino

tag: smoking status

value: Former

tag: histology

value: NX

value: MX

value: PD

value: Low


title: Patient sample BACI203

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2102

value: White

value: Transitional cell carcinoma

tag: overall survival

tag: alive

value: Bladder

value: Yes


title: Patient sample BACI204

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2086

value: Current

value: TCC with other histologies mixed

value: Transitional cell with squamous differentiation

tag: primary tumor location

tag: ecog

value: N

value: Pembrolizumab


title: Patient sample BACI201

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2084

value: F

value: Y

tag: pfs

tag: progressed


title: Patient sample BACI199

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2082

value: Not Hispanic or Latino

value: Never

value: Transitional cell with micropapillary features

value: No

value: Atezolizumab

tag: tmb

value: Intermediate


title: Patient sample BACI195

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2079

value: White

value: Former

value: Ureter/renal pelvis

value: PD

value: FAIL


title: Patient sample BACI202

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2085

value: M

value: Black or African American

value: TCC with other histologies mixed

value: Bladder

value: Yes

value: Low


title: Patient sample BACI193

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2078

value: F

value: Not Hispanic or Latino

value: Transitional cell carcinoma

value: N

value: Y


title: Patient sample BACI194

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2126

value: Pembrolizumab

value: High


title: Patient sample BACI196

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2080

value: White

value: Former

value: Transitional cell with small nested variant

value: No


title: Patient sample BACI191

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2077

value: M

value: Light

value: SD

value: Intermediate


title: Patient sample BACI190

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2076

value: non-TCC

value: Small cell neuroendocrine

value: Bladder

value: Atezolizumab

value: PD

value: Yes


title: Patient sample BACI192

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2117

value: F

value: Black or African American

value: Not Hispanic or Latino

value: Transitional cell carcinoma

value: N

value: Y

value: PR


title: AAV-GFP infected 2

source_name: ventral midbrain

tag: tissue

value: Pooled Ventral Midbrain from AAV-GFP infected animal

tag: strain


title: Patient sample BACI189

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2075

value: White

value: Never

value: TCC with other histologies mixed

value: Transitional cell with sarcomatoid features

value: No

value: Pembrolizumab

value: Low


title: Patient sample BACI188

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2074

value: Transitional cell with squamous differentiation

value: Ureter/renal pelvis

value: Durvalumab

value: PD

value: Intermediate


title: Patient sample BACI186

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2100

value: F

value: Black or African American

value: Not Hispanic or Latino

value: Former

value: TCC w/ micropapillary and glandular diff

value: Yes

value: Bladder

value: Atezolizumab

value: CR


title: Patient sample BACI206

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2087

value: M

value: White

value: Transitional cell carcinoma

value: No

value: N

value: Y


title: Patient sample BACI185

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2073

value: Never

value: TCC with other histologies mixed

value: TCC w/ nested and clear cell morphology

value: PD

value: Low


title: Patient sample BACI209

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2089

value: F

value: Not Hispanic or Latino

value: Transitional cell with squamous differentiation

value: Pembrolizumab

value: High


title: Patient sample BACI180

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2068

value: Current

value: Bladder

value: Atezolizumab

value: SD

value: Yes

value: Intermediate


title: Patient sample BACI174

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2115

value: M

value: White

value: Former

value: Transitional cell carcinoma

value: No

value: N

value: Y


title: Patient sample BACI177

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2116

value: Not Hispanic or Latino

value: PD

value: Low


title: Patient sample BACI173

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2064

value: Never

value: Pembrolizumab


title: Patient sample BACI182

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2070

value: F

value: Black or African American

value: TCC with other histologies mixed

value: TCC w/ small nested/signet-ring cell morph

value: Bladder


title: Patient sample BACI172

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2063

value: M

value: TCC w/ smallcell/neuroendocrine and glandular diff

value: Yes

value: Atezolizumab

value: PR

value: High


title: Patient sample BACI170

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2062

value: Current

value: Transitional cell carcinoma

value: No

value: N

value: Y

value: Intermediate


title: Patient sample BACI175

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2065

value: White

value: Not Hispanic or Latino

value: Former

value: Nivolumab

value: PD


title: Patient sample BACI181

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2069

value: M

value: Bladder

value: Pembrolizumab

value: Low


title: Patient sample BACI178

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2099

value: F

value: Never

value: Yes


title: Patient sample BACI169

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2061

value: Transitional cell carcinoma

value: Ureter/renal pelvis


title: Patient sample BACI167

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2059

value: TCC with other histologies mixed

value: Transitional cell with squamous features

value: No

value: N


title: Patient sample BACI164

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2056

value: White

value: Not Hispanic or Latino


title: Patient sample BACI165_1

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2057

value: Transitional cell with micropapillary features

value: Y

value: Atezolizumab

value: Intermediate


title: Patient sample BACI165_2

value: M

value: Bladder

value: PD


title: Patient sample BACI162

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2113

value: Former

value: Low


title: Patient sample BACI187

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2101

value: Transitional cell carcinoma

value: Yes


title: Patient sample BACI197

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2081

value: Never

value: Pembrolizumab


title: Patient sample BACI159

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2054

value: PR

value: No

value: High


title: Patient sample BACI163

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2055

value: White

value: Not Hispanic or Latino

value: N


title: Patient sample BACI158

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2053

value: F

value: TCC with other histologies mixed

value: TCC w/ squamous diff and focal glandular diff

value: Y


title: Patient sample BACI157

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2052

value: M

value: Transitional cell with squamous differentiation

value: Ureter/renal pelvis


title: Patient sample BACI183

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2071

value: Former

value: Sarcomatoid w/ small cell and TCC w/ squam diff

value: Bladder

value: Nivolumab

value: PD

value: Low


title: Patient sample BACI160

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2124

value: Transitional cell carcinoma

value: No

value: Avelumab

value: Yes

value: High


title: Patient sample BACI156

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2051

value: White

value: Not Hispanic or Latino

value: N

value: Atezolizumab

value: Intermediate


title: Patient sample BACI161

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2125

value: F

value: Y


title: Patient sample BACI184

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2072

value: M

value: Former


title: Patient sample BACI155

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2050

value: Black or African American

value: Bladder

value: Pembrolizumab


title: Patient sample BACI153

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2048

value: Never

value: Transitional cell carcinoma

value: Durvalumab

value: PD


title: Patient sample BACI152

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2123

value: TCC with other histologies mixed

value: Transitional cell with myxoid stroma

value: Yes

value: SD


title: Patient sample BACI151

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2047

value: White

value: Not Hispanic or Latino

value: N

value: Atezolizumab

value: PR


title: Patient sample BACI144

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2043

value: M

value: No

value: Y

value: Intermediate


title: Patient sample BACI148

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2112

value: Former

value: Transitional cell with squamous differentiation

value: Bladder

value: Pembrolizumab


title: Patient sample BACI149

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2045

value: Black or African American

value: Light

value: Transitional cell carcinoma

value: PD


title: Patient sample BACI139

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2039

value: F

value: Never

value: TCC with other histologies mixed

value: TCC w/ focal squamous differentiation

value: Yes


title: Patient sample BACI142

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2041

value: M

value: Not Hispanic or Latino

value: Current

value: N


title: Patient sample BACI136

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2037

value: Asian

value: Former

value: Ta

value: No

value: Ureter/renal pelvis

value: Y

value: Low


title: Patient sample BACI138

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2111

value: White

value: Transitional cell with squamous differentiation

value: Bladder

value: Atezolizumab

value: CR

value: High


title: Patient sample BACI137

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2038

value: M

value: Never

value: Transitional cell carcinoma

value: PD

value: Yes

value: Intermediate


title: Patient sample BACI133

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2098

value: Not Hispanic or Latino

value: Current

value: N


