title: Visium of tumor and adjcent liver tissues Chow IgG D1

city: Indianapolis

first: Yamei

state: Indiana

address: 975 W. Walnut St., IB552

institute: Indiana University

description: Library name: Visium_liver_Chow_IgG_D1

data_processing:
Raw sequencing data from 10x Genomics Visium slides were processed using the Space Ranger pipeline (v4.0.1) to align reads to the mouse reference genome GRCm39 and generate spot-level gene expression matrices. Downstream analyses were performed in Seurat (v5.3.0) in R (v4.4.3, The R Foundation).
Assembly: refdata-gex-mm10-2020-A/mm10 (GRCm38)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv: spatial feature enrichment scores
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Liver cancer

extract_protocol:
The isolated RNA was quality-checked using Agilent RNA 6000 Pico kit (#5067-1513) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). DV200 of the RNA samples need more than 30% to qualify for the assay.
The qualified samples after H&E staining and image were decrosslinked based the protocol (CG000409) and the library preparation followed the protocol (CG000407). The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA), and the library concentrations were determined by qPCR using Collibri Library Quantification kit (#A38524500, Thermo Fisher Scientific). The libraries were pooled evenly and went for the paired-end 75-cycle sequencing on an Illumina NextSeq 550 System (Illumina, Inc., USA) using High Output Kit v2.5 (#20024907, Illumina, Inc., USA).

value: Liver cancer


title: Visium of tumor and adjcent liver tissues MASH IgG D2

status: Public on Feb 11 2026

type: SRA

last: Chen

country: USA

description: Library name: Visium_liver_NASH_IgG_D2

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue


title: PETER001_HK2_6H_X1.A2_B46:A08

type: RNA

city: New York

first: Avi

last: Ma'ayan

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate

scan_protocol: Following treatment and lysis, gene expression was profiled using the L1000 platform, a high-throughput assay that measures the expression of ∼1,000 landmark genes and computationally infers the expression of nonmeasured transcripts.

data_processing: The data was normalized relative to the expression of 80 invariant landmark control genes. The expression of additional genes was inferred via a linear model trained on thousands of Affymetrix gene expression datasets from the gene expression omnibus (GEO). In this study, we utilized the L1000 data with the 12,328 measured and inferred mRNAs.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HK2 treated with Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM for 6.0 h

label_protocol: biotin labeling. Processing was done by th Broad Institute as previously described (10.1016/j.cell.2017.10.049)

growth_protocol:
HepG2 cells (5000 cells/well; ATCC, HB-8065) were cultured in Eagle's Minimum Essential Medium (EMEM; ATCC, cat. no.  30-2003), supplemented with 10% FBS and 1% P/S  at 37°C, 5% CO2.
HK-2 cells (5000 cells/well; ATCC, cat. no. CRL-2190) were cultured in Keratinocyte Serum Free Medium (K-SFM), Kit (Gibco, cat. no. 17005-042)  at 37°C, 5% CO2.
THP-1 cells (10,000 cells/well; ATCC, cat. no. TIB-202) were cultured in RPMI-40 medium (Gibco, cat. no. 11875-093) supplemented with 10% fetal bovine serum (FBS, Gibco, cat. no. 10438026) and 1% penicillin/streptomycin (P/S, Corning, cat. no. 30-002) at 37°C, 5% CO2. Macrophage differentiation was induced in vitro with phorbol-12-myristate-13-acetate (PMA, 50 ng/mL; Sigma) for 72 hours at 37°C in 5% CO2

extract_protocol: After treatment, cells were lysed using the TCL Buffer (Qiagen, cat. no. 1031576) and incubated for 30 minutes at 37°C. The lysates were then stored at -80°C. RNA was extracted by the Broad Institute, according to their protocol.

treatment_protocol: After 24 hours of culture for HepG2 and HK-2 cells, and 72 hours for THP-1 macrophages, the cells were placed in their respected culture media supplemented with 2% FBS for 16 hours. Subsequently, they were treated for 6 or 24 hours with either vehicle (DMSO) or with ART medications at a concentration of 0.1, or 0.5 µM.

tag: cell line

tag: treatment

tag: duration

tag: plate

tag: well


title: Visium of tumor and adjcent liver tissues MASH anti-PD-1 A2

description: Library name: Visium_liver_NASH_AntiPD1_A2


title: HaCaT, Ro60 and La sequential IP (IP)

city: Frederick

first: Sandra

middle: L

last: Wolin

state: Maryland

address: 1050 Boyles Street, BLDG 560 Room 11-39

department: NCI

institute: NIH

description: Library name: Ro60_La_IP

data_processing:
Demultiplexing and adapter trimming by Ultraplex v1.2.5.
Read alignment to UCSC hg38 using Novoalign v4.03.08 (parameters -t 15,3 -l 15 -x 4 -g 20 -s 1 -o SAM -R 0 -r All --umi2 bc --matchReward 3 --softclip 0,0).
Deduplication by UMI using UMI-tools v1.1.5.
Read counting for annotations using featureCounts of Subread v2.0.6 with -M --fraction.
Assembly: hg38
Supplementary files format and content: Tab-separated count tables.

