title: Donor 10 (older) 67 yo

first: Guilherme

last: de Sena Brandine

address: 1050 Child's Way

department: Quantitative and Computational Biology

institute: University of Southern California

description: Donor 10 (older) 67 yo

data_processing:
FASTQ files were trimmed using trim-galore version 0.6.7
Trimmed reads were mapped to the human telomere-to-telomere assembly v2.0 using abismal v3.1.1
mapped reads were processed using DNMTools v1.1.0. Paired-end mates were merged using dnmtools format
The resulting single-end SAM output was sorted using SAMTools v1.13 through the samtools sort command
Duplicates were removed using the dnmtools uniq command
Counts files for individual cytosines were generated through the dnmtools counts command using each SAM file and the human reference FASTA genome as input.
Symmetric CpG counts were generated using the dnmtools sym command
Assembly: Human telomere-to-telomere assembly (hs1) v2.0
Supplementary files format and content: DNMTools counts file for symmetric CpGs. See https://dnmtools.readthedocs.io/en/latest/counts/ and https://dnmtools.readthedocs.io/en/latest/sym/

source_name: sperm

extract_protocol:
Using a Qiagen DNA extraction kit, DNA was extracted and purified for all sperm samples.
Samples were sent to the Beijing Genomics Institute for bisulfite conversion and sequencing.

tag: subject

value: Donor 10

value: sperm

tag: age

value: 67 yo

tag: age group

value: older


title: Donor 9 (older) 65 yo

status: Public on Mar 01 2023

type: SRA

city: Los Angeles

state: CA

country: USA

description: Donor 9 (older) 65 yo

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

value: Donor 9

tag: tissue

value: 65 yo


title: Donor 9 (younger) 52 yo

description: Donor 9 (younger) 52 yo

value: 52 yo

value: younger


title: WT_2i_72h bis

city: Saarbrücken

first: Jörn

last: Walter

state: Saarland

address: Campus A2.4

department: Genetics and Epigenetics

country: Germany

institute: Saarland University

data_processing:
(a) The hidden states i.e. the estimated distribution of C, 5mC and 5hmC. More precisely: uu (unmethylated on both DNA strands), um or mu (methylated only on upper or lower strand, respectively), uh or hu (hydroxylated on upper or lower and unmethylated on the other strand), mm (methylated on both DNA strands), hh (hydroxylated on both DNA strands), mh or hm (methylated on one and hydroxylated on the other strand) and toth (total frequency of all states that contain at least one 5hmC).
(b) The efficiencies i.e. the activity of Dnmts and Tets given as De_novo (de novo methylation efficiency for Dnmts), maint (maintenance methylation efficiency for Dnmts) or hydroxyl (hydroxylation efficiency of Tet enzymes).
(c) The standard deviations of the estimated Efficiencies given as De_novo_sd (standard deviation given of de novo methylation efficiency) maint_sd (standard deviation of maintenance efficiency), hydroxyl_sd (standard deviation of hydroxylation efficiency).
Column 1 - Chromosome: name of the chromosome e.g. 1 for chromosome 1
Column 10 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was only methylated on the lower strands i.e. C/5mC.
Column 11 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was unmethylated on both DNA strands i.e. C/C.
Column 2 - Position of the cytosine: e.g. 3003721
Column 3 - DNA Strand: Either C (upper strand) or G (lower strand). Indicates to which DNA strand the methylation has been mapped. This is only relevant for the non-hairpin information given in columns 4, 5 and 6.
Column 4 - Coverage: lists the coverage of the analyzed cytosine.
Column 5 - Methylation: lists how often an analyzed cytosine has been methylated
Column 6 - Unmethylated: lists how often an analyzed cytosine has been unmethylated
Column 7 - Sequence context: Gives the sequence context of the analyzed cytosine. Can be âCGâ for CpG, âGCâ for GpC or âothersâ for CpH.
Column 8 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was methylated on both DNA strands i.e. 5mC/5mC.
Column 9 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was only methylated on the upper strands i.e. 5mC/C.
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: DSI file format: the abbreviation âdsiâ stands for âdouble strand informationâ. The dsi file is a tab separated text file without header and contains the sequencing results of the hairpin bisulfite sequencing experiment, visualizing the four different states of a given CpG position i.e. both dna strand are methylated - 5mC/5mC; DNA is only methylated at the upper strand - 5mC/C, DNA only methylated on the lower strand - C/5mC or both DNA strands are unmethylated at a given CpG - C/C. DSI files can be visualized using the Integrative Genomics Viewer (IGV) (http://software.broadinstitute.org/software/igv/). The file contains the following elven columns:

organism: Mus musculus

source_name: cell culture

growth_protocol: Embryonic stem cells were cultured as discribed in Ficz et al. 2013. Briefly, ES cells were cultured without feeders either in standard serum-containing media (DMEM 4,500 mg/l glucose, 4 mM L-glutamine, 110 mg/l sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 microg/ml streptomycin, 0.1 mM nonessential amino acids, 50 microM Î²-mercaptoethanol, and 103 U/ml LIF ESGRO) or under 2i culturing conditions (Ying et al., 2008) (serum-free N2B27 [Cat. DMEM/F12: GIBCO 21331; Neurobasal: GIBCO 21103; N2: Stem Cells SF-NS-01-005; B27: GIBCO 17504-044] supplemented with 103 U/ml LIF and Mek inhibitor PD0325901 [1 microM] and Gsk3Î² inhibitor CHIR99021 [3 microM]).

extract_protocol: Genomic DNA was prepared using QIAamp DNA Micro Kit or AllPrep DNA/RNA mini kit (QIAGEN).  1.2 μg DNA is divided equally into three 0.5ml reaction tubes and digested in a 20 μl reaction using 20 U of HaeIII (NEB), AluI (NEB) and 10 U HpyCH4V (NEB), respectively. The reactions are incubated overnight for a minimum of 12 h at 37 °C. Restriction enzymes are inactivated at 80 °C for 30 min. The reactions are pooled and subjected to a ligation step. During this process, hairpin linker and sequencing adapter are introduced to the opposed ends of each restriction fragment. For this, 200 mM biotin labeled hairpin linker and 100 mM sequencing adapter are added to the digested DNA, incubatedwith 1 mM ATP and 2000 U T4 DNA Ligase (NEB) for 16 h at 16 °C. The reaction is purified using AMPureXP beadsfollowed by enrichment for hairpin containing fragments with streptavidin beads. The library is then subjected to BS/oxBS work-flow of the TrueMethyl kit from CEGX according tomanufacturer’s instructions. Amplification of the library was done with HotStarTaq® polymerase (Qiagen) and sequencing was performed on an Illumina HiSeq 2500 platform in a 150 bp paired-end sequencing mode.

tag: cell type

value: embryonic stem cell

tag: strain

tag: treatment


title: Donor 7 (older) 55 yo

description: Donor 7 (older) 55 yo

value: Donor 7

value: 55 yo


title: Donor 8 (older) 57 yo

description: Donor 8 (older) 57 yo

value: Donor 8

value: 57 yo


title: Donor 7 (younger) 45 yo

description: Donor 7 (younger) 45 yo

value: 45 yo


title: WT_heart 2

type: RNA

first: Vasu

last: Punj

address: Biggy Street

institute: USC

hyb_protocol: 10 µg of cRNA were hybridized for 16hr on  Affymetrix Mouse Genome 430 2.0 Array as recommended by manufacturer

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing:
The data was analyzed with   Affy – an Bioconductor package (http://www.bioconductor.org).  Briefly, after background correction, data was normalized using RMA (Robust Multiarray Average). Probe level data was summarized to gene level data.
Differential expression between Wt and mutant mouse was calculated using a One-way ANOVA

label: biotin

molecule: total RNA

label_protocol: Starting from 10 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer's instructions

growth_protocol: mouse heart Samples

extract_protocol: RNA was extracted from mouse heart using  RNeasy mini kit (Qiagen Valenica, CA)

tag: genotype/variation

value: wild type

value: heart


title: Donor 8 (younger) 46 yo

description: Donor 8 (younger) 46 yo

value: 46 yo


title: Donor 6 (younger) 40 yo

description: Donor 6 (younger) 40 yo

value: Donor 6

value: 40 yo


title: Donor 2 (older) 44 yo

description: Donor 2 (older) 44 yo

value: Donor 2

value: sperm

value: 44 yo


title: Donor 5 (younger) 36 yo

description: Donor 5 (younger) 36 yo

value: Donor 5

value: 36 yo


title: Donor 6 (older) 57 yo

description: Donor 6 (older) 57 yo

value: older


title: Donor 1 (older) 33 yo

description: Donor 1 (older) 33 yo

value: Donor 1

value: 33 yo


title: Donor 2 (younger) 27 yo

description: Donor 2 (younger) 27 yo

value: 27 yo

value: younger


title: Donor 4 (older) 51 yo

description: Donor 4 (older) 51 yo

value: Donor 4

value: 51 yo


title: Donor 3 (younger) 33 yo

description: Donor 3 (younger) 33 yo

value: Donor 3


title: Donor 1 (younger) 23 yo

description: Donor 1 (younger) 23 yo

value: 23 yo


title: Donor 10 (younger) 56 yo

description: Donor 10 (younger) 56 yo

value: Donor 10

value: 56 yo


title: lung-normal-3(Cap3) MeDIP-seq

city: 上海

first: Yani

last: Kang

address: 东川路800号

country: China

institute: Shanghai Jiaotong University

data_processing:
Low-quality reads were filtered using trimmomatic. Then clean reads were mapped to the reference genome (GRCh38) using bowite2.
The SAM files were sorted to BAM files using samtools, and duplicates were removed using picard.
We calculated the MeDIP-seq reads per gene using htseq.
The edgeR package was used for the differential methylation analysis, with p value < 0.01 considered to be differentially methylated significantly.
Assembly: hg38
Supplementary files format and content: Xlsx file includes matrix table with results of edgeR analysis between lung cancer samples and adjacent normal samples

source_name: lung

extract_protocol:
Genomic DNA from human lung tissue samples  were extracted using the Axygen gDNA Extraction kit (Axygen, CA, USA) according to the protocol described by the manufacturer.
MeDIP-seq library was constructed using the EpiQuik™ MeDIP Ultra Kit (Cat # P-1052; Epigentek,NY,USA) according to the protocol described by the manufacturer.

value: lung

tag: disease

value: normal


title: Donor 5 (older) 54 yo

description: Donor 5 (older) 54 yo

value: sperm

value: 54 yo


title: Patient derived xenograft (PDX), 5415hxxtm

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description:
hg19_raw_counts_df.NCohort.txt
mm10_raw_counts_df.NCohort.txt

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to human (hg19) and mouse (mm10) genomes using STAR aligner v.2.6.1.
Disambiguate algorithm [PMID: 27990269] was used to assign reads to human or mouse genome
featureCounts v.1.6.4 was used to quantify gene expression for hg19 and mm10 transcriptome
Assembly: hg19, mm10
Supplementary files format and content: plain text gene expression count tables

source_name: subcutaneous tumor

growth_protocol: PDX passaged in athymic nude mice

extract_protocol:
Qiagen ALLPrep DNA/RNA Mini Kit
Illumina mRNA-Seq Sample Prep Kit ot TruSeq RNA Sample Prep Kit v2-SertsA/B
 Illumina HiSeq2000/2500

value: PDX (not a cell line)