title: Patient sample BACI135

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2036

value: Black or African American

value: No

value: Y

value: Pembrolizumab


title: Patient sample BACI128

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2033

value: F

value: White

value: Bladder

value: Low


title: Patient sample BACI131

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2097

value: M

value: Atezolizumab


title: Patient sample BACI123

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2096

value: Light

value: Transitional cell carcinoma


title: Patient sample BACI124

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2030

value: PD

value: Yes


title: Patient sample BACI117

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2027

value: Not Hispanic or Latino

value: Intermediate


title: Patient sample BACI154

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2049

value: Never

value: TCC with other histologies mixed

value: TCC w/ squamous diff and sarcomatoid features

value: Ureter/renal pelvis

value: N


title: Patient sample BACI118

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2094

value: F

value: No

value: Y

value: Pembrolizumab


title: Patient sample BACI122

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2029

value: White

value: Former

value: Bladder

value: High


title: Patient sample BACI126

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2032

value: M

value: Small cell with TCC component

value: Nivolumab

value: PD

value: Low


title: Patient sample BACI121

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2110

value: Black or African American

value: Not Hispanic or Latino

value: Light

value: Transitional cell carcinoma

value: Yes


title: Patient sample BACI114

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2026

value: F

value: N

value: PR

value: No


title: Patient sample BACI150

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2046

value: White

value: Never

value: Y

value: Pembrolizumab

value: Intermediate


title: Patient sample BACI120

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2095

value: M

value: Current

value: Bladder

value: Atezolizumab

value: CR

value: High


title: Patient sample BACI113

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2025

value: Not Hispanic or Latino

value: Former

value: Transitional cell carcinoma


title: Patient sample BACI119

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2028

value: TCC with other histologies mixed

value: Transitional cell with sarcomatoid features

value: N

value: PD

value: Yes


title: Patient sample BACI111

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2023

value: White

value: No

value: Y

value: PR


title: Patient sample BACI116

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2122

value: F

value: NX

value: Low


title: Patient sample BACI110

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2109

value: M

value: Ureter/renal pelvis

value: Atezolizumab


title: Patient sample BACI112

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2024

value: Not Hispanic or Latino

value: Never

value: Bladder

value: CR

value: Intermediate


title: Patient sample BACI109

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2022

value: Transitional cell carcinoma

value: N

value: Pembrolizumab

value: SD

value: High


title: Patient sample BACI143

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2042

value: Black or African American

value: Former

value: TCC with other histologies mixed

value: Transitional cell with squamous differentiation

value: No

value: Y

value: PD

value: Yes


title: Patient sample BACI107

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2021

value: M

value: White

value: Not Hispanic or Latino

value: Atezolizumab


title: HSC_d20_IL1_1_E061316

status: Public on Apr 09 2021

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
DIFFERENTIAL EXP. - cufflinks-2.0.2 (cuffdiff) "--library-type fr-firststrand --FDR 0.05 -u -b GENOME" and deSeq2_1.12.3
Genome_build: GRCm38.p4 + Gencode-M6 Annotation
Supplementary_files_format_and_content: raw gene counts

source_name: SLAM_IL-1β 20 days

extract_protocol:
RNA was purified from sorted SLAM cells using RNEasy Micro kit (Qiagen) according to manufacturer's instructions.
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA) per manufacturer’s recommendations. RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated by the HiSeq2500 (Illumina, San Diego, CA).

treatment_protocol: IL-1 beta or PBS was injected intraperitoneally into mice (0.5 microg/mouse/day) for 1 or 20 days.

value: Bone marrow

tag: cell type

value: SLAM cells (LSK/Flk2-/CD48-/CD150+)

tag: treatment

value: IL-1β 20 days  (0.5 ug/day)


title: HSC_d20_IL1_2_E061316


title: HSC_d20_ctrl_2_E061316

source_name: SLAM_PBS 20 days

value: PBS 20 days


title: HSC_d1_IL1_10k

source_name: SLAM_IL-1β 1 day

value: IL-1β 1 day  (0.5 ug/day)


title: HSC_d1_IL1_2_E060216


title: HSC_20d_ctrl_4


title: HSC_d20_ctrl_1_E061316


title: HSC_20d_ctrl_3


title: Ctrl_HSC_10k

source_name: SLAM_PBS 1 day

value: PBS 1 day


title: HSC_20d_IL1_3


title: HSC_d1_ctrl_1_E060216


title: HSC_20d_IL1_4


title: HSC_d1_IL1_1_E060216


title: T-ALL_sample_730

status: Public on Mar 01 2021

city: Paris

first: Vahid

last: Asnafi

address: 149 rue de Sèvres

country: France

institute: Universite de Paris (Descartes)

description: genomic data from T-ALL leukemic blasts

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

scan_protocol: Standard Illumina Protocol

data_processing:
Raw IDAT files were processed with RnBeads bioconductor package and background normalized to produce methylation beta values
Mat_processed.tsv includes normalized data matrix includes normalized (NOOB) beta values
Mat_signal_intesities.tsv includes Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Leukemic Bone Marrow

label_protocol: Standard Illumina Protocol

extract_protocol: DNA isolation using Qiagen blood and tissue isolation kit according to manufacturer's protocol

tag: gender

value: Female

tag: diagnosis

value: T-ALL

value: T-ALL Bone Marrow


title: T-ALL_sample_724

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_727

description: genomic data from T-ALL leukemic blasts

value: Male


title: T-ALL_sample_733

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_RAD_MI

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_728

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_732

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_POT_EL

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_726

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_701

description: genomic data from T-ALL leukemic blasts


title: HSC_ctrl_2_E060216


title: T-ALL_sample_702

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_723

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_699

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_690

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_698

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_689

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_691

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_677

description: genomic data from T-ALL leukemic blasts


title: Patient sample BACI140

source_name: Patient with metastatic UC treated with ICB at a single academic medical center from 2014-2040

tag: race

value: Unknown

tag: ethnicity

value: Hispanic or Latino

value: Current

value: Transitional cell carcinoma

value: Bladder

value: N

value: Y

value: Pembrolizumab

value: Low


title: T-ALL_sample_679

description: genomic data from T-ALL leukemic blasts

tag: age


title: T-ALL_sample_676

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_667

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_655

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_661

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_638

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_670

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_649

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_623

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_607

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_599

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_624

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_626

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_642

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_646

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_666

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_621

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_635

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_622

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_627

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_628

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_617

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_601

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_595

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_592

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_587

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_590

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_600

description: genomic data from T-ALL leukemic blasts


title: HU-1-32_untreated_timepoint1

status: Public on Mar 15 2021

city: Ulm

first: Deyan

middle: Yordanov

last: Yosifov

address: Albert-Einstein-Allee 23

department: Internal Medicine III

institute: University Hospital Ulm

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChips using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan reader with standard recommended settings

data_processing: The raw data were processed using the RnBeads package in R/Bioconductor. Probes known to be cross-reactive (43 230) or overlapping known single-nucleotide polymorphisms (SNPs; 8 710), as well as probes giving unreliable measurements (1039 as determined by the Greedycut algorithm) were excluded from analysis. The data from the remaining 432 598 probes were subjected to background subtraction using the Noob method and beta-mixture quantile normalization (BMIQ). This normalization strategy successfully mitigated the inherent bias in β-value distributions between the two different types of probes (Infinium I and II) that are present on the HumanMethylation450 BeadChip. In a subsequent step, probes of non-CpG context (1 242), probes binding to sequences on sex chromosomes (9 941), probes with missing values (198) and probes with low standard deviation (57 109) were filtered out. The data obtained by the remaining 364 108 probes were used in downstream analyses.

