title: RNA from sample #2 from trial f, collected after 4 days of repeated exposure to treatment E (TIC+Tat-50ng)

city: Philadelphia

first: Micheal

last: Nonnemacher

address: 245 N Broad St

institute: Drexel University

description: Library name: f_4X_E_2

data_processing:
Raw sequences were processed using the Nextflow RNA-seq pipeline as described in the instructions using the --pseudo_aligner salmon to use Salmon based pseudo-alignment quantification. `https://github.com/nf-core/rnaseq` [hungry_curran] DSL2 - revision: b89fac3265 [master]
Assembly: hg38
Supplementary files format and content: TSV of a matrix of gene-level length-scaled estimated counts across all samples

source_name: CNS

growth_protocol: Primary human fetal astrocytes harvested from 16 to 18-week aborted fetuses were obtained prior to 2018 from the Temple University / Drexel University Comprehensive NeuroHIV Center (CNHC) Core (Philadelphia, PA, USA) in full compliance with National Institutes of Health and Temple University ethical guidelines. Astrocytes were cultured in Dulbecco's Modified Eagle Medium (DMEM; Thermo-Fisher Scientific, Waltham, MA, USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Gibco; Thermo-Fisher Scientific, Waltham, MA, USA) and 1% penicillin-streptomycin (Corning, Glendale, AZ, USA) on 100 mm TPP Tissue Culture dishes (Midwest Scientific, Fenton, MO, USA). Experiments were only performed with astrocytes between passages 2 - 6. On 6-well plates (Falcon, Corning, Glendale, AZ, USA), astrocytes were seeded at a density of 90,000 cells/plate and grown to functional confluence.

extract_protocol:
Astrocyte whole cell lysate was collected from the monocultures for protein analysis and RNA extraction. RNA extraction and purification was completed using the RNeasy Micro procedure (Qiagen, Germantown, MD, USA). Following the extraction protocol, RNA purity was assessed with a spectrophotometer (Nanodrop, ND-1000) to measure absorbance at 260 nm and 280 nm, quantity by Qubit fluorometry using the RNA HS Assay procedure, and quality using Agilent Bioanalyzer nano RNA chips. RNA samples with RNA integrity number (RIN) values ≥ 8.0 were selected for sequencing.
Sequencing libraries were produced using the Illumina TruSeq Stranded mRNA library preparation with poly-A selection and sequenced on an Illumina NovaSeq SP chip at 2 x 100 nt paired-end reads with a target of >30 million clusters per sample.

treatment_protocol: Media changes were performed every 24 hours, either with control or freshly treated low serum media. To induce A1-like polarization of astrocytes, activated microglia signaling was simulated with a pro-inflammatory cocktail. This specific formulation had been used to induce an A1-like state in rodent-derived astrocytes in vitro [9]. The treatment consisted of IL1-α (3 ng/ml; Sigma-Aldrich, St. Louis, MO, USA), TNF-α (30 ng/ml; Sigma-Aldrich, St. Louis, MO, USA), and C1q (400 ng/ml; Sigma-Aldrich, St. Louis, MO, USA). To examine the effects of chronic Tat exposure, the viral protein was administered at 50 ng/ml (low dose) or 250 ng/ml (moderate-high dose) [50]. Treatment re-administration or control media replacement occurred every 24 hours for up to 6 days to simulate both acute and chronic exposure.

value: CNS

tag: cell type

value: Astrocyte

value: TIC + Tat (50 ng)

value: f


title: RNA from sample #3 from trial f, collected after 4 days of repeated exposure to treatment E (TIC+Tat-50ng)

status: Public on Jun 25 2025

type: SRA

country: USA

description: Library name: f_4X_E_3

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: treatment

tag: batch


title: blood, Day 3, UGA4, 402

city: Bethesda

first: Megan

last: Hockman

state: MD

address: 50 South Drive

department: NIAID

institute: National Institutes of Health

data_processing:
Sequencing reads were aligned using the nf-core RNASeq pipeline, version 3.0, and standard parameters. Alignment and quanficiation were performed using STAR and Salmon.
Assembly: GRCh38
Supplementary files format and content: Length scaled gene counts. Rows = Genes, Columns = Subjects

molecule: total RNA

source_name: Whole Blood

extract_protocol:
For each study day, total RNA was isolated from blood samples in randomized batches using the PAXgene Blood RNA kit (QIAGEN, Hilden, Germany) according to the manufacturer’s recommendations. Isolated RNA was stored at -80° C in a LoBind twin-tec 96-well PCR plate (Eppendorf). Sample concentrations were determined using the Qubit BR RNA Assay on a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Sample fragment size distributions were measured using an RNA Screentape on a 4200 TapeStation System.
Sequencing libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB), according to the manufacturer’s protocols. In cases of sufficient RNA concentration, 1 μg of input RNA was used, but in cases of low-yield samples, the maximum possible input mass was used. AMPure XP Beads (Beckman Coulter) were used in place of the supplied NEBNext Sample Purification Beads. Libraries for each study day were prepared in separate batches across multiple 96-well plates due to high sample number. Each plate included two negative controls to monitor for reagent or sample-to-sample contamination. Libraries were barcoded with NEBNext Multiplex Oligos for Illumina (NEB), with each pool containing a unique set of barcodes. Libraries were quantified using the Qubit dsDNA HS Assay on a Qubit 2.0 Fluorometer and fragment size was measured with an HSD1000 Screentape (Agilent) on a 4200 TapeStation System to ensure sufficient molarity and quality for pooling and sequencing. Libraries were pooled with equimolar input to a final concentration of 3nM.

value: Whole Blood

tag: time

value: Day 3

tag: Sex

value: male

tag: vaccine response

value: High Responder

tag: bmi

tag: age


title: RNA from sample #1 from trial f, collected after 4 days of repeated exposure to treatment D (Tat-250ng)

description: Library name: f_4X_D_1

value: Tat (250 ng)


title: RNA from sample #1 from trial f, collected after 4 days of repeated exposure to treatment E (TIC+Tat-50ng)

description: Library name: f_4X_E_1


title: RNA from sample #3 from trial f, collected after 4 days of repeated exposure to treatment A (control)

description: Library name: f_4X_A_3

value: Control


title: blood, Day 3, UGA4, 380

value: Non Responder


title: RNA from sample #3 from trial f, collected after 4 days of repeated exposure to treatment C (Tat-50ng)

description: Library name: f_4X_C_3

value: Tat (50 ng)


title: RNA from sample #2 from trial f, collected after 4 days of repeated exposure to treatment B (TIC)

description: Library name: f_4X_B_2

value: TIC


title: P162PE BC scATAC

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

description: Library name: P162PE

library_source: genomic single cell

data_processing:
The initial processing of scATAC-seq data to generate barcoded and aligned read bam files was performed using the ATAC-Seq Analysis Toolkit (Bio-Rad). Sequencing data were then processed by converting BAM files into fragment files using Rsamtools (https://bioconductor.org/packages/Rsamtools).
Assembly: hg19
Supplementary files format and content: fragment file

molecule: genomic DNA

source_name: Breast cancer

extract_protocol:
BC specimens were obtained via core needle biopsy of surgically removed tumors. The specimens were dissociated into single cells using a MACS Tumor Dissociation Kit and gentleMACS dissociation (Miltenyi Biotec), following manufacturer’s instructions. For pleural effusion samples, the drainage fluid was collected after trocar placement, centrifuged, and purified using a Red Blood Cell Lysis Solution lysis buffer (Miltenyi Biotec).
The scATAC-seq libraries were prepared according to the droplet-based combinatorial indexing method, with some modifications. The indexed-Tn5 transposase was prepared as previously described. After segmentation with the custom indexed-Tn5, the library was prepared using the SureCell ATAC-Seq Library Prep Kit (Bio-Rad) and a ddSEQ Single-Cell Isolator system (Bio-Rad). Q5 HiFi DNA Polymerase and USER II Enzyme (both from NEB) were used for a subset of samples in the Barcode Reaction mix and Enzyme Reaction mix. Then, the complete scATAC-seq libraries were loaded at 1.5 pM on a NextSeq 550 platform (Illumina) and sequencing was performed using the following read protocol: Read 1, 118 cycles; i7 index read, 8 cycles; and Read 2, 40 cycles.

value: Breast cancer


title: blood, Day 3, UGA4, 287

value: Low Responder


title: M1

city: New York

first: Davit

middle: A.

last: Goukassian

state: NY

address: One Gustave L. Levy Place, Box 1014

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

description: Library name: W7-2

data_processing:
FastQC (version 0.11.9) was used for the quality assessment of raw sequencing reads (Q30% was greater than 94%). Next, we aligned the reads to the mouse reference genome (mm39) using the STAR aligner (version 2.7.8a) in gene count quantification mode and obtained raw gene counts. The GRCm39 release 110 GTF file was used for gene annotation.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: right ventricular tissue

extract_protocol:
Total RNA was extracted from RV tissues using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol and stored at -80°C until further use.
A poly-A selected mRNA library was prepared using the NEBNextUltra™II RNA Library Prep Kit.

value: right ventricular tissue

tag: strain

tag: diet

value: Normal

tag: field

value: Mix

tag: dose

value: 50 cGy

tag: rin


title: RNA from sample #3 from trial e, collected after 6 days of repeated exposure to treatment C (Tat-50ng)

description: Library name: e_6X_C_3

value: CNS

value: Astrocyte

value: e


title: blood, Day 3, UGA4, 362

value: Whole Blood

value: Day 3


title: RNA from sample #1 from trial e, collected after 6 days of repeated exposure to treatment C (Tat-50ng)

description: Library name: e_6X_C_1


title: RNA from sample #2 from trial e, collected after 6 days of repeated exposure to treatment C (Tat-50ng)

description: Library name: e_6X_C_2


title: Multiome, MLN, TCDD, ATAC, Illumina NovaSeq 6000

city: Solna

first: Oscar

last: Diaz Perez

address: Nobels väg 13

country: Sweden

institute: Karolinska Institutet

description: Library name: MLN_TCDD_ATAC_NS6000

data_processing:
Quantification using Cell Ranger ARC 2.0.1 and the 10x refdata-cellranger-arc-mm10-2020-A-2.0.0 reference
Analysis using Seurat 5.0.1 and Signac 1.14.0 in R 4.4.1
Assembly: mm10
Supplementary files format and content: Cell Ranger ARC filtered h5
Supplementary files format and content: Cell Ranger ARC ATAC fragments TSV
Supplementary files format and content: Cell Ranger ARC summary statistics CSV
Supplementary files format and content: 10x Loupe Browser file
Supplementary files format and content: TSV file of metadata from Seurat object after filtering

source_name: Colon-draining mensenteric lymph nodes

extract_protocol:
CD45+ immune cells and dendritic cells were isolated from the colon lamina propria and from the colon-draining mesenteric lymph nodes of C. rodentium infected mice. Single nuclei suspensions were prepared isolated according to the Demonstrated Protocol: Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing (CG00053 – Rev C, 10x Genomics), using the Low Cell Input Nuclei isolation protocol.
Isolated single nuclei were transposed, then loaded on Chromium Chip and partitioned in nanolitre scale droplets using the Chromium Controller and Chromium Next GEM Single Cell Reagents (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide, User Guide, CG000338)

value: Colon-draining mensenteric lymph nodes

value: CD45+ cells and dendritic cells

tag: genotype

value: AhrCAIR/CAIR

value: Infected with C. rodentium


title: RNA from sample #2 from trial e, collected after 6 days of repeated exposure to treatment B (TIC)

description: Library name: e_6X_B_2


title: Multiome, MLN, CAIR, ATAC, Illumina NovaSeq 6000

description: Library name: MLN_CAIR_ATAC_NS6000

value: WT


title: Multiome, MLN, Vehicle, ATAC, Illumina NovaSeq 6000

description: Library name: MLN_Vehicle_ATAC_NS6000


title: blood, Day 3, UGA4, 221

value: female


title: RNA from sample #3 from trial e, collected after 6 days of repeated exposure to treatment A (control)

description: Library name: e_6X_A_3

value: Control


title: M5

description: Library name: W10-2

value: male


title: RNA from sample #1 from trial e, collected after 6 days of repeated exposure to treatment B (TIC)

description: Library name: e_6X_B_1

value: TIC


title: RNA from sample #2 from trial e, collected after 6 days of repeated exposure to treatment A (control)

description: Library name: e_6X_A_2


title: blood, Day 3, UGA4, 272

value: Low Responder


title: Multiome, Colon, Vehicle, ATAC, Illumina NovaSeq 6000

description: Library name: Colon_Vehicle_ATAC_NS6000

source_name: Colon lamina propria

value: Colon lamina propria


title: RNA from sample #1 from trial e, collected after 6 days of repeated exposure to treatment A (control)

