title: genomic_DNAmethylation_QF0368_vcN

value: Male


title: TSA treated Min6 cells_rep_1

status: Public on Aug 08 2023

type: SRA

city: Lille

first: Frederik

last: Oger

address: Faculté de Médecine - Pôle Recherche - 2eme etage - 1 place de Verdun

country: France

institute: Université de Lille

description: RNA polyA

library_source: transcriptomic

data_processing:
The demultiplexing of sequence data (from BCL files generated by Illumina sequencing systems to standard FASTQ file formats) was performed using bcl2fastq Conversion Software (Illumina; version 2.19.1).
Trimming of residuals adapters and low-quality reads was performed using Cutadapt software (version 1.7.1).
Sequence reads from FASTQ files were mapped to the mouse genome (mm10) or human genome (Hg38) using STAR Aligner (version 2.5.2b). On average, 38M reads were generated per sample, and 93.5 % +/- 0.9% of them were accurately mapped.
The counting of the different genes and isoforms was performed using RSEM (version 1.3). Finally, differential expression was performed using DESeq2 package
Assembly: mm10 (mouse) and Hg38 (human)
Supplementary files format and content: Tab-delimited text files include TPM and FPKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Min6 cells

growth_protocol: Min6 cells (Addexbio, C0018008) were cultured in DMEM high Glucose glutaMAX medium (Gibco, 31966-021) supplemented with 15 % SVF, 0.1 % β-mercaptoethanol and antibiotics (penicillin/streptomycin).

extract_protocol:
Total RNA was extracted from EndoCβH1, Min6, mouse pancreatic islets and human pancreatic islets using RNeasy Plus mini kit (Qiagen, 74136) according to the manufacturer’s instructions. Total RNA sample concentrations were determined using a Nanodrop spectrophotometer (Implen). RNA quality was verified using RNA 6000 nanochips (Agilent, 5067-1511) on the Agilent 2100 bioanalyzer (Agilent, G2939A). 500 ng of purified RNA with RNA integrity number (RIN) ≥8 was subsequently used for library preparation
500 ng of purified RNA with RNA integrity number (RIN) ≥8 was subsequently used for library preparation with the TrueSeq Stranded mRNA library Prep (Illumina, 20020594) and sequenced in paired end 2x75 on the NextSeq device.
Libraries were prepared with the TruSeq Stranded mRNA library Prep (Illumina, #20020594) and sequenced on the Illumina NextSeq500 system using a paired-end 2×75 bp protocol.

treatment_protocol: EndoCβH1, Min6, mouse pancreatic islets and human pancreatic islets were treated either with DMSO (0.1%) or TSA (0.5µM) for 16h.

tag: cell type

value: Mouse beta cell model - Min6

tag: treatment


title: WT sham microglia 1

city: Pittsburgh

first: Yejie

last: Shi

state: PA

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

country: USA

institute: University of Pittsburgh

data_processing:
Genome alignment to GRCm38 using HISAT2 in Chipster v3.15
Counting reads using HTSeq in Chipster v3.15
Assembly: GRCm38
Supplementary files format and content: tsv files include read counts for each sample

source_name: brain

extract_protocol:
Single-cell suspensions were prepared from mouse brains 3 days after stroke or sham operation. Mice were transcardially perfused with sterile 0.9% NaCl. The ipsilesional brain hemisphere was harvested, and cell suspensions were prepared using the Neural Tissue Dissociation Kit and gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec). Suspensions were passed through a 70 μm cell strainer, and fractionated on a 30% and 70% Percoll gradient at 500 g for 30 min. Mononuclear cells at the interface were collected. Isolated mononuclear cells were washed, resuspended at 1×10^6 per mL, and stained with fluorophore-conjugated antibodies and the appropriate isotype controls. Fluorescence-activated cell sorting was performed using the FACS Aria I sorter and FACS Diva software (BD Biosciences). Microglia were gated as CD11c–Ly6G–CD11b+CD45low and sorted for bulk RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: brain

value: microglia

tag: genotype


title: DMSO treated Min6 cells_rep_3

description: RNA polyA


title: DMSO treated Min6 cells_rep_2

description: RNA polyA


title: CMe-vco-538

city: Guangzhou

first: Cui

last: Guizhong

state: Guangdong

address: 188 KaiYuan Road, Huangpu District

department: Center of Cell Lineage and Atlas

country: China

institute: Guangzhou Laboratory

data_processing:
Sequencing quality of raw sequencing data was evaluated by fastp (Chen et al., 2018).
Reads were mapped to the mm10 genome assemblies by HISAT2 (Pertea et al., 2016) using default settings. Mapping ratio was calculated based on the number of mapped reads and total reads for each sample.
All mapped reads were processed by StringTie (Pertea et al., 2016) to quantify gene expression levels (measured by FPKM, Fragment Per Kilobase per Million mapped reads respectively) using default parameters.
Assembly: mm10/GRCm38.91
Supplementary files format and content: tab-delimited text files include log10(FPKM+1) values for each samples

molecule: polyA RNA

source_name: Mes

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using Vayzme TD503 DNA sample preparation kit

treatment_protocol: Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.

value: Mes

value: mvco

value: Embryonic day 14.5


title: CR-dt-567

source_name: RPE

value: RPE

value: dt


title: DMSO treated Min6 cells_rep_1

description: RNA polyA


title: genomic_DNAmethylation_PM151_vc

type: genomic

city: Boston

first: Maitreyi

last: Mazumdar

state: MA

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridised to the Illumina Infinium  MethylationEPIC Beadchips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using an HiSCAN with standard recommended Illumina scanner settings.

data_processing:
See original publication
Beta values with dasen + noob normalization, filtered for quality probes.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: V-NORM and V-SSRI samples: 1.5-2 cm3 samples of chorionic villi were taken from each of four distinct cotyledons (sites) from below the surface of the fetal-facing side of the placental disc. The samples were washed thoroughly to remove blood, and any thick vessels were removed. Samples were frozen at -20°C until use. DNA was then extracted from all four cotyledon samples using a salting-out DNA extraction procedure, and extracted DNA from the four sites was pooled in equimolar proportions to provide a representative sample of each placenta. The second sampling process involved the QF-2011 placentas, which were processed in Brisbane, Australia within 60 minutes of delivery, and eight sites (1 cm3 each) representing different cotyledons were sampled across the fetal-facing side of each placenta. These samples were snap frozen in liquid nitrogen and subsequently shipped frozen to Montreal, Canada. Samples were pooled and ground while snap frozen over liquid nitrogen. DNA was extracted using a commercial kit  from pooled samples in Montreal, before shipping to Vancouver on dry ice for DNAme processing.

tag: cohort

value: V-NORM

tag: batch

value: NIH Batch 3

tag: sentrix

value: FALSE

tag: Sex

value: Female

value: East Asian

tag: syncytiotrophoblast

tag: cytotrophoblast

tag: stromal

tag: endothelial

tag: hofbauer

tag: nrbc


title: Untreated Min6 cells - Input DNA

library_source: genomic

data_processing:
The demultiplexing of sequence data (from BCL files generated by Illumina sequencing systems to standard FASTQ file formats) was performed using bcl2fastq Conversion Software (Illumina; version 2.20).
Trimming of residuals adapters and low-quality reads was performed using TrimGalore (version 0.4.5)
Sequence reads from FASTQ files were mapped to the mouse genome (mm10) using Bowtie2 Aligner (version 2.3.5.1)
Finally peak-calling was performed using MACS2 software (version 2.2.7.1)
Assembly: mm9 (samples 1 to 8) and mm9 (samples 9 to 14)
Supplementary files format and content: BigWig were generated using Bamcoverage

growth_protocol: Min6 cells (Addexbio) were cultured in DMEM high Glucose glutaMAX medium (Gibco, 31966-021) supplemented with 15 % SVF, 0.1 % β-mercaptoethanol and antibiotics (penicillin/streptomycin).

extract_protocol:
20.106 Min6 cells were treated with formaldehyde at a final concentration of 1% to cross link DNA and protein complexes during 10 min. The reaction was stopped by the addition of glycine 0.125 M during 5 min. Cells were lysed and DNA-protein complexes were sheared using the Bioruptor Pico (Diagenode, ref B01060010) for 8 minutes. The sheared chromatin was followed by immunoprecipitation with either the non-specific antibody IgG ( Santa Cruz, sc2025), H3K4me3 (Active motif, 61379), H3K27me3 (Active motif, 61017), H3K27ac (Active motif, 3968S), H3K9ac (Abcam, ab47915) or H3K4me1 (Active Motif, 39297).
1 ng of eluted and purified DNA was used to prepare DNA sequencing library with the Nextflex rapid DNA seq kit 2.0 (Perkin Elmer, NOVA-5188-01) on NextSeq HighOutput Sequencer in single read 100 base pairs

treatment_protocol: Min6 cells were treated either with DMSO (0.1%) or TSA (0.5µM) for 16h.

tag: antibody

value: Untreated


title: genomic_DNAmethylation_M0023_vcN

value: European/Caucasian


title: CMe-vct-538

value: mvct


title: genomic_DNAmethylation_PM220_vc

value: Male


title: Untreated Min6 cells - H3K9ac

value: Mouse beta cell model - Min6

value: Abcam (#ab4441)


title: genomic_DNAmethylation_PM353_vc

value: TRUE

value: Mixed


title: Untreated Min6 cells - H3K4me3

value: Active motif (#61379)


title: Untreated Min6 cells - H3K27ac

value: Active motif (#39685)


title: Untreated Min6 cells - H3K27me3

value: Active motif (#61017)


title: genomic_DNAmethylation_PM212_vc


title: genomic_DNAmethylation_QF0357_vcN


title: TSA Min6 cells - IgG

value: Santa Cruz (#sc2025)


title: TSA treated Min6 cells - H3K9ac


title: CMe-dco-538

value: Mes

value: mdco

value: Embryonic day 14.5


title: CMe-dct-538

value: mdct


title: TSA treated Min6 cells - H3K27ac


title: genomic_DNAmethylation_PM353_vc_R

value: V-NORM

value: NIH Batch 3

value: FALSE


title: TSA treated Min6 cells - H3K27me3


title: DMSO Min6 cells - IgG


title: genomic_DNAmethylation_PM178_vc

value: European/Caucasian


title: CMe-do-538

value: mdo


title: DMSO treated Min6 cells - H3K27me3

value: Mouse beta cell model - Min6


title: CMe-dt-538

value: mdt


title: genomic_DNAmethylation_PM202_vc

value: Female


title: CMe-vo-538

value: mvo


title: genomic_DNAmethylation_QF0185_vcN

value: Male


title: Untreated Min6 cells - H3K4me1

value: Active motif (#39297)

value: Untreated


title: CMe-vt-538

value: mvt


title: CR-vco-538

value: RPE

value: vco


title: DMSO treated Min6 cells - H3K27ac

value: Active motif (#39685)


title: genomic_DNAmethylation_PM184_vc


title: Mouse Lung tumor_KrasLA1_641_rep2

city: Houston

first: Raisa

last: Reyes-Castro

state: Texas

address: 6767 Bertner Ave

department: Genetics

institute: UT Health MD Anderson Cancer Center

data_processing:
Reads were mapped to mouse mm10 reference genome using BWA (v0.7.12) algorithm and saved as BAM files.
Reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome were used for further analysis. In addition, duplicate reads (“PCR duplicates”) were removed.
Genomic regions with a high level of transposition/tagging events were determined using the MACS3 (v3.0.0) peak calling algorithm with a cut off of p-value 1e-7
For comparative analysis, normalization was achieved by reducing the number of alignments per sample to match the number of alignments in the sample with fewer number of alignments. Reduction was done through random sampling
To identify the density of transposition events along the genome, the genome was divided into 32 bp bins and the number of fragments in each bin was determined
The histograms showing the density of each signal (peaks) was stored in a bigWig file and visualized using the USCC Genome browser
BigWig files were generated using deeptools (v3.5.1)
A FRIP (fraction of reads in peaks) value of 10% or higher was used to define good data quality and false peaks were defined within the ENCODE blacklist (Consortium, 2012) and removed from analysis
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: Lung tumor

extract_protocol:
A total of 40-50 mg of lung tumors were dissected from euthanized mice, snap frozen in liquid nitrogen and submitted for ATAC-sequencing
Samples were send to Active Motif for library prep, sequencing and analysis

value: Lung tumor

tag: strain

tag: age in_weeks

tag: assay

value: Atac-sequencing


title: Mouse Lung tumor_KrasLA1;DicerS2D_697_rep1


title: genomic_DNAmethylation_PM187_vc

value: V-NORM

value: NIH Batch 3


title: SCAR_643_dTAG_H4K20me0_T0_rep3

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.20.2)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Samples were normalized based on Drosphila spike-In abundance and corresponding ClickedInputs.
Assembly: mm10/dm6
Supplementary files format and content: SCAR-seq Partition scores in bigwig format
Library strategy: SCAR-seq

source_name: Cell line

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE.

