title: 207760740041_R03C03


title: 207760740041_R07C03

status: Public on May 15 2024

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

country: USA

institute: Children's Hospital of Philadelphia

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.
Normalized average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Human cell line DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from 30-70 mg of tissue or 5.0 x 10^6 cells for cell lines using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol. DNA was quantified using a Qubit 4 Fluorometer (Invitrogen).

tag: modification

tag: tissue

value: Illumina DVT (Coriell)


title: 207760740030_R07C03


title: 207760740030_R03C03


title: 207760740030_R05C03


title: 207760740030_R01C03


title: 207760740056_R05C03


title: 207760740083_R16C02


title: 207760740056_R16C02


title: 207760740056_R10C02


title: 207760740083_R14C02


title: 207760740041_R16C02


title: 207760740083_R10C02


title: 207760740056_R03C03


title: 207760740056_R14C02


title: 207760740056_R12C02


title: 207760740030_R16C02


title: 207760740041_R14C02


title: 207760740083_R12C02


title: 207760740041_R10C02


title: 207760740041_R12C02


title: 207760740030_R14C02


title: 207760740030_R12C02


title: 207760740030_R10C02


title: 207760740083_R08C02


title: 207760740083_R06C02


title: 207760740083_R02C02


title: 207760740041_R08C02


title: 207760740041_R02C02


title: 207760740056_R02C02


title: 207760740056_R04C02


title: 207760740041_R06C02


title: 207760740056_R06C02


title: 207760740030_R08C02


title: 207760740056_R08C02


title: 207760740030_R06C02


title: 207760740030_R02C02


title: 207760740041_R04C02


title: 207760740083_R09C02


title: 207760740083_R13C02


title: 207760740056_R15C02


title: 207760740083_R15C02


title: 207760740056_R13C02


title: 207760740083_R11C02


title: 207760740041_R13C02


title: 207760740056_R11C02


title: 207760740030_R13C02


title: 207760740041_R11C02


title: 207760740041_R15C02


title: 207760740030_R15C02


title: 207760740030_R11C02


title: 207760740083_R04C02


title: 207760740083_R14C01

value: Raji

value: Illumina DVT (Cell Line)


title: 207760740083_R16C01


title: 207760740041_R12C01


title: 207760740083_R12C01


title: 207760740030_R09C02


title: 207760740030_R16C01


title: 207760740056_R14C01


title: 207760740041_R16C01


title: 207760740083_R04C01


title: 207760740041_R10C01


title: 207760740083_R08C01


title: 207760740056_R16C01


title: 207760740083_R10C01


title: 207760740083_R02C01


title: 207760740083_R06C01


title: 207760740056_R12C01


title: 207760740030_R04C02


title: 207760740041_R14C01


title: 207760740041_R09C02


title: 207760740056_R10C01


title: 207760740030_R14C01


title: 207760740041_R08C01


title: 207760740030_R12C01


title: 207760740041_R04C01


title: 207760740030_R06C01


title: 207760740030_R10C01


title: 207760740030_R02C01


title: 207760740056_R08C01


title: 207760740083_R05C02


title: 207760740056_R02C01


title: 207760740083_R01C02


title: 207760740056_R04C01


title: 207760740056_R06C01


title: 207760740030_R08C01


title: 207760740041_R06C01


title: 207760740056_R03C02


title: 207760740041_R03C02


title: 207760740083_R03C02


title: 207760740083_R07C02


title: 207760740056_R01C02


title: 207760740041_R02C01


title: 207760740056_R07C02


title: 207760740030_R05C02


title: 207760740056_R05C02


title: 207760740041_R05C02


title: 207760740030_R01C02


title: 207760740083_R15C01

value: Jurkat


title: 207760740083_R13C01


title: 207760740030_R07C02


title: 207760740056_R15C01


title: 207760740030_R03C02


title: 207760740041_R07C02


title: 207760740083_R11C01


title: 207760740030_R04C01


title: 207760740041_R01C02


title: 207760740056_R11C01


title: 207760740056_R13C01


title: 207760740056_R09C01


title: 207760740041_R13C01


title: 207760740041_R09C01


title: 207760740083_R05C01

value: Hela


title: 207760740041_R11C01


title: 207760740041_R15C01


title: 207760740030_R15C01


title: 207760740030_R11C01


title: 207760740083_R01C01


title: 207760740083_R09C01


title: 207760740056_R05C01


title: 207760740056_R07C01


title: 207760740083_R07C01


title: 207760740041_R01C01


title: 207760740030_R07C01


title: 207760740030_R05C01


title: 207760740056_R03C01


title: 207760740056_R01C01


title: 207760740030_R09C01


title: 207760740041_R03C01


title: 207760740030_R13C01


title: 207760740041_R05C01


title: 207760740030_R03C01


title: 207760740083_R03C01


title: 207675480016_R06C02

value: 50% Epigen Control

value: Illumina Alpha Test (Titration Control)


title: 207760740030_R01C01


title: 207675480016_R10C02

value: 100% Epigen Control


title: 207675480016_R11C03


title: 207675480016_R08C02


title: 207760740041_R07C01


title: 207675480016_R07C03


title: 207675480016_R12C02


title: 207675480016_R05C03


title: 207675480016_R03C03

value: 0% Epigen Control


title: 207675480016_R01C03


title: 207675480016_R02C02


title: 207675480016_R04C02


title: 207675480011_R14C02

value: Illumina Alpha Test (Coriell)


title: 207675480011_R08C02


title: 207675480016_R09C03


title: 207675480011_R16C02


title: 207675480011_R12C02


title: 207675480011_R10C02


title: 207675480011_R02C02


title: 207675480011_R01C03


title: 207675480011_R07C03


title: 207675480011_R04C02


title: 207675480011_R11C03


title: 207675480011_R09C03


title: 207675480011_R15C03


title: 207675480011_R13C02


title: 207675480011_R05C03


title: 207675480011_R07C02


title: 207675480011_R08C01


title: 207675480011_R06C01


title: 207675480011_R15C02


title: 207675480011_R03C02


title: 207675480011_R04C01


title: 207675480011_R05C02


title: 207675480011_R16C03


title: 207675480011_R16C01


title: 207675480011_R03C03


title: 207675480011_R14C01


title: 207675480004_R14C02


title: 207675480011_R10C01


title: 207675480011_R01C02


title: 207675480011_R13C03


title: 207675480004_R10C02


title: 207675480011_R11C02


title: 207675480011_R02C01


title: 207675480011_R08C03


title: 207675480004_R02C02


title: 207675480011_R09C02


title: 207675480004_R06C02


title: 207675480011_R12C01


title: 207675480004_R12C03


title: 207675480004_R16C03


title: 207675480004_R10C03


title: 207675480004_R06C03


title: 207675480004_R15C03

value: Illumina Alpha Test (Cell Line)


title: 207675480004_R09C03


title: 207760740056_R09C02


title: 207675480004_R05C03


title: 207675480004_R07C03


title: 207675480004_R11C02


title: 207675480004_R12C02


title: 207675480004_R08C02


title: 207675480004_R09C02


title: 207675480004_R04C03


title: 207675480011_R06C02


title: 207675480004_R08C03


title: 207675480011_R13C01


title: 207675480004_R15C02


title: 207675480004_R04C02


title: 207675480004_R16C02


title: 207675480011_R11C01


title: 207675480011_R09C01


title: 207675480004_R14C03


title: 207675480011_R12C03


title: 207675480004_R05C02


title: 207675480011_R06C03


title: 207675480004_R03C03


title: 207675480011_R04C03


title: 207675480004_R02C03


title: 207675480004_R01C03


title: 207675480004_R11C03


title: 207675480004_R13C03


title: 207675480004_R08C01


title: 207675480016_R16C02

value: HeLa


title: 207675480011_R10C03


title: 207675480004_R03C02


title: 207675480004_R04C01


title: 207675480004_R06C01


title: 207675480004_R13C02


title: 207675480016_R09C02


title: 207675480016_R13C02


title: 207675480004_R01C02


title: 207675480011_R15C01


title: 207675480004_R10C01


title: 207675480004_R16C01


title: 207675480016_R11C02


title: 207675480011_R07C01


title: 207675480011_R01C01


title: 207675480011_R14C03


title: 207675480004_R07C02


title: 207675480011_R05C01


title: 207675480004_R14C01


title: 207675480016_R07C02


title: 207675480016_R15C02


title: 207675480004_R02C01


title: 207675480016_R05C02


title: 207675480016_R03C02


title: 207675480016_R01C02


title: 207675480011_R03C01


title: 207675480004_R13C01


title: 207675480004_R12C01


title: 207675480011_R02C03


title: 207675480004_R15C01


title: 207675480004_R05C01


title: 207675480004_R09C01


title: 207675480004_R07C01


title: 207675480004_R03C01


title: 207675480004_R11C01


title: 207675480004_R01C01


title: 207854510042_R15C03

source_name: Human primary cell DNA

value: skin

value: 8. Tissue-specific 5hmC


title: 207854510042_R08C03


title: 207854510042_R11C03


title: 207854510042_R10C02


title: 207854510042_R06C02


title: 207854510042_R16C02

value: pancreas


title: 207854510042_R03C03


title: 207854510042_R07C03


title: 207854510042_R01C03


title: 207854510042_R14C02


title: 207854510042_R05C03

value: colon (ileum)


title: 207854510042_R08C02

value: colon (small bowel)


title: 207854510042_R06C03

value: colon


title: 207854510042_R13C03

value: heart (mitral valve)


title: 207854510042_R12C02


title: 207854510042_R04C02


title: 207854510042_R04C03


title: 207854510042_R02C03


title: 207854510042_R13C01

value: cerebellum

value: 7a. Brain-region 5hmC


title: 207854510042_R09C01

value: motor


title: 207854510042_R10C01


title: 207854510042_R12C03


title: 207854510042_R14C01


title: 207854510042_R10C03


title: 207854510042_R11C01


title: 207854510042_R09C03


title: 207760740037_R16C02

status: Public on May 11 2024

description: EpigenDx standard_100

data_processing: SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings

value: 3. Methylation Titration


title: 207760740037_R01C03

description: Jurkat standard 100


title: 207760740037_R16C01

value: 1. Cell line reproducibility


title: 207760740037_R06C02

description: EpigenDx standard_5


title: 207760740037_R07C02

value: 2. EPICv2 and WGBS Comparison


title: 207760740037_R03C03

description: Jurkat standard 50


title: 207760740037_R05C02


title: 207760740037_R14C02

description: EpigenDx standard_75


title: 207760740037_R02C02

description: LNCaP


title: 207760740037_R15C02

description: LNCaP


title: 207760740037_R08C02

description: EpigenDx standard_10


title: 207760740037_R11C01


title: 207760740037_R13C02

description: LNCaP


title: 207760740037_R11C02


title: 207760740037_R10C02

description: EpigenDx standard_25


title: 207760740037_R12C02

description: EpigenDx standard_50


title: 207760740037_R04C01


title: 207760740037_R01C02


title: 207760740037_R05C01

description: Illumina Control DNA

value: 0. Illumina Control


title: 207760740037_R14C01


title: 207760740037_R09C01


title: 207760740037_R12C01


title: 207760740037_R15C01


title: 207760740037_R08C01

description: LNCaP


title: 207760740037_R13C01


title: 207760740001_R16C03

description: cerebellum

value: 7. Brain-region methylation


title: 207760740037_R09C02


title: 207760740037_R04C02

description: EpigenDx standard 0


title: 207760740001_R08C03

description: motor cortex


title: 207760740037_R03C01

description: Illumina Control DNA


title: 207760740001_R13C03

description: CD4+ T cells

value: 6. Sorted immune cell


title: 207760740037_R07C01

description: Illumina Control DNA


title: 207760740037_R02C01


title: 207760740001_R04C03

description: NK cells


title: 207760740001_R14C02

description: NK cells


title: 207760740037_R05C03

description: Jurkat standard 0


title: 207760740001_R01C03

description: Total T cells


title: 207760740001_R06C03

description: PBMC


title: 207760740001_R09C03

description: PBMC


title: 207760740001_R12C03

description: motor cortex


title: 207760740001_R02C03

description: Monocytes


title: 207760740037_R01C01

description: Illumina Control DNA


title: 207760740001_R13C02

description: NK cells


title: 207760740001_R12C02

description: Monocytes


title: 207760740001_R03C03

description: CD4+ T cells


title: 207760740001_R08C02

description: heart

value: 5. Tissue-specific methylation


title: 207760740001_R15C03

description: CD8+ T cells


title: 207760740001_R11C03

description: Total T cells


title: 207760740001_R10C03

description: motor cortex


title: 207760740001_R15C02

description: colon


title: 207760740001_R09C02

description: colon


title: 207760740001_R05C02

description: colon


title: 207760740001_R07C02

description: CD4+ T cells


title: 207760740001_R02C02

description: colon


title: 207760740001_R14C01

description: pancreas


title: 207760740001_R10C01

description: pancreas


title: 207760740001_R05C03

description: CD8+ T cells


title: 207760740001_R04C02

description: colon


title: 207760740001_R10C02

description: Total T cells


title: 207760740001_R16C02

description: PBMC


title: 207760740001_R04C01

description: skin


title: 207760740001_R07C03

description: Monocytes


title: 207760740001_R01C02

description: colon


title: 207760740001_R11C02

description: colon


title: 207760740001_R03C02

description: colon


title: 207760740001_R07C01

description: skin


title: 207760740037_R10C03

description: LNCaP

value: 4. Low input


title: 207760740001_R06C01

description: pancreas


title: F1-AGVT iPSC

status: Public on Apr 24 2024

type: SRA

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: F1-AGVT (NCLCN-261), iPSC day6