description: Library name: e_6X_A_1


title: RNA from sample #4 from trial d, collected after 4 days of repeated exposure to treatment D (Tat-250ng)

description: Library name: d_4X_D_4

value: Tat (250 ng)

value: d


title: Multiome, MLN, AHR KO, ATAC, Illumina NovaSeq 6000

description: Library name: MLN_AHR_KO_ATAC_NS6000

value: AHR KO/KO


title: blood, Day 3, UGA4, 062

value: High Responder


title: RNA from sample #3 from trial d, collected after 4 days of repeated exposure to treatment D (Tat-250ng)

description: Library name: d_4X_D_3

value: CNS

value: Astrocyte


title: RNA from sample #2 from trial d, collected after 4 days of repeated exposure to treatment C (Tat-50ng)

description: Library name: d_4X_C_2

value: Tat (50 ng)


title: Multiome, Colon, TCDD, ATAC, Illumina NovaSeq 6000

description: Library name: Colon_TCDD_ATAC_NS6000

value: CD45+ cells and dendritic cells


title: RNA from sample #1 from trial d, collected after 4 days of repeated exposure to treatment C (Tat-50ng)

description: Library name: d_4X_C_1


title: blood, Day 3, UGA4, 299

value: Whole Blood

value: Day 3


title: RNA from sample #6 from trial d, collected after 4 days of repeated exposure to treatment B (TIC)

description: Library name: d_4X_B_6


title: Multiome, Colon, AHR KO, ATAC, Illumina NovaSeq 6000

description: Library name: Colon_AHR_KO_ATAC_NS6000

value: Infected with C. rodentium


title: RNA from sample #3 from trial e, collected after 6 days of repeated exposure to treatment B (TIC)

description: Library name: e_6X_B_3

value: e


title: blood, Day 3, UGA4, 454

value: female


title: PROSER1 KO LSK RNA-seq biol rep 3

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

country: United Kingdom

institute: School of Life Sciences, University of Dundee

description: Library name: sample7

data_processing:
Raw paired-end RNA-seq reads from the biological replicates were trimmed using Trimmomatic and mapped to the mouse genome (mm10) using RNA-STAR with paired-end settings.
Gene annotation ‘gencode.vM25.annotation.gtf.gz’ was obtained from GENCODE release 25 (GRCm38.p6) and gene expression was summarized from mapped reads using FeatureCounts, with option (--countReadPairs) to enable counting of fragments from paired-end data.
Differential expression was determined using DESeq2 with default parameters
Assembly: mm10
Supplementary files format and content: Normalised counts: Tabular file generated by DESeq2 normalisation

source_name: Bone Marrow

growth_protocol: LSK (Lin-Sca1+cKit+) cells were FACS purified from lethally irradiated (9.5 Gy in two equal doses 3 hr apart) recipient mice transplanted with wildtype or PROSER1 knockout bone marrow at 77 days after transplantation

extract_protocol:
Total RNA was isolated from biological replicate samples using a RNeasy Plus Mini kit (Qiagen, 74134). RNA integrity was checked by gel electrophoresis on an Agilent Tapestation system.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit (NEB, E7765) according to manufacturer’s instructions.

treatment_protocol: No treatment

value: Bone Marrow

tag: cell line

value: Bone marrow chimeric mice

value: LSK (Lin-Sca1+cKit+) cells

value: PROSER1 KO


title: RNA from sample #3 from trial d, collected after 4 days of repeated exposure to treatment B (TIC)

description: Library name: d_4X_B_3

value: TIC


title: neuron_ipsc_Y155H_tic; 73-Y115H-Plus_S33

city: London

first: Oliver

last: Ziff

address: Institute of Neurology, Queen Square

institute: University College London

description:
Library name: 73-Y115H-Plus_S33
neuron_ipsc_Y155H_tic

data_processing:
Adapter trimming with TrimGalore!
Alignment with STAR
Read quantification with Salmon
Sort and index alignments with Samtools
Quality control with RSeQC, Qualimap, dupRadar, Preseq, MultiQC
Assembly: Ensembl Homo_sapiens GRCh38 99
Supplementary files format and content: TPM read counts for each gene in each sample in TSV file

source_name: ipsc

growth_protocol: iPSC-dereived neurons were differentiated in N2B27 media and grown to 100DIV. iPSC astrcoytes were generated from neuronal cultures via FGF2-mediated enrichment in N2B27 media, before being matured in N2B27 media with BMP4+LIF.

extract_protocol:
RNA was isolated using NEB Monarch Total RNA miniprep kit
KAPA mRNA Hyper Prep (Roche)

treatment_protocol: Cells were untreated, or treated with TNFa+IL1a+C1q for 24 hours priors to harvesting.

value: ipsc

value: tic

tag: strandedness

value: forward


title: PROSER1 KO LSK RNA-seq biol rep 2

description: Library name: sample6

tag: cell type


title: blood, Day 3, UGA4, 357

tag: tissue

value: male

value: Low Responder


title: blood, Day 3, UGA4, 208

value: High Responder


title: RNA from sample #5 from trial d, collected after 4 days of repeated exposure to treatment A (control)

description: Library name: d_4X_A_5

value: CNS

value: Astrocyte

tag: treatment

value: Control

value: d


title: RNA from sample #3 from trial d, collected after 4 days of repeated exposure to treatment A (control)

description: Library name: d_4X_A_3

tag: batch


title: neuron_ipsc_Y155H_nil; 73-Y115H-0_S32

description:
Library name: 73-Y115H-0_S32
neuron_ipsc_Y155H_nil


title: PROSER1 KO LSK RNA-seq biol rep 1

description: Library name: sample5


title: neuron_ipsc_ctrl4_nil; 73-WT-0_S24

description:
Library name: 73-WT-0_S24
neuron_ipsc_ctrl4_nil

value: wildtype


title: wildtype LSK RNA-seq biol rep 4

description: Library name: sample4

value: WT


title: neuron_ipsc_R278I_tic; 73-R278I-Plus_S35

description:
Library name: 73-R278I-Plus_S35
neuron_ipsc_R278I_tic


title: blood, Day 3, UGA4, 313

value: Whole Blood

tag: time

value: Day 3


title: neuron_ipsc_R278I_nil; 73-R278I-0_S34

description:
Library name: 73-R278I-0_S34
neuron_ipsc_R278I_nil


title: blood, Day 3, UGA4, 135

tag: Sex

value: Non Responder


title: neuron_ipsc_DI4_tic; 73-dI4-Plus_S31

description:
Library name: 73-dI4-Plus_S31
neuron_ipsc_DI4_tic


title: neuron_ipsc_ctrl3_tic; 73-Ctrl3-Plus_S23

description:
Library name: 73-Ctrl3-Plus_S23
neuron_ipsc_ctrl3_tic


title: wildtype LSK RNA-seq biol rep 2

description: Library name: sample2

value: Bone Marrow

value: Bone marrow chimeric mice

value: LSK (Lin-Sca1+cKit+) cells


title: neuron_ipsc_ctrl3_nil; 73-Ctrl3-0_S36

description:
Library name: 73-Ctrl3-0_S36
neuron_ipsc_ctrl3_nil

value: ipsc


title: wildtype LSK RNA-seq biol rep 1

description: Library name: sample1


title: neuron_ipsc_ctrl2_tic; 73-Ctrl2-Plus_S22

description:
Library name: 73-Ctrl2-Plus_S22
neuron_ipsc_ctrl2_tic

value: tic

value: forward


title: blood, Day 3, UGA4, 332

value: female

tag: vaccine response

value: Low Responder


title: neuron_ipsc_ctrl1_tic; 73-Ctrl1-Plus_S20

description:
Library name: 73-Ctrl1-Plus_S20
neuron_ipsc_ctrl1_tic


title: Trap-Ai9 male, 2 months, tamoxifen at p24 rep4

city: Jerusalem

first: Tamar

last: Licht

address: Hadassah ein karem

department: Medical Neurobiology

country: Israel

institute: Hebrew University

description:
Library name: sample 7
columns U, AB in processed data

data_processing:
10 ng of RNA from each sample was processed using the SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara).
Samples were eluted in 25 μL of 10 mM elution buffer, then all of them were pooled into 10 nM final concentration into a single tube. The library was sequenced using NovaSeq6000 machine (Illumina) with 100 cycles and single-Read sequencing conditions.
Raw reads were quality-trimmed with cutadapt using a quality threshold of 32 for both ends, poly-G sequences (NextSeq’s no signal) and adapter sequences were removed from the 3' end, and poly-T stretches were removed from the 5' end (being the reverse-complement of poly-A tails).
Processed reads were aligned to the mouse GRCm39 genome with Tophat, v2.2.1, allowing for 5 mismatches, using gene annotations from Ensembl release 106.
Raw counts per gene per sample were obtained with htseq-count, v2.0.1, then normalization was done with the DESeq2 package, v1.26.0.
Assembly: GRCm39 ,Ensembl release 106
Supplementary files format and content: excel table of DESeq2

source_name: Medial amygdala

growth_protocol: mice housed in normal SPF conditions with food and water ad lib. Age 2m at sacrifice.

extract_protocol:
300 µm coronal slices were made by vibratome (Leica) in ice-cold  aCSF solution equilibrated with 95% O2/5% CO2 44. Slices containing the MeA were inspected under a fluorescent stereoscope (Nikon SMZ25) and the DIMPLE area of both hemispheres was carefully dissected, imaged to evaluate % DIMPLE in the dissected tissue, and immediately processed by Zymo Quick-RNA™ Microprep kit (cat#R1050).
ScreenTape (5067-5579) along with the Qubit® RNA HS Assay Kit (Invitrogen; Q32852).

treatment_protocol: Tamoxifen was given orally to females at 6w and to males at p24.