extract_protocol: Native SCAR-seq: After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 30 min  and then  collected (T0).

value: Cell line

tag: cell line

tag: cell type

value: Embryonic stem cells

value: CAF-1 p150 dTAG

tag: treatment

value: dTAG


title: CR-vt-538

tag: tissue

value: vt

tag: genotype

value: Embryonic day 14.5


title: CR-vo-538

value: vo


title: SCAR_643_dTAG_stranded_input_Me0_T0_rep3


title: Mouse Lung tumor_KrasLA1_695_rep1

value: Female


title: SCAR_643_dTAG_H3K27me3_T0_rep3


title: CR-vct-538

value: vct


title: DMSO treated Min6 cells - H3K9ac

value: Mouse beta cell model - Min6

value: Abcam (#ab4441)


title: genomic_DNAmethylation_QF0325_vcN

tag: cohort

tag: batch

tag: sentrix

value: FALSE

value: European/Caucasian


title: SCAR_643_DMSO_stranded_input_Me0_T0_rep3

value: DMSO


title: genomic_DNAmethylation_PM139_vc_R

tag: Sex

value: Male

value: East Asian

tag: syncytiotrophoblast

tag: cytotrophoblast


title: Mouse Lung tumor_KrasLA1;DicerS2D_657_rep2

value: Lung tumor

value: Atac-sequencing


title: SCAR_643_DMSO_stranded_input_K27_T0_rep3

value: Cell line

value: Embryonic stem cells


title: SCAR_643_DMSO_H3K27me3_T0_rep3

value: CAF-1 p150 dTAG


title: SCAR_643_dTAG_stranded_input_T0_rep2

value: dTAG


title: CR-do-538

value: RPE

value: do

value: Embryonic day 14.5


title: CR-dco-538

value: dco


title: SCAR_643_dTAG_H3K27me3_T0_rep2


title: CR-dt-538

value: dt


title: SCAR_643_DMSO_stranded_input_T0_rep2


title: SCAR_643_dTAG_H4K20me0_T0_rep2


title: genomic_DNAmethylation_PM355_vc

value: V-NORM

value: NIH Batch 3

value: Female

tag: stromal

tag: endothelial

tag: hofbauer


title: FMe-vco-518

value: Mes

value: mvco

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)


title: SCAR_643_dTAG_stranded_input_K27_T0_rep3


title: SCAR_643_DMSO_H4K20me0_T0_rep2

value: DMSO


title: SCAR_643_dTAG_stranded_input_Me0_T0_rep1


title: FMe-vct-518

value: mvct


title: SCAR_643_dTAG_stranded_input_K27_T0_rep1

value: Cell line


title: SCAR_643_dTAG_H4K20me0_T0_rep1

value: Embryonic stem cells


title: CR-dct-538

value: dct


title: SCAR_643_DMSO_H4K20me0_T0_rep3

value: CAF-1 p150 dTAG


title: FMe-vo-518

value: mvo


title: SCAR_643_DMSO_stranded_input_Me0_T0_rep1


title: SCAR_643_dTAG_H3K27me3_T0_rep1

value: dTAG


title: SCAR_643_DMSO_stranded_input_K27_T0_rep1


title: SCAR_643_DMSO_H4K20me0_T0_rep1


title: FMe-dco-518

value: mdco

value: Embryonic day 14.5


title: FMe-vt-518

value: mvt


title: FMe-dct-518

value: mdct


title: FMe-do-518

value: mdo


title: SCAR_643_DMSO_H3K27me3_T0_rep2


title: ZS+OT1-2

city: Philadelphia

first: Ben

middle: Z

last: Stanger

address: 421 Curie Blvd

institute: Perelman School of Medicine

data_processing:
Illumina bcl2fastq was used to convert bcl to fastq files
Sequencing reads were aligned to the mouse (GRCm39) reference genomes using Bowtie2 with default settings.
Reads were dedeuplicated
Peaks were called with Genrich in ATAC mode. Blacklisted peaks (https://sites.google.com/site/anshulkundaje/projects/blacklists), were excluded in all subsequent analysis.
Assembly: GRCm39
Supplementary files format and content: Genrich-called peaks in narrowPeak format

source_name: pancreatic cancer cells

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum, 10% glutamine, and 150 µg/mL gentamicin at 37°C, 5% CO2, 21% O2, and 100% humidity.

extract_protocol:
Nuclei were extracted and permeabilized using nuclei isolation buffer (NIB). Details in Methods section.
Genomic DNA was simultaneously fragmented and tagged with Illumina sequencing adapters using the Tn5 transposase. Libraries were amplified for 5 PCR cycles. Details in Methods section.

treatment_protocol: cells were co-cultured with OT-1 cells if indicated

value: pancreatic cancer cells

value: Zeb1/Snail overexpression

value: OT-1 co-culture


title: ZS+OT1-1


title: EV+OT1-1

value: wildtype


title: FMe-dt-518

value: Mes

value: mdt

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)


title: ZS2


title: ZS1


title: EV2


title: FR-vco-518

value: RPE

value: vco


title: SCAR_643_DMSO_H3K27me3_T0_rep1

value: Cell line

value: Embryonic stem cells

value: CAF-1 p150 dTAG

value: DMSO


title: FR-vct-518

value: vct

value: Embryonic day 14.5


title: EV+OT1-2


title: antiCtBP2

city: Tsukuba

first: Motohiro

last: Sekiya

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
Sequencing was performed with Illumina NextSeq500.
The paired-end reads were mapped onto mouse genome mm9 with BWA algorithm.
The mapped reads were converted to BED files using Samtools (version 0.1.19) and bedtools (version 2.17.0).
Assembly: mouse reference genome mm9
Supplementary files format and content: bigWig and bed files.

extract_protocol:
MIN6 cells were washed and fixed in 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched by adding glycine to a final concentration of 125 mM. Thereafter, ChIP assay was carried out using Magna ChIP HiSens Chromatin Immunoprecipitation system (EMD Millipore). Chromatin shearing was achieved by sonication (Bronson sonifier 250). Chromatin was immunoprecipitated either with control IgG (Cell Signaling) or anti-CtBP2 (Active Motif, 61261).
The library was constructed with NEBNext UltraII DNA Library Prep Kit for Illumina.

value: MIN6 pancreatic beta cells

tag: chip antibody

value: anti-CtBP2 (Active Motif 61261)


title: Runx1 KO Ov 6

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

data_processing:
Analysis was performed by Active Motif. The paired-end 42 bp sequencing reads generated by Illumina sequencing (using NextSeq 500) are mapped to the mouse mm10 reference genome using the STAR algorithm with default settings.
The number of fragments overlapping predefined genomic features of interest (e.g. genes) are counted. Only read pairs that have both ends aligned were counted. Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands were discarded. The gene annotations were obtained from Subread package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were merged into one gene.
Data normalization, filtering and differential analysis was perform using DESeq2 with 0.1 FDR
Assembly: mm10
Supplementary files format and content: Excel file containing the DESeq2 normalized counts for each Sample

source_name: ovary 4.5m

extract_protocol:
RNA from 4.5 months old ovaries was extracted using RNeasy mini kit (Qiagen).
Libraries were prepared by Active Motif. For each sample, 1 ug of total RNA was used for library preparation using Illumina’s TruSeq Stranded mRNA Library kit

value: ovary 4.5m

value: Sf1-Cre+/Tg; Runx1f/-


title: EV1

value: pancreatic cancer cells


title: FR-vo-518

value: vo


title: Runx1 KO Ov 4


title: FR-vt-518

value: vt


title: Runx1 KO Ov 5


title: Runx1 KO Ov 3


title: FR-dco-518

value: dco


title: Runx1 KO Ov 1


title: LEB1020

city: Doha

first: Georges

last: Nemer

address: Education City

country: Qatar

institute: Hamad Bin Khalifa university

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium EPIC Human Methylation Beadchip using standard Illumina protocol

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

data_processing: Standard Illumina Protocol

label: Unaffected sister of LEB1010

source_name: Blood

extract_protocol: Standard Illumina Protocol

tag: sample type

value: Control

tag: gender

value: Female

tag: age

tag: mutation type


title: Runx1 Control Ov 6

value: Sf1-Cre+/+; Runx1+/f


title: FR-dct-518

value: RPE

tag: cell type

value: dct

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)

tag: treatment


title: Runx1 Control Ov 5

tag: tissue

tag: genotype


title: input

tag: cell line


title: LEB2020

label: Unaffected brother of LEB2010

value: Male


title: Runx1 KO Ov 2


title: PERU1050

label: Unaffected father of PERU1010

value: Carrier

value: Heterozygous

tag: mutation


title: PERU2040

label: Unaffected sister of PERU2010


title: FR-do-518

value: do

value: Embryonic day 14.5


title: Runx1 Control Ov 3

value: ovary 4.5m


title: FR-dt-518

value: dt


title: 10_CRB_ko

city: Milan

first: Francesca

last: Maltecca

state: Milan

address: Via Olgettina, 58

department: Division of Neuroscience

country: Italy

institute: Ospedale San Raffaele

description: Cerebellar tissues of  Sacs KO  mouse - replicate 5

data_processing:
Raw data obtained after sequencing were demultiplexed using bcl2fasq (Illumina).
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39).
The remaining reads were mapped to the reference murine genome GRCm38, using STAR aligner (version 2.5.3a).
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts (version1.6.4). Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (GENCODE release M22).
Assembly: GRCm38
Supplementary files format and content: all.counts.txt: Raw gene counts for each sample, in a tab-delimited format.

source_name: Cerebella

extract_protocol:
Total RNA extracted from cerebellum with RNeasy kit (Qiagen).
NGS libraries were generated with the TruSeq stranded mRNA protocol (Illumina), starting from 50ng of RNA. Libraries were barcoded, pooled and sequenced on an Illumina NextSeq 500 sequencing system in SR (single read) mode, generating an average of 30M reads 100 nt long.