source_name: CLL, untreated

extract_protocol: Genomic DNA was extracted from CD19+ fractions of patients' peripheral blood mononuclear cells (PBMCs) using Qiagen AllPrep Kit according to standard instructions

tag: Sex

value: male

tag: treated

value: no

tag: response to therapy

value: not applicable

value: unmutated


title: T-ALL_sample_583

description: genomic data from T-ALL leukemic blasts


title: HU-1-31_untreated_timepoint1


title: T-ALL_sample_557

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_552

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_584

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_572

description: genomic data from T-ALL leukemic blasts


title: HU-1-12_untreated_timepoint1

value: female


title: T-ALL_sample_576

description: genomic data from T-ALL leukemic blasts

value: Female

value: T-ALL


title: T-ALL_sample_567

description: genomic data from T-ALL leukemic blasts

value: Male

value: T-ALL Bone Marrow


title: HU-1-11_untreated_timepoint1


title: T-ALL_sample_571

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_586

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_570

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_585

description: genomic data from T-ALL leukemic blasts


title: HU-1-07_untreated_timepoint1


title: HU-1-19_untreated_timepoint1


title: T-ALL_sample_569

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_565

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_597

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_551

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_573

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_549

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_547

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_593

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_546

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_534

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_558

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_528

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_515

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_522

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_507

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_533

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_523

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_532

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_529

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_525

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_506

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_486

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_487

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_489

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_494

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_491

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_498

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_485

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_481

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_482

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_680

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_539

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_477

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_527

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_550

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_479

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_474

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_497

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_470

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_469

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_421

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_428

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_451

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_429

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_460

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_468

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_466

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_389

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_415

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_409

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_407

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_417

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_419

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_392

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_420

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_464

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_380

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_375

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_480

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_381

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_371

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_244

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_256

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_255

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_242

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_243

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_465

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_238

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_231

description: genomic data from T-ALL leukemic blasts


title: T-ALL_sample_366

description: genomic data from T-ALL leukemic blasts


title: bone_marrow_PMF_stable_disease_sample_26

status: Public on Feb 08 2021

city: Hannover

first: Helge

last: Stark

address: Carl-Neuberg-Straße 1

department: Institute of Pathology

institute: Medical School Hannover

description: SD-26 (failed QC sample)

hyb_protocol: EZ-96 DNA Methylation-Lightning Kit and according to Infinium HD AssayMethylation Protocol

scan_protocol: According to Infinium HD AssayMethylation Protocol

data_processing: R packages: MethylAid (version 1.12.0), ChAMP (version 2.9.10)

label: QuDye dsDNA

source_name: bone marrow

label_protocol: Qubit dsDNA HS assay kit (Life Technologies, Carlsbad, U.S.A.)

extract_protocol: Maxwell RSC DNA FFPE Kit (Promega, Madison, U.S.A.) on a Maxwell RSC instrument (Promega)

value: total bone marrow


title: bone_marrow_PMF_fibrotic_progression_sample_74

description: FP-74 (training sample)


title: bone_marrow_PMF_stable_disease_sample_8

description: SD-8 (training sample)


title: bone_marrow_PMF_stable_disease_sample_10

description: SD-10 (training sample)


title: bone_marrow_PMF_stable_disease_sample_4

description: SD-4 (failed QC sample)


title: bone_marrow_PMF_stable_disease_sample_25

description: SD-25 (validation sample)


title: bone_marrow_PMF_stable_disease_sample_1

description: SD-1 (failed QC sample)


title: bone_marrow_PMF_fibrotic_progression_sample_72

description: FP-72 (training sample)


title: bone_marrow_PMF_stable_disease_sample_16

description: SD-16 (training sample)


title: bone_marrow_PMF_fibrotic_progression_sample_9

description: FP-9 (training sample)


title: bone_marrow_PMF_stable_disease_sample_7

description: SD-7 (training sample)


title: bone_marrow_PMF_stable_disease_sample_14

description: SD-14 (training sample)


title: bone_marrow_PMF_fibrotic_progression_sample_6

description: FP-6  (validation sample)


title: bone_marrow_PMF_stable_disease_sample_6

description: SD-6 (validation sample)


title: bone_marrow_PMF_stable_disease_sample_18

description: SD-18 (training sample)


title: bone_marrow_PMF_stable_disease_sample_24

description: SD-24 (validation sample)


title: bone_marrow_PMF_fibrotic_progression_sample_54

description: FP-54 (validation sample)


title: bone_marrow_PMF_fibrotic_progression_sample_8

description: FP-8 (training sample)


title: bone_marrow_PMF_stable_disease_sample_12

description: SD-12 (validation sample)


title: 199_smp_82

status: Public on Jan 27 2021

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Processed data matrix includes Average Beta values.

source_name: bone marrow aspirate

extract_protocol: DNA was extracted  using the QIAamp DNA Blood Mini Kit (Qiagen, Werfen).

value: bone marrow aspirate

value: high-risk Myelodysplastic Syndromes and secondary Acute Myeloid Leukemia

tag: time afer diagnosis

value: DX

value: AZA

tag: response

value: YES


title: 187_smp_78

value: other


title: bone_marrow_PMF_fibrotic_progression_sample_47

description: FP-47 (training sample)


title: 201_smp_83


title: bone_marrow_PMF_stable_disease_sample_23

description: SD-23 (validation sample)


title: 170_smp_74


title: bone_marrow_PMF_stable_disease_sample_11

description: SD-11 (training sample)


title: 164_smp_71


title: bone_marrow_PMF_stable_disease_sample_9

description: SD-9 (training sample)


title: bone_marrow_PMF_stable_disease_sample_5

description: SD-5 (training sample)


title: bone_marrow_PMF_fibrotic_progression_sample_42

description: FP-42 (validation sample)


title: 154_smp_65


title: bone_marrow_PMF_fibrotic_progression_sample_70

description: FP-70 (training sample)


title: 157_smp_67


title: 156_smp_66


title: bone_marrow_PMF_fibrotic_progression_sample_62

description: FP-62 (training sample)


title: 145_smp_62


title: 144_smp_61

value: NO


title: 149_smp_64


title: 130_smp_57


title: 136_smp_59


title: 112_smp_51


title: 110_smp_50

value: > or equal to 12M


title: 106_smp_48


title: bone_marrow_PMF_stable_disease_sample_27

description: SD-27 (validation sample)

value: male


title: 126_smp_55


title: 104_smp_46


title: 93_smp_42


title: 100_smp_45


title: 90_smp_41


title: 108_smp_49


title: bone_marrow_PMF_stable_disease_sample_13

description: SD-13 (validation sample)


title: 79_smp_38


title: 69_smp_32


title: bone_marrow_PMF_stable_disease_sample_20

description: SD-20 (training sample)


title: 64_smp_29


title: 66_smp_31


title: 61_smp_26


title: 49_smp_21


title: 27_smp_13


title: 21_smp_10


title: 58_smp_25


title: 29_smp_14


title: 56_smp_24


title: MII-12m-6-D

status: Public on Jan 08 2021

first: Thomas

last: Chan

address: Room623, Area 39, CUHK, Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
RNA-seq: Raw reads were trummed by Trim Galore
Trimmed reads were aligned to reference genome(mm10) using Tophat.
Expression levels of transcripts and genes were calculated, and differential expression was compared with Cufflinks.
Bisulfite-seq: Reads with poor quality and adapter contaminations were filtered when Trim Galore. The trimmed reads were mapped to the mouse reference genome (mm10) using Bismark in single-end mode to increase mapping efficiency, and two seperated bams from the same sample were merged. Duplication removal and methylation call extraction were also performed by Bismark
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include FPKM values for each Sample ; Bisulfite-seq: bedgraph files include methylation level of all called cytosine sites.