value: Medial amygdala

value: brain

value: male

value: tamoxifen given p24

tag: % dimple_in_tissue


title: neuron_ipsc_ctrl1_nil; 73-Ctrl1-0_S19

description:
Library name: 73-Ctrl1-0_S19
neuron_ipsc_ctrl1_nil

value: wildtype


title: Trap-Ai9 male, 2 months, tamoxifen at p24 rep3

description:
Library name: sample 6
columns T, AA in processed data


title: neuron_ipsc_ctrl4_nil; 71-WT-0_S7

description:
Library name: 71-WT-0_S7
neuron_ipsc_ctrl4_nil


title: neuron_ipsc_ctrl4_tic; 73-WT-Plus_S25

description:
Library name: 73-WT-Plus_S25
neuron_ipsc_ctrl4_tic


title: Trap-Ai9 male, 2 months, tamoxifen at p24 rep2

description:
Library name: sample 5
columns S, Z in processed data


title: wildtype LSK RNA-seq biol rep 3

description: Library name: sample3

value: WT


title: neuron_ipsc_APP1_tic; 71-APP1-Plus_S29

description:
Library name: 71-APP1-Plus_S29
neuron_ipsc_APP1_tic


title: neuron_ipsc_Y155H_tic; 70-Y115H-Plus_S16

description:
Library name: 70-Y115H-Plus_S16
neuron_ipsc_Y155H_tic


title: Trap-Ai9 male, 2 months, tamoxifen at p24 rep1

description:
Library name: sample 4
columns R, Y in processed data


title: neuron_ipsc_Y155H_nil; 70-Y115H-0_S15

description:
Library name: 70-Y115H-0_S15
neuron_ipsc_Y155H_nil


title: blood, Day 3, UGA4, 196

value: Whole Blood

tag: bmi

tag: age


title: neuron_ipsc_R278I_tic; 70-R278I-Plus_S18

description:
Library name: 70-R278I-Plus_S18
neuron_ipsc_R278I_tic


title: blood, Day 3, UGA4, 294

value: Day 3


title: Trap-Ai9 female, 2 months tamoxifen at 1.5 month rep3

description:
Library name: sample 3
columns Q, X in processed data

value: tamoxifen given 1.5 months


title: blood, Day 3, UGA4, 262

value: Non Responder


title: neuron_ipsc_DI4_nil; 73-dI4-0_S30

description:
Library name: 73-dI4-0_S30
neuron_ipsc_DI4_nil


title: neuron_ipsc_ctrl2_nil; 73-Ctrl2-0_S21

description:
Library name: 73-Ctrl2-0_S21
neuron_ipsc_ctrl2_nil


title: Trap-Ai9 female, 2 months tamoxifen at 1.5 month rep2

description:
Library name: sample 2
columns P, W in processed data


title: neuron_ipsc_DI4_nil; 70-dI4-0_S13

description:
Library name: 70-dI4-0_S13
neuron_ipsc_DI4_nil


title: blood, Day 3, UGA4, 348


title: blood, Day 3, UGA4, 001

value: High Responder


title: neuron_ipsc_ctrl4_tic; 71-WT-Plus_S8

description:
Library name: 71-WT-Plus_S8
neuron_ipsc_ctrl4_tic


title: neuron_ipsc_ctrl2_tic; 70-Ctrl2-Plus_S4

description:
Library name: 70-Ctrl2-Plus_S4
neuron_ipsc_ctrl2_tic


title: blood, Day 3, UGA4, 046


title: blood, Day 3, UGA4, 275


title: blood, Day 3, UGA4, 477


title: neuron_ipsc_ctrl3_tic; 70-Ctrl3-Plus_S6

description:
Library name: 70-Ctrl3-Plus_S6
neuron_ipsc_ctrl3_tic


title: neuron_ipsc_ctrl3_nil; 70-Ctrl3-0_S5

description:
Library name: 70-Ctrl3-0_S5
neuron_ipsc_ctrl3_nil


title: blood, Day 3, UGA4, 359


title: neuron_ipsc_ctrl1_nil; 70-Ctrl1-0_S1

description:
Library name: 70-Ctrl1-0_S1
neuron_ipsc_ctrl1_nil


title: neuron_ipsc_ctrl2_nil; 70-Ctrl2-0_S3

description:
Library name: 70-Ctrl2-0_S3
neuron_ipsc_ctrl2_nil


title: neuron_ipsc_APP1_tic; 70-APP1-Plus_S10

description:
Library name: 70-APP1-Plus_S10
neuron_ipsc_APP1_tic


title: neuron_ipsc_APP1_nil; 70-APP1-0_S9

description:
Library name: 70-APP1-0_S9
neuron_ipsc_APP1_nil


title: blood, Day 3, UGA4, 244


title: neuron_ipsc_R278I_nil; 70-R278I-0_S17

description:
Library name: 70-R278I-0_S17
neuron_ipsc_R278I_nil


title: RNA-E115-brain_CD1_AA330_female_TP185-7

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 804

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

description: Library name: 67065

data_processing:
Reads were trimmed with cutadapt, aligned with STAR, reads counted using featureCounts and TPM caclulated using RSEM
Assembly: mm10
Supplementary files format and content: gene counts using featureCounts
Supplementary files format and content: TPM values using RSEM

source_name: E11.5 brain

extract_protocol:
RNA was extracted using RNeasy plus mini kit (Qiagen, 74136)
TruSeq Stranded mRNA Library Prep kit (Illumina, 20020594)

treatment_protocol: Supply VitC at 3.3 g/l in drinkin water for +VitC (AAplus) samples, or  nothing for -VitC Aamin) samples. Other concentrations or phenotypes are indicated

value: E11.5 brain

tag: background

tag: condition

tag: timed pregnancy


title: RNA-E115-brain_CD1_AA3300_female_TP178-7

description: Library name: 67067


title: neuron_ipsc_ctrl1_tic; 70-Ctrl1-Plus_S2

description:
Library name: 70-Ctrl1-Plus_S2
neuron_ipsc_ctrl1_tic

value: ipsc


title: neuron_ipsc_APP12_nil; 65-APP2-0_S28

description:
Library name: 65-APP2-0_S28
neuron_ipsc_APP12_nil


title: RNA-E115-brain_CD1_AA330_male_TP185-3

description: Library name: 67064


title: neuron_ipsc_APP1_tic; 56-APP1-Plus_S27

description:
Library name: 56-APP1-Plus_S27
neuron_ipsc_APP1_tic

value: tic


title: blood, Day 3, UGA4, 396


title: blood, Day 3, UGA4, 279


title: RNA-E115-brain_CD1_AA100-NTD_female_TP199-14

description: Library name: 67063


title: TP19M6-14 Fixed Liver HFO snRNA-seq

city: Pittsburgh

first: Alexander

middle: Chih-Chieh

last: Chang

state: PA

address: 5051 Centre Ave

institute: University of Pittsburgh

description: Library name: TP19M6-14_Fixed

library_source: transcriptomic single cell

data_processing:
CellRanger v7.1.0
Assembly: GrCh38
Supplementary files format and content: .h5 files

molecule: nuclear RNA

source_name: Liver metastases

extract_protocol:
snPathoSeq
3' V3.1 Kit for Frozen NextGEM FLEX kit for Fixed.

value: Liver metastases


title: blood, Day 3, UGA4, 326


title: blood, Day 3, UGA4, 054

value: female


title: RNA-E115-brain_CD1_AA100-NTD_male_TP203-5

description: Library name: 67062


title: RNA-E115-brain_CD1_AA3300_male_TP178-3

description: Library name: 67066


title: neuron_ipsc_APP12_nil; 70-APP2-0_S11

description:
Library name: 70-APP2-0_S11
neuron_ipsc_APP12_nil

value: forward


title: blood, Day 3, UGA4, 267


title: TP20M204-13 Fixed Liver HFO snRNA-seq

description: Library name: TP20M204-13_Fixed


title: blood, Day 3, UGA4, 312

value: Low Responder


title: Trap-Ai9 female, 2 months tamoxifen at 1.5 month rep1

description:
Library name: sample 1
columns O, V in processed data

value: Medial amygdala

value: brain


title: E10.0 posterior

first: Sergio

last: Menchero

address: 1 Midland Road

institute: The Francis Crick Institute

description: 10X Genomics

data_processing:
Quantification by kallisto (0.46.2) bustools (0.40.0) workflow
Cell selection using DropletUtils (1.12.1)
Analysis using Seurat (4.0.3)
Assembly: ASM229v1 with Y chromosome
Supplementary files format and content: kallisto bustools expression matrix in cell ranger-format in tarball
Supplementary files format and content: 10x loupe for embryonic cells
Supplementary files format and content: Seurat rds object for embryonic cells
Supplementary files format and content: Metadata table for embryonic cells in CSV format

organism: Monodelphis domestica

source_name: embryo (posterior region)

extract_protocol:
Samples were incubated on FACSmax Cell Dissociation Solution (Amsbio, T200100) with 10% Papain (30 U/mg, Sigma-Aldrich, 10108014001) for 11-12 min at 37°C to dissociate the cells. Samples were then resuspended in HBSS with 5% FBS, 10 µM rock inhibitor (Stemcell Technologies, Y-27632), and 1x non-essential aminoacids (Life Technologies, 11140050). Cells were filtered through 35 µm cell strainers (Falcon, 352235) and 20 µm filters (Miltenyi Biotec, 130-101-812).
Libraries were prepared using the Single Index Kit T Set A (PN-1000213) from the 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (PN-1000121)

value: embryo (posterior region)

tag: developmental stage


title: ESC, ATAC, Rep2

city: Cologne

first: Robert

last: Hänsel-Hertsch

department: CMMC

country: Germany

institute: University of Cologne

description:
ESC-ATAC.merged_cpm.bw
ESC-ATAC_master_peaks.bed

library_source: genomic

data_processing:
basecalls were performed using BaseSpace DRAGEN Analysis - Version: 1.3.0
Assembly: mm39
Supplementary files format and content: bigwig, bed (peak file), tsv (gene set enrichment analysis ouput)

source_name: Stem cells

growth_protocol: cultured on gelatine-coated (Sigma-Aldrich, ES-006-B) dishes in 2i/L medium (GMEM (Gibco, 11710035), 20 % foetal bovine serum (Merck, ES-009-C), 1X NEAA (Gibco, 11140-035), 1X L-glutamine (Gibco, 35035-038), 1000 ng/mL LIF (Gibco, A35934), 0.1 mM 2-mercaptoethanol (Gibco, 21985023), 1 mM sodium pyruvate (Gibco, 113060039), 3µM GSK3βi (AXON, 1386), 1 µM MEKi (AXON, 1408) at 37 °C with 5 % CO2 and passaged every other day.

extract_protocol:
Nuclei isolation from in vitro cultured cells. For nuclei isolation, cells were incubated in NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1 % Triton X-100, 20 % glycerol, 1X cOmplete Proteinase Inhibitor) for 3 min on ice. Nuclei were fixed with 0.1 % formaldehyde (Thermo Scientific, 28906) in PBS for 1 min at room temperature. Formaldehyde was quenched with 74 mM glycine and nuclei were pelleted by centrifugation at 450 xg for 3 min at 4 °C. RNA isolation and RNA-seq from in vitro cultured cells. Total RNA from cultured cells were extracted using the NucleoSpin RNA Kit (Macherey-Nagel, 740955.50) according to the manufacturer’s protocol. RNA-seq libraries were generated with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with Unique Dual Indices for Illumina (Lexogen, 115.384) and sequenced on an Illumina NovaSeq 6000 platform using NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) (Illumina, 20028401). All RNA-seq experiments were conducted in four independent technical replicates.
10,000 nuclei were transferred into new 0.2 mL PCR tubes and incubated for 3 h at 58 °C in 50 µL Denaturation buffer (10 mM Tris pH 8.0 (HCl), 50 mM NaCl, 0.2 % (w/v) SDS, 0.5 ng/mL proteinase K). Denaturation was stopped by purification of the tagmented DNA fragments using the MinElute Reaction Cleanup Kit (QIAGEN, 28204). DNA was eluted in 23 µL EB buffer and amplified analogously to CUT&Tag (https://www.nature.com/articles/s41467-019-09982-5) for 12-20 cycles. Appropriate number of cycles can be estimated via qPCR and will depend on epitope abundancy. Amplified sequencing libraries were one-sided size-selected using first a 0.5 X SPRI beads ratio to remove large fragments followed by purification with 1.3 X SPRI beads ratio followed by elution in 26 µL EB buffer.

treatment_protocol: For epiblast-like cell differentiation, 200,000 embryonic stem cells were plated onto fibronectin-coated (Corning, 354008) in 2i/L medium and allowed to attach overnight. The next morning, medium was changed to EpiLC-Diff medium (0.5 X DMEM/F-12 (Gibco, 10565-018), 0.5 X Neurobasal Medium (Gibco, 21103049), 1 X N2 (Gibco, 17502048), 1 X B27 (Gibco, 17504044), 20 ng/mL activin A (STEMCELL, 78132.1), 12 ng/mL bFGF (STEMCELL, 78134), 1 % KSR (Gibco, 10828010), 0.1 mM 2-mercaptoethanol (Gibco, 21985023), 0.04 ng/mL bovine serum albumin (Gibco, 15260037) for 48 h.

value: Stem cells


title: RNA-E115-brain_CD1_AA100_male_TP199-15

description: Library name: 67060

tag: genotype

value: male


title: ESC, ATAC, Rep1


title: RNA-E115-brain_CD1_AA33_male_TP190-4

description: Library name: 67056


title: blood, Day 3, UGA4, 185

value: Whole Blood


title: EpiLC, ATAC, Rep2

description:
EpiLC-ATAC.merged_cpm.bw
EpiLC-ATAC_master_peaks.bed

source_name: Epiblast like cells

value: Epiblast like cells


title: RNA-E115-brain_CD1_AA33_female_TP190-10

description: Library name: 67057


title: EpiLC, ATAC, Rep1


title: ESC, YAP1, G2, Rep1, DynaTag

description:
ESC-YAP1-G2.merged_cpm.bw
ESC-YAP1-G2_master_peaks.bed


title: blood, Day 3, UGA4, 338

value: Day 3


title: ESC, YAP1, S, Rep1, DynaTag

description:
ESC-YAP1-S.merged_cpm.bw
ESC-YAP1-S_master_peaks.bed


title: RNA-E115-brain_CD1_AA100_female_TP203-4

description: Library name: 67061


title: neuron_ipsc_APP1_nil; 56-APP1-0_S26

description:
Library name: 56-APP1-0_S26
neuron_ipsc_APP1_nil

tag: cell line


title: E10.0 anterior

description: 10X Genomics

source_name: embryo (anterior region)

value: embryo (anterior region)

value: wildtype


title: blood, Day 3, UGA4, 282


title: RNA-E85-HF_B6_AAplus_male_TP158-5

description: Library name: 67042

data_processing:
Reads were trimmed with cutadapt, aligned with STAR, deduplicated using UMI-tools, reads counted using featureCounts and TPM caclulated using RSEM
Assembly: mm10
Supplementary files format and content: gene counts using featureCounts
Supplementary files format and content: TPM values using RSEM

source_name: E8.5 headfold

extract_protocol:
RNA was extracted using RNeasy micro kit (Qiagen, 74004)
SMARTer® Stranded Total RNA-Seq v3 - Pico Input Mammalian kit (Takara, 634485)

treatment_protocol: Supply VitC at 3.3 g/l in drinkin water for +VitC (AAplus) samples, or  nothing for -VitC Aamin) samples