value: Cerebella

tag: Sex

value: 5 months

value: CRB KO

value: untreated


title: Runx1 Control Ov 2


title: PERU3050

label: Unaffected father of PERU3010


title: CMe-vco-517

value: Mes

value: mvco


title: PERU1060

label: Unaffected mother of PERU1010

value: Female


title: PERU2060

label: Unaffected mother of PERU2010


title: 9_CRB_ko

description: Cerebellar tissues of  Sacs KO  mouse - replicate 4


title: 8_CRB_ko

description: Cerebellar tissues of  Sacs KO  mouse - replicate 3


title: Runx1 Control Ov 1

value: Sf1-Cre+/+; Runx1+/f


title: CMe-vct-517

value: mvct


title: PERU2050

label: Unaffected father of PERU2010


title: 7_CRB_ko

description: Cerebellar tissues of  Sacs KO  mouse - replicate 2


title: CMe-vo-517

value: mvo


title: 5_CRB_wt

description: Cerebellar tissues of WT mouse - replicate 5

value: WT


title: 6_CRB_ko

description: Cerebellar tissues of  Sacs KO  mouse - replicate 1


title: 4_CRB_wt

description: Cerebellar tissues of WT mouse - replicate 4


title: 3_CRB_wt

description: Cerebellar tissues of WT mouse - replicate 3


title: CMe-vt-517

value: mvt


title: CMe-dco-517

value: mdco


title: PERU2010

label: CGL2 patient PERU family 2

value: Patient

value: Male

value: Homozygous


title: LEB1010

label: CGL2 patient LEB family 1


title: LEB2010

label: CGL2 patient LEB family 2


title: Runx1 Control Ov 4

value: ovary 4.5m


title: CMe-dct-517

value: mdct

value: Embryonic day 14.5


title: 2_CRB_wt

description: Cerebellar tissues of WT mouse - replicate 2

value: Cerebella

value: 5 months


title: 1_CRB_wt

description: Cerebellar tissues of WT mouse - replicate 1

value: untreated


title: PERU1010

label: CGL2 patient PERU family 1


title: PERU3060

label: Unaffected mother of PERU3010

value: Carrier

value: Heterozygous


title: Refeed+rapa

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
Illumina NextSeq 500 using v3 chemistry. Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq cellranger mkfastq (see characteristics for version)
Single-cell RNAseq data was produced using the 10x genomics platform. Data were processed using cellranger version 3.1.0 with alignment to a modified version of the GENCODE mouse genome (GRCm38, build accession NCBI:GCA_000001635.8) with 2018-03 genebuild target provided by 10x genomics. The modification was the addition of the GFP selectable marker. Cellranger filtered data was imported into R version 4.1.0 (R Core Team 2021) and analyzed with Seurat version 4.0.3 (Stuart et al. 2019).
Genome_build: mm10 (NCBI:GCA_000001635.8) with 2018-03 genebuild
Supplementary_files_format_and_content: D20-1014.al.tar.gz is a tar archive of filtered_feature_bc_matrix
Supplementary_files_format_and_content: D20-1015.f.tar.gz is a tar archive of filtered_feature_bc_matrix
Supplementary_files_format_and_content: D20-1016.rf.tar.gz is a tar archive of filtered_feature_bc_matrix
Supplementary_files_format_and_content: D20-1017.rf.rapa.tar.gz is a tar archive of filtered_feature_bc_matrix

source_name: Intestinal Stem Cells and Progenitor Cells

growth_protocol: 8-12 week old mice

extract_protocol:
10x Genomics Single Cell 3' v3
scRNA-Seq

tag: strain

value: Lgr5-EGFP-IRES-CreERT2 (strain name:B6.129P2-Lgr5tm1(cre/ERT2)Cle/J, stock number 008875)

tag: diet

value: refeeding for 24 hours following 24 hour fast plus rapamycin

tag: rapamycin

value: intraperitoneal injection at 10 mg/kg Rapamycin in EtOH


title: Refeed

value: refeeding for 24 hours following 24 hour fast.


title: Fast

value: fasting (24 hours)


title: AL

value: feeding at will


title: PERU3010

label: CGL2 patient PERU family 3

value: Patient

value: Female


title: CMe-do-517

value: Mes

value: mdo


title: PERU3030

value: Homozygous


title: Colletotrichum panacicola treated for 24h, rep3

city: Changchun

first: Shouan

last: Liu

address: Xi-An-Da Road 5333

institute: Jilin University

description:
CP_24h3
2-year-old ginseng plant
Colletotrichum panacicola treated sample 24h- 3

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 Panax ginseng whole genome (http://ginsengdb.snu.ac.kr/index.php) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps. Prior to assembly, the low quality reads (1, reads containing sequencing adaptors; 2, reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed. software CutAdapter, parameters -o 5 -p 100.
Read alignment software, software HISAT, version 2.0, parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9.
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie, version 1.3.0, parameters -b dta -q phred33-quals.
Assembly: Panax ginseng whole genome (http://ginsengdb.snu.ac.kr/index.php).
Supplementary files format and content: 4_genes_fpkm_expression.xlsx: Excel file includes counts and FPKM values for each Sample.

organism: Panax ginseng

source_name: leaf

growth_protocol: The ginseng were grown in soil under a microbe free climate chamber with the 10 h light and 14 h dark. The plants were watered once a week and kept growing for about 2 years.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. 10ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The Colletotrichum panacicola were grown in PDA (200 g potato, 20 g glucose, 20 g agar and 1 L water) plate to produce the conidia spores. For incubation, the plant leaves were spray infected with 1*10^6 spores mL-1. The buffer without any spores were sprayed as untreated control (CK). All leaves were harvested at 14hours and 24 hours and frozen at -80℃ for RNA sequencing.

value: leaf

value: 2 years

value: wildtype


title: Colletotrichum panacicola treated for 24h, rep2

description:
CP_24h2
2-year-old ginseng plant
Colletotrichum panacicola treated sample 24h- 2


title: CMe-dt-517

value: mdt

value: Embryonic day 14.5


title: CR-vco-517

value: RPE

value: vco


title: Colletotrichum panacicola treated for 24h, rep1

description:
CP_24h1
2-year-old ginseng plant
Colletotrichum panacicola treated sample 24h- 1


title: Colletotrichum panacicola treated for 14h, rep2

description:
CP_14h2
2-year-old ginseng plant
Colletotrichum panacicola treated sample 14h- 2


title: Colletotrichum panacicola treated for 14h, rep3

description:
CP_14h3
2-year-old ginseng plant
Colletotrichum panacicola treated sample 14h- 3


title: CR-vct-517

value: vct


title: PERU3020


title: Colletotrichum panacicola treated for 14h, rep1

description:
CP_14h1
2-year-old ginseng plant
Colletotrichum panacicola treated sample 14h- 1


title: CK, rep3

description:
CK3
2-year-old ginseng plant
Uninfected control samples replicate 3

value: control


title: CR-vo-517

value: vo


title: CK, rep2

description:
CK2
2-year-old ginseng plant
Uninfected control samples replicate 2


title: CR-vt-517

value: vt


title: CK, rep1

description:
CK1
2-year-old ginseng plant
Uninfected control samples replicate 1


title: CR-dco-517

value: dco


title: 1-3_Plus_DOX1

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

data_processing:
Reads were aligned and mapped to reference genome hg38 using STAR 2.7.3a
Peaks from bigwig flies were visualized using IGV
TPM values were calculated using DESeq2
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Human Ewing Sarcoma cell line TC-71( DSMZ-German collection) was cultured in complete RPMI medium (Hyclone; #SH30027.02) with 10% fetal bovine serum (Gibco; #10437-028), 10 mM HEPES (Hyclone; #SH30237.01), 1 mM each of sodium pyruvate (Corning; #25-000-CI), nonessential amino acids (Hyclone; #SH30238.01), and L-glutamine (Gibco; #25030-081), 50 μM 2-ME (Gibco; #21985-023), and 1% penicillin/ streptomycin (#15140-122; Gibco).

extract_protocol:
Total RNA was isolated using Qiagen RNeasy RNA extraction kit (#74104) and further cleaned using the RNeasy PowerClean Pro Cleanup kit (#13997-50), as per manufacturer’s protocols. The purity of RNA was assessed on a Bioanalyzer in the UNMC Next Generation Sequencing Facility.
1 µg of cleaned RNA samples were used to generate RNA-seq libraries using the TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer's protocols and sequenced using the 2 x 75 bases paired-end protocol on a NextSeq550 instrument (Illumina).

treatment_protocol: TC71 cells engineered with shNTC and shEHD1 lentivirus were treated with doxycycline(0.5 ug/ml) for 3 days.

tag: shRNA


title: 1-3_Plus_DOX3


title: 1-3_Plus_DOX2


title: NTC_Plus_DOX2

value: shNTC+dox


title: Blood, Case8

city: Zhengzhou

first: yong

last: qi

state: Henan

address: Weiwu Road

department: Department of Respiratory and Critical Care Medicine

institute: Henan Provincial People’s Hospital

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using an Illumina iScan

data_processing: ChAMP package. The average beta values of the 16 samples were normalized corrected using BMIQ (beta-mixture quantile normalization).

extract_protocol: Whole blood samples from 8 subjects before and after smoking cessation intervention were collected to extract genomic DNA.

tag: individual

value: subject 8

tag: smoking status

value: short-term smoking cessation

value: whole blood


title: NTC_Plus_DOX1


title: CR-dct-517

value: dct


title: Blood, Case7

value: subject 7


title: CR-do-517

value: do


title: Gut-STAT3ko-PD-1ko-to-WT-CD8-2-β

city: Duarte

first: Defu

last: Zeng

state: CA

address: 1500 E Duarte Rd

department: Immunology & Theranostics

institute: City of Hope National Medical Center

data_processing:
Reads were aligned to mouse TRA and TRB reference (NG_007044.1 and NG_006980.1) using miXCR v2.1 with default settings.
Clone assembly and extraction were also done using miXCR v2.1 with default settings
Assembly: mouse mm10
Supplementary files format and content: text delimited text files containing the TRA and TRB clones

source_name: Gut

growth_protocol: Lethally irradiated WT BALB/c recipients were given TCD-BM cells (5 x 106) from WT C57BL/6 donors with  WT , STAT3-/-, or STAT3-/-PD-1-/- CD90.2+ T cells (1 x 106)  from C57BL/6 donors on day 0

extract_protocol:
RNA from equal numbers of sorted H-2Kb+TCRβ+CD4+ and H-2Kb+TCRβ+CD8+ cells were extracted with the RNeasy Mini Kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
TCR-CDR3 libraries were prepared using Takara Smarter Mouse TCR a/b Profiling kit following manufacturer's recommendations

treatment_protocol: On day 6 after HCT, lymphocytes from liver and gut were isolated, each sample represents lymphocytes combine from 3 recipients.Then sorted H-2Kb+TCRβ+CD4+ and H-2Kb+TCRβ+CD8+ cells for RNA extract.

value: Gut

tag: tcr

value: TCR-[beta]

value: CD8 T cell

value: hematopoietic cell transplantation

tag: time

value: Day 6 after HCT


title: Blood, Case4

value: subject 4


title: NTC_Plus_DOX3


title: DRG_Tumor

type: RNA

city: Suita

first: Kenji

last: Hata

state: Osaka

address: 1-8 Yamadaoka

department: Biochemistry

institute: Osaka University graduate school of dentistry

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label: biotin

organism: Rattus norvegicus

source_name: dorsal root ganglion(DRG)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

extract_protocol: Rat pulmonary carcinoma cells (IP-B12) which show osteolytic tumor growth in bone marrow were inoculated into the bone marrow cavity of the right tibiae in rat under general anesthesia. DRGs were collected from rat followed by the isolation of RNA using NucleoSpin RNA Plus. DRGs of left tibia were used as control.

value: dorsal root ganglion

tag: disease

value: Tumor


title: CR-dt-517

value: RPE

value: dt

value: Embryonic day 14.5


title: Liver, high-fat-diet with heat-moisture treatment sample,bio rep4

city: Tokyo

first: Sihui

last: Ma

address: Yayoi 1-1-1

institute: The university of Tokyo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genom 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After washing and staining, array scanning was performed using GeneChip Hybridization and Affymetrix Gene Array Scanner 3000

data_processing: The data were analyzed with R using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Liver, high-fat-diet with heat-moisture treatment condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: 29 Male Wistar rats (5-week-old) were purchased from Charles River Japan (Kanagawa, Japan) and kept in a room maintained at 22 ± 2°C with a relative humidity of 40–60% and a 12 h light (8:00–20:00) and 12 h darkness (20:00–8:00) cycle. The ani-mals were allowed free access to water and food throughout the experiments.

extract_protocol: Total RNA was isolated from homogenized liver tissue using the Nucleo-Spin®RNA (Takara Bio, Shiga, Japan) according to the manufacturer’s instructions. The total RNA concentration was measured using a NanoDrop® spectrophotometer (ND-1000, NanoDrop, DE, USA). The quality of the RNA was determined by assessing the A260/280 and A260/230 ratios and agarose gel electrophoresis.

treatment_protocol: Then the rats were randomly divided into four groups with the same average weight with three kinds of diets: a control diet (CON) and a high fat diet (HFD), whose car-bohydrate contents are rice flours obtained from low-amylose Koshihikari rice species, without HMT (CON, n = 10 and HFD, n = 10); an HFD, whose carbohydrate content is rice flour obtained from high-amylose Koshinokaori rice species, with HMT (HMT-HFD, n = 10).

value: Liver

value: High-fat-diet with heat-moisture treatment


title: Gut-WT-to-WT-CD8-2-β

value: WT


title: FMe-vco-569

data_processing:
Sequencing quality of raw sequencing data was evaluated by fastp (Chen et al., 2018).
Reads were mapped to the mm10 genome assemblies by HISAT2 (Pertea et al., 2016) using default settings. Mapping ratio was calculated based on the number of mapped reads and total reads for each sample.
All mapped reads were processed by StringTie (Pertea et al., 2016) to quantify gene expression levels (measured by FPKM, Fragment Per Kilobase per Million mapped reads respectively) using default parameters.
Assembly: mm10/GRCm38.91
Supplementary files format and content: tab-delimited text files include log10(FPKM+1) values for each samples

