title: U251, TMZ-sensitive cell line-3

city: Nanjing

first: Yali

last: Zhou

address: 22 Hankou Road

institute: Nanjing University

description: LncRNA and mRNA expression profiles from TMZ-sensitive cell line

hyb_protocol: 0.1 µg Cy5-labeled aRNA of the respective sample was fragmented and hybridized onto HlncOA 1.0 using Phalanx OneArray hybridization kit (Phalanx Biotech Group). Hybridization was performed for 17h, rotating at a speed of 10rpm at 65℃ in an Agilent hybridization oven (G2545A). After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 and 1 minute with 37℃ Wash buffer 2.

scan_protocol: HlncOA 1.0arrays were scanned by Agilent Microarray Scanner (G2505C) HD_1X color protocol (Dye channel: R ; Scan resolution: 2 um; Tiff: 20-bit; Red PMT gain: 100%; XDR: No) and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by R language (v3.3.0). The probes will filter out control probes and normalized by median scaling method between all samples. Pair-wise comparisons between samples were calculated by Bioconductor limma package and presented by log2 fold change and p-value.

source_name: glioblastoma multiforme (GBM)

label_protocol: 0.5 µg of total RNA was reverse-transcribed and amplified using Onearray Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group). Indirect labeled the aa-UTP by NHS-Cy5 (AAT Bioquest ). Dye incorporation and aRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Trizol Reagent (Thermo Fisher Scientific) following the manufacture’s instructions. RNA quality was assessed by spectrophotometry (NanoDrop, ND1000) and gel electrophoresis. To be considered as high-quality, the RNA had to have the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

value: brain

tag: phenotype

value: TMZ-sensitive


title: R099-H-015

status: Public on Jul 02 2020

type: SRA

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

country: United Kingdom

institute: Cardiff University

description: Zeb1-/- CLP 3

library_source: transcriptomic

data_processing:
Trimming to remove adapter sequencer and poor quality ends of reads was performed by Trim Galore ( a wrapper to cutadapt). Trimming was performed using default parameters in paired-end mode.
Trimmed paired-end reads were aligned to the GRCm38 reference using STAR (v2.5.1b), an ultrafast universal RNA-seq aligner, following the 2-pass method.  STAR mapping was carried out using the MultimapNMax=1 flag, whereby reads that map to more than one genomic location are treated as being unmapped so as to excluded them from downstream analysis*.
Transcript level counts were calculated using Subread featureCounts Version 1.5.1. Transcript and locations used in the analysis derive from the GENCODE GRCm38 v17 gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files containing: ensemble transcript ID, chromosome, start and end locations, strand, transcripts length and counts in STAR mapped bam file.

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Cells were resuspended in RLT Plus buffer (Qiagen) and stored at -80 degrees. RNA extraction was carried out using a RNAeasy Plus micro kit (Qiagen) following the manufacturers instructions. Total RNA quality and quantity was assessed using Agilent 2100 Bioanalyser and a RNA Nano 6000 kit (Agilent Technologies). 30-260ng of Total RNA with a RIN value >8 was depleted of ribosomal RNA using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), (New England BioLabs, NEB)
Sequencing libraries were prepared using the NEB® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB). The steps included RNA fragmentation and priming, 1st strand cDNA synthesis, 2nd strand cDNA synthesis, adenylation of 3’ ends, adapter ligation, PCR amplification (11-cycles) and validation. The manufacturer’s instructions were followed. The libraries were validated using the Agilent 2100 Bioanalyser and a high-sensitivity kit (Agilent Technologies) to ascertain the insert size, and the Qubit® (Life Technologies) was used to perform the fluorometric quantitation. Following validation, the libraries were normalized to 10nM, pooled together and clustered on the cBot™2 following the manufacturer’s recommendations. The pool was then sequenced using a 75-base paired-end (2x75bp PE) dual index read format on the Illumina® HiSeq4000 according to the manufacturer’s instructions.

tag: strain

tag: genotype

value: Zeb1 KO

tag: tissue

value: bone marrow

tag: immunophenotype

value: Lin- Sca-1 low C-kit low CD127+


title: U251, TMZ-sensitive cell line-1

status: Public on Jul 03 2020

type: RNA

country: China

organism: Homo sapiens

tag: cell line


title: R099-H-014

description: Zeb1-/- CLP 2


title: U251, TMZ-resistant cell line-2

description: LncRNA and mRNA expression profiles from TMZ-resistant cell line

value: TMZ-resistant


title: R099-H-013

description: Zeb1-/- CLP 1


title: U251, TMZ-sensitive cell line-2


title: U251, TMZ-resistant cell line-3


title: R099-H-007

description: Wild Type CLP 3

value: Zeb1 WT


title: U251, TMZ-resistant cell line-1


title: R099-H-006

description: Wild Type CLP 2


title: R099-H-009

description: Zeb1-/- HSC 1

value: LSK CD48- CD150+ (HSC)


title: MM_VQ_D5_rep2

city: Milwaukee

first: Robert

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

country: USA

institute: Blood Research Institute, Versiti

data_processing:
Fastq data were aligned using STAR v2.6.1d using additional parameters: --quantMode GeneCounts --clip5pNbases 3
The number of reads aligning to the sense strand of each gene were retained for further analysis (present within the processed data file)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: csv of unnormalized read counts per gene per sample

source_name: Bone marrow donor derived plasma cells (CD138+ B220-)

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions.
RNA-Seq libraries were prepared using SMARTer® Stranded Total RNA-Seq Kit v1 - Pico Input Mammalian (Takara Bio USA/Clontech) as per manufacturer's protocol

tag: cell type

tag: background strain

value: V{kappa}*MYC; Nras LSL Q61R/+; IgG1-Cre (recipient)


title: tVk12653_rep2

value: Bone marrow donor derived plasma cells (CD138+ B220-)

value: tVk12653 (recipient)


title: V_rep2

source_name: Bone marrow derived plasma cells (CD138+ B220-)

value: V{kappa}*MYC; IgG1-Cre


title: V_rep3

value: Bone marrow derived plasma cells (CD138+ B220-)


title: MM_VQ_D4_rep1


title: tVk12653_rep1


title: MM_VQ_D1_rep2


title: WT_rep2

value: Wild-type


title: MM_VQ_D5_rep1


title: WT_rep3


title: WT_rep1


title: R099-H-005

description: Wild Type CLP 1


title: R099-H-008

description: Wild Type CLP 4


title: R3

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus_musculus/Ensembl/GRCm38.PatchesSkipped
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: MEFs

extract_protocol:
cell pellets were flash frozen. Cells were lysed using the QiaShredder kit. RNA was isolated with the Qiagen Rneasy Micro Kit including DNase digestion. After isolation, RNA quality was checked on a Fragment analyzer and concentrqation was meausred with the Qubit. RNA was diluted to a concentration of 20 ng/ul and frozen until library preparation.
The stranded TruSeq RNA Sample Prep Kit v2 (Illumina, Inc, CA, USA) was used in the succeeding steps. Briefly, mRNA was enriched from total RNA samples (100-1000 ng) using poly-A selection and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using the Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc.,). The libraries were normalized to 10 nM in 10 mM Tris-Cl/0.1% Tween 20, pH8.5.

value: mouse embryonic fibroblasts

tag: microbiota

value: not applicable

tag: treatment

value: untreated


title: M2T

source_name: m-ICc12 cells

value: m-ICc12 cells

value: 5 ng/ml TNF 8h


title: R2


title: M3


title: R1


title: M3T


title: M1T


title: MM_VQ_D1_rep1


title: Z918OT

source_name: Organoid Germ-free

value: Organoid

value: germ-free


title: M1


title: Z919OT


title: Z917OT


title: M2


title: Z917O


title: V_rep1


title: Z913O

source_name: Organoid SPF Facility 2


title: Z912O


title: Z911O


title: Z910O

source_name: Organoid SPF Facility 1


title: Z911OT


title: Z910OT


title: Z909O


title: Z908OT


title: Z913OT


title: Z909OT


title: Z912OT


title: Input

city: Portland

first: Theodore

middle: Paul

last: Braun

state: OR

address: 3181 SW Sam Jackson Park Road

department: Knight Cancer Institute

institute: OHSU

description: Input DNA

library_source: genomic

data_processing:
Raw reads were aligned to mm10 with Bowtie.
Chromatin Segmentation was Performed with ChromHMM.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bed files containing chromatin segmentation.

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: CEBPA/CSF3R murine leukemia cells were cultured in IMDM +20% FBS.

extract_protocol:
ChIP Seq performed using CST SimpleChIP Kit.
Libraries were constructed using NEB Ultra II library prep kit for Illumina.

treatment_protocol: Cells were treated with DMSO or 4 nM GSK-LSD1 for 48 hours.

tag: strain/background

value: BALB/c

value: CEBPA/CSF3R leukemia cells

tag: chip antibody


title: Z919O


title: Z918O


title: GSKLSD1-H3K27Ac

description:
ChIP DNA
processed data file: GSK_6_segments.bed


title: GSKLSD1-H3K4me3


title: DMSO-H3K27Ac

description:
ChIP DNA
processed data file: DMSO_6_segments.bed

value: DMSO


title: DMSO-H3K4me3


title: GSKLSD1-H3K4me1


title: IFT88_4hr_R2

city: Oxford

first: Angus

last: Wann

address: Roosevelt Drive, Headington

department: Kennedy Institute of Rheumatology

institute: University of Oxford

data_processing:
Sequence reads were aligned to the mouse genome with Hisat2 (version 2.1.0) using a “genome_trans” index built from the GRCm38 release of the mouse genome and Ensembl version 91 annotations (two-pass strategy to discover novel splice sites; with parameters: --dta and --score-min L,0.0,-0.2).
Mapped reads were counted using featureCounts (Subread version 1.6.3; Ensembl version 91 annotations; default parameters).
TPMs were estimated with salmon (salmon version 0.9.1); using a quasi-index (built with Ensembl version 91 annotations and k=31) and gc bias correction (parameter “--gcBias”)
Genome_build: GRCm38
Supplementary_files_format_and_content: (1) "featureCounts_raw_counts.txt" is a tab-delimited text file containing the table of gene-by-sample read counts computed with the featureCounts algorithm. (2) "salmon_tpms.txt" is a tab-delimited text file containing the table of gene-by-sample raw TPMs computed with salmon.