value: E8.5 headfold

value: AAplus


title: ESC, YAP1, S, Rep2, DynaTag


title: blood, Day 3, UGA4, 304

value: High Responder


title: ESC, SOX2, S, Rep1, DynaTag

description:
ESC-SOX2-S.merged_cpm.bw
ESC-SOX2-S_master_peaks.bed


title: blood, Day 3, UGA4, 175


title: RNA-E115-brain_CD1_AAR65_female_TP72-10

description: Library name: 67055

value: E11.5 brain


title: ESC, SOX2, G2, Rep2, DynaTag

description:
ESC-SOX2-G2.merged_cpm.bw
ESC-SOX2-G2_master_peaks.bed


title: ESC, YAP1, G1, Rep2, DynaTag

description:
ESC-YAP1-G1.merged_cpm.bw
ESC-YAP1-G1_master_peaks.bed


title: RNA-E115-brain_CD1_AAR65_male_TP72-9

description: Library name: 67054


title: ESC, YAP1, G1, Rep1, DynaTag


title: blood, Day 3, UGA4, 420

value: female


title: ESC, YAP1, G2, Rep2, DynaTag


title: ESC, SOX2, S, Rep2, DynaTag


title: ESC, SOX2, G1, Rep1, DynaTag

description:
ESC-SOX2-G1.merged_cpm.bw
ESC-SOX2-G1_master_peaks.bed


title: RNA-E85-HF_B6_AAplus_male_TP158-4

description: Library name: 66204


title: blood, Day 3, UGA4, 124

value: Non Responder


title: RNA-E85-HF_B6_AAplus_female_TP158-7

description: Library name: 66203


title: ESC, SOX2, G1, Rep2, DynaTag


title: blood, Day 3, UGA4, 397

value: Low Responder


title: RNA-E85-HF_B6_AAplus_male_TP154-7

description: Library name: 66202


title: ESC, OCT4, S, Rep2, DynaTag

description:
ESC-OCT4-S.merged_cpm.bw
ESC-OCT4-S_master_peaks.bed


title: ESC, OCT4, S, Rep1, DynaTag


title: RNA-E85-HF_B6_AAplus_female_TP155-5

description: Library name: 66207


title: ESC, OCT4, G2, Rep2, DynaTag

description:
ESC-OCT4-G2.merged_cpm.bw
ESC-OCT4-G2_master_peaks.bed


title: ESC, OCT4, G1, Rep1, DynaTag

description:
ESC-OCT4-G1.merged_cpm.bw
ESC-OCT4-G1_master_peaks.bed


title: ESC, NANOG, S, Rep2, DynaTag

description:
ESC-NANOG-S.merged_cpm.bw
ESC-NANOG-S_master_peaks.bed


title: RNA-E85-HF_B6_AAplus_female_TP158-6

description: Library name: 67043


title: blood, Day 3, UGA4, 442


title: ESC, NANOG, S, Rep1, DynaTag


title: ESC, OCT4, G1, Rep2, DynaTag


title: ESC, OCT4, G2, Rep1, DynaTag


title: ESC, NANOG, G2, Rep1, DynaTag

description:
ESC-NANOG-G2.merged_cpm.bw
ESC-NANOG-G2_master_peaks.bed


title: blood, Day 3, UGA4, 232


title: blood, Day 3, UGA4, 243


title: blood, Day 3, UGA4, 356


title: ESC, SOX2, G2, Rep1, DynaTag


title: ESC, NANOG, G2, Rep2, DynaTag


title: RNA-E85-HF_B6_AAmin_male_TP140-2

description: Library name: 67044

value: AAmin


title: RNA-E85-HF_B6_AAmin_male_TP159-5

description: Library name: 66212


title: ESC, NANOG, G1, Rep2, DynaTag

description:
ESC-NANOG-G1.merged_cpm.bw
ESC-NANOG-G1_master_peaks.bed


title: ESC, NANOG, G1, Rep1, DynaTag


title: ESC, MYC, S, Rep2, DynaTag

description:
ESC-MYC-S.merged_cpm.bw
ESC-MYC-S_master_peaks.bed


title: RNA-E85-HF_B6_AAmin_male_TP149-6

description: Library name: 66210


title: blood, Day 3, UGA4, 169


title: RNA-E85-HF_B6_AAmin_male_TP140-1

description: Library name: 66208


title: blood, Day 3, UGA4, 085


title: ESC, MYC, G2, Rep2, DynaTag

description:
ESC-MYC-G2.merged_cpm.bw
ESC-MYC-G2_master_peaks.bed


title: ESC, MYC, S, Rep1, DynaTag


title: blood, Day 3, UGA4, 203


title: ESC, MYC, G2, Rep1, DynaTag


title: P209PE BC scATAC

description: Library name: P209PE

value: Breast cancer


title: blood, Day 3, UGA4, 296


title: ESC, MYC, G1, Rep2, DynaTag

description:
ESC-MYC-G1.merged_cpm.bw
ESC-MYC-G1_master_peaks.bed


title: ESC, MYC, G1, Rep1, DynaTag


title: RNA-E85-HF_B6_AAmin_female_TP159-4

description: Library name: 67045


title: blood, Day 3, UGA4, 349


title: ESC, H3K4me3, W300, Rep2, CUTTag


title: RNA-E85-HF_B6_AAmin_female_TP159-3

description: Library name: 66209


title: ESC, H3K4me3, W300, Rep1, CUTTag


title: blood, Day 3, UGA4, 372


title: ESC, H3K4me3, ICS, Rep2, DynaTag


title: blood, Day 3, UGA4, 281


title: ESC, H3K4me3, ICS, Rep1, DynaTag


title: ESC, H3K27me3, ICS, Rep2, DynaTag


title: RNA-E85-HF_B6_AAmin_female_TP149-9

description: Library name: 66211


title: ESC, H3K27me3, W300, Rep2, CUTTag


title: RNA-E85-HF_129_AAplus_male_TP160-2

description: Library name: 66216


title: blood, Day 3, UGA4, 418


title: ESC, H3K27me3, ICS, Rep1, DynaTag


title: RNA-E85-HF_129_AAplus_male_TP152-5

description: Library name: 66214


title: ESC, CTCF, W300, Rep2, CUTTag


title: blood, Day 3, UGA4, 416


title: ESC, CTCF, W300, Rep1, CUTTag


title: blood, Day 3, UGA4, 070


title: RNA-E85-HF_129_AAplus_male_TP114-5

description: Library name: 67048


title: RNA-E85-HF_129_AAplus_male_TP114-2

description: Library name: 67046


title: blood, Day 3, UGA4, 412


title: ESC, CTCF, ICS, Rep2, DynaTag


title: ESC, CTCF, ICS, Rep1, DynaTag


title: RNA-E85-HF_129_AAplus_female_TP160-6

description: Library name: 66217


title: EpiLC, YAP1, S, Rep1, DynaTag

description:
EpiLC-d2-YAP1-S.merged_cpm.bw
EpiLC-YAP1-S_master_peaks.bed


title: EpiLC, YAP1, G2, Rep2, DynaTag

description:
EpiLC-d2-YAP1-G2.merged_cpm.bw
EpiLC-YAP1-G2_master_peaks.bed


title: RNA-E85-HF_129_AAplus_female_TP160-1

description: Library name: 67047


title: EpiLC, YAP1, G2, Rep1, DynaTag


title: blood, Day 3, UGA4, 344


title: blood, Day 3, UGA4, 459


title: EpiLC, SOX2, G2, Rep2, DynaTag

description:
EpiLC-d2-SOX2-G2.merged_cpm.bw
EpiLC-SOX2-G2_master_peaks.bed


title: EpiLC, YAP1, G1, Rep2, DynaTag

description:
EpiLC-d2-YAP1-G1.merged_cpm.bw
EpiLC-YAP1-G1_master_peaks.bed


title: EpiLC, YAP1, G1, Rep1, DynaTag


title: RNA-E85-HF_129_AAplus_female_TP152-4

description: Library name: 66215


title: EpiLC, SOX2, S, Rep2, DynaTag

description:
EpiLC-d2-SOX2-S.merged_cpm.bw
EpiLC-SOX2-S_master_peaks.bed


title: blood, Day 3, UGA4, 364


title: blood, Day 3, UGA4, 445


title: RNA-E85-HF_129_AAplus_female_TP156-6

description: Library name: 67049


title: RNA-E85-HF_129_AAmin_male_TP198-4

description: Library name: 67052


title: EpiLC, YAP1, S, Rep2, DynaTag


title: RNA-E85-HF_129_AAmin_male_TP197-4

description: Library name: 67050


title: EpiLC, SOX2, S, Rep1, DynaTag


title: blood, Day 3, UGA4, 069


title: EpiLC, SOX2, G1, Rep2, DynaTag

description:
EpiLC-d2-SOX2-G1.merged_cpm.bw
EpiLC-SOX2-G1_master_peaks.bed


title: EpiLC, SOX2, G1, Rep1, DynaTag


title: EpiLC, OCT4, S, Rep2, DynaTag

description:
EpiLC-d2-OCT4-S.merged_cpm.bw
EpiLC-OCT4-S_master_peaks.bed


title: EpiLC, SOX2, G2, Rep1, DynaTag


title: blood, Day 3, UGA4, 440


title: ESC, H3K27me3, W300, Rep1, CUTTag


title: EpiLC, OCT4, G2, Rep1, DynaTag

description:
EpiLC-d2-OCT4-G2.merged_cpm.bw
EpiLC-OCT4-G2_master_peaks.bed


title: RNA-E85-HF_129_AAmin_male_TP153-5

description: Library name: 66220


title: EpiLC, OCT4, G2, Rep2, DynaTag


title: RNA-E85-HF_B6_AAmin_female_TP159-7

description: Library name: 66213


title: EpiLC, OCT4, S, Rep1, DynaTag


title: EpiLC, OCT4, G1, Rep2, DynaTag

description:
EpiLC-d2-OCT4-G1.merged_cpm.bw
EpiLC-OCT4-G1_master_peaks.bed


title: blood, Day 3, UGA4, 300


title: blood, Day 3, UGA4, 422


title: EpiLC, OCT4, G1, Rep1, DynaTag


title: RNA-E85-HF_129_AAmin_female_TP198-2

description: Library name: 67053


title: EpiLC, NANOG, S, Rep2, DynaTag

description:
EpiLC-d2-NANOG-S.merged_cpm.bw
EpiLC-NANOG-S_master_peaks.bed


title: RNA-E85-HF_129_AAmin_female_TP153-6

description: Library name: 66221


title: blood, Day 3, UGA4, 209


title: blood, Day 3, UGA4, 382


title: RNA-E85-HF_129_AAmin_female_TP197-3

description: Library name: 67051


title: EpiLC, NANOG, G2, Rep2, DynaTag

description:
EpiLC-d2-NANOG-G2.merged_cpm.bw
EpiLC-NANOG-G2_master_peaks.bed


title: RNA-E85-HF_129_AAmin_male_TP145-6

description: Library name: 66222


title: blood, Day 3, UGA4, 353


title: EpiLC, NANOG, S, Rep1, DynaTag


title: EpiLC, NANOG, G1, Rep1, DynaTag

description:
EpiLC-d2-NANOG-G1.merged_cpm.bw
EpiLC-NANOG-G1_master_peaks.bed


title: EpiLC, MYC, S, Rep1, DynaTag

description:
EpiLC-2d-MYC-S.merged_cpm.bw
EpiLC-MYC-S_master_peaks.bed


title: WGBS-E115-brain_CD1_AA100_male_TP199-1

description: Library name: 67070

data_processing:
Reads were trimmed with Trimgalore, and aligned using Bismark.
Assembly: mm10
Supplementary files format and content: bismark coverage file
Supplementary files format and content: CpG report
Supplementary files format and content: CpG bedgraph

extract_protocol:
gDNA was extracted using the Purelink genomic DNA Mini Kit (Invitrogen, K182001)
IDT xGen™ Methyl-Seq DNA library prep kit (IDT, 10009824)


title: EpiLC, MYC, S, Rep2, DynaTag


title: WGBS-E115-brain_CD1_AA100-NTD_male_TP199-3

description: Library name: 67071


title: EpiLC, NANOG, G2, Rep1, DynaTag


title: blood, Day 3, UGA4, 125


title: EpiLC, NANOG, G1, Rep2, DynaTag


title: EpiLC, MYC, G2, Rep2, DynaTag

description:
EpiLC-2d-MYC-G2.merged_cpm.bw
EpiLC-MYC-G2_master_peaks.bed


title: EpiLC, MYC, G2, Rep1, DynaTag


title: EpiLC, MYC, G1, Rep2, DynaTag

description:
EpiLC-2d-MYC-G1.merged_cpm.bw
EpiLC-MYC-G1_master_peaks.bed


title: blood, Day 3, UGA4, 217


title: WGBS-E115-brain_CD1_AA3300_male_TP178-9

description: Library name: 66653


title: blood, Day 3, UGA4, 220


title: EpiLC, MYC, G1, Rep1, DynaTag


title: WGBS-E115-brain_CD1_AA330_male_TP185-10

description: Library name: 66652


title: blood, Day 3, UGA4, 050


title: blood, Day 3, UGA4, 385


title: WGBS-E115-brain_CD1_AA33_male_TP190-3

description: Library name: 66651


title: WGBS-E115-brain_CD1_AA33-del_male_TP190-8

description: Library name: 66650


title: blood, Day 3, UGA4, 410


title: mESc 2i LIF 2 (scRNA-seq)

city: Illkirch

first: Nacho

last: Molina

address: 1 Rue Laurent Fries

country: France

institute: Institut de génétique et de biologie moléculaire et cellulaire

description:
Library name: QCKG4
nuclear RNA 10x Genomics

data_processing:
Raw data was processed using CellRanger-arc-2.0.2 with the 10X reference genome cellranger-arc-mm10-2020-A-2.0.0
Assembly: mm10
Supplementary files format and content: h5 file: contains both RNA-seq counts and ATAC-seq counts; tsv.gz: frangments file for ATAC-seq; tsv.gz.tbi: frangments file index for ATAC-seq

growth_protocol: Mouse ES cells E14 were cultivated without feeders on 0.1% gelatine-coated dishes in DMEM high glucose (4.5 g/L) with GlutaMAX supplemented with 15% fetal calf serum heat inactivated, 0.001% B-mercaptoethanol, 1X non-essential amino acids, 1X NaPyr, 1X LIF, 1 mM MEK Inhibitor PD 0325901, and 3 mM GSK3  inhibitor CHIR99021.