source_name: MII oocyte

extract_protocol:
Bisulfite-seq: To construct the scBS-seq libraries, 60fg of unmethylated lambda DNA was added into the retained lysis solution containing a nucleus. Pico Methyl-Seq Library Prep Kit (Zymo) was used for library construction strictly followed by the manufacturer’s manual. The quality of all constructed libraries was assessed by Agilent Bioanalyzer 2100 with High Sensitivity DNA Kit (Agilent Technologies). Qualified libraries were sequenced on Illumina HiSeq4000 to generate 150bp pair-end reads."
RNA and gDNA were separated from a single oocyte followed by the published protocol with minor modification. Frozen oocytes in PCR tubes were thawed at room temperature for around 5 minutes. The 7µl of soft lysis buffer (500mM KCl, 100 mM Tris-HCl pH=8, 1.35mM MgCl2, 4.5mM DTT, 0.45% Nonidet P-40, 0.18U SUPERase-In and 0.36U RNase-inhibitor) was added into each PCR tube containing a single oocyte, and the lysate was inhibited at 4˚C for 30 min. The tubes were vortexed at room temperature for one minute and then were centrifuged at 1000xg for 5 min. RNA in the cytoplasm was released to the lysate and gDNA storing in the nucleus was at the bottom of the tube. The 6.5µl of lysate supernatant was carefully transferred to another PCR tube for the following RNA-seq. The remaining nucleus with around 2.5µl of lysis buffer was subjected for performing bisulfite sequencing.

treatment_protocol: For collecting oocytes in the stage of metaphase II (MII oocyte), female mice underwent superovulation according to the established protocol. Briefly, mice were injected intraperitoneally with ten units of pregnant mare’s serum gonadotropin (PMSG, Sigma) at 7 pm on the first day. Then, at 7 pm on the third day, they underwent the intraperitoneal injection of 10 units of human chorionic gonadotropin (hCG, Sigma). 14 hours later, mice were sacrificed by cervical dislocation. Ovary tying with oviduct and part of the uterus were dissected out and put in M2 medium (Sigma). Though chopping the ampulla of oviduct by needle, oocyte-cumulus-complex (COC) were harvested and transferred to a droplet of 100 µl M2 medium containing 1% hyaluronidase (Sigma) to detach cumulus cells from oocytes. After incubation at room temperature for 1-2 minutes, cumulus-free metaphase II (MII) oocytes were successively transferred to two droplets of M2 medium and three droplets of PBS by mouth pipette for washing. Finally, each oocyte within 1-2 µl of PBS was transferred into one PCR tube and was kept in -80˚C freezer for further experiments.

value: 12 months

value: MII oocyte


title: 3_smp_2


title: bone_marrow_PMF_fibrotic_progression_sample_34

description: FP-34 (training sample)


title: MII-12m-4-D


title: MII-12m-3-D


title: 48_smp_20


title: MII-12m-5-D


title: bone_marrow_PMF_fibrotic_progression_sample_30

description: FP-30 (training sample)


title: MII-12m-1-D


title: MII-12m-6-R

extract_protocol:
RNA-seq: Library preparation for scRNA-seq was according to the modified protocol of Smart-seq2. In brief, the mixture of 2µl of 10mM oligo-dT30VN primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’) and 2µl of 10mM dNTP mix was added into the lysate supernatant, and the sample was inhibited at 72˚C for 3 min. Then, the 9.5µl of reverse transcription mixture (200U SuperScript II reverse transcriptase, 20U RNAse inhibitor, 1x Superscript II first-strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1µM TSO (5’-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’) was added into the tube for RNA reverse transcription. The tubes containing total 20µl mixture were put into ProFlex PCR System (Thermo Fisher Scientific) and the reaction condition was as follows: 42˚C for 90min, followed by ten cycles of 50 ˚C for 2 min and 42 ˚C for 2 min. The final enzyme inactivation was performed at 70˚C for 15 min. After finishing the first-strand reaction, the 30µl of PCR preamplification mix (1x KAPA HiFi HotStart ReadyMix, 0.1µM IS PCR primers (5’-AAGCAGTGGTATCAACGCAGAGT-3’)) were added into the tube containing 20µl of the first-strand reaction. PCR preamplification reaction was performed in ProFlex PCR System by using the following program: 98˚C for 3 min, 18 cycles of 98˚C for 20s, 67˚C for 15s and 72˚C for 6min, with the final extension cycle of 72˚C for 5min. Amplified cDNA was purified by using Ampure XP beads (1:1 ratio) according to the manufacturer’s manual and was eluted in 15µl of ddH2O in the end. To check the quality of the cDNA library, 1µl of amplified cDNA was removed to perform additional same PCR amplification reaction as mentioned above and PCR product was run on a 1% agarose gel at 100 Volts for 45min. The yield of amplified cDNA was measure by Qubit3.0 fluorometer. 5ng of amplified cDNA with good quality were used for library construction with TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme) followed by the instruction.
RNA and gDNA were separated from a single oocyte followed by the published protocol with minor modification. Frozen oocytes in PCR tubes were thawed at room temperature for around 5 minutes. The 7µl of soft lysis buffer (500mM KCl, 100 mM Tris-HCl pH=8, 1.35mM MgCl2, 4.5mM DTT, 0.45% Nonidet P-40, 0.18U SUPERase-In and 0.36U RNase-inhibitor) was added into each PCR tube containing a single oocyte, and the lysate was inhibited at 4˚C for 30 min. The tubes were vortexed at room temperature for one minute and then were centrifuged at 1000xg for 5 min. RNA in the cytoplasm was released to the lysate and gDNA storing in the nucleus was at the bottom of the tube. The 6.5µl of lysate supernatant was carefully transferred to another PCR tube for the following RNA-seq. The remaining nucleus with around 2.5µl of lysis buffer was subjected for performing bisulfite sequencing.


title: MII-12m-2-D


title: MII-12m-4-R


title: MII-12m-2-R


title: bone_marrow_PMF_fibrotic_progression_sample_26

description: FP-26 (training sample)


title: MII-12m-1-R


title: 43_smp_17


title: 25_smp_12


title: bone_marrow_PMF_fibrotic_progression_sample_11

description: FP-11 (validation sample)


title: MII-12m-3-R


title: MII-12m-5-R


title: Cell86_scHiC

status: Public on Oct 22 2020

city: Cambridge

first: Aleksandra

last: Galitsyna

state: Massachusetts

address: 77 Massachusetts Avenue

department: IMES

institute: Massachusetts Institute of Technology

data_processing:
The reads for both population and single cell .fastq.gz files were mapped to dm3 reference genome with bwa-mem with default parameters. Only reads that mapped to chromosomes chr2L, chr2R, chr3L, chr3R and chr4 were selected.
Population data files were processed with an early version of pairtools (a timestamp at https://github.com/agalitsyna/pairsamtools) with --walks-policy mask, replicates were merged and deduplicated (--max-mismatch 1).
The pairs were binned at 1 Kb resolution with cooler (https://github.com/mirnylab/cooler version 0.7.6), balanced with default options and stored in .cool format.
Bam files were processed with an early version of pairtools (a timestamp at https://github.com/agalitsyna/pairsamtools) with an adapted annotation and filtering protocol (--walks-policy ligation_junctions --add-columns rfrag).
In this adapted protocol only chimeric reads traversing DpnII restriction sites were considered as contact pairs. Both ends of chimeric parts at the junction should map closer than 10 base pairs to DpnII restriction site in order to be considered a true contact pair observed in the experiment.
Replicates were merged by concatenation of files with pairs.
WGA duplicates were filtered out by retaining only one contact per each pair of restriction fragments. The best 20 cells were selected based on the number of retrieved contacts (Cell1-Cell20) and retained for subsequent processing.
The pairs were binned at 1 Kb resolution with cooler and stored in .cool format. No correction was used for single cells. .cool files were used for downstream analysis.
Full processing procedure can be found at GitHub repository https://github.com/agalitsyna/sc_dros.
Genome_build: dm3
Supplementary_files_format_and_content: We provide .cool processed files for population and 20 individual cell of the best quality as 10 kb resolution .cool files (https://github.com/mirnylab/cooler). We also provide file with merged contacts from all the cells.

organism: Drosophila melanogaster

source_name: ML-DmBG3-c2 cells

growth_protocol: Drosophila melanogaster ML-DmBG3-c2 cell line (Drosophila Genomics Resource Center) was grown at 25°C in a mixture (1:1 v/v) of Shields and Sang M3 insect medium (Sigma) and Schneider’s Drosophila Medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), 50 units/ml penicillin, and 50 µg/ml streptomycin.