library_source: genomic

data_processing:
Paired-end reads were processed with Trim_Galore! V0.6.3 and mapped on the GRCh38.p12 genome using Bismark v0.22.1 and Bowtie2 v2.3.4.1 with the “-X 2000” option.  BAM files were, then, processed with deduplicate_bismark script to remove PCR duplicates, and bismark_methylation_extractor to count methyl- and unmehyl-Cytosine per at CpG or CpA sequences.
Assembly: GRCh38.p12
Supplementary files format and content: bismark report file
Library strategy: EM-seq

source_name: NCLCN(XX) AGVT261

extract_protocol:
Gemomic DNA extraction was integrated in "library construction protocol" process.
EM-seq libraries were generated as described previously (Gyobu-Motani, 2023).
EM-seq, (Vaisvila, 2021)

tag: cell line

tag: cell type

value: human iPSC

tag: transgene

value: TFAP2C-EGFP, DDX4-tdTomato knock-in

tag: genotype

value: WT


title: 207760740001_R08C01

description: pancreas


title: 207760740001_R03C01

description: skin


title: 207760740001_R15C01

description: Illumina Control DNA


title: Recurrent HGSOC (R5)

status: Public on Apr 18 2024

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

country: South Korea

institute: Incheon National University

description: Fresh frozen10x Genomics Visium Spatial transcriptome sequencing

library_source: transcriptomic

data_processing:
All specimens from patients with cancer were obtained with appropriate consent and approval from the institutional review board of Seoul St. Mary’s Hospital, The Catholic University of Korea, College of Medicine (KC22SISI0687). We obtained ovarian cancer tissues from eight treatment-naïve patients who underwent cytoreductive surgery.
Visium Spatial Gene Expression Solution was used to measure total mRNA in the tissue sections and locations where gene activity occurred (10x Genomics).
Libraries were prepared according to the Visium Spatial Gene Expression Guide CG000239 (10x Genomics, Pleasanton, CA, USA). Libraries were sequenced on the NovaSeq platform (Illumina, San Diego, CA, USA).
10x Genomics Space Ranger v2.0.0 was used to perform gene counting of the Visium sequencing data. Fastq files were processed using the GRCh38 reference, and raw gene expression matrices were used for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered gene expression count data in h5 Format
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: image.tif: image of tissue
Supplementary files format and content: scalefactors_json.json
Supplementary files format and content: tissue_positions_list.csv
Library strategy: Spatial Transcriptomics

molecule: total RNA

source_name: high-grade serous ovarian cancer

extract_protocol:
Visium Spatial Gene Expression Solution was used to measure total mRNA in the fresh frozen tissue sections and locations where gene activity occurred (10x Genomics). The tissue sections were fixed, stained on Visium Spatial Tissue Optimization Slide, and permeabilized.
Libraries were prepared according to the Visium Spatial Gene Expression Guide CG000239 (10x Genomics, Pleasanton, CA, USA). The tissue sections placed on Visium Spatial Gene Expression Slide were fixed and stained, and cellular mRNA was captured using primers at gene expression spots.

value: high-grade serous ovarian cancer

tag: group

value: Recurrent

tag: Sex

value: Female

tag: stage (figo)

value: III

tag: age

tag: treatment

value: treatment-naïve


title: 207760740001_R13C01

description: Illumina Control DNA


title: 207760740001_R16C01

description: pancreas


title: 207760740037_R12C03

description: LNCaP


title: 207760740001_R09C01

description: Illumina Control DNA


title: Recurrent HGSOC (R4)

value: IV


title: 207760740001_R05C01

description: CD8+ T cells


title: 207760740037_R02C03


title: 207760740037_R14C03

description: LNCaP


title: 207760740037_R07C03

description: Human blood standard 100

value: 3. Methylation Titration


title: Recurrent HGSOC (R1)


title: 207760740037_R11C03

description: Human blood standard 0


title: Recurrent HGSOC (R2)


title: 207760740037_R15C03


title: Non-recurrent HGSOC (NR3)

value: Non-recurrent


title: 207760740001_R12C01

description: pancreas


title: 207760740001_R11C01

description: Illumina Control DNA


title: Recurrent HGSOC (R3)


title: 207760740037_R04C03


title: 207760740037_R08C03


title: 207760740037_R03C02

value: 2. EPICv2 and WGBS Comparison


title: 207760740037_R10C01

description: LNCaP

value: 1. Cell line reproducibility


title: Non-recurrent HGSOC (NR1)


title: 207760740037_R13C03


title: 207760740001_R01C01

description: skin


title: 207760740037_R16C03

description: skin


title: K19-HIF2dPA_24M_WT_4

status: Public on Mar 27 2024

type: RNA

first: Makarand

last: Risbud

address: 1015 Walnut Street

institute: Thomas Jefferson University

description: Total RNA from 24M WT NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.7

hyb_protocol: Affymetrix Gene chips, Mouse Clariom S, were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail.

scan_protocol: Array scanning was performed on an Affymetrix GeneChip Scanner 3000 7G using Command Console Software (Affymetrix).

data_processing: Raw data were processed and .CHP files were generated by sst-rma normalization from Affymetrix .CEL files, and quality control of the experiment was performed in Transcriptome Analysis Console (TAC) v4.0.2 (Affymetrix). The experimental group was compared to the control group in the TAC, including all probe sets where at least 50% of the samples had a DABG (detected above background) p < 0.05. Inclusion cutoffs were defined at a 1.7-fold change and p-value < 0.05.

label: biotin

organism: Mus musculus

source_name: 24M WT

label_protocol: Single-stranded cDNA was generated, then fragmented and biotin-labeled using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: dPA and K19-dPA mice were aged to 3 months, and were injected with tamoxifen for three consecutive days to activate K19-CreERT driver. Tissues were collected at 11 months and 21 months following the initial injection at 3 months. Genotypes were confirmed by PCR.

extract_protocol: NP tissues were micro-dissected from caudal intervertebral discs of 4 dPA and 4 K19-dPA overexpression animals and immediately placed in RNAlater® Reagent (INVITROGEN). Tissues were homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971) and RNA was extracted from tissue lysates using RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

value: Nucleus Pulposus

value: female


title: K19-HIF2dPA_24M_WT_3


title: K19-HIF2dPA_24M_WT_2


title: 207760740037_R09C03

description: Human blood standard 50


title: K19-HIF2dPA_24M_WT_1

value: male


title: 207760740037_R06C01

description: LNCaP


title: 207760740037_R06C03

value: 4. Low input


title: K19-HIF2dPA_24M_MUT_1

description: Total RNA from 24M MUT NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.7

source_name: 24M MUT


title: K19-HIF2dPA_24M_MUT_4


title: KJ7 Top2-AID

status: Public on Jan 30 2024

city: Bunkyo-ku

first: Naoko

last: Yokota

state: Tokyo

address: 1-1-1 yayoi

department: Department of Cell and Molecular Biology

institute: The University of Tokyo

data_processing:
Sequenced paired-end 150-bp reads were mapped to the yeast genome using Juicer with default parameters.
Assembly: Saccharomyces Genome Database (SGD), identical with sacCer3
Supplementary files format and content: hic files were generated by juicertools version 1.9.9 pre with "-r 1000" option . The total hic contact number of Hi-C samples was normalized  (see the manuscript for detail).

organism: Saccharomyces cerevisiae

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose, or 2 % galactose, as stated, and at 30°C if not stated otherwise.

extract_protocol:
Hi-C was performed as detailed in Jeppsson et al., 2022. Briefly, S. cerevisiae cells were crosslinked with 3 % formaldehyde for 20 minutes at room temperature. Following spheroplasting and gentle lysis, restriction digestion of crosslinked chromatin by DpnII (NEB, R0543M) was performed overnight at 37°C, after which the restriction enzyme was inactivated by incubation at 62°C for 20 minutes. The presence of intact and individual DNA masses throughout the spheroplasting, digestion and ligation steps were confirmed by DAPI (4′,6-diamidino-2-phenylindole)-staining and microscopy. Marking and repairing DNA ends, proximity ligation, crosslink reversal, DNA shearing, size selection, biotin pull-down, preparation for Illumina sequencing, final amplification (15 cycles) and purification were then performed as in Jeppsson et al., 2022.
Marking and repairing DNA ends, proximity ligation, crosslink reversal, DNA shearing, size selection, biotin pull-down, preparation for Illumina sequencing, final amplification (15 cycles) and purification was performed as in ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014).

treatment_protocol: For synchronization in G1-phase, 3 μg ml-1 α-factor mating pheromone (Merck, custom peptide WHWLQLKPGQPMY) was added every hour (a total of three additions) to cells growing logarithmically. For G2/M cell cycle arrest, benomyl (Merck, 381586) was added to the YEPD media for a final concentration 80 µg ml-1. A complete G2/M-arrest of logarithmically growing cells was achieved after 90 minutes at 30°C, or 120 minutes at 23°C. For G2/M-arrest following synchronization in G1-phase, cells were released into benomyl-containing YEPD for 60 minutes. For depletion of Scc2, Wpl1, Top1, Smc6, Nse4, Nse5 and Top2 in Figures 1A, 1D, 4A, S10C, auxin (3-indoleacetic acid, 1 mM final concentration, Merck, I2886) and doxycycline (5 μg ml-1 final concentration, Merck, D9891) were added to simultaneously degrade the proteins and inhibit their transcription, respectively. For degradation of Smc5 and Smc6 in Figure S9C, auxin (3-indoleacetic acid, Merck, I2886) was added at a final concentration of 1 mM. For transcription inhibition, thiolutin (Abcam, ab143556) was added to cell cultures for the final concentration of 20 µg ml-1 for 30 minutes.

tag: strain

value: Auxin+doxycycline


title: K19-HIF2dPA_14M_MUT_1

description: Total RNA from 14M MUT NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.7

source_name: 14M MUT


title: K19-HIF2dPA_14M_MUT_3


title: K19-HIF2dPA_24M_MUT_2


title: K19-HIF2dPA_14M_WT_1

description: Total RNA from 14M WT NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.7

source_name: 14M WT

value: Nucleus Pulposus (NP)


title: KJ61 top2-4 -b

value: G2/M-arrest following an S-phase at 35°C


title: K19-HIF2dPA_14M_MUT_2


title: K19-HIF2dPA_14M_MUT_4


title: KJ6 WT

value: WT


title: KJ60 top2-4 -a


title: KJ57 WT-b


title: Non-recurrent HGSOC (NR2)

value: high-grade serous ovarian cancer


title: K19-HIF2dPA_14M_WT_3


title: UCSD-AML1

status: Public on Jan 14 2024

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

data_processing:
For sequencing data with fastq files, read quality was assessed with FastQC (version 0.11.5). Illumina adapter sequences from raw fastq files were trimmed using Trimmomatic (version 0.39). The trimmed fastq files were aligned to the GRCh38 human reference genome (hg38, release 86) using HISAT2 (version 2.1.0) and gene counts were obtained using featureCounts, downloaded from Subread package. All downstream analyses were performed in R Studio (version, 1.4.1106) using the Bioconductor framework.
Assembly: GrCh38.86
Supplementary files format and content: .csv file contains raw counts for each gene per sample

source_name: Acute myeloid leukemia cell line

growth_protocol: Human AML cell lines were cultured as previously described (Pearson et al. Mol. Cancer Research, 2020).