molecule: polyA RNA

source_name: chondrocyte cell line

growth_protocol: Cells were maintained in low glucose DMEM supplemented with 10% FCS, transfected using lipofectamine at 60% confluence, before growing to confluence and starting timecourse 48hrs later.

extract_protocol:
Total RNA was isolated using a QIAGEN RNAeasy microkit.
The mRNA fraction was selected from the total RNA provided before conversion to cDNA. The cDNA was end-repaired, A-tailed and adapter-ligated. The prepared libraries were size selected, multiplexed and QC’ed before paired end sequencing over three lanes of a flow cell.

treatment_protocol: Chondrocytes were treated with IL-1b 10ng/ml or vehicle. siRNA knock down: 50-60% confluent murine chondrocytes were incubated in murine primary media. Cells were transfected with 50nM of siRNA for IFT88 (IFT88 pool siRNA) or a non-targeting control siRNA (non-targeting pool).

value: fibroblastic chondrocyte cell line

value: IL-1 beta 10ng/ml

value: IFT88 pool siRNA


title: IFT88_2hr_R3


title: IFT88_8hr_R3


title: IFT88_8hr_R1


title: IFT88_8hr_R2


title: IFT88_4hr_R3


title: IFT88_4hr_R1


title: IFT88_24hr_R3


title: IFT88_1hr_R3


title: IFT88_24hr_R1


title: IFT88_2hr_R2


title: IFT88_1hr_R2


title: IFT88_24hr_R2


title: IFT88_1hr_R1


title: IFT88_0hr_R3

value: No IL-1 beta


title: IFT88_2hr_R1


title: IFT88_0hr_R1


title: Z908O


title: control_8hr_R3

value: WT + NT siRNA pool


title: control_8hr_R1


title: control_4hr_R2


title: control_4hr_R3


title: DMSO-H3K4me1


title: control_8hr_R2


title: IFT88_0hr_R2


title: control_4hr_R1


title: control_24hr_R3


title: control_2hr_R3


title: control_1hr_R3


title: control_1hr_R2


title: control_24hr_R2


title: control_24hr_R1


title: control_1hr_R1


title: control_0hr_R3


title: control_0hr_R2


title: control_0hr_R1


title: vehicle control for ebastine

city: Houston

first: Guangyu

last: Wang

address: 6670 Bertner Ave

institute: Houston methodist research institute

description: Sample "C" in processed data file.

data_processing:
Sequenced reads were mapped to hg19 whole genome using tophat2
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Prostate cancer cell line

growth_protocol: C4-2 cells were cultured in RPMI-1640 (GenDEPOT) supplemented with 10% FBS (GenDEPOT).

extract_protocol:
Total RNA was isolated from cells to generate cDNA using the RNA MiniPrep kit (Direct-zol, R2052, ZYMO Research).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: C4-2 cells were re-plated in 2-well plates and allowed for adherence in the next 24 hours. The growth medium were then replaced with medium respectively supplemented with vehicle, ebastine.

value: C4-2 cell

tag: passages

value: vehicle control


title: ebastine

description: Sample "T" in processed data file.

value: ebastine


title: Breast cancer FFPE tissue Case 27 IN

type: genomic

city: Brescia

first: Edoardo

last: Abeni

address: Viale Europa n. 11

department: Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy.

country: Italy

institute: University of Brescia

description: Fraction: input DNA

hyb_protocol: Array Washing and Staining was performed with the use of the Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 7G (Affymetrix) and raw data were extracted with the GeneChip Operating System (GCOS) software from Affymetrix.

data_processing:
The CEL files were imported into Partek Genomics Suite (PGS) software version 6.6, normalized with the RMA algorithm and converted to log2 values. For each breast cancer case, the IP CEL files was normalized through subtraction of log2 IN signal intensity of each of 4.6 million array probes to log2 IP signal.
We performed 9 different comparisons according to gender and mutation status (BRCA1, BRCA2 and BRCAX):
1: FBC vs MBC All cases
2: FBC vs MBC BRCAX cases
3: BRCAX vs BRCA1 and BRCA2 All cases
4: BRCA1 vs BRCA2 Female cases only
5: BRCA1 vs BRCAX Female cases only
6: BRCA2 vs BRCAX Female cases only
7: BRCA1 vs BRCA2 and BRCAX Female cases only
8: BRCA2 vs BRCA1 and BRCAX Female cases only
9: BRCAX vs BRCA1 and BRCA2 Female cases only
Based on the number of breast cancer cases present in the various comparisons considered, we performed different array normalization with the RMA algorithm. Significantly differentially methylated regions (DMR) were obtained using ANOVA followed by MAT algorithm (model-based analysis of tiling arrays algorithm) for each comparison performed. Using PGS function, each DMR was associated to its nearest gene of human genome. The genomic coordinates of each DMR were calculated based on UCSC human genomic assembly version 18.
The resulting txt file is generated by the Partek Genomics Suite Software version 6.6 using ANOVA followed by Mat algorithm, using the following parameters:
1. FBC VS MBC (All cases): MAT algorithm parameters: p-value threshold: 0.0001, sliding window: 1400 bp, minimum number of probes in a region: 10.
2. FBC VS MBC (BRCAX cases only): MAT algorithm parameters: p-value threshold: 0.0001, sliding window: 1400 bp, minimum number of probes in a region: 10.
3. BRCAX VS BRCA1 and BRCA2 (All cases): MAT algorithm parameters: p-value threshold: 0.0001, sliding window: 1400 bp, minimum number of probes in a region: 10.
4. BRCA1 VS BRCA2 (Female cases only): MAT algorithm parameters: p-value threshold: 0.0001, sliding window: 600 bp, minimum number of probes in a region: 10.
5. BRCA1VS BRCAX (Female cases only): MAT algorithm parameters: p-value threshold: 0.0001, sliding window: 600 bp, minimum number of probes in a region: 10.
6. BRCA2 VS BRCAX (Female cases only): MAT algorithm parameters: p-value threshold: 0.0001, sliding window: 600 bp, minimum number of probes in a region: 10.
7. BRCA1 VS BRCA2 and BRCAX (Female cases only): MAT algorithm parameters: p-value threshold: 0.0001, sliding window: 350 bp, minimum number of probes in a region: 10.
8. BRCA2 VS BRCAX  and BRCA1 (Female cases only): MAT algorithm parameters: p-value threshold: 0.0001, sliding window: 350 bp, minimum number of probes in a region: 10.
9. BRCAX VS BRCA2 and BRCA1 (Female cases only): MAT algorithm parameters.: p-value threshold: 0.0001, sliding window: 350 bp, minimum number of probes in a region: 10.

label: biotin

source_name: Breast cancer FFPE tissue Case 27

label_protocol: A total of 200 ng of IN and IP DNA was amplified with the Affymetrix Chromatin Immunoprecipitation Assay Protocol. Hybridation on Human Promoter 1.0R array was performed using the reagents contained in GeneChip®Hybridization, Wash, and Stain Kit (Affymetrix) using GeneChip® hybridization oven 640 (Affymetrix).

extract_protocol: The global DNA methylation profiles of 24 breast cancer cases were obtained by methylated DNA immunoprecipitation coupled with Affymetrix Human Promoter 1.0R Tiling Arrays (MeDip-chip). The genomic DNA from 24 breast cancer FFPE tissues was extracted using QIAamp DNA FFPE Tissue Kit supplied by Qiagen- The genomic DNA was digested using micrococcal nuclease (New England Biolabs) to obtain DNA fragments ranging from 200 to 500 nucleotides and used them as input (IN) DNA. Agilent Bioanalyzer with the RNA 6000 Nano LabChip Kit was used to check the size of fragmented DNA. Part of IN DNA (4 µg) was immunoprecipitated (IP) with 10 µl of anti-5-MethylCytosine Antibody (Eurogentec, BI-MECY-0100) using the MeDip protocol. The antibody-DNA complexes were immunoprecipitated using Dynabeads® Protein G immunoprecipitation kit (Life Technologies) and the methylated enriched DNA was purified by standard phenol/chloroform procedure and precipitated with isopropanol.

tag: gender

value: Male

value: Breast cancer FFPE tissue

tag: mutation

value: BRCA X

tag: antibody


title: Breast cancer FFPE tissue Case 33 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 33


title: Breast cancer FFPE tissue Case 26 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 26 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 26 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 26


title: Breast cancer FFPE tissue Case 33 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 33 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 27 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 27 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 18 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 18 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 25 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 25


title: Breast cancer FFPE tissue Case 18 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 18


title: Breast cancer FFPE tissue Case 25 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 25 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 17 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 17


title: Breast cancer FFPE tissue Case 03 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 03 + anti-5-MethylCytosine

value: BRCA 2 delA9158FS + 29 stop


title: control_2hr_R2


title: Breast cancer FFPE tissue Case 17 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 17 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 23 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 23 + anti-5-MethylCytosine

value: Female


title: Breast cancer FFPE tissue Case 23 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 23


title: Breast cancer FFPE tissue Case 03 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 03


title: Breast cancer FFPE tissue Case 21 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 21 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 21 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 21


title: Breast cancer FFPE tissue Case 22 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 22 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 20 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 20 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 16 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 16 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 19 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 19

value: BRCA1 M1652I


title: Breast cancer FFPE tissue Case 19 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 19 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 20 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 20


title: Breast cancer FFPE tissue Case 07 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 07 + anti-5-MethylCytosine

value: BRCA 1 C64R


title: Breast cancer FFPE tissue Case 08 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 08


title: Breast cancer FFPE tissue Case 08 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 08 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 22 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 22


title: Breast cancer FFPE tissue Case 11 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 11 + anti-5-MethylCytosine

value: BRCA 2 Q2960X


title: Breast cancer FFPE tissue Case 12 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 12


title: Breast cancer FFPE tissue Case 10 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 10 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 15 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 15


title: Breast cancer FFPE tissue Case 12 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 12 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 13 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 13


title: Breast cancer FFPE tissue Case 13 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 13 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 10 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 10


title: Breast cancer FFPE tissue Case 11 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 11


title: Breast cancer FFPE tissue Case 15 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 15 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 16 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 16


title: Breast cancer FFPE tissue Case 06 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 06 + anti-5-MethylCytosine

value: BRCA 2 T703N


title: Breast cancer FFPE tissue Case 02 IN

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 02

value: BRCA 2 458stop


title: Breast cancer FFPE tissue Case 05 IN

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 05


title: Breast cancer FFPE tissue Case 02 IP

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 02 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 06 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 06


