title: Brain Organoid LT-ampseq day 42 Rep2

city: Vienna

first: Simon

middle: Emanuel

last: Haendeler

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: LT barcodes amplified for 234527 (scRNAseq day 42 Rep2)

library_source: other

data_processing:
Per sample, sequenced reads were aligned to the GRCh38 2020-A human reference genome with Cell Ranger version 7.01 (10× Genomics) using default parameters. Resulting cell-by-gene, unique molecular identifier (UMI) count matrices were analysed in R using Seurat version 4.3.0.1.We filtered for high-quality cells based on doublet detection performed with scrublet (version 0.2.3), number of uniquely detected genes (“nFeature”), number of UMIs (“nCount”), percentage of mitochondrial reads and percentage of ribosomal reads.
Assembly: GRCh38 2020-A
Supplementary files format and content: Tab seperated values files, matrix files and comma seperated values files

molecule: other

source_name: Brain Organoid

extract_protocol:
Organoids were dissociated at day 18 or 42 by incubation in a 9:1 mixture of Accutase (Sigma Aldrich, cat # A6954) and 10x Trypsin (Gibco, cat # 15400) at 37 degrees on a Thermo-shaker (800rpm). Cells were filtered through a 35 um strainer followed by dilution with 0.1% BSA in DPBS-/- and stained with Draq7 viability dye (Biostatus; DR70250, 0.3 mM). Live, single, GFP positive cells were sorted with a BD FACSAria III (70 nm nozzle) and directly collected in a 96-well PCR plate pre-loaded with 10 uL of 0.5% BSA in DPBS-/-.
A whole organoid was sorted to completion into a single well and the entire resulting cell suspension was subject to single cell transcriptomic analysis using the Chromium Single Cell 3′ Reagent Kit (v.3.1) following the 10X user guide with the following modification. During cDNA amplification (2.2), the PCR reaction is paused at 72 degrees after 6 cycles. 75 uL of sample is removed for targeted amplification (below) and replaced with 37.5 uL of Amp Mix, 11.25 uL cDNA Primers and 26.25 uL H2O before continuing for a total of 13 cycles

value: Brain Organoid

value: hESC


title: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 8TF [AP58]

status: Public on Mar 01 2024

type: SRA

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

country: USA

institute: Childrens National Hospital

description:
skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 8TF
AP58

library_source: transcriptomic

data_processing:
BCL files generated from sequencer were converted using bcl2fastq (Illumina) to fastq files, quality-checked using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapter and quality trimming was performed using trimgalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Summary QC files for before and after quality trimming was performed using MultiQC.
Alignment to was performed using STAR, followed by count estimation using RSEM.
For differential expression analysis, read counts were estimated using tximport, followed by normalization and differential expression analysis performed using Deseq2.
Assembly: hg38 reference
Supplementary files format and content: rawCounts_Sertoli.csv
Supplementary files format and content: TPMCounts_Sertoli.csv

molecule: total RNA

organism: Homo sapiens

source_name: Fibroblasts

growth_protocol: Normal human adult 46, XY primary dermal fibroblast (HDFa) (Cat. ATCC PCS-201-012) was purchased from American Type Culture Collection repository (ATCC). The following cell lines were purchased from Coriell cell repository:  GM03651: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; GM00083: Gonadal fibroblasts derived from a 1-year-old 46, XY female; SRXY1; GM06938: fibroblasts derived from a 3-week-old male with a WT1 deletion; GM21894: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia; and GM03368: gonadal fibroblasts derived from a 17-year-old 46, XY woman). HDFa was cultured in Medium 106 (Thermo Cat.M106-500), completed with low serum growth supplement (LSGS) (Thermo Cat. S00310), and 1X penicillin-streptomycin antibiotic (P/S) (Thermo Cat. 15140122). GM03651, GM00083, GM06938 and GM12896 were cultured in Eagle’s minimum essential medium (Thermo Cat. M0325) completed with 15% non-inactivated FBS (Thermo Cat. 16000044) and 1X P/S (Thermo Cat. 15140122).  GM21894 was cultured in DMEM (Genesee Cat. 25-500) completed with 10% non-inactivated FBS and 1X P/S. All these cells were grown as adherent monolayer cultures in tissue culture-treated T25 flasks (Genesee Cat. 25-207), harvested by trypsinization upon 80-90% confluence, quenched by trypsin neutralization solution (Thermo Cat. R002100), spun down at 150g for 4 min at RT and sub-cultured in 5ml of suitable complete media. The media was replaced every alternate day in all these cultures until they reached confluency.

extract_protocol:
Cells were lysed and total RNA was isolated using RNeasy micro kit (Qiagen Cat. 74004) following the manufacturer’s instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit from Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: For the trans-differentiation culture, fibroblasts were seeded at 2.25x104 into each well of 6 well dishes (Millipore Sigma Cat. CLS3516) in 2ml complete M106 on Day 0 and grown overnight. On Day 1, cells were counted from an extra well to determine the number of lentiviral particles required to transduce the cells at a multiplicity of infection (MOI) of five. Three transduction sets were designed: A. GFP; B. 8 TFs:  FGF2, GATA6, GATA4, MXI1, JUNB, NFYB, NR5A1 and EBF1; C. 6TFs: FGF2, GATA6, GATA4, MXI1, JUNB, and NFYB. The old media in wells was replaced with transduction media consisting of 2 mL complete M106 mixed with an appropriate amount of respective lentivirus cocktail and 2 μL of 100 mg/mL Polybrene (Millipore Sigma Cat. TR-1003-G). The cells were left to transduce for 12 hours/overnight. On Day 2, transduction media was replaced with fresh complete M106 and cultured in it for 4 days with alternate days media change. On day 5, M106 was replaced with 2 mL of trans-differentiation media consisting of basal Sertoli Cell Media (SerCM) completed with 5% FBS, 1X Sertoli cell growth supplement (SerCGS) and 1X P/S  (ScienCell Cat. 4521). The culture was maintained in this media for another 24 days until day 30 with alternate days media change.

tag: tissue

value: Fibroblasts

tag: cell line

tag: genotype

tag: treatment


title: Brain Organoid LT-ampseq day 42 Rep1

description: LT barcodes amplified for 234526 (scRNAseq day 42 Rep1)


title: hypoxia_3

city: Hangzhou

first: Jun-Kai

last: Ma

address: Yuhangtang road No.866

country: China

institute: Zhejiang University

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19. No quality trimming was performed for deposited fastq files.
Sequenced reads were quality trimmed using Cutadapt v1.16.5.
Reads were mapped to mm10 whole genome using HISAT2 v2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v1.6.4 and DESeq2 v2.11.40.6 were applied for differentially expression analysis.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

organism: Mus musculus

source_name: Bone marrow cells

extract_protocol:
Bone marrow cells were obtained from normoxia- or hypoxia-treated mice.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were exposed to 5000 m altitude hypoxia for 1 week.

tag: cell type

value: Bone marrow cells

value: WT

value: hypoxia


title: AB7406

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
20190727_M4_tumor_ID3_WT_CD8_3
MARSseq

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q.txt

molecule: polyA RNA

source_name: tumor

growth_protocol: 8 to 10 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were sacrificed at various time points by cervical dislocation. Tumor, spleen, and tdLN were collected and put through a process of mechanical and enzymatic digestion. For single-cell suspensions, tumors were chopped into small pieces and suspended in RPMI supplemented with DNase (2mg/ml, Sigma-Aldrich) and collagenase IV (100mg/ml, Worthington). Tumors were homogenized by GentleMacs tissue homogenizer (Miltenyi Biotec) and incubated at 37oC for 30min, with frequent agitation. Following dissociation procedures, cells were washed with cold PBS, filtered through a 70-μm cell strainer, and centrifuged at 300g for 5 min at 4 °C. Spleen and tdLN were mashed through a 100uM cell strainer and washed with ice-cold MACS buffer (PBS supplemented with 0.2mM EDTA, pH 8, and 0.5% BSA). Cells were centrifuged at 300g, 5 min, and 4°C. Spleen was suspended in red blood lysis buffer (Sigma-Aldrich) and DNase (0.33U/ml, Sigma-Aldrich), incubated for 5min at room temperature, washed with cold PBS, passed through a 70μm mesh strainer, centrifuged at 300g, 5 min, 4°C and then resuspended in ice-cold MACS buffer.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol:
Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
mice were treated with 250ug of aPD1 or/and 200ug of a41BB.

value: tumor

value: endogenous CD8+

tag: experiment id

tag: days post_adoptive_transfer

tag: mouse number


title: AB7032

description:
20190620_D10_Tumor4_endoPD1+_1
MARSseq


title: hypoxia_2


title: Brain Organoid LT-ampseq day 16 Rep2

description: LT barcodes amplified for 232029 (scRNAseq day 16 Rep2)


title: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 6TF [AP63]

description:
skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 6TF
AP63


title: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 6TF [AP62]

description:
skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 6TF
AP62


title: hypoxia_1


title: AB7030

description:
20190620_D10_Tumor4_endoCD3+_2
MARSseq


title: normoxia_3

value: normoxia


title: Brain Organoid sc-RNA day 42 Rep2


title: WT_3

source_name: Bone marrow

extract_protocol:
Central macrophages were sorted from TFPIf/f mice or TFPIf/f;EpoR mice.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Bone marrow

value: Central macrophages


title: Brain Organoid LT-ampseq day 16 Rep1

description: LT barcodes amplified for 232028 (scRNAseq day 16 Rep1)


title: AB7029

description:
20190620_D10_Tumor4_endoCD3+_1
MARSseq


title: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 6TF [AP61]

description:
skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 6TF
AP61


title: Brain Organoid sc-RNA day 42 Rep1


title: skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 8TF [AP60]

description:
skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 8TF
AP60


title: normoxia_2


title: Brain Organoid sc-RNA day 16 Rep2


title: AB7027

description:
20190620_D10_Tumor3_endoPD1+_1
MARSseq


title: AB7028

description:
20190620_D10_Tumor3_endoPD1+_2
MARSseq


title: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with GFPC [AP18]

description:
Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with GFPC
AP18

value: GFPC


title: AB7031

description:
20190620_D10_Tumor4_endoCD3+_3
MARSseq


title: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with GFPC [AP17]

description:
Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with GFPC
AP17


title: Brain Organoid sc-RNA day 16 Rep1


title: WT_1


title: AB7026

description:
20190620_D10_Tumor3_endoCD3+_2
MARSseq


title: normoxia_1


title: AB7025

description:
20190620_D10_Tumor3_endoCD3+_1
MARSseq


title: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 8TF [AP21]

description:
Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 8TF
AP21


title: mouse with dissection

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

country: Japan

institute: Kobe University Graduate School of Medicine

description: 10x Genomics

data_processing: Cell Ranger Single Cell Software (v 6.1.2) by 10X Genomics against the GRCh38 human reference genome or the mm10 murine reference genome with default parameter

source_name: aorta

extract_protocol: Each sample was washed, cut into small pieces, and digested in enzymatic digestion buffer with 3 mg/ml collagenase type II (LS004176, Worthington), 0.15 mg/ml collagenase type XI (H3506, Sigma), 0.25 mg/ml soybean trypsin inhibitor (LS003571, Worthington), 0.1875 mg/ml elastase lyophilized (LS002292, Worthington), 0.24 mg/ml hyaluronidase type I (H3506, Sigma), and 2.38 mg/ml 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES, H4034, Sigma) in PBS with Ca2+ and Mg2+ at 37 °C for 60 minutes while shaking.