extract_protocol:
We used previously published protocol of single-nucleus Hi-C [PMID:28355183] with minor modifications. 5-10 million cells were fixed in 1× phosphate buffered solution (PBS) with 2% formaldehyde for 10 minutes with occasional mixing. The reaction was quenched with by addition of 2 M glycine to a final concentration of 125 mM. Cells were pelleted by centrifugation (1,000 g, 10 minutes, 4 °C), resuspended in 50 μl of 1× PBS, snap-frozen in liquid nitrogen and stored at -80 °C. Cells were lysed in 1.5 ml of isotonic buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.5% (v/v) NP-40 substitute (Fluka), 1% (v/v) Triton-X100 (Sigma), 1× Halt™ Protease Inhibitor Cocktail (Thermo Scientific)) on ice for 15 minutes. Cells were pelleted by centrifugation at 2,500g for 5 minutes, resuspended in 100 μl of 1× DpnII buffer (NEB) and pelleted again. The pellet was resuspended in 200 μl of 0.3% SDS in 1.1× DpnII buffer and incubated at 37 °C for 1 hour. Then 330 μl of 1.1× DpnII buffer and 53 μl of 20% Triton X-100 (Sigma) were added, and the suspension was incubated at 37 °C for 1 hour. Next, 600 U of DpnII enzyme (NEB) were added, and the chromatin was digested overnight (14-16 hours) at 37 °C with shaking (1,400 rpm). In the morning, 200 U of DpnII enzyme were added and the cells were incubated for additional 2 hours. DpnII was then inactivated by incubation at 65 °C for 20 minutes. Nuclei were pelleted by centrifugation at 3,000 g for 5 minutes, resuspended in 100 μl of 1× T4 DNA ligase buffer (Fermentas) and pelleted again. The pellet was resuspended in 400 μl of 1× T4 DNA ligase buffer, and 75 U of T4 DNA ligase (Fermentas) were added. Chromatin fragments were ligated at 16 °C for 6 hours. Next, the nuclei were pelleted by centrifugation at 5,000 g for 5 minutes, resuspended in 100 μl of sterile 1× PBS, stained with Hoechst, and single nuclei were isolated into wells of a standard 96-well PCR plate (Thermo Fisher) using FACS (BD FACSAriaTMIII). Each well contained 3 μl of sample buffer from illustra GenomiPhi v2 DNA amplification kit (GE Healthcare). Sample buffer drops containing isolated nuclei were covered by 5 μl of mineral oil (Thermo Fisher), incubated at 65 °C for 3 hours to reverse formaldehyde cross-links. Total DNA was amplified according to a previously published protocol [PMID:18533898]. The amplification was considered successful if the sample contained ≥1 μg DNA.
Samples were prepared for sequencing using Illumina TruSeq reagents (NEB) according to the manufacturer's instruction.

tag: cell line


title: Cell87_scHiC


title: Cell81_scHiC


title: population_HiC


title: Cell85_scHiC


title: Cell82_scHiC


title: Cell84_scHiC


title: Cell80_scHiC


title: Cell77_scHiC


title: Cell88_scHiC


title: Cell78_scHiC


title: Cell72_scHiC


title: Cell73_scHiC


title: Cell75_scHiC


title: Cell76_scHiC


title: Cell74_scHiC


title: Cell71_scHiC


title: Cell70_scHiC


title: Cell68_scHiC


title: Cell67_scHiC


title: Cell83_scHiC


title: Cell66_scHiC


title: Cell65_scHiC


title: Cell64_scHiC


title: Cell79_scHiC


title: Cell69_scHiC


title: Cell62_scHiC


title: Cell58_scHiC


title: Cell61_scHiC


title: Cell59_scHiC


title: Cell53_scHiC


title: Cell60_scHiC


title: Cell51_scHiC


title: Cell54_scHiC


title: Cell56_scHiC


title: Cell52_scHiC


title: Cell45_scHiC


title: Cell57_scHiC


title: Cell46_scHiC


title: Cell48_scHiC


title: Cell50_scHiC


title: Cell42_scHiC


title: Cell43_scHiC


title: Cell40_scHiC


title: Cell41_scHiC


title: Cell38_scHiC


title: Cell39_scHiC


title: Cell55_scHiC


title: Cell47_scHiC


title: bone_marrow_PMF_fibrotic_progression_sample_32

description: FP-32 (training sample)

value: female


title: Cell44_scHiC


title: Cell37_scHiC


title: Cell63_scHiC


title: Cell49_scHiC


title: Cell35_scHiC


title: Cell36_scHiC


title: bone_marrow_PMF_fibrotic_progression_sample_21

description: FP-21 (training sample)


title: Cell34_scHiC


title: Cell32_scHiC


title: Cell29_scHiC


title: Cell30_scHiC


title: Cell24_scHiC


title: Cell26_scHiC


title: Cell22_scHiC


title: Cell23_scHiC


title: Cell27_scHiC


title: Cell25_scHiC


title: Cell21_scHiC


title: Cell20_scHiC


title: Cell16_scHiC


title: Cell18_scHiC


title: Cell17_scHiC


title: Cell19_scHiC


title: Cell14_scHiC


title: Cell13_scHiC


title: Cell12_scHiC


title: Cell11_scHiC


title: Cell10_scHiC


title: Cell31_scHiC


title: Cell8_scHiC


title: Cell7_scHiC


title: Cell6_scHiC


title: Cell33_scHiC


title: Cell9_scHiC


title: Cell4_scHiC


title: Cell28_scHiC


title: Cell2_scHiC


title: DNA methylation from T-ALL ALL_1994 EPICarray

status: Public on Sep 24 2020

city: South San Francisco

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium HumanMethylationEPIC BeadChip (Illumina) using standard Illumina protocol

data_processing:
RnBeads.hg19 in R (versions >3.4). β values were obtained after filtering and normalization using the default preprocessing pipeline.
Normalized (RnBeads, SWAN normalization) Average Beta

source_name: Blast from the bone marrow

extract_protocol: genomic DNA was extracted by a SDS-containing lysis buffer containing proteinase K and purified by isopropanol precipitation. 250ng of DNA was used for bisulfite conversion by the EZ DNA methylation Kit (Zymo Research).