extract_protocol:
Nuclei were isolated from 4X105 mouse ES cells using 100 µL of cold lysis buffer (10 mM Tris-HCl (pH7.4), 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% IGEPAL CA-630, 0.01% Digitonin, 1% BSA, 1mM DTT, 1 U/µL RNase inhibitor). Cells were incubated for 5 min at 4°C, then resuspended in 1 mL chilled wash buffer (10 mM Tris-HCl (pH7.4), 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1mM DTT, 1 U/µL RNase inhibitor) and centrifuged at 500 rcf for 5 min at 4°C. Pellet was rinsed two more times with 1 mL wash buffer, for a total of 3 washes. The nuclei pellet was resuspended in 40 µL Diluted Nuclei Buffer (1X Nu- clei buffer (10X Genomics, PN-1000280), 1 mM DTT, 1 U/µL RNase inhibitor), and passed through a 40 µm Flowmi Cell Strainer (Merck)
Library preparation was performed at the GenomEast platform at the Institut de Génétique et de Biologie Moléculaire et Cellulaire. Transposition was performed using the 10X Genomics kit (PN-1000280) and nuclei were loaded into the 10X Genomics Chromium Controller with a target capture of 6,000 single nuclei. Li- braries for the ATAC and 3′ mRNA were produced according to the Chromium Next GEM instructions (10X Genomics, Document CG000338 Rev F), and sequenced using the Illumina NextSeq 2000. Libraries were sequenced on an Illumina NextSeq 2000 sequencer as paired-end 28 + 85 base reads for 3′ mRNA, 50 base reads for ATAC. Image analysis and base calling were performed using RTA version 2.7.7 and BCL Convert version 3.8.4

value: embryonic


title: mESc 2i LIF 1 (scRNA-seq)

description:
Library name: QCKG3
nuclear RNA 10x Genomics


title: mESc 2i LIF 1 (scATAC-seq)

description:
Library name: QCKG1
chromatin accessibility 10x Genomics


title: mESc 2i LIF 2 (scATAC-seq)

description:
Library name: QCKG2
chromatin accessibility 10x Genomics


title: WGBS-E115-brain_CD1_AAR65_male_TP72-5

description: Library name: 66647


title: blood, Day 3, UGA4, 225


title: 4T1 cells, fully edited, lineage tracing cassette library

city: Cambridge

first: Kathryn

last: Yost

state: Massachusetts

address: 455 Main St

department: Biology

institute: Whitehead Institute

description: Library name: PEtracer_4T1_fully_edited_LTC

data_processing:
All scRNA-seq data was processed using the Cellranger software package (version 7.1.0). To capture lineage information a custom reference genome was constructed by appending the 2171 lineage tracing cassette sequences to the human hg38 genome build. Both gene expression and lineage tracing cassette libraries were then aligned to this reference using default parameters. Since the reference contains all 2171 30bp barcode sequences the integration barcode (intBC) of each lineage tracing cassette read can be determined based on which element in the reference it aligns to. A custom Python script was used to extract lineage information from the bam alignment file generated by Cellranger. This script iterated through all reads aligned to a tracing cassette sequence. For each read the lineage mark (LM) sequence at each edit site was determined based on the alignment. For each UMI the number of supporting reads was calculated and the LM for each site set to the LM with the most read support (ties broken randomly). UMIs were then aggregated by intBC, cellBC, and the set of LMs detected across the three edit sites to generate a final LM table. scRNA-seq data for puromycin and blasticidin barcode libraries was aligned using Cellranger to a custom reference. This reference included puromycin and blasticidin resistance cassette sequences with ‘N’s indicating the positions of the 10nt random barcodes. A custom Python script was used to extract the barcode sequence from each read aligned to these elements, generate a consensus barcode for each UMI, and aggregate UMIs by barcode for each cell. To separate barcode calls corresponding to real integrations from sequencing errors and ambient RNA, for each 10x capture a Gaussian mixture model was fitted to the distribution of UMIs per barcode per cell. Barcode calls corresponding to the lower peak were excluded as likely errors. pegRNA libraries were processed using the “CRISPR Guide Capture” feature of Cellranger. pegRNA protospacer mismatch calls supported by <3 UMIs were filtered out and careful quality control performed to exclude cells with multiple pegRNA integrations as these cells could confound our estimation of protospacer mismatch kinetics. Cells with multiple pegRNA calls were removed as well as cells with lineage cassette reads where more than one edit site had an LM installed.
Assembly: mm10
Supplementary files format and content: Processed data barcodes/features/matrix and filtered_counts.h5 files contain the filtered_feature_bc_matrix transcript count matrix outputs from Cellranger. BlastBC_counts.csv, PuroBC_counts.csv, allele_counts.csv, and mapping_counts.csv files contain unfiltered static barcode, lineage tracing cassette allele, and intBC mapping count data.

extract_protocol:
Single cell suspensions were washed with PBS + 0.04% BSA and captured using the 10X Genomics Next GEM Single Cell 3ʹ Kit v3.1
Gene expression libraries were prepared using the 10X Genomics Next GEM Single Cell 3ʹ Kit v3.1 according to the manufacturer's instructions. Targeted lineage tracing cassette, puromycin/blasticidin barcode, and pegRNA libraries were prepared from amplified cDNA using two or three rounds of PCR with target-specific amplification primers and sample indexing primers.


title: 4T1 cells, fully edited, intBC library

description: Library name: PEtracer_4T1_fully_edited_intBC


title: 4T1 cells, in vitro heterogeneity, intBC library, rep 1

description: Library name: PEtracer_4T1_invitro_rep1_intBC


title: blood, Day 3, UGA4, 293


title: blood, Day 3, UGA4, 155


title: 4T1 cells, in vitro heterogeneity, intBC library, rep 2

description: Library name: PEtracer_4T1_invitro_rep2_intBC


title: WGBS-E115-brain_CD1_AA0_male_TP181-6

description: Library name: 66649


title: 4T1 cells, in vitro heterogeneity, gene expression library, rep 1

description: Library name: PEtracer_4T1_invitro_rep1_GEX


title: 4T1 cells, in vitro heterogeneity, gene expression library, rep 2

description: Library name: PEtracer_4T1_invitro_rep2_GEX


title: WGBS-E85-HF_129_AAmin-norm_male_TP229-7

description: Library name: 69245

extract_protocol:
gDNA was extracted using 1x AMPure XP beads (Beckman Coultier, A63881), after incubation with lysis buffer (10 mM Tris–HCl pH 8.3, 50 mM KCl, 2.5 mM MgCl2, 0.5% NP-40) and 0.4 mg/ml Proteinase K (Thermo Fisher Scientific, AM2546) for 1 h at 56°C and subsequently 30 min with 2 mg/ml RNAse A (Qiagen, 19101) at 37°C.
IDT xGen™ Methyl-Seq DNA library prep kit (IDT, 10009824)

value: AAmin-norm


title: WGBS-E85-HF_129_AAmin-norm_male_TP229-4

description: Library name: 69244

value: male


title: transcriptomes of T cells from choroid plexus  of aged mice

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

description: Library name: OCP

data_processing:
Primary analysis was performed using the Cellrange pipeline. Reference genome mouse (mm10) was used for read alignment and gene expression quantification using Cellranger v5.1.0 pipelines. The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines. These pipelines combine Chromium specific algorithms with the RNA-seq aligner STAR.
Assembly: mm10
Supplementary files format and content: mtx and tsv for processed data, bam for each sample

source_name: choroid plexus

extract_protocol:
Primary T cells were obtained from freshly isolated meninges and choroid plexus tissue from young and aged mice by FACS.
Libraries were constructed using 10xgenomics 5' gene expression kit, according to the manufacture's instructions.

value: choroid plexus

value: primary cell

value: T cells

tag: age group

value: aged


title: transcriptomes of T cells from meninges of young mice

description: Library name: YM

source_name: meninges

value: meninges

tag: cell type

value: young


title: WGBS-E85-HF_129_AAmin-norm_male_TP197-1

description: Library name: 67074

tag: tissue

value: E8.5 headfold


title: transcriptomes of T cells from choroid plexus  of young mice

description: Library name: YCP


title: transcriptomes of T cells from meninges of aged mice

description: Library name: OM


title: blood, Day 3, UGA4, 246

source_name: Whole Blood

extract_protocol:
For each study day, total RNA was isolated from blood samples in randomized batches using the PAXgene Blood RNA kit (QIAGEN, Hilden, Germany) according to the manufacturer’s recommendations. Isolated RNA was stored at -80° C in a LoBind twin-tec 96-well PCR plate (Eppendorf). Sample concentrations were determined using the Qubit BR RNA Assay on a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Sample fragment size distributions were measured using an RNA Screentape on a 4200 TapeStation System.
Sequencing libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB), according to the manufacturer’s protocols. In cases of sufficient RNA concentration, 1 μg of input RNA was used, but in cases of low-yield samples, the maximum possible input mass was used. AMPure XP Beads (Beckman Coulter) were used in place of the supplied NEBNext Sample Purification Beads. Libraries for each study day were prepared in separate batches across multiple 96-well plates due to high sample number. Each plate included two negative controls to monitor for reagent or sample-to-sample contamination. Libraries were barcoded with NEBNext Multiplex Oligos for Illumina (NEB), with each pool containing a unique set of barcodes. Libraries were quantified using the Qubit dsDNA HS Assay on a Qubit 2.0 Fluorometer and fragment size was measured with an HSD1000 Screentape (Agilent) on a 4200 TapeStation System to ensure sufficient molarity and quality for pooling and sequencing. Libraries were pooled with equimolar input to a final concentration of 3nM.

value: Whole Blood

value: Day 3


title: WGBS-E85-HF_129_AAmin-norm_female_TP197-2

description: Library name: 67073

value: female


title: blood, Day 3, UGA4, 436

value: High Responder


title: blood, Day 3, UGA4, 320

value: Low Responder


title: blood, Day 3, UGA4, 450


title: WGBS-E85-HF_129_AAmin-pheno_male_TP145-3

description: Library name: 63947

value: AAmin-pheno


title: blood, Day 3, UGA4, 305


title: Endo, ibuprofen, uterus, rep6

city: San Francisco

first: Marina

last: Sirota

state: CA

address: 490 Illinois St.

institute: UCSF

description:
Library name: Ibuprofen_U6
Column name in counts.txt: 7780.EE.0078

data_processing:
Adapter sequences in the raw read files were trimmed using cutadapt (v4.9) with an error rate of 0.1, minimum overlap of 3 bps, minimum 3’ base quality score of 25, and minimum length after trimming of 55 bps. We also set to remove poly-A tails and ploy-G with lengths over 20 bps. The trimmed reads were mapped to Rattus Norvegicus reference genome GRCr8 with exon and splice site information using Hisat2 (v2.2.0). The SAM files were converted to BAM files and sorted using samtools (v1.21). The gene counts were summarized by featureCounts (v2.0.6).
Assembly: GRCr8
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: uterus

extract_protocol:
RNAs were extracted using miRNeasy mini Kit (Qiagen). 1.5ug of total RNA was used for library construction.
RNA libraries were prepared using the Illumina Stranded Total RNA Prep with Ribo-ZeroTM Plus kit.