value: aorta


title: Matrigel/scMN-Organs,day21 bio rep3

city: Beijing

first: sun

last: zheng

address: NO.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: scMN-Organs_21day_gene counts.txt

data_processing:
Raw data of fastq format were firstly processed through fastq software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built  using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Feature counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based  on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0). The resulting P-values were adjusted using  the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by  DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the cluster Profiler R package,  in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by  differential expressed genes. GO analysis was performed on differentially expressed genes using cluster Profiler v4.2.2. Heat maps  of differentially expressed genes were generated using TBtools software.

extract_protocol:
Total RNA was extracted with the use of the Ultrapure RNA kit (#CW0567S, CWBIO) according to the manufacturer's instructions.
Total RNA was used as input material for the RNA sample preparations. The clustering of the index-coded samples was performed  on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.  After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: spinal cord motor neuron cells

value: neuronal differentiation


title: AB7024

description:
20190620_D10_Tumor2_endoPD1+_1
MARSseq


title: mouse without dissection

description: 10x Genomics


title: Matrigel/scMN-Organs,day21 bio rep2

description: scMN-Organs_21day_gene counts.txt


title: Matrigel/scMN-Organs,day21 bio rep1

description: scMN-Organs_21day_gene counts.txt


title: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with GFPC [AP16]

description:
Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with GFPC
AP16


title: AB7023

description:
20190620_D10_Tumor2_endoCD3+_3
MARSseq


title: RNA-seq_RagCtrl_rep2

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

description: In vitro cultured cell line

data_processing:
Hi-C and capture Hi-C raw reads were processed to the mouse reference genome mm10 by HiCUP (v0.7.2) with the settings of Arima. High-quality and unique paired-end tags (PETs) from HiCUP were further processed to the HIC file through Juicer (v1.6.0) for visualization with Juicebox. These PETs were also processed with cLoops2 (v0.0.2) for quantifications. Chromosome X was excluded from the analysis. Compartment analysis of eigenvectors (PC1) were obtained by hicPCA in HiCExplorer3 package (v3.6) with parameters of -noe 1 at the resolution of 100 kb. Hi-C TADs were called by Juicer arrowhead with parameters of -r 25000 -k KR and quantified by cLoops2. Hi-C or capture Hi-C virtual 4C tracks were generated by the cLoops2 dump module.
CTCF and Rad21 ChIP-seq raw reads were mapped to the mouse reference genome mm10 by Bowtie2 (v2.3.5). Only non-redundant reads with MAPQ >=10 were used for the following analysis. BigWig tracks were generated by bamCoverage in deepTools (v3.3.0) with parameters of --ignoreDuplicates --minMappingQuality 10 --normalizeUsing CPM for visualization and quantification aggregation analysis.
RNA-seq raw reads were mapped to mm10 by STAR (v2.7.3a) and quantified into RPKM with Cufflinks (v2.2.1). BigWig tracks were also generated by STAR as signal quantified as RPKM.
Assembly: mm10
Supplementary files format and content: BEDPE files for Hi-C and capture Hi-C samples were provided for valid interactions.
Supplementary files format and content: BED files for single-end ChIP-seq samples were provided for processed high quality unique reads.
Supplementary files format and content: TEXT files for processed gene expression in FPKM from RNA-seq data were also provided.

source_name: progenitor B cells

growth_protocol:
For Rag2-/- mice, total bone marrow was extracted from tibia and femurs and erythrocytes are lysed. Pro-B cells were purified by combining positive selection using CD19+ selective beads (Stem Cell Technology, Cat #18954) and sorting by CD19+ and B220+ markers.
Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+ and Rag2-/-Ebf1+/−Pax5+/− pro-B cell lines are cultured as previous described (Ramamoorthy et al., 2020).

extract_protocol:
For the capture Hi-C libraries, whole genome Hi-C libraries were first generated as previously described. To enrich the IgH locus (mm10, chr12: 113,201,001 - 116,030,000), SureSelect Target Enrichment probes (Table S3) with 2× tiling density were designed and manufactured by Agilent (Agilent Technologies Inc.). Hi-C libraries were hybridized to probes as specified by the manufacturer. Enriched libraries were sequenced using Illumina NextSeq sequencer to generate paired-end 150-bp reads.
Genome-wide in situ Hi-C was performed with Rag2-/- young and old primary pro-B cells, and Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+ and Rag2-/-Ebf1+/−Pax5+/− pro-B cell lines using the Arima Hi-C Kit (Arima Genomics), including KAPA Hyper Prep indexing and library amplification (catalog no. KK8500, Roche Molecular Systems Inc) according to the manufacturer’s instructions. For each assay, 1X10^6 cells to be used as the input materials and two biological replicates were performed for each group. Samples were sequenced 2×150 bp on an Illumina NovaSeq instrument.
For the ChIP-seq libraries, Young and old primary Rag2-/- pro-B cells were crosslinked with 1% formaldehyde (Sigma) for 10 min, quenched with 125 mM of glycine and lysed in lysis buffer containing 1% SDS. Chromatin was sheared by Bioruptor (Diagenode) and followed by immunoprecipitation with specific antibodies. For each immunoprecipitation assay, 1×10^6 cells was used. Antibody information anti-H3K27ac (Active Motif, # 39133; 1:500), anti-H3K27me3 (Diagonode, #C1541005; 1:500), anti-CTCF (Abcam, # ab70303; 1:250), anti-Rad21 (Abcam, # ab992; 1:500).
Total RNA was prepared using the Direct-zol RNA Miniprep Kit (# R2051, Zymo Research) according to manufacturer’s instructions. RNA libraries for Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+ and Rag2-/-Ebf1+/−Pax5+/− pro-B cell lines (two replicates for each group) were prepared using SMARTer Stranded Total RNA-Seq Kit v2 (# 634412, Takara Bio USA, Inc.) and sequenced 1×100 bp on an Illumina NovaSeq instrument.
Total RNA was prepared using the Direct-zol RNA Miniprep Kit (# R2051, Zymo Research) according to manufacturer’s instructions. The RNA libraries for young and old Rag2-/- primary pro-B cells (four biological replicates for each group) were prepared using the NEXTFLEX Rapid Directional RNA-Seq Kit (NOVA-5138-07, PerkinElmer) and sequenced 2×75 bp on an Illumina NovaSeq instrument.

tag: strain

value: progenitor B cells


title: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 8TF [AP20]

description:
Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 8TF
AP20


title: mouse control

description: 10x Genomics


title: DASCM/scMN-Organs,day21 bio rep3

description: scMN-Organs_21day_gene counts.txt


title: AB7022

description:
20190620_D10_Tumor2_endoCD3+_2
MARSseq


title: RNA-seq_RagCtrl_rep1

description: In vitro cultured cell line


title: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 8TF [AP19]

description:
Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 8TF
AP19


title: DASCM/scMN-Organs,day21 bio rep2

description: scMN-Organs_21day_gene counts.txt


title: AB7021

description:
20190620_D10_Tumor2_endoCD3+_1
MARSseq


title: DASCM/scMN-Organs,day21 bio rep1

description: scMN-Organs_21day_gene counts.txt


title: RNA-seq_Ebf1Pax5Heter_rep2

description: In vitro cultured cell line


title: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 6TF [AP23]

description:
Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 6TF
AP23


title: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 6TF [AP22]

description:
Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 6TF
AP22


title: AB7020

description:
20190620_D10_Tumor1_endoPD1+_3
MARSseq


title: RNA-seq_Ebf1Pax5Heter_rep1

description: In vitro cultured cell line


title: AB7019

description:
20190620_D10_Tumor1_endoPD1+_2
MARSseq


title: DNSCM/scMN-Organs,day21 biol rep3

description: scMN-Organs_21day_gene counts.txt


title: Fibroblasts derived from a 3-week-old male with a WT1 deletion with GFPC [AP45]

description:
Fibroblasts derived from a 3-week-old male with a WT1 deletion with GFPC
AP45


title: DNSCM/scMN-Organs,day21 biol rep2

description: scMN-Organs_21day_gene counts.txt


title: RNA-seq_Ebf1Heter_rep2

description: In vitro cultured cell line


title: Fibroblasts derived from a 3-week-old male with a WT1 deletion with GFPC [AP44]

description:
Fibroblasts derived from a 3-week-old male with a WT1 deletion with GFPC
AP44


title: DNSCM/scMN-Organs,day21 biol rep1

description: scMN-Organs_21day_gene counts.txt


title: RNA-seq_Ebf1Heter_rep1

description: In vitro cultured cell line


title: AB7017

description:
20190620_D10_Tumor1_endoCD3+_1
MARSseq


title: AB7018

description:
20190620_D10_Tumor1_endoPD1+_1
MARSseq


title: ChIP-seq_Young_Rad21_rep2

description: Primary pro-B cells by CD19+ selection

library_source: genomic

molecule: genomic DNA

tag: age

value: young

tag: chip antibody


title: pre_OSKM_92_3

city: İstanbul

first: Tamer

last: Önder

state: ANKARA

address: Rumelifeneri Yolu 34450, Sarıyer, İstanbul

country: Turkey

institute: Koc University

data_processing:
Fastqc run (fastq input, html output)
Multiqc run (input from fastqc results, html output)
Alignment with STAR (input fastq, output bam)
Quantification with Salmon (input bam, output quant.sf)
Second Multiqc run (input quant.sf, output html)
Normalisation in R (median of ratios)

source_name: dH1f fibroblasts

growth_protocol: Fibroblasts were grown in DMEM containing 10 % inactivated fetal bovine serum (FBS), 1% Pen-Strep.