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using Vayzme TD503 DNA sample preparation kit

value: Mes

value: mvco

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)


title: DRG_Cont

value: control


title: Blood, Case6

value: subject 6

value: short-term smoking cessation

value: whole blood


title: FMe-vct-569

value: mvct


title: Br 86

city: Morgantown

first: Dajie

last: Luo

state: West Virginia

address: P.O. Box 9300 Room 2816 HSS

institute: West Virginia University

description: Raw data in Block 13-18 of 2010-10-05_14223523_550PMT_532.txt

hyb_protocol: Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Tag RNA labeling Kit manual.

scan_protocol: The microarrays were scanned on an Axon Genepix 4000B scanner, and data was extracted from images using GenePix V4.1 software.

data_processing: The raw data were preprocessed and then re-scaled by quantile normalization using R V2.12.0 software.  We employed SAM t test to select genes, which were then used for classifiers of cancer and normal samples using 'siggenes' package V1.24.0 in R.

source_name: breast cancer

label_protocol: The samples were DNAse digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).

growth_protocol: Patient tissue samples were procured from the West Virginia University Tissue Bank and the Cooperative Human Tissue Network and were stored at -80oC.

extract_protocol: Total RNA was isolated from all samples using the mirVana miRNA Isoloation Kit, following the manufacture's protocol (Ambion, Austin, TX). Breifly, a guanidinium thiocyanate-based lysis buffer to release the RNA from the cells while deactivating nucleases. An acid-phenol chloroform solution was then used to separate the RNA from other biomolecules. Then, a solid-phase extraction step was performed, using a glass fiber column, to further purify the RNA.

treatment_protocol: Patient samples include snap frozen tumor tissue samples as well as snap frozen normal tissue samples.

tag: ajcc stage

tag: samples of same patient (patient id)

value: Br 86

tag: age

tag: histology

tag: tumor grade


title: Gut-STAT3ko-PD-1ko-to-WT-CD8-1-β

tag: tissue

value: Gut

value: TCR-[beta]

tag: cell type

value: CD8 T cell

tag: genotype

tag: treatment

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: Gut-STAT3ko-to-WT-CD8-2-β


title: Liver, high-fat-diet with heat-moisture treatment sample,bio rep3

value: Liver


title: Liver, high-fat-diet with heat-moisture treatment sample,bio rep2

value: High-fat-diet with heat-moisture treatment


title: Blood, Case5

value: subject 5


title: Liver, high-fat-diet with heat-moisture treatment sample,bio rep1


title: Br 78

description: Raw data in Block 1-6 of 2010-10-14_14240387_550PMT_532_REDIP.txt

value: Br 78

value: Invasive lobular carcinoma


title: Br 77

description: Raw data in Block 19-24 of 2010-10-14_14240386_550PMT_532_REDIP.txt

value: normal

value: Normal Tissue


title: Br 83

description: Raw data in Block 7-12 of 2010-10-14_14240387_550PMT_532_REDIP.txt

value: Br 83

value: Invasive ductal carcinoma


title: Blood, Case1

value: subject 1

value: short-term smoking cessation

value: whole blood


title: Blood, Case3

value: subject 3


title: Br 76

description: Raw data in Block 13-18 of 2010-10-07_14223529_550PMT_532.txt


title: FMe-vo-569

city: Guangzhou

first: Cui

last: Guizhong

institute: Guangzhou Laboratory

value: Mes

value: mvo

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)

value: Embryonic day 14.5


title: FMe-vt-569

value: mvt


title: Gut-STAT3ko-to-WT-CD8-1-β

value: Gut

value: TCR-[beta]

value: CD8 T cell

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: B70

description: Raw data in Block 7-12 of 2010-10-05_14223522_550PMT_532.txt


title: Liver, high-fat-diet sample,bio rep3

source_name: Liver, high-fat-diet-fed condition

value: Liver

value: High-fat-diet


title: Liver, high-fat-diet sample,bio rep4


title: Gut-WT-to-WT-CD8-1-β

value: WT


title: Gut-STAT3ko-to-WT-CD4-2-β

value: CD4 T cell


title: Gut-STAT3ko-PD-1ko-to-WT-CD4-2-β


title: FMe-dco-569

value: mdco


title: Blood, Control6

value: subject 6

value: before short-term smoking cessation

value: whole blood


title: FMe-dct-569

value: Mes

value: mdct


title: Liver, high-fat-diet sample,bio rep2


title: Blood, Control4

value: subject 4


title: Blood, Case2

value: subject 2

value: short-term smoking cessation


title: B61

description: Raw data in Block 19-24 of 2010-10-05_14223521_550PMT_532.txt

value: Invasive ductal carcinoma


title: Liver, high-fat-diet sample,bio rep1


title: B63

description: Raw data in Block 1-6 of 2010-10-05_14223522_550PMT_532.txt


title: FMe-do-569

value: mdo

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)

value: Embryonic day 14.5


title: FR-vco-569

value: RPE

value: vco


title: B55

description: Raw data in Block 13-18 of 2010-10-05_14223521_550PMT_532.txt


title: FMe-dt-569

value: mdt


title: Gut-STAT3ko-to-WT-CD4-1-β

value: Gut

value: TCR-[beta]

value: CD4 T cell

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: Gut-STAT3ko-PD-1ko-to-WT-CD4-1-β


title: Liver, control sample,bio rep4

source_name: Liver, control condition

value: Liver

value: CONTROL


title: Gut-WT-to-WT-CD4-1-β

value: WT


title: Liver, control sample,bio rep2


title: Blood, Control7

value: subject 7

value: before short-term smoking cessation

value: whole blood


title: Gut-WT-to-WT-CD4-2-β


title: Blood, Control2

value: subject 2


title: Blood, Control5

value: subject 5


title: B54

description: Raw data in Block 1-6 of 2010-10-05_14223521_550PMT_532.txt

value: Invasive ductal carcinoma


title: FR-vct-569

value: RPE

value: vct

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)

value: Embryonic day 14.5


title: Liver, control sample,bio rep3


title: B9

description: Raw data in Block 7-12 of 2010-10-05_14223521_550PMT_532.txt


title: Blood, Control1

value: subject 1


title: Liver, control sample,bio rep1


title: Liver-STAT3ko-PD-1ko-to-WT-CD8-2-β

source_name: Liver

value: TCR-[beta]

value: CD8 T cell


title: NR.3

data_processing:
Illumina bcl2fastq was used to convert bcl to fastq files
Sequencing reads were aligned to the mouse (GRCm39) reference and quantified using salmon (v2.5.1) with default settings.
differential analysis performed with DESeq2
Assembly: GRCm39

extract_protocol:
RNA was prepared from cultured tumor cells or sorted cells using the or RNeasy Mini Kit (Qiagen) according to manufacturer's protocol,
Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. Libraries were constructed by Novogene (Beijing, China)

value: pancreatic cancer cells

value: wildtype


title: FR-vo-569

value: vo


title: Blood, Control8

value: subject 8


title: Blood, Control3

value: subject 3


title: Liver-STAT3ko-to-WT-CD8-2-β

value: Liver

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: Bn76

description: Raw data in Block 13-18 of 2010-10-14_14240386_550PMT_532_REDIP.txt

value: normal

value: Normal Tissue


title: FR-vt-569

value: RPE

value: vt


title: Bn75

description: Raw data in Block 1-6 of 2010-10-07_14223529_550PMT_532.txt


title: FR-dco-569

value: dco

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)


title: Liver-WT-to-WT-CD8-2-β

value: WT


title: NR.2


title: FR-dct-569

value: dct

value: Embryonic day 14.5


title: Liver-STAT3ko-PD-1ko-to-WT-CD8-1-β

value: TCR-[beta]

value: CD8 T cell


title: NR.1

value: pancreatic cancer cells

value: wildtype


title: Bn39

description: Raw data in Block 1-6 of 2010-10-05_14223520_550PMT_532.txt


title: FR-do-569

value: do


title: parental.ZS.OT1.2

value: Zeb1/Snail overexpression

value: OT1 co-culture


title: Liver-STAT3ko-to-WT-CD8-1-β

value: Liver

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: FMe-vco-563

source_name: Mes

value: Mes

value: mvco


title: FR-dt-569

source_name: RPE

value: RPE

value: dt


title: parental.EV.OT1.2


title: Liver-STAT3ko-PD-1ko-to-WT-CD4-2-β

value: CD4 T cell


title: Liver-WT-to-WT-CD8-1-β

value: WT


title: Bn70

description: Raw data in Block 7-12 of 2010-10-05_14223520_550PMT_532.txt

value: normal

value: Normal Tissue


title: FMe-vct-563

value: mvct

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)

value: Embryonic day 14.5


title: parental.EV.OT1.1

value: pancreatic cancer cells

value: wildtype


title: Liver-STAT3ko-to-WT-CD4-2-β

value: TCR-[beta]


title: Liver-WT-to-WT-CD4-2-β

value: Liver


title: FMe-vo-563

value: mvo


title: escape7.OT1.2

value: OT1 co-culture


title: B52

description: Raw data in Block 7-12 of 2010-10-05_14223519_550PMT_5um_0532.txt

value: Invasive ductal carcinoma


title: B53

description: Raw data in Block 13-18 of 2010-10-05_14223519_550PMT_5um_0532.txt


title: B51

description: Raw data in Block 1-6 of 2010-10-05_14223519_550PMT_5um_0532.txt


title: B50

description: Raw data in Block 19-24 of 2010-10-05_14223518_550PMT_5um_0532.txt


title: escape7.OT1.1


title: B49

description: Raw data in Block 13-18 of 2010-10-05_14223518_550PMT_5um_0532.txt


title: FMe-vt-563

value: Mes

value: mvt


title: Bn38

description: Raw data in Block 19-24 of 2010-10-05_14223519_550PMT_5um_0532.txt


title: Liver-STAT3ko-to-WT-CD4-1-β

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: FMe-dco-563

value: mdco


title: B48

description: Raw data in Block 7-12 of 2010-10-05_14223518_550PMT_5um_0532.txt


title: escape3.OT1.2


title: FMe-dct-563

value: mdct


title: escape3.OT1.1


title: parental.ZS.OT.1

value: Zeb1/Snail overexpression


title: Liver-WT-to-WT-CD4-1-β

value: CD4 T cell

value: WT


title: B47

description: Raw data in Block 1-6 of 2010-10-05_14223518_550PMT_5um_0532.txt


title: FMe-do-563

value: mdo

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)

value: Embryonic day 14.5


title: STAT3ko-PD-1ko-Naive-CD8-β

source_name: Spleen

value: Spleen

value: TCR-[beta]

value: CD8 T cell

value: before HCT


title: escape2.OT1.2

value: pancreatic cancer cells

value: wildtype

value: OT1 co-culture


title: FMe-dt-563

value: Mes

value: mdt


title: Liver-STAT3ko-PD-1ko-to-WT-CD4-1-β

value: Liver

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: STAT3ko-Naive-CD8-β


title: FR-vco-563

value: RPE

value: vco


title: WT-Naïve-CD8-β

value: WT


title: FR-vct-563

value: vct

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)


title: B45

description: Raw data in Block 13-18 of 2010-10-02_14223516_550PMT_0532.txt

value: Mucinous carcinoma


title: escape1.OT1.1


title: FR-vo-563

value: vo

value: Embryonic day 14.5


title: STAT3ko-PD-1ko-Naive-CD4-β

value: Spleen

value: TCR-[beta]

value: CD4 T cell

value: before HCT


title: B41

description: Raw data in Block 1-6 of 2010-10-02_14223516_550PMT_0532.txt

value: Invasive ductal carcinoma


title: parental.OT1.3

value: pancreatic cancer cells

value: wildtype

value: OT1 co-culture


title: FR-vt-563

value: vt


title: escape1.OT1.2


title: WT-Naïve-CD4-β


title: B39

description: Raw data in Block 19-24 of 2010-10-02_14223515_550PMT_0532.txt


title: escape2.OT1.1


title: Gut-STAT3ko-PD-1-ko-to-WT-CD8-2-α

value: Gut

value: TCR-[alpha]