value: Blast from the bone marrow

tag: disease state


title: DNA methylation from T-ALL ALL_1890 EPICarray

value: T-ALL


title: DNA methylation from T-ALL ALL_2000 EPICarray


title: DNA methylation from T-ALL ALL_1895 EPICarray


title: DNA methylation from T-ALL ALL_1886 EPICarray


title: DNA methylation from T-ALL ALL_1865 EPICarray


title: Cell1_scHiC


title: DNA methylation from T-ALL ALL_1909 EPICarray


title: DNA methylation from T-ALL ALL_1752 EPICarray


title: DNA methylation from T-ALL ALL_1606 EPICarray


title: DNA methylation from T-ALL ALL_1583 EPICarray


title: DNA methylation from T-ALL ALL_1743 EPICarray


title: DNA methylation from T-ALL ALL_1603 EPICarray


title: DNA methylation from T-ALL ALL_1654 EPICarray


title: DNA methylation from T-ALL ALL_1450 EPICarray


title: DNA methylation from T-ALL ALL_1490 EPICarray


title: Cell5_scHiC


title: DNA methylation from T-ALL ALL_1428 EPICarray


title: DNA methylation from T-ALL ALL_1264 EPICarray


title: DNA methylation from T-ALL ALL_1260 EPICarray


title: DNA methylation from T-ALL ALL_1256 EPICarray


title: DNA methylation from T-ALL ALL_1381 EPICarray


title: DNA methylation from T-ALL ALL_2003 EPICarray


title: DNA methylation from T-ALL ALL_1230 EPICarray


title: DNA methylation from T-ALL ALL_1413 EPICarray


title: DNA methylation from T-ALL ALL_1228 EPICarray


title: Cell3_scHiC


title: DNA methylation from T-ALL ALL_1472 EPICarray


title: DNA methylation from T-ALL ALL_0984 EPICarray


title: DNA methylation from T-ALL ALL_1121 EPICarray


title: DNA methylation from T-ALL ALL_1025 EPICarray


title: DNA methylation from T-ALL ALL_1095 EPICarray


title: DNA methylation from T-ALL ALL_1090 EPICarray


title: DNA methylation from T-ALL ALL_1192 EPICarray


title: DNA methylation from T-ALL ALL_0882 EPICarray


title: DNA methylation from T-ALL ALL_0933 EPICarray


title: DNA methylation from T-ALL ALL_0949 EPICarray


title: DNA methylation from T-ALL ALL_0940 EPICarray


title: DNA methylation from T-ALL ALL_1006 EPICarray


title: DNA methylation from T-ALL ALL_0859 EPICarray


title: DNA methylation from T-ALL ALL_0788 EPICarray


title: DNA methylation from T-ALL ALL_0858 EPICarray


title: DNA methylation from T-ALL ALL_0677 EPICarray


title: DNA methylation from T-ALL ALL_0630 EPICarray


title: DNA methylation from T-ALL ALL_0601 EPICarray


title: DNA methylation from T-ALL ALL_0698 EPICarray


title: DNA methylation from T-ALL ALL_0501 EPICarray


title: DNA methylation from T-ALL ALL_0473 EPICarray


title: DNA methylation from T-ALL ALL_0330 EPICarray


title: DNA methylation from T-ALL ALL_0388 EPICarray


title: DNA methylation from T-ALL ALL_0319 EPICarray


title: DNA methylation from T-ALL ALL_0398 EPICarray


title: Cell15_scHiC


title: DNA methylation from T-ALL ALL_0286 EPICarray


title: DNA methylation from T-ALL ALL_0310 EPICarray


title: DNA methylation from T-ALL ALL_0252 EPICarray


title: DNA methylation from T-ALL ALL_0207 EPICarray


title: DNA methylation from T-ALL ALL_0170 EPICarray


title: DNA methylation from T-ALL ALL_0221 EPICarray


title: DNA methylation from T-ALL ALL_0062 EPICarray


title: DNA methylation from T-ALL ALL_0070 EPICarray


title: DNA methylation from T-ALL ALL_0168 EPICarray


title: DNA methylation from T-ALL ALL_0116 EPICarray


title: DNA methylation from T-ALL ALL_0001 EPICarray


title: DNA methylation from T-ALL ALL_2495 EPICarray


title: DNA methylation from T-ALL ALL_2373 EPICarray


title: DNA methylation from T-ALL ALL_1939 EPICarray


title: DNA methylation from T-ALL ALL_2095 EPICarray


title: DNA methylation from T-ALL ALL_1633 EPICarray


title: DNA methylation from T-ALL ALL_2245 EPICarray


title: DNA methylation from T-ALL ALL_2428 EPICarray


title: DNA methylation from T-ALL ALL_0291 EPICarray


title: DNA methylation from T-ALL ALL_1829 EPICarray


title: DNA methylation from T-ALL ALL_2160 EPICarray


title: DNA methylation from T-ALL ALL_2408 EPICarray


title: DNA methylation from T-ALL ALL_2237 EPICarray


title: DNA methylation from T-ALL ALL_1489 EPICarray


title: DNA methylation from T-ALL ALL_2425 EPICarray


title: DNA methylation from T-ALL ALL_2523 EPICarray


title: DNA methylation from T-ALL ALL_1389 EPICarray


title: DNA methylation from T-ALL ALL_0073 EPICarray


title: DNA methylation from T-ALL ALL_2341 EPICarray


title: DNA methylation from T-ALL ALL_2223 EPICarray


title: DNA methylation from T-ALL ALL_0060 EPICarray


title: DNA methylation from T-ALL ALL_1701 EPICarray


title: DNA methylation from T-ALL ALL_0019 EPICarray


title: DNA methylation from T-ALL ALL_2042 EPICarray


title: DNA methylation from T-ALL ALL_2049 EPICarray


title: DNA methylation from T-ALL ALL_2067 EPICarray


title: DNA methylation from T-ALL ALL_1422 EPICarray


title: DNA methylation from T-ALL ALL_2205 EPICarray


title: DNA methylation from T-ALL ALL_2155A EPICarray


title: DNA methylation from T-ALL ALL_1853 EPICarray


title: DNA methylation from T-ALL ALL_1357 EPICarray


title: DNA methylation from T-ALL ALL_2156A EPICarray


title: DNA methylation from T-ALL ALL_2101 EPICarray


title: DNA methylation from T-ALL ALL_2452 EPICarray


title: DNA methylation from T-ALL ALL_2362 EPICarray


title: DNA methylation from T-ALL ALL_2374 EPICarray


title: DNA methylation from T-ALL ALL_2513 EPICarray


title: HepLPC rep2

status: Public on Jul 30 2020

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

country: China

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks.
and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: liver progenitor cells

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The paired-end libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: 8-week-old of lineage tracing models including tdTomato mice with AAV8-TBG-Cre and AlbCreERT/R26GFP were purified for hepatocytes and non-parenchymal cells respectively, and cultured for transition to progenitor-like cells in transision and expansion media.The differences between these two were clarified by RNA sequencing.

value: liver progenitor-like cells derived from hepatocytes and non-parenchymal cells

value: 6-8 weeks


title: HepLPC rep1


title: DNA methylation from T-ALL ALL_1660 EPICarray


title: NPC_LPCs rep1

value: liver progenitor-like cells derived from non-parenchymal cells


title: NPC_LPCs rep2


title: Donor 3: intermediate cell phenotype (D2)

status: Public on Jul 01 2020

description: RiboZero depleted RNAseq

data_processing:
Raw reads were aligned to the genome using Tophat2.1
BAM files were used to construct BigWig files for visualization
Genome_build: hg19

source_name: primary alveolar epithelial cells taken from human remnant transplant lung

growth_protocol: PurifiedAT2 cells were harvested from a human lung donor without prior history of lung disease and differentiated in vitro for 6 days

extract_protocol:
RNA was isolated using whole-cell extract by performing RNA purification using the Illustra TriplePrep kit.
Library construction was performed at the USC Epigenome center.
Barcodes were attached;  Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Sample underwent Paired End 50 cycling. Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1.

value: intermediate differentiation AEC cells

tag: donor


title: Donor 3: AT1-like cells (D4)

description: RiboZero depleted RNAseq

value: AT1-like cells


title: Donor 2: AT1-like cells (D6)

description: RiboZero depleted RNAseq


title: Donor 3: AT1-like cells (D6)

description: RiboZero depleted RNAseq


title: Donor 3: purified AT2 cells (D0)

description: RiboZero depleted RNAseq

value: Purified primary AT2 cells


title: Donor 2: purified AT2 cells (D0)

description: RiboZero depleted RNAseq


title: Donor 2: intermediate cell phenotype (D2)

description: RiboZero depleted RNAseq


title: DNA methylation from T-ALL ALL_2221 EPICarray

tag: tissue


title: Donor 1: purified AT2 cells (D0)

description: RiboZero depleted RNAseq


title: Donor 1: AT1-like cells (D6)

description: RiboZero depleted RNAseq


title: Donor 1: AT1-like cells (D4)

description: RiboZero depleted RNAseq


title: Donor 2: AT1-like cells (D4)

description: RiboZero depleted RNAseq


title: Donor 1: intermediate cell phenotype (D2)

description: RiboZero depleted RNAseq


title: DNA methylation from T-ALL ALL_1702 EPICarray


title: D4 cells Replicate 1

description: total miRNA from D4 cells

hyb_protocol: unknown

scan_protocol: Scan date 5/13/11 10:36 using Agilent Technologies Scanner G2505C US45102918 using one-color scanning

data_processing: MicroRNA array data were processed using AgiMicroRNA package  in R. Microarray data identification of significantly affected miRNAs over the course of alveolar transdifferentiation utilized ANOVA with a Benjamini-Hochburg FDR correction.