extract_protocol:
Total RNA was isolated from AML patient PBMCs and AML cell lines by resuspending pellets in Trizol and purifying RNA with Direct-zol RNA Miniprep (Zymo Research # R2052). DNase treatment was done using RNase-Free DNase Set (Qiagen # 79254). RNA integrity was analyzed using the Agilent TapeStation system according to the manufacturer’s protocol. RNA samples with RIN scores higher than 5.3 were sent to Novogene for mRNA library prep and sequencing. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
100 ng total RNA isolated using trizol standard protocol (according to the manufacturer’s instructions) was used for sequencing using TruSeq Stranded Total RNA Ribo Zero kit (Human/Mouse/Rat) on NovaSeq6000 S4, 150 bp paired-end.

tag: library preparation

value: Stranded


title: KJ56 WT-a


title: U937

value: Unstranded


title: K19-HIF2dPA_14M_WT_4


title: K19-HIF2dPA_24M_MUT_3


title: TF-1


title: TF1


title: SKNO-1


title: SKM-1


title: PPBL9542

source_name: AML Primary sample


title: 207760740001_R14C03

description: cerebellum

value: 7. Brain-region methylation


title: SET2


title: PPBL9785


title: PPBL8426


title: K19-HIF2dPA_14M_WT_2


title: PBL10278


title: PBL10261


title: P933


title: 207760740001_R02C01

description: skin

value: 5. Tissue-specific methylation


title: THP-1


title: P1356


title: P998


title: P934


title: P218


title: P1361


title: P1343


title: P850


title: P801


title: THP1


title: P1316


title: P136


title: P1313


title: P1257


title: P109


title: P1044


title: P1266


title: P1021


title: P1065


title: PPBL10173


title: P1006


title: OCIM2


title: OCIAML4


title: P1304


title: MV411


title: NOMO

description: NOMO

value: NOMO


title: P1321


title: OCI-3


title: MOL16


title: ML2


title: MUTZ-2


title: Mol13


title: OCI-5


title: ME-1


title: OCI1


title: MKPL

description: MKPL

value: MKPL


title: MOL14


title: MonoMac6


title: KG1


title: ME1


title: KG1ABTR


title: KG1aABTR


title: KG-1


title: KAS-4


title: KAS-3


title: KASUMI1


title: OCI-2


title: HL60ABTR


title: KAS-1


title: KG1a


title: K562


title: HL60VCR


title: OCI-4


title: HL60-1


title: HL60-2


title: CMK

description: CMK

value: CMK


title: 7CR20HFD_PIT

status: Public on Jan 04 2024

city: LITTLE ROCK

first: Melanie

last: MacNicol

state: Arkansas

address: 4301 W Markham St

department: Neuroscience

institute: UAMS

data_processing:
Quality of sequencing for RNA reads were checked using FastQC. The adaptors and low-quality bases (Q < 20) were trimmed to a minimum of 36 base pairs using Trimmomatic (27). STAR was used to align Mus musculus GRCm39.104 reference genome with reads that passed quality control (28). To obtain raw counts, BAM files using Subread's features Count function were transformed to log2 counts per million (CPM) (29). Genes with a low expression were filtered out and libraries normalized by trimmed mean of M values (30). R package, Limma, using the voom “With Quality Weights” function was used for differential expression and linear modeling (31).  Genes with an FDR adjusted p-values < 0.055 and a Log2FC ≥ 0.58 (1.5-fold increase) were considered significant and designated as differentially expressed genes (DEGs).
Assembly: Mus musculus GRCm39.104
Supplementary files format and content: tab-delimited csv

source_name: Pituitary

growth_protocol: For the diet induced obesity (DIO) studies, additional offspring were generated using the CR20 model as described above (see 2.2). FED and CR20 offspring were weaned at PND21 and separated by sex. Offspring weight and length (nose to anus) were measured weekly from weaning to 8 weeks of age. Female pups were inspected daily from PND 21 until the day of vaginal opening to determine the timing of puberty.

extract_protocol:
At euthanasia, trunk serum, pituitaries, eWAT, and liver were collected.
Libraries for RNAseq were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina Inc) according to the manufacturer’s protocol.

treatment_protocol: At 8 weeks of age, pups from each dam were blindly assigned to either a CTRL or HFD feeding group. Offspring were introduced to either a 10% fat (CTRL) diet (Envigo, TD.110675) or a 45% high fat diet (HFD) (Envigo, TD.06415) which they consumed for 10 weeks or 16 weeks. For each sex, this resulted in four experimental groups with 5±1 mice/group: FED control (FED-CTRL); FED high fat diet (FED-HFD) and calorie restricted control (CR20-CTRL) and HFD (CR20-HFD).  Food intake, an average of food consumed divided by the number of mice per cage, and individual mouse weights were measured weekly for the duration of the experiment

value: Pituitary


title: 6CR20HFD_PIT


title: 6CR20HFD_FAT

source_name: Epididymal white adipose tissue(eWAT)

value: Epididymal white adipose tissue(eWAT)


title: 5CR20CTRL_FAT


title: 7CR20HFD_LIV

source_name: Liver

value: Liver


title: FKH

description: FKH

value: FKH


title: 4CR20CTRL_FAT


title: 49CR20CTRL_PIT


title: EOL

value: EOL


title: 6CR20HFD_LIV


title: F36P


title: 4CR20CTRL_PIT


title: 4CR20CTRL_LIV


title: 48CR20CTRL_PIT


title: 49CR20CTRL_FAT


title: 47CR20CTRL_LIV


title: 5CR20CTRL_LIV


title: 46CR20HFD_LIV


title: 48CR20CTRL_LIV


title: 47CR20CTRL_PIT


title: 48CR20CTRL_FAT


title: 46CR20HFD_PIT


title: 47CR20CTRL_FAT


title: HEL

description: HEL

value: HEL


title: 7CR20HFD_FAT


title: 45CR20HFD_PIT


title: 45CR20HFD_LIV


title: 46CR20HFD_FAT


title: 49CR20CTRL_LIV


title: 42FEDCTRL_FAT


title: 42FEDCTRL_PIT


title: 33CR20CTRL_PIT


title: 40FEDHFD_FAT


title: 5CR20CTRL_PIT


title: 41FEDCTRL_PIT


title: 45CR20HFD_FAT


title: 40FEDHFD_LIV


title: 41FEDCTRL_LIV


title: 42FEDCTRL_LIV


title: 23FEDHFD_PIT


title: 33CR20CTRL_FAT


title: 31CR20HFD_PIT


title: 24FEDCTRL_FAT


title: 31CR20HFD_LIV


title: 33CR20CTRL_LIV


title: 23FEDHFD_LIV


title: 24FEDCTRL_LIV


title: 32CR20HFD_LIV


title: 31CR20HFD_FAT


title: 23FEDHFD_FAT


title: 24FEDCTRL_PIT


title: 41FEDCTRL_FAT


title: 32CR20HFD_FAT


title: 16FEDCTRL_LIV


title: 40FEDHFD_PIT


title: 32CR20HFD_PIT


title: 16FEDCTRL_FAT


title: 16FEDCTRL_PIT


title: Male High Fat Diet Pituitary 15 wk rep2

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexed fastq files generated by the UAMS Genomics Core were analyzed with the 10x Genomics Cell Ranger 3.1.0 count function for sequence alignment and gene counting
The reads were aligned to the University of California, Santa Cruz (UCSC) mm10 reference transcriptome using STAR and transcript counts are generated (37,38).
The R package Seurat was used to further analyze the filtered, aggregated, and depth normalized counts generated by cellranger count and cellranger aggr (http://software.10xgenomics.com/single-cell/overview/welcome, Butler et al, 2018).
Cells with unique feature counts over more the 75th percentile plus 1.5 times the interquartile range (IQR) or less 200 unique features, total gene counts more than more the 75th percentile plus 1.5 times the IQR or less than 1000 counts, and/or mitochondrial feature percentage more the 75th percentile plus 1.5 times the IQR or less than the 25th percentile minus 1.5 times the IQR were filtered out of the data. Next, the 2000 highest variable features are selected. The data is then scaled by a linear transformation and variation associated with cell death and cell cycling where regressed out of the scaled data using mitochondrial feature percentage and cell cycle scoring values. Counts were normalized using the SCTransform and PCA was performed on the scaled data. A Uniform Manifold Approximation and Projection (UMAP) was used to visualize and explore the clustering results. Seurat’s FindNeighbors and FindClusters functions were optimized to label clusters based on the visual clustering in the projections. Seurat FindAllMarkers function was used to identify gene markers that define cluster cell types. These gene markers were compared to known markers of expected cell types in order to assign appropriate cell type labels (Frazén et al, 2019). Differential expression analysis was performed using the FindMarkers to compare similar cell types across diet and gender. The MAST test, a GLM-framework that treats cellular detection rate as a covariate, was used to determine statistically different transcription (Finak et al, 2015). Genes with an FDR adjusted p-values < 0.055 and a Log2FC ≥ 0.58 (fold increase 1.5) were considered significant.
Assembly: University of California, Santa Cruz (UCSC) mm10 reference transcriptome
Supplementary files format and content: filtered_feature_bc_matrix.h5

extract_protocol:
Pituitaries were removed for dispersion/centrifugation, cells were washed gently, centrifuged, and resuspended in DMEM with no gentamicin.
individual pituitary cell suspensions were pooled within treatment groups (2-3 pituitaries/pool) and counted.  Concentration of the cells within each pool was adjusted to optimally target 10,000 cells according to 10X Genomics guidelines.   Samples were then submitted to the UAMS Cancer Institute Genomics Core facility, where cells were resuspended in PBS with 0.04% BSA, filtered, recounted, and assessed for viability.  Then, 10,000 cells from each pool were targeted for scRNA-seq according to the 10X Genomics protocol.

treatment_protocol: Each group was first acclimated to the thermoneutral environment for 1 week (beginning at 12 weeks of age) and then exposed to the HFD  or normal control diet (ND) for either 10 weeks or 15 weeks. For all groups, the HFD (fat, 60 kcal%; carbohydrate, 36 kcal%; protein, 19 kcal%) was supplied as palatable pellets. The sources of fat were lard and soybean oil (ENVIGO, TD.06414). Mice receiving the control, normal diet (ND) received ENVIGO Reduced Sucrose Control Diet (10% fat, TD.08806).

value: FVB.129P2-Pde6b + Tyr c-ch/AntJ

value: male

value: High Fat Diet


title: Female High Fat Diet Pituitary 15 wk rep2

description: 10X Genomics

value: Female


title: Male High Fat Diet Pituitary 15 wk rep1

description: 10X Genomics


title: 15FEDCTRL_PIT


title: 15FEDCTRL_FAT


title: Female High Fat Diet Pituitary 15 wk rep1

description: 10X Genomics


title: 14FEDCTRL_PIT


title: 15FEDCTRL_LIV


title: Male Control Pituitary 15 wk rep2

description: 10X Genomics

value: Control


title: 14FEDCTRL_LIV


title: Male Control Pituitary 15 wk rep1

description: 10X Genomics


title: 14FEDCTRL_FAT


title: 13FEDHFD_PIT


title: Female Control Pituitary 15 wk rep2

description: 10X Genomics


title: 13FEDHFD_FAT


title: 13FEDHFD_LIV


title: Male High Fat Diet Pituitary 10 wk

description: 10X Genomics


title: 12FEDHFD_PIT


title: Female Control Pituitary 15 wk rep1

description: 10X Genomics


title: Male Control Pituitary 10 wk

description: 10X Genomics


title: Female Control Pituitary 10 wk

description: 10X Genomics


title: Female High Fat Diet Pituitary 10 wk

description: 10X Genomics


title: 12FEDHFD_LIV


title: 12FEDHFD_FAT


title: 11FEDHFD_PIT


title: 10FEDHFD_FAT


title: 10FEDHFD_LIV


title: Hashing reads for scGEX-1 & scBCR-1 (HC013, HC017, HC020)

status: Public on Nov 16 2023

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

data_processing:
GRCh38
Compressed tar files contain output from CellRanger, as well as sample-level metadata and sample hashing information.