value: CD8 T cell

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: parental.OT1.1


title: B46

description: Raw data in Block 19-24 of 2010-10-02_14223516_550PMT_0532.txt

value: In Situ carcinoma


title: escape2.steadystate.3


title: Gut-STAT3ko-to-WT-CD8-2-α


title: FR-do-563

value: RPE

value: do

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)


title: B36

description: Raw data in Block 1-6 of 2010-10-02_14223515_550PMT_0532.txt

value: Ductal Adenocarcinoma


title: B43

description: Raw data in Block 7-12 of 2010-10-02_14223516_550PMT_0532.txt

value: Predominantly Lobular


title: B34

description: Raw data in Block 19-24 of 2010-10-02_14223513_550PMT_0532.txt


title: escape2.steadystate.2


title: Gut-WT-to-WT-CD8-2-α

value: WT


title: FR-dt-563

value: dt

value: Embryonic day 14.5


title: STAT3ko-Naive-CD4-β

value: Spleen

value: TCR-[beta]

value: CD4 T cell

value: before HCT


title: B32

description: Raw data in Block 13-18 of 2010-10-02_14223513_550PMT_0532.txt

value: Invasive ductal carcinoma


title: Gut-STAT3ko-PD-1-ko-to-WT-CD8-1-α

value: Gut

value: TCR-[alpha]

value: CD8 T cell


title: parental.OT1.2

value: pancreatic cancer cells

value: wildtype

value: OT1 co-culture


title: Gut-STAT3ko-to-WT-CD8-1-α

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: escape2.steadystate.1


title: B30

description: Raw data in Block 7-12 of 2010-10-02_14223513_550PMT_0532.txt

value: Invasive lobular carcinoma


title: B38

description: Raw data in Block 13-18 of 2010-10-02_14223515_550PMT_0532.txt


title: CMe-vct-564

value: Mes

value: mvct

value: BAF155f/f; BAF170f/f


title: FR-dco-563

value: RPE

value: dco

value: BAF155f/f; BAF170f/f; DCT-Cre (FcKO)

value: Embryonic day 14.5


title: Gut-WT-to-WT-CD8-1-α

value: WT


title: escape1.steadystate.3


title: escape1.steadystate.2


title: B37

description: Raw data in Block 7-12 of 2010-10-02_14223515_550PMT_0532.txt

value: Invasive ductal carcinoma


title: B29

description: Raw data in Block 1-6 of 2010-10-02_14223513_550PMT_0532.txt


title: FR-dct-563

value: dct


title: CMe-vo-564

value: mvo


title: B28

description: Raw data in Block 19-24 of 2010-10-02_14223512_550PMT_0532.txt


title: Gut-STAT3ko-PD-1-ko-to-WT-CD4-2-α

value: Gut

value: TCR-[alpha]

value: CD4 T cell


title: escape1.steadystate.1

value: pancreatic cancer cells

value: wildtype


title: CMe-vt-564

value: mvt


title: Gut-STAT3ko-to-WT-CD4-2-α

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: B27

description: Raw data in Block 13-18 of 2010-10-02_14223512_550PMT_0532.txt


title: CMe-dco-564

value: Mes

value: mdco

value: BAF155f/f; BAF170f/f


title: parental.steadystate.3


title: B24

description: Raw data in Block 7-12 of 2010-10-02_14223512_550PMT_0532.txt


title: parental.steadystate.2


title: CMe-vco-564

value: mvco


title: Gut-STAT3ko-PD-1-ko-to-WT-CD4-1-α


title: CMe-dct-564

value: mdct

value: Embryonic day 14.5


title: parental.steadystate.1


title: Gut-STAT3ko-to-WT-CD4-1-α


title: B22

description: Raw data in Block 1-6 of 2010-10-02_14223512_550PMT_0532.txt

value: Invasive ductal carcinoma


title: CMe-do-564

value: mdo


title: B21

description: Raw data in Block 19-24 of 2010-10-02_14223511_550PMT_0532.txt


title: human cervical epidermoid carcinoma cells, shVPS13C_3

city: Wuhan

first: xiangyu

last: Tan

state: Hubei

address: 1095 Jiefang Avenue

department: Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
For analysis of RNA-Seq data, the DEGseq software package was used to identify the differentially expressed genes (DEGs) and DEGs were defined as | log2 (fold change) | >1 and Q value <0.05.. KEGG pathway analysis and gene set enrichment analysis (GSEA) were conducted with the Dr. Tom program.
Assembly: hg38

source_name: SiHa

growth_protocol: SiHa cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) and 100 U/ml penicillin and streptomycin (Invitrogen) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the tissues using TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Subsequently, total RNA was qualified and quantified using a NanoDrop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
The final library was amplified with phi29 to make DNA nanoballs (DNBs), which had more than 300 copies of one molecule. DNBs were loaded into the patterned nanoarray, and single-end 50-base reads were generated on the DNBSEQ platform (BGI-Shenzhen, China).

treatment_protocol: The cells were treated with 20μM cisplatin for 48h.

tag: cell line

value: SiHa

value: cervical epidermal cancer cells

value: VPS13C knockdown

value: treated with cisplatin


title: Gut-WT-to-WT-CD4-1-α

value: Gut

value: TCR-[alpha]

value: CD4 T cell

value: WT


title: CMe-dt-564

address: 188 KaiYuan Road, Huangpu District

value: mdt


title: Liver-STAT3ko-PD-1-ko-to-WT-CD8-2-α

value: Liver

value: CD8 T cell

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: human cervical epidermoid carcinoma cells, shVPS13C_2


title: human cervical epidermoid carcinoma cells, shVPS13C_1


title: Liver-STAT3ko-to-WT-CD8-2-α


title: CR-vco-564

value: RPE

value: vco

value: BAF155f/f; BAF170f/f


title: B19

description: Raw data in Block 13-18 of 2010-10-02_14223511_550PMT_0532.txt

value: Invasive ductal carcinoma


title: B18

description: Raw data in Block 7-12 of 2010-10-02_14223511_550PMT_0532.txt


title: CR-vct-564

value: vct

value: Embryonic day 14.5


title: B16

description: Raw data in Block 1-6 of 2010-10-02_14223511_550PMT_0532.txt


title: human cervical epidermoid carcinoma cells, shcontrol_3

value: SiHa

value: cervical epidermal cancer cells

value: control


title: Liver-WT-to-WT-CD8-2-α

value: TCR-[alpha]


title: Gut-WT-to-WT-CD4-2-α

value: Gut

value: CD4 T cell


title: B12

description: Raw data in Block 19-24 of 2010-10-02_14223510_550PMT_0532.txt

value: normal

value: Normal Tissue


title: human cervical epidermoid carcinoma cells, shcontrol_2

value: treated with cisplatin


title: CR-vo-564

value: vo


title: CR-vt-564

value: vt


title: Liver-STAT3ko-PD-1-ko-to-WT-CD8-1-α

value: Liver

value: CD8 T cell

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: CR-dco-564

value: RPE

value: dco

value: BAF155f/f; BAF170f/f


title: human cervical epidermoid carcinoma cells, shcontrol_1

value: SiHa

value: cervical epidermal cancer cells


title: Liver-STAT3ko-to-WT-CD8-1-α

value: TCR-[alpha]


title: CR-dct-564

value: dct

value: Embryonic day 14.5


title: CR-do-564

value: do


title: Liver-WT-to-WT-CD8-1-α

value: WT


title: B10

description: Raw data in Block 7-12 of 2010-10-14_14240386_550PMT_532_REDIP.txt

value: Invasive ductal carcinoma


title: B8

description: Raw data in Block 7-12 of 2010-10-02_14223510_550PMT_0532.txt


title: CR-dt-564

value: dt


title: B5

description: Raw data in Block 19-24 of 2010-10-02_14223509_550PMT_0532.txt

value: Spindle Cell Sarcoma


title: B7

description: Raw data in Block 1-6 of 2010-10-02_14223510_550PMT_0532.txt

value: Metaplastic carcinoma


title: human cervical epidermoid carcinoma cells ,sgVPS13C_1

growth_protocol: ME180 cells were maintained in McCoy's 5A supplemented with 10% fetal bovine serum(FBS) and 100 U/ml penicillin and streptomycin (Invitrogen) in humidified atmosphere with 5% CO2 at 37℃

treatment_protocol: The cells were treated with 2μM cisplatin for 48h.

value: Retinal metastasis of epidermoid carcinoma of cervix

value: VPS13C knockout

value: treated with cisplatin


title: B4

description: Raw data in Block 13-18 of 2010-10-02_14223509_550PMT_0532.txt


title: human cervical epidermoid carcinoma cells ,vector_3

value: vector


title: human cervical epidermoid carcinoma cells ,sgVPS13C_3


title: Liver-WT-to-WT-CD4-2-α

value: Liver

value: CD4 T cell

value: hematopoietic cell transplantation

value: Day 6 after HCT


title: human cervical epidermoid carcinoma cells ,sgVPS13C_2


title: human cervical epidermoid carcinoma cells ,vector_2


title: Bulk RNAseq, Whole Mouse Brain, Ref004

city: Los Angeles

first: Hugo

middle: Jae Mun

last: Kim

address: 4760 Templeton St, Unit 3113

department: Neuroscience

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

description:
Patch-seq
Ref_004

data_processing:
The demultiplexing, barcoded processing, gene counting and STAR aligner was used to align the sample.
Assembly: mm22
Supplementary files format and content: Tap delimited expression table and phenotype table

source_name: Brain

extract_protocol:
The mice are sacrificed under perfusion of sucrose cutting solution, bubbling. The brain was sliced in 200-300um by viubratome, bubbling with CO2/O2. Tissue were recovered in the recovery chamber, bubbling. Using Patch Clamp approach, I generated giga-seal and extract the cell contents to the ppet. Then I freeze the cell in liquid nitrogen until the library prep
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
We amplified RNA using modified aRNA protocol for 2 cycles, followed by illumina Truseq mRNA prep.

treatment_protocol: At 8 weeks, I injected AAV-retro-cre to spinal cord, after 4 weeks, I apply spinal cord Injury, dorsal hemisection above the injection site. After 6 weeks, I injected AAV-retro-GFP to the 500um below the injury.  site.

value: Motor Cortex

value: Brain

tag: strain

value: PTEN SOCS3 tdTomato

value: 26 weeks old


title: Liver-STAT3ko-PD-1-ko-to-WT-CD4-1-α

value: TCR-[alpha]


title: human cervical epidermoid carcinoma cells ,vector_1


title: B3

description: Raw data in Block 7-12 of 2010-10-02_14223509_550PMT_0532.txt

value: Invasive ductal carcinoma


title: Liver-STAT3ko-to-WT-CD4-1-α


title: Bulk RNAseq, Whole Mouse Brain, Ref002

description:
Patch-seq
Ref_002

value: 24 weeks old


title: Bulk RNAseq, Whole Mouse Brain, Ref003

description:
Patch-seq
Ref_003

value: 25 weeks old


title: B2

description: Raw data in Block 1-6 of 2010-10-02_14223509_550PMT_0532.txt


title: genomic DNA from HeLa-EBSS-Rep3

city: Hangzhou

first: Liyuan

last: Zhu

address: NO.3, Qingchun Road, Shangcheng District

institute: Zhejiang University

description:
HeLa-EBSS-Rep3
AllNormMethyl.anno-12 samples.txt

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850K Beadchip using standard Illumina protocol

data_processing:
BeadStudio software v3.2
matrix processed value definition: Average Beta

source_name: Cervical carcinoma cell

extract_protocol: Total DNA from SGC7901 and SGC-R cells with corresponding treatment as indicated was extracted using TIANamp Genomic DNA Kit Extraction, quantified (>50ng/μL) and fullfilled Quality Inspection (OD260/280=1.8-2.0 & OD260/280>2.0).