source_name: human AT differentiating (D4) cells Replicate 1

label_protocol: MiRNA expression was assessed on the Agilent MicroRNA Array v2.0 platform

growth_protocol: Primary AEC were isolated and cultured as described previously (Marconett et al., PLoS genetics 2013).

extract_protocol: RNA was harvested from each biological replicate on Day 0 (D0), D2, D4, D6, and D8. miRNA was extracted with the MirVana miRNA isolation kit (Thermo Fisher Scientific)

treatment_protocol: No Treatment

value: 61 years old

value: caucasian


title: D2 cells Replicate 2

description: total miRNA from D2 cells

source_name: human AT differentiating (D2) cells Replicate 2

value: 49 years old


title: D6 cells Replicate 3

description: total miRNA from D6 cells

source_name: human AT1-like (D6) cells Replicate 3

value: 47 years old


title: D6 cells Replicate 1

description: total miRNA from D6 cells

source_name: human AT1-like (D6) cells Replicate 1


title: D4 cells Replicate 2

description: total miRNA from D4 cells

source_name: human AT differentiating (D4) cells Replicate 2


title: D8 cells Replicate 3

description: total miRNA from D8 cells


title: D8 cells Replicate 2

description: total miRNA from D8 cells

source_name: human AT1-like (D6) cells Replicate 2


title: D8 cells Replicate 1

description: total miRNA from D8 cells


title: D6 cells Replicate 2

description: total miRNA from D6 cells


title: D4 cells Replicate 3

description: total miRNA from D4 cells

source_name: human AT differentiating (D4) cells Replicate 3


title: K562_rep2_Red-C

status: Public on May 15 2020

description:
purified RNA-DNA chimeras
Red-C for K562 replicate 2

data_processing:
Library strategy: Red-C
For Red-C, we filtered out possible PCR duplicates with FastUniq based on the first 50 bp of both forward and reverse reads. We cut low-quality ends of reads with TRIMMOMATIC (window size: 5, quality threshold: 26).
Each read was scanned for the adapter, bridge sequence and GGG/CCC oligonucleotides. DNA sequence was extracted from the forward read, parts of RNA sequence could be present at both forward and reverse reads resulting in two sequences, RNA 3' and RNA 5'.  We used parameters: “-k 100 --no-spliced-alignment --no-softclip” for DNA and “-k 100 --no-softclip --dta-cufflinks” for RNAs (--known-splicesite-infile, splicing sites annotation was taken from gencode v19 for hg19 genome and gencode v34 for hg38 genome). SAM files were filtered for unique mappings with at most two mismatches relative to the reference genome with samtools and converted to BED with bedtools. Only reads with DNA, 3’ RNA and 5' RNA parts uniquely mapped to canonical chromosomes were selected.
The mapped parts were annotated by MmeI and NlaIII restriction sites. We deleted contacts for which either 3' or 5' RNA end was mapped close to NlaIII or MmeI cut. We required 3' RNA and 5' RNA parts to be mapped to the opposite strands of the same chromosome at a distance of no more than 10 Kb from each other.
Resulting files were saved as TSV files with the header. For more details see Methods section of the paper and github: https://github.com/agalitsyna/RedClib
For RNA-Seq, we run hisat2 with the same parameters as for RNA parts for Red-C (see above).
RNA-Seq reads were intersected with gene annotation from GENCODE (release 27 (GRCh37); basic gene annotation); piRNAs annotation from piRNABank; tRNAs annotation from UCSC (track: tRNA Genes; table: tRNAs); set of rRNAs, snRNAs, scRNAs, tRNAs, RNAs, srpRNAs from UCSC (track: RepeatMAsker; table: rmsk); vlinc from G. Laurent et al. (https://link.springer.com/article/10.1186/gb-2013-14-7-r73)
Genome_build: hg19, hg38
Supplementary_files_format_and_content: Processed RedC data files are available as TSV files with individual mapped RNA-DNA contacts (for both hg19 and hg38 genome versions). Each row corresponds to an individual RNA-DNA contact that passed filtering steps. Columns represent information about 3' RNA, 5' RNA and DNA mapping position (chromosome, start, end, strand), CIGAR string and mapped sequence length.
Supplementary_files_format_and_content: RNA-Seq results are available as TSV file with annotated genes counts per replicateswih columns: gene name, gene type, counts of genes per replicate.

source_name: chronic myelogenous leukemia immortalized cell line K562

growth_protocol: Human K562 cells (ATCC® CCL-243™) were cultured in RPMI supplemented with 10% FBS and penicillin/streptomycin. Normal human skin fibroblasts (female 46XX) were cultured in DMEM supplemented with 10% FBS and penicillin/streptomycin. All cells were grown at 37°C and 5% CO2 in a conventional humidified CO2 incubator.

extract_protocol:
In Red-C experiments, cells were fixed with 1% formaldehyde, nuclei were isolated, DNA was fragmented with a restriction enzyme NlaIII, and the ends were blunted and A-tailed. RNA 3’ ends were ligated with a bridge adapter containing a biotinylated nucleotide followed by ligation of the opposite ends of the bridge with DNA ends in a spatial proximity. RNA-DNA chimeras were purified and excessive DNA was cut off with MmeI restriction enzyme whose recognition site is in the bridge. After biotin-pull down, reverse transcription was initiated from the bridge with template switching at the 5’ end of RNA (SMART technology) allowing for incorporation of a custom Illumina adapter. Finally, another Illumina adapter was ligated to DNA ends and the chimeras were amplified and paired-end sequenced on an Illumina platform. In the control experiment without DNA ligase, water was added instead of DNA ligase at the proximity ligation step. In the control experiment with RNase treatment, purified RNA-DNA chimeras were treated with RNase A prior to MmeI digestion.
In RNA-seq experiments, we isolated total cellular RNA from K562 cells using RNeasy Mini Kit (Qiagen) followed by removal of ribosomal RNA using Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina).
Red-C uses custom oligos and adapters resulting in libraries ready for sequencing on the Illumina platform. For RNA-seq we prepared strand-specific libraries using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

tag: cell cycle

value: asynchronous


title: K562_rep1_add_Red-C

description:
purified RNA-DNA chimeras
Red-C for K562 replicate 1 additional sequencing

tag: cell type


title: D2 cells Replicate 1

description: total miRNA from D2 cells

source_name: human AT differentiating (D2) cells Replicate 1


title: K562_rep1_RNASeq_RNA-Seq

description:
Total K562 cellular RNA depleted from ribosomal RNA replicate 1
The processed data file available at the foot of this record includes data for both replicate 1 (GSM4041596) and replicate 2 (GSM4041597).

data_processing:
For Red-C, we filtered out possible PCR duplicates with FastUniq based on the first 50 bp of both forward and reverse reads. We cut low-quality ends of reads with TRIMMOMATIC (window size: 5, quality threshold: 26).
Each read was scanned for the adapter, bridge sequence and GGG/CCC oligonucleotides. DNA sequence was extracted from the forward read, parts of RNA sequence could be present at both forward and reverse reads resulting in two sequences, RNA 3' and RNA 5'.  We used parameters: “-k 100 --no-spliced-alignment --no-softclip” for DNA and “-k 100 --no-softclip --dta-cufflinks” for RNAs (--known-splicesite-infile, splicing sites annotation was taken from gencode v19 for hg19 genome and gencode v34 for hg38 genome). SAM files were filtered for unique mappings with at most two mismatches relative to the reference genome with samtools and converted to BED with bedtools. Only reads with DNA, 3’ RNA and 5' RNA parts uniquely mapped to canonical chromosomes were selected.
The mapped parts were annotated by MmeI and NlaIII restriction sites. We deleted contacts for which either 3' or 5' RNA end was mapped close to NlaIII or MmeI cut. We required 3' RNA and 5' RNA parts to be mapped to the opposite strands of the same chromosome at a distance of no more than 10 Kb from each other.
Resulting files were saved as TSV files with the header. For more details see Methods section of the paper and github: https://github.com/agalitsyna/RedClib
For RNA-Seq, we run hisat2 with the same parameters as for RNA parts for Red-C (see above).
RNA-Seq reads were intersected with gene annotation from GENCODE (release 27 (GRCh37); basic gene annotation); piRNAs annotation from piRNABank; tRNAs annotation from UCSC (track: tRNA Genes; table: tRNAs); set of rRNAs, snRNAs, scRNAs, tRNAs, RNAs, srpRNAs from UCSC (track: RepeatMAsker; table: rmsk); vlinc from G. Laurent et al. (https://link.springer.com/article/10.1186/gb-2013-14-7-r73)
Genome_build: hg19, hg38
Supplementary_files_format_and_content: Processed RedC data files are available as TSV files with individual mapped RNA-DNA contacts (for both hg19 and hg38 genome versions). Each row corresponds to an individual RNA-DNA contact that passed filtering steps. Columns represent information about 3' RNA, 5' RNA and DNA mapping position (chromosome, start, end, strand), CIGAR string and mapped sequence length.
Supplementary_files_format_and_content: RNA-Seq results are available as TSV file with annotated genes counts per replicateswih columns: gene name, gene type, counts of genes per replicate.