source_name: Peripheral Blood

extract_protocol:
Peripheral blood was collected in heparin tubes (BD, #367874) and processed within 24 hours. Blood was spun at 1,500 rpm for 10 min. The plasma layer was collected and stored at -80°C. PBMCs were separated by Ficoll-Paque Plus density gradient centrifugation (Sigma-Aldrich, #GE17-1440-02) using Leucosep tube (Grainer Bio-One, #227288) following the manufacturer’s instructions. After the isolation, the PBMCs were counted and resuspended in 500 ul of 5% AB serum in RPMI and 500 ul of 20% DMSO in AB serum at 0.5 – 10 x 106 PBMCs per cryovial and cryopreserved.
10X Genomics libraries:B cells were isolated from 17 million to 100 million PBMC from 5 peanut allergic children with sIgE>100 and 3 non-allergic children by EasySepTM Human B cell Isolation Kit (STEMCELL technologies, #17954). Hash tagged antibodies were added to 3 million B cells from each sample. B cells from 2 peanut allergic subjects were combined in experiment 1. In experiment 2, B cells from 3 non-allergic subjects were combined, and B cells from 3 non-allergic children were combined. The cells were then stained with BV421 anti-human CD19 and FITC anti-human CD27 antibodies and CD19+CD27+ memory B cell populations were sorted on a FACSAria (BD). After confirming cell number and viability, B cells were run on a Chromium 10X controller using 5’ chemistry (10X Genomics) in one lane (experiment 1) or two lanes (experiment 2) with an expected recovery rate of 10,000 cells per lane, according to the manufacturer’s instructions. Libraries were generated and run on a HiSeq2500 apparatus.  PacBio Libraries: Ara h 2 multimers were generated by associating biotinylated Ara h 2 with PE-labeled streptavidin or AF647-labeled streptavidin. Similarly, detoxified diphtheria toxin (DT) (CRM197, PFENEX Biopharmaceuticals) was used to generate DT multimers. Ara h 2 (or DT) binding B cells were sorted into 96 well plates with lysis buffer containing RNAse inhibitor, dNTPs and oligo dT-VN30 anchored with template switch oligo sequence (Table S4). Plates were flash frozen in dry ice and stored at -80°C. Plates were thawed on ice, then oligo dT was added and annealing was performed at 70°C for 5 min. cDNA synthesis and cDNA amplification was performed with template switching oligo (TSO) using template switching RT enzyme mix (NEB) according to the manufacturer’s instruction. The first PCR was performed to amplify BCR heavy and light chains using outer primers targeting human immunoglobulin constant regions (IgG, IgM for heavy chains, kappa and lambda for light chains) and TSO inner primer (Table S4), respectively. After cleaning up the PCR products, BCR heavy and light chains were further amplified with inner primers with plate and row specific ID (5’) and column specific ID (3’) to enable the identification of BCR sequences derived from each well (Table S4). Afterwards, all PCR products were combined as one library. PacBio sequencing was performed to obtain long amplicon reads to cover 500 to 1000 bp. All PCR reactions were performed using NEBNext UltraTM II Q5 master mix (NEB).
BCR sequence data from 10X Genomics scRNA-seq + BCR sequencing began with the filtered V(D)J contigs from Cell Ranger version 3.1. To obtain V and J gene assignments, these contigs were aligned to the IMGT GENE-DB germline reference allele database (obtained 8/3/2019)43. Non-productive heavy and light chain BCR sequences were removed. BCRs were annotated by B cell subtype based on matching their single cell barcodes to the gene expression information. Only cells that had both gene expression and BCR sequence data were retained. In cells with multiple heavy chains, only one heavy chain with the highest unique molecular identifier count was retained. In the event of a tie, the first heavy chain identified was retained.
For BCR sequencing data from sorted single cell PacBio sequencing data, adaptor ligation, sequencing reactions, and initial sequence processing were conducted at GENEWIZ, LLC/Azenta US, Inc (South Plainfield, NJ, USA) using standard PacBio circular consensus sequence (CCS) tools and guidelines. Further processing was performed using presto v0.6.244. To remove reads too short to likely contain functional BCRs and associated constant regions, reads shorter than 500bp were removed. After initial processing, PacBio BCR sequence reads were assembled into consensus sequences. As with 10X Genomics BCR sequence data, consensus sequences were aligned to the IMGT GENE-DB database43 to obtain V and J germline annotations. Non-productive heavy and light chain BCR sequences were removed.
BCRs from both 10X Genomics and PacBio were processed using the Immcantation suite.

value: Peripheral Blood

value: B-Lymphocyte


title: Hashing reads for scGEX-3 & scBCR-3 (FA007, FA048)


title: 11FEDHFD_LIV


title: Hashing reads for scGEX-2 & scBCR-2 (FA028, FA053, FA011)


title: 10FEDHFD_PIT


title: 11FEDHFD_FAT


title: Hashed scBCR sample (FA007, FA048)


title: Hashed scGEX sample (HC013, HC017, HC020)


title: Hashed scGEX sample (FA028, FA053, FA011)


title: Hashed PacBio scBCR library 1


title: Hashed scBCR sample (HC013, HC017, HC020)


title: GFP+ cells, organoid, Day 20

status: Public on Oct 04 2023

city: Glendale

first: Crystal

last: Marconett

state: CA

address: 1856 Kirkby Rd

department: Translational Genomics

institute: Keck School of Medicine

description: 10x Genomics

data_processing:
Cell Ranger pipeline (v7.0.1) was applied to generate a data matrix
Assembly: custom mm10 with EGFP and tdTomodo sequence added
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Lung

growth_protocol: Sorted GFP+ cells were seeded with 100,000 MLg fibroblasts in growth factor-reduced Matrigel on Transwell filter inserts in DMEM/F-12 containing 10% fetal bovine serum, insulin transferrin, glutamine, penicillin/streptomycin and SB 431542.

extract_protocol:
Flow cytometry sorted GFP+ cells were defined as day 0. On days 8, 13, and 20 of 3D culture, to obtain single cells, colonies were dissociated with dispase and TrypLE express. Biotinylated EpCAM Ab, anti-biotin microbeads, and MS columns were used to enrich for epithelial cells. For each time point, cells were counted, and viability was measured using an automated cell counter.
Single-cell suspensions were processed for library construction using Chromium Single Cell 3’ Reagent Kits v3.1. Briefly, cells resuspended in the reaction mix were loaded into the Chromium Single Cell Chip G, as well as the 10x Barcoded Gel Beads and the partitioning oil. The Chip G was placed into the 10x Chromium controller for cell partitioning, targeting a final number of 10 thousand cells per sample. After partition was concluded, the Gel Bead-In Emulsions were transferred to the C1000 Touch Thermal Cycler for the first phase of reverse transcription and samples proceed to library preparation following manufacturer’s instructions.

value: Lung

value: Alveolar epithelial cells

tag: time

value: Day 20


title: GFP+ cells, Day 0

description: 10x Genomics

value: Day 0


title: TG_FD_Untreated_5905

status: Public on Sep 28 2023

city: Boston

first: Susan

last: Slaugenhaupt

state: Massachusetts

address: 185 Cambridge Street, CPZN-5254

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
RNASeq reads were mapped against a custom referenceby STAR (version 2.5.22b) allowing 5% mismatch
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.36)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using HTSeq(v0.11.2) and DESeq2 (v1.34.0).
Assembly: human ELP1 gene (ENSG00000070061) Ensemble Human transcriptome reference GRCh37.75 to the Ensembl Mouse Transcriptome GRCm38.83
Supplementary files format and content: Supplementary Table S1 - DEG_stats.txt

source_name: Trigeminal Ganglion

growth_protocol: We developed a mouse model that faithfully recapitulates the the FD phenotype seen in patients using the TgFD9 hypomorphic mouse and human transgene.

extract_protocol:
RNA was harvested using QIAzol Reagent as per manufacturrers instructions. 100 ng of total RNA was used for the construction of sequencing libraries.
Tru-Seq Stranded® mRNA library Prep Kit (Illumina, 20020594) following manufacturer's protocols.

value: Trigeminal Ganglion

value: WT


title: GFP+ cells, organoid, Day 8

description: 10x Genomics

value: Day 8


title: GFP+ cells, organoid, Day 13

description: 10x Genomics

value: Day 13


title: TG_FD_Untreated_5901


title: TG_FD_Untreated_5906


title: TG_FD_Untreated_5877


title: TG_FD_Untreated_5780


title: Hashed scBCR sample (FA028, FA053, FA011)


title: TG_FD_Untreated_5881


title: TG_FD_Untreated_5822


title: TG_FD_Untreated_5378


title: TG_FD_Untreated_5753


title: Hashed scGEX sample (FA007, FA048)


title: TG_Control_Untreated_5902


title: TG_FD_Untreated_5376


title: TG_Control_Untreated_5900


title: TG_FD_Untreated_5441


title: TG_FD_Untreated_5374


title: TG_Control_Untreated_5875


title: TG_Control_Untreated_5779


title: TG_FD_Untreated_5373


title: TG_Control_Untreated_5821


title: TG_Control_Untreated_5880


title: Hashed PacBio scBCR library 2


title: TG_Control_Untreated_5776


title: TG_Control_Untreated_5752


title: TG_Control_Untreated_5377


title: SC_FD_Untreated_5905

source_name: Spinal Cord

value: Spinal Cord

value: Familial Dysautonomia (FD)