tag: cell line background

value: HeLa

value: Cervical carcinoma cell

tag: disease state

value: Cancer

value: EBSS


title: B1

description: Raw data in Block 19-24 of 2010-10-02_14223508_550PMT_0532.txt


title: Bulk RNAseq, Whole Mouse Brain, Ref001

description:
Patch-seq
Ref_001

value: 23 weeks old


title: Liver-STAT3ko-PD-1-ko-to-WT-CD4-2-α

value: Liver


title: genomic DNA from HeLa-EBSS-Rep2

description:
HeLa-EBSS-Rep2
AllNormMethyl.anno-12 samples.txt


title: Liver-STAT3ko-to-WT-CD4-2-α

value: CD4 T cell


title: STAT3ko-PD-1-ko-Naive-CD8-α

value: Spleen

value: CD8 T cell

value: before HCT


title: sc-Patch-seq,Red only,Regenerating CSMN203

description:
Patch-seq
NoRegen_CSMN_203

value: Cortical Spinal Motor Neuron

value: Brain

value: 22 weeks old


title: EtOH_IP

city: shenyang

first: Ruina

last: Luan

state: Liaoning

address: shenbei district

institute: china medical university

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the human genome hg38 assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Assembly: hg38
Supplementary files format and content: bw files were generated using python

source_name: Breast

extract_protocol:
Primary analyze of ChIP-seq: The threshold of the number of the valid peak was selected within a false discovery rate (FDR) of 0.01. We used the default parameters from HOMER to distinguish genomic distribution, while promoter peaks were defined as those with peak center falling between 100 bp downstream and 5,000 bp upstream of transcript start sites (TSS). Exon, intron, and transcript terminate site (TTS) regions were exported from the National Center for Biological Information (NCBI), and the other regions were suggested as intergenic regions. To define meaningful MYSM1 binding sites, we defined the fold enrichment of a peak was larger than 2 in IP versus input and the fold change (FC) of tag density was considered at least p<10e-5.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Breast

value: human breast cancer cell

tag: agent

value: EtOH


title: genomic DNA from HeLa-EBSS-Rep1

description:
HeLa-EBSS-Rep1
AllNormMethyl.anno-12 samples.txt


title: EtOH_Input


title: genomic DNA from HeLa-Con-Rep3

description:
HeLa-Con-Rep3
AllNormMethyl.anno-12 samples.txt

value: Con


title: STAT3ko-Naïve-CD8-α

tag: tcr

value: TCR-[alpha]


title: E2_Input


title: Liver-WT-to-WT-CD4-1-α

value: WT

value: hematopoietic cell transplantation

tag: time

value: Day 6 after HCT


title: WT-Naïve-CD8-α


title: genomic DNA from HeLa-Con-Rep2

description:
HeLa-Con-Rep2
AllNormMethyl.anno-12 samples.txt

value: HeLa

value: Cervical carcinoma cell

value: Cancer


title: genomic DNA from HeLa-Con-Rep1

description:
HeLa-Con-Rep1
AllNormMethyl.anno-12 samples.txt


title: vHC_2699_Pop5

city: Atlanta

first: Weirong

last: Chen

state: GA

address: 615 Michael Street

department: School of Medicine

institute: Emory University

data_processing:
Raw fastq files were mapped to the human genome using TopHat2 v.2.0.13 with the hg19 version and the UCSC KnownGene reference transcriptome.
All duplicate reads were excluded with PICARD v.1.127, followed by quantification with Partek Flow Genomics Suite (Partek Inc.) using the union model in HTSeq with the default setting, and library-size normalization using the DESeq2 with default parameters.
Differential gene expression analysis was determined with a generalized linear effect model.
For disease differences covariates included cell type and patients; for cell type differences covariates included disease status and patients. Genes with at least a two-fold change and an FDR value < 0.05 among comparison were considered significant and termed as differentially expressed genes (DEGs).
Quantile normalized RPKM values were used in the heat maps and z-score values were plotted for genes visualization.
Supplementary files format and content: Tab delimited text file include RPKM values for each sample

source_name: Peripheral Blood

extract_protocol:
Populations including Pop 2 (CD19+ CD138-), Pop 3 (CD19+ CD138+), Pop 5 (CD19- CD138+), and naïve B cells (CD19+ IgD+ CD27-), isolated from active SLE patients or influenza-vaccinated healthy subjects (vHC)were sorted directly into lysis buffer. RNA was isolated using the AllPrep DNA/RNA Mini kit (Qiagen) according to the manufacturer’s instruction.
Total RNA (50pg) was used as input for the ten cycles of PCR amplification by using SMART-seq v3 cDNA synthesis kit (Takara). Libraries were quantified by qPCR and size distribution was examined by Bioanalyer before pooling and sequencing

value: Peripheral Blood

tag: subject status

value: vHC

tag: subject id

tag: population


title: sc-Patch-seq,Red only,Regenerating CSMN202

description:
Patch-seq
NoRegen_CSMN_202

value: PTEN SOCS3 tdTomato

tag: age


title: sc-Patch-seq,Red only,Regenerating CSMN199

description:
Patch-seq
NoRegen_CSMN_199

value: Cortical Spinal Motor Neuron


title: vHC_2699_Pop3


title: E2_IP


title: sc-Patch-seq,Red only,Regenerating CSMN201

description:
Patch-seq
NoRegen_CSMN_201

value: Brain


title: STAT3ko-PD-1-ko-Naïve-CD4-α

value: Spleen

value: CD4 T cell

value: before HCT


title: vHC_2699_Pop2


title: sc-Patch-seq,Red only,Regenerating CSMN200

description:
Patch-seq
NoRegen_CSMN_200

value: 22 weeks old


title: genomic DNA from SGC7901-EBSS-Rep3

description:
SGC-EBSS-Rep3
all_sample_methylation_quatify-15 samples.txt

source_name: Gastric cancer cell

value: Gastric cancer cell

value: EBSS


title: genomic DNA from SGC7901-EBSS-Rep2

description:
SGC-EBSS-Rep2
all_sample_methylation_quatify-15 samples.txt


title: WT-Naïve-CD4-α

value: TCR-[alpha]

value: WT


title: sc-Patch-seq,Red only,Regenerating CSMN197

description:
Patch-seq
NoRegen_CSMN_197


title: vHC_2687_Pop5


title: genomic DNA from SGC7901-EBSS-Rep1

description:
SGC-EBSS-Rep1
all_sample_methylation_quatify-15 samples.txt


title: o/eRNase H1 CIN612 cells_2

city: Chicago

first: Conor

last: Templeton

address: 300 E Superior Street

institute: Northwestern University

description: DeSeq2 of RNaseH1-overexpressing CIN 612 cells compared to scrm CIN 612 cells

data_processing:
FastQC (version v0.11.8) was applied to check the quality of raw reads.
Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting.
STAR Aligner version 2.7.1a was used to align the reads.
Picard tools (version 2.20.4) was applied to mark duplicates of mapping.
The StringTie version 2.0.4 was used to assemble the RNA-Seq alignments into potential transcripts. The featureCounts (version 1.6.0)/HTSeq was used to count mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. The De-Seq2 (version 1.14.1) was used to do the differential analysis. The Gene Ontology Analysis was done using ClusterProfiler package in R.
Assembly: Hg18
Supplementary files format and content: The FastQ files remain in GZ format
Supplementary files format and content: The DeSeq2 files are in Microsoft excel comma separated values format

source_name: Cervical

growth_protocol: CIN 612 cells were maintained in E-media containing 10% FBS DMEM

extract_protocol:
RNA was extracted using an Rneasy mini plus kit (Qiagen).
RNAseq-PolyA technique was applied by Admera Biosciences. Briefly, PolyA+RNA was captured and then fragmented and primed for cDNA synthesis. Following cDNA synthesis, 3' ends were adenylated and 5' ends repaired. DNA sequencing adapters were ligated and the ligated fragments were PCR amplified.

value: Cervical

value: CIN612 cells

value: Keratinocytes

value: o/eRNase H1

value: Neomycin selection


title: o/eRNase H1 CIN612 cells


title: genomic DNA from SGC7901-Con-Rep3

description:
SGC-Con-Rep3
all_sample_methylation_quatify-15 samples.txt

value: Cancer

value: Con


title: vHC_2687_Pop3

value: Peripheral Blood

value: vHC


title: shRNase H1 Cin612 cells_2

description: DeSeq2 of RNaseH1-depleted CIN612 compared to scrm CIN 612 cells

value: shRNAse H1

value: Puromycin selection


title: genomic DNA from SGC7901-Con-Rep2

description:
SGC-Con-Rep2
all_sample_methylation_quatify-15 samples.txt


title: sc-Patch-seq,Red only,Regenerating CSMN195

description:
Patch-seq
NoRegen_CSMN_195

value: Cortical Spinal Motor Neuron

value: Brain

value: PTEN SOCS3 tdTomato


title: sc-Patch-seq,Red only,Regenerating CSMN196

description:
Patch-seq
NoRegen_CSMN_196

value: 22 weeks old


title: vHC_2687_Pop2


title: shRNase H1 CIN612 cells


title: STAT3ko-Naive-CD4-α

value: Spleen

value: TCR-[alpha]

value: CD4 T cell

value: before HCT


title: genomic DNA from SGC7901-Con-Rep1

description:
SGC-Con-Rep1
all_sample_methylation_quatify-15 samples.txt

value: Gastric cancer cell


title: vHC_2687_Naive

value: Naive


title: sc-Patch-seq,Red only,Regenerating CSMN193

description:
Patch-seq
NoRegen_CSMN_193


title: sc-Patch-seq,Red only,Regenerating CSMN198

description:
Patch-seq
NoRegen_CSMN_198


title: Scrm CIN612 cells_2

description:
DeSeq2 of RNaseH1-depleted CIN612 compared to scrm CIN 612 cells
DeSeq2 of RNaseH1-overexpressing CIN 612 cells compared to scrm CIN 612 cells

value: Cervical

value: CIN612 cells

value: Keratinocytes

value: Scrm control


title: genomic DNA from SGC7901/DDP siLinc00942#2-Rep3

description:
si942#2-Rep3
all_sample_methylation_quatify-15 samples.txt

source_name: DDP resistant GC cell

value: Cancer


title: Scrm CIN612 cells


title: genomic DNA from SGC7901/DDP siLinc00942#2-Rep2

description:
si942#2-Rep2
all_sample_methylation_quatify-15 samples.txt


title: sc-Patch-seq,Red only,Regenerating CSMN192

description:
Patch-seq
NoRegen_CSMN_192


title: vHC_2686_Pop3

value: Peripheral Blood

value: vHC


title: vHC_2699_Naive


title: genomic DNA from SGC7901/DDP siLinc00942#2-Rep1

description:
si942#2-Rep1
all_sample_methylation_quatify-15 samples.txt


title: vHC_2686_Pop2


title: OUD-_38

city: Orange

first: Janitza

middle: L

last: Montalvo-Ortiz

state: CT

address: 200 Edison Road

department: Psychiatry

institute: Yale School of Medicine; West Haven VA Medical Center, VA Connecticut Health Care

data_processing:
Mapping of sequencing reads to CRCh38 human genome and detection of converted and unconverted cytosines were conducted using the Bismark bisulfite read mapper.
Differential analysis was conducted using the methylkit R package
Assembly: Homo_sapiens.GRCh38.84.gtf
Supplementary files format and content: Comma delimited csv file includes the beta values (% unconverted cytosines) of methylation and hydroxymethylation sites for all samples

source_name: orbitofrontal cortex

extract_protocol:
Between 0.5-1 M NeuN+ nuclei were collected via FANS. DNA extraction were processed following the manufacturer’s protocol of the DNeasy Blood and Tissue Kit (Cat. #69504, Qiagen).
Two libraries were prepared for methylation and hydroxymethylation analysis. The first library (BS) underwent bisulfite treatment to convert unmethylated cytosines to uracils. The second library (oxBS) underwent oxidation prior to bisulfite sequencing to convert both unmethylated and hydroxymethylated cytosines to uracils.
Reduced Representation Oxidative Bisulfite Sequencing

treatment_protocol: Fluorescence-activated nuclear sorting (FANS) procedures were carried out at the Icahn School of Medicine Flow Cytometry CoRE using a BD 5-laser cell sorting system.