title: Breast cancer FFPE tissue Case 05 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 05 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 07 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 07


title: Breast cancer FFPE tissue Case 14 IP

description: Fraction: MeDip DNA

source_name: Breast cancer FFPE tissue Case 14 + anti-5-MethylCytosine


title: Breast cancer FFPE tissue Case 14 IN

description: Fraction: input DNA

source_name: Breast cancer FFPE tissue Case 14


title: Trank1-shRNA1-3

city: Kunming

first: Ming

last: Li

state: Yunnan

address: NO 32 Jiao-Chang Donglu

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

data_processing:
Trimmomatic v0.32 were used to examine the sequencing quality and trim reads.
Clean paired-end reads were aligned to the reference genome using Hisat2.
We quantified gene-level expression using featureCounts.FPKM (fragments per kilobase of exon per million fragments mapped) was calculated to measure gene-level expression according to the formula: FPKM=F×103/L×106/N, where F was the number of the fragments assigned to the gene annotation, L was the length of gene and N was the total number of mapped fragments.
Genome_build: Rnor6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: cortex

growth_protocol: Dissociated cortical neurons were prepared from infant Sprague Dawley rats at E18 days of gestation. In brief, cortices were dissected, trypsinized and gently triturated into single cell suspension. Neurons in this suspension were then counted, and seeded at a density of 1×106 viable cells/well in 6 well culture-plates pre-coated with poly-D-lysine (10 μg ml−1) for at least 12 hours at 37 °C. Cultures were maintained at 37 °C with 5% CO2, supplemented with Neurobasal medium with 2% B27 (Invitrogen) and 2.0 mM glutamax.

extract_protocol:
Total RNAs from infected neurons were purified by TRIzol reagent according to the manufactor’s instruction.
For RNA-Seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Lentiviruses of pSicoR-Ef1a-mCh-Puro vector carrying Trank1-shRNA#1, Trank1-shRNA#2 or empty were generated according to the manufacturer’s protocol. Rat neurons were infected at 14-15 days in vitro (DIV) with Trank1-shRNAs or control shRNA.

value: Sprague Dawley Rat

value: rat primary cortical neuron

value: infected Trank1-shRNA1 lentivirus


title: Trank1-shRNA2-1

value: infected Trank1-shRNA4 lentivirus


title: Trank1-shRNA2-3


title: Trank1-shRNA1-2


title: Trank1-shRNA2-2


title: Trank1-shRNA1-1


title: control shRNA-3

value: infected control shRNA lentivirus


title: control shRNA-1


title: control shRNA-2


title: 2wk_re3

city: Copenhagen

first: Kyoung

middle: Jae

last: Won

state: Hovedstaden

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Mapping: TopHat  2.0.8b
Differential expression analysis using EdgeR 3.30.3
Supplementary_files_format_and_content: normalized counts in tsv

source_name: pancreatic islet cells

extract_protocol:
Total RNA was extracted from freshly isolated islets using TRIzol® Reagent, followed by Qiagen RNeasy® Mini kit following manufacturer’s instructions.
Multiplexed libraries were created using the Illumina TruSeq Stranded Total RNA LT Sample prep kit with Ribo-Zero Gold following manufacturer’s instructions

value: Neonatal pancreatic islet cells

value: pancreatic islet

tag: age

value: postnatal week 4


title: e19_re3

value: Fetal pancreatic islet cells

value: Embryonic day 19


title: e19_re1


title: e19_re2


title: 2wk_re1

value: postnatal week 2


title: 23_CR

city: St. Louis

first: Nathan

last: Singh

state: MO

institute: Washington University School of Medicine

data_processing:
Fastq files were processed for data QC, read mapping, transcript assembly, and transcript abundance estimation. A number of quality control metrics were assessed including data quality and GC content on per base and sequence levels, sequence length distribution and duplication levels, and insert size distribution. Finally, HTSeq was used to count the number of reads mapping to each gene46. Data normalization for differential expression analysis was carried out with the edgeR R package47. The logCPM value of each gene was z-normalized and gene set scores were calculated as the mean of the normalized gene expression for each gene in a given gene set.
Supplementary_files_format_and_content: Normalized count matrix

source_name: bone marrow

extract_protocol:
Total RNA was extracted from bone marrow cells stored in PAXgene tubes according to the manufacturer’s instructions (Qiagen).
Integrity was checked on the Agilent TapeStation (RIN), followed by preparation for sequencing using the TruSeq RNA v2 prep (Illumina).
High-throughput sequencing was performed on an Illumina HiSeq 2500 platform to a target depth of 50 million paired-end reads per sample.

value: bone marrow

tag: patient diagnosis

value: B-cell acute lymphoblastic leukemia

tag: patient response

value: CR


title: 27_CR


title: 26_NR

value: NR


title: 25_CR


title: 22_CR


title: 19_CR


title: 20_CR


title: 18_CR


title: 21_CR


title: 14_CR


title: 17_CR


title: 16_CR


title: 15_CR


title: 2wk_re2

value: postnatal week 3


title: 12_CR


title: 13_NR


title: 24_NR


title: 11_CR


title: 8_CR


title: 7_CR


title: 9_CR


title: 6_NR


title: 5_NR


title: 2_NR


title: 4_NR


title: 1_CR


title: Patient10

city: Dunedin

first: Amber

last: Helliwell

address: 710 Cumberland Road

department: Biochemistry Department

country: New Zealand

institute: University of Otago

data_processing:
reads were adaptor trimmed using bismark that used a file of adaptor sequences and trimmed three bases back from any detected adaptor to delete the C invorporated and rejecting any reads that were trimmed to less than 10bp
reads were aligned to the hg19 genome using bismark with the following specifications: a tolerance for one non-bisulfite mismatch per read, the default minimum alignment score (L,O, -02), and with ignore - quals in order to calculate the mismatch penalty by considering the quality value at the mismatched position to be the highest possible
bam files generated by Bismark alignment were then processed using DMAP to compare control vs. patients with  the following specifications: ANOVA F test on fragments 40-220bp in length, with the fragment requireing at lest 2 CpGs  to have 10 or more sequence reads. The differential methylation file was then annotated with protein coding gene information using the DMAP command identgeneloc. DMAPmatrix.csv file contains this data.
the bam files were additionally analysed following a MethylKit based pipeline where first the data was filtered for low read coverage (less than 10 times coverage) and normalised basde on mean coverage distribution before comparing pooled patient and control groups using a Fisher's test. Methmatrix.csv file contains this data
Genome_build: hg19
Supplementary_files_format_and_content: Individual .txt files for each sample containing C and T frequency per base and coverage. Matrix (csv file) containing methylation percentages for each sample used in the control vs patient analysis for the MethylKit single CpG pipeline.
Supplementary_files_format_and_content: A matrix containing the DMAP output data (individual sample percentages, significance values, associated genomic features, fragment length, CpG per fragment). .

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
DNA was extracted from 200ul of PBMCs
MSPI digestion (purify), end repair (purify), A-tialing and adaptor ligation (purify), PCR amplification (purify), Gel size selection and gel extraction (purify)

tag: disease state

value: Patient


title: 3_NR

tag: tissue


title: Patient9


title: Patient8


title: Patient6


title: Patient7


title: 10_CR


title: Patient2


title: Control10

value: Control


title: Patient1


title: Control7


title: Control8


title: Patient4


title: Control9


title: Control4


title: Control6


title: Control3


title: Control2


title: BLANCO

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
FASTQs were trimmed using cutadapt for TGGAATTCTCGGGTGCCAAGG  adapter and random barcode length 4 (on 5' and 3' ends).
We used bowtie 1.01 to align reads against the human genome (GRCh38) no allowing mismatches.
Mapped reads were quantified to known mature microrna ( miRBase version 22) using Partek E/M method.
Genome_build: GRCh38
Supplementary_files_format_and_content: Quantified read counts

source_name: Cerebrospinal fluid (CSF)

extract_protocol:
Total RNA was extracted from 200 µL of cleared CSF using the Plasma/Serum RNA Purification kit (Norgen #55000). Isolated RNA was eluted in 50 µL of nuclease-free water (Ambion #AM9930).
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).

treatment_protocol: CSF samples were obtained via lumbar puncture, centrifuged to remove contaminant cells (500 xg for 10 min), aliquoted, and immediately stored at -80°C until their processing. Then, samples were thawed at 4°C, centrifuged to remove cell debris (3,000 xg for 15 min at 4°C), and aliquoted in a 200 µL format (cleared CSF).

tag: age (years)


title: EXOLCR25


title: EXOLCR29


title: EXOLCR19


title: Control1


title: EXOLCR17


title: EXOLCR16


title: EXOLCR13


title: EXOLCR14


title: EXOLCR20


title: Patient5


title: Patient3


title: EXOLCR12


title: EXOLCR05


title: EXOLCR03


title: EXOLCR11


title: EXOLCR02


title: Control5


title: EXOLCR01


title: SkMel-23_TR: Tcell resistant cell line SkMel-23

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequence samples were mapped to the human genome (Homo.sapiens.GRCh38.v82) using STAR(2.6.0c) with default settings. Sequence reads were counted using HTSeq-count. Normalization and statistical analysis of the expression of genes was performed using DESeq2
Genome_build: HG38
Supplementary_files_format_and_content: Un-processed read count data

growth_protocol: All cells were cultured with DMEM plus 9% FBS and pen/strep in 5% CO2 incubator at 37 degree

extract_protocol: RNA was extracted using Trizol. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We subjected a series of established melanoma cell lines, which all endogenously express HLA-A*02:01+ and MART-1, in vitro to healthy donor CD8 T cells that had been retrovirally transduced with a T cell receptor recognizing MART-1. These melanoma cell lines initially displayed high sensitivity to the T cells, being largely eliminated in a 24-hour co-culture. However, a small fraction of tumor cells remained viable after this treatment. We expanded these rare cells and subsequently repeated the cycles of T cell challenge to up to 15 times. This stringent selection procedure yielded three independent melanoma populations from as many different parental cell lines, which had spontaneously acquired resistance to T cells (“TR” cell lines)

value: Melanoma cell line

tag: cell line


title: D10_parental: Parental cell line D10


title: M009R.X1_CL_TR: Tcell resistant  cell line M009R.X1_CL

value: Melanoma PDX cell line


title: NHD13/Setd2 KO (Bisulfite-Seq)

city: Shanghai

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

data_processing:
Clean sequenced reads were alignmented to mm10 by bowtie2(2.2.9) with parameters: -N 1; alignmented SAM files were handled using samtools(1.7); peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set; BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing CPM.(ChIP-seq)
Clean sequenced reads were alignmented to mm10 by HISAT2 (2.0.5) with default parameters; alignmented SAM files were handled using samtools(1.7); aligned reads were extracted by Htseq(0.9.1) with default parameters; FPKM were calculated by R script on its defination, differential genes were generated by R package Deseq2(1.22.2).(RNA-seq)
Raw reads were filtered by trimmomatic with parameter: SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, ILLIMINACLIP:adaper.fa:2:30:7:1:true, HEADCROP:10; clean sequenced reads were alignmented to mm10 by bismark(0.19.0) with parameters: deduplicated alignments were removed by deduplicate_bismark(bismark 0.19.0); coverage files were extracted by bismark_methylation_extractor(bismark 0.19.0); DMR regions were generated by R package DSS(2.26.0). (Bisulfite-Seq)
Genome_build: mm10
Supplementary_files_format_and_content: coverage files, bed, bigwig, peak, FPKMs, raw counts

source_name: Bone marrow

extract_protocol:
Fluorescence activated Cell Sorting
(For ChIP-seq): Library preparation was according to the manufacture’s guidelines (KAPA Biosystems KK8503) and sequencing procedures were carried out according to Illumina protocols with minor modifications (Illumina, San Diego).  (For RNA-seq): Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  (For Bisulfite-Seq): A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR.