title: SC_FD_Untreated_5901


title: SC_FD_Untreated_5906


title: TG_Control_Untreated_5907


title: SC_FD_Untreated_5822


title: SC_Control_Untreated_5902


title: SC_Control_Untreated_5907


title: SC_FD_Untreated_5378


title: SC_FD_Untreated_5374


title: SC_FD_Untreated_5376


title: SC_FD_Untreated_5753


title: SC_FD_Untreated_5881


title: SC_FD_Untreated_5877


title: SC_FD_Untreated_5373


title: SC_FD_Untreated_5780


title: SC_Control_Untreated_5880


title: SC_Control_Untreated_5779


title: SC_Control_Untreated_5875


title: SC_Control_Untreated_5776


title: SC_Control_Untreated_5377


title: SC_Control_Untreated_5821


title: SC_Control_Untreated_5375


title: MED_FD_Untreated_5906

source_name: Medulla

value: Medulla


title: TG_Control_Untreated_5372


title: TG_Control_Untreated_5375


title: SC_Control_Untreated_5752


title: SC_Control_Untreated_5372


title: SC_Control_Untreated_5900


title: MED_FD_Untreated_5905


title: MED_FD_Untreated_5822


title: SC_FD_Untreated_5441


title: MED_FD_Untreated_5441


title: MED_FD_Untreated_5753


title: MED_FD_Untreated_5881


title: MED_FD_Untreated_5877


title: MED_FD_Untreated_5374


title: MED_Control_Untreated_5821


title: MED_FD_Untreated_5373


title: MED_FD_Untreated_5378


title: MED_Control_Untreated_5779


title: MED_FD_Untreated_5780


title: MED_FD_Untreated_5376


title: MED_Control_Untreated_5900


title: MED_Control_Untreated_5880


title: MED_Control_Untreated_5907


title: MED_Control_Untreated_5902


title: MED_Control_Untreated_5375


title: MED_Control_Untreated_5377


title: MED_Control_Untreated_5752


title: DRG_FD_Untreated_5905

source_name: Dorsal Root Ganglion

value: Dorsal Root Ganglion


title: DRG_FD_Untreated_5881


title: MED_Control_Untreated_5875


title: MED_Control_Untreated_5372


title: DRG_FD_Untreated_5901


title: DRG_FD_Untreated_5906


title: DRG_FD_Untreated_5877


title: MED_FD_Untreated_5901


title: DRG_FD_Untreated_5441


title: DRG_FD_Untreated_5822


title: DRG_FD_Untreated_5378


title: DRG_FD_Untreated_5753


title: DRG_FD_Untreated_5780


title: DRG_FD_Untreated_5376


title: DRG_Control_Untreated_5880


title: MED_Control_Untreated_5776


title: DRG_FD_Untreated_5374


title: DRG_Control_Untreated_5907


title: DRG_FD_Untreated_5373


title: DRG_Control_Untreated_5902


title: DRG_Control_Untreated_5900


title: DRG_Control_Untreated_5752


title: DRG_Control_Untreated_5377


title: DRG_Control_Untreated_5821


title: DRG_Control_Untreated_5776


title: Cortex_FD_Untreated_5881

source_name: Cortex

value: Cortex


title: DRG_Control_Untreated_5875


title: Cortex_FD_Untreated_5901


title: DRG_Control_Untreated_5372


title: Cortex_FD_Untreated_5906


title: DRG_Control_Untreated_5375


title: Cortex_FD_Untreated_5822


title: Cortex_FD_Untreated_5441


title: Cortex_FD_Untreated_5753


title: Cortex_FD_Untreated_5877


title: Cortex_FD_Untreated_5780


title: Cortex_FD_Untreated_5905


title: Cortex_FD_Untreated_5378


title: Cortex_FD_Untreated_5373


title: Cortex_FD_Untreated_5374


title: Cortex_Control_Untreated_5776


title: Cortex_Control_Untreated_5880


title: Cortex_Control_Untreated_5907


title: Cortex_Control_Untreated_5902


title: Cortex_Control_Untreated_5779


title: Cortex_Control_Untreated_5752


title: Cortex_Control_Untreated_5821


title: Cortex_Control_Untreated_5875


title: Nfe2l2fl/fl, scRNAseq

status: Public on Aug 25 2023

description: 10X Genomics

data_processing:
CellRanger v4.0.0 (10x Genomics) was used to perform single-cell 5’ gene counting using mouse genome GRCm38.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mice were anesthetized with isoflurane and intranasally administrated with a mixture of 7 ug of PAO and 20 µg of Ova every other day for 9 days (day 0, 2, 4, 6, 8). In house dust mite (HDM)-induced lung inflammation experiments, mice were sensitized on day 0 by 1 µg of Der f 1 via intranasal route. After 1 week, mice were intranasally administered with 10 µg of Der f 1 every day for a total five times (day 7, 8, 9, 10, 11). Sixteen hours after the last administration, all mice were euthanized and bronchoalveolar lavage (BAL) fluid, lung, and mediastinal lymph node were obtained for further analysis. For mixed bone marrow transplantation experiment, donor bone marrow cells from WT control (CD45.1+/+) and Cd4creNfe2l2fl/fl (CD45.2+/+) mice were mixed at 1:1 ratio and adoptively transferred into irradiated recipient Rag1-/- mice. After 4-week reconstitution period, the recipients were intranasally injected with a mixture of PAO/Ova as previously described.
To generate single cell Gel Beads-in-Emulsion (GEMs), the 10x Genomics Chromium platform was used to capture and barcode the cells by following the manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA). Cell suspensions were loaded on to 10x Genomics Chromium Next GEM Chip K along with the reverse transcription master mix. Along with gel beads coated with oligonucleotides, cells were divided into the GEMs. These oligonucleotides were used for mRNA capture inside the droplet by 13 bp oligo-dT after cell lysis. After reverse transcription, cDNAs with barcodes were amplified and qualified using BioAnalyzer 2100 (Agilent technologies, Santa Clara, CA, USA). The libraries were constructed from these DNA products with the Single Cell Reagent Kit (5’ v2 chemistry) for each sample. Adapters were ligated on to the cDNAs and amplified with indexing primer.

value: CD4+ cells

value: 8-15 weeks old


title: Cd4cre Nfe2l2fl/fl, scRNAseq

description: 10X Genomics


title: 15-7 [ssBCR-Seq]

status: Public on Aug 20 2023

data_processing:
Library strategy: scBCR-seq
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Quality control was performed removing sequences with nonproductive arrangements, lacking valid V or J gene annotation. Cells were further filtered that have exactly one heavy chain sequence.
B cell clones were inferred based on heavy chain sequences using hierarchical clustering with single-linkage (Gupta 2017) for each subject with day 0 and day 7 cells combined. Sequences were first partitioned based on common V and J gene annotations and junction lengths. Within each partition, sequences whose junction sequences were within 0.12 normalized Hamming distances between each other were clustered as clones. The cutoff was chosen based on manual inspection of the bimodal distance-to-nearest distribution.
Somatic hypermutation frequency was computed using the “calcObservedMutations” function from SHazaM v1.0.2 package (Gupta 2015) and was the number of nucleotide mismatches from the germline sequences of the heavy chain variable segments leading up to the CDR3.
Genome_build: GRCh38
Supplementary_files_format_and_content: BCR-seq results were saved in AIRR-tsv format and gzip compressed.
Supplementary_files_format_and_content: Tar archives include cell ranger output files.

source_name: single-cell BCR-seq of human: adult male PBMC seven days post vaccination

extract_protocol:
B cells were isolated from PBMCs using the EasySepTM Human Pan-B cell Enrichment Kit (immunomagnetic negative selection kit, StemCell) per the manufacturer’s instructions.
Single-cell emulsions and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol using the Chromium Controller (10x Genomics). The NovaSeq 6000 with 150x150 paired-end reads was used to sequence gene expression libraries.

tag: timepoint

value: seven days post vaccination

value: PBMC

value: B-cell

value: male

tag: ethnicity

value: Hispanic or Latino

tag: race

value: White

tag: library type

value: scBCR-seq


title: Cortex_Control_Untreated_5372

value: WT


title: Cortex_FD_Untreated_5376


title: Cortex_Control_Untreated_5377


title: 15-0 [ssBCR-Seq]

source_name: single-cell BCR-seq of human: adult male PBMC pre-vaccination

value: pre-vaccination

tag: tissue


title: 93-7 [ssBCR-Seq]

source_name: single-cell BCR-seq of human: adult female PBMC seven days post vaccination

value: female

value: Not Hispanic or Latino


title: 94-7 [ssBCR-Seq]


title: 94-0 [ssBCR-Seq]

source_name: single-cell BCR-seq of human: adult female PBMC pre-vaccination


title: 09-7 [ssBCR-Seq]


title: 93-0 [ssBCR-Seq]


title: 09-0 [ssBCR-Seq]


title: 48-0 [ssBCR-Seq]


title: 67-7 [ssBCR-Seq]


title: 67-0 [ssBCR-Seq]


title: Cortex_Control_Untreated_5900


title: 15-0 [ssRNA-Seq]

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the cellranger count subcommand.
Gene expression analysis of CellRanger output was performed using Seurat v.3.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files barcodes.tsv & features.tsv. The tar.gz file also contains a feature-barcode matrix file named matrix.mtx, stored in the Market Exchange Format for sparse matrices. The matrix file contains indexes to barcodes and gene/features, as well as total UMI count per cell and gene/feature combination.

source_name: single-cell RNA-seq of human: adult male PBMC pre-vaccination

extract_protocol:
B cells were isolated from PBMCs using the EasySepTM Human Pan-B cell Enrichment Kit (immunomagnetic negative selection kit, StemCell) per the manufacturer’s instructions.
Single-cell emulsions and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol using the Chromium Controller (10x Genomics). The NovaSeq 6000 with 100x100 paired-end reads was used to sequence gene expression libraries.
ssRNA-Seq

value: scRNA-seq


title: Cortex_Control_Untreated_5375


title: 48-7 [ssBCR-Seq]


title: 09-7 [ssRNA-Seq]

source_name: single-cell RNA-seq of human: adult female PBMC seven days post vaccination


title: 09-0 [ssRNA-Seq]

source_name: single-cell RNA-seq of human: adult female PBMC pre-vaccination


title: 94-7 [ssRNA-Seq]


title: 93-7 [ssRNA-Seq]


title: 94-0 [ssRNA-Seq]


title: 67-7 [ssRNA-Seq]


title: 93-0 [ssRNA-Seq]


title: 48-7 [ssRNA-Seq]

source_name: single-cell RNA-seq of human: adult male PBMC seven days post vaccination


title: 67-0 [ssRNA-Seq]


title: 48-0 [ssRNA-Seq]


title: shGFP_1_S19

status: Public on Aug 10 2023

city: Pamplona

first: Silvestre

last: Vicent

address: Avenida Pío XII 55

department: Oncology

country: Spain

institute: Center for Applied Medical Research (CIMA)

data_processing:
The quality of the samples was verified using FastQC v0.11.3 software.
FASTQ files were mapped to hg19 human assembly using STAR v2.5.2b with default parameters.
featureCounts v1.5.0 software and Gencode v19 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: H358 cell line

growth_protocol: Cells were grown in RPMI1640 (10% FBS and 1% antibiotics)

extract_protocol:
RNA was processed using Trizol and cleaned using Qiagen columns. RNA quality was analysed using Experion™ (Bio-Rad) and only RNAs with RQI>7 were included in the experiment.
Library construction was done as reported in Jaitin, D.A., et al., Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science, 2014. 343(6172): p. 776-9.
Low input RNA-seq (mars-seq)

treatment_protocol: Cells were infected with 3 different shRNAs (GFPsh, FOSL1sh or KRASsh) for 2 days, then selected with puromycin for 3 days. Upon expansion of selected cells, shRNAs were induced by addition of 1 ug/ml doxycycline for 4 days, then trypsinized and plated for 24 h before RNA was harvested

value: shGFP


title: sh2_3

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR v2.6.1c with default parameters.
featureCounts v1.6.0 software and Gencode v35 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: pancreatic cancer cells (HPAFII)

growth_protocol: HPAFII cell lines was grown in DMEM (10% serum and 1% antibiotics) and transduced with constitutive shRNAs (GFPsh or LAMC2sh) for 48 h. Cells were selected with 2 ug/ml puromycin for 3 days and then plated overnight before RNA was harvested.

extract_protocol:
Trizol
Illumina protocol

tag: cell line

value: HPAFII


title: shFOSL1_2_S20


title: GFP_3


title: shKRAS_1_S18

value: shKRAS


title: shGFP_3_S25


title: Tram_1

data_processing:
The quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to hg38 human assembly using STAR v2.5.3a with default parameters.
featureCounts v1.6.0 software and Gencode v28 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: H1792 cell line treated with Trametinib (MEKi) for 16 hours

growth_protocol: H1792 were grown in 10% FBS-supplemented RPMi1640

extract_protocol:
RNA was processed using Trizol and cleaned using Qiagen columns. RNA quality was analysed using Experion™ (Bio-Rad) and only RNAs with RQI>7 were included in the experiment.
Library construction was done as reported in Jaitin, D.A., et al., Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science, 2014. 343(6172): p. 776-9; Low input RNA-seq (mars-seq)

treatment_protocol: Cells were treated with 0.5 uM trametinib and 0.625 uM lestaurtinib for 16 hours


title: GFP_1


title: sh2_2


title: shFOSL1_1_S17


title: shGFP_2_S22


title: Tram_3


title: shKRAS_3_S24


title: shFOSL1_3_S23


title: shKRAS_2_S21


title: sh2_1


title: GFP_2


title: Lest_2

source_name: H1792 cell line treated with Lestaurtinib (multikinase FLT3i) for 16 hours


title: Lest_3


title: CTL_3

source_name: H1792 cell


title: 15-7 [ssRNA-Seq]

tag: cell type


title: CTL_2


title: Lest_1


title: PITPNC1sh7_2

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR v2.6.1c with default parameters.
featureCounts v1.6.0 software and Gencode v35 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: lung cancer cells

growth_protocol: A549 cell line was grown in RPMI (10% serum and 1% antibiotics) and transduced with constitutive shRNAs (GFPsh, PITPNC1sh6 and PITPNC1sh7) for 48 h. Cells were selected with 2 ug/ml puromycin for 3 days and then plated overnight before RNA was harvested.