value: orbitofrontal cortex

value: neurons

tag: Sex

value: Male

tag: opioid use_disorder

value: OUD-

tag: age of_death

tag: ancestry

value: W

tag: pmi


title: OUD-_37

tag: tissue

tag: cell type


title: genomic DNA from SGC7901/DDP siLinc00942#1-Rep3

description:
si942#1-Rep3
all_sample_methylation_quatify-15 samples.txt

tag: genotype


title: vHC_2686_Naive


title: sc-Patch-seq,Red only,Regenerating CSMN190

description:
Patch-seq
NoRegen_CSMN_190

value: Cortical Spinal Motor Neuron

value: Brain

tag: strain

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: sc-Patch-seq,Red only,Regenerating CSMN189

description:
Patch-seq
NoRegen_CSMN_189


title: genomic DNA from SGC7901/DDP siLinc00942#1-Rep2

description:
si942#1-Rep2
all_sample_methylation_quatify-15 samples.txt

tag: cell line background

value: Gastric cancer cell

tag: disease state


title: OUD-_36


title: sc-Patch-seq,Red only,Regenerating CSMN194

description:
Patch-seq
NoRegen_CSMN_194


title: OUD-_35


title: genomic DNA from SGC7901/DDP siLinc00942#1-Rep1

description:
si942#1-Rep1
all_sample_methylation_quatify-15 samples.txt


title: sc-Patch-seq,Red only,Regenerating CSMN188

description:
Patch-seq
NoRegen_CSMN_188


title: vHC_2671_Pop5


title: genomic DNA from SGC7901/DDP siNC-Rep3

description:
siNC-Rep3
all_sample_methylation_quatify-15 samples.txt

value: siNC


title: vHC_2671_Pop3


title: vHC_2686_Pop5


title: OUD-_34

value: AA


title: sc-Patch-seq,Red only,Regenerating CSMN191

description:
Patch-seq
NoRegen_CSMN_191


title: sc-Patch-seq,Red only,Regenerating CSMN187

description:
Patch-seq
NoRegen_CSMN_187


title: genomic DNA from SGC7901/DDP siNC-Rep2

description:
siNC-Rep2
all_sample_methylation_quatify-15 samples.txt


title: sc-Patch-seq,Red only,Regenerating CSMN185

description:
Patch-seq
NoRegen_CSMN_185


title: OUD-_33


title: sc-Patch-seq,Red only,Regenerating CSMN186

description:
Patch-seq
NoRegen_CSMN_186


title: genomic DNA from SGC7901/DDP siNC-Rep1

description:
siNC-Rep1
all_sample_methylation_quatify-15 samples.txt


title: OUD-_32

value: CAUC


title: vHC_2670_Pop5


title: vHC_2671_Naive

value: Naive


title: OUD+_31

value: OUD+


title: genomic DNA from SGC7901/DDP-Rep3

description:
SD-Rep3
AllNormMethyl.anno-12 samples.txt

value: Cancer


title: sc-Patch-seq,Red only,Regenerating CSMN184

description:
Patch-seq
NoRegen_CSMN_184


title: sc-Patch-seq,Red only,Regenerating CSMN183

description:
Patch-seq
NoRegen_CSMN_183


title: vHC_2670_Pop3

value: Peripheral Blood

value: vHC


title: genomic DNA from SGC7901/DDP-Rep2

description:
SD-Rep2
AllNormMethyl.anno-12 samples.txt


title: vHC_2670_Pop2


title: OUD-_29

value: orbitofrontal cortex

value: neurons


title: vHC_2670_Naive


title: OUD+_28

value: Male


title: vHC_2669_Pop5


title: vHC_2671_Pop2


title: sc-Patch-seq,Red only,Regenerating CSMN181

description:
Patch-seq
NoRegen_CSMN_181


title: OUD-_27

value: OUD-


title: genomic DNA from SGC7901/DDP-Rep1

description:
SD-Rep1
AllNormMethyl.anno-12 samples.txt


title: sc-Patch-seq,Red only,Regenerating CSMN180

description:
Patch-seq
NoRegen_CSMN_180

value: Cortical Spinal Motor Neuron


title: vHC_2669_Pop2


title: genomic DNA from SGC7901-Rep2

description:
SGC-Rep2
AllNormMethyl.anno-12 samples.txt


title: Crohn's diesease biopsy, metastatic, replicate 2, fragment BC

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zürich

library_source: other

data_processing:
deMULTIplex (v1.0.2)
Assembly: GRCh38 v2020-A genecode, GRCm38 vM25, GFP 3'UTR
Supplementary files format and content: 3 UMI and 3 read count tables; gene-wise counts for exon, intron and exon+intron (.rds format)
Supplementary files format and content: UMI count matrix for MULTI-seq barcodes per cell; column "Barcode" contains the allocated MULTI-seq BC (.txt format)
Supplementary files format and content: Cell barcodes in first column and total UMI counts in second column (.txt format)

molecule: other

source_name: Gut

extract_protocol:
in-vitro digestion
MULTI-seq cell hashing

value: Gut cells

value: Gut

value: Crohn's dieseas


title: OUD+_26

value: W


title: vHC_2669_Naive


title: sc-Patch-seq,Red only,Regenerating CSMN179

description:
Patch-seq
NoRegen_CSMN_179

value: Brain

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: OUD+_25


title: genomic DNA from SGC7901-Rep1

description:
SGC-Rep1
AllNormMethyl.anno-12 samples.txt

value: Gastric cancer cell


title: sc-Patch-seq,Red only,Regenerating CSMN178

description:
Patch-seq
NoRegen_CSMN_178


title: sc-Patch-seq,Red only,Regenerating CSMN177

description:
Patch-seq
NoRegen_CSMN_177


title: OUD-_30


title: vHC_2666_Pop5


title: OUD+_24

value: OUD+


title: Crohn's disease biopsy, replicate 2, WTA

library_source: transcriptomic single cell

data_processing:
zUMIs (v. 2.9.4)
Assembly: GRCh38 v2020-A genecode, GRCm38 vM25, GFP 3'UTR
Supplementary files format and content: 3 UMI and 3 read count tables; gene-wise counts for exon, intron and exon+intron (.rds format)
Supplementary files format and content: UMI count matrix for MULTI-seq barcodes per cell; column "Barcode" contains the allocated MULTI-seq BC (.txt format)
Supplementary files format and content: Cell barcodes in first column and total UMI counts in second column (.txt format)

extract_protocol:
in-vitro digestion
BD Rhapsody: WTA kit


title: OUD-_23


title: vHC_2666_Pop3


title: Crohn's diesease biopsy, metastatic, replicate 1, fragment BC


title: sc-Patch-seq,Red only,Regenerating CSMN182

description:
Patch-seq
NoRegen_CSMN_182


title: sc-Patch-seq,Red only,Regenerating CSMN176

description:
Patch-seq
NoRegen_CSMN_176


title: sc-Patch-seq,Red only,Regenerating CSMN175

description:
Patch-seq
NoRegen_CSMN_175


title: vHC_2666_Pop2


title: genomic DNA from SGC7901-Rep3

description:
SGC-Rep3
AllNormMethyl.anno-12 samples.txt

value: Cancer


title: OUD-_22


title: Crohn's disease biopsy, replicate 1, WTA


title: sc-Patch-seq,Red only,Regenerating CSMN174

description:
Patch-seq
NoRegen_CSMN_174


title: OUD+_21

value: AA


title: vHC_2666_Naive

value: Peripheral Blood

value: vHC

value: Naive


title: SLE_2696_Pop5

value: SLE


title: OUD-_20

value: orbitofrontal cortex

value: neurons

value: Male

value: OUD-

value: CAUC


title: sc-Patch-seq,Red only,Regenerating CSMN173

description:
Patch-seq
NoRegen_CSMN_173

value: Cortical Spinal Motor Neuron


title: SLE_2696_Pop2


title: OUD-_19


title: OUD+_18

value: W


title: PN96_hESC_+PF127_24h_rep2

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

institute: Peking University

data_processing:
Fastq data were quality-checked by FastQC (version 0.11.9). 150bp paired-end reads with adapters were trimmed by TrimGalore (v0.6.7) and cutadapt (v4.1).
Trimmed reads from each sample were mapped to the human genome (hg38) using STAR (v2.7.10a) with parameters outFilterMismatchNoverLmax=0.1 and outFilterMultimapNmax=1.
Gene read counts were quantified against the GENCODE v40 gene annotation using Subread featureCounts (v2.0.1).
Differentially expressed genes (DEGs) were identified by DESeq2 (v1.36.0) in R software (v4.2.0), where gene raw counts were inputted.
Assembly: GRCh38
Supplementary files format and content: Excel file includes TPM values for each sample and DESeq2 results of NEAT1 knockout versus control samples for hESC and four types of organoids.

source_name: human embryonic stem cells

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Magen) and reverse transcribed into cDNA using the HiScript II 1st Strand cDNA Synthesis Kit (Vazyme) following the manufacturer’s instruction.
RNA-Seq libraries were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer’s instructions. Briefly, total RNA was purified twice using poly-T oligo-attached magnetic beads before the synthesis of double-stranded (ds) cDNA. The ds-cDNA was ligated to adaptors (Vazyme) and sequenced by Illumina (Novogene).

value: human embryonic stem cells

tag: cell line

value: WT

tag: treatment

value: 24 hours


title: sc-Patch-seq,Red only,Regenerating CSMN172

description:
Patch-seq
NoRegen_CSMN_172

value: Brain

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: sc-Patch-seq,Red only,Regenerating CSMN171