tag: strain

value: Bone marrow

tag: cell type

value: Hematopoietic stem and progenitor cells (HSPCs)

tag: genotype


title: NHD13/Setd2 flox/flox (Bisulfite-Seq)

value: NHD13/SETD2 flox/flox


title: MCSF+IL-10+GdA (2)

city: Hong Kong

first: Jian

last: Wu

state: Hong Kong

address: 5 Sassoon Road, Pokfulam

country: Hong Kong

institute: HKU

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The number of raw reads mapped to genes was calculated by RSEM(rsem-1.2.4), the reference genome using hg38, then put all the samples results together and normalized by EDAseq(1.99.1),  genes expression fold change were calculated using TPM.
Genome_build: hg38
Supplementary_files_format_and_content: TPMs

source_name: human monocyte-derived macrophage

growth_protocol: Primary monocytes were isolated by Ficoll-Paque density gradient centrifugation. Monocyte isolated by negative immunomagnetic separation. Culture in RPMI1640 + 10% FBS

extract_protocol:
Total RNA was extracted by RNA spin column
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

treatment_protocol: Macrophages were prepared by treating monocytes with 50 ng/ml  MCSF for 9 days in the presence or absence of IL-10 (5 ng/ml) and/or GdA (10 μg/ml)

value: human blood monocyte-derived macrophage

tag: treatment


title: C57BL/6 (Bisulfite-Seq)

value: WT


title: NHD13/Setd2 KO_3 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
KO_3


title: NHD13/Setd2 KO - AML_1 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
AML_1

source_name: Spleen

value: Spleen

value: C-Kit+ cells


title: NHD13/Setd2 KO - AML_2 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
AML_2


title: NHD13/Setd2 KO_2 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
KO_2


title: NHD13/Setd2 KO_1 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
KO_1


title: MCSF+GdA (1)

value: MCSF+GdA


title: SkMel-23_parental: Parental cell line SkMel-23


title: D10_TR: Tcell resistant cell line D10


title: NHD13/Setd2 flox/flox_3 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
NHD13_3


title: Donor 2 CD39+ tTreg

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: Human tTreg 4

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Pico Kit User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: CD39+ tTreg

label_protocol: 500pg of total RNA were amplified and labeled using the Affymetrix 3` IVT Pico Kit (Catalog Number 902789, Affymetrix, Santa Clara, CA)

growth_protocol: cells were immediately FACS-sorted after isolation from peripheral blood

extract_protocol: RNeasy micro kit according to the manufacturers' instructions; Qiagen, Hilden, Germany

tag: subject status

value: healthy donor 2

value: peripheral blood

value: magnetic-beads enriched  CD4+ T-cells

tag: cell population


title: Donor 1 CD39+ tTreg

description: Human tTreg 2

value: healthy donor 1


title: Donor 1 CD39- tTreg

description: Human tTreg 1

source_name: CD39- tTreg


title: Donor 2 CD39- tTreg

description: Human tTreg 3


title: Donor 3 CD39+ tTreg

description: Human tTreg 6

value: healthy donor 3


title: Donor 3 CD39- tTreg

description: Human tTreg 5


title: MCSF+IL10 (1)


title: MCSF+IL10 (2)


title: C57BL/6_3 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
WT_3

tag: chip antibody


title: NHD13/Setd2 KO - AML_3 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
AML_3


title: MCSF+IL-10+GdA (1)


title: M009R.X1_CL_parental: Parental cell line M009R.X1_CL


title: NHD13/Setd2 flox/flox_1 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
NHD13_1


title: MCSF (2)

value: MCSF


title: MCSF (1)


title: NHD13/Setd2 KO - AML (Bisulfite-Seq)


title: control_2hr_R1

source_name: chondrocyte cell line

value: fibroblastic chondrocyte cell line

value: IL-1 beta 10ng/ml

value: WT + NT siRNA pool


title: C57BL/6_1 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
WT_1

value: Bone marrow


title: DM (2)

source_name: human decidual macrophage

value: human macrophage


title: NHD13/Setd2 flox/flox_2 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
NHD13_2

value: Hematopoietic stem and progenitor cells (HSPCs)

value: NHD13/SETD2 flox/flox


title: DM (1)


title: NSC-3 [re-analysis; R6_MEL1]

city: New York

first: Lorenz

last: Studer

state: NY

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
MEL1_R6
R6_MEL1

data_processing:
Basecalls performed using CASAVA version 1.4
RNASeq - FASTQ files were aligned using the STAR aligner to hg38.  BAM files were then processed into a counts table using HTSeq and imported into DESeq2 for further analysis
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited files.  RNA seq - fold change compared to rosette cells

source_name: hPSC-deived

growth_protocol: ES cell differentiation were routinely generated using the dual SMAD inhibition method to obtain forebrain restricted NSCs (d20). NSCs were then either maintained in culture to generate OCC cells or treated with FGF8 (50ng/ml) and SHH (25ng/ml) to skew the differentiation towards PFC. Both OCC and PFC were harvested at d40 of differentiation.

extract_protocol:
RNA was extracted using Trizol reagent followed by chloroform extraction. RNA was precipitated in isopropanol and resuspended in ddH2O.
RNA was sent to the integrated genomics core at MSKCC where standard library preparation and sequencing was performed without modification to Illumina protocols.

tag: psc line

tag: growth condition

value: N2 media containing EGF/FGF2


title: C57BL/6_2 (RNA-seq)

description:
FPKM.txt
Raw_Matrix.txt
Differential_expression_gene.xlsx
WT_2

value: WT


title: PFC differentiation to d40-1 [Sample_0913]

description:
Sample_0913
913_IGO_07381_D_2_S3

source_name: hESC differentiation/cell culture_PFC differentiation to d40

tag: cell type source

value: H9 ESCs

tag: cell subtype

value: hPSC-derived prefrontal (PFC)


title: NSC-2 [re-analysis; R6_UMOD]

description:
UMOD_R6
R6_UMOD


title: PFC differentiation to d40-3 [Sample_1071]

description:
Sample_1071
1071_IGO_07381_D_8_S9


title: PFC differentiation to d40-2 [Sample_0919]

description:
Sample_0919
919_IGO_07381_D_4_S5


title: PFC differentiation to d40-4 [Sample_1113]

description:
Sample_1113
1113_IGO_07381_D_10_S1


title: NSC-1 [re-analysis; UMOD_d20]

description:
UMOD_d20
UMOD_d20


title: OCC differentiation to d40-1 [Sample_0912]

description:
Sample_0912
912_IGO_07381_D_1_S2

source_name: hESC differentiation/cell culture_OCC differentiation to d40

value: hPSC-derived occipital (OCC)


title: MCSF+GdA (2)

value: human blood monocyte-derived macrophage

value: MCSF+GdA


title: Arabidopsis root cells - sc_53

city: Durham

first: Philip

middle: N.

last: Benfey

state: North Carolina

address: 130 Science Drive

department: Biology

institute: Duke University

description:
Arabidopsis root cells - Benfey Lab
Single-cell RNA-seq

data_processing:
Processed by COPILOT (https://github.com/Hsu-Che-Wei/COPILOT).
Genome_build: TAIR10
Supplementary_files_format_and_content: *_mtx.tar: Include gene-by-cell count matrices.
Supplementary_files_format_and_content: *_COPILOT.rds: Seurat objects.

organism: Arabidopsis thaliana

source_name: Arabidopsis root cells

growth_protocol: Seeds from wildtype Arabidopsis thaliana ecotype Columbia (Col-0), shortroot-2 (Col-0 background), and scarecrow-4 (Landsberg background backcrossed to Col-0 at least 5 times) were surface sterilized with a 50% (v/v) bleach, 0.05% (v/v) Tween-20 solution for 10 minutes and subsequently stratified for 48 hours at 4°C. Seeds were sown at a density of ~150-300 seeds/row on 1X Linsmaier and Skoog (LSP03-1LT, Caisson Labs; pH 5.7), 1% sucrose media covered by 100/ 47 µm mesh. Plates were placed vertically in a Percival chamber programmed to 16h light, 8h dark conditions at 22°C.

extract_protocol: Chromium Single Cell 3ʹ GEM Kit v3.

tag: ecotype/background

value: Root

tag: use for atlas

value: No


title: Arabidopsis root cells - sc_52


title: Arabidopsis root cells - col0

value: Wild type

value: Yes


title: genomic DNA from buffy coat Sample75 [X200400320079]

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA from buffy coat averaged across 12 individuals on the same chip (SENTRIX ID)

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

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

data_processing: Noob normalization using the R function preprocessNoob from the minfi R package

label: Cy3 and Cy5

source_name: manifest_buffy coat

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from buffy coat samples

extract_protocol: genomic DNA was extracted and purified from EDTA tubes using the RecoverEase DNA Isolation Kit.