title: fibr_rep1_add_Red-C

description:
purified RNA-DNA chimeras
Red-C for fibroblasts replicate 1 additional sequencing

source_name: normal human skin fibroblasts (female 46XX)

value: fibrroblasts


title: K562_rep1_rnase_Red-C

description:
purified RNA-DNA chimeras
Red-C control with Rnase for K562


title: fibr_rep2_Red-C

description:
purified RNA-DNA chimeras
Red-C for fibroblasts replicate 2


title: fibr_rep1_Red-C

description:
purified RNA-DNA chimeras
Red-C for fibroblasts replicate 1


title: D0 cells Replicate 2

description: total miRNA from D0 cells

source_name: human AT2 (D0) cells Replicate 2


title: K562_rep1_wo-ligase_Red-C

description:
purified RNA-DNA chimeras
Red-C control without ligase for K562


title: K562_rep2_RNASeq_RNA-Seq

description:
Total K562 cellular RNA depleted from ribosomal RNA replicate 2
Processed data for this sample are available in the supplementary file available on GSM4041596.


title: D0 cells Replicate 1

description: total miRNA from D0 cells

source_name: human AT2 (D0) cells Replicate 1


title: K562_rep1_Red-C

description:
purified RNA-DNA chimeras
Red-C for K562 replicate 1


title: D0 cells Replicate 3

description: total miRNA from D0 cells

source_name: human AT2 (D0) cells Replicate 3

value: male


title: Genomic DNA from T-cell lymphoblastic lymphoma 46

status: Public on May 04 2020

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850K Human Methylation BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
DNA methylation data were analyzed using the methylation analysis module within BeadStudio software employing default parameters (Illumina, Inc., San Diego CA, USA).
normalized_data.txt: Tab-delimited text file includes Normalized (Beta-Mixture Quantile dilation method) Average Beta.

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from T-LBL samples using Qiagen DNeasy Kit according to standard instructions.

value: T-cell lymphoblastic lymphoma

value: Relapse-free T-LBL


title: Genomic DNA from T-cell lymphoblastic lymphoma 44


title: Genomic DNA from T-cell lymphoblastic lymphoma 49

value: Relapse T-LBL


title: Genomic DNA from T-cell lymphoblastic lymphoma 48


title: D2 cells Replicate 3

description: total miRNA from D2 cells

source_name: human AT differentiating (D2) cells Replicate 3


title: Genomic DNA from T-cell lymphoblastic lymphoma 41


title: Genomic DNA from T-cell lymphoblastic lymphoma 40


title: Genomic DNA from T-cell lymphoblastic lymphoma 39


title: Genomic DNA from T-cell lymphoblastic lymphoma 37


title: Genomic DNA from T-cell lymphoblastic lymphoma 38


title: Genomic DNA from T-cell lymphoblastic lymphoma 42


title: Genomic DNA from T-cell lymphoblastic lymphoma 34


title: Genomic DNA from T-cell lymphoblastic lymphoma 33


title: Genomic DNA from T-cell lymphoblastic lymphoma 31


title: Genomic DNA from T-cell lymphoblastic lymphoma 29


title: Genomic DNA from T-cell lymphoblastic lymphoma 28


title: Genomic DNA from T-cell lymphoblastic lymphoma 32


title: Genomic DNA from T-cell lymphoblastic lymphoma 45


title: Genomic DNA from T-cell lymphoblastic lymphoma 36


title: Genomic DNA from T-cell lymphoblastic lymphoma 23


title: Genomic DNA from T-cell lymphoblastic lymphoma 22


title: Genomic DNA from T-cell lymphoblastic lymphoma 20


title: Genomic DNA from T-cell lymphoblastic lymphoma 24


title: Genomic DNA from T-cell lymphoblastic lymphoma 26


title: Genomic DNA from T-cell lymphoblastic lymphoma 27


title: Genomic DNA from T-cell lymphoblastic lymphoma 15


title: Genomic DNA from T-cell lymphoblastic lymphoma 21


title: Genomic DNA from T-cell lymphoblastic lymphoma 14


title: Genomic DNA from T-cell lymphoblastic lymphoma 16


title: Genomic DNA from T-cell lymphoblastic lymphoma 19


title: Genomic DNA from T-cell lymphoblastic lymphoma 13


title: Genomic DNA from T-cell lymphoblastic lymphoma 35


title: Genomic DNA from T-cell lymphoblastic lymphoma 12


title: Genomic DNA from T-cell lymphoblastic lymphoma 10


title: Genomic DNA from T-cell lymphoblastic lymphoma 3


title: Genomic DNA from T-cell lymphoblastic lymphoma 4


title: Genomic DNA from T-cell lymphoblastic lymphoma 1


title: Genomic DNA from T-cell lymphoblastic lymphoma 25


title: RNA_epi_WT_rep1

status: Public on Apr 06 2020

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

data_processing:
Basecalling pipeline: HiSeq Control Software 2.2.58 ; RTA 1.18.64.0 ; CASAVA-1.8.2
small RNA FASTQ file generation, demultiplexing and adapter removal was done by Fasteris.
Small RNA reads were filtered to 17-30nt long reads for analysis. Reads with identical sequence were grouped using the processReads function from the ncPRO-seq pipeline and aligned against A.thaliana’s genome (TAIR10) using bowtie2 (options : -k 100 --score-min L,0,0)
mRNA FASTQ file generation and demultiplexing was done by Fasteris.
Reads were timmed using Trimmomatic (v0.36) with parameters ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:50
Mapping to Arabidopsis genome (TAIR10) with Tophat (v2.0.11)  and Bowtie2 (v2.2.1.0)
Reads count with the featureCounts function from the Subread package with options -S rf -p -s 1 -C -B -O
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files including distinct sequences and reads count values.
Supplementary_files_format_and_content: Tab delimited text files of fragments count

organism: Arabidopsis thaliana

source_name: epidermis

growth_protocol: Plants were grown in soil under 12:12 light:dark conditions

extract_protocol:
Total cellular RNA was extracted using TRIzol reagent (Invitrogene)
Extracted RNA was processed into sequencing libraries using adapted Illumina protocols and sequenced at Fasteris (http://www.fasteris.com, Switzerland) using the Illumina HiSeq sequencer

tag: ecotype

tag: genotype

value: Col0 WT

value: epidermis

tag: development stage

value: 4-5 weeks old rosettes


title: Genomic DNA from T-cell lymphoblastic lymphoma 17


title: RNA_epi_WT_rep2


title: sarcoma classifier reference case 919

status: Public on Mar 01 2020

city: Heidelberg

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 919

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
Average Beta

source_name: sarcoma sample

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

value: sarcoma

tag: material preparation

value: FFPE


title: sarcoma classifier reference case 891

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 891