treatment_protocol: Endometriosis was surgically induced in rats as described by Vernon and Wilson. Animals were anesthetized with a combination of ketamine (73 mg/kg) and xylazine (8.8 mg/kg), and a midline abdominal incision was made. A 1 cm segment of the left uterine horn with surrounding fat was excised and transferred to sterile saline. This tissue was cut into four 2x2 mm fragments and sutured onto the mesenteric arteries supplying the small intestine. After the surgical procedure, the incision was closed, and the rats were closely monitored during recovery. The operation had no complications and estrous cycles resumed within a few days. The experimental groups were treated with one of three conditions: simvastatin (40 mg/kg/day) (n=6), primaquine (40 mg/kg/day) (n=6), or a vehicle solution (control) (n=6). Treatments were administered via daily oral gavage for a 4-week period following the induction of endometriosis. Simvastatin and primaquine were selected based on their potential anti-inflammatory and analgesic properties, respectively. The vehicle control group received the same volume of vehicle solution but no active drug.

value: uterus

tag: treatment

value: Endometriosis Induction+Ibuprofen


title: blood, Day 3, UGA4, 354

data_processing:
Sequencing reads were aligned using the nf-core RNASeq pipeline, version 3.0, and standard parameters. Alignment and quanficiation were performed using STAR and Salmon.
Assembly: GRCh38
Supplementary files format and content: Length scaled gene counts. Rows = Genes, Columns = Subjects


title: Endo, ibuprofen, uterus, rep4

description:
Library name: Ibuprofen_U4
Column name in counts.txt: 7780.EE.0061


title: WGBS-E85-HF_129_AAplus_female_TP160-5

description: Library name: 67072

value: AAplus


title: WGBS-E85-HF_129_AAplus_male_TP156-5

description: Library name: 63945

value: male


title: WGBS-E85-HF_129_AAplus_male_TP152-6

description: Library name: 63943


title: WGBS-E85-HF_129_AAmin-pheno_female_TP153-4

description: Library name: 63950


title: Endo, ibuprofen, uterus, rep1

description:
Library name: Ibuprofen_U1
Column name in counts.txt: 7780.EE.0005


title: Endo, ibuprofen, uterus, rep5

description:
Library name: Ibuprofen_U5
Column name in counts.txt: 7780.EE.0074


title: Endo, ibuprofen, uterus, rep3

description:
Library name: Ibuprofen_U3
Column name in counts.txt: 7780.EE.0014


title: WGBS-E85-HF_129_AAplus_female_TP152-2

description: Library name: 63944


title: blood, Day 3, UGA4, 066

value: Non Responder


title: Endo, ibuprofen, lesion, rep6

description:
Library name: Ibuprofen_L6
Column name in counts.txt: 7780.EE.0079

source_name: lesion

value: lesion


title: Endo, ibuprofen, uterus, rep2

description:
Library name: Ibuprofen_U2
Column name in counts.txt: 7780.EE.0011


title: Endo, ibuprofen, lesion, rep5

description:
Library name: Ibuprofen_L5
Column name in counts.txt: 7780.EE.0050


title: blood, Day 3, UGA4, 030


title: WGBS-E85-HF_B6_AAmin_female_TP149-10

description: Library name: 63942

value: AAmin


title: blood, Day 3, UGA4, 373


title: WGBS-E85-HF_B6_AAmin_male_TP149-1

description: Library name: 63941


title: Endo, ibuprofen, lesion, rep4

description:
Library name: Ibuprofen_L4
Column name in counts.txt: 7780.EE.0039


title: blood, Day 3, UGA4, 290


title: Endo, ibuprofen, lesion, rep3

description:
Library name: Ibuprofen_L3
Column name in counts.txt: 7780.EE.0022


title: Endo, ibuprofen, lesion, rep2

description:
Library name: Ibuprofen_L2
Column name in counts.txt: 7780.EE.0021


title: WGBS-E85-HF_B6_AAmin_female_TP159-2

description: Library name: 63940


title: Endo, ibuprofen, lesion, rep1

description:
Library name: Ibuprofen_L1
Column name in counts.txt: 7780.EE.0019


title: blood, Day 3, UGA4, 224


title: blood, Day 3, UGA4, 308


title: Endo, simvastatin, uterus, rep6

description:
Library name: Simvastatin_U6
Column name in counts.txt: 7780.EE.0060

value: Endometriosis Induction+Simvastatin


title: Endo, simvastatin, uterus, rep5

description:
Library name: Simvastatin_U5
Column name in counts.txt: 7780.EE.0054


title: WGBS-E85-HF_B6_AAmin_male_TP159-1

description: Library name: 63939


title: blood, Day 3, UGA4, 146


title: Endo, simvastatin, uterus, rep4

description:
Library name: Simvastatin_U4
Column name in counts.txt: 7780.EE.0032


title: WGBS-E85-HF_B6_AAplus_female_TP155-7

description: Library name: 63938


title: blood, Day 3, UGA4, 438


title: Endo, simvastatin, uterus, rep3

description:
Library name: Simvastatin_U3
Column name in counts.txt: 7780.EE.0029


title: Endo, simvastatin, uterus, rep2

description:
Library name: Simvastatin_U2
Column name in counts.txt: 7780.EE.0012


title: Endo, simvastatin, lesion, rep6

description:
Library name: Simvastatin_L6
Column name in counts.txt: 7780.EE.0059


title: Endo, simvastatin, uterus, rep1

description:
Library name: Simvastatin_U1
Column name in counts.txt: 7780.EE.0010


title: WGBS-E85-HF_B6_AAplus_female_TP138-6

description: Library name: 63936


title: blood, Day 3, UGA4, 099


title: Endo, simvastatin, lesion, rep5

description:
Library name: Simvastatin_L5
Column name in counts.txt: 7780.EE.0058


title: WGBS-E85-HF_B6_AAplus_male_TP155-8

description: Library name: 63937


title: blood, Day 3, UGA4, 297


title: Endo, simvastatin, lesion, rep3

description:
Library name: Simvastatin_L3
Column name in counts.txt: 7780.EE.0037


title: Endo, simvastatin, lesion, rep4

description:
Library name: Simvastatin_L4
Column name in counts.txt: 7780.EE.0046


title: WGBS-E85-HF_B6_AAplus_male_TP138-5

description: Library name: 63935


title: Endo, simvastatin, lesion, rep2

description:
Library name: Simvastatin_L2
Column name in counts.txt: 7780.EE.0027


title: blood, Day 3, UGA4, 386


title: Endo, simvastatin, lesion, rep1

description:
Library name: Simvastatin_L1
Column name in counts.txt: 7780.EE.0023


title: PCBP1/2KO β cells

first: Doris

middle: A

last: Stoffers

address: 3400 Civic Center Blvd

department: IDOM

institute: University of Pennsylvania

description:
Library name: Sample 2
10X genomics

data_processing:
Data was processed using the Cell Ranger pipeline (10x Genomics, v.3.1.0) for demultiplexing and alignment of sequencing reads to the mm10 genome and creation of feature-barcode matrices.
The cell ranger output files were read into R and processed utilizing the standard Seurat workflow (version 3).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barocodes.tsv, features.tsv, matrix.mtx).

source_name: Pancreatic islet

extract_protocol:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent kit v3.2 per manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer run by the CHOP Center for Applied Genomics.
scRNA_seq

treatment_protocol: Islets were washed with PBS, and dispersed to single cells with 0.25% trypsin at 37°C with gentle pipetting. FBS was added to the solution and the cell suspension was filtered through a 40μm cell strainer to facilitate further breakup of cells (Corning, Cat#: 352340). Debris and dead cells were then removed from the cell suspension using Dead Cell and Debris Removal kits (Miltenyi Biotec, Cat#: 130-090-101/130-109-398). Cells were counted and resuspended in 1X PBS with 0.04% ultra-pure BSA (Millipore Sigma Cat#: 820452) for library preparation by the Children’s Hospital of Philadelphia Center for Applied Genomics core.

value: Pancreatic islet

value: Beta cell

value: Male

value: 4-5 weeks


title: Endo, primaquine, uterus, rep6

description:
Library name: Primaquine_U6
Column name in counts.txt: 7780.EE.0053

value: Endometriosis Induction+Primaquine


title: Endo, primaquine, uterus, rep5

description:
Library name: Primaquine_U5
Column name in counts.txt: 7780.EE.0049


title: Control β cells

description:
Library name: Sample 1
10X genomics

value: WT


title: Endo, primaquine, uterus, rep4

description:
Library name: Primaquine_U4
Column name in counts.txt: 7780.EE.0031


title: Endo, primaquine, uterus, rep3

description:
Library name: Primaquine_U3
Column name in counts.txt: 7780.EE.0030


title: Endo, primaquine, uterus, rep1

description:
Library name: Primaquine_U1
Column name in counts.txt: 7780.EE.0008


title: blood, Day 3, UGA4, 280

value: Whole Blood

value: Day 3

value: female

value: High Responder


title: Duodenal epithelium; Control; H. polygyrus (7 d.p.i.)

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description:
Library name: Epithelium_Control
10x Genomics (3' v3.1 dual index chemistry)

data_processing:
After sequencing, BCL files were demultiplexed to individual libraries and aligned against the mouse reference genome (GRCm38 / mm10) with Cell Ranger v7.0.1 (10x Genomics) ran through the Cumulus pipeline to generate count matrices.
Assembly: Mouse GRCm38 / mm10
Supplementary files format and content: .h5 files

source_name: Small intestinal epithelium (duodenum)

extract_protocol:
To generate muscularis single-cell suspensions, the distal 12 centimeters of small intestines were dissected on ice, cut longitudinally along the mesenteric border, and laid flat (luminal side down) on C-fold towels dampened with ice-cold holding buffer (HBSS without Ca2+ and Mg2+, 5% FCS, 10mM HEPES) on a metal tray in an ice bucket. Muscularis propria were isolated from lamina propria by stereomicroscope-aided microdissection performed on an ice-cold metal block lined with buffer-dampened C-fold towels, rinsed 2-3x in holding buffer to limit epithelial cell contaminants, minced with scissors, and digested in digestion buffer (HBSS with Ca2+ and Mg2+, 5% FCS, 10mM HEPES, 100 μg/mL DNase I, 200 μg/mL Liberase TH) for 15-30 minutes at 37°C in flasks with stir-bars spinning at 550 rpm. After digestion, samples were gently triturated with 3-5 passes through an 18G needle attached to a syringe and single-cell suspensions were strained through 40μm nylon meshes, washed, and further processed for fluorescence-activated cell sorting (FACS). To enrich for muscularis glial and stromal cells, our input consisted of 50% single, live, CD45neg, Itgβ1+ cells and 50% all single, live cells, purified by FACS. Biological replicates (n = 2; 1 female, 1 male) from each respective group were pooled into the same 10x Genomics channel for single-cell encapsulation. To generate duodenal crypt epithelium single-cell suspensions, the proximal 10 centimeters of small intestines were dissected on ice, cut longitudinally along the mesenteric border, and luminal contents were gently removed. Intestines were cut into ~1 cm segments and placed in epithelial dissociation buffer (PBS with 5mM EDTA) for 30 min on ice with mild shaking. The first fraction of buffer was discarded, and fresh epithelial dissociation buffer was added to the samples and tubes were kept on ice for 30 min with occasional vigorous shaking. The second fraction of buffer was saved and the previous step was repeated with a third fraction of epithelial dissociation buffer. The second and third fractions containing epithelial cells enriched for crypts were combined and strained through a sterile 70 μm mesh filter and pelleted by centrifugation. Epithelial crypts were further dissociated with the addition of 10 mL of pre- warmed (37°C) TrypLE solution (Gibco) for 3 min. Ice-cold DMEM/F-12 media supplemented with 5% FBS was added to quench the reaction and cells were filtered through a sterile 40 μm mesh strainer. Cells were counted and resuspended in PBS supplemented with 0.4% BSA for 10x Genomics scRNA-seq encapsulation.
Sorted muscularis cells and duodenal epithelial cells were each pelleted and resuspended in PBS with 0.4% BSA. A maximum of 10,000 cells from each group was loaded on a Chromium controller (10X Genomics) following the protocol for 3' v3.1 dual index chemistry single cell RNA sequencing (CG000315_RevE and attached products, 10x Genomics). For the muscularis, cells sorted from the control Il13ra1 flox group (~10,000 sort-enriched cells pooled from 1 male and 1 female mouse) and the Calb2ΔIl13ra1 cKO group (~10,000 sort-enriched cells pooled from 1 male and 1 female mouse) were loaded into two separate channels of the Chromium controller (10X Genomics). For epithelial samples, cells from the control Il13ra1flox group (~5,000 manually counted cells from 1 female mouse; male sample compromised) and the Calb2ΔIl13ra1 cKO group (~10,000 manually counted cells pooled from 1 male and 1 female mouse) were loaded into two separate channels, respectively, of the Chromium controller (10X Genomics). Libraries were prepared according to manufacturer’s instructions, pooled in equimolar ratios and sequenced on a NovaSeq sequencer (Illumina) in the following read configuration: R1:28, I1:10, I2:10, R2:90bp.