treatment_protocol: Standard Illumina Protocol

tag: huntingtondiseasestatus

value: manifest

tag: averageage

tag: averagebodymassindex

tag: dnamage


title: genomic DNA from buffy coat Sample66 [X200397540094]

source_name: control_buffy coat

value: control


title: OCC differentiation to d40-3 [Sample_1068]

description:
Sample_1068
1068_IGO_07381_D_7_S8


title: OCC differentiation to d40-2 [Sample_0918]

description:
Sample_0918
918_IGO_07381_D_3_S4


title: genomic DNA from buffy coat Sample71 [X200397870067]


title: genomic DNA from buffy coat Sample70 [X200397870050]


title: genomic DNA from buffy coat Sample76 [X200406080062]


title: genomic DNA from buffy coat Sample69 [X200397870042]

source_name: pre-manifest_buffy coat

value: pre-manifest


title: genomic DNA from buffy coat Sample58 [X200397540058]


title: genomic DNA from buffy coat Sample63 [X200397540083]


title: genomic DNA from buffy coat Sample72 [X200397870075]


title: genomic DNA from buffy coat Sample77 [X200406080063]


title: genomic DNA from buffy coat Sample59 [X200397540064]


title: genomic DNA from buffy coat Sample61 [X200397540066]


title: genomic DNA from buffy coat Sample68 [X200397870039]


title: genomic DNA from buffy coat Sample67 [X200397870038]


title: genomic DNA from buffy coat Sample62 [X200397540072]


title: OCC differentiation to d40-4 [Sample_1110]

description:
Sample_1110
1110_IGO_07381_D_9_S10


title: genomic DNA from buffy coat Sample56 [X200397540056]


title: genomic DNA from buffy coat Sample60 [X200397540065]


title: genomic DNA from buffy coat Sample74 [X200397870109]


title: day 60 replicate 5

city: Esch-sur-Alzette

first: Rashi

last: Halder

address: 7, Avenue des Hauts-Fourneaux

country: Luxembourg

institute: Luxembourg Center for Systems Biomedicine

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D60_4

data_processing:
Illumina bcl2fastq.
Sequenced reads were mapped using tophat (v.2.1.1) and fragments per kilobase of transcript per million (FPKM) were calculated using Cufflinks (v 2.2.1).
Genome_build: Not provided
Supplementary_files_format_and_content: genes.fpkm_table_annotation1.txt: Tab-delimited text file including FPKM values for each sample generated using Cufflinks.

source_name: iPSC derived human brain organoids

extract_protocol:
RNA from all the samples was isolated using Machery-Nagel RNA isolation kit (cat. no. 740955) according to the kits protocol.
RNA sequencing libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Cat. no. RS-122-2201).

value: fetal brain-like cells in a collagen hydrogel

tag: age

value: 60 days after differentiation


title: genomic DNA from buffy coat Sample73 [X200397870108]


title: genomic DNA from buffy coat Sample65 [X200397540091]


title: Arabidopsis root cells - sc_51

description:
Arabidopsis root cells - Benfey Lab
Single-cell RNA-seq
WT generated in the same batch as sc_52 and sc_53.

tag: tissue


title: genomic DNA from buffy coat Sample55 [X200397540055]


title: genomic DNA from buffy coat Sample54 [X200397540047]


title: day 60 replicate 6

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D60_5

tag: cell type


title: day 60 replicate 4

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D60_3


title: genomic DNA from buffy coat Sample53 [X200397540046]


title: Arabidopsis root cells - sc_36

value: Landsberg background backcrossed to Col-0 at least 5 times

tag: genotype


title: genomic DNA from buffy coat Sample57 [X200397540057]


title: day 60 replicate 3

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D60_2


title: Arabidopsis root cells - sc_31

description:
Arabidopsis root cells - Benfey Lab
Single-cell RNA-seq
WT generated in the same batch as sc_36.


title: day 60 replicate 2

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D60_1


title: genomic DNA from buffy coat Sample64 [X200397540085]


title: day 60 replicate 1

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D60_0


title: Arabidopsis root cells - sc_30


title: day 50 replicate 4

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D50_3

value: early brain-like cells in a collagen hydrogel

value: 50 days after differentiation


title: Arabidopsis root cells - sc_25


title: day 50 replicate 3

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D50_2


title: Arabidopsis root cells - sc_21

description:
Arabidopsis root cells - Benfey Lab
Single-cell RNA-seq
WT generated in the same batch as sc_25.


title: Arabidopsis root cells - sc_20


title: day 50 replicate 2

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D50_1


title: Arabidopsis root cells - sc_12

description:
Arabidopsis root cells - Benfey Lab
Single-cell RNA-seq
The best quality sample used as reference for building atlas.


title: day 50 replicate 1

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D50_0


title: Arabidopsis root cells - sc_11


title: genomic DNA from buffy coat Sample52 [X200397540037]


title: day 40 replicate 5

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D40_4

value: 40 days after differentiation


title: Arabidopsis root cells - sc_10_at

description:
Arabidopsis root cells - Benfey Lab
Single-cell RNA-seq
The raw data also contains root cells of rice (Oryza sativa).


title: day 40 replicate 4

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D40_3


title: Arabidopsis root cells - sc_9_at


title: genomic DNA from buffy coat Sample47 [X200397540032]

description: genomic DNA from buffy coat averaged across 12 individuals on the same chip (SENTRIX ID)


title: day 40 replicate 1

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D40_0


title: Arabidopsis root cells - sc_1

description:
Arabidopsis root cells - Benfey Lab
Single-cell RNA-seq


title: genomic DNA from buffy coat Sample48 [X200397540033]


title: genomic DNA from buffy coat Sample49 [X200397540034]


title: day 40 replicate 3

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D40_2


title: genomic DNA from buffy coat Sample44 [X200397540026]


title: genomic DNA from buffy coat Sample46 [X200397540028]


title: genomic DNA from buffy coat Sample45 [X200397540027]


title: genomic DNA from buffy coat Sample40 [X200397540008]


title: day 40 replicate 2

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D40_1


title: genomic DNA from buffy coat Sample43 [X200397540022]


title: genomic DNA from buffy coat Sample38 [X200397540004]


title: genomic DNA from buffy coat Sample34 [X200394970126]


title: day 28 replicate 4

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D28_3

value: early embryonic-like brain cells in a collagen hydrogel

value: 28 days after differentiation


title: genomic DNA from buffy coat Sample30 [X200394970117]


title: genomic DNA from buffy coat Sample37 [X200394970138]


title: genomic DNA from buffy coat Sample35 [X200394970132]


title: genomic DNA from buffy coat Sample39 [X200397540006]


title: genomic DNA from buffy coat Sample32 [X200394970124]


description:
genomic DNA methylation from sheepBloodHD382Control
HD382

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: cy3, cy5

organism: Ovis aries

extract_protocol: genomic DNA was extracted

tag: genotype huntington

value: Control

tag: age (years)

tag: Sex

value: female

value: Blood

tag: basename


title: genomic DNA from buffy coat Sample42 [X200397540018]


title: day 28 replicate 2

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D28_1


title: genomic DNA from buffy coat Sample36 [X200394970137]


title: genomic DNA from buffy coat Sample33 [X200394970125]


title: genomic DNA from buffy coat Sample31 [X200394970120]


description:
genomic DNA methylation from sheepBloodHD868Transgenic
HD868

value: Transgenic

value: male


title: genomic DNA from buffy coat Sample51 [X200397540036]


title: genomic DNA from buffy coat Sample28 [X200394970111]


title: genomic DNA from buffy coat Sample23 [X200394970038]


title: genomic DNA from buffy coat Sample41 [X200397540012]


title: day 28 replicate 3

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D28_2


title: genomic DNA from buffy coat Sample29 [X200394970116]


title: genomic DNA from buffy coat Sample25 [X200394970100]


title: day 28 replicate 1

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D28_0


title: genomic DNA from buffy coat Sample21 [X200394870111]


title: day 15 replicate 4

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D15_3

value: differentiating cells in a collagen hydrogel

value: 15 days after differentiation


description:
genomic DNA methylation from sheepBloodHD876Transgenic
HD876


description:
genomic DNA methylation from sheepBloodHD854Control
HD854


title: genomic DNA from buffy coat Sample27 [X200394970102]

value: control


title: genomic DNA from buffy coat Sample24 [X200394970039]

value: manifest


title: genomic DNA from buffy coat Sample20 [X200394870108]


title: day 15 replicate 3

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D15_2


description:
genomic DNA methylation from sheepBloodHD920Control
HD920


title: day 15 replicate 5

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D15_4


description:
genomic DNA methylation from sheepBloodHD866Transgenic
HD866


title: genomic DNA from buffy coat Sample26 [X200394970101]

description: genomic DNA from buffy coat averaged across 12 individuals on the same chip (SENTRIX ID)


title: genomic DNA from buffy coat Sample50 [X200397540035]


description:
genomic DNA methylation from sheepBloodHD1074Transgenic
HD1074


title: day 15 replicate 2

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D15_1


title: day 15 replicate 1

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D15_0


title: day 8 replicate 3

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D8_2

value: 8 days after differentiation


title: genomic DNA from buffy coat Sample16 [X200394870081]


description:
genomic DNA methylation from sheepBloodHD911Control
HD911


title: genomic DNA from buffy coat Sample18 [X200394870092]


description:
genomic DNA methylation from sheepBloodHD886Control
HD886


description:
genomic DNA methylation from sheepBloodHD1073Transgenic
HD1073


title: genomic DNA from buffy coat Sample13 [X200394870037]


title: genomic DNA from buffy coat Sample22 [X200394870112]


description:
genomic DNA methylation from sheepBloodHD888Control
HD888


title: day 8 replicate 1

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D8_0


description:
genomic DNA methylation from sheepBloodHD810Transgenic
HD810


description:
genomic DNA methylation from sheepBloodHD1077Transgenic
HD1077


title: day 3 replicate 4

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D3_3

value: 3 days after differentiation


title: day 8 replicate 2

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D8_1


description:
genomic DNA methylation from sheepBloodHD873Control
HD873


title: genomic DNA from buffy coat Sample14 [X200394870079]


title: genomic DNA from buffy coat Sample12 [X200394870033]


title: day 3 replicate 2

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D3_1


title: genomic DNA from buffy coat Sample3 [X200325530032]


title: genomic DNA from buffy coat Sample9 [X200394870023]

value: pre-manifest


title: genomic DNA from buffy coat Sample2 [X200325530031]


title: genomic DNA from buffy coat Sample11 [X200394870031]


title: genomic DNA from buffy coat Sample8 [X200394870022]


description:
genomic DNA methylation from sheepBloodHD881Control
HD881


title: day 3 replicate 3

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D3_2


title: genomic DNA from buffy coat Sample15 [X200394870080]

description: genomic DNA from buffy coat averaged across 12 individuals on the same chip (SENTRIX ID)


title: genomic DNA from buffy coat Sample6 [X200379120093]


description:
genomic DNA methylation from sheepBloodHD820Transgenic
HD820


title: day 3 replicate 1

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D3_0


title: genomic DNA from buffy coat Sample5 [X200379120091]


title: genomic DNA from buffy coat Sample7 [X200379120131]


title: genomic DNA from PBMC HIV-High49

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol

label: Cy5 and Cy3

source_name: PBMC

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA was extracted from frozen PBMC using QiaAmp kit.