extract_protocol: Total RNA was extracted from culture plates for each sample using Nucleospin RNA Isolation Kit (Macherey-Nagel)

value: dH1f fibroblasts

tag: reprogramming viral infection

value: Uninfected

value: MEN1 sg2


title: Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 6TF [AP24]

description:
Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 6TF
AP24

value: Fibroblasts


title: AB7016

description:
20190627_D17_Tumor2_endoPD1+_3
MARSseq


title: ChIP-seq_Young_Rad21_rep1

description: Primary pro-B cells by CD19+ selection


title: Fibroblasts derived from a 3-week-old male with a WT1 deletion with GFPC [AP43]

description:
Fibroblasts derived from a 3-week-old male with a WT1 deletion with GFPC
AP43


title: Fibroblasts derived from a 3-week-old male with a WT1 deletion with 8TF treatment [AP48]

description:
Fibroblasts derived from a 3-week-old male with a WT1 deletion with 8TF treatment
AP48


title: ChIP-seq_Young_CTCF_rep2

description: Primary pro-B cells by CD19+ selection

value: CTCF


title: Fibroblasts derived from a 3-week-old male with a WT1 deletion with 8TF treatment [AP47]

description:
Fibroblasts derived from a 3-week-old male with a WT1 deletion with 8TF treatment
AP47


title: pre_OSKM_92_2


title: pre_OSKM_92_1


title: AB7014

description:
20190627_D17_Tumor2_endoPD1+_1
MARSseq


title: pre_OSKM_NT1_3

value: Non-targeting


title: ChIP-seq_Young_CTCF_rep1

description: Primary pro-B cells by CD19+ selection


title: ChIP-seq_Old_Rad21_rep2

description: Primary pro-B cells by CD19+ selection

value: old


title: Fibroblasts derived from a 3-week-old male with a WT1 deletion with 6TF treatment [AP50]

description:
Fibroblasts derived from a 3-week-old male with a WT1 deletion with 6TF treatment
AP50


title: pre_OSKM_NT1_2


title: AB7012

description:
20190627_D17_Tumor2_endoCD3+_1
MARSseq

value: tumor

value: endogenous CD8+


title: AB7013

description:
20190627_D17_Tumor2_endoCD3+_2
MARSseq


title: ChIP-seq_Old_Rad21_rep1

description: Primary pro-B cells by CD19+ selection

value: Bone marrow


title: pre_OSKM_NT1_1


title: Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with GFPC [AP33]

description:
Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with GFPC
AP33


title: AB7011

description:
20190627_D17_Tumor1_endoPD1+_3
MARSseq


title: OSKM_92_3

value: OSKM


title: AB7010

description:
20190627_D17_Tumor1_endoPD1+_2
MARSseq


title: AB7015

description:
20190627_D17_Tumor2_endoPD1+_2
MARSseq


title: OSKM_92_2


title: Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with GFPC [AP32]

description:
Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with GFPC
AP32

value: GFPC


title: AB7009

description:
20190627_D17_Tumor1_endoPD1+_1
MARSseq


title: Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 8TF treatment [AP35]

description:
Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 8TF treatment
AP35


title: OSKM_92_1


title: Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with Green Fluroscent protein  (GFPC) [AP31]

description:
Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with Green Fluroscent protein  (GFPC)
AP31


title: OSKM_NT1_3


title: Fibroblasts derived from a 3-week-old male with a WT1 deletion with 6TF treatment [AP51]

description:
Fibroblasts derived from a 3-week-old male with a WT1 deletion with 6TF treatment
AP51


title: AB7007

description:
20190627_D17_Tumor1_endoCD3+_1
MARSseq


title: HiC_Ebf1Pax5Heter_rep1

description: In vitro cultured cell line


title: HiC_Ebf1Heter_rep2

description: In vitro cultured cell line


title: Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 6TF treatment [AP39]

description:
Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 6TF treatment
AP39


title: OSKM_NT1_2


title: Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 6 transcription factor (TF) treatment [AP37]

description:
Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 6 transcription factor (TF) treatment
AP37


title: AB7006

description:
20190617_D7_Tumor2_endoPD1+_3
MARSseq


title: OSKM_NT1_1


title: HiC_Ebf1Heter_rep1

description: In vitro cultured cell line


title: AB7005

description:
20190617_D7_Tumor2_endoPD1+_2
MARSseq


title: HiC_RagCtrl_rep2

description: In vitro cultured cell line


title: ChIP-seq_Old_CTCF_rep2

description: Primary pro-B cells by CD19+ selection


title: pre_OSKM_DMSO_3

value: DMSO


title: Vestibular schwannoma, vs4, replicate 1

city: Nashville

first: Taha

last: Jan

state: TN

address: 2220 Pierce Ave, PRB 752

department: Otolaryngology

institute: VUMC

description: 10x Genmoics

data_processing:
Following sequencing, data were processed through CellRanger pipeline, including cell calling steps. Next, filtered counts, barcodes, and features were merged into a Seurat object in R for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: 3 files for each sample representing the matrix (counts), barcodes (cells), and features (genes)

source_name: utricle (inner ear)

extract_protocol:
Human utricle were harvested from the operating room and underwent cell dissociation using enzymatic treatment and mechanical tirturation prior to filtering and cell capture on 10X chromium platform
10x v3

value: utricle (inner ear)

tag: individual

value: Patient #4

tag: vestibular symptoms

value: Y


title: HiC_Ebf1Pax5Heter_rep2

description: In vitro cultured cell line

value: progenitor B cells


title: ChIP-seq_Old_CTCF_rep1

description: Primary pro-B cells by CD19+ selection


title: HiC_RagCtrl_rep1

description: In vitro cultured cell line


title: AB7008

description:
20190627_D17_Tumor1_endoCD3+_2
MARSseq


title: Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 8TF treatment [AP34]

description:
Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 8TF treatment
AP34


title: Sample-16, Nurr2c

city: Irvine

first: Samuel

last: Morabito

state: CA

address: Biological Sciences III

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Cellranger count (v 6.0.0) was used to map snRNA-seq reads to the reference transcriptome (mm10 2020-A, downloaded from the 10X Genomics website) to quantify gene expression in single nuclei from each sample. The “include-introns” option was used in cellranger count to account for pre-mRNA molecules present in the snRNA-seq data. Downstream data processing (e.g. normalization, dimensionality reduction, clustering) was performed using the SCANPY software ecosystem.
Assembly: mm10
Supplementary files format and content: Processed SeuratObject containing UMI counts matrix, normalized gene expression, cluster assignments, and UMAP representation.

molecule: nuclear RNA

source_name: habenula

extract_protocol:
Using a 0.5 mm biopsy punch and a dissecting microscope, habenula samples were collected from two 400 um slabs made on a Leica 1850 CM cryostat.
From habnenula biopsy punches, single nuclei were extracted into droplets containing barcoded GEMs (Gel Bead-In Emulsions) using the 10X v3.1 3’ snRNA-seq kit.  After a cleanup step, cDNA were amplified, and libraries were constructed for sequencing.

value: habenula

tag: strain background

value: heterozygous ChAT-Cre

tag: Sex

value: male


title: organ donor Left ear, replicate 2

description: 10x Genmoics

value: Organ Donor #4

tag: inner ear_analyzed

value: L

value: N


title: AB7003

description:
20190617_D7_Tumor2_endoCD3+_2
MARSseq

tag: tissue


title: AB7002

description:
20190617_D7_Tumor2_endoCD3+_1
MARSseq


title: pre_OSKM_DMSO_2

value: dH1f fibroblasts

value: Uninfected


title: Vestibular schwannoma, vs3, replicate 1

description: 10x Genmoics

value: Patient #3


title: pre_OSKM_DMSO_1


title: pre_OSKM_VTP_3


title: AB7001

description:
20190617_D7_Tumor1_endoPD1+_3
MARSseq

value: tumor

value: endogenous CD8+


title: Sample-13, GFP

value: GFP


title: Sample-14, Nurr2c


title: pre_OSKM_VTP_2


title: PF382_SB37_STAG2KO

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

data_processing:
Sequencing reads were mapped to GRCh38 human genome reference by STAR. RSEM was used for the count data.
Assembly: hg38
Supplementary files format and content: text file for read counts

source_name: cell line

growth_protocol: Cell lines were grown in RPMI 1640 supplemented with 10% fetal bovine serum and 50 U/ml penicillin, 50 ug/ml streptomycin and 2 mM L-glutamine.

extract_protocol:
Freshly cultured cells were counted using trypan blue and a cell suspension volume corresponding to 5 million live cells was washed once with PBS (-Ca2+ -Mg2+) and then RNA was isolated by using AllPrep DNA/RNA Mini kit (Qiagen).
All RNAseq experiments were performed using Illumina compatible total RNA library kit.

treatment_protocol: no treatment

value: leukemia

value: STAG2 knockout by using Cas9-gRNA ribonucleoprotein (RNP) delivery

tag: cell line


title: AB7000

description:
20190617_D7_Tumor1_endoPD1+_2
MARSseq


title: PF382_SB23_STAG2KO


title: PF382_SA20_STAG2KO


title: OSKM_DMSO_3

value: OSKM

value: DMSO


title: Sample-11, Nurr2c


title: Sample-9, GFP


title: AB6998

description:
20190617_D7_Tumor1_endoCD3+_2
MARSseq


title: Sample-8, GFP


title: AB7004

description:
20190617_D7_Tumor2_endoPD1+_1
MARSseq


title: Sample-5, GFP


title: PF382_SA28_WT

value: no treatment


title: OSKM_DMSO_2


title: pre_OSKM_VTP_1


title: AB6997

description:
20190617_D7_Tumor1_endoCD3+_1
MARSseq


title: Sample-4, GFP

value: habenula


title: AB6969

description:
20190511_day20_tumor2_CD45.1_1
MARSseq

value: OT1 CD8+


title: MOLT14_STAG2

value: Transduction of STAG2


title: AB6968

description:
20190511_day20_spleen3_CD45.1_1
MARSseq

source_name: spleen

value: spleen


title: OSKM_VTP_3


title: MOLT14_EV

value: Transduction of empty vector


title: OSKM_VTP_2


title: AB6999

description:
20190617_D7_Tumor1_endoPD1+_1
MARSseq


title: PF382_SA19_WT


title: organ donor Left ear, replicate 1

description: 10x Genmoics

value: utricle (inner ear)

value: Organ Donor #3

value: L

value: N


title: AB6967

description:
20190506_day15_tumor5_CD45.1_2
MARSseq

value: tumor


title: PF382_SB23_STAG2KO_homo_STAG2

data_processing:
HiChIP data were mapped to hg19 human genome reference and analyzed using MAPS41 v2.0 as implemented within the Arima Genomics bioinformatics pipeline available at https://github.com/ijuric/MAPS. ChIP-seq reads were mapped to GRCh38 human genome reference by BWA. MACS2 (version 2.1.1) was used for peak calls.
Assembly: hg19/hg38
Supplementary files format and content: BigWig and Hic for HiChIP. BigWig for ChIP

extract_protocol:
Freshly cultured cells were counted using trypan blue and a cell suspension volume corresponding to 6 million live cells was washed once with PBS (-Ca2+ -Mg2+) and then crosslinked in a volume of 5 mL PBS with 2% formaldehyde for 10 minutes at room temperature, followed by quenching with Stop Solution 1 according to the Arima protocol for HiChIP, or  Glycine Solution (10X, Cell Signaling, #7005S) according to SimpleChiP kit (Cell Signaling, #56383) for ChIP-seq.
All H3K27ac HiChIP experiments were performed using the Arima-HiC+ kit (Arima Genomics A101020) according precisely to the manufacturer’s protocols (Arima-HiC+ Document numbers A160168 v00 (HiChIP) and A160169 v00 (library preparation)). All ChIPseq experiments were performed using the SimpleChiP kit (Cell Signaling, #56383) according precisely to the manufacturer’s protocols.

value: STAG2 (abcam, #ab4463)


title: OSKM_VTP_1

value: dH1f fibroblasts


title: AB6966

description:
20190506_day15_tumor5_CD45.1_1
MARSseq


title: Sample-1, Nurr2c

value: heterozygous ChAT-Cre

value: male


title: PF382_SB23_STAG2KO_homo_STAG1

value: leukemia

value: STAG1 (abcam, #ab4457)

value: STAG2 knockout by using Cas9-gRNA ribonucleoprotein (RNP) delivery


title: AB6965

description:
20190506_day15_tumor2_CD45.1_2
MARSseq


title: PF382_SB23_STAG2KO_homo_input

value: IgG Input


title: S2577 (Cpt1aCKO)

city: St. Louis

first: Leslie

middle: Stuart

last: Gewin

state: MO

address: 660 S Euclid Ave, McDonnell Science Building, Rm 718

department: Medicine (Nephrology)

institute: Washington University in St. Louis

data_processing:
Alignment was performed using STAR aligner, raw read counts were estimated using HTSeq and normalized using DESeq2 to get normalized counts. Read length 100/150
Aligned reads were used for estimating expression of genes using cufflinks (v2.2.1). Expression values reported in FPKM (fragments per kilobase per million units for each gene).
RNA sequencing and analysis were done by Medgenome.
Assembly: Alignmnet was performed using STAR v2.7.3a. Reads mapping to ribosomal and mitochondrial genome were removed before alignmnet.
Supplementary files format and content: Raw read counts of genes across sample and p values, adjusted for multiple comparison

source_name: kidney

growth_protocol: Mice were aged in a pathogen-free environment for 2 years.