value: Stomach Carcinoid-Endocrine Tumour Of The Soft Tissue


title: Donor 4 (younger) 35 yo

description: Donor 4 (younger) 35 yo

value: 35 yo


title: Patient derived xenograft (PDX), 4163hxxtm

value: Soft Tissue Sarcoma Of The Abdominal Wall


title: Patient derived xenograft (PDX), 2283hxxtm

value: Pancreas Carcinoma Of The Lung


title: Patient derived xenograft (PDX), 5077hxxtm

value: Pancreas Carcinoma


title: Patient derived xenograft (PDX), 5717hxxtm


title: Patient derived xenograft (PDX), 4927hxxtm


title: Patient derived xenograft (PDX), 4833hxxtm


title: Patient derived xenograft (PDX), 6030hxxtm


title: Donor 3 (older) 48 yo

description: Donor 3 (older) 48 yo

value: 48 yo

value: older


title: Patient derived xenograft (PDX), 4649hxxtm


title: Patient derived xenograft (PDX), 4676hxxtm


title: Patient derived xenograft (PDX), 4664hxxtm


title: Patient derived xenograft (PDX), 4379hxxtm


title: Patient derived xenograft (PDX), 4378hxxtm


title: Patient derived xenograft (PDX), 4244hxxtm


title: Patient derived xenograft (PDX), 4316hxxtm


title: Patient derived xenograft (PDX), 4226hxxtm


title: Patient derived xenograft (PDX), 4015hxxtm


title: Patient derived xenograft (PDX), 4018hxxtm


title: Patient derived xenograft (PDX), 3982hxxtm


title: Patient derived xenograft (PDX), 4173hxxtm


title: Patient derived xenograft (PDX), 3990hxxtm


title: Patient derived xenograft (PDX), 4215hxxtm


title: Patient derived xenograft (PDX), 3947hxxtm


title: Patient derived xenograft (PDX), 3898hxxtm


title: Patient derived xenograft (PDX), 3800hxxtm


title: Patient derived xenograft (PDX), 3801hxxtm


title: Patient derived xenograft (PDX), 3816hxxtm


title: Patient derived xenograft (PDX), 3782hxxtm


title: Patient derived xenograft (PDX), 3268hxxtm


title: Patient derived xenograft (PDX), 3052hxxtm


title: Patient derived xenograft (PDX), 2684hxxtm


title: Patient derived xenograft (PDX), 3038hxxtm


title: Patient derived xenograft (PDX), 2997hxxtm


title: Patient derived xenograft (PDX), 2564hxxtm


title: Patient derived xenograft (PDX), 2470hxxtm


title: Patient derived xenograft (PDX), 2428hxxtm


title: Patient derived xenograft (PDX), 2406hxxtm


title: Patient derived xenograft (PDX), 2220hxxtm


title: Patient derived xenograft (PDX), 2339hxxtm


title: Patient derived xenograft (PDX), 2116hxxtm


title: Patient derived xenograft (PDX), 2219hxxtm


title: Patient derived xenograft (PDX), 2081hxxtm


title: Patient derived xenograft (PDX), 3846hxxtm


title: Patient derived xenograft (PDX), 2043hxxtm


title: Patient derived xenograft (PDX), 2046hxxtm


title: Patient derived xenograft (PDX), 20810hxxtm


title: Patient derived xenograft (PDX), 2026hxxtm


title: Patient derived xenograft (PDX), 1633hxxtm


title: Patient derived xenograft (PDX), 1948hxxtm


title: Patient derived xenograft (PDX), 1317hxxtm


title: Patient derived xenograft (PDX), 1963hxxtm


title: Patient derived xenograft (PDX), 1362hxxtm


title: Patient derived xenograft (PDX), 1959hxxtm


title: Patient derived xenograft (PDX), 5205hxxtm

value: Pancreas Carcinoid-Endocrine Tumour Of The Pancreas


title: Patient derived xenograft (PDX), 3028hxxtm


title: Patient derived xenograft (PDX), 3559hxxtm

value: Ovary Germ Cell Tumour


title: Patient derived xenograft (PDX), 4852hxxtm

value: Ovary Carcinoma Of The Omentum


title: Patient derived xenograft (PDX), 3766hxxtm

value: Ovary Carcinoma Of The Pelvic Mass


title: Patient derived xenograft (PDX), 4579hxxtm


title: Patient derived xenograft (PDX), 1786hxxtm


title: Patient derived xenograft (PDX), 3604hxxtm

value: Ovary Carcinoma Of The Lymph Node


title: Patient derived xenograft (PDX), 1318hxxtm


title: Patient derived xenograft (PDX), 1199hxxtm


title: Patient derived xenograft (PDX), 3867hxxtm

value: Ovary Carcinoma Of The Ascites


title: Patient derived xenograft (PDX), 2526hxxtm

value: Ovary Carcinoma Of The Liver


title: Patient derived xenograft (PDX), 5018hxxtm

value: Ovary Carcinoma Of The Abdomina Cavity


title: Patient derived xenograft (PDX), 5493hxxtm

value: Ovary Carcinoma


title: Patient derived xenograft (PDX), 5462hxxtm

value: PDX (not a cell line)


title: Patient derived xenograft (PDX), 5094hxxtm


title: Patient derived xenograft (PDX), 5024hxxtm


title: Patient derived xenograft (PDX), 4886hxxtm


title: Patient derived xenograft (PDX), 4829hxxtm


title: Patient derived xenograft (PDX), 4826hxxtm


title: Patient derived xenograft (PDX), 4138hxxtm


title: Patient derived xenograft (PDX), 4412hxxtm


title: Patient derived xenograft (PDX), 3615hxxtm


title: Patient derived xenograft (PDX), 4261hxxtm


title: Patient derived xenograft (PDX), 4863hxxtm


title: Patient derived xenograft (PDX), 3694hxxtm


title: Patient derived xenograft (PDX), 1289hxxtm


title: Patient derived xenograft (PDX), 3783hxxtm


title: Patient derived xenograft (PDX), 3861hxxtm


title: Patient derived xenograft (PDX), 3575hxxtm


title: Patient derived xenograft (PDX), 3939hxxtm


title: Patient derived xenograft (PDX), 3102hxxtm


title: Patient derived xenograft (PDX), 3001hxxtm


title: Patient derived xenograft (PDX), 2757hxxtm


title: Patient derived xenograft (PDX), 2681hxxtm


title: Patient derived xenograft (PDX), 2725hxxtm


title: Patient derived xenograft (PDX), 2471hxxtm


title: Patient derived xenograft (PDX), 2263hxxtm


title: Patient derived xenograft (PDX), 2607hxxtm


title: Patient derived xenograft (PDX), 1433hxxtm

value: Oesophagus Carcinoma Of The Lung


title: Patient derived xenograft (PDX), 2300hxxtm

value: Oesophagus Carcinoma Of The Cerebellum


title: Patient derived xenograft (PDX), 3931hxxtm


title: Patient derived xenograft (PDX), 5532hxxtm

value: Oesophagus Carcinoma


title: Patient derived xenograft (PDX), 3787hxxtm


title: Patient derived xenograft (PDX), 3682hxxtm


title: Patient derived xenograft (PDX), 3136hxxtm


title: Patient derived xenograft (PDX), 5135hxxtm


title: Patient derived xenograft (PDX), 5189hxxtm

value: Melanoma Of The Soft Tissue, Left Lateral Mallelos


title: Patient derived xenograft (PDX), 4530hxxtm

value: Melanoma Of The Right Popliteal


title: Patient derived xenograft (PDX), 2430hxxtm


title: Patient derived xenograft (PDX), 2723hxxtm

value: Melanoma Of The Vulva


title: Patient derived xenograft (PDX), 2530hxxtm


title: Patient derived xenograft (PDX), 3050hxxtm

value: Melanoma Of The Pericardium


title: Patient derived xenograft (PDX), 2805hxxtm


title: Patient derived xenograft (PDX), 2838hxxtm

value: Melanoma Of The Small Intestine


title: Patient derived xenograft (PDX), 5694hxxtm

value: Melanoma Of The Lymph Node


title: Patient derived xenograft (PDX), 4157hxxtm

value: Melanoma Of The Right Inguinal Mass


title: Patient derived xenograft (PDX), 5808hxxtm


title: Patient derived xenograft (PDX), 2306hxxtm


title: Patient derived xenograft (PDX), 5584hxxtm

value: Melanoma Of The Lung


title: Patient derived xenograft (PDX), 3211hxxtm

value: Melanoma Of The Scalp And Right Parotid


title: Patient derived xenograft (PDX), 1906hxxtm


title: Patient derived xenograft (PDX), 5566hxxtm

value: Melanoma Of The Lower Extremity


title: Patient derived xenograft (PDX), 1655hxxtm

value: Melanoma Of The Left Vulva


title: Patient derived xenograft (PDX), 3773hxxtm

value: Melanoma Of The Liver


title: Patient derived xenograft (PDX), 2753hxxtm


title: Patient derived xenograft (PDX), 4538hxxtm

value: Melanoma Of The Left Upper Lobe Lung


title: Patient derived xenograft (PDX), 3439hxxtm

value: PDX (not a cell line)

value: Oesophagus Carcinoma Of The Gastroesophageal Junction


title: Patient derived xenograft (PDX), 4644hxxtm

value: Melanoma Of The Left Posterior Shoulder


title: Patient derived xenograft (PDX), 3503hxxtm

value: Melanoma Of The Left Temple


title: Patient derived xenograft (PDX), 2884hxxtm

value: Oesophagus Carcinoma


title: Patient derived xenograft (PDX), 5696hxxtm

value: Melanoma Of The Colon


title: Patient derived xenograft (PDX), 3676hxxtm


title: Patient derived xenograft (PDX), 4832hxxtm


title: Patient derived xenograft (PDX), 5643hxxtm


title: Patient derived xenograft (PDX), 4339hxxtm

value: Melanoma Of The Brain (Right Cerebellum, Right Parietal)


title: Patient derived xenograft (PDX), 3746hxxtm

value: Melanoma Of The Chest Wall/Subcutaneous Mass Ribs 3-6


title: Patient derived xenograft (PDX), 3486hxxtm

value: Melanoma Of The Axilla


title: Patient derived xenograft (PDX), 5959hxxtm

value: Melanoma


title: Patient derived xenograft (PDX), 2163hxxtm

value: Melanoma Of The Adrenal


title: Patient derived xenograft (PDX), 4797hxxtm


title: Patient derived xenograft (PDX), 4668hxxtm


title: Patient derived xenograft (PDX), 4455hxxtm


title: Patient derived xenograft (PDX), 5645hxxtm


title: Patient derived xenograft (PDX), 4849hxxtm


title: Patient derived xenograft (PDX), 3880hxxtm


title: Patient derived xenograft (PDX), 5727hxxtm


title: Patient derived xenograft (PDX), 3127hxxtm


title: Patient derived xenograft (PDX), 2613hxxtm


title: Patient derived xenograft (PDX), 2700hxxtm


title: Patient derived xenograft (PDX), 2602hxxtm


title: Patient derived xenograft (PDX), 5267hxxtm

value: Lung Carcinoma Of The Adrenal Gland


title: Patient derived xenograft (PDX), 3400hxxtm

value: Lung Carcinoma Of The Shoulder


title: Patient derived xenograft (PDX), 4819hxxtm

value: Lung Carcinoma


title: Patient derived xenograft (PDX), 3843hxxtm


title: Patient derived xenograft (PDX), 4213hxxtm


title: Patient derived xenograft (PDX), 3020hxxtm


title: Patient derived xenograft (PDX), 3029hxxtm


title: Patient derived xenograft (PDX), 3408hxxtm


title: Patient derived xenograft (PDX), 2336hxxtm


title: Patient derived xenograft (PDX), 2088hxxtm


title: Patient derived xenograft (PDX), 4426hxxtm


title: Patient derived xenograft (PDX), 2148hxxtm


title: Patient derived xenograft (PDX), 2030hxxtm


title: Patient derived xenograft (PDX), 2082hxxtm


title: Patient derived xenograft (PDX), 2096hxxtm


title: Patient derived xenograft (PDX), 2129hxxtm


title: Patient derived xenograft (PDX), 1934hxxtm


title: Patient derived xenograft (PDX), 2017hxxtm


title: Patient derived xenograft (PDX), 1870hxxtm


title: Patient derived xenograft (PDX), 1865hxxtm


title: Patient derived xenograft (PDX), 1834hxxtm


title: Patient derived xenograft (PDX), 1993hxxtm


title: Patient derived xenograft (PDX), 1835hxxtm


title: Patient derived xenograft (PDX), 1980hxxtm


title: Patient derived xenograft (PDX), 1787hxxtm


title: Patient derived xenograft (PDX), 1823hxxtm


title: Patient derived xenograft (PDX), 2921hxxtm


title: Patient derived xenograft (PDX), 3237hxxtm


title: Patient derived xenograft (PDX), 1795hxxtm


title: Patient derived xenograft (PDX), 1725hxxtm


title: Patient derived xenograft (PDX), 1755hxxtm


title: Patient derived xenograft (PDX), 1726hxxtm


title: Patient derived xenograft (PDX), 1658hxxtm


title: Patient derived xenograft (PDX), 1481hxxtm


title: Patient derived xenograft (PDX), 1586hxxtm


title: Patient derived xenograft (PDX), 2042hxxtm


title: Patient derived xenograft (PDX), 1499hxxtm


title: Patient derived xenograft (PDX), 1442hxxtm


title: Patient derived xenograft (PDX), 1367hxxtm


title: Patient derived xenograft (PDX), 1323hxxtm


title: Patient derived xenograft (PDX), 1156hxxtm


title: Patient derived xenograft (PDX), 1172hxxtm


title: Patient derived xenograft (PDX), 5556hxxtm

value: Liver Carcinoma


title: Patient derived xenograft (PDX), 5555hxxtm

value: Liver Carcinoma Of The Liver


title: Patient derived xenograft (PDX), 5498hxxtm


title: Patient derived xenograft (PDX), 4950hxxtm


title: Patient derived xenograft (PDX), 1979hxxtm


title: Patient derived xenograft (PDX), 2969hxxtm


title: Patient derived xenograft (PDX), 3239hxxtm

value: Large Intestine Carcinoma Of The Rectum And Distal Sigmoid


title: Patient derived xenograft (PDX), 1867hxxtm

value: PDX (not a cell line)