tag: gender

value: Male

tag: group

value: HIV-High


title: genomic DNA from buffy coat Sample10 [X200394870024]


description:
genomic DNA methylation from sheepBloodHD902Control
HD902


title: day 0 replicate 2

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D0_1

value: induced Pluripotent cells in a collagen hydrogel

value: differentiation day


title: genomic DNA from PBMC HIV-High50


title: genomic DNA from buffy coat Sample17 [X200394870083]


title: day 0 replicate 1

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D0_0


description:
genomic DNA methylation from sheepBloodHD890Transgenic
HD890


description:
genomic DNA methylation from sheepBloodHD1071Control
HD1071


title: day 0 replicate 3

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D0_2


title: genomic DNA from PBMC HIV-High35


title: genomic DNA from PBMC HIV-High39


title: genomic DNA from PBMC HIV-High43


title: genomic DNA from PBMC HIV-High42


title: day -1 replicate 4

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D-1_3

value: induced Pluripotent cells in a monolayer culture

value: one day before differentiation


title: genomic DNA from buffy coat Sample4 [X200379120041]


title: genomic DNA from PBMC HIV-High48


title: day -1 replicate 3

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D-1_2


description:
genomic DNA methylation from sheepBloodHD1057Transgenic
HD1057

value: female


title: genomic DNA from buffy coat Sample19 [X200394870099]


description:
genomic DNA methylation from sheepBloodHD921Control
HD921

value: Control

value: Blood


title: genomic DNA from PBMC HIV-High44


title: day -1 replicate 2

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D-1_1


title: day -1 replicate 1

description:
processed data file: genes.fpkm_table_annotation1.txt
Column in genes.fpkm_table_annotation1.txt: D-1_0


description:
genomic DNA methylation from sheepBloodHD1065Control
HD1065

value: male


description:
genomic DNA methylation from sheepBloodHD984Transgenic
HD984

value: Transgenic


description:
genomic DNA methylation from sheepBloodHD917Transgenic
HD917


description:
genomic DNA methylation from sheepBloodHD840Control
HD840


description:
genomic DNA methylation from sheepBloodHD912Transgenic
HD912


title: skin_isogenic_transplantation_1

city: Bochum

first: Stephan

middle: A

last: Hahn

address: Universitaetsstrasse 150

department: MGO

country: Germany

institute: Ruhr-University Bochum

description: mRNA expression

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions  for 17 hours at 65C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C ) using standard settings

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028282_D_F_20190102) to obtain background subtracted and spatially detrended Processed Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hind limb skin tissue

label_protocol: 100 ng of total RNA were labeled using the QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with  cyanine-5-CTP (Cy5)

growth_protocol: Orthotopic hindlimb-transplantations were performed either from Lewis to Lewis (isogenic group) or from Fischer344 to Lewis (chronic rejection group). Skin and muscle samples were obtained from the transplanted hind limbs by post operative day 100.

extract_protocol: Total RNA isolation from 20 mg frozen tissue (skin and muscle) per animal were isolated using the RNeasy™ Fibrous Tissue Mini Kit (Qiagen) according to the manufacture`s protocol. RNA integrity was analysed using standard RNA-gel electrophoresis. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: Treatment consisted of 10 mg/kg cyclosporine A and 2 mg/kg dexamethasone (Dexa 4 mg inject, Jenapharm, Jena, Germany) intraperitoneal and was administered daily until clinical signs of rejection completely disappeared.

tag: rejection

value: no rejection


title: genomic DNA from PBMC HIV-High24


title: genomic DNA from PBMC HIV-High34


title: genomic DNA from PBMC HIV-High23


title: genomic DNA from PBMC HIV-High22


title: genomic DNA from PBMC HIV-High21


title: skin_isogenic_transplantation_2

description: mRNA expression


description:
genomic DNA methylation from sheepBloodHD994Transgenic
HD994


title: skin_chronic_rejection_2

description: mRNA expression

value: chronic rejection


title: genomic DNA from PBMC HIV-High32


title: genomic DNA from PBMC HIV-High14

value: Female


title: muscle_chronic_rejection_2

description: mRNA expression

source_name: hind limb muscle tissue


title: skin_chronic_rejection_1

description: mRNA expression


description:
genomic DNA methylation from sheepBloodHD860Control
HD860


description:
genomic DNA methylation from sheepBloodHD366Transgenic
HD366


title: genomic DNA from PBMC HIV-High19


title: genomic DNA from PBMC HIV-High30


title: genomic DNA from PBMC HIV-High15


title: genomic DNA from PBMC HIV-High12


title: genomic DNA from PBMC HIV-Low50

value: HIV-Low


title: genomic DNA from PBMC HIV-High07


title: muscle_isogenic_transplantation_2

description: mRNA expression


title: genomic DNA from PBMC HIV-High01


title: muscle_chronic_rejection_1

description: mRNA expression


title: genomic DNA from PBMC HIV-High02


title: genomic DNA from PBMC HIV-Low46


title: genomic DNA from PBMC HIV-High11


title: genomic DNA from PBMC HIV-Low39


title: muscle_isogenic_transplantation_1

description: mRNA expression


description:
genomic DNA methylation from sheepBloodHD831Transgenic
HD831


description:
genomic DNA methylation from sheepBloodHD930Control
HD930


title: genomic DNA from PBMC HIV-Low43


description:
genomic DNA methylation from sheepBloodHD1094Control
HD1094


title: genomic DNA from PBMC HIV-High06


title: 3730CHDI_820493_RRBS

description: The provided FASTQ files are not the raw FASTQ files from the sequencer; they have been processed by adapter trimming, and further processed using a custom script to make the file suitable for alignment.

data_processing:
To analyze the sequence data, a reference genome is created that contains only the 36 base pairs adjacent to every MspI site and every C in those sequences is changed to T. A converted sequence read file is then created by changing each C in the original sequence reads to a T. The converted sequence reads are aligned to the converted reference genome, and only reads that map uniquely to the reference genome are kept. Once reads are aligned the percent methylation is calculated for each CpG using the original sequence reads. The percent methylation and number of reads is reported for each CpG.
Genome_build: mm10

source_name: Striatum

extract_protocol:
DNA methylation at CpG sites was assayed with a modified version of Reduced Representation Bisulfite Sequencing (RRBS; Meissner et al., 2008). RRBS was carried out by the HudsonAlpha Institute for Biotechnology. Genomic DNA is isolated from each cell line using the QIAGEN DNeasy Blood & Tissue Kit according to the instructions provided by the manufacturer. DNA concentrations for each genomic DNA preparation are determined using fluorescent DNA binding dye and a fluorometer (Invitrogen Quant-iT dsDNA High Sensitivity Kit and Qubit Fluorometer). 1 µg of DNA was used to make an RRBS library.
RRBS library construction starts with MspI digestion of genomic DNA , which cuts at every CCGG regardless of methylation status. Klenow exo- DNA Polymerase is then used to fill in the recessed end of the genomic DNA and add an adenosine as a 3prime overhang. Next, a methylated version of the Illumina paired-end adapters is ligated onto the DNA. Adapter ligated genomic DNA fragments between 105 and 185 basepairs are selected using agarose gel electrophoresis and Qiagen Qiaquick Gel Extraction Kit. The selected adapter-ligated fragments are treated with sodium bisulfite using the Zymo Research EZ DNA Methylation Gold Kit, which converts unmethylated cytosines to uracils and leaves methylated cytosines unchanged. Bisulfite treated DNA is amplified in a final PCR reaction which has been optimized to uniformly amplify diverse fragment sizes and sequence contexts in the same reaction. During this final PCR reaction uracils are copied as thymines resulting in a thymine in the PCR products wherever an unmethylated cytosine existed in the genomic DNA. The sample is now ready for sequencing on the Illumina sequencing platform. These libraries were sequenced with an Illumina Genome Analyzer IIx according to the manufacturer's recommendations.

value: Striatum


title: genomic DNA from PBMC HIV-High09


title: 3730CHDI_820513_RRBS

source_name: Cerebellum

value: Cerebellum


title: genomic DNA from PBMC HIV-Low42

value: Male


title: genomic DNA from PBMC HIV-Low37


title: genomic DNA from PBMC HIV-Low38


title: genomic DNA from PBMC HIV-Low40


title: 3730CHDI_820491_RRBS


description:
genomic DNA methylation from sheepBloodHD992Control
HD992


title: 3730CHDI_820506_RRBS


title: genomic DNA from PBMC HIV-High45

value: HIV-High


title: genomic DNA from PBMC HIV-Low45


title: 3730CHDI_820501_RRBS


title: 3730CHDI_820505_RRBS


description:
genomic DNA methylation from sheepBloodHD829Control
HD829


description:
genomic DNA methylation from sheepBloodHD835Transgenic
HD835


description:
genomic DNA methylation from sheepBloodHD1075Control
HD1075


description:
genomic DNA methylation from sheepBloodHD996Transgenic
HD996


description:
genomic DNA methylation from sheepBloodHD372Transgenic
HD372


title: 3730CHDI_820499_RRBS


title: 3730CHDI_820497_RRBS


title: genomic DNA from PBMC HIV-Low35


title: genomic DNA from PBMC HIV-Low36


title: genomic DNA from PBMC HIV-Low32


title: genomic DNA from PBMC HIV-Low33


description:
genomic DNA methylation from sheepBloodHD989Transgenic
HD989


title: genomic DNA from PBMC HIV-High17


title: 3730CHDI_820514_RRBS


description:
genomic DNA methylation from sheepBloodHD903Transgenic
HD903


description:
genomic DNA methylation from sheepBloodHD915Control
HD915


title: genomic DNA from PBMC HIV-High27


title: 3730CHDI_820510_RRBS


title: 3730CHDI_820509_RRBS


title: genomic DNA from PBMC HIV-Low30


title: genomic DNA from PBMC HIV-High29


description:
genomic DNA methylation from sheepBloodHD851Transgenic
HD851


title: genomic DNA from PBMC HIV-Low28


title: genomic DNA from PBMC HIV-Low47


description:
genomic DNA methylation from sheepBloodHD932Control
HD932


description:
genomic DNA methylation from sheepBloodHD844Transgenic
HD844


title: 3730CHDI_820492_RRBS


title: 3730CHDI_820483_RRBS


title: genomic DNA from PBMC HIV-Low14


title: genomic DNA from PBMC HIV-Low16


title: genomic DNA from PBMC HIV-Low21


title: genomic DNA from PBMC HIV-Low23


description:
genomic DNA methylation from sheepBloodHD865Control
HD865


title: genomic DNA from PBMC HIV-Low19


title: 3730CHDI_820490_RRBS


title: genomic DNA from PBMC HIV-Low24


description:
genomic DNA methylation from sheepBloodHD337Control
HD337


title: TCQA 2

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the top 3000 DEGs between T7 and D0 hAECs and for all DEGs between T7 and D7 hAECs to test whether a priori-defined groups of genes associated with neural differentiation were significantly related to the DEGs between RA-treated and control cells on day 0 and day 7
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HG-U219
program-name = Expression Console
program-version = 1.4.1.46