extract_protocol:
RNA isolation performed with Qiagen Rneasy Kit plus DNAse step
Library prepared with Illumina TruSeq stranded mRNA kit

treatment_protocol: Mice were treated with doxycyline-containing food at aged 5-8 wks for a total of 3 weeks to induce recombination

value: kidney

value: mixed

tag: genotype

value: aged for 2 years


title: OSKM_DMSO_1

value: OSKM

tag: treatment

value: DMSO


title: PROTAC_d3NPC_ATACseq_rep2

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

description:
filtered.d3npc.nfr.bed
merged.hESC_d3npc.nfr.bed
d3NPC_ATACseq_sample8

data_processing:
Paired-end reads were trimmed with cutadapt, aligned to hg19 with bowtie2, and deduplicated with picardtools. Nucleosome free reads were defined with bamtools by keeping reads with insert sizes less than 101 bases. NFR were identified by calling peaks with macs2 with mfold limits of 10 and 200 and FDR cutoff of 0.001. NFR were merged with bedtools and filtered to only keep NFR that were called in more than one replicate of at least one treatment group. Nucleosome free reads within NFR were quantified with FeatureCounts and differential analysis was performed with DESeq2 with fold change > 2 and adjusted p-value < 0.01 cutoffs.
genome build/assembly:hg19
processed data files format and content: NFR coverage bigwig files and bed files of peaks

source_name: H1 human embryonic stem cells

growth_protocol: ESCs were cultured as described and collected as single cell suspensions using the TrypLE Express reagent. Cells were then cultured according to the STEMCELL Technologies instructions for the STEMDiff Dual Neural Induction System for the generation of neural progenitor cells (NPC) using dual SMAD inhibition. Briefly, ESCs were plated as single cells at a density of 2.0E05cells/cm2 in STEMDiff Neural Induction Media with SMADi, and 10uM Y-27632, on Matrigel coated plates, and incubated in a 5% CO2 atmosphere at 37°C. Media was changed daily with STEMDiff Neural Induction Media with SMADi.

extract_protocol:
NPCs were collected using Accutase and single cell suspensions were prepared at a concentration of 0.8-1.2x106 cells/ml and with cell viability of 80% or above.
Tagmentation was performed on 0.5E04 cells using Tn5 enzyme in tagmentation buffer on 3 biological replicates per condition

treatment_protocol: Doxycycline treatment for induction of shRNA expression was performed using 1ug/ml doxycycline in TeSR-E8 media for 3 days and maintained in NPC differentiation media until collection. PROTAC treatment for BRG1 degradation was performed using 0.5uM PROTAC in TeSR-E8 media for 1 day and maintained in NPC differentiation media until collection.

value: H1 human embryonic stem cells

value: PROTAC

value: NPC differentiation media


title: PROTAC_d3NPC_ATACseq_rep3

description:
filtered.d3npc.nfr.bed
merged.hESC_d3npc.nfr.bed
d3NPC_ATACseq_sample9


title: S7763 (Cpt1aCKO)


title: AB6964

description:
20190506_day15_tumor2_CD45.1_1
MARSseq

value: tumor

tag: cell type

value: OT1 CD8+


title: S7602 (Cpt1aCKO)


title: PF382_SB23_STAG2KO_homo_H3K27ac

value: H3K27ac (Active Motif am91193)


title: Sample-3, Nurr2c

value: habenula

value: heterozygous ChAT-Cre


title: PF382_SA28_WT_STAG2

value: leukemia

value: STAG2 (abcam, #ab4463)

value: no treatment


title: BRG1KD_d3NPC_ATACseq_rep3

description:
filtered.d3npc.nfr.bed
merged.hESC_d3npc.nfr.bed
d3NPC_ATACseq_sample6

value: Doxycycline


title: PROTAC_d3NPC_ATACseq_rep1

description:
filtered.d3npc.nfr.bed
merged.hESC_d3npc.nfr.bed
d3NPC_ATACseq_sample7


title: AB6963

description:
20190506_day15_spleen2_CD45.1_1
MARSseq

value: spleen

tag: experiment id


title: AB6962

description:
20190506_day15_tumor3_CD45.1_1
MARSseq

tag: days post_adoptive_transfer


title: S2397 (Cpt1aCKO)

value: kidney

value: mixed

value: male


title: PF382_SA28_WT_STAG1

value: STAG1 (abcam, #ab4457)


title: S2394 (Cpt1aCKO)

value: aged for 2 years


title: PF382_SA28_WT_input

value: IgG Input


title: BRG1KD_d3NPC_ATACseq_rep2

description:
filtered.d3npc.nfr.bed
merged.hESC_d3npc.nfr.bed
d3NPC_ATACseq_sample5

value: H1 human embryonic stem cells

value: NPC differentiation media


title: BRG1KD_d3NPC_ATACseq_rep1

description:
filtered.d3npc.nfr.bed
merged.hESC_d3npc.nfr.bed
d3NPC_ATACseq_sample4


title: AB6961

description:
20190430_day9_tumor4_CD45.1_2
MARSseq

value: tumor

value: OT1 CD8+

tag: mouse number


title: Control_d3NPC_ATACseq_rep3

description:
filtered.d3npc.nfr.bed
merged.hESC_d3npc.nfr.bed
d3NPC_ATACseq_sample3

value: Untreated


title: AB6959

description:
20190430_day9_spleen4_CD45.1_1
MARSseq


title: S2155 (Cpt1aCKO)


title: PF382_SA28_WT_H3K27ac

value: H3K27ac (Active Motif am91193)


title: PF382_SA20_STAG2KO_homo_STAG2

value: leukemia

value: STAG2 knockout by using Cas9-gRNA ribonucleoprotein (RNP) delivery


title: Control_d3NPC_ATACseq_rep2

description:
filtered.d3npc.nfr.bed
merged.hESC_d3npc.nfr.bed
d3NPC_ATACseq_sample2


title: AB6958

description:
20190430_day9_tumor2_CD45.1_2
MARSseq


title: S2582 (floxed control)

value: floxed control


title: PF382_SA20_STAG2KO_homo_STAG1


title: S7762 (floxed control)


title: Control_d3NPC_ATACseq_rep1

description:
filtered.d3npc.nfr.bed
merged.hESC_d3npc.nfr.bed
d3NPC_ATACseq_sample1


title: PF382_SA20_STAG2KO_homo_input


title: PROTAC_ESC_ATACseq_rep3

description:
filtered.hESC.nfr.bed
merged.hESC_d3npc.nfr.bed
ESC_ATACseq_sample9

value: PROTAC


title: AB6957

description:
20190430_day9_tumor2_CD45.1_1
MARSseq


title: S7601 (floxed control)


title: AB6956

description:
20190430_day9_spleen2_CD45.1_1
MARSseq

value: spleen


title: PF382_SA20_STAG2KO_homo_H3K27ac


title: PROTAC_ESC_ATACseq_rep2

description:
filtered.hESC.nfr.bed
merged.hESC_d3npc.nfr.bed
ESC_ATACseq_sample8


title: S2152 (floxed control)

value: kidney


title: AB6955

description:
20190430_day9_tumor1_CD45.1_2
MARSseq


title: AB6960

description:
20190430_day9_tumor4_CD45.1_1
MARSseq


title: BRG1KD_ESC_ATACseq_rep3

description:
filtered.hESC.nfr.bed
merged.hESC_d3npc.nfr.bed
ESC_ATACseq_sample6

value: Doxycycline


title: AB6953

description:
20190430_day9_spleen1_CD45.1_1
MARSseq


title: BRG1KD_ESC_ATACseq_rep2

description:
filtered.hESC.nfr.bed
merged.hESC_d3npc.nfr.bed
ESC_ATACseq_sample5


title: PF382_SA19_WT_input

value: no treatment


title: PROTAC_ESC_ATACseq_rep1

description:
filtered.hESC.nfr.bed
merged.hESC_d3npc.nfr.bed
ESC_ATACseq_sample7


title: PF382_SA19_WT_STAG1

value: STAG1 (abcam, #ab4457)


title: AB6954

description:
20190430_day9_tumor1_CD45.1_1
MARSseq


title: S2578 (floxed control)

value: mixed

value: male

value: aged for 2 years


title: Sample-2, Nurr2c

value: habenula

value: heterozygous ChAT-Cre


title: Seq03_Tfh5_4e4_1

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

country: Germany

institute: University Hospital Bonn

data_processing:
Fastq files were demultiplexes with Multi Demultiplex (Galaxy Version 1.0) using Illumina Index file
All raw fastq data were mapped to the mouse genome (mm10) using STAR 2.7.2b (Dobin et al., 2013)
Count matrices were generated using FeatureCount 1.6.4 (Liao et al., 2014) with the gene annotation file for mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts

source_name: activated murine CD4 T cells in vitro

growth_protocol: Isolated naive CD4 T cells were cultured in cRPMI for 3.5 days

extract_protocol:
Cells were stained for flow cytometry and and sorted directly into Trizol LS. RNA was isolated using Chloroform-Extraction followed by a RNA-purification via spin-columns.
Libraries were generated according to manufacturer´s guidelines with the 3‘ mRNA-Seq Library Prep Kit FWD with Unique Dual Indices (Lexogen) using 50 ng total RNA as input.

treatment_protocol: The cells were activated with plate-bound anti-CD3 and anti-CD28 and differentiated in the indicated conditions

value: CD4 T cell

tag: strain

tag: condition


title: AB6951

description:
20190427_day6_tumor3_CD45.1_1
MARSseq

value: tumor

value: OT1 CD8+


title: Seq03_Tfh2_1e4_3


title: Seq03_Tfh5_4e4_4


title: Seq03_Tfh2_1e4_6


title: Control_ESC_ATACseq_rep3

description:
filtered.hESC.nfr.bed
merged.hESC_d3npc.nfr.bed
ESC_ATACseq_sample3

value: H1 human embryonic stem cells

value: Untreated


title: Seq03_TfhA_4e4_3


title: AB6952

description:
20190427_day6_tumor3_CD45.1_2
MARSseq


title: Seq03_TfhA_4e4_6


title: MOLT14_STAG2_STAG1_rep2

value: leukemia

tag: chip antibody

value: Transduction of STAG2


title: Control_ESC_ATACseq_rep1

description:
filtered.hESC.nfr.bed
merged.hESC_d3npc.nfr.bed
ESC_ATACseq_sample1


title: PF382_SA19_WT_H3K27ac

value: H3K27ac (Active Motif am91193)


title: MOLT14_STAG2_STAG2_rep2

value: STAG2 (abcam, #ab4463)


title: AB6771

description:
20190427_Day2_OT1_PD1_Tumor6_2
MARSseq

value: PD1/OT1 time course


title: PF382_SA19_WT_STAG2

value: no treatment


title: AB6770

description:
20190427_Day2_OT1_PD1_Tumor6_1
MARSseq


title: AB6767

description:
20190427_Day2_OT1_PD1_Tumor5_1
MARSseq


title: MOLT14_STAG2_input_rep1

value: IgG Input


title: Seq03_Tfh2_4e4_4


title: Control_NPC_day6_scRNAseq_rep2

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample10

data_processing:
Fastq files were processed with CellRanger v3.0.1 using GRCm38 genome and Gencode annotation provide by 10X to generate the initial cell by gene matrix for each sample. Matrices were read into Seurat v4 using R-4.2.1 and merged into a single Seurat object. Cells with greater than 10% mitochondrial reads or less than 4000 UMI were removed from the object. UMAP dimensional reduction was performed using the top 15 principal components and clusters were called with resolution = 1.5. From this object, the raw counts matrix was exported for cell annotation using the online tool at celltypist.org. Data were visualized with built-in Seurat tools or with ggplot2
genome build/assembly:hg38
processed data files format and content: comma separated data matrixes of raw counts and seurat-normalized data

extract_protocol:
NPCs were collected using Accutase and single cell suspensions were prepared at a concentration of 0.8-1.2x106 cells/ml and with cell viability of 80% or above.
Briefly, approximately 5000 cells were used together with the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10x Genomics, 1000268) onto the 10x single cell chromium chip to generate a single cell emulsion in Chromium Controller (10x Genomics, 120263). Reverse transcription of mRNA and cDNA amplification were carried out following the manufacture’s instruction (10x Genomics, 1000268). The amplified cDNA was further fragmented to construct NGS libraries.