value: Large Intestine Carcinoma Of The Sigmoid


title: Patient derived xenograft (PDX), 3671hxxtm

value: Large Intestine Carcinoma Of The Sigmoid/Rectum


title: Patient derived xenograft (PDX), 3684hxxtm

value: Large Intestine Carcinoma Of The Ovary


title: Patient derived xenograft (PDX), 5223hxxtm


title: Patient derived xenograft (PDX), 5446hxxtm

value: Large Intestine Carcinoma Of The Liver


title: Patient derived xenograft (PDX), 2538hxxtm


title: Patient derived xenograft (PDX), 4087hxxtm

value: Large Intestine Carcinoma Of The Omentum


title: Patient derived xenograft (PDX), 4454hxxtm


title: Patient derived xenograft (PDX), 2697hxxtm


title: Patient derived xenograft (PDX), 2573hxxtm

value: Large Intestine Carcinoma Of The Sigmoid Colon And Distal Anastomotic Margin


title: Patient derived xenograft (PDX), 1290hxxtm


title: Patient derived xenograft (PDX), 1855hxxtm


title: Patient derived xenograft (PDX), 2239hxxtm

value: Large Intestine Carcinoma Of The Distal Transverse Colon


title: Patient derived xenograft (PDX), 1443hxxtm


title: Patient derived xenograft (PDX), 5563hxxtm

value: Large Intestine Carcinoma Of The Cecum


title: Patient derived xenograft (PDX), 1746hxxtm

value: Liver Carcinoma Of The Lung


title: Patient derived xenograft (PDX), 5578hxxtm


title: Patient derived xenograft (PDX), 2846hxxtm

value: Large Intestine Carcinoma Of The Colon, Sigmoid


title: Patient derived xenograft (PDX), 2761hxxtm

value: Large Intestine Carcinoma Of The Ascending Colon


title: Patient derived xenograft (PDX), 2991hxxtm

value: Large Intestine Carcinoma Of The Ampulla


title: Patient derived xenograft (PDX), 2182hxxtm


title: Patient derived xenograft (PDX), 3019hxxtm


title: Patient derived xenograft (PDX), 1479hxxtm

value: Large Intestine Carcinoma Of The Caecum


title: Patient derived xenograft (PDX), 1234hxxtm


title: Patient derived xenograft (PDX), 4304hxxtm

value: Large Intestine Carcinoma Of The Abdominal Wall


title: Patient derived xenograft (PDX), 3765hxxtm


title: Patient derived xenograft (PDX), 5536hxxtm

value: Large Intestine Carcinoma


title: Patient derived xenograft (PDX), 5441hxxtm


title: Patient derived xenograft (PDX), 4484hxxtm

value: Large Intestine Carcinoma Of The Abdomen


title: Patient derived xenograft (PDX), 5495hxxtm

value: PDX (not a cell line)


title: Patient derived xenograft (PDX), 5494hxxtm


title: Patient derived xenograft (PDX), 5594hxxtm


title: Patient derived xenograft (PDX), 5439hxxtm


title: Patient derived xenograft (PDX), 5438hxxtm


title: Patient derived xenograft (PDX), 3224hxxtm

value: Large Intestine Carcinoma Of The Inguinal Mass


title: Patient derived xenograft (PDX), 5421hxxtm


title: Patient derived xenograft (PDX), 5405hxxtm


title: Patient derived xenograft (PDX), 5285hxxtm


title: Patient derived xenograft (PDX), 3570hxxtm


title: Patient derived xenograft (PDX), 3205hxxtm


title: Patient derived xenograft (PDX), 2484hxxtm


title: Patient derived xenograft (PDX), 3792hxxtm


title: Patient derived xenograft (PDX), 5254hxxtm


title: Patient derived xenograft (PDX), 3093hxxtm


title: Patient derived xenograft (PDX), 3135hxxtm


title: Patient derived xenograft (PDX), 2659hxxtm


title: Patient derived xenograft (PDX), 2822hxxtm


title: Patient derived xenograft (PDX), 2514hxxtm


title: Patient derived xenograft (PDX), 2483hxxtm


title: Patient derived xenograft (PDX), 2403hxxtm


title: Patient derived xenograft (PDX), 2374hxxtm


title: Patient derived xenograft (PDX), 1538hxxtm


title: Patient derived xenograft (PDX), 2145hxxtm


title: Patient derived xenograft (PDX), 1493hxxtm


title: Patient derived xenograft (PDX), 1333hxxtm


title: Patient derived xenograft (PDX), 1303hxxtm


title: Patient derived xenograft (PDX), 1270hxxtm


title: Patient derived xenograft (PDX), 1210hxxtm


title: Patient derived xenograft (PDX), 1329hxxtm


title: Patient derived xenograft (PDX), 3267hxxtm


title: Patient derived xenograft (PDX), 1173hxxtm


title: Patient derived xenograft (PDX), 1167hxxtm


title: Patient derived xenograft (PDX), 1683hxxtm

value: Lung Carcinoma


title: Patient derived xenograft (PDX), 1055hxxtm


title: Patient derived xenograft (PDX), 1027hxxtm


title: Patient derived xenograft (PDX), 0992hxxtm


title: Patient derived xenograft (PDX), 1119hxxtm


title: Patient derived xenograft (PDX), 1095hxxtm


title: Patient derived xenograft (PDX), 2742hxxtm


title: Patient derived xenograft (PDX), 0933hxxtm


title: Patient derived xenograft (PDX), 2861hxxtm


title: Patient derived xenograft (PDX), 5374hxxtm

value: Kidney Carcinoma Of The Lung


title: Patient derived xenograft (PDX), 5739hxxtm

value: Kidney Carcinoma


title: Patient derived xenograft (PDX), 3829hxxtm

value: Kidney Carcinoma Of The Diaphragm


title: Patient derived xenograft (PDX), 5523hxxtm

value: Kidney Carcinoma Of The Femur


title: Patient derived xenograft (PDX), 1536hxxtm


title: Patient derived xenograft (PDX), 5395hxxtm


title: Patient derived xenograft (PDX), 1480hxxtm


title: Patient derived xenograft (PDX), 5510hxxtm


title: Patient derived xenograft (PDX), 4073hxxtm


title: Patient derived xenograft (PDX), 3629hxxtm


title: Patient derived xenograft (PDX), 3717hxxtm


title: Patient derived xenograft (PDX), 3083hxxtm


title: Patient derived xenograft (PDX), 4536hxxtm


title: Patient derived xenograft (PDX), 2967hxxtm


title: Patient derived xenograft (PDX), 2597hxxtm


title: Patient derived xenograft (PDX), 2863hxxtm


title: Patient derived xenograft (PDX), 1169hxxtm


title: Patient derived xenograft (PDX), 2198hxxtm

value: Intraductal Carcinoma


title: Patient derived xenograft (PDX), 2207hxxtm


title: Patient derived xenograft (PDX), 1569hxxtm


title: Patient derived xenograft (PDX), 1473hxxtm


title: Patient derived xenograft (PDX), 3972hxxtm

value: Esophagus Carcinoma


title: Patient derived xenograft (PDX), 2983hxxtm

value: Endometrium Carcinoma Of The Uterus


title: Patient derived xenograft (PDX), 1381hxxtm


title: Patient derived xenograft (PDX), 4870hxxtm


title: Patient derived xenograft (PDX), 3877hxxtm


title: Patient derived xenograft (PDX), 3736hxxtm

value: Endometrium Carcinoma Of The Bowel


title: Patient derived xenograft (PDX), 4074hxxtm


title: Patient derived xenograft (PDX), 3274hxxtm

value: Endometrium Carcinoma Of The Abdomen


title: Patient derived xenograft (PDX), 4653hxxtm


title: Patient derived xenograft (PDX), 3200hxxtm

value: Endometrium Carcinoma


title: Patient derived xenograft (PDX), 5700hxxtm


title: Patient derived xenograft (PDX), 4367hxxtm


title: Patient derived xenograft (PDX), 2880hxxtm


title: Patient derived xenograft (PDX), 2781hxxtm


title: Patient derived xenograft (PDX), 2914hxxtm


title: Patient derived xenograft (PDX), 5974hxxtm

value: Breast Carcinoma Of The Lymph Node


title: Patient derived xenograft (PDX), 5001hxxtm


title: Patient derived xenograft (PDX), 2347hxxtm


title: Patient derived xenograft (PDX), 3468hxxtm


title: Patient derived xenograft (PDX), 1916hxxtm


title: Patient derived xenograft (PDX), 3201hxxtm

value: Breast Carcinoma Of The Chest Wall


title: Patient derived xenograft (PDX), 5541hxxtm

value: Breast Carcinoma In Situ


title: Patient derived xenograft (PDX), 6017hxxtm

value: Breast Carcinoma


title: Patient derived xenograft (PDX), 5490hxxtm

value: PDX (not a cell line)


title: Patient derived xenograft (PDX), 5975hxxtm


title: Patient derived xenograft (PDX), 6047hxxtm


title: Patient derived xenograft (PDX), 1678hxxtm


title: Patient derived xenograft (PDX), 5885hxxtm


title: Patient derived xenograft (PDX), 5931hxxtm


title: Patient derived xenograft (PDX), 5502hxxtm


title: Patient derived xenograft (PDX), 5593hxxtm


title: Patient derived xenograft (PDX), 5249hxxtm


title: Patient derived xenograft (PDX), 5355hxxtm


title: Patient derived xenograft (PDX), 5367hxxtm


title: Patient derived xenograft (PDX), 5440hxxtm


title: Patient derived xenograft (PDX), 3888hxxtm


title: Patient derived xenograft (PDX), 2793hxxtm


title: Patient derived xenograft (PDX), 5141hxxtm


title: Patient derived xenograft (PDX), 5115hxxtm


title: Patient derived xenograft (PDX), 4949hxxtm


title: Patient derived xenograft (PDX), 5938hxxtm


title: Patient derived xenograft (PDX), 5057hxxtm


title: Patient derived xenograft (PDX), 5213hxxtm


title: Patient derived xenograft (PDX), 4970hxxtm


title: Patient derived xenograft (PDX), 4948hxxtm


title: Patient derived xenograft (PDX), 4888hxxtm


title: Patient derived xenograft (PDX), 4824hxxtm


title: Patient derived xenograft (PDX), 4347hxxtm


title: Patient derived xenograft (PDX), 4132hxxtm


title: Patient derived xenograft (PDX), 3873hxxtm


title: Patient derived xenograft (PDX), 3697hxxtm


title: Patient derived xenograft (PDX), 3453hxxtm


title: Patient derived xenograft (PDX), 3904hxxtm


title: Patient derived xenograft (PDX), 3450hxxtm


title: Patient derived xenograft (PDX), 3147hxxtm


title: Patient derived xenograft (PDX), 3298hxxtm


title: Patient derived xenograft (PDX), 3078hxxtm


title: Patient derived xenograft (PDX), 3077hxxtm


title: Patient derived xenograft (PDX), 3202hxxtm


title: Patient derived xenograft (PDX), 2780hxxtm


title: Patient derived xenograft (PDX), 2487hxxtm


title: Patient derived xenograft (PDX), 2640hxxtm


title: Patient derived xenograft (PDX), 2524hxxtm


title: Patient derived xenograft (PDX), 2353hxxtm


title: Patient derived xenograft (PDX), 2376hxxtm


title: Patient derived xenograft (PDX), 2195hxxtm


title: Patient derived xenograft (PDX), 1970hxxtm


title: Patient derived xenograft (PDX), 2344hxxtm


title: Patient derived xenograft (PDX), 2127hxxtm


title: Patient derived xenograft (PDX), 1921hxxtm


title: Patient derived xenograft (PDX), 1784hxxtm


title: Patient derived xenograft (PDX), 1832hxxtm


title: Patient derived xenograft (PDX), 1828hxxtm


title: Patient derived xenograft (PDX), 1631hxxtm


title: Patient derived xenograft (PDX), 1600hxxtm


title: Patient derived xenograft (PDX), 4567hxxtm


title: Patient derived xenograft (PDX), 1543hxxtm


title: Patient derived xenograft (PDX), 1383hxxtm


title: Patient derived xenograft (PDX), 1371hxxtm


title: Patient derived xenograft (PDX), 1407hxxtm


title: Patient derived xenograft (PDX), 1468hxxtm


title: Patient derived xenograft (PDX), 1349hxxtm


title: Patient derived xenograft (PDX), 1298hxxtm


title: Patient derived xenograft (PDX), 1286hxxtm


title: Patient derived xenograft (PDX), 5143hxxtm

value: Biliary Tract Carcinoma Of The Liver


title: Patient derived xenograft (PDX), 1008hxxtm


title: Patient derived xenograft (PDX), 2357hxxtm


title: Patient derived xenograft (PDX), 1004hxxtm


title: Patient derived xenograft (PDX), 4836hxxtm

value: Biliary Tract Carcinoma


title: GSC11 TAZ 4SA + HDACi_ Input DNA [GSCS-V4SA_G]