description:
Patch-seq
NoRegen_CSMN_171


title: PN96_hESC_+PF127_24h_rep1

tag: time


title: PN96_hESC_-PF127_24h_rep1


title: PN96_hESC_-PF127_24h_rep2


title: sc-Patch-seq,Red only,Regenerating CSMN170

description:
Patch-seq
NoRegen_CSMN_170


title: OUD-_17


title: SLE_2696_Naive

value: Peripheral Blood

tag: subject status

tag: subject id


title: SLE_2479_Pop5

tag: population


title: sc-Patch-seq,Red only,Regenerating CSMN169

description:
Patch-seq
NoRegen_CSMN_169

tag: age


title: OUD-_16

tag: Sex

tag: opioid use_disorder


title: PN96_hESC_+PF127_4h_rep1

value: 4 hours


title: OUD-_15

tag: age of_death

tag: ancestry


title: sc-Patch-seq,Red only,Regenerating CSMN168

description:
Patch-seq
NoRegen_CSMN_168

tag: tissue


title: PN96_hESC_-PF127_4h_rep2

tag: cell type


title: OUD-_14

tag: pmi


title: sc-Patch-seq,Red only,Regenerating CSMN167

description:
Patch-seq
NoRegen_CSMN_167

tag: strain


title: OUD-_13


title: SLE_2696_Pop3


title: PN96_hESC_-PF127_4h_rep1

tag: genotype


title: sc-Patch-seq,Red only,Regenerating CSMN166

description:
Patch-seq
NoRegen_CSMN_166


title: PN96_hESC_+PF127_1h_rep2

value: 1 hour


title: SLE_2479_Naive

value: SLE

value: Naive


title: OUD-_12

value: orbitofrontal cortex

value: neurons


title: sc-Patch-seq,Red only,Regenerating CSMN165

description:
Patch-seq
NoRegen_CSMN_165


title: SLE_2161_Pop5


title: sc-Patch-seq,Red only,Regenerating CSMN164

description:
Patch-seq
NoRegen_CSMN_164


title: PN96_hESC_+PF127_1h_rep1


title: SLE_2161_Pop2


title: OUD+_11

value: Male

value: OUD+


title: PN96_hESC_-PF127_1h_rep2


title: PN96_hESC_+PF127_4h_rep2


title: SLE_2161_Naive


title: sc-Patch-seq,Red only,Regenerating CSMN163

description:
Patch-seq
NoRegen_CSMN_163

value: Cortical Spinal Motor Neuron


title: OUD+_10

value: W


title: SLE_1763_Pop5


title: SLE_2479_Pop3


title: sc-Patch-seq,Red only,Regenerating CSMN162

description:
Patch-seq
NoRegen_CSMN_162


title: PN96_hESC_-PF127_1h_rep1

value: human embryonic stem cells


title: SLE_2479_Pop2


title: sc-Patch-seq,Red only,Regenerating CSMN161

description:
Patch-seq
NoRegen_CSMN_161


title: PN96_hESC_+PF127_0h_rep2

value: WT

value: 0 hours


title: OUD-_8

value: OUD-

value: AA


title: SLE_1763_Pop3


title: SLE_1763_Pop2


title: OUD+_7


title: sc-Patch-seq,Red only,Regenerating CSMN160

description:
Patch-seq
NoRegen_CSMN_160

value: Brain

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: SLE_1763_Naive

value: Peripheral Blood


title: OUD+_6


title: PN96_hESC_-PF127_0h_rep2


title: PN96_hESC_-PF127_0h_rep1


title: SLE_690_Pop5

value: SLE


title: PN96_Lung_NEAT1ko-clone2_day19_rep2

source_name: lung organoids derived from human embryonic stem cells

value: day 19


title: sc-Patch-seq,Red only,Regenerating CSMN158

description:
Patch-seq
NoRegen_CSMN_158


title: sc-Patch-seq,Red only,Regenerating CSMN157

description:
Patch-seq
NoRegen_CSMN_157


title: SLE_690_Pop3


title: OUD-_9

value: orbitofrontal cortex


title: PN96_Lung_NEAT1ko-clone2_day19_rep1

value: lung organoids derived from human embryonic stem cells


title: SLE_690_Pop2


title: sc-Patch-seq,Red only,Regenerating CSMN156

description:
Patch-seq
NoRegen_CSMN_156


title: OUD-_3

value: neurons

value: Male


title: SLE_690_Naive

value: Naive


title: PN96_hESC_+PF127_0h_rep1


title: sc-Patch-seq,Red only,Regenerating CSMN155

description:
Patch-seq
NoRegen_CSMN_155

value: Cortical Spinal Motor Neuron


title: PN96_Lung_NEAT1ko-clone1_day19_rep2


title: OUD-_2


title: sc-Patch-seq,Red only,Regenerating CSMN154

description:
Patch-seq
NoRegen_CSMN_154


title: SLE_235_Pop5


title: PN96_Lung_NEAT1ko-clone1_day19_rep1


title: OUD-_1

value: W


title: sc-Patch-seq,Red only,Regenerating CSMN159

description:
Patch-seq
NoRegen_CSMN_159


title: PN96_Lung_CTR_day19_rep2

value: CTR


title: SLE_235_Pop3


title: PN96_Lung_CTR_day19_rep1


title: SLE_235_Pop2


title: PBMC, healthy, rep4-6

city: Aurora

first: Liyen

last: Loh

state: Colorado

address: 12800 E 19th Ave, Research 1 North, P18-8401K

institute: University of Colorado

description:
BD Rhapsody
LRS08
LRS09
LRS11

data_processing: Quality control, demultiplexing, and read mapping were performed using the BD Rhapsody WTA Analysis Pipeline (v1.0) on the Seven Bridges server.

source_name: PBMC

extract_protocol:
KIR3DL3+ lymphocytes were enriched with PE-magnetic beads from cryopreserved PBMC. Cell subsets for the populations from different donors were labelled simultaneously with the cell surface sorting panel an oligonucleotide-tagged antibody sample tag (BD Biosciences) prior to cell sorting on a FACSAria3 (BD Biosciences).
Library was performed according to the manufacter’s instructions (TCR/BCR Full Length, mRNA Whole Transcriptome Analysis (WTA),  BD® AbSeq, and Sample Tag Library Preparation Protocol, BD Biosciences). Prior to cDNA library preparation for the WTA and VDJ libraries, all cell subsets from the different donors were pooled, up to 12 unique sample tags were combined per library. Briefly, cells were captured with beads in a microwell plate, followed by cell lysis, bead retrieval, cDNA synthesis, template switching, Klenow extension, and library preparation.

value: NK, CD8+ T, gd T cells

value: PBMC

tag: disease state

value: healthly control


title: sc-Patch-seq,Red only,Regenerating CSMN152

description:
Patch-seq
NoRegen_CSMN_152

value: Brain


title: OUD-_4

value: OUD-

value: CAUC


title: PBMC, healthy, rep1-3

description:
BD Rhapsody
LRS03
LRS04
LRS07


title: sc-Patch-seq,Red only,Regenerating CSMN153

description:
Patch-seq
NoRegen_CSMN_153

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: OUD+_5

value: OUD+

value: AA


title: PN96_Hepatic_NEAT1ko-clone2_day21_rep2

source_name: hepatic organoids derived from human embryonic stem cells

tag: cell line

value: day 21


title: sc-Patch-seq,Red only,Regenerating CSMN151

description:
Patch-seq
NoRegen_CSMN_151


title: SLE_235_Naive

value: Peripheral Blood

value: SLE


title: sc-Patch-seq,Red only,Regenerating CSMN150

description:
Patch-seq
NoRegen_CSMN_150


title: SLE_215_Pop5


title: PN96_Hepatic_NEAT1ko-clone1_day21_rep2

value: hepatic organoids derived from human embryonic stem cells

tag: treatment


title: SLE_215_Pop3


title: sc-Patch-seq,Red only,Regenerating CSMN149

description:
Patch-seq
NoRegen_CSMN_149

value: Cortical Spinal Motor Neuron


title: sc-Patch-seq,Red only,Regenerating CSMN148

description:
Patch-seq
NoRegen_CSMN_148


title: FACS HTO library 2

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

data_processing:
scRNA-seq reads were analyzed by pseudoalignment using kallisto v0.46.2 (GRCh38 with Gencode v24 annotation) and bustools v0.40.0. CITE-seq and hashtag barcodes were demultiplexed and extracted using DropSeqPipeline8 (https://github.com/simslab/DropSeqPipeline8). Hashtags were demultiplexed by CLR normalization, k-means clustering, and statistical identification of singlets by fitting a negative binomial model as described in Stoeckius et al, Genome Biology, 2018.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with cell-identifying barcodes, hashtags, and count matrix

source_name: blood

extract_protocol:
Mononuclear cells (MNCs) were isolated from organ donor tissues from two subjects (D496 and D503) as described in Dominguez-Conde et al, Science, 2022.  A detailed protocol for each tissue site appears in the supplementary materials. For the FAC-sorted sample corresponding to PDC100-PDC101, we obtained peripheral blood from  a consenting, healthy volunteer (35  year-old male) by venous puncture. Peripheral blood mononuclear cells (PBMCs) were isolated using RosetteSep Granulocyte Depletion Cocktail (StemCell Technologies), following manufacturer’s protocols for density gradient centrifugation. Briefly, samples were incubated with the cocktail at 20°C for 10 minutes, diluted 1:1 with FACS buffer (DPBS 10% FBS 2mM EDTA), then layered over Ficoll-Plaque in SepMate PBMC isolation tubes (StemCell Technologies). Samples were centrifuged at 1200 x g for 10 minutes at 20°C, and PBMC layers were isolated according to instructions. Samples were washed (400 x g for 10 minutes) with FACS buffer. For further erythrocyte removal, pellets were resuspended in ACK lysis buffer (Gibco) incubated for 2 minutes at 37°C and washed with FACS buffer.  PBMCs were stained with Zombie NIR Fixable Viability dye (Biolegend) for 30 minutes. Samples were kept at 4°C in the dark. Cells were washed thrice with FACS buffer, resuspended in TrueStain FcX and TrueStain Monocyte Blocker (Biolegend) and incubated for 10 minutes. Cells were incubated with the FACS antibody cocktail for 30 minutes, then washed thrice with FACS buffer. Cells were incubated in TrueStain FcX (Biolegend) for 10 minutes, then stained using a custom Total Seq-A Universal Human Panel (Biolegend) for 30 minutes, according to manufacturer instructions. Samples were washed thrice with FACS buffer. Cells were sorted using a FACS Aria III (BD Biosciences). Seven T cell memory populations (CD4+ Naive, CD4+ TCM, CD4+ TEM,  CD8+ Naive, CD8+ TCM, CD8+ TEM,  CD8+ TEMRA), and monocytes were sorted into sterile, heat inactivated FBS. All sorts were high purity, with mean purity 94.4% (ranging from 97.1% to 91.8%).
For the organ donor tissues (D496 and D503), each single-cell suspension was hashtagged to allow pooling of samples for loading on the 10x Genomics Chromium instrument. Approximately 1M MNCs per tissue were transferred to 4 mL flow cytometry tubes. Cells were centrifuged at 400 x g for 5 minutes at 4C, supernatant removed, and re-suspended in PBS containing 5% (v/v) FBS and 2 mM EDTA. Cells were treated with Trustain FcX (Biolegend, 422302) and FcR Blocking Reagent (Miltenyi, 130-059-901) to reduce background labeling and incubated at 4C for 10 minutes. Each hashtag was spun at 14,000 x g for 10 minutes, and 1 uL of hashtag was added to each tube. The samples were incubated at 4C for 30 minutes, and subsequently centrifuged at 400 x g for 5 minutes at 4C and washed three times with PBS containing 5% (v/v) FBS and 2 mM EDTA. 200,000 cells from each sample was added to a single 4 mL flow cytometry tube. This tube was centrifuged at 400 x g for 5 minutes at 4C and re-suspended in PBS containing 5% (v/v) FBS and 2 mM EDTA. For each donor, the hashtagged cells were pooled and stained with the TotalSeq-A Human Universal Cocktail panel according to the manufacturer's instructions (Biolegend) and loaded across 16 channels of the 10x Genomics Chromium instrument for library construction using the 10x Genomics Single Cell 3' Solution (v3.1 1000121) according to the manufacturer's instructions with the manufacturer's recommended modifications for compatibility with the TotalSeqA cell hashing and CITE-seq reagents (Biolegend).
For the FACS-sorted PBMCs (PDC100-101), samples were counted, diluted to the appropriate volume, and loaded across two lanes of a 10x Genoimcs NextGEM chip. cDNA synthesis and amplification was performed using the 10x Genomics NextGEM 3' Kit v3.1 with the manufacturer's recommended modifications for compatibility with the TotalSeqA cell hashing and CITE-seq reagents (Biolegend). In this experiment, the hashtags correspond to FAC-sorted immune cell subsets (HTO1: Naive CD4 T cells, HTO2: Central Memory CD4 T cells, HTO3: Effector Memory CD4  T cells, HTO4: Naive CD8 T cells, HTO5: Central Memory CD8 T cells, HTO6: Effector Memory CD8 T cells, HTO7: CD8 TEMRA, HTO8: Monocytes).
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: blood

value: T cells and monocytes

tag: library type

value: HTO

tag: antibodies/tags


title: FACS HTO library 1


title: SLE_215_Pop2

tag: subject status

tag: subject id


title: FACS ADT library 2

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

value: ADT

value: TotalSeq-A Human Universal Cocktail


title: SLE_215_Naive

tag: population

value: Naive


title: PN96_Hepatic_CTR_day21_rep1

value: CTR

tag: time


title: FACS ADT library 1


title: sc-Patch-seq,Red only,Regenerating CSMN147

description:
Patch-seq
NoRegen_CSMN_147

value: Brain

tag: age


title: FACS GEX library 2

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: sc-Patch-seq,Red only,Regenerating CSMN146

description:
Patch-seq
NoRegen_CSMN_146

value: PTEN SOCS3 tdTomato

value: 22 weeks old


title: PN96_Nephron_NEAT1ko-clone2_day13_rep1

source_name: nephron organoids derived from human embryonic stem cells

value: day 13


title: PN96_Nephron_NEAT1ko-clone2_day13_rep2

value: nephron organoids derived from human embryonic stem cells


title: PN96_Hepatic_NEAT1ko-clone2_day21_rep1

value: day 21


title: PN96_Hepatic_NEAT1ko-clone1_day21_rep1


title: SLE_165_Pop2

value: Peripheral Blood

value: SLE


title: sc-Patch-seq,Red only,Regenerating CSMN145

description:
Patch-seq
NoRegen_CSMN_145

value: Cortical Spinal Motor Neuron


title: PN96_Hepatic_CTR_day21_rep2

value: hepatic organoids derived from human embryonic stem cells


title: PN96_Nephron_CTR_day13_rep2


title: SLE_165_Pop5


title: D503 HTO library 12

source_name: various

value: various

value: mononuclear cells (MNCs)


title: PN96_Nephron_NEAT1ko-clone1_day13_rep2


title: D503 HTO library 16

value: HTO


title: SLE_165_Naive


title: sc-Patch-seq,Red only,Regenerating CSMN143

description:
Patch-seq
NoRegen_CSMN_143


title: D503 HTO library 14


title: SLE_165_Pop3


title: D503 HTO library 11


title: PN96_Nephron_NEAT1ko-clone1_day13_rep1