treatment_protocol: Calb2-cre; Il13ra1 flox/flox (Calb2ΔIl13ra1) cKO mice (n = 2) and littermate control Il13ra1 flox/flox mice (n = 2) were administered 200 L3 H. polygyrus larvae by oral gavage and euthanized at 7 d.p.i.

value: Small intestinal epithelium (duodenum)

value: 9 weeks 1 day

value: Epithelial and intra-epithelial leukocytes (manually counted cells)

value: Il13ra1 flox/flox (control)

value: 200 L3 H. polygyrus larvae

tag: batch


title: Endo, primaquine, lesion, rep5

description:
Library name: Primaquine_L5
Column name in counts.txt: 7780.EE.0063

value: lesion


title: Ileal muscularis cells; cKO; H. polygyrus (7 d.p.i.)

description:
Library name: Muscularis_cKO
10x Genomics (3' v3.1 dual index chemistry)

source_name: Small intestinal muscularis propria (ileum)

value: pooled male and female

value: 50% all single, live cells and 50% single, live, CD45neg, Itgb1+ cells (FACS-purified muscularis cells)

value: Calb2 cre/+; Il13ra1 flox/flox (cKO)


title: Endo, primaquine, lesion, rep4

description:
Library name: Primaquine_L4
Column name in counts.txt: 7780.EE.0051


title: Ileal muscularis cells; Control; H. polygyrus (7 d.p.i.)

description:
Library name: Muscularis_Control
10x Genomics (3' v3.1 dual index chemistry)

value: Small intestinal muscularis propria (ileum)


title: blood, Day 3, UGA4, 014

first: Megan

last: Hockman

institute: National Institutes of Health

tag: time


title: Endo, primaquine, lesion, rep2

description:
Library name: Primaquine_L2
Column name in counts.txt: 7780.EE.0015


title: Replicate 3, ATF1/CREB1/CREM-KO

first: Lihe

last: Chen

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

description: Library name: Sample 22

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 106). Transcript per million (TPM) and expected counts were generated by RSEM. Unless otherwise specified, the computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform
Assembly: Ensemble release 106
Supplementary files format and content: CREB_family_raw.txt

source_name: Kidney

growth_protocol: Cells were maintained in DMEM/F-12 media with 2% Fetal Bovine Serum and supplemented with 5 μg/mL insulin, 50 nM dexamethasone, 1 nM triiodothyronine, 10 ng/mL epidermal growth factor, 60 nM sodium selenite, 5 μg/mL transferrin; all from Sigma). In order to polarize cells, they were grown in permeable membrane supports (Transwell) and grown with complete media for 4 days, prior to changing to simple media (DMEM/F-12 media only supplemented with 50 nM dexamethasone, 60 nM sodium selenite and 5 μg/mL transferrin) for 3 days, with 0.1 nM dDAVP (1-desamino-8-D-arginine-vasopressin).

extract_protocol:
RNA was extracted using Direct-zol RNA MicroPrep kit
Trizol-extracted RNA was proceeded to cDNA generation using the SMARTer V4 Ultra Low RNA Kit (Takara Bio). cDNA was generated with 8 PCR cycles. 1 ng of the resulting cDNA was “tagmented” and barcoded by using the Nextera XT DNA Sample Preparation Kit (Illumina) to generate sequencing libraries for high throughput sequencing. Libraries were purified by AmPure XP magnetic beads (Beckman Coulter), and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). An equal amount of index libraries were pooled and sequenced (paired-end 50 bp) on an Illumina platform.

treatment_protocol: dDAVP 0.1nM added for 72 hours

value: Kidney

value: mpkCCD

value: Immortalized mouse collecting duct

value: dDAVP 0.1nM 72 hrs


title: blood, Day 3, UGA4, 051

address: 50 South Drive

value: Whole Blood

value: Day 3

tag: Sex

value: male

value: Low Responder


title: blood, Day 3, UGA4, 086

tag: vaccine response

value: Non Responder


title: Replicate 2, ATF1/CREB1/CREM-KO

description: Library name: Sample 21


title: blood, Day 3, UGA4, 458

value: High Responder


title: Endo, Fenoprofen, uterus, rep5

description:
Library name: Fenoprofen_U5
Column name in counts.txt: 7780.EE.0068

value: uterus

value: Endometriosis Induction+Fenoprofen


title: Endo, Fenoprofen, uterus, rep4

description:
Library name: Fenoprofen_U4
Column name in counts.txt: 7780.EE.0067


title: Replicate 1, ATF1/CREB1/CREM-KO

description: Library name: Sample 20


title: Duodenal epithelium; cKO; H. polygyrus (7 d.p.i.)

description:
Library name: Epithelium_cKO
10x Genomics (3' v3.1 dual index chemistry)

value: Small intestinal epithelium (duodenum)

value: 9 weeks 1 day

value: Epithelial and intra-epithelial leukocytes (manually counted cells)

value: 200 L3 H. polygyrus larvae


title: blood, Day 3, UGA4, 016

value: female


title: Endo, primaquine, uterus, rep2

description:
Library name: Primaquine_U2
Column name in counts.txt: 7780.EE.0013

value: Endometriosis Induction+Primaquine


title: blood, Day 3, UGA4, 430


title: Endo, Fenoprofen, uterus, rep2

description:
Library name: Fenoprofen_U2
Column name in counts.txt: 7780.EE.0056


title: Replicate 11, control clone

description: Library name: Sample 19

value: Kidney

value: mpkCCD

value: WT


title: blood, Day 3, UGA4, 263

value: Whole Blood


title: Endo, primaquine, lesion, rep3

description:
Library name: Primaquine_L3
Column name in counts.txt: 7780.EE.0044

value: lesion


title: Endo, primaquine, lesion, rep6

description:
Library name: Primaquine_L6
Column name in counts.txt: 7780.EE.0077


title: Endo, Fenoprofen, lesion, rep5

description:
Library name: Fenoprofen_L5
Column name in counts.txt: 7780.EE.0069


title: Endo, primaquine, lesion, rep1

description:
Library name: Primaquine_L1
Column name in counts.txt: 7780.EE.0009


title: blood, Day 3, UGA4, 038

value: Day 3

value: male


title: blood, Day 3, UGA4, 343

value: Non Responder


title: Replicate 9, control clone

description: Library name: Sample 17

value: Immortalized mouse collecting duct

value: dDAVP 0.1nM 72 hrs


title: Endo, Fenoprofen, uterus, rep1

description:
Library name: Fenoprofen_U1
Column name in counts.txt: 7780.EE.0024

value: uterus

value: Endometriosis Induction+Fenoprofen


title: Endo, Fenoprofen, lesion, rep4

description:
Library name: Fenoprofen_L4
Column name in counts.txt: 7780.EE.0055


title: Endo, Fenoprofen, uterus, rep6

description:
Library name: Fenoprofen_U6
Column name in counts.txt: 7780.EE.0073


title: Endo, Fenoprofen, lesion, rep2

description:
Library name: Fenoprofen_L2
Column name in counts.txt: 7780.EE.0018


title: Endo, Fenoprofen, uterus, rep3

description:
Library name: Fenoprofen_U3
Column name in counts.txt: 7780.EE.0065


title: Endo, Fenoprofen, lesion, rep3

description:
Library name: Fenoprofen_L3
Column name in counts.txt: 7780.EE.0040


title: blood, Day 3, UGA4, 473

value: High Responder


title: Endo, Fenoprofen, lesion, rep1

description:
Library name: Fenoprofen_L1
Column name in counts.txt: 7780.EE.0006


title: Endo, no treatment, uterus, rep6

description:
Library name: Vehicle_U6
Column name in counts.txt: 7780.EE.0064

value: Endometriosis Induction


title: Replicate 2, ATF1/CREB1-KO

description: Library name: Sample 15


title: Endo, no treatment, uterus, rep4

description:
Library name: Vehicle_U4
Column name in counts.txt: 7780.EE.0041


title: blood, Day 3, UGA4, 128


title: Endo, no treatment, uterus, rep3

description:
Library name: Vehicle_U3
Column name in counts.txt: 7780.EE.0036


title: Endo, Fenoprofen, lesion, rep6

description:
Library name: Fenoprofen_L6
Column name in counts.txt: 7780.EE.0075


title: Endo, no treatment, uterus, rep5

description:
Library name: Vehicle_U5
Column name in counts.txt: 7780.EE.0062


title: Endo, no treatment, uterus, rep2

description:
Library name: Vehicle_U2
Column name in counts.txt: 7780.EE.0034


title: blood, Day 3, UGA4, 309


title: Endo, no treatment, uterus, rep1

description:
Library name: Vehicle_U1
Column name in counts.txt: 7780.EE.0033


title: Replicate 1, ATF1/CREB1-KO

description: Library name: Sample 14


title: Replicate 10, control clone

description: Library name: Sample 18


title: Replicate 8, control clone

description: Library name: Sample 13


title: Endo, no treatment, lesion, rep6

description:
Library name: Vehicle_L6
Column name in counts.txt: 7780.EE.0080


title: Replicate 7, control clone

description: Library name: Sample 12


title: Endo, no treatment, lesion, rep3

description:
Library name: Vehicle_L3
Column name in counts.txt: 7780.EE.0025


title: Endo, no treatment, lesion, rep5

description:
Library name: Vehicle_L5
Column name in counts.txt: 7780.EE.0052


title: blood, Day 3, UGA4, 064


title: blood, Day 3, UGA4, 270


title: Replicate 5, ATF1-KO

description: Library name: Sample 10


title: Replicate 3, ATF1/CREB1-KO

description: Library name: Sample 16


title: Endo, no treatment, lesion, rep1

description:
Library name: Vehicle_L1
Column name in counts.txt: 7780.EE.0016


title: blood, Day 3, UGA4, 371


title: Replicate 4, ATF1-KO

description: Library name: Sample 9


title: blood, Day 3, UGA4, 446

value: Low Responder


title: No endo, no treatment, uterus, rep4

description:
Library name: WT4
Column name in counts.txt: 7780.EE.0071

value: No treatment


title: No endo, no treatment, uterus, rep3

description:
Library name: WT3
Column name in counts.txt: 7780.EE.0057


title: blood, Day 3, UGA4, 295

value: female


title: Endo, no treatment, lesion, rep4

description:
Library name: Vehicle_L4
Column name in counts.txt: 7780.EE.0028


title: blood, Day 3, UGA4, 211


title: No endo, no treatment, uterus, rep5

description:
Library name: WT5
Column name in counts.txt: 7780.EE.0072


title: blood, Day 3, UGA4, 213


title: Replicate 6, control clone

description: Library name: Sample 11

value: Kidney


title: Replicate 3, ATF1-KO

description: Library name: Sample 8

value: mpkCCD


title: No endo, no treatment, uterus, rep2

description:
Library name: WT2
Column name in counts.txt: 7780.EE.0045


title: Endo, no treatment, lesion, rep2

description:
Library name: Vehicle_L2
Column name in counts.txt: 7780.EE.0020


title: RCC4A_2

first: Genomics-core-facility

last: WCM

address: 1300 York Ave.

institute: Weill Cornell Medicine

description:
Library name: Sample 5
RCC4 ATF4 KO cells 2

data_processing:
Raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing. FASTQ files were trimmed for adaptor sequences and low-quality bases using cutadapt. Trimmed reads were aligned to the human reference genome (GRCh38) using STAR aligner. Raw gene counts were quantified using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes gene counts for each sample

extract_protocol:
Cortices of kidneys from 3 - 4 mice from each of the cohorts were dissected for mRNA-seq. Five -10 mg of each cortex section was transferred into a tube containing beads (Benchmark Scientific Prefilled Tubes for Homogenizer, Catalogue #, D1032-15) and a 500 μl mixture of RLT (from Qiagen RNeasy Plus Mini Kit (Cat. No. 74134)) and β-mercaptoethanol. Tissues were homogenized twice for 30 seconds each with a Bead Bug homogenizer (Benchmark Scientific, Fort Lauderdale, FL). After homogenization, total RNA was extracted by following the protocol from the kit. Total RNA from RCC4 cells was extracted by following the protocol from the kit.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), following manufacturer's protocols.