city: Houston

first: Mahinur

last: Mattohti

state: TX

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

data_processing:
ChIPseq reads were aligned to hg19 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 and MACS2 using pvalue cutoff of 1e-5, and was further filtered for downstream analysis using a more stringent cutoff of 1e-10
bigwig files were generated by deeptools bamCoverage normalized by RPKM
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14

source_name: GSC11 TAZ 4SA + HDACi

growth_protocol: All GSCs were expanded and maintained in Dulbecco's modified Eagle’s medium/F12 50/50 supplemented with B-27, 20 ng/mL EGF and 20 ng/mL FGF

extract_protocol:
Crosslinked samples were thawed on ice and resuspended in RIPA lysis buffer supplemented with protease inhibitor, lysed the cells on ice then sheared the chromatin by sonication. After centrifuge, the clean sonicated cell lysate mixed with protein G magnetic dynabeads (Invitrogen) coupled to antibodies described above and incubated over night at 4 degrees. Samples was washed 5 times with cold RIPA, twice with high salt RIPA, twice with LiCl buffer, twice with TE, and then eluted in elution buffer. The eluate was reverse crosslinked at 65C. Solid-phase reversible immobilization (SPRI) cleanup steps were performed. Beads were washed twice on the magnet with 70% ethanol and then air-dried. The DNA was eluted in EB buffer.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

value: GBM GSC cell line

tag: chip antibody


title: GSC8-18 IDH WT TAZ high Mesenchymal_Input DNA [GSCS-OO20_G]

source_name: GSC8-18 IDH WT TAZ high Mesenchymal

value: glioblastoma stem cell (GSC) line

value: GSC8-18 IDH WT TAZ high Mesenchymal


title: GSC8-18 IDH WT TAZ low_H3K27ac_ChIPseq [GSCS-8-18_C]

source_name: GSC8-18 IDH WT TAZ low

value: GSC8-18 IDH WT TAZ low


title: GSC8-18 IDH WT TAZ high Mesenchymal_H3K27ac_ChIPseq [GSCS-OO20_C]


title: GSC8-18 IDH WT TAZ low_Input DNA [GSCS-8-18_G]


title: GSC11 TAZ 4SA + HDACi_H3K27ac [GSCS-V4SA_C]


title: GSC8-11 IDH Mutant TAZ low_Input DNA [GSCS-8-11_G]

source_name: GSC8-11 IDH Mutant TAZ low

value: GSC8-11 IDH Mutant TAZ low


title: GSC8-11 IDH Mutant TAZ low_H3K27ac_ChIPseq [GSCS-8-11_C]


title: GSC11 TAZ S51A_Input DNA [GSCS-S51A_G]

source_name: GSC11 TAZ S51A

value: GSC11 TAZ S51A


title: GSC11 TAZ S51A_H3K27ac_ChIPseq [GSCS-S51A_C]


title: GSC11 TAZ 4SA_H3K4me3_ChIPseq [GBMC-GSC3_E]

source_name: GSC11 TAZ 4SA

value: GSC11 TAZ 4SA


title: GSC11 TAZ 4SA_H3K4me1_ChIPseq [GBMC-GSC3_A]


title: GSC11 TAZ 4SA_H3K79me2_ChIPseq [GBMC-GSC3_D]


title: GSC11 TAZ 4SA_H3K9me3_ChIPseq [GBMC-GSC3_B]


title: Patient derived xenograft (PDX), 5238hxxtm

value: Large Intestine Carcinoma Of The Liver


title: GSC11 TAZ WT_H3K79me2_ChIPseq [GBMC-GSC2_D]

source_name: GSC11 TAZ WT

value: GSC11 TAZ WT


title: GSC11 TAZ WT_H3K4me3_ChIPseq [GBMC-GSC2_E]


title: GSC11 Vector_Input DNA [GBMC-GSC1_G]

source_name: GSC11 Vector

value: GSC11 Vector


title: GSC11 TAZ WT_H3K9me3_ChIPseq [GBMC-GSC2_B]


title: GSC11 TAZ WT_H3K4me1_ChIPseq [GBMC-GSC2_A]


title: GSC11 Vector_H3K4me3_ChIPseq [GBMC-GSC1_E]


title: GSC11 Vector_H3K27ac_ChIPseq [GBMC-GSC1_C]


title: GSC11 Vector_H3K9me3_ChIPseq [GBMC-GSC1_B]


title: GSC11 Vector_H3K79me2_ChIPseq [GBMC-GSC1_D]


title: GSC11 TAZ 4SA_Input DNA [GBMC-GSC3_G]


title: GSC11 TAZ 4SA_H3K27ac_ChIPseq [GBMC-GSC3_C]


title: FOB-Free

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

description: processed data file: all.counts.Homosapiens.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting
Genome_build: GRCh38; Rnor_6.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: cell

growth_protocol: 10%FBS high-glucose DMEM were used as culture medium for primary cell culture. When cells reach 80% confluent, the cell were lysed with trypsin for passage.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Ion  Proton Sequencing Protocol

treatment_protocol: 100ng/ml uMSC derived exosomes were added to the indicated sample for 48h before total RNA extraction. All samples were treated with 1% exosome-free FBS/DMEM 48h before RNA extraction.

tag: cell line

value: human osteoblast cell line

value: Exosome-free supernatent


title: FOB-exo

value: 100ng/ml uMSC-derived exosomes


title: mimics negative control_rep2 (NC-m-2)

city: Guangzhou

first: Sijia

last: Liang

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Sun Yat-Sen University

data_processing:
Quality control.Clean datas were obtained by removing low quality reads with Fastp.
Reads mapping.Clean reads were mapped to mouse reference genome mm10 by hisat2.
Differential expression analysis of two conditions/groups was performed using the feartureCounts.
Assembly: mm10
Supplementary files format and content: xlsx

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow cells were isolated and cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% HEPES, 1% penicillin/streptomycin, and 30% L929 conditioned medium (source of M-CSF) for 7 d to differentiate into bone marrow-derived macrophages.

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. 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.

treatment_protocol: The cells were transfected with miRNA mimics negative control or miRNA-204-3p mimics for 24 h.

value: Bone marrow-derived macrophages

value: transfected with mimics negative control


title: KI, replicate 1, VDJ repertoire

city: Erlangen

first: Simon

last: Schaefer

state: Bavaria

address: Glueckstr. 6

department: Genetics

institute: FAU Erlangen

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw data from the V(D)J library run was analysed with the Cell Ranger platform and further processed.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
To retrieve single cell suspensions from spleen, freshly-isolated organs were injected with Collagenase D/DNAse I solution (2mg/ml and 1mg/ml) with a syringe followed by a 15-minute incubation at 37°C. The organs were transferred into GentleMACS C-Tube containing 3ml PBS and subjected to the pre-defined “37 SDK” program in the gentleMACS Octo Dissociator. Retrieved cell suspensions were filtered through a 70 𝜇m filter and cells were pelleted, washed with PBS and subjected to erythrocyte lysis. Splenocytes were enriched for T cells with the MACS T cell isolation kit II (Milteny) according to manufacturer’s protocol. Enriched T cells from spleen were subjected to antibody surface staining (B220, CD3, CD11c, TCR𝛿, TCR𝛽) after Fc receptor blockage. The stained cell suspensions were subjected to flow cytometry sorting (Astrios II).
After sorting, viable cell numbers were determined and subjected to 10X library preparation (Next GEM Single Cell 5’ Lib Kit V1.1) according to the manufacturer’s protocol using the 10X Chromium device. After generation of full length 10X barcoded cDNA, a part of the cDNA library was subjected to enrichment amplification of V(D)J transcripts according to manufacturer’s protocol with custom primers for TCRγ (round 1: TCRG_Cg1_2_Outer, TCRG_Cg3_Outer, TCRG_Cg4_Outer at 10mM concentration, round 2: TCRG_Cg1_3_Inner, TCRG_Cg4_Inner at 20mM concentration) and TCRδ (round 1: TRD_Outer at 10mM concentration, round 2: TCRD Inner at 20mM concentration) constant regions. The  VDJ library was run twice on a HiSeq platform with 100/8/100 bp parameters.

value: gamma delta T cells

value: spleen

value: 10 weeks old


title: WT, replicate 1, VDJ repertoire

description: 10x Genomics


title: GSC11 TAZ WT_Input DNA [GBMC-GSC2_G]

value: glioblastoma stem cell (GSC) line


title: mimics negative control_rep1 (NC-m-1)


title: KI, replicate 2, VDJ repertoire

description: 10x Genomics


title: WT, replicate 2, VDJ repertoire

description: 10x Genomics


title: GSC11 TAZ WT_H3K27ac_ChIPseq [GBMC-GSC2_C]


title: KI, replicate 2, scRNAseq

description: 10x Genomics

data_processing:
Raw data from the 5’Gene Expression library (5’GEX) run was analysed with the Cell Ranger platform and further processed.
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
To retrieve single cell suspensions from spleen, freshly-isolated organs were injected with Collagenase D/DNAse I solution (2mg/ml and 1mg/ml) with a syringe followed by a 15-minute incubation at 37°C. The organs were transferred into GentleMACS C-Tube containing 3ml PBS and subjected to the pre-defined “37 SDK” program in the gentleMACS Octo Dissociator. Retrieved cell suspensions were filtered through a 70 𝜇m filter and cells were pelleted, washed with PBS and subjected to erythrocyte lysis. Splenocytes were enriched for T cells with the MACS T cell isolation kit II (Milteny) according to manufacturer’s protocol. Enriched T cells from spleen were subjected to antibody surface staining (B220, CD3, CD11c, TCR𝛿, TCR𝛽) after Fc receptor blockage. The stained cell suspensions were subjected to flow cytometry sorting (Astrios II).
After sorting, viable cell numbers were determined and subjected to 10X library preparation (Next GEM Single Cell 5’ Lib Kit V1.1) according to the manufacturer’s protocol using the 10X Chromium device. The 5’GEX library was consequentially sequenced on a HiSeq platform with 100/8/100 bp and 28/9/91 bp parameters.


title: WT, replicate 2, scRNAseq

description: 10x Genomics


title: WT, replicate 1, scRNAseq

description: 10x Genomics


title: KI, replicate 1, scRNAseq

description: 10x Genomics


title: miR-204-3p mimice_rep2 (miR-204-3p-m-2)

value: transfected with miR-204-3p mimics


title: miR-204-3p mimice_rep1 (miR-204-3p-m-1)


title: HFDp3

city: Illkirch

first: Gérard

last: Gradwohl

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2 and reads mapping to rRNA were discarded.
Reads were mapped onto the mm10 assembly of mouse genome using Tophat v2.0.10 with bowtie v2.1.0.
Gene expression was quantified using HTSeq version 0.5.4p3 and gene annotations from Ensembl release 74.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: jejunum

growth_protocol: 8 week Neurog3eYFP+/ adult mice (C56BL/6N background) fed with normal diet (Safe D04) were shifted (n=3) to a high fat diet (D12492; Research Diets) for 4 weeks or kept on normal diet (n=3)

extract_protocol:
RNeasy QIAGEN columns
Double stranded cDNA were prepared from total RNA using Ovation RNA-Seq System V2 (NuGEN Part #7102-32), and libraries were then generated using Ovation SP Ultralow Library Systems (NuGeN, Part #8033) following manufacturer instructions.

treatment_protocol: Villi were enriched by EDTA treatment, cells dissociated using dispase and eYFPplus and eYFPminus cells sorted (FACS AriaII)

tag: genetic background

value: jejunum

tag: Sex

value: male

value: EEC

value: 12 weeks

tag: genotype

tag: diet

value: high fat diet


title: HFDp2


title: HFDm2

value: non-EEC


title: HFDm3

value: non EEC


title: HFDp1


title: GSC11 Vector_H3K4me1_ChIPseq [GBMC-GSC1_A]

value: GSC11 Vector


title: FOB-NC

value: human osteoblast cell line


title: NDm2

value: normal diet


title: NDp3


title: NDm1


title: NDp2


title: NDp1


title: CT26-Input

city: New York

first: Gurkan

last: Mollaoglu

state: New York

address: Hess Center for Science and Medicine 5th Floor 302

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

description:
ChIP-seq control
Please note that the fastq file was lost due to hard drive failure but the sequence record is complete.