source_name: cell treated with TCQA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: AECs were isolated from delivered term placenta and were maintained in Placenta Epithelial Cell Basal Medium (PromoCell, Cat. # C-26140) in 2D culture plate. Finally, 3D spheroids were formed by seeding 1×10^6 AECs in Placenta Basal Epithelial Cell Medium into each well of the 24-well plate.

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour culture, the medium was changed with 20 μM of TCQA every 48 hours for three times (7days) for the treatment samples. Control samples were maintained in Placental medium that was also changed every 48 hours. Finally, we collected the treatment and control samples from one-week culture. Day 0 control samples were collected after the initial treatment.

value: Human amnion epithelial cells (hAECs)

tag: treatment

tag: time point

value: day 7


title: genomic DNA from PBMC HIV-Low20


title: genomic DNA from PBMC HIV-Low15


title: genomic DNA from PBMC HIV-Low22


title: 3730CHDI_820507_RRBS


title: genomic DNA from PBMC HIV-Low26


title: genomic DNA from PBMC HIV-Low06


title: genomic DNA from PBMC HIV-Low13


title: genomic DNA from PBMC HIV-Low18


title: genomic DNA from PBMC HIV-Low12


title: genomic DNA from PBMC HIV-Low08


description:
genomic DNA methylation from sheepBloodHD929Transgenic
HD929


title: D0 Control 1

source_name: cell treated with water

value: none (control)

value: day 0


title: 3730CHDI_820508_RRBS


title: genomic DNA from PBMC HIV-Low10


title: genomic DNA from PBMC HIV-Low11


title: D7 Control 2


title: Patient 63 omental mets [SO1709_063; PanCancer Progression]

first: Sandra

last: Orsulic

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

institute: David Geffen School of Medicine at UCLA

hyb_protocol: As per Nanostring Technologies standard protocol.

scan_protocol: NanoString cartridges were scanned on a digital analyzer under default settings set by the manufacturer.  555 field of view (FOV) were scanned for each lane and the images were processed by the digital analyzer to quantify fluorescent barcodes

data_processing: Raw data in RCC file format were downloaded from the digital analyzer and imported into nSolver software (NanoString Technologies) for further processing.  ERCC positive control probes were used to normalize lane to lane technical variations, and ERCC negative control probes were used to estimate the background noise level.  After adjusting for technical variation and background noise, data were further normalized by geometric mean of housekeeping genes to account for sample RNA input differences.  Normalized data were log2 transformed and used in downstream analyses including differential expression analysis.

label: fluorescent barcode

source_name: Omental metastasis

extract_protocol: FFPE tissue was collected at the time of surgery. Whole tissue sections from 152 tumors were profiled. Total RNA was isolated by the FFPE kit according to the manufacturer’s instruction (Qiagen). RNA quantity and quality was assessed by Nanodrop and Bioanalyser, respectively.

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: weight

value: nd

tag: bmi

tag: race

value: CAUCASIAN

tag: ethnicity

value: NON-HISPANIC

tag: brca mutation description

tag: patient mutant history

tag: debulking

value: optimal

tag: Stage

value: IIIC

tag: pfs

tag: os


title: Patient 66 omental mets [SO1709_066; PanCancer Progression]

label_protocol: As per Nanostring Technologies standard protocol.

tag: tissue

tag: brca mutation status

value: W

value: WT - No Mut


title: D0 Control 2

tag: cell type


title: genomic DNA from PBMC HIV-Low31

tag: gender

tag: age

tag: group

value: HIV-Low


description:
genomic DNA methylation from sheepBloodHD804Transgenic
HD804

tag: genotype huntington

value: Transgenic

tag: age (years)

tag: Sex

value: male

value: Blood

tag: basename


title: Patient 64 omental mets [SO1709_064; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

tag: ethnicity

value: IV


title: Patient 62 omental mets [SO1709_062; PanCancer Progression]

value: M

tag: brca mutation description

tag: patient mutant history

value: BRCA2 exon11 6174delT

tag: debulking

tag: Stage

tag: pfs

tag: os


title: 3730CHDI_820494_RRBS

description: The provided FASTQ files are not the raw FASTQ files from the sequencer; they have been processed by adapter trimming, and further processed using a custom script to make the file suitable for alignment.

tag: genotype

tag: tissue

value: Striatum


title: genomic DNA from PBMC HIV-Low05

tag: gender

value: Male

tag: age

tag: group


description:
genomic DNA methylation from sheepBloodHD997Transgenic
HD997

tag: genotype huntington

tag: age (years)

tag: Sex

tag: basename


title: 3730CHDI_820498_RRBS

value: Cerebellum


description:
genomic DNA methylation from sheepBloodHD1084Control
HD1084

value: Control

value: female


title: Patient 61 omental mets [SO1709_061; PanCancer Progression]

value: Omental metastasis

tag: age at diagnosis

tag: height

value: nd

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

value: UNKNOWN


title: genomic DNA from PBMC HIV-Low04


title: Patient 60 omental mets [SO1709_060; PanCancer Progression]

tag: ethnicity

tag: brca mutation description

tag: patient mutant history

tag: debulking

tag: Stage

value: IIIC


title: 3730CHDI_820486_RRBS

tag: genotype

tag: tissue


title: genomic DNA from PBMC HIV-Low29

tag: gender

value: Female

tag: age

tag: group

value: HIV-Low


title: TCQA 1

tag: cell type

value: Human amnion epithelial cells (hAECs)

tag: treatment

value: 20 μM of TCQA every 48 hours for three times (7days)

tag: time point

value: day 7


title: 3730CHDI_820484_RRBS


description:
genomic DNA methylation from sheepBloodHD334Control
HD334

tag: genotype huntington

tag: age (years)

tag: Sex

value: male

value: Blood

tag: basename


title: genomic DNA from PBMC HIV-Low07


title: Patient 58 omental mets [SO1709_058; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

tag: ethnicity

tag: brca mutation status

value: W

value: WT - No Mut

value: optimal

value: IIC

tag: pfs

tag: os


title: Patient 57 omental mets [SO1709_057; PanCancer Progression]

tag: tissue

tag: brca mutation description

tag: patient mutant history

tag: debulking

tag: Stage


title: Patient 59 omental mets [SO1709_059; PanCancer Progression]

value: HISPANIC


title: 3730CHDI_820511_RRBS

tag: genotype

value: Cerebellum


title: Patient 56 omental mets [SO1709_056; PanCancer Progression]

value: Omental metastasis

value: nd

value: NON-HISPANIC


title: genomic DNA from PBMC HIV-Low01

tag: gender

value: Male

tag: age

tag: group


description:
genomic DNA methylation from sheepBloodHD260Transgenic
HD260

tag: genotype huntington

value: Transgenic

tag: age (years)

tag: Sex

value: female

tag: basename


title: D7 Control 1

tag: cell type

value: Human amnion epithelial cells (hAECs)

tag: treatment

value: none (control)

tag: time point


title: Patient 65 omental mets [SO1709_065; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

tag: ethnicity

tag: brca mutation status

value: M

value: BRCA2 6174delT

value: IIIC

tag: pfs

tag: os


title: 3730CHDI_820500_RRBS

tag: genotype

tag: tissue

value: Striatum


description:
genomic DNA methylation from sheepBloodHD373Control
HD373

tag: genotype huntington

value: Control

tag: age (years)

value: Blood


title: 3730CHDI_820502_RRBS


title: genomic DNA from PBMC HIV-Low02

tag: gender

value: Female

tag: age

tag: group

value: HIV-Low


title: Patient 54 omental mets [SO1709_054; PanCancer Progression]

value: Omental metastasis

tag: brca mutation description

tag: patient mutant history

tag: debulking

value: suboptimal

tag: Stage


title: Patient 52 omental mets [SO1709_052; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight

value: nd

tag: bmi

value: UNKNOWN


title: Patient 53 omental mets [SO1709_053; PanCancer Progression]

tag: race

tag: ethnicity

tag: pfs


description:
genomic DNA methylation from sheepBloodHD878Transgenic
HD878

value: Transgenic

tag: Sex

tag: tissue

tag: basename


title: 3730CHDI_820485_RRBS

tag: genotype


title: Patient 50 omental mets [SO1709_050; PanCancer Progression]

value: NON-HISPANIC

value: optimal

tag: os


title: Patient 55 omental mets [SO1709_055; PanCancer Progression]


title: 3730CHDI_820496_RRBS

value: Cerebellum


title: Patient 48 omental mets [SO1709_048; PanCancer Progression]

value: CAUCASIAN

tag: brca mutation status

value: W

value: WT - No Mut

value: IV


description:
genomic DNA methylation from sheepBloodHD1056Transgenic
HD1056

tag: genotype huntington

tag: age (years)

value: female


description:
genomic DNA methylation from sheepBloodHD918Control
HD918

value: Control


description:
genomic DNA methylation from sheepBloodHD1087Control
HD1087

value: male

value: Blood


description:
genomic DNA methylation from sheepBloodHD1088Control
HD1088


title: Patient 51 omental mets [SO1709_051; PanCancer Progression]