treatment_protocol: Doxycycline treatment for induction of shRNA expression was performed using 1ug/ml doxycycline in TeSR-E8 media for 3 days and maintained in NPC differentiation media until collection

value: NPC differentiation media


title: BRG1KD_ESC_ATACseq_rep1

description:
filtered.hESC.nfr.bed
merged.hESC_d3npc.nfr.bed
ESC_ATACseq_sample4

value: Doxycycline


title: AB6769

description:
20190427_Day2_OT1_PD1_Spleen6_1
MARSseq

value: spleen


title: Control_NPC_day9_scRNAseq_rep2

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample12


title: MOLT14_STAG2_STAG1_rep1

value: STAG1 (abcam, #ab4457)


title: MOLT14_STAG2_input_rep2


title: Control_NPC_day6_scRNAseq_rep1

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample9


title: Seq03_Tfh2_6e4_2


title: Control_NPC_day3_scRNAseq_rep1

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample7


title: Control_NPC_day9_scRNAseq_rep1

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample11


title: Seq03_Tfh2_4e4_1


title: AB6764

description:
20190427_Day2_OT1_Tumor4_1
MARSseq


title: AB6766

description:
20190427_Day2_OT1_PD1_Spleen5_1
MARSseq


title: Seq03_Tfh2_1e4_5


title: AB6765

description:
20190427_Day2_OT1_Tumor4_2
MARSseq


title: Seq03_Tfh2_2e4_6


title: Control_ESC_ATACseq_rep2

description:
filtered.hESC.nfr.bed
merged.hESC_d3npc.nfr.bed
ESC_ATACseq_sample2


title: Control_NPC_day3_scRNAseq_rep2

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample8


title: MOLT14_EV_STAG2_rep1

value: Transduction of empty vector


title: MOLT14_STAG2_H3K27ac_rep2


title: AB6768

description:
20190427_Day2_OT1_PD1_Tumor5_2
MARSseq


title: AB6762

description:
20190427_Day2_OT1_Tumor3_2
MARSseq


title: MOLT14_EV_STAG2_rep2


title: Seq03_Tfh5_4e4_3

value: CD4 T cell


title: Seq03_Tfh2_1e4_2


title: MOLT14_EV_STAG1_rep2


title: BRG1KD_NPC_day9_scRNAseq_rep1

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample5


title: MOLT14_STAG2_H3K27ac_rep1


title: AB6761

description:
20190427_Day2_OT1_Tumor3_1
MARSseq

value: tumor


title: BRG1KD_NPC_day6_scRNAseq_rep2

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample4


title: Seq03_Tfh5_4e4_6


title: Seq03_TfhA_4e4_2


title: BRG1KD_NPC_day9_scRNAseq_rep2

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample6


title: MOLT14_EV_STAG1_rep1


title: MOLT14_EV_input_rep2


title: AB6763

description:
20190427_Day2_OT1_Spleen4_1
MARSseq

value: OT1 CD8+


title: BRG1KD_NPC_day6_scRNAseq_rep1

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample3

value: H1 human embryonic stem cells


title: AB6751

description:
20190427_day6_spleen3_CD45.1_1
MARSseq


title: Seq03_TfhA_4e4_5


title: MOLT14_EV_input_rep1


title: BRG1KD_NPC_day3_scRNAseq_rep2

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample2


title: AB6750

description:
20190427_day6_tumor2_CD45.1_2
MARSseq


title: MOLT14_EV_H3K27ac_rep2


title: MOLT14_EV_H3K27ac_rep1


title: Seq03_Tfh2_6e4_4


title: PC3_miR375_OE_rep2

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

data_processing:
RNA-seq reads were filtered by fastp software with default parameters.
RNA-seq reads were aligned to the Ensembl hg38 genome using STAR v2.7.1a with default settings.
The featurecounts software was utilized to quantify gene expression.
The DESeq2 package was utilized to identify differentially expressed genes.
Assembly: hg38
Supplementary files format and content: txt, gene count

growth_protocol: RPMI-1640, 10% (for LNCaP) or 20% (for PC3) fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells with miRNeasy Tissue/Cells Advanced Mini Kit (QIAGEN, Dusseldorf, German) according to the manufacturer's protocol.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Human prostate cancer

value: miR-375 overexpression


title: Seq03_Tfh2_6e4_1


title: BRG1KD_NPC_day3_scRNAseq_rep1

description:
NPC_scRNAseq_counts.csv
NPC_scRNAseq_data.csv
NPC_scRNAseq_sample1


title: AB6760

description:
20190427_Day2_OT1_Spleen3_1
MARSseq


title: AB6749

description:
20190427_day6_tumor2_CD45.1_1
MARSseq


title: Seq03_Tfh2_4e4_3


title: PER-117_HiChIP_H3K27ac

data_processing:
HiChIP data were mapped to hg19 human genome reference and analyzed using MAPS41 v2.0 as implemented within the Arima Genomics bioinformatics pipeline available at https://github.com/ijuric/MAPS. ChIP-seq reads were mapped to GRCh38 human genome reference by BWA. MACS2 (version 2.1.1) was used for peak calls.
Assembly: hg19/hg38
Supplementary files format and content: BigWig and Hic for HiChIP. BigWig for ChIP
Library strategy: HiChIP

value: leukemia


title: PC3_miR375_OE_rep1


title: Control_ESC_RNAseq_rep3

description:
ESC_RNAseq_gene_expression.csv
ESC_RNAseq_sample6

data_processing:
Transcript abundance was quantified using Salmon version 1.3.0, (doi:10.1038/nmeth.4197) with an index containing Gencode version v32lift37 comprehensive transcripts (doi:10.1093/nar/gkaa1087), human Class I and II enhancers (Rada-Iglesias et al.), and the hg19 human genome as decoy. Data were imported into R-3.6.1 for analysis, summarized to gene level with tximport version 1.14.2 (doi:10.12688/f1000research.7563.1), then statistical contrasts were performed using limma-voom version 3.42.2 (https://doi.org/10.1093/nar/gkv007) moderated t-tests
genome build/assembly: hg19
processed data files format and content: Comma separated values of normalized gene expression

growth_protocol: ESCs were cultured feeder-free in TeSR-E8 media, on Matrigel coated tissue culture vessels, and incubated in a 5% CO2 atmosphere and at 37°C.

extract_protocol:
RNA was isolated from ESCs using the total RNA purification kit (Norgen, 48300)
ribosome RNA removal, library preparation, and sequencing by Expression Analysis, an IQVIA company

treatment_protocol: Doxycycline treatment of ESC cultures for induction of shRNA expression was performed using 1ug/ml doxycycline in TeSR-E8 media for 3 days

value: Untreated


title: Seq03_Tfh2_2e4_2


title: Seq03_Tfh2_6e4_5


title: Seq03_Tfh2_4e4_6


title: AB6747

description:
20190427_day6_tumor1_CD45.1_2
MARSseq


title: AB6745

description:
20190427_day6_spleen1_CD45.1_1
MARSseq


title: PC3_miR375_NC_rep2

value: control


title: MOLT-14_HiChIP_H3K27ac

value: H3K27ac (Active Motif am91193)


title: AB6746

description:
20190427_day6_tumor1_CD45.1_1
MARSseq


title: PC3_miR375_NC_rep1


title: Control_ESC_RNAseq_rep2

description:
ESC_RNAseq_gene_expression.csv
ESC_RNAseq_sample5


title: LNCaP_miR375_OE_rep2

source_name: LNCaP

value: LNCaP


title: Seq03_Tfh2_2e4_5


title: LNCaP_miR375_NC_rep2


title: AB6742

description:
20190424_day3_spleen3_CD45.1_1
MARSseq


title: Seq03_Tfh2_1e4_4


title: AB6748

description:
20190427_day6_spleen2_CD45.1_1
MARSseq


title: Seq03_Tfh5_4e4_2


title: AB6744

description:
20190424_day3_tumor3_CD45.1_2
MARSseq


title: Seq03_Tfh2_1e4_1


title: Seq03_Tfh5_4e4_5


title: AB6740

description:
20190424_day3_tumor2_CD45.1_1
MARSseq


title: LNCaP_miR375_OE_rep1


title: 24h LPS, rep 3

city: Jena

first: Charlotte

middle: Sophie

last: Ehle

address: Hans-Knoell Str. 2

department: Institute of Biochemistry and Biophysics

institute: Friedrich-Schiller-University

description: Sequencing by GENEWIZ/Azenta Life Sciences

data_processing:
Quality control (by GENEWIZ): In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Mapping (by GENEWIZ): Hisat2 (v2.0.1) was used to index the reference genome sequence and to aligne clean data to the reference genome. Resulting BAM files were uploaded to the Galaxy.eu platform for further analysis.
Counting (by Ehle, C. on Galaxy.eu web platform): featureCounts (Galaxy Version 2.0.1+galaxy1) was used to measure gene expression from BAM files.
Differential Expression Analysis (by Ehle, C. on Galaxy.eu web platform): DESeq2 (Galaxy Version 2.11.40.6+galaxy2) was used to determine differentially expressed features from count tables.
Assembly: hg19
Supplementary files format and content: comma-delimited text files include read counts for each sample
Supplementary files format and content: supplementary file: comma-delimited text files including normalized counts for each sample

source_name: HepaRG

growth_protocol: HepaRG WT cells were grown in supplemented Williams Medium E for one week at confluency and then differentiated by consecutively growing them with 1% and 2% DMSO added to the medium for  one week, respectively.

extract_protocol:
Total RNA was extracted using TRIZol Reagent (Invitrogen) according to manufactuer's instructions. 1µg total RNA with RIN value above 6.5 was used for library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: Differentiated HepaRG were treated with 100 ng/ml LPS (Sigma-Aldrich, N0636) for 6 h or 24 h. Untreated cells (0 h) served as control.