data_processing:
Sequenced reads containing barcode contamination were filtered using Cutadapt.
Reads were aligned to the mm9 mouse reference genome using Bowtie. Duplicated reads were removed using samtools.
Peak calling was performed using MACS2 and a p-value cutoff of 1e-6.
Assembly: mm9
Supplementary files format and content: Bigwig tracks were generated and visualized on the IGV browser (Broad).

source_name: CT26, N-nitroso-N-methylurethane-(NNMU) induced, undifferentiated colon carcinoma cell line.

growth_protocol: CT26 cells were cultured in RPMI1640 supplemented with 10% heat-inactivated FBS, 100 U/ml penicillin/streptomycin, and 2mM L-Glutamine.

extract_protocol:
For colon epithelium, a normal mouse colon was dissected distal to the cecum and proximal to the rectum. The colon was flushed with ice-cold PBS and split open longitudinally. Epithelial cells were collected using a cell scraper to separate them from the underlying mesenchyme. For CT26 cells, the cells were collected from culture plates. For both samples, the cells were rinsed with PBS and double-cross-linked at room temperature, first using 0.25 M disuccinimidyl glutarate for 45 minutes followed by 1% formaldehyde for 10 minutes. Formaldehyde crosslinking was quenched with 2.5 M glycine for 5 minutes. The cells were collected in PBS and incubated in nuclear lysis buffer on ice for 10 minutes (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS). The cells were sonicated using a Diagenode Bioruptor for 15 cycles in alternating 30 s on/off cycles on the low setting. Difficult to sonicate cell lines, including primary mouse colonic epithelium, were first incubated in 0.25% trypsin for 3 minutes with agitation at room temperature followed by inactivation with media containing 10% FBS. Sonicated chromatin was diluted 1:4 in IP dilution buffer (20 mM Tris pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS) and precleared with overheard rotation at 4 C for two hours using Protein A+G conjugated magnetic beads (Millipore). Chromatin was incubated with primary antibody against mouse p53 (CM5, Leica) overnight followed by two hours of conjugation to Protein A+G conjugated magnetic beads. Beads were washed once with IP Wash Buffer 1 (20 mM Tris pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), twice with High Salt Wash Buffer (20 mM Tris pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP Wash Buffer II (10 mM Tris pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% NP-40, 1% deoxycholic acid), and twice with TE buffer. Beads were eluted with buffer containing 1% SDS and 0.1 mM NaHCO3 with agitation at 37 C. Reverse crosslinking was performed overnight at 65 C with high NaCl and RNase treatment. Proteinase K digestion was performed for 2 hours at 42 C before DNA was purified using QIAQuick PCR purification kits according to the manufacturer’s instructions.
End repair of ChIP DNA was performed using Klenow DNA Polymerase, T4 DNA Polymerase, and T4 PNK (NEB). Polyadenylation was performed using Klenow Exo (NEB). NEXTFLEX barcodes were ligated using the Quick Ligation Kit (NEB). Libraries were amplified for 15 cycles using HotStart HiFi Ready Mix (KAPA). Libraries were run on a 2% low melt agar gel, and 300-400 bp fragments were excised using the DNA Gel Extraction Kit (QIAGEN). Libraries underwent quality control using Qubit and Bioanalyzer High Sensitivity assays before being sequenced on an Illumina NextSeq 2500 at the Oncological Sciences Sequencing Core Facility at Mount Sinai. p53 ChIP libraries were sequenced to a target depth of 30 M reads and input libraries of 60 M reads.

value: BALB/c

value: Colon

value: undifferentiated colon carcinoma cell


title: Gut epithelium

description: ChIP-seq for TP53

source_name: Colon epithelium

value: normal gut epithelium


title: CT26-TP53 ChIP

description:
ChIP-seq for TP53
Please note that the fastq file was lost due to hard drive failure but the sequence record is complete.


title: Tet_TKO_168h-2i-BS

description: processed data file: Tet_TKO_Enzyme_Efficiencies.igv.gz

data_processing:
library strategy: hairpin oxidative bisulfite-seq (reduced reprsentation)
The sequences were aligned as suggested by Porter et al. 2015. In detail; reads were trimmed for adapter, hairpin-linker and3’ quality (Q≥20) with TrimGalore! (Krüger et al. 2019) and cutadapt (Martin M. 2011). Trimmed read pairs were aligned with the Smith-Waterman algorithm allowing for bisulfite induced mismatches. The two bisulfite converted strands were used to deduce the original genomic sequence. Mismatches other than G-to-A and T-to-C were replaced with N. The resulting sequences were aligned to the mouse genome (mm10) with GEM-mapper (beta build1.376) (Marco-Sola et al.), after which the methylation information wasreintroduced with a custom pileup function based on HTSJDK (Li et al. 2009) and ratios for the four methylation states were calculated for each cytosine. The pipeline was implemented with the Ruffus pipeline framework (Goodstadt et al. 2010).
Genome_build: mm10
Supplementary_files_format_and_content: IGV files : IGV files are tab-delimited text files with header, which defines tracks. While the first three columns define the location of a genomic feature - in our case individual cytosine, the following columns define individual tracks - in our case the output of our hidden Markov model. The columns include:
(a) The hidden states i.e. the estimated distribution of C, 5mC and 5hmC. More precisely: uu (unmethylated on both DNA strands), um or mu (methylated only on upper or lower strand, respectively), uh or hu (hydroxylated on upper or lower and unmethylated on the other strand), mm (methylated on both DNA strands), hh (hydroxylated on both DNA strands), mh or hm (methylated on one and hydroxylated on the other strand) and toth (total frequency of all states that contain at least one 5hmC).
(b) The efficiencies i.e. the activity of Dnmts and Tets given as De_novo (de novo methylation efficiency for Dnmts), maint (maintenance methylation efficiency for Dnmts) or hydroxyl (hydroxylation efficiency of Tet enzymes).
(c) The standard deviations of the estimated Efficiencies given as De_novo_sd (standard deviation given of de novo methylation efficiency) maint_sd (standard deviation of maintenance efficiency), hydroxyl_sd (standard deviation of hydroxylation efficiency).
Supplementary_files_format_and_content: DSI file format: the abbreviation “dsi” stands for “double strand information”. The dsi file is a tab separated text file without header and contains the sequencing results of the hairpin bisulfite sequencing experiment, visualizing the four different states of a given CpG position i.e. both dna strand are methylated - 5mC/5mC; DNA is only methylated at the upper strand - 5mC/C, DNA only methylated on the lower strand - C/5mC or both DNA strands are unmethylated at a given CpG - C/C. DSI files can be visualized using the Integrative Genomics Viewer (IGV) (http://software.broadinstitute.org/software/igv/). The file contains the following elven columns:
Column 1 - Chromosome: name of the chromosome e.g. 1 for chromosome 1
Column 2 - Position of the cytosine: e.g. 3003721
Column 3 - DNA Strand: Either C (upper strand) or G (lower strand). Indicates to which DNA strand the methylation has been mapped. This is only relevant for the non-hairpin information given in columns 4, 5 and 6.
Column 4 - Coverage: lists the coverage of the analyzed cytosine.
Column 5 - Methylation: lists how often an analyzed cytosine has been methylated
Column 6 - Unmethylated: lists how often an analyzed cytosine has been unmethylated
Column 7 - Sequence context: Gives the sequence context of the analyzed cytosine. Can be “CG” for CpG, “GC” for GpC or “others” for CpH.
Column 8 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was methylated on both DNA strands i.e. 5mC/5mC.
Column 9 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was only methylated on the upper strands i.e. 5mC/C.
Column 10 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was only methylated on the lower strands i.e. C/5mC.
Column 11 - Applies only to symmetric CpG or GpC positions. Indicates how often a given CpG or GpC was unmethylated on both DNA strands i.e. C/C.

source_name: cell culture

growth_protocol: Embryonic stem cells were cultured as discribed in Ficz et al. 2013. Briefly, ES cells were cultured without feeders either in standard serum-containing media (DMEM 4,500 mg/l glucose, 4 mM L-glutamine, 110 mg/l sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 μg/ml streptomycin, 0.1 mM nonessential amino acids, 50 μM β-mercaptoethanol, and 103 U/ml LIF ESGRO) or under 2i culturing conditions (Ying et al., 2008) (serum-free N2B27 [Cat. DMEM/F12: GIBCO 21331; Neurobasal: GIBCO 21103; N2: Stem Cells SF-NS-01-005; B27: GIBCO 17504-044] supplemented with 103 U/ml LIF and Mek inhibitor PD0325901 [1 μM] and Gsk3β inhibitor CHIR99021 [3 μM]).

extract_protocol:
Genomic DNA was prepared using QIAamp DNA Micro Kit or AllPrep DNA/RNA mini kit (QIAGEN).
1.2 μg DNA is divided equally into three 0.5ml reaction tubes and digested in a 20 μl reaction using 20 U of HaeIII (NEB), AluI (NEB) and 10 U HpyCH4V (NEB), respectively. The reactions are incubated overnight for a minimum of 12 h at 37 °C. Restriction enzymes are inactivated at 80 °C for 30 min. The reactions are pooled and subjected to a ligation step. During this process, hairpin linker and sequencing adapter are introduced to the opposed ends of each restriction fragment. For this, 200 mM biotin labeled hairpin linker and 100 mM sequencing adapter are added to the digested DNA, incubatedwith 1 mM ATP and 2000 U T4 DNA Ligase (NEB) for 16 h at 16 °C. The reaction is purified using AMPureXP beadsfollowed by enrichment for hairpin containing fragments with streptavidin beads. The library is then subjected to BS/oxBS work-flow of the TrueMethyl kit from CEGX according tomanufacturer’s instructions. Amplification of the library was done with HotStarTaq® polymerase (Qiagen) and sequencing was performed on an Illumina HiSeq 2500 platform in a 150 bp paired-end sequencing mode.

treatment_protocol: no treatment

tag: strain background

value: embryonic stem cell


title: Tet_TKO_48h-2i-BS


title: WT-144h-2i-BS

description: processed data file: WT_Enzyme_Efficiencies.igv.gz

value: wild type


title: HFDm1


title: WT-72h-2i-oxBS


title: Tet_TKO_Serum-BS

value: Serum/LIF


title: WT-Serum-BS


title: WT-144h-2i-oxBS


title: WT-Serum-oxBS


title: Tet_TKO_96h-2i-BS


title: WT-72h-2i-BS


title: NDm3

value: jejunum


title: d0-si-ctrl-r2

city: LILLE

first: souhila

last: amanzougarene

address: 1 place de Verdun

institute: CNRS

data_processing:
the demultiplexing of sequence data was performed using bcl2fastq Conversion Software (Illumina; bcl2fastq v2.19.1). Trimming of adapter sequences was performed using cutadapt software (version 1.7.1). Reads quality control was assessed using FastQC (v0.11.5). Subsequently, sequence reads from FASTQ files were aligned to the human genome GRCh38, downloaded from Ensembl. Alignement was performed using STAR aligner (version 2.5.2b). Over 19 million of 75 base pairs PE-reads reads were generated per sample.The normalized counts of the different genes and isoforms was performed using RSEM (v1.2.31) using a GTF from Ensembl 89. Finally differential expression was performed using R version 3.6.3 and DESeq2 package v1.24.0.
Assembly: the human genome GRCh38
Supplementary files format and content: Excel file include Differential expression DE_D0_D10
Supplementary files format and content: Excel file include Differential expression DE_Ctrl_Cdkn_D0
Supplementary files format and content: Excel file include Differential expression DE_Ctrl_Cdkn_D10

source_name: hiPSC-BAP 3D cells, siCTRL D0

growth_protocol: hiPSC-BAPs, derived from the hiPSC line NOK6 as previously described (Mohsen-Kanson et al., 2014) were grown in standard tissue culture conditions at 37C with 5% CO2. The growth medium is DMEM low glucose supplemented with L-glutamine (2mM), penicillin–streptomycin 5,000 IU/ml–5,000 g/ml (Pen/Strep), 10% FBS and 2.5 ng/ml FGF2.

extract_protocol:
Total RNA was extracted from hiPSC-BAP 3D at D0 and D10 of differentiation using TRIzolTM Reagent (Sigma).
The libraries were sequenced on the NextSeq system (Illumina), using a paired-end 2x75 bp protocol.