tag: brca mutation description

tag: patient mutant history

tag: debulking

value: IIIC


title: 3730CHDI_820488_RRBS


title: Patient 46 omental mets [SO1709_046; PanCancer Progression]

value: Omental metastasis

tag: age at diagnosis

tag: height

value: ASIAN

tag: Stage


title: genomic DNA from PBMC HIV-Low09

tag: gender

value: Male

tag: age

tag: group

value: HIV-Low


title: Patient 45 omental mets [SO1709_045; PanCancer Progression]

tag: weight

tag: bmi

tag: race

tag: ethnicity

value: nd

value: IIC

tag: pfs


title: Patient 44 omental mets [SO1709_044; PanCancer Progression]

tag: tissue

value: NON-HISPANIC

tag: brca mutation status

value: optimal

tag: os


title: Patient 49 omental mets [SO1709_049; PanCancer Progression]

value: CAUCASIAN

tag: brca mutation description


title: 3730CHDI_820504_RRBS

tag: genotype

value: Striatum


title: 3730CHDI_820503_RRBS

value: Cerebellum


title: 3730CHDI_820495_RRBS


title: Patient 47 omental mets [SO1709_047; PanCancer Progression]

tag: patient mutant history

tag: debulking


title: Patient 42 omental mets [SO1709_042; PanCancer Progression]

tag: age at diagnosis

tag: height

value: suboptimal


title: Patient 41 omental mets [SO1709_041; PanCancer Progression]

value: M

value: BRCA1 187delAG

tag: Stage


title: 3730CHDI_820489_RRBS


title: Patient 39 omental mets [SO1709_039; PanCancer Progression]

value: W

value: WT - No Mut


title: Patient 43 omental mets [SO1709_043; PanCancer Progression]

value: III


title: Patient 37 omental mets [SO1709_037; PanCancer Progression]

value: Omental metastasis

value: UNKNOWN

value: IV


title: Patient 40 omental mets [SO1709_040; PanCancer Progression]


title: Patient 38 omental mets [SO1709_038; PanCancer Progression]

value: IIIC


description:
genomic DNA methylation from sheepBloodHD379Control
HD379

tag: genotype huntington

value: Control

tag: age (years)

tag: Sex

value: male

value: Blood

tag: basename


description:
genomic DNA methylation from sheepBloodHD839Transgenic
HD839

value: Transgenic


title: 3730CHDI_820512_RRBS


title: Patient 36 omental mets [SO1709_036; PanCancer Progression]

value: nd

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

value: optimal


title: Human infant foreskin epidermis - Donor 5

city: Irvine

first: Scott

last: Atwood

state: California

address: 4340 McGaugh Hall, Ring Rd

department: Department of Developmental & Cell Biology

institute: University of California, Irvine

description:
ds7
RNA from single cells

data_processing:
Transcripts were mapped to the reference genome (GRCh38) using Cell Ranger Version 2.1.0 with the following standard parameters:
Quality control of all data sets was performed using Seurat (Version 3.0.0) and SoptSC
Processed files were analyzed with Seurat V3.1.0 and Velocyto.R and SoptSC
Genome_build: GRCh38

source_name: Foreskin epidermis

extract_protocol:
Human neonatal foreskin epidermis (n=5). Samples were surgically excised and placed in HBSS + 10% FBS at 4C until retrieved from the hospital that collected the tissue samples. The tissue was placed in dispase at 37C for several hours until the epidermis could be peeled apart from the dermis. The epidermis was then trypsinized for 30 min, and the dermis was discarded. Epidermal cells were incubated with DNAse for 5 min, filtered over 40um cell strainer, and flow sorted for live cells for library preparation.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v2 chemistry. Library metrics were as follow: 550.19 pg/µl with an avg. size ~454 bps. Libraries were sequenced on an Illumina Next-Seq4000 platform (Illumina). Cell counting, capture, library preparation, quality control, and sequencing was performed at the Genomics High Throughput Sequencing facility at the University of California, Irvine.
Single Cell 3’ v2 chemistry - 10X Genomics

tag: tissue

value: Human foreskin

tag: age

value: Infant / Newborn


title: Patient 34 omental mets [SO1709_034; PanCancer Progression]

value: ASIAN

tag: ethnicity

value: NON-HISPANIC

tag: pfs

tag: os


title: Patient 35 omental mets [SO1709_035; PanCancer Progression]

value: BLACK

tag: brca mutation description

tag: patient mutant history


title: Patient 33 omental mets [SO1709_033; PanCancer Progression]

tag: age at diagnosis

tag: debulking

value: IIA


description:
genomic DNA methylation from sheepBloodHD339Transgenic
HD339


title: Human infant foreskin epidermis - Donor 3

description:
ds5
RNA from single cells


title: Patient 32 omental mets [SO1709_032; PanCancer Progression]

value: Omental metastasis

tag: height

tag: Stage


title: Patient 31 omental mets [SO1709_031; PanCancer Progression]

tag: brca mutation status

value: M

value: BRCA1 5382insC


title: Patient 30 omental mets [SO1709_030; PanCancer Progression]

value: BRCA2 5193delC

value: IIIC


description:
genomic DNA methylation from sheepBloodHD364Control
HD364

tag: genotype huntington

value: Control

tag: age (years)

tag: Sex

value: male


title: Patient 29 omental mets [SO1709_029; PanCancer Progression]

tag: weight

tag: bmi

value: BRCA2 6174delT


description:
genomic DNA methylation from sheepBloodHD1067Transgenic
HD1067

value: Transgenic

value: female

tag: tissue

value: Blood

tag: basename


title: Human infant foreskin epidermis - Donor 4

description:
ds6
RNA from single cells

value: Human foreskin

tag: age


title: Patient 28 omental mets [SO1709_028; PanCancer Progression]

value: nd

tag: race

value: CAUCASIAN

tag: ethnicity

value: UNKNOWN

tag: pfs


description:
genomic DNA methylation from sheepBloodHD1054Transgenic
HD1054


description:
genomic DNA methylation from sheepBloodHD919Control
HD919


description:
genomic DNA methylation from sheepBloodHD924Control
HD924


title: Patient 26 omental mets [SO1709_026; PanCancer Progression]

tag: brca mutation description

tag: patient mutant history

value: suboptimal

tag: os


title: Patient 27 omental mets [SO1709_027; PanCancer Progression]

tag: age at diagnosis

tag: height

value: NON-HISPANIC

value: W

value: WT - No Mut

tag: debulking

value: optimal


title: Human infant foreskin epidermis - Donor 2

description:
ds4
RNA from single cells

value: Infant / Newborn


title: VQ-D2_LN_plasma_cells

city: Milwaukee

first: Robert

last: Burns

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

data_processing:
Fastq data for each sample were aligned and processed using the Illumina SureCell Single-Cell RNA BaseSpace application v1.2.0
Genome_build: mm10
Supplementary_files_format_and_content: csv of UMI counts per gene per cell

source_name: Lymph node donor derived plasma cells (CD138+ B220-)

extract_protocol:
scRNA-Seq was performed using the Illumina® Bio-Rad® Single-Cell Sequencing Solution, which consists of Bio-Rad's ddSEQ™ Single-Cell Isolator with Illumina's SureCell WTA 3ʹ Library Prep Kit as per manufacturer's instructions
scRNA-Seq libraries were constructed using Illumina's SureCell WTA 3ʹ Library Prep Kit as per manufacturer's instructions

tag: cell type

tag: background strain

tag: genotype

value: V{kappa}*MYC; Nras LSL Q61R/+; IgG1-Cre (recipient)

tag: disease state

value: Multiple myeloma


description:
genomic DNA methylation from sheepBloodHD848Transgenic
HD848

tag: genotype huntington

tag: age (years)

tag: Sex

value: male


title: Patient 25 omental mets [SO1709_025; PanCancer Progression]

tag: tissue

value: Omental metastasis

tag: weight

tag: bmi

value: BLACK

tag: Stage

value: IIIC


description:
genomic DNA methylation from sheepBloodHD910Transgenic
HD910

value: Transgenic

value: female

value: Blood

tag: basename


description:
genomic DNA methylation from sheepBloodHD374Control
HD374

value: Control


title: VQ-D2_BM_plasma_cells_rep2

source_name: Bone marrow donor derived plasma cells (CD138+ B220-)


title: Patient 23 omental mets [SO1709_023; PanCancer Progression]

value: nd

tag: race

value: CAUCASIAN

tag: ethnicity

value: UNKNOWN

tag: brca mutation description

tag: patient mutant history

tag: pfs


title: Human infant foreskin epidermis - Donor 1

description:
ds0
RNA from single cells

value: Human foreskin

tag: age


title: WT_BM_plasma_cells

source_name: Bone marrow derived plasma cells (CD138+ B220-)

tag: cell type

tag: background strain

value: Wild-type


title: Patient 22 omental mets [SO1709_022; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: debulking

value: optimal

tag: os


title: Patient 21 omental mets [SO1709_021; PanCancer Progression]

tag: tissue

tag: brca mutation status

value: W

value: WT - No Mut


title: GC_B_cell_creControl_RNAseq_Repl5

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were aligned using STAR and annotated to RefSeq annotation using Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited counts per million

source_name: GC B-cells

extract_protocol: Total RNA was extracted using Trizol (LifeTechnologies) and RNeasy isolation Kit (Qiagen).  Library was prepared using TruSeq stranded kit as described in manuscript.

tag: genotype


title: Patient 20 omental mets [SO1709_020; PanCancer Progression]

tag: weight

tag: bmi

value: NON-HISPANIC

tag: Stage

value: IV


title: Patient 16 omental mets [SO1709_016; PanCancer Progression]

value: Omental metastasis

tag: race

tag: ethnicity


title: Patient 19 omental mets [SO1709_019; PanCancer Progression]

tag: brca mutation description

tag: patient mutant history

value: suboptimal


title: Patient 18 omental mets [SO1709_018; PanCancer Progression]

value: IIIC

tag: pfs


title: Patient 15 omental mets [SO1709_015; PanCancer Progression]


description:
genomic DNA methylation from sheepBloodHD879Control
HD879

tag: genotype huntington

tag: age (years)

tag: Sex

value: male

tag: basename


title: GC_B_cell_creControl_RNAseq_Repl4