value: PITPNC1sh7-expressing cells


title: CTL_1


title: PITPNC1sh7_1


title: PITPNC1sh6_3

value: PITPNC1sh6-expressing cells


title: Tram_2


title: PITPNC1sh6_2


title: PITPNC1sh7_3


title: GFPsh_1

value: GFPsh-transduced A549 cells


title: GFPsh_2


title: S6.Msi.IP.TSTRLT

status: Public on Jul 31 2023

data_processing:
Fastq quality check:FastQC,v0.11.8
Fastq trimming: Trimmomatic, v0.39
Alignment: STAR, version 2.7.1a
Assembly: Mus musculus GRCm39.104
Supplementary files format and content: counts

extract_protocol:
Pituitaries from sighted FVB males and females (FVB.129P2‐Pde6b+Tyrc‐ch/Ant, The Jackson Laboratory) were collected and placed into DBPS with RNase inhibitor to be stored at -20 degrees C.
Libraries for RNAseq were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina Inc) according to the supplier’s protocol.

treatment_protocol: Musashi1 was immunoprecipitated from lysate from six adult 8-10 week old control mouse pituitaries equally split between Musashi1 antibody (Abcam, ab52865) plus Musashi2 antibody (Abcam, ab114107) or control rabbit IgG (Millipore Sigma PP64) as per the kit supplier’s protocol (Invitrogen Dynabeads Protein A IP kit, Fisher Scientific, catalog # 10006).  Musashi IP was done with both antibodies pooled together. Protein was degraded, and RNA was isolated, precipitated and utilized for RNAseq.  The immunoprecipitation experiments were performed on six separate occasions (three for male pituitaries, three for female pituitaries).

value: pituitary

tag: rip antibody

value: 8-10 weeks

value: Female


title: S7.IgG.TSTRLT

source_name: Pituitaries from sighted FVB males and females (FVB.129P2‐Pde6b+Tyrc‐ch/Ant,

value: IgG

value: Male


title: S5.IgG.TSTRLT


title: PITPNC1sh6_1


title: EGI1_TET_FOSL1sh10_2

status: Public on Jul 22 2023

source_name: cholangiocarcinoma cell line

growth_protocol: EGI-1 cell were grown in 10% FBS DMEM using 10 cm plates

treatment_protocol: Cells were treated with 2ug/ml doxycycline for 4 days and seeded for 24 h. Then cells were harvested and RNA isolated.

value: cholangiocarcinoma (CCA)


title: S3.IgG.TSTRLT


title: EGI1_TET_FOSL1sh10_1


title: EGI1_TET_FOSL1sh10_3


title: S6.IgG.TSTRLT


title: S3.Msi.IP.TSTRLT


title: EGI-1 flag-tagged FOSL1 overexpressing cells

data_processing:
The quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to hg38 human assembly using Bowtie2 v2.5.3a with default parameters.
MACS 2.1.0.20151222 was the peak calling algorithm used with default parameters.
SAM files were converted to BAM files and sorted with SAMtools v1.9-foss-2018b
BAM files were converted to bedGraph files with the bedtools suite v2.27.1
bedGraph files were converted to BigWig files using bedGraphToBigWig v4
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files generated from bedGraph files.

extract_protocol: Library preparation was performed with the NEBNext® Ultra™ II DNA Library Prep Kit


title: EGI1_TET_FOSL1sh3_2


title: EGI1_TET_FOSL1sh3_3


title: EGI1_TET_FOSL1sh3_1


title: EGI1_TET_GFPsh_3


title: S2.IgG.TSTRLT


title: EGI1_TET_GFPsh_1


title: EGI1_TET_GFPsh_2


title: GFPsh_3


title: EGI-1 Input


title: Platelet Sample from Subject 182493, 28 Days Post Vaccination

status: Public on May 31 2023

data_processing:
Raw data was demultiplexed and converted to FASTQ format using bcl2fastq.
FASTQ files were quality trimmed using Trimmomatic.
FASTQ files were quality assessed with FASTQC.
Quality-trimmed FASTQ files were aligned against human reference with STAR aligner.
Read counts for each gene were genereated with htseq-count.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Each processed file contains the read counts for each gene for one sample. The format is plain text, gzip compressed.

source_name: platelet

extract_protocol:
Whole blood was collected in a yellow-cap tube and stored at room temperature. The tube was centrifuged and the platelet-rich plasma (PRP) was collected. The PRP was aliquoted and further centrifuged to isolate the platelet pellet. The platelet pellet was dissolved in 700 microliter Qiasol/TRISol. RNA was extracted using the Qiagen miRNA Easy Kit (Cat. # 217004) following the manufacturer’s instructions using a QIACUBE.
RNA-seq libraries were prepared using the Takara Bio SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian per the manufacturer’s instructions.

tag: subject id

tag: gender

value: Young

tag: time point relative to flu vaccination

value: 28 Days Post-Vaccination


title: Gramd2-CreERT2 control

status: Public on Jul 20 2023

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Paired-end sequencing (2x100) was performed on an Illumina instrument. Sequencing data was pre-processed using the Space Ranger pipelines (10x Genomics,https://cloud.10xgenomics.com/cloud-analysis).
BCL data was demultiplexed and converted to FASTQ format using the spaceranger mkfastq pipeline.
The spaceranger count pipeline was then used for read alignment to human reference genome mm10, Unique Molecular Identifier (UMI) counting, and generation of feature-spot matrices corresponding to the microscopic tissue image. The pipeline also performs automatic tissue detection and fiducial alignment from the image.
Assembly: mm10
Supplementary files format and content: UMI count matrices
Library strategy: Spatial transcriptomics

source_name: Lung

growth_protocol: The Sftpc-CreERT2 mouse line has been used previously to track AT2 cell fate. Gramd2-CreERT2 mice were generated by homologous recombination insertion of a cassette including CreERT2- downstream of the endogenous Gramd2 gene stop codon within exon 12. These were separately crossed to heterozygous KrasLSL-G12D mice (Jackson laboratory, Stock: #008179). Gramd2-CreERT2 and Sftpc-CreERT2 mice were in a B6/129 mixed strain background (129 N1), while KrasLSL-G12D mice are in a B6/129S4 mixed strain background (C57BL/6 N10).

extract_protocol:
Spatial transcriptomic profiling was performed at the Molecular Genomics Core, a part of the Norris Comprehensive Cancer Center and under manufacturer’s instructions. Briefly, two biological replicates (one block for each) of Gramd2:KrasG12D and Sftpc:KrasG12D underwent initial 10μM sectioning at the Tissue Pathology Core, part of the Norris Comprehensive Cancer Center. Sections were H&E stained (as above) and underwent pathology review. Regions of Interest (ROIs) then underwent sample preparation including test slide sample sequencing using the Visium Tissue Section Test Slide (PN-2000460, 10X Genomics, Dublin, CA, USA). RNA quality assessment of test slides was determined by first extracting RNA using the Qiagen RNeasy FFPE kit (#73504, Qiagen, Hilden, Germany) and measuring RNA concentration using a Qubit fluorometer (#Q33238, ThermoFisher Scientific, Waltham, MA, USA). To determine The percentage of total fragments >200nt in length was determined by running the samples using a 4200 Tapestation (#G2991AA, Agilent, Santa Clara, CA). Once samples were determined to be of high enough quality to continue, 5μM FFPE sections were then placed in a 42C water bath and once rehydrated adhered to the Visium Spatial Gene Expression Slide (PN-2000233, 10X Genomics). Subsequently, samples were dried at 42C for 3hrs in a desiccation chamber and underwent deparrafinization using Qiagen Deparaffinization Solution (Cat # 19093) at 60C for 2 hr. Subsequently H&E staining (#MHS16, #HT110116 Millipore Sigma, Burlington MA, USA) was performed according to Visium technical parameters (CG000409) and images were captured with a Zeiss Axioscan2 microscope using a 10x objective. Decrosslinking was performed according to 10X standard protocol (CG000407) and immediately hybridized to the Visium Mouse Transcriptome probe set V1.0, which contained 20,551 genes targeted by 20,873 probes.
Post-probe extension, sequencing library construction was performed using unique sample indices using the Dual Index Kit TS, Set A (PN-1000251) for Illumina-compatible sequencing.

treatment_protocol: Tamoxifen (Sigma, CAS: 10540-29-1) powder was first dissolved in 100% ethanol (SHBJ8384, Sigma-Aldrich) and then diluted to a final concentration of 40 mg/mL with corn oil (Sigma, CAS: 8001-30-7). To ensure that tamoxifen was fully dissolved, the mixture was gently shaken in a shaking incubator (SHEL LAB, model: SSI5R; cat: #33-804R) at 55℃ for 2 hours. Six-week-old mice were injected with tamoxifen via intraperitoneal injection. For Gramd2-CreERT2; Sftpc-CreERT2, KrasLSL-G12D and WT mice, 40 mg/mL tamoxifen was injected via intraperitoneal injection. The dosage of tamoxifen was 200 mg/Kg according to the body weight of each mouse. Tamoxifen was given three times over a period of one week. For Sftpc::KrasLSL-G12D mice, 40mg/mL tamoxifen was injected via intraperitoneal injection. The dosage of tamoxifen was 100 mg/Kg according to the body weight of each mouse. Tamoxifen was given twice over a period of one week.

value: Lung

tag: genotype

value: Tamoxifen


title: Gramd2:KrasG12D Lung 3

value: Gramd2-CreERT2; Kras-LSL-G12D


title: Sftpc:KrasG12D Lung 3

value: Sftpc-CreERT2; Kras-LSL-G12D


title: S7.Msi.IP.TSTRLT

tag: age

tag: Sex


title: S5.Msi.IP.TSTRLT


title: S2.Msi.IP.TSTRLT


title: Platelet Sample from Subject 182492, 28 Days Post Vaccination


title: Platelet Sample from Subject 182493, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Platelet Sample from Subject 182493, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: Platelet Sample from Subject 182492, 2 Days Post Vaccination