treatment_protocol: To generate spheroids, a suspension of hiPSC-BAPs at 0.5~1x 106 cells/ml was prepared in growth medium, and 1ml of the cell suspension was seeded in one well of 24 well Ultra-Low Attachment (ULA) plate (Corning 3473). The plate was maintained for 3 days to generate spheroids. Then, to differentiate spheroids, the growth medium was changed to differentiation medium composed of EBM-2 (Lonza) supplemented with 0.1% FCS, IBMX (0.5 mM), dexamethasone (0.25 μM), T3 (0.2 nM), insulin (170 nM), rosiglitazone (1 μM), SB431542 (5 μM), and EGM-2 cocktail (Lonza, CC-3121) including ascorbic acid, hydrocortisone and EGF. IBMX and dexamethasone were maintained only for the first 3 days of differentiation. SB431542 and EGF were removed after the first 9 days of differentiation. Spheroids were maintained in differentiation medium up to 20 to 30 days, with medium changed once a week.

value: hiPSC-BAP

value: Human induced pluripotent stem cells differentiated into brown adipocytes progenitors

value: Control

value: adipogenic differentiation

tag: time

value: Day 0


title: d0-si-cdkn-r3

source_name: hiPSC-BAP 3D cells, siCDKN2A D0

value: CDKN2A knockdown


title: d10-si-ctrl-r1

source_name: hiPSC-BAP 3D cells, siCTRL D10

value: Day 10


title: d10-si-cdkn-r1

source_name: hiPSC-BAP 3D cells, siCDKN2A D10


title: d0-si-ctrl-r1


title: d10-si-ctrl-r3


title: d0-si-cdkn-r1


title: d10-si-cdkn-r2


title: d0-si-ctrl-r3


title: d0-si-cdkn-r2


title: PBMC, S1, ADT-derived cDNA

city: Seattle

first: Chetan

last: Seshadri

state: WA

address: 750 Republican Street

institute: University of Washington

description:
Antibody-derived oligonucleotide (ADT) and hashtag-derived oligonucleotide (HTO)
s1_filtered_barcodes.tsv.gz
s1_filtered_features.tsv.gz
s1_filtered_matrix.mtx.gz
s1_raw_barcodes.tsv.gz
s1_raw_features.tsv.gz
s1_raw_matrix.mtx.gz

library_source: other

data_processing:
The Cell Ranger multi pipeline (v5.0.1, 10x Genomics) was used to conduct the alignment and feature expression quantification of the single-cell sequencing data. mRNA and V(D)J reads were aligned to the GRCh38 human reference genome. HTO and ADT reads were aligned to a feature reference containing the appropriate barcode sequences.
Further processing was done with Seurat v4.1.0 (quality control, hashtag demultiplexing, dimensional reduction, clustering, differential gene expression analysis). Cell barcodes classified as singlets by HTO enrichment were kept and then filtered by gene expression data using the following parameters: (1) >200 unique genes/cell and (2) <5% mitochondrial counts. Within each cell barcode, the mRNA count data were log-normalized, and the ADT count data were CLR normalized.
From the filtered V(D)J output given by the Cell Ranger multi pipeline, cell barcodes with less than four productive TCR chains or a single productive TCR-β chain were retained. If a given cell barcode was associated with two TCR-ɑ or TCR-β chains, the chain with the greater number of unique molecular identifiers (UMIs) was retained.
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, contig_annotations.csv
Library strategy: CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing)

molecule: protein

source_name: Peripheral blood mononuclear cells (PBMC)

extract_protocol:
Cryopreserved PBMC from SARS-CoV-2-naive (n = 4) or convalescent (n = 4) donors collected approximately 10 days post vaccination were thawed in sterile-filtered RPMI 1640 (Thermo Fisher Scientific) with 10% FBS (Hyclone) and 0.2% Benzonase (MilliporeSigma) and then centrifuged at 300xg for 10 minutes at room temperature. Viable cells were counted using the Guava easyCyte. Cells were centrifuged at 300xg for 10 minutes at room temperature and plated at a density of 2x106 167 cells/well in a 96-well U-bottom plate. Next, cells were blocked with 1 ug/mL antiCD40 (clone HB14, Miltenyi Biotec) at 37degreeC. The following day, cells were stained with Fixable Aqua viability dye (Invitrogen) for 30 minutes at room temperature. An antibody cocktail was prepared for sorting with the following markers: antiCD7 FITC (clone CD7-6B7, BioLegend), antiCD69 BV711 (clone FN50, BioLegend), antiCD137 APC/Fire 750 (clone 4B4-1, BioLegend), and antiCD40L/CD154 PE-Cy5 (clone TRAP1, BD Biosciences). Additionally, eight cocktails were prepared with the following TotalSeq-C antibody-derived tags (ADTs): antiCD3 (clone UCHT1, BioLegend), antiCD4 (clone RPA-T4, BioLegend), antiCD8a (clone RPA-T8, BioLegend), antiGD (clone B1, BioLegend), antiTRAV1-2 (clone 3C10, BioLegend), antiCD62L (clone DREG-56, BioLegend), antiCCR7 (clone G043H7, BioLegend), antiCD45RA (clone HI100, BioLegend), antiCD28 (clone CD28.2, BioLegend), antiCD127 (clone A019D5, BioLegend), antiCD95 (clone DX2, BioLegend), antiCXCR3 (clone G025H7, BioLegend), antiCXCR5 (clone J252D4, BioLegend), antiCCR4 (clone L291H4, BioLegend), antiCCR5 (clone J418F1, BioLegend), antiCCR6 (clone G034E3, BioLegend), antiCD25 (clone BC96, BioLegend), antiCD38 (clone HIT2, BioLegend), antiCD26 (clone BA5b, BioLegend), antiHLA-DR (clone L243, BioLegend), antiCD161 (clone HP-3G10, BioLegend), antiCD103 (clone Ber-ACT8, BioLegend), antiCD14 (clone M5E2, BioLegend), antiCD16 (clone 3G8, BioLegend), antiCD56 (clone 5.1H11, BioLegend), antiCD11b (clone ICRF44, BioLegend), antiCD11c (clone S-HCL-3, BioLegend), antiCD169 (clone 7-239, BioLegend), antiPD185 L1 (clone 29E.2A3, BioLegend), antiCD19 (clone HIB19, BioLegend), antiCD20 (clone 2H7, BioLegend), antiCD163 (clone GHI/61, BioLegend), antiCD86 (clone IT2.2, BioLegend), antimouse IgG2a isotype control (clone MOPC-173, BioLegend), antimouse IgG1 isotype control (clone MOPC-21, BioLegend), antimouse IgG2b isotype control (clone MPC-11, BioLegend). One of the following TotalSeq-C anti-human hashtag oligonucleotides (HTOs) were also included in each of the TotalSeq cocktails for cell hashing: Hashtag 1 (clones LNH-94/2M2, BioLegend), Hashtag 2 (clones LNH-94/2M2, BioLegend), Hashtag 3 (clones LNH-94/2M2, BioLegend), Hashtag 4 (clones LNH-94/2M2, BioLegend), Hashtag 5 (clones LNH-94/2M2, BioLegend), Hashtag 6 (clones LNH-94/2M2, BioLegend), Hashtag 7 (clones LNH-94/2M2, BioLegend), and Hashtag 8 (clones LNH-94/2M2, BioLegend). Cells were stained with the sorting antibody cocktail and the appropriate TotalSeq cocktail for 30 minutes at 4degreeC. Next, cells stimulated with S1 or S2 peptides were separately pooled together and passed through a 35 um cell strainer. Activated T cells defined as Live/Dead-, CD7+, CD69+ and CD137+ or CD154+ were sorted using a BD FACSAria III Cell Sorter. Two wells of a Chromium Next GEM Chip G were loaded with either the pooled S1-activated or S2-activated T cells.
The Chromium Next GEM Single Cell V(D)J Reagent kit (v1.1, 10x Genomics) was used to prepare mRNA, TCR, and surface protein libraries. cDNA amplification and target enrichment were quantified using a Qubit 3 Fluorometer (Invitrogen) and assessed for quality using a 4200 TapeStation System (Agilent). Libraries were constructed and sequenced to a depth of approximately 11,900 reads per cell using the NextSeq 500 system (Illumina).

tag: condition

value: S1 peptide pool stimulation


title: PBMC, S2, mRNA-derived cDNA

description:
polyA RNA
s2_filtered_barcodes.tsv.gz
s2_filtered_features.tsv.gz
s2_filtered_matrix.mtx.gz
s2_raw_barcodes.tsv.gz
s2_raw_features.tsv.gz
s2_raw_matrix.mtx.gz

data_processing:
The Cell Ranger multi pipeline (v5.0.1, 10x Genomics) was used to conduct the alignment and feature expression quantification of the single-cell sequencing data. mRNA and V(D)J reads were aligned to the GRCh38 human reference genome. HTO and ADT reads were aligned to a feature reference containing the appropriate barcode sequences.
Further processing was done with Seurat v4.1.0 (quality control, hashtag demultiplexing, dimensional reduction, clustering, differential gene expression analysis). Cell barcodes classified as singlets by HTO enrichment were kept and then filtered by gene expression data using the following parameters: (1) >200 unique genes/cell and (2) <5% mitochondrial counts. Within each cell barcode, the mRNA count data were log-normalized, and the ADT count data were CLR normalized.
From the filtered V(D)J output given by the Cell Ranger multi pipeline, cell barcodes with less than four productive TCR chains or a single productive TCR-β chain were retained. If a given cell barcode was associated with two TCR-ɑ or TCR-β chains, the chain with the greater number of unique molecular identifiers (UMIs) was retained.
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, contig_annotations.csv

molecule: polyA RNA

value: Peripheral blood mononuclear cells (PBMC)

value: S2 peptide pool stimulation


title: PBMC, S2, TCR V(D)J-enriched cDNA

description: polyA RNA


title: PBMC, S2, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT) and hashtag-derived oligonucleotide (HTO)
s2_filtered_barcodes.tsv.gz
s2_filtered_features.tsv.gz
s2_filtered_matrix.mtx.gz
s2_raw_barcodes.tsv.gz
s2_raw_features.tsv.gz
s2_raw_matrix.mtx.gz


title: PBMC, S1, TCR V(D)J-enriched cDNA

description: polyA RNA


title: d10-si-cdkn-r3


title: DIPG6_BDNF-treated_1

city: Stanford

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

department: Neurology

institute: Stanford University

description: poly(A)+ RNA-seq

data_processing:
Reads were mapped to hg19 annotation using Tophat2 (Kim et al 2013) (version 2.0.13) and transcript expression ("DIPGVI_BDNF-treatedvsUntreated_RAWtpm") was quantified against RefSeq gene annotations using featureCounts (Liao et al, 2014). Differential gene expression and log2 fold change calculations ("DIPGVI_BDNF-treatedvsUntreated_DESEQ2_results.csv") were determined using the DESeq2 package in R (Love, 2014).
Assembly: hg19
Supplementary files format and content: Raw tpm counts of gene expression abundance for SU-DIPGVI cells (in csv format)
Supplementary files format and content: Metadata table with sample key (in csv format)
Supplementary files format and content: DESeq2 results table of differential gene expression changes in BDNF-treated SU-DIPGVI cells compared to vehicle-treated SU-DIPGVI cells (in csv format)

source_name: Brain

growth_protocol: Cells are grown in Tumor Stem Media (TSM), consisting of Neurobasal (-A), DMEM F12, B27 (-A), bFGF, EGF, PDGF-AB, and heparin. See Grasso et al 2015.

extract_protocol:
RNA was extracted from pelleted cell culture samples using the RNeasy Isolation kit (Qiagen #74004) as per manufacturer’s instructions. Total RNA samples were submitted to Stanford Functional Genomics Facility. RNA integrity was established with Bioanalyzer trace (Agilent). The mRNA was prepared for sequencing using the KAPA Stranded mRNAseq Library prep kit (KK8420), and libraries were indexed with Truseq RNA UD from Illumina (#20021454) as per manufacturer’s instructions. The sequencing was performed on the Illumina NextSeq 500.
KAPA Stranded mRNAseq Library prep (KK8420)

treatment_protocol: SU-DIPGVI cells were treated with 100 nM BDNF recombinant protein ("DIPG6_BDNF-treated") or vehicle ("DIPG6_ctrl"). RNA was extracted for sequencing 16 hours post-treatment.