value: ATF4 KO


title: RCC4A_1

description:
Library name: Sample 4
RCC4 ATF4 KO cells 1


title: Replicate 2, ATF1-KO

description: Library name: Sample 7


title: No endo, no treatment, uterus, rep6

description:
Library name: WT6
Column name in counts.txt: 7780.EE.0076


title: blood, Day 3, UGA4, 253

value: Whole Blood


title: RCC4A_3

description:
Library name: Sample 6
RCC4 ATF4 KO cells 3


title: Replicate 1, ATF1-KO

description: Library name: Sample 6


title: RCC4P_3

description:
Library name: Sample 3
RCC4 Parental cells 3

value: Wild Type


title: RCC4P_2

description:
Library name: Sample 2
RCC4 Parental cells 2


title: blood, Day 3, UGA4, 126

value: Day 3


title: RCC4P_1

description:
Library name: Sample 1
RCC4 Parental cells 1


title: Replicate 5, control clone

description: Library name: Sample 5

value: WT


title: blood, Day 3, UGA4, 323


title: Replicate 4, control clone

description: Library name: Sample 4


title: TP19M6-10 Fixed Liver HFO snRNA-seq

description: Library name: TP19M6-10_Fixed

value: Liver metastases


title: blood, Day 3, UGA4, 378


title: Replicate 1, control clone

description: Library name: Sample 1

value: Immortalized mouse collecting duct


title: blood, Day 3, UGA4, 383

value: Non Responder


title: Replicate 2, control clone

description: Library name: Sample 2

value: dDAVP 0.1nM 72 hrs


title: blood, Day 3, UGA4, 350

value: male


title: No endo, no treatment, uterus, rep1

description:
Library name: WT1
Column name in counts.txt: 7780.EE.0002

value: uterus


title: blood, Day 3, UGA4, 238

value: High Responder


title: GCERAdT_3

description:
Library name: Sample 16
TRAnsgenic model of Cancer of the Kidney (TRACK)- ATF4 KO mouse 3

data_processing:
Raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing. FASTQ files were trimmed for adaptor sequences and low-quality bases using cutadapt. Trimmed reads were aligned to the mouse reference genome (GRCm38) using STAR aligner. Raw gene counts were quantified using HTSeq-count.
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file includes gene counts for each sample

value: TRACK-ATF4 KO


title: blood, Day 3, UGA4, 065


title: blood, Day 3, UGA4, 136


title: Replicate 3, control clone

description: Library name: Sample 3


title: GCERAdT_2

description:
Library name: Sample 15
TRAnsgenic model of Cancer of the Kidney (TRACK)- ATF4 KO mouse 2


title: blood, Day 3, UGA4, 055


title: Lung, Myh11, control, scRNAseq

city: Cincinnati

first: Jichao

address: 3333 Burnet Avenue

department: Pediatrics

institute: University of Cincinnati and Cincinnati Children's Hospital Medical Center

description:
Library name: Myh11-control
10X Genomics

data_processing:
Raw sequencing data (fastqfile) was demultiplexed and analyzed using 10X Genomics cell Ranger ARC software
Chromium single-cell RNA-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”. Further analysis was carried out using R package Seurat 2.3.4 (https://satijalab.org/seurat/pbmc3k_tutorial.html).
Assembly: mm10
Supplementary files format and content: tsv and mtx files can be opened and analyzed with Seurat&Signac (R package)

source_name: Lung

extract_protocol:
Lungs from young adult mice were freshly collected after perfusion and kept in cold 1X Leibovitz media until dissociation. All the lung lobes except for the accesory lobe were separated and dissociated in 1X Lebovitz media with Collagenase type I (2mg/ml), DNAse I  (0.5 mg/ml) and Elastase (2mg/ml) for 45  minutes at 37˚C. Then, the lung cells were filtered, red blood cells lysated and lung cells were incubated  with conjugated antibodies for each lineage for 30 min. All the samples were stained with CD45-PE/Cy7 (BioLegend, 103114), ECAD-PE (BioLegend, 147304), and ICAM2-A647 (Invitrogen, A15452) antibodies (1:250 dilutions for all antibodies) for 30 min Then washed and stain with the viability dye Sytox blue. Cells were filtered with a 35 mm cell strainer into a 5 mL glass tube again and sorted by a BD FACSAria  with a 70 mm nozzle.
FACS-purified lung cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10x Genomics) using the Chromium Single Cell 3’ Library and Gel Bead Kit in accordance with the manufacturer’s user guide. The libraries were sequenced on an Illumina NextSeq500 using a 26X124 sequencing run format with 8 bp index.

treatment_protocol: All mice were injected once with 500ug of tamoxifen at early alveologenesis between postanatal day 7-9.

value: Lung

tag: group

value: two males

value: Endothelial, epithelial, immue and mesenchymal cells

value: Myh11-CreER;  Rosa26 tdT/+

value: Tamoxifen= 500 ug


title: adjacent_2075354, Sup

type: RNA

city: sheng yang

first: li

middle: rui

last: ming

address: san hao jie

country: China

institute: china medical school

hyb_protocol: Cy3 and Cy5 labeled cRNAs were  combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed to show the distinguishable m6A-methylation pattern among samples.

source_name: Rcc normal tissue

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: RCC and matched non-tumor hepar tissues

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: fraction

value: Sup


title: Rcc tissue_2075354, Sup

source_name: Rcc tumor tissue

tag: age


title: Rcc tissue_1599104, Sup


title: adjacent_2080951, Sup

value: female


title: Rcc tissue_2080951, IP

value: IP


title: adjacent_1599104, Sup


title: Rcc tissue_2080951, Sup


title: adjacent_2075354, IP


title: adjacent_1599104, IP


title: Rcc tissue_2075354, IP


title: Rcc tissue_1599104, IP


title: adjacent_2080951, IP


title: Lung, Myh11, mutant, scRNAseq

description:
Library name: Myh11-mutant
10X Genomics

value: Myh11-CreER;  Rosa26 Bcl2/+


title: Lung,Pdgfrb, control, scRNA seq

description:
Library name: Pdgfrb-control
10X Genomics

value: pooled male and female

value: one female, one male

value: PdgfrbcreER/+; Rosa26 Bcl2/+


title: GCERAdT_4

description:
Library name: Sample 17
TRAnsgenic model of Cancer of the Kidney (TRACK)- ATF4 KO mouse 4

value: Kidney


title: Lung, Pdgfrb, mutant, scRNAsq

description:
Library name: Pdgfrb-mutant
10X Genomics

value: male

value: PdgfrbcreER/+; Rosa26 tdT/+


title: Lung,Pdgfra, mutant, scRNAseq

description:
Library name: Pdgfra-mutant
10X Genomics

value: PdgfracreER/+; Rosa26 tdT/+


title: (Rosa26) Wild type chondrocytes

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

description:
Library name: AdenoGFP
10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation made using CellRanger software v.7.0.1  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-2020-A
Supplementary files format and content: .h5 filtered features, matrix, barcoded files
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Chondrocyte

growth_protocol: Plated wt cells on tissue culture treated plates.

extract_protocol:
Trypsinize lifted and proceed to single cell protocol.
A 10x genomics kit for library construction.

treatment_protocol: 24 hr adenoviral GFP and Cre infection for RosaNICD2 with 24 hr recovery

value: Chondrocyte

value: Wild type

value: AdenoGFP


title: blood, Day 3, UGA4, 431

city: Bethesda

value: Whole Blood

value: Day 3

value: Non Responder

tag: bmi


title: blood, Day 3, UGA4, 184


title: Notch2tm1.1Ecan Experimental chondrocytes

description:
Library name: Het
10x Genomics

value: no treatment


title: Rosa26NICD2 Experimental chondrocytes

description:
Library name: AdenoCre
10x Genomics

value: AdenoCre


title: blood, Day 3, UGA4, 249

value: female

value: Low Responder


title: Lung,Pdgfra,control, scRNA seq

description:
Library name: Pdgfra-control
10X Genomics

value: Lung

value: pooled male and female

value: Endothelial, epithelial, immue and mesenchymal cells

value: PdgfracreER/+; Rosa26 Bcl2/+

value: Tamoxifen= 500 ug


title: TRACK_3

city: New York

description:
Library name: Sample 13
TRAnsgenic model of Cancer of the Kidney (TRACK) mouse 3

value: Kidney

value: TRACK


title: GCERAd_5

description:
Library name: Sample 10
ATF4 KO mouse 5

value: ATF4 KO


title: GCERAdT_1

description:
Library name: Sample 14
TRAnsgenic model of Cancer of the Kidney (TRACK)- ATF4 KO mouse 1

value: TRACK-ATF4 KO


title: blood, Day 3, UGA4, 334

value: male


title: TRACK_1

description:
Library name: Sample 11
TRAnsgenic model of Cancer of the Kidney (TRACK) mouse 1


title: Rosa26NICD2 Experimental chondrocytes, biological rep 4

description: Library name: Canalis-8

data_processing:
Libraries were validated for length and adapter dimer removal using the Agilent TapeStation 4200 D1000 High Sensitivity assay (Agilent Technologies), and then they were quantified and normalized using the dsDNA High Sensitivity Assay for Qubit 3.0 (Thermo Fisher Scientific).
Sample libraries were prepared for Illumina sequencing by denaturing and diluting the libraries per manufacturer’s protocol (Illumina).
All samples were pooled into one sequencing pool, equally normalized, and run as one sample pool across the Illumina NextSeq 500 using version 2.5 chemistry.
Target read depth was achieved for each sample with paired end 75bp reads.
Raw reads were trimmed with Sickle, with a quality threshold of 30 and length threshold of 45, following that the trimmed reads were mapped to Mus Musculus genome (GRCm38) with HISAT2 .
The resulting SAM files then converted into BAM format using samtools, and the PCR duplicates were removed using PICARD (http://broadinstitute.github.io/picard/).
The counts were generated against the features with htseq-count.
The differential expression of genes between conditions was evaluated using DESeq2.
Covariates were introduced in the DESeq2 analysis to increase the accuracy of results, and genes showing less than 10 counts across the compared samples were excluded from the analysis.
Genes with a false discovery rate (FDR) < 0.05 were considered significant and used in the downstream analysis.
Assembly: Mus Musculus genome (GRCm39 ensembl release 105)
Supplementary files format and content: COUNTS File (*.counts) and counts

extract_protocol:
Cells were lifted and the RNA extracted using Qiagen Rneasy Mini Kit.
Total RNA samples were prepared for mRNA-Sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation kit following the manufacturer’s protocol (Illumina, San Diego, CA).

value: Chondrocyte


title: (Notch2) Wild type chondrocytes

description:
Library name: WT
10x Genomics

value: Wild type


title: blood, Day 3, UGA4, 393

value: Whole Blood

value: Day 3


title: GCERAd_4

description:
Library name: Sample 9
ATF4 KO mouse 4


title: Rosa26NICD2 Experimental chondrocytes, biological rep 3

description: Library name: Canalis-7

value: AdenoCre


title: GCERAd_3

description:
Library name: Sample 8
ATF4 KO mouse 3


title: Rosa26NICD2 Experimental chondrocytes, biological rep 2

description: Library name: Canalis-6


title: blood, Day 3, UGA4, 166

value: Non Responder


title: (Rosa26) Wild type chondrocytes, biological rep 4

description: Library name: Canalis-4

value: AdenoGFP


title: GCERAd_2

description:
Library name: Sample 7
ATF4 KO mouse 2


title: blood, Day 3, UGA4, 083

value: female


title: (Rosa26) Wild type chondrocytes, biological rep 2

description: Library name: Canalis-2


title: GCERAd_1

description:
Library name: Sample 6
ATF4 KO mouse 1


title: Rosa26NICD2 Experimental chondrocytes, biological rep 1

description: Library name: Canalis-5


title: Notch2tm1.1Ecan Experimental chondrocytes, biological rep 3

description: Library name: Hajdu-7

value: no treatment


title: blood, Day 3, UGA4, 469


title: blood, Day 3, UGA4, 194


title: Notch2tm1.1Ecan Experimental chondrocytes, biological rep 4

description: Library name: Hajdu-8


title: blood, Day 3, UGA4, 452

value: High Responder


title: Notch2tm1.1Ecan Experimental chondrocytes, biological rep 2

description: Library name: Hajdu-6


title: blood, Day 3, UGA4, 029


title: (Rosa26) Wild type chondrocytes, biological rep 1

description: Library name: Canalis-1


title: (Notch2) Wild type chondrocytes, biological rep 2

description: Library name: WT-2


title: blood, Day 3, UGA4, 222


title: WT_3

description:
Library name: Sample 3
wild type mouse 3

value: Wild Type


title: WT_4

description:
Library name: Sample 4
wild type mouse 4


title: (Notch2) Wild type chondrocytes, biological rep 1

description: Library name: WT-1