value: HepaRG

value: hepatocyte

value: WT

value: LPS

tag: time


title: Control_ESC_RNAseq_rep1

description:
ESC_RNAseq_gene_expression.csv
ESC_RNAseq_sample4


title: AB6739

description:
20190424_day3_spleen2_CD45.1_1
MARSseq

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q.txt

extract_protocol:
Mice were sacrificed at various time points by cervical dislocation. Tumor, spleen, and tdLN were collected and put through a process of mechanical and enzymatic digestion. For single-cell suspensions, tumors were chopped into small pieces and suspended in RPMI supplemented with DNase (2mg/ml, Sigma-Aldrich) and collagenase IV (100mg/ml, Worthington). Tumors were homogenized by GentleMacs tissue homogenizer (Miltenyi Biotec) and incubated at 37oC for 30min, with frequent agitation. Following dissociation procedures, cells were washed with cold PBS, filtered through a 70-μm cell strainer, and centrifuged at 300g for 5 min at 4 °C. Spleen and tdLN were mashed through a 100uM cell strainer and washed with ice-cold MACS buffer (PBS supplemented with 0.2mM EDTA, pH 8, and 0.5% BSA). Cells were centrifuged at 300g, 5 min, and 4°C. Spleen was suspended in red blood lysis buffer (Sigma-Aldrich) and DNase (0.33U/ml, Sigma-Aldrich), incubated for 5min at room temperature, washed with cold PBS, passed through a 70μm mesh strainer, centrifuged at 300g, 5 min, 4°C and then resuspended in ice-cold MACS buffer.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

value: spleen


title: AB6743

description:
20190424_day3_tumor3_CD45.1_1
MARSseq


title: MOLT14_STAG2_STAG2_rep1

value: STAG2 (abcam, #ab4463)

value: Transduction of STAG2


title: BRG1KD_ESC_RNAseq_rep2

description:
ESC_RNAseq_gene_expression.csv
ESC_RNAseq_sample2

value: Doxycycline


title: LNCaP_miR375_NC_rep1


title: AB6741

description:
20190424_day3_tumor2_CD45.1_2
MARSseq

value: tumor

value: OT1 CD8+


title: H1 ESCs, H3K27ac, XMD.2

city: macau

first: Chengcheng

last: SONG

address: universtiy of macau

department: fhs

country: Macau

institute: university of macau

data_processing:
All raw data was subjected to Fastp
Differential enriched peaks (FDR) Reads were identified through MCAS2
ChIPseeker v1.32.1 was used to identify the promoter and annotate the features of peaks
the alignment results were converted to bigwig format using a series of softwares, e.g., MACS2 bdgcmp, Bedtools slop v2.29.0 and UCSC toolkits (http://hgdownload.cse.ucsc.edu/admin/exe/) including bedClip V 332 and Bedgraphtobigwig V 323
The peaks and alignment results were visualized through IGV v2.6.3
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: H1 ESCs  was maintained in E8 medium supplemented with  antibiotics  with 5% CO2 at 37C. E8 medium contained DMEM/F12, sodium selenite, ascorbic acid trisodium, transferrin, insulin, FGF2 and TGFβ.

extract_protocol:
H1 ESCs was processed cross-linking reaction by 1 % PFA and 125 mM Glycine. Cell lysates were sonicated with Diagenode BioRuptor Sonicator.
ChIP-seq library building was processed as published (Xu, Ye et al. 2020). The DNA library was generated by Tn5. The DNA library was sequenced using Illumina Novaseq 6000.

treatment_protocol: XMD892 1uM was treated with E8 medium for 12/24/48hr in H1 ESCs.

value: H3K27ac (abcam#ab4729)

value: Human embryonic stem cells

value: XMD892 1 uM treatment for 24h


title: H1 ESCs, H3K4me3, XMD.2

value: XMD892 1 uM treatment for 48h


title: H1 ESCs, H3K4me3, XMD.1


title: Seq03_TfhA_4e4_1

value: CD4 T cell


title: 6h LPS, rep 2

value: 6 h


title: H1 ESCs, H3K27ac, XMD.1


title: Seq03_Tfh2_6e4_3


title: BRG1KD_ESC_RNAseq_rep3

description:
ESC_RNAseq_gene_expression.csv
ESC_RNAseq_sample3

value: H1 human embryonic stem cells


title: 24h LPS, rep 2

value: HepaRG


title: AB6595

description:
20190330_day13_PD1_M3_tumor_CD45.1_1
MARSseq


title: Seq03_Tfh2_2e4_4


title: AB6738

description:
20190424_day3_tumor1_CD45.1_2
MARSseq


title: Seq03_Tfh2_2e4_1


title: control, rep 3

value: hepatocyte

value: 0 h


title: H1 ESCs, H3K27ac, E8.1

value: WT

value: E8 for 24h, H3


title: Seq03_Tfh2_6e4_6


title: H1 ESCs, H3K4me3, E8.1

value: E8 for 24h,


title: 24h LPS, rep 1

value: LPS


title: Seq03_Tfh2_4e4_2


title: 6h LPS, rep 3


title: Seq03_Tfh2_4e4_5


title: AB6596

description:
20190330_day13_PD1_M3_tumor_CD45.2_1
MARSseq

value: endogenous CD8+


title: BRG1KD_ESC_RNAseq_rep1

description:
ESC_RNAseq_gene_expression.csv
ESC_RNAseq_sample1

value: Doxycycline


title: AB6736

description:
20190424_day3_spleen1_CD45.1_1
MARSseq

value: spleen

value: OT1 CD8+


title: H1 ESCs, H3K4me3, E8.2

value: Human embryonic stem cells

value: E8 for 24h


title: control, rep 2


title: H1 ESCs, H3K27ac, E8.2

value: H3K27ac (abcam#ab4729)


title: Con 11 RNAseq BA10 cortex

city: Austin

first: Tanya

middle: T.

last: Paull

state: TX

address: 2500 Speedway MBB 2.448

department: Molecular Biosciences

institute: Univ. of Texas at Austin

data_processing:
Sequencing reads were cleaned using FASTP in paired end mode and mapped to the genome using STAR aligner and GRCh38 (hg38). Aligned reads were converted to bedgraph format via MACS2 (61). Output bedgraph files were processed again using MACS2’s bdgcmp command with the ppois flag to approximately remove the ChIP input influence from the ChIP bedgraph files. Finally, bedgraph output was read depth normalized to make files equivalent in total signal.
Sequencing reads were cleaned using FASTP in paired end mode, transcript abundance levels were determined using Salmon pseudoaligner and GRCh38 (hg38), and differentially abundant transcripts were quantified using Swish in the Gene mode. Statistically significant differences between density plots were determined using empirical cumulative distribution function tests via DTS R package with 5000 bootstraps. GSEA information was computed via the Fast Gene Set Enrichment Analysis (FGSEA) R package.
Assembly: HG38
Supplementary files format and content: bigwig, input adjusted and read depth normalized
Supplementary files format and content: text file showing read counts

source_name: BA10 cortex

extract_protocol:
PAR ChIP: The protocol was adapted from (16). Briefly, SH-SY5Y cells were differentiated as described above and two 15 cm dishes were used for each ChIP replicate (approximately 20M cells). Cells were removed from dishes using trypsin and then resuspended in media in a volume of 36 ml. Formaldehyde (37%, Sigma F1635) was added to 1% final concentration and incubated at 37°C for 7 min. with occasional inversion of the tube. 2.5M glycine was added to a final concentration of 0.125M. The tube was inverted several times and cells recovered by centrifugation at 550xg for 5 min. at 4°C. The pellet was washed twice with 10 ml cold PBS using 550xg centrifugation for 5 min. each time. The pellets were snap frozen using liquid nitrogen and stored at -80°C for later use. Each cell pellet was resuspended in 1mL cold PAR ChIP RIPA buffer (10 mM Tris-HCl, pH7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) containing protease inhibitor (Fisher, A32955). Samples were sonicated using a Diagenode Bioruptor UCD-200 instrument on high power with 15 sec on/ 15 sec off cycles for 45 min. at 4°C. Under these conditions, fragmented chromatin was 200 to 500 bp. Samples were centrifuged at 20,000xg for 10 minutes at 4°C. The supernatant was transferred to another tube; 50 μl were reserved as input DNA. 40 μl of Protein A/G magnetic beads was incubated with 5 μg anti-pan-ADP-ribose binding reagent (Millipore Sigma, MABE1016) per IP sample in 100 μl PBS for 30 min. then washed with 200μl PBS twice. The beads were then added to the supernatant and incubated at 4°C overnight. The following day, beads were washes for 10 min. at 4°C with the following sequence of buffers: 2x with 1 mL of RIPA buffer, 2x with 1 mL of RIPA buffer + 0.3M NaCl, 1x with 1 mL of TE pH 8 + 0.2% Triton X-100, 1x with 1 mL of TE pH 8. The beads were resuspended in 100μl TE; 3μl 10% SDS and 5μl 20 mg/ml proteinase K were added and the samples incubated at 65°C for 4 hrs while rocking. The tubes were vortexed every 30 to 50 min. The DNA was removed from beads using a magnetic stand; 100μl TE + 0.5M NaCl was added to the beads and then removed and combined with the first sample. 200 μl phenol/chloroform/isoamyl alcohol was added and samples were added to Phase Lock gel columns (VWR, 10847-802) and processed according to manufacturer instructions. Samples were then ethanol precipitated by adding 2μl glycogen (20 mg/ml), 20μl 3M NaOAc pH 5.2, and 500 μl cold ethanol (100%). After incubation on dry ice for 15 min., samples were centrifuged at 20,000xg for 15 min. at 4°C. Pellets were washed with 70% ethanol twice; the supernatant was removed and pellets dried at room temp. Pellets were resuspended in 22 μl 10 mM Tris-HCl pH 8.0, vortexed, and stored at -20°C.  R-ChIP  The protocol was adapted from (24). Briefly, SH-SY5Y cells were differentiated as described above and two 15 cm dishes were used for each ChIP replicate (approximately 20M cells). Cells were crosslinked in the dishes with the addition of formaldehyde to 1% final concentration and incubated for 7 min. while shaking (120 RPM). 2.5M glycine was added to a final concentration of 0.125M. Cells were removed by scraping and transferred to conical tubes with an additional 5 ml PBS to wash the dishes. Cells were centrifuged at 2187xg for 15 min. at 4°C, then washed with cold PBS and pelleted again. The pellets were snap frozen using liquid nitrogen and stored at -80°C for later use. Each cell pellet was resuspended in 2.3 mL cold R-ChIP RIPA buffer (50 mM Tris-HCl, pH 8.0, 0.15M NaCl, 2 mM EDTA, 0.1% SDS, 0.5% sodium deoxycholate, 0.1% Igepal CA-630 (NP40) containing protease inhibitor (Fisher, A32955) and incubated on ice for 10 min. Samples were sonicated using a Diagenode Bioruptor UCD-200 instrument on high power with 15 sec on/ 15 sec off cycles for 45 min. at 4°C. Samples were centrifuged at 3,889xg for 10 minutes at 4°C. The supernatant was transferred to another tube; 50 μl were reserved as input DNA. 25 μl of Protein A/G magnetic beads per IP sample were washed with 1 ml wash buffer (20 mM Tris-HCl pH 8.0, 0.15M NaCl, 2 mM EDTA, 1% Triton X-100) using a magnetic separator; this step was repeated for a total of 3 washes. Beads were resuspended in bead blocking buffer (0.2 μg/ml BSA, 0.2 mg/ml glycogen in PBS) and incubated for 1 hr at RT. Beads were then washed 3 times with antibody binding buffer (5 μg/ml BSA in PBS), resuspended in 250 μl antibody binding buffer and 2.5 μg FLAG M2 antibody (Sigma) per 25 μl of Protein A/G magnetic beads and incubated overnight at 4°C with rotation. After removal of unbound antibody, beads were resuspended in 1 ml sonicated lysate and incubated overnight at 4°C with rotation. The following day, beads were washed 3 times for 3 min. at room temperature with 1 ml wash buffer I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) containing protease inhibitor, then 3 times with wash buffer II (wash buffer I containing 0.5M NaCl), then once with wash buffer III (20 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP40, 0.25M LiCl), then once with TE. Samples were moved to a new tube and eluted with 100 μl elution buffer (0.1 M sodium bicarbonate, 1% SDS) at 30 °C for 30 min. Beads were removed, 1 μl RNase A (20 mg/ml) was added to each sample and supernatants were decrosslinked at 65°C for 22 hrs. 1 μl Proteinase K (20 mg/ml) was added to each sample and incubated for an additional 2 hrs at 65°C. Samples were purified using the nucleotide removal kit (Qiagen) according to manufacturer instructions.
RNA extraction from SH-SY5Y cells: Total RNA extraction was performed using NEB Monarch Total RNA Miniprep Kit (New England Biolabs Cat #T2010S). RNAseq library prep was performed using NEBNext Ultra II RNA Library Prep for Illumina (NEB Cat# E7770S). The NEB protocol was followed using the Poly(A) mRNA Magnetic Isolation Module and SPRIselect beads (Beckman Coulter Cat #B23317). Library adapter was diluted 5-fold. The additional SPRIselect cleanup step referred to at 1.11.3 in the NEB protocol was followed.RNA extraction from patient tissues: Fresh-frozen A-T patient and control tissues were obtained from the NIH Neurobiobank (Table S1). 50mg patient tissue RNA was extracted in an RNase free environment using RNA Extraction kit for Bioruptor Plus (Diagenode Cat# C20000010). The additional protocol listed for DNaseI treatment was followed for 10ug of extracted RNA per sample. DNaseI treated RNA was cleaned using RNeasy Mini Kit (Qiagen Cat# 74104).
ChIP library preparation and sequencing  For PAR and R-ChIP, the eluted DNA (2 biological replicates per condition) as well as input samples were used to make sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) with NEBNext Multiplex dual index primers using 12 amplification cycles and 2 additional AMPure XP clean-up steps at 0.8X. Libraries were sequenced by the UT Genomic Sequencing and Analysis Facility (RRID:SCR_021713) using the Illumina NovaSeq SP platform with PE150 runs.
RNAseq library prep was performed using NEBNext Ultra II RNA Library Prep for Illumina (NEB Cat# E7770S). The NEB protocol was followed using the Poly(A) mRNA Magnetic Isolation Module and SPRIselect beads (Beckman Coulter Cat #B23317). Library adapter was diluted 5-fold. The additional SPRIselect cleanup step referred to at 1.11.3 in the NEB protocol was followed.