value: Brain

value: SU-DIPGVI

value: Patient-derived diffuse intrinsic pontine glioma (DIPG)

value: 100 nM BDNF (16 hours)


title: DIPG6_BDNF-treated_2

description: poly(A)+ RNA-seq


title: IgD-neg, replicate 1, scRNAseq

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
B cells were negative selected using column purification (EasySep Pan-B cell purification kit, StemCell Technologies), treated with neuraminidase, stained with HA tetramers, fluorophore-labeled Abs, and Abs conjugated with TotalSeq C oligomer hashtags. HA-binding IgDneg CD38lo/med cells were sort-purified and barcoded.
Chromium Single Cell 5’ Library and Gel Bead Kit (Nest GEM 5’ Kit v 1.1) as well as the Single Cell 5’ Feature Barcode Library Kit (10XGenomics)

value: B cell

value: Blood


title: A, replicate 1, scRNAseq

description: 10x Genomics


title: DIPG6_ctrl_1

description: poly(A)+ RNA-seq

value: None (vehicle)


title: DIPG6_BDNF-treated_3

description: poly(A)+ RNA-seq


title: d10-si-ctrl-r2

value: hiPSC-BAP


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_3 [PRO-seq]

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 512 B Preston Research Building

department: Biochemistry

institute: Vanderbilt University

description: biotinylated RNA

data_processing:
Adaptors were trimmed and short/low quality sequence filtered by Trimmomatic-0.32: ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15 MINLEN:15
Reverse complement sequence was generated using fastx_reverse_complement from the FASTX toolkit(v 0.0.13)
Reverse complement sequences were aligned to the human genome (hg19)+ S2 genome  using bowtie2 (v2.2.2)
Raw Counts tables for promoter proximal counts and gene body counts were calculated with Nascent RNA Sequencing Analysis (NRSA) pipeline - pause_PROseq.pl. The counts tables were normalized with DESeq2 and differential analysis was performed
Assembly: hg19
Supplementary files format and content: differential gene transcription analysis generated by NRSA and DESeq2
Library strategy: PRO-seq

source_name: Kasumi-1 cells

growth_protocol: Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine.

extract_protocol:
following nuclear run-on, total RNA was isolated by Trizol extraction and biotinylated RNA isolated by streptavidin bead binding
follwing hydrolysis of RNA, 3'adaptors were ligated to biotinylated RNA fragments. After 5'Cap removal and end repair, 5' adaptors were also ligated. Adaptor-ligated RNA fragments were reverse transcribed and cDNA libraries amplified using indexed primers.

treatment_protocol: cells were treated with 500 nM dTAG-47 for the indicated timepoints

value: Kasumi-1 cells


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_3 [PRO-seq]

description: biotinylated RNA


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_5 [PRO-seq]

description: biotinylated RNA

value: untreated


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_4 [PRO-seq]

description: biotinylated RNA


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_4 [PRO-seq]

description: biotinylated RNA


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_3 [PRO-seq]

description: biotinylated RNA


title: DFAM22359_NPM1c_SNDX5613_7d_rep3

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

description: polyA enriched mRNAseq

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl). Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Assembly: GRCh38/hg38
Supplementary files format and content: IGVtools tiled data file (TDF)
Supplementary files format and content: rlog_normalized gene counts_DESeq2 (csv)
Supplementary files format and content: z-scores_from rlog counts_DESEq2 (txt)
Supplementary files format and content: differentially expressed genes_DESeq2 (csv)

source_name: bone marrow

growth_protocol: human leukemia cells were trnsplanted into non-conditioned NXG mice and leukemia burden mas monitored in the peripheral blood

extract_protocol:
1Mio MV4;11 cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions for cell ine experiments. PDX-derived human leukemia cells from the bone marrow were depleted for mouse cells using magnetic cell sorting (mouse cell depletion kit, Milteny)
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 37bp, paired-end reads.

treatment_protocol: upon confirmation of engraftment mice were treated for 1 week (7d) with SNDX-5613 (0.1% supplemented rodent special diet) or vehicle as control.

value: bone marrow

value: Patient-derived xenograft (PDX)

value: leukemia cells

value: SNDX5613 (0.1% rodent diet) for 7 days


title: DFAM22359_NPM1c_SNDX5613_7d_rep1

description: polyA enriched mRNAseq


title: DFAM22359_NPM1c_vehicle_7d_rep1

description: polyA enriched mRNAseq

value: vehicle for 7 days


title: CBAM68552_MLL-AF6_SNDX5613_7d_rep3

description: polyA enriched mRNAseq


title: DFAM22359_NPM1c_SNDX5613_7d_rep2

description: polyA enriched mRNAseq


title: PBMC, S1, mRNA-derived cDNA

description:
polyA RNA
s1_filtered_barcodes.tsv.gz
s1_filtered_features.tsv.gz
s1_filtered_matrix.mtx.gz
s1_raw_barcodes.tsv.gz
s1_raw_features.tsv.gz
s1_raw_matrix.mtx.gz

extract_protocol:
Cryopreserved PBMC from SARS-CoV-2-naive (n = 4) or convalescent (n = 4) donors collected approximately 10 days post vaccination were thawed in sterile-filtered RPMI 1640 (Thermo Fisher Scientific) with 10% FBS (Hyclone) and 0.2% Benzonase (MilliporeSigma) and then centrifuged at 300xg for 10 minutes at room temperature. Viable cells were counted using the Guava easyCyte. Cells were centrifuged at 300xg for 10 minutes at room temperature and plated at a density of 2x106 167 cells/well in a 96-well U-bottom plate. Next, cells were blocked with 1 ug/mL antiCD40 (clone HB14, Miltenyi Biotec) at 37degree. The following day, cells were stained with Fixable Aqua viability dye (Invitrogen) for 30 minutes at room temperature. An antibody cocktail was prepared for sorting with the following markers: antiCD7 FITC (clone CD7-6B7, BioLegend), antiCD69 BV711 (clone FN50, BioLegend), antiCD137 APC/Fire 750 (clone 4B4-1, BioLegend), and antiCD40L/CD154 PE-Cy5 (clone TRAP1, BD Biosciences). Additionally, eight cocktails were prepared with the following TotalSeq-C antibody-derived tags (ADTs): antiCD3 (clone UCHT1, BioLegend), antiCD4 (clone RPA-T4, BioLegend), antiCD8a (clone RPA-T8, BioLegend), antiGD (clone B1, BioLegend), antiTRAV1-2 (clone 3C10, BioLegend), antiCD62L (clone DREG-56, BioLegend), antiCCR7 (clone G043H7, BioLegend), antiCD45RA (clone HI100, BioLegend), antiCD28 (clone CD28.2, BioLegend), antiCD127 (clone A019D5, BioLegend), antiCD95 (clone DX2, BioLegend), antiCXCR3 (clone G025H7, BioLegend), antiCXCR5 (clone J252D4, BioLegend), antiCCR4 (clone L291H4, BioLegend), antiCCR5 (clone J418F1, BioLegend), antiCCR6 (clone G034E3, BioLegend), antiCD25 (clone BC96, BioLegend), antiCD38 (clone HIT2, BioLegend), antiCD26 (clone BA5b, BioLegend), antiHLA-DR (clone L243, BioLegend), antiCD161 (clone HP-3G10, BioLegend), antiCD103 (clone Ber-ACT8, BioLegend), antiCD14 (clone M5E2, BioLegend), antiCD16 (clone 3G8, BioLegend), antiCD56 (clone 5.1H11, BioLegend), antiCD11b (clone ICRF44, BioLegend), antiCD11c (clone S-HCL-3, BioLegend), antiCD169 (clone 7-239, BioLegend), antiPD185 L1 (clone 29E.2A3, BioLegend), antiCD19 (clone HIB19, BioLegend), antiCD20 (clone 2H7, BioLegend), antiCD163 (clone GHI/61, BioLegend), antiCD86 (clone IT2.2, BioLegend), antimouse IgG2a isotype control (clone MOPC-173, BioLegend), antimouse IgG1 isotype control (clone MOPC-21, BioLegend), antimouse IgG2b isotype control (clone MPC-11, BioLegend). One of the following TotalSeq-C anti-human hashtag oligonucleotides (HTOs) were also included in each of the TotalSeq cocktails for cell hashing: Hashtag 1 (clones LNH-94/2M2, BioLegend), Hashtag 2 (clones LNH-94/2M2, BioLegend), Hashtag 3 (clones LNH-94/2M2, BioLegend), Hashtag 4 (clones LNH-94/2M2, BioLegend), Hashtag 5 (clones LNH-94/2M2, BioLegend), Hashtag 6 (clones LNH-94/2M2, BioLegend), Hashtag 7 (clones LNH-94/2M2, BioLegend), and Hashtag 8 (clones LNH-94/2M2, BioLegend). Cells were stained with the sorting antibody cocktail and the appropriate TotalSeq cocktail for 30 minutes at 4degreeC. Next, cells stimulated with S1 or S2 peptides were separately pooled together and passed through a 35 um cell strainer. Activated T cells defined as Live/Dead-, CD7+, CD69+ and CD137+ or CD154+ were sorted using a BD FACSAria III Cell Sorter. Two wells of a Chromium Next GEM Chip G were loaded with either the pooled S1-activated or S2-activated T cells.
The Chromium Next GEM Single Cell V(D)J Reagent kit (v1.1, 10x Genomics) was used to prepare mRNA, TCR, and surface protein libraries. cDNA amplification and target enrichment were quantified using a Qubit 3 Fluorometer (Invitrogen) and assessed for quality using a 4200 TapeStation System (Agilent). Libraries were constructed and sequenced to a depth of approximately 11,900 reads per cell using the NextSeq 500 system (Illumina).

value: Peripheral blood mononuclear cells (PBMC)

value: S1 peptide pool stimulation


title: CBAM68552_MLL-AF6_SNDX5613_7d_rep2

description: polyA enriched mRNAseq


title: CBAM68552_MLL-AF6_SNDX5613_7d_rep1

description: polyA enriched mRNAseq


title: CBAM68552_MLL-AF6_vehicle_7d_rep3

description: polyA enriched mRNAseq


title: 19C7j

city: Princeton

first: Namit

last: Kumar

state: NJ

address: 3551 lawrenceville

department: Informatics & Predictive Sciences

institute: Bristol-Myers Squibb

description:
10x Genomics
matrix.mtx;barcodes.tsv;genes.tsv

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2.
Assembly: Grch38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx), cell.metadata

source_name: Whole Blood

extract_protocol:
Tissue samples were enzymatically dissociated using a human Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s recommendations, and red blood cells were lysed using 1X RBC solution (eBioscience™, Thermo Fisher Scientific, Waltham, MA, USA) for 5 minutes at room temperature before quenching with cold phosphate-buffered saline. Subsequently, single cell suspensions were Fc-blocked using TruStain FcX (1:125 dilution; BioLegend, San Diego, CA, USA) for 5 minutes on ice. Surface CD45 was stained with anti-CD45-FITC (1:50; #REA747, Miltenyi Biotech) for 20 minutes at 4°C. Washed cells were stained with propidium iodide (PI; BD Biosciences, Franklin Lakes, NJ, cat: 556463) and with DRAQ5 (#62251, Thermo Fisher Scientific, Waltham, MA, USA) diluted 1:5000 in cold 1% bovine serum albumin in phosphate-buffered saline and stained for 10 minutes at room temperature. Single cells were sorted for live, nucleated CD45+ and CD45− cells to enrich for immune and non-immune cells.
single cell libraries (10X Genomics 5' V3 Chemistry) were prepared using the Chromium Single Cell Controller, version 3.16 (10x Genomics, Pleasanton, CA) according to the respective protocol.
NextSeq500/550

tag: patient id

tag: tumor type

value: RCC

value: Blood cells

value: Whole Blood

tag: age


title: 19C12e

value: CRC

tag: cell type

tag: tissue


title: CBAM68552_MLL-AF6_vehicle_7d_rep1

description: polyA enriched mRNAseq

tag: treatment


title: 19C26a

source_name: Tumor

value: CD45.pos Immune.cells

value: Tumor


title: 19A8b


title: 19A4d

source_name: Normal Adjacent

value: Normal Adjacent


title: 19A4b


title: 19A10a


title: 19C7g


title: 19A9b


title: 19A9a

value: CD45.neg Non.Immune.cells


title: DIPG6_ctrl_2

description: poly(A)+ RNA-seq

value: Brain

value: SU-DIPGVI

value: Patient-derived diffuse intrinsic pontine glioma (DIPG)

value: None (vehicle)


title: CBAM68552_MLL-AF6_vehicle_7d_rep2

description: polyA enriched mRNAseq

value: bone marrow

value: Patient-derived xenograft (PDX)

value: leukemia cells


title: 19A4a


title: 19A4c


title: 19C12a


title: DFAM22359_NPM1c_vehicle_7d_rep3

description: polyA enriched mRNAseq

value: vehicle for 7 days


title: 19C7f


title: DFAM22359_NPM1c_vehicle_7d_rep2

description: polyA enriched mRNAseq


title: 19B27a


title: 18M19a


title: 19B26b


title: 19C28b


title: 19C12d


title: 19C5d


title: 18M19b


title: 19C5b


title: 19C22b


title: 19B27b


title: 19C14b


title: 19C12b


title: 19C26b


title: 19C5a


title: 19C22a


title: 19B26a


title: 19C14a


title: deltaiPS-fibro-C

first: Ksenia

middle: S

last: Anufrieva

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

description:
MB-PO5
B2M KO iPSCs-derived fibroblast-like cells (donor C)

data_processing:
RNA-seq reads were trimmed for quality, paired reads were cropped using Trim Galore.
Trimmed RNAseq reads were quantified against Homo sapiens GRCh38.12 genome annotation at the transcript level using Salmon (v.1.4). Results were aggregated to gene level using the R package tximport.
Differentially expressed genes were identified using the R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: iPS-fibro_TPM.tsv: Space-delimited text file includes TPM values for every gene and every sample.