title: Platelet Sample from Subject 182491, 28 Days Post Vaccination


title: Platelet Sample from Subject 182489, 2 Days Post Vaccination


title: Platelet Sample from Subject 182489, 28 Days Post Vaccination


title: Platelet Sample from Subject 182492, 7 Days Post Vaccination


title: Platelet Sample from Subject 182490, 7 Days Post Vaccination


title: Platelet Sample from Subject 182487, 28 Days Post Vaccination


title: Platelet Sample from Subject 182491, 2 Days Post Vaccination


title: Sftpc-CreERT2 control

tag: treatment


title: Platelet Sample from Subject 182487, 2 Days Post Vaccination


title: Platelet Sample from Subject 182490, 2 Days Post Vaccination


title: Platelet Sample from Subject 182490, 28 Days Post Vaccination


title: Platelet Sample from Subject 182488, 28 Days Post Vaccination


title: Platelet Sample from Subject 182487, 7 Days Post Vaccination


title: Platelet Sample from Subject 182488 Pre-vaccination

value: Pre-vaccination


title: Platelet Sample from Subject 182487 Pre-vaccination


title: Platelet Sample from Subject 182488, 2 Days Post Vaccination


title: Platelet Sample from Subject 182486, 7 Days Post Vaccination


title: Platelet Sample from Subject 182486, 2 Days Post Vaccination


title: Platelet Sample from Subject 182420, 28 Days Post Vaccination

value: Older


title: Platelet Sample from Subject 182486, 28 Days Post Vaccination


title: Platelet Sample from Subject 182420, 2 Days Post Vaccination


title: Platelet Sample from Subject 182420, 7 Days Post Vaccination


title: Platelet Sample from Subject 182419, 28 Days Post Vaccination


title: Platelet Sample from Subject 182419, 2 Days Post Vaccination


title: Platelet Sample from Subject 182489, 7 Days Post Vaccination


title: Platelet Sample from Subject 182418, 28 Days Post Vaccination


title: Platelet Sample from Subject 182488, 7 Days Post Vaccination


title: Platelet Sample from Subject 182419, 7 Days Post Vaccination


title: Platelet Sample from Subject 182491, 7 Days Post Vaccination


title: Platelet Sample from Subject 182418 Pre-vaccination


title: Platelet Sample from Subject 182418, 7 Days Post Vaccination


title: Platelet Sample from Subject 182418, 2 Days Post Vaccination


title: Platelet Sample from Subject 182417, 28 Days Post Vaccination


title: Platelet Sample from Subject 182416, 2 Days Post Vaccination


title: Platelet Sample from Subject 182416, 7 Days Post Vaccination


title: Platelet Sample from Subject 182417, 2 Days Post Vaccination


title: Platelet Sample from Subject 182417, 7 Days Post Vaccination


title: Platelet Sample from Subject 182415, 2 Days Post Vaccination


title: Platelet Sample from Subject 182416, 28 Days Post Vaccination


title: Platelet Sample from Subject 182414, 28 Days Post Vaccination


title: Platelet Sample from Subject 182414 Pre-vaccination


title: Platelet Sample from Subject 182414, 7 Days Post Vaccination


title: Platelet Sample from Subject 182417 Pre-vaccination


title: Platelet Sample from Subject 182413, 28 Days Post Vaccination


title: Platelet Sample from Subject 182414, 2 Days Post Vaccination


title: Platelet Sample from Subject 182416 Pre-vaccination


title: Platelet Sample from Subject 182412, 28 Days Post Vaccination


title: Platelet Sample from Subject 182415, 7 Days Post Vaccination


title: Platelet Sample from Subject 182413, 2 Days Post Vaccination


title: Platelet Sample from Subject 182413, 7 Days Post Vaccination


title: Platelet Sample from Subject 182412, 7 Days Post Vaccination


title: Platelet Sample from Subject 182411, 7 Days Post Vaccination


title: Platelet Sample from Subject 182411, 2 Days Post Vaccination


title: Platelet Sample from Subject 182411, 28 Days Post Vaccination


title: Platelet Sample from Subject 182412, 2 Days Post Vaccination


title: Platelet Sample from Subject 182409, 28 Days Post Vaccination


title: Platelet Sample from Subject 182415, 28 Days Post Vaccination


title: Platelet Sample from Subject 182410, 28 Days Post Vaccination


title: Platelet Sample from Subject 182410, 7 Days Post Vaccination


title: Platelet Sample from Subject 182409, 2 Days Post Vaccination


title: Platelet Sample from Subject 182410, 2 Days Post Vaccination


title: Platelet Sample from Subject 182408, 2 Days Post Vaccination


title: Platelet Sample from Subject 182408, 28 Days Post Vaccination


title: Platelet Sample from Subject 182406, 7 Days Post Vaccination


title: Platelet Sample from Subject 182407 Pre-vaccination


title: Platelet Sample from Subject 182407, 7 Days Post Vaccination


title: Platelet Sample from Subject 182408, 7 Days Post Vaccination


title: Platelet Sample from Subject 182407, 2 Days Post Vaccination


title: Platelet Sample from Subject 182405, 28 Days Post Vaccination


title: Platelet Sample from Subject 182406, 2 Days Post Vaccination


title: Platelet Sample from Subject 182404, 28 Days Post Vaccination


title: Platelet Sample from Subject 182409, 7 Days Post Vaccination


title: Platelet Sample from Subject 182405, 7 Days Post Vaccination


title: Platelet Sample from Subject 182405, 2 Days Post Vaccination


title: Platelet Sample from Subject 182404, 2 Days Post Vaccination


title: Platelet Sample from Subject 182404, 7 Days Post Vaccination


title: Platelet Sample from Subject 182343 Pre-vaccination


title: Platelet Sample from Subject 182343, 28 Days Post Vaccination


title: Platelet Sample from Subject 182341 Pre-vaccination


title: Platelet Sample from Subject 182342, 2 Days Post Vaccination


title: Platelet Sample from Subject 182340, 2 Days Post Vaccination


title: Platelet Sample from Subject 182342 Pre-vaccination


title: Platelet Sample from Subject 182341, 2 Days Post Vaccination


title: Platelet Sample from Subject 182407, 28 Days Post Vaccination


title: Platelet Sample from Subject 182340 Pre-vaccination


title: Platelet Sample from Subject 182406, 28 Days Post Vaccination


title: Platelet Sample from Subject 182340, 28 Days Post Vaccination


title: Platelet Sample from Subject 182341, 7 Days Post Vaccination


title: Platelet Sample from Subject 182339, 28 Days Post Vaccination


title: Platelet Sample from Subject 182340, 7 Days Post Vaccination


title: Platelet Sample from Subject 182343, 7 Days Post Vaccination


title: Platelet Sample from Subject 182336, 28 Days Post Vaccination


title: Platelet Sample from Subject 182337, 28 Days Post Vaccination


title: Platelet Sample from Subject 182338, 28 Days Post Vaccination


title: Platelet Sample from Subject 182338 Pre-vaccination


title: Platelet Sample from Subject 182337, 2 Days Post Vaccination


title: Platelet Sample from Subject 182337, 7 Days Post Vaccination


title: Platelet Sample from Subject 182336, 7 Days Post Vaccination


title: Platelet Sample from Subject 182335, 7 Days Post Vaccination


title: Platelet Sample from Subject 182335, 28 Days Post Vaccination


title: Platelet Sample from Subject 182335 Pre-vaccination


title: Platelet Sample from Subject 182339, 7 Days Post Vaccination


title: Platelet Sample from Subject 182335, 2 Days Post Vaccination


title: Platelet Sample from Subject 182336, 2 Days Post Vaccination


title: Platelet Sample from Subject 182333, 28 Days Post Vaccination


title: Platelet Sample from Subject 182334, 28 Days Post Vaccination


title: Platelet Sample from Subject 182334, 7 Days Post Vaccination


title: Platelet Sample from Subject 182333, 2 Days Post Vaccination


title: Platelet Sample from Subject 182333, 7 Days Post Vaccination


title: Platelet Sample from Subject 182332, 28 Days Post Vaccination


title: Platelet Sample from Subject 182331, 28 Days Post Vaccination


title: Platelet Sample from Subject 182332, 7 Days Post Vaccination


title: Platelet Sample from Subject 182332, 2 Days Post Vaccination


title: Platelet Sample from Subject 182338, 2 Days Post Vaccination


title: Platelet Sample from Subject 182330, 2 Days Post Vaccination


title: Platelet Sample from Subject 182331, 2 Days Post Vaccination


title: Platelet Sample from Subject 182331 Pre-vaccination


title: Platelet Sample from Subject 182331, 7 Days Post Vaccination


title: Platelet Sample from Subject 182330, 28 Days Post Vaccination


title: Platelet Sample from Subject 182328, 7 Days Post Vaccination


title: Platelet Sample from Subject 182329 Pre-vaccination


title: Platelet Sample from Subject 182329, 7 Days Post Vaccination


title: Platelet Sample from Subject 182330, 7 Days Post Vaccination


title: Platelet Sample from Subject 182330 Pre-vaccination


title: Platelet Sample from Subject 182328 Pre-vaccination


title: Platelet Sample from Subject 182328, 2 Days Post Vaccination


title: Platelet Sample from Subject 182334, 2 Days Post Vaccination


title: Platelet Sample from Subject 182327, 7 Days Post Vaccination


title: Platelet Sample from Subject 182327, 28 Days Post Vaccination


title: Platelet Sample from Subject 182332 Pre-vaccination


title: Platelet Sample from Subject 182327, 2 Days Post Vaccination


title: Platelet Sample from Subject 182326, 2 Days Post Vaccination


title: Platelet Sample from Subject 182327 Pre-vaccination


title: Platelet Sample from Subject 182325, 7 Days Post Vaccination


title: Platelet Sample from Subject 182325, 2 Days Post Vaccination


title: Platelet Sample from Subject 182325, 28 Days Post Vaccination


title: Platelet Sample from Subject 182328, 28 Days Post Vaccination


title: Platelet Sample from Subject 182324, 7 Days Post Vaccination


title: Platelet Sample from Subject 182324, 28 Days Post Vaccination


title: Platelet Sample from Subject 182323, 2 Days Post Vaccination


title: Platelet Sample from Subject 182324 Pre-vaccination


title: Platelet Sample from Subject 182323, 28 Days Post Vaccination


title: Platelet Sample from Subject 182324, 2 Days Post Vaccination


title: Platelet Sample from Subject 182321, 7 Days Post Vaccination


title: Platelet Sample from Subject 182323, 7 Days Post Vaccination


title: Platelet Sample from Subject 182326 Pre-vaccination


title: Platelet Sample from Subject 182322, 2 Days Post Vaccination


title: Platelet Sample from Subject 182321, 2 Days Post Vaccination


title: Platelet Sample from Subject 182322, 7 Days Post Vaccination


title: Platelet Sample from Subject 182318, 28 Days Post Vaccination


title: Platelet Sample from Subject 182319, 28 Days Post Vaccination


title: Platelet Sample from Subject 182321, 28 Days Post Vaccination


title: Platelet Sample from Subject 182320, 2 Days Post Vaccination


title: Platelet Sample from Subject 182319, 2 Days Post Vaccination


title: Platelet Sample from Subject 182318, 7 Days Post Vaccination


title: Platelet Sample from Subject 182319 Pre-vaccination


title: Platelet Sample from Subject 182318 Pre-vaccination


title: Platelet Sample from Subject 182318, 2 Days Post Vaccination


title: Platelet Sample from Subject 182316, 28 Days Post Vaccination


title: Platelet Sample from Subject 182320, 28 Days Post Vaccination


title: Platelet Sample from Subject 182317, 28 Days Post Vaccination


title: Platelet Sample from Subject 182317, 2 Days Post Vaccination


title: Platelet Sample from Subject 182316, 7 Days Post Vaccination


title: Platelet Sample from Subject 182317, 7 Days Post Vaccination


title: Platelet Sample from Subject 182319, 7 Days Post Vaccination


title: Platelet Sample from Subject 182322, 28 Days Post Vaccination


title: Platelet Sample from Subject 182315, 28 Days Post Vaccination


title: Platelet Sample from Subject 182320 Pre-vaccination


title: Platelet Sample from Subject 182315, 7 Days Post Vaccination


title: Platelet Sample from Subject 182317 Pre-vaccination


title: Platelet Sample from Subject 182314 Pre-vaccination


title: Platelet Sample from Subject 182314, 28 Days Post Vaccination


title: Platelet Sample from Subject 182315, 2 Days Post Vaccination


title: Platelet Sample from Subject 182314, 7 Days Post Vaccination


title: Platelet Sample from Subject 182312, 7 Days Post Vaccination


title: Platelet Sample from Subject 182312, 28 Days Post Vaccination


title: Platelet Sample from Subject 182316, 2 Days Post Vaccination


title: Platelet Sample from Subject 182313, 7 Days Post Vaccination


title: Platelet Sample from Subject 182313, 28 Days Post Vaccination


title: Platelet Sample from Subject 182311, 7 Days Post Vaccination


title: Platelet Sample from Subject 182313, 2 Days Post Vaccination


title: Platelet Sample from Subject 182312, 2 Days Post Vaccination


title: Platelet Sample from Subject 182310, 28 Days Post Vaccination


title: Platelet Sample from Subject 182310, 7 Days Post Vaccination


title: Platelet Sample from Subject 182311, 28 Days Post Vaccination


title: Platelet Sample from Subject 182309, 28 Days Post Vaccination