value: BA10 cortex


title: control, rep 1


title: Con 11 RNAseq cerebellum

source_name: cerebellum

value: cerebellum


title: AB6593

description:
20190330_day13_PD1_M3_spleen_CD45.1_1
MARSseq


title: AB6594

description:
20190330_day13_PD1_M3_spleen_CD45.2_1
MARSseq


title: AB6737

description:
20190424_day3_tumor1_CD45.1_1
MARSseq

value: tumor


title: GPRR_4

city: Shenzhen

first: lu

middle: xi

last: feng

state: Guangdong

address: Taoyuan

institute: Shenzhen University

description:
mRNA from aortic arch was extracted and sequenced
mRNA_Expression_ReadCount.txt
mRNA_Expression_FPKM.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5.
Transcript abundance readcount values were obtained from gene-level count matrices were generated by featureCounts v1.5.0, and FPKM values were generated by  StringTie v1.3.3b.
Differential gene expression was performed on normalized gene counts use edgeR  v3.32.0 with parameters dispersion 0.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes gene abundance(Readcounts and FPKM values) for each sample

source_name: LDLR-/- mice fed with 42% Western type diet for 4 weeks and received (P)RR G-ASOs

growth_protocol: LDLR-/- mice were fed with 42% WTD for 4 weeks

extract_protocol:
Aortic arch was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Subcutaneously injection of saline or (P)RR G-ASOs (3.0 mg/kg/week) on a weekly basis for 4 weeks

tag: age

value: 12 weeks

value: LDLR-/-

value: aorta arch


title: Con 7 RNAseq BA9 cortex

source_name: BA9 cortex

value: BA9 cortex

value: WT


title: MM09, RNAseq, biorep1

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
counts across GENCODE v42 features by featureCounts
Assembly: hg38
Supplementary files format and content: tsv, counts generated by featureCounts

source_name: Bone marrow

extract_protocol:
Bone marrow (BM) samples derived from patients diagnosed with MM. CD138 positive plasma cells purified from BM aspirates using immunomagnetic bead selection. Total RNA extracted from CD138+ cells using miRNeasy Mini Kit followed by Ribosomal RNA depletion with NEB Ribo-Zero Plus rRNA Depletion Kit.
NEBNext® UltraTM II Directional RNA Library Prep Kit

value: Bone marrow

tag: disease state

value: Multiple Myeloma

tag: tumor stage

value: Newly Diagnosed MM

value: Plasma Cell Myeloma

value: Female


title: AB6591

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

institute: Weizmann Institute of Science

description:
20190330_day13_PD1_M2_spleen_CD45.2_1
MARSseq

value: spleen

value: endogenous CD8+


title: AB6592

description:
20190330_day13_PD1_M2_tumor_CD45.2_1
MARSseq

source_name: tumor


title: Con_0wk

source_name: untreated 8 week-old LDLR-/- mice

value: untreated

value: 8 weeks


title: Con 7 RNAseq cerebellum


title: MM07, RNAseq, biorep1

tag: Sex

value: Male


title: H139-070-6-4_S6

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

country: Netherlands

institute: Erasmus MC

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
H139-070-6-4_S6_L001

data_processing:
Raw FASTQ files were uploaded to the ARResT/Interrogate immunoprofiler for annotation and initial exploratory analysis. The full productive IGH repertoire for each sample was downloaded in .csv format and processed in R (R Core Team, 2020) during further analysis.
Assembly: GRCh38
Supplementary files format and content: Tab delimited tekst file containing: sample,QC.status,scenario,rearrangements,raw.count,w.junction.count,w.junction.percent,artefacts.count,artefacts.percent,usable.count,usable.percent,w.most.pop.cln.s..count,w.most.pop.cln.s..percent,uniq.usable.seq.count,clonotypes.count,diversity..norm.ed..count,effective.species.count,R1.Q.mean.stdev.count,R2.Q.mean.stdev.count,joined.normally.count,joined.normally.percent,joined.loosely.count,joined.loosely.percent,total.joined.count,total.joined.percent,saved.from.unjoined.count,saved.from.unjoined.percent,low.quality..ee.nt...0.01..count,low.quality..ee.nt...0.01..percent,short...50nt..count,short...50nt..percent,annotated.count,annotated.percent,w.TR.receptor.count,w.TR.receptor.percent,w.B.chain.count,w.B.chain.percent,w.VJ.Vb..Db..Jb.count,w.VJ.Vb..Db..Jb.percent,w.VJ.Vb..Db..Jb.cln

source_name: PBMCs

extract_protocol:
gDNA was available from the HOVON-139/GIVE trial. 2-12 ug DNA was amplified through multiplex PCR of IGHV-IGHD-IGHJ gene rearrangements following the EC-NGS leader primer protocol. After amplification, PCR products were purified on Agencourt AMPURE beads (Beckman Coulter, Brea, CA, USA) and eluted using H2O. The purified product was checked for primer dimers using the Agilent Tapestation (Agilent,Santa Clara, CA, USA).
The intitial multiplex PCR already attached the indexes to the PCR products, so library construction was simply pooling the purified PCR product in equilmolar fashion.

value: PBMCs

tag: sample type

value: HOVON139/GIVE post-Tx

tag: patient number

tag: timepoint

value: 12 months after randomization


title: AB6589

description:
20190330_day13_ctrl_M2_spleen_CD45.2_1
MARSseq

tag: tissue

value: ctrl


title: AB6590

description:
20190330_day13_ctrl_M2_tumor_CD45.2_1
MARSseq

value: tumor

tag: treatment


title: Con 7 RNAseq BA10 cortex

value: BA10 cortex

tag: genotype


title: H139-039-6-4_S4

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
H139-039-6-4_S4_L001


title: H139-054-6-4_S5

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
H139-054-6-4_S5_L001


title: Saline_4

source_name: LDLR-/- mice fed with 42% Western type diet for 4 weeks and received saline treatment