source_name: Differentiated Induced Pluripotent Stem Cells

growth_protocol: All cells were cultivated at 37°C under humidified atmosphere with 5% CO2. Human dermal fibroblasts and iPS-fibro were maintained in F3 medium containing DMEM medium (PanEco company) supplemented with 10% FBS (Gibco), and 5 ng/ml bFGF (Miltenyi Biotec). The culture medium was changed every 3-4 days. To differentiate iPSCs into iPS-fibro, we modified a previously reported protocol (Hewitt et al., 2011). 3D-spheroids were formed from iPSCs suspension using AggreWell™800 24-well Plates (STEMCELL Technologies Inc) according to the manufacturer's recommendations. The next day, 3D spheroids were harvested into F1 medium containing 3/1 DMEM/F12 (Gibco), 5% FBS (Gibco), 0,1 μg/ml hydrocortisone (Gedeon Richter Ltd), 10 ng/ml EGF (Miltenyi Biotec) and 5 μg/ml insulin (Sigma). Further cultivation was carried out in special homemade mini bioreactors (Eremeev et al., 2019) on an orbital shaker (70 rpm). From day 4, 2 ng/ml BMP-4 (R&D Systems) were added to the F1 medium. On day 8, the medium was shifted to the F3 medium. Onwards, the medium was changed every three days. On day 14, 3D spheroids were collected and plated on Matrigel-coated plates. In the next few days, 3D spheroids tightly adhered to the substrate, and the active migration of fibroblast-like derivatives was observed. From day 23, depending on the migration rate, iPS-fibro were dissociated with 0.25% Trypsin-EDTA solution (Gibco) and plated at the ratio of 1:4 in fresh F3 medium.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The on-column DNase treatment was performed with RNase-Free DNase Set (Qiagen). RNA quality was checked by 2100 Bioanalyzer (Agilent, USA). Enrichment of polyadenylated RNA and library preparation were performed with NEBNext Ultra II Directional RNA Library Prep Kit (NEB), according to the manufacturer’s protocol. The library underwent a final cleanup using the Agencourt AMPure XP system (Beckman Coulter) after which the libraries’ size distribution and quality were assessed using a high sensitivity DNA chip (Agilent Technologies). Libraries were subsequently quantified by Quant-iT DNA Assay Kit, High Sensitivity (ThermoFisher). Samples were sequenced on NextSeq 500 System (Illumina, USA) with NextSeq 500/550 High Output Kit v2.5 (75 Cycles).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cells were treated with 100 ng/ml IFNγ (Celltera-Pharm) for 48 hours.

value: Fibroblast-like cell

value: Differentiated iPSC

value: beta-2-microglobulin knockout

value: intact

tag: donor

value: C


title: deltaiPS-fibro-C+IFNg

description:
MB-PO6
B2M KO iPSCs-derived fibroblast-like cells stimulated with IFNg (donor C)

value: 100 ng/ml interferon gamma


title: fibro-C+IFNg

description:
MB-PO2
Dermal fibroblasts stimulated with IFNg (donor C)

source_name: Human Dermal Fibroblast

value: Fibroblast

value: tissue

value: WT


title: fibro-C

description:
MB-PO1
Dermal fibroblasts (donor C)


title: iPS-fibro-C

description:
MB-PO3
iPSCs-derived fibroblast-like cells (donor C)


title: iPS-fibro-B

description:
MB-FD3
iPSCs-derived fibroblast-like cells (donor B)

value: B


title: deltaiPS-fibro-B+IFNg

description:
MB-FD7
B2M KO iPSCs-derived fibroblast-like cells stimulated with IFNg (donor B)


title: iPS-fibro-C+IFNg

description:
MB-PO4
iPSCs-derived fibroblast-like cells stimulated with IFNg (donor C)


title: fibro-B+IFNg

description:
MB-FD2
Dermal fibroblasts stimulated with IFNg (donor B)


title: iPS-fibro-B+IFNg

description:
MB-FD4
iPSCs-derived fibroblast-like cells stimulated with IFNg (donor B)


title: deltaiPS-fibro-A+IFNg

description:
MB-FF7
B2M KO iPSCs-derived fibroblast-like cells stimulated with IFNg (donor A)

value: A


title: fibro-B

description:
MB-FD1
Dermal fibroblasts (donor B)


title: iPS-fibro-A+IFNg

description:
MB-FF4
iPSCs-derived fibroblast-like cells stimulated with IFNg (donor A)


title: deltaiPS-fibro-A

description:
MB-FF6
B2M KO iPSCs-derived fibroblast-like cells (donor A)


title: fibro-A+IFNg

description:
MB-FF2
Dermal fibroblasts stimulated with IFNg (donor A)


title: iPS-fibro-A

description:
MB-FF3
iPSCs-derived fibroblast-like cells (donor A)


title: fibro-A

description:
MB-FF1
Dermal fibroblasts (donor A)


title: 19C28a

value: CRC

value: CD45.pos Immune.cells

value: Tumor


title: P8.1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data from the first experiment to study effect of Nutlin in individuals with P47S and Y107H was aligned using STAR against hg19 version of human genome and RSEM was used for estimation of read counts and FPKM values using Ensemble transcriptome information
For the RNA-Seq experiment to identify a p53 hypomorph gene signature alignment was done using bowtie2 against hg19 version of human genome and Ensemble transcriptome information followed by RSEM to estimate read counts on gene level.
Assembly: hg19
Supplementary files format and content: RSEM raw gene counts

source_name: LCL

growth_protocol: LCLs were cultured in RPMI 1640 supplemented with 15% fetal bovine serum, 1% penicillin/streptomycin, and 2mM L-glutamine

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and on-column DNase digestions, according to the manufacturer’s protocol
Libraries were prepared using Quantseq 3’-mRNA kit (Lexogen) and sequencing was performed on Illumina Nextseq500 on high-output mode in a 75 bp single end run

treatment_protocol: Cells were treated with 10μM Nutlin-3a (Sigma-Aldrich)

value: LCL

tag: group

value: classifier

tag: set

value: testing

tag: batch

tag: unique patient_id

tag: hypomorph

value: untreated

tag: replicate


title: P14.1


title: P4.1

value: wt


title: P4.2


title: P3.2


title: P3.1


title: deltaiPS-fibro-B

description:
MB-FD5
B2M KO iPSCs-derived fibroblast-like cells (donor B)

value: Fibroblast-like cell

tag: cell line

value: Differentiated iPSC

tag: genotype

value: beta-2-microglobulin knockout


title: P2.2


title: P1.2


title: P2.1


title: P1.1


title: wt.P2.8

value: training


title: wt.P2.7


title: Y107H.P1.8


title: G334R.P1.1


title: G334R.P1.2


title: G334R.P2.1


title: Y107h.P1.5


title: wt.P8.2


title: Y107h.P1.6


title: wt.P9.2


title: wt.P9.1


title: G334R.P2.2


title: P8.2


title: Y107H.P1.7


title: P14.2


title: wt.P8.1


title: CRC0472PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

source_name: Colorectal Cancer

growth_protocol: Please check the linked publication

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded

treatment_protocol: Please check the linked publication

value: Colorectal Cancer

value: X

value: PR


title: CRC0471LMX0A02003TUMR01000, LMX_BASALE, bio rep 2, QC ok

value: LM

value: WT


title: CRC0473PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC failed


title: CRC0471LMX0A05007TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: NT


title: CRC0471LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0471LMX0A05002TUMR01000, LMX_cetux_6w, bio rep 1, QC ok

value: CET


title: CRC0474PRX0B02001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0468PRH0000000000R01000, PRH, bio rep 1, QC ok

value: H


title: CRC0468LMX0B03012TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: wt.P8.3

value: LCL


title: Y107h.P1.4

value: classifier


title: CRC0468LMX0B03004TUMR01000, LMX_cetux_6w_NT, bio rep 2, QC ok


title: CRC0468LMX0B03010TUMR05000, LMX_cetux_6w, bio rep 2, QC ok


title: CRC0468LMX0B03006TUMR01000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0468LMX0B03002TUMR05000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0468LMX0B02001TUMR05000, LMX_BASALE, bio rep 2, QC ok


title: CRC0471LMX0A05006TUMR01000, LMX_cetux_6w, bio rep 2, QC ok


title: CRC0467LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0474PRH0000000000R05000, PRH, bio rep 1, QC ok


title: CRC0466PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0465LMX0A02004TUMR08000, LMX_BASALE, bio rep 1, QC ok


title: CRC0464LMO0A04014001R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: CRC0464LMO0A04010001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0464LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0463PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0461LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0463PRX0A01001TUMR05000, PRX_BASALE, bio rep 1, QC failed


title: CRC0456LMX0B03003TUMR01000, LMX_cetux_h_NT, bio rep 2, QC ok


title: CRC0456LMX0B02001TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0460PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0458LMX0B02004TUMR08000, LMX_BASALE, bio rep 1, QC ok


title: CRC0460PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0456LMX0B03012TUMR01000, LMX_cetux_h, bio rep 2, QC ok


title: CRC0456LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0468LMX0B03005TUMR05000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0456LMX0A03004TUMR01000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0454LMX0A02001TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0466PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0452LMX0A02004TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0468LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0468LMH0000000000R01000, LMH, bio rep 1, QC ok


title: CRC0451LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0449PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0445PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0446PRX0A01001TUMR05000, PRX_BASALE, bio rep 1, QC failed


title: CRC0442LMX0B02001TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0448PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0441LMO0A04011001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC0440PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0440LMX0B03009TUMR05000, LMX_cetux_h_NT, bio rep 2, QC ok


title: CRC0441LMX0A02001TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0440LMX0B03012TUMR01000, LMX_cetux_h, bio rep 2, QC ok


title: CRC0440LMX0A03002TUMR05000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0440LMH0000000000R05000, LMH, bio rep 1, QC ok


title: CRC0440LMX0A02002TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0439PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC failed


title: CRC0440LMX0A03001TUMR04000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0438LMX0A03002TUMR01000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0438LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0439PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0438LMX0A03011TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0456LMX0A03003TUMR01000, LMX_cetux_h_NT, bio rep 1, QC ok


title: CRC0438LMX0A02003TUMR01000, LMX_BASALE, bio rep 2, QC ok


title: CRC0438LMX0A03003TUMR01000, LMX_cetux_6w, bio rep 2, QC ok


title: CRC0435LMX0A03005TUMR03000, LMX_cetux_6w, bio rep 1, QC ok


title: CRC0449LMX0A01001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0435LMX0A03002TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: CRC0435LMX0A02001TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0431LMX0A02003TUMR08000, LMX_BASALE, bio rep 1, QC ok


title: CRC0431LMH0000000000R02000, LMH, bio rep 1, QC ok


title: CRC0419LMX0A02003TUMR04000, LMX_BASALE, bio rep 1, QC ok


title: CRC0428PRH0000000000R01000, PRH, bio rep 1, QC ok


title: CRC0428PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0419LMH0000000000R09000, LMH, bio rep 1, QC ok


title: CRC0422LMX0B02002TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0429LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0416LMX0A03012TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC failed


title: CRC0416LMX0A02001TUMR03000, LMX_BASALE, bio rep 1, QC failed


title: CRC0420LMX0A02001TUMR06000, LMX_BASALE, bio rep 1, QC ok


title: CRC0416LMX0A03006TUMR05000, LMX_cetux_6w, bio rep 1, QC failed


title: CRC0426LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0409PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0418LMX0A02005TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0419LMX0B03001TUMR04000, LMX_cetux_h_NT, bio rep 2, QC ok


title: CRC0419LMX0A03009TUMR05000, LMX_cetux_h_NT, bio rep 1, QC ok