title: Platelet Sample from Subject 182314, 2 Days Post Vaccination


title: Platelet Sample from Subject 182309, 7 Days Post Vaccination


title: Platelet Sample from Subject 182308, 7 Days Post Vaccination


title: Platelet Sample from Subject 182311, 2 Days Post Vaccination


title: Platelet Sample from Subject 182309, 2 Days Post Vaccination


title: Platelet Sample from Subject 182308, 28 Days Post Vaccination


title: Platelet Sample from Subject 182308, 2 Days Post Vaccination


title: Platelet Sample from Subject 182307, 28 Days Post Vaccination


title: Platelet Sample from Subject 182308 Pre-vaccination


title: Platelet Sample from Subject 182307, 2 Days Post Vaccination


title: Platelet Sample from Subject 182306, 28 Days Post Vaccination


title: Platelet Sample from Subject 182306, 2 Days Post Vaccination


title: Platelet Sample from Subject 182305, 28 Days Post Vaccination


title: Platelet Sample from Subject 182305 Pre-vaccination


title: Platelet Sample from Subject 182304, 28 Days Post Vaccination


title: Platelet Sample from Subject 182305, 2 Days Post Vaccination


title: Platelet Sample from Subject 182304, 2 Days Post Vaccination


title: Platelet Sample from Subject 182420 Pre-vaccination


title: Platelet Sample from Subject 182305, 7 Days Post Vaccination


title: Platelet Sample from Subject 182492 Pre-vaccination


title: Platelet Sample from Subject 182489 Pre-vaccination


title: Platelet Sample from Subject 182491 Pre-vaccination


title: Platelet Sample from Subject 182304, 7 Days Post Vaccination


title: Platelet Sample from Subject 182419 Pre-vaccination


title: Platelet Sample from Subject 182490 Pre-vaccination


title: Platelet Sample from Subject 182493 Pre-vaccination


title: Platelet Sample from Subject 182486 Pre-vaccination


title: Platelet Sample from Subject 182413 Pre-vaccination


title: Platelet Sample from Subject 182411 Pre-vaccination


title: Platelet Sample from Subject 182409 Pre-vaccination


title: Platelet Sample from Subject 182412 Pre-vaccination


title: Platelet Sample from Subject 182408 Pre-vaccination


title: Platelet Sample from Subject 182404 Pre-vaccination


title: Platelet Sample from Subject 182415 Pre-vaccination


title: Platelet Sample from Subject 182339 Pre-vaccination


title: Platelet Sample from Subject 182325 Pre-vaccination


title: Platelet Sample from Subject 182323 Pre-vaccination


title: Platelet Sample from Subject 182336 Pre-vaccination


title: Platelet Sample from Subject 182337 Pre-vaccination


title: Platelet Sample from Subject 182334 Pre-vaccination


title: Platelet Sample from Subject 182315 Pre-vaccination


title: Platelet Sample from Subject 182333 Pre-vaccination


title: Platelet Sample from Subject 182322 Pre-vaccination


title: Platelet Sample from Subject 182321 Pre-vaccination


title: Platelet Sample from Subject 182309 Pre-vaccination


title: Platelet Sample from Subject 182316 Pre-vaccination


title: Platelet Sample from Subject 182310 Pre-vaccination


title: Platelet Sample from Subject 182306 Pre-vaccination


title: Platelet Sample from Subject 182304 Pre-vaccination


title: Platelet Sample from Subject 182311 Pre-vaccination


title: muscle, polymyositis patient 1

status: Public on Apr 25 2023

data_processing:
Standard preprocessing for V(D)J repertoires was carried out using pRESTO v0.5.4 (http://presto.readthedocs.io).
V(D)J germline genes were then assigned with IgBLAST v1.7.0 (23) using the March 30, 2017 version of the IMGT gene database
Mutations and selection strength of FWR and CDR regions was quantified using the implementation of BASELINe in SHazaM v0.1.8 in R v3.4.2
Alakazam v0.2.7 in R was used for analysis of CDR3 physiochemical properties and diversity analysis (27).
For the single cell libraries, the cellranger mkfastq function from 10X Genomics v2.2.0 was used to convert base calls to fastq sequences and perform demultiplexing; sequences were then aligned to the GCRhg38 genome supplied by 10X Genomics. Sparse count matrices, barcode assignments and feature calls were made using the cellranger count function and Seurat v.2.3.4 was used for visualization and cluster assignment.
Assembly: GCRhg38
Supplementary files format and content: BCR repertoire sequences in Change-O format.
Library strategy: BCR-seq

source_name: muscle

extract_protocol:
The IIM biopsy tissue was prepared for sequencing by first isolating RNA from frozen sections using the Qiagen RNA Mini kit according to the manufacturer’s instructions. B cells were isolated from frozen PBMCs using a human Pan B immunomagnetic negative selection kit (StemCell).
IBM RNA libraries were made using reagents supplied by New England BioLabs as part of the NEBNext Immune Sequencing Kit. B cells were loaded directly into the Chromium Controller (10x Genomics) and prepared using the Chromium Single Cell 5′ Reagent Kit (10x Genomics) for version 3 chemistry per the manufacturer’s protocol.

tag: isolate

value: polymyositis patient 1

value: muscle

tag: disease

value: polymyositis

tag: sample type

value: frozen section

tag: anatomic site

value: left thigh

tag: biomaterial provider

value: UConn Health


title: Platelet Sample from Subject 182406 Pre-vaccination

value: Female


title: Platelet Sample from Subject 182410 Pre-vaccination


title: muscle, inclusion body myositis  patient 4

value: inclusion body myositis patient 4

value: inclusion body myositis

value: right biceps


title: Platelet Sample from Subject 182405 Pre-vaccination


title: muscle, polymyositis patient 3

value: polymyositis patient 3

value: right quadriceps


title: muscle, inclusion body myositis  patient 2

value: inclusion body myositis patient 2


title: muscle, inclusion body myositis  patient 3

value: inclusion body myositis patient 3

value: left biceps


title: muscle, polymyositis patient 2

value: polymyositis patient 2


title: Platelet Sample from Subject 182312 Pre-vaccination

value: Older

value: Pre-vaccination


title: Platelet Sample from Subject 182313 Pre-vaccination

value: Male


title: muscle, dermatomyositis patient 3

value: dermatomyositis patient 3

value: muscle

value: dermatomyositis

value: not available


title: muscle, inclusion body myositis  patient 1

value: inclusion body myositis patient 1

value: frozen section

value: UConn Health


title: Platelet Sample from Subject 182307 Pre-vaccination


title: muscle, dermatomyositis patient 1

value: dermatomyositis patient 1

value: Female

value: right thigh


title: muscle, dermatomyositis patient 2

value: dermatomyositis patient 2

value: left thigh


title: Islet118/119_MS20087

status: Public on Mar 30 2023

city: Farmington

first: Efthymios

last: Motakis

address: 10 Farmington Drive

department: Computational Sciences

institute: The Jackson Laboratory

description: 10x Genomics

data_processing:
Reads alignment with STARsolo
Estimation and removal of ambient RNA by SoupX
Genetic demultiplexing for the 12 mutiplexed libraries by Demuxlet and removal of doublets
Cluster-based cell QC: the cell clusters are generated by Seurat's processing pipeline and the cells with > 500 features & < 50% MT & >1000 UMIs are kept for further analysis
Doublet identification by Scrublet, DoubletFinder and doublet visualization in the cell clusters
Second step cluster-based cell QC: the cell clusters are re-generated with the cleaner data by Seurat's processing pipeline and the cells with > 1400 features & < 40% MT are kept for further analysis. Keep cells of particular cell types (marker-based pre-annotation) even if the do not satisfy the features criterion.
Data integration by Harmony and integrated data clustering
Visualize the estimated doublets on the integrated data clusters, remove all scrublet doublets plus while custers if they are enriched in such doublets
Keep the clean data for downstream analysis: final cell annotation, differential expression, subclustering
Assembly: HG38
Supplementary files format and content: CellRanger output files

source_name: Pancreatic islets

growth_protocol: Cultured overnight in PIM(S) [ProdoLabs] prior to dissociation and 10X Genomics single cell capture

extract_protocol:
10X Genomics standard procedures for sample dilution and single cell capture
10X Genomcis standard procedures for library construction

treatment_protocol: Islets treated with Accutase for 10 minutes at 37 degrees Celsius and gentle pipetting

value: Pancreatic islets

tag: chemistry

tag: disease state

value: Male/Female

tag: bmi

tag: race

value: White/AfricanAmerican

tag: center

value: Scharp-Lacy/Southern California IsletCell Resource Center

tag: Cause of death

value: Head trauma/NA

tag: library id


title: Islet127

description: 10x Genomics

tag: tissue

value: PreDiabetic

value: Male

value: White

value: UPenn

value: Anoxia


title: Islet123

description: 10x Genomics

value: NonDiabetic

value: Hispanic

value: Scharp-Lacy

value: Head trauma


title: Islet128

description: 10x Genomics

value: southern California IsletCell Resource Center

value: Cerebrovascular/stroke


title: Islet126

description: 10x Genomics

value: Female

value: AfricanAmerican


title: Islet101

description: 10x Genomics

value: Pancreatic islets


title: Islet107

description: 10x Genomics


title: Islet118/119_MS20086

description: 10x Genomics

value: Male/Female

value: White/AfricanAmerican


title: Islet91

description: 10x Genomics


title: Islet73

description: 10x Genomics


title: Islet84/85_MS19042

description: 10x Genomics

value: Male/Male

value: Hispanic/Hispanic

value: Scharp-Lacy/Miami


title: Islet68

description: 10x Genomics

value: Male

value: White

value: Wisconsin


title: Islet104

description: 10x Genomics

value: NonDiabetic


title: Islet70/71_MS19035

description: 10x Genomics

value: Female/Male

value: White/White

value: Southern California IsletCell Resource Center/Scharp-Lacy


title: Islet84/85_MS19043

description: 10x Genomics


title: Islet70/71_MS19034

description: 10x Genomics


title: Islet63

description: 10x Genomics

value: PreDiabetic

value: Scharp-Lacy

value: Anoxia


title: Islet61

description: 10x Genomics

value: Female

value: Cerebrovascular/stroke


title: Islet59/60_MS19021

description: 10x Genomics

value: Pancreatic islets

value: Wisconsin/Scharp-Lacy


title: Islet57/58_MS19016

description: 10x Genomics

value: NonDiabetic/PreDiabetic

value: White/Hispanic

value: Scharp-Lacy/Southern California IsletCell Resource Center

value: Cerebrovascular/stroke / Anoxia


title: Islet57/58_MS19017

description: 10x Genomics


title: Islet59

description: 10x Genomics

value: Male

value: White


title: Islet59/60_MS19020

description: 10x Genomics

value: Male/Male


title: Islet80

description: 10x Genomics

value: NonDiabetic

value: AfricanAmerican

value: Miami

value: Head trauma


title: Islet60

description: 10x Genomics

value: Scharp-Lacy


title: Islet62

description: 10x Genomics

value: PreDiabetic

value: Anoxia


title: Islet58

description: 10x Genomics

value: Hispanic

value: Southern California IsletCell Resource Center


title: Islet57

description: 10x Genomics

value: Pancreatic islets

value: Female

value: Cerebrovascular/stroke


title: Islet55

description: 10x Genomics


title: Islet53

description: 10x Genomics


title: Islet54

description: 10x Genomics


title: Islet56

description: 10x Genomics

value: Wisconsin


title: Islet47/48_MS19007

description: 10x Genomics

value: Female/Female

value: White/Hispanic

value: Cerebrovascular/stroke / Head trauma


title: Islet89

description: 10x Genomics


title: Islet50

description: 10x Genomics

value: Male

value: White


title: Islet42

description: 10x Genomics

value: NonDiabetic


title: Islet47

description: 10x Genomics


title: Islet41

description: 10x Genomics

value: AfricanAmerican

value: NR


title: Islet34

description: 10x Genomics

value: Scharp-Lacy

value: Head trauma


title: Islet47/48_MS19006

description: 10x Genomics


title: Islet45

description: 10x Genomics

value: Miami


title: Islet39

description: 10x Genomics


title: Islet48

description: 10x Genomics

value: Hispanic


title: Islet31

description: 10x Genomics


title: Islet37

description: 10x Genomics

value: Head trauma - gunshot wound/suicide


title: Islet30

description: 10x Genomics

value: Pancreatic islets


title: Islet38

description: 10x Genomics


title: Islet52

description: 10x Genomics

value: Female


title: Islet44

description: 10x Genomics

value: UPenn

value: Cerebrovascular/stroke


title: Islet40

description: 10x Genomics

value: PreDiabetic

value: Southern California IsletCell Resource Center


title: Islet33

description: 10x Genomics


title: Islet32

description: 10x Genomics


title: Islet29

description: 10x Genomics

value: Wisconsin