value: 12 weeks

value: LDLR-/-

value: aorta arch


title: MM05, RNAseq, biorep1

value: Bone marrow

value: Multiple Myeloma

value: Newly Diagnosed MM

tag: cell type


title: MM06, RNAseq, biorep1

value: Plasma Cell Myeloma


title: MM10, RNAseq, biorep1


title: Con 4 RNAseq BA10 cortex

value: WT


title: Con 1 RNAseq BA10 cortex


title: Con 4 RNAseq cerebellum

value: cerebellum


title: AB6587

description:
20190330_day13_ctrl_M1_tumor_CD45.1_1
MARSseq

value: OT1 CD8+

tag: experiment id

tag: days post_adoptive_transfer


title: 6h LPS, rep 1

description: Sequencing by GENEWIZ/Azenta Life Sciences

tag: cell line

value: HepaRG

value: hepatocyte

value: LPS

value: 6 h


title: AB6588

description:
20190330_day13_ctrl_M1_tumor_CD45.2_1
MARSseq

value: endogenous CD8+

value: ctrl

tag: mouse number


title: MM03, RNAseq, biorep1

value: Relapsed MM

value: Male


title: 9-T7_S17

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
9-T7_S17_L001

value: PBMCs

value: HOVON139/GIVE post-Tx

value: 24 months after randomization


title: MM01, RNAseq, biorep1

value: Bone marrow

value: Multiple Myeloma

value: Female


title: AB6586

description:
20190330_day13_ctrl_M1_spleen_CD45.2_1
MARSseq

value: spleen


title: 9-6t4_S7

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
9-6t4_S7_L001

value: 12 months after randomization


title: 9-t7_S9

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
9-t7_S9_L001


title: Con 1 RNAseq BA9 cortex

value: BA9 cortex

value: WT


title: AB6585

description:
20190330_day13_ctrl_M1_spleen_CD45.1_1
MARSseq

value: OT1 CD8+


title: AB6584

description:
20190323_day6_PD1_tumor_CD45.2_2
MARSseq

value: tumor


title: Con 1 RNAseq cerebellum

value: cerebellum


title: AT 11 RNAseq cerebellum

value: AT


title: AT 10 RNAseq BA10 cortex

value: BA10 cortex


title: AB6583

description:
20190323_day6_PD1_tumor_CD45.2_1
MARSseq

value: endogenous CD8+


title: H139-014-6-4_S3

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
H139-014-6-4_S3_L001


title: 8-6t2_S3

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
8-6t2_S3_L001

value: 6 months after randomization


title: AB6582

description:
20190323_day6_PD1_tumor_CD45.1_2
MARSseq


title: 8-6t4A_S5

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
8-6t4A_S5_L001

value: PBMCs


title: AT 11 RNAseq BA10 cortex


title: AT 10 RNAseq cerebellum


title: 7-6t2_S6

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
7-6t2_S6_L001

value: HOVON139/GIVE post-Tx


title: 7-6t4_S20

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
7-6t4_S20_L001


title: 7-6t2_S15

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
7-6t2_S15_L001


title: AB6581

description:
20190323_day6_PD1_tumor_CD45.1_1
MARSseq


title: AB6580

description:
20190323_day6_PD1_spleen_CD45.2_1
MARSseq


title: AT 7 RNAseq cerebellum


title: 7-3t4_S3

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
7-3t4_S3_L001

value: Venetoclax ramp-up


title: AB6579

description:
20190323_day6_PD1_spleen_CD45.1_1
MARSseq


title: 69-6t4_S2

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
69-6t4_S2_L001


title: AB6578

description:
20190323_day6_ctrl_tumor_CD45.2_2
MARSseq

value: ctrl


title: AT 7 RNAseq BA9 cortex


title: AB6577

description:
20190323_day6_ctrl_tumor_CD45.2_1
MARSseq


title: AT 4 RNAseq BA10 cortex


title: 69-6t4_S14

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
69-6t4_S14_L001


title: AT 4 RNAseq cerebellum


title: AT 1 RNAseq BA9 cortex


title: AB6575

description:
20190323_day6_ctrl_tumor_CD45.1_1
MARSseq


title: 69-6t2_S23

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
69-6t2_S23_L001


title: RNAseq ATMi NAC rep2

value: neuroblastoma, differentiated

value: AZD1390 (ATMi) + N-acetyl cysteine (NAC)


title: AB6573

description:
20190323_day6_ctrl_spleen_CD45.1_1
MARSseq

value: spleen


title: kd (CDH11 knockdown, rep3)

city: Cleveland

first: Pranab

last: Mukherjee

state: OH

address: 9500 Euclid Avenue

department: Infection and Immunity

institute: Cleveland Clinic

data_processing:
Paired-ended reads were checked for quality with FastQC (v0.11.3) [ref: http://www.bioinformatics.babraham.ac.uk/projects]
Reads were aligned using Rsubread::Subread
Gene counts were determined by the number of uniquely aligned, unambiguous reads (Subread: featureCounts, v1.5.2) and annotated by alignment to the human genome (GRCh38.p10 using Gencode Release 27 annotations).
Raw counts were loaded into R (v3.6.2 and 4.1.2, R Core Team 2021), and Counts were filtered to exclude transcripts that were expressed at low levels (counts per million reads mapped [CPM] < 1)
Differential expression (DE) analysis was conducted using R packages edgeR and Limma, subsequent analyses were performed using standard R packages (tidyverse, dunn.test, EnhancedVolcano, clusterProfiler)
Assembly: GRCh38.p10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: intestine

extract_protocol:
Qiagen Mini kit
Illumina instructions

value: intestine

value: Primary human intestinal epithelial cells

value: myofibroblasts

value: CDH11 knockdown

value: CDH11 siRNA


title: AB6574

description:
20190323_day6_ctrl_spleen_CD45.2_1
MARSseq


title: 67-6t4_S22

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
67-6t4_S22_L001

value: 12 months after randomization


title: kd (CDH11 knockdown, rep4)


title: kd (CDH11 knockdown, rep2)


title: AB6572

description:
20181227_M29_tumor_CD8_2
MARSseq

value: tumor

value: melanoma_CD8+_PD1 treatment


title: kd (CDH11 knockdown, rep1)


title: 68-3t4_S22

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
68-3t4_S22_L001


title: AB6322

description:
20181227_M26_tumor_CD8_2
MARSseq

value: endogenous CD8+


title: 67-5_S2

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
67-5_S2_L001

value: End of induction treatment


title: RNAseq ATMi NAC rep1

value: WT


title: scr (control-rep3)

value: wild type

value: scrambled (si)RNA


title: RNAseq NAC rep1

value: N-acetyl cysteine (NAC)


title: RNAseq ATMi rep2

value: neuroblastoma, differentiated

value: AZD1390 (ATMi)


title: AB6321

description:
20181227_M26_tumor_CD8_1
MARSseq


title: scr (control-rep4)


title: 67-3t4_S21

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
67-3t4_S21_L001

value: PBMCs

value: HOVON139/GIVE post-Tx

value: Venetoclax ramp-up


title: 6-6t4_S23

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
6-6t4_S23_L001


title: AB6576

description:
20190323_day6_ctrl_tumor_CD45.1_2
MARSseq

value: OT1 CD8+

value: ctrl


title: scr (control-rep2)

value: intestine

value: Primary human intestinal epithelial cells

value: myofibroblasts


title: 69-5A_S23

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
69-5A_S23_L001

value: End of induction treatmentA


title: AT 1 RNAseq cerebellum

value: cerebellum

value: AT


title: AB6320

description:
20181227_M26_spleen_CD8_1
MARSseq

value: spleen

value: endogenous CD8+

value: melanoma_CD8+_PD1 treatment


title: 66-6t4_S21

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
66-6t4_S21_L001

value: 12 months after randomization


title: RNAseq DMSO rep2

value: neuroblastoma, differentiated

value: WT


title: 67-6t2_S23

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
67-6t2_S23_L001

value: PBMCs

value: 6 months after randomization


title: scr (control-rep1)

value: wild type

value: scrambled (si)RNA


title: 66-6t2_S20

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
66-6t2_S20_L001

value: HOVON139/GIVE post-Tx


title: AB6319

description:
20181227_M15_tumor_CD8_2
MARSseq

value: tumor


title: AB6571

description:
20181227_M29_tumor_CD8_1
MARSseq


title: AB6318

description:
20181227_M15_tumor_CD8_1
MARSseq


title: RNAseq NAC rep2

value: N-acetyl cysteine (NAC)


title: vestibular schwannoma right ear, replicate 1, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: vestibular schwannoma right ear

extract_protocol:
Utricles from vestibular schwannoma patients or organ donors were placed in DMEM/F12 with 5% FBS during transport to the laboratory. Following cleaning, the whole utricle was then incubated with thermolysin (0.5 mg/mL) for 45 min at 37C prior to mechanical separation of the sensory epithelium from underlying stroma. Next, the sensory epithelium was digested using Accutase for 20 min at 37C and single cell suspension was obtained by trituration using a 1 ml pipette. Single cell suspension was achieved using a 40 μm filter. Cells were then centrifuged at 300 rcf for 5 min at 4oC. The supernatant was removed and cells were resuspended in media.   The single cell suspension was then loaded onto a 10x Genomics controller using manufacturer’s recommended protocols at the Stanford Genomics Facility.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics)

value: utricle (inner ear)

tag: individual

value: Patient #21

value: male

tag: inner ear_analyzed

value: R

tag: vestibular symptoms

value: Y


title: 66-5_S21

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
66-5_S21_L001

value: End of induction treatment


title: RNAseq DMSO rep1


title: AB6317

description:
20181227_M15_spleen_CD8_1
MARSseq

source_name: spleen

value: spleen

value: endogenous CD8+

value: melanoma_CD8+_PD1 treatment


title: R ChIP input, ATMi NAC, rep1

tag: chip antibody

value: expressed in SH-SY5Y cells:Flag-tagged human RNaseH(D210N)(R-ChIP)

value: neuroblastoma, differentiated

value: WT

value: AZD1390 (ATMi) + N-acetyl cysteine (NAC)


title: organ donor Right ear, replicate 2, scRNAseq

description: 10x Genomics

source_name: organ donor Right ear

value: Organ Donor #5

tag: age

value: female

value: N


title: 66-3t4_S13

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
66-3t4_S13_L001

value: PBMCs

value: HOVON139/GIVE post-Tx

value: Venetoclax ramp-up


title: vestibular schwannoma left ear, replicate 1, scRNAseq

description: 10x Genomics

source_name: vestibular schwannoma left ear

value: utricle (inner ear)

value: Patient #17

tag: Sex

value: male

value: L


title: 66-3t4_S1

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
66-3t4_S1_L001

tag: sample type


title: R ChIP input, ATMi NAC, rep2


title: R ChIP input, NAC, rep2

value: N-acetyl cysteine (NAC)


title: RNAseq ATMi rep1

value: AZD1390 (ATMi)


title: AB6315

description:
20181227_M13_tumor_CD8_1
MARSseq

value: tumor

value: endogenous CD8+

value: melanoma_CD8+_PD1 treatment


title: AB6316

description:
20181227_M13_tumor_CD8_2
MARSseq


title: R ChIP input, NAC, rep1

value: expressed in SH-SY5Y cells:Flag-tagged human RNaseH(D210N)(R-ChIP)

value: neuroblastoma, differentiated

value: WT


title: 65-6t4_S22

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
65-6t4_S22_L001

tag: patient number

value: 12 months after randomization


title: 65-6t2_S20

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
65-6t2_S20_L001

tag: timepoint

value: 6 months after randomization


title: AB6314

description:
20181227_M13_spleen_CD8_1
MARSseq

tag: tissue

value: spleen


title: CRC-404 PDOX, rep3

city: Durham

first: Ergang

last: Wang

state: NC

address: C215, LSRC

department: PCB

institute: Duke University

data_processing:
ATAC seq data was processed using the pipeline developed for ENCODE to perform quality control filtering of low0quality reads and PCR duplicates analysis of reproducibility, reference genome alignment, peaks calling, and fold-enrichment or p-value signal tracks generation.
Reads were aligned to reference genome hg19 using Bowtie2. Duplicate an mitochondrial reads were removed, and peaks were called by MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig for genome track visualization

extract_protocol:
The nuclei were extracted from samples (PT, PDO, PDX and PDOX). For each sample type in one PT-PDO-PDX/PDOX set, three replciates were included. Intact nuclei (5x10^4) were used for each replicate. Transposase, digitonin, and Tween-20 were added, and the mixture was incubated at 37C for 30 minutes. The tranposed fragments were amplified.
The Omni-ATAC protocol was utilized for ATAC library preparations.

tag: replicate

value: PDOX


title: 65-5_S22

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
65-5_S22_L001

value: PBMCs

value: HOVON139/GIVE post-Tx

value: End of induction treatment


title: AB6313

description:
20181227_M12_tumor_CD8_2
MARSseq

tag: treatment


title: R ChIP input, ATMi, rep1

tag: cell type

tag: genotype


title: CRC-404 PDOX, rep2


title: AB6312

description:
20181227_M12_tumor_CD8_1
MARSseq

tag: experiment id

tag: days post_adoptive_transfer


title: CRC-404 PDO, rep3

value: PDO


title: 65-3t4_S19

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
65-3t4_S19_L001

value: Venetoclax ramp-up


title: R ChIP input, DMSO, rep2

tag: cell line


title: AB6311

description:
20181227_M12_spleen_CD8_1
MARSseq

tag: mouse number


title: R ChIP input, DMSO, rep1


title: CRC-404 PDO, rep2


title: 6-3t4_S14

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
6-3t4_S14_L001


title: 62-6t4_S21

description:
B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of post-treatment samples from CLL patients enrolled in the HOVON139/GIVE trial
62-6t4_S21_L001