source_name: HaCaT

extract_protocol:
Cells were washed once in Dulbecco’s Phosphate-Buffered Saline (Gibco) and harvested in NET-2 (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 2.5 mM MgCl2, 0.5 % NP-40) containing 1 mM phenylmethylsulfonyl fluoride (PMSF) and protease inhibitor cocktail. Cells were sonicated in a Bioruptor (Diagenode) and the lysate cleared by centrifuging for 5 min at 10,000 x g at 4 °C. Lysates were incubated with MagStrep Streptactin XT beads (IBA) for 1.5 hrs at 4 °C with rotation. After washing three times with NET-2, beads were incubated with NET-2 containing 50 mM biotin (Sigma) for 30 minutes at 4°C to elute Twin-Strep-Ro60 RNPs. To isolate La-containing RNPs, half the eluate was incubated with Protein G Dynabeads (Thermo Fisher Scientific) pre-coupled to a patient anti-La serum (a gift of John Harley, University of Cincinnati) at 4 °C for 1.5 hours with rotation. The remaining eluate was incubated with Protein G Dynabeads (Thermo Fisher Scientific) coupled to normal human sera. After three washes with NET-2, RNAs were extracted with phenol:chloroform:isoamyl alcohol (25:24:1) followed by addition of glycoblue (Invitrogen) and ethanol precipitation.
The cDNA library was prepared as described by Buchbender et al. (10.1016/j.ymeth.2019.10.003) except that 20 ng of purified RNA was ligated to the 3’ adapter with T4 RNA ligase 2 (truncated KQ) (New England Biolabs).

value: HaCaT

tag: cell type

value: human keratinocyte

tag: genotype

value: RO60-/- + twin-strep-RO60

tag: antibody

value: patient anti-La serum


title: Visium of tumor and adjcent liver tissues MASH anti-PD-1 B2

description: Library name: Visium_liver_NASH_AntiPD1_B2


title: Visium of tumor and adjcent liver tissues Chow IgG C1

description: Library name: Visium_liver_Chow_IgG_C1


title: Visium of tumor and adjcent liver tissues MASH IgG C2

description: Library name: Visium_liver_NASH_IgG_C2


title: Visium of tumor and adjcent liver tissues Chow anti-PD-1 B1

description: Library name: Visium_liver_Chow_AntiPD1_B1


title: PETER001_HK2_6H_X1.A2_B46:A07

value: Efavirenz|Emtricitabine|Tenofovir Disoproxil Fumarate 0.5|0.1|0.1 uM


title: RM-1 tumors treated with vehicle.

city: Jinan

first: Lin

last: Gao

address: No.44, Wenhua Xi Road

country: China

institute: shandong university

description:
Library name: vehicle-1
SeekOne DD

library_source: transcriptomic single cell

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: RM-1 tumors

extract_protocol:
Tumor tissues were dissociated into single-cell suspensions, and CD45⁺ cells were isolated by flow cytometry. CD45⁺ cells were then mixed with tumor cells at a ratio of 3:1 and subjected to single-cell RNA sequencing.Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol,SeekOne DD). RNA libraries were prepared for sequencing using standard Illumina protocols

value: RM-1 tumors

value: prostate cancer cell line

value: WT

value: vehicle


title: RM-1 tumors treated with RP-6306.

description:
Library name: RP-6306-1
SeekOne DD


title: Visium of tumor and adjcent liver tissues Chow anti-PD-1 A1

description: Library name: Visium_liver_Chow_AntiPD1_A1


title: PETER001_HK2_6H_X1.A2_B46:A06

description: L1000 inferred profile; pert_id: Abacavir|Dolutegravir|Emtricitabine

source_name: HK2 treated with Abacavir|Dolutegravir|Emtricitabine 0.5|0.1|0.1 uM for 6.0 h


title: Old normal diet replicate 5

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

description:
Library name: OND_18
colnames in ND_raw_counts.txt: 18_OND_5-146032949/ (29532739.0 total)
ND_raw_counts.txt

data_processing:
Alignment to GrCM38/mm10 using STAR aligner, tag counting using HOMER.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: whole liver

extract_protocol:
RNA extracted using Trizol-chloroform methodology.
NEB polyA mRNA library prep kits.

tag: strain

value: whole liver

tag: age

value: Old

tag: diet

value: ND

tag: Sex

value: male


title: PETER001_HK2_6H_X1.A2_B46:A05


title: Old normal diet replicate 2

description:
Library name: OND_15
colnames in ND_raw_counts.txt: 15_OND_2-146037913/ (27002902.0 total)
ND_raw_counts.txt


title: F00374662

type: protein

city: Silver Spring

first: Paula

last: Hyland

state: MD

address: 10903 New Hampshire Avenue

department: CDER

institute: FDA

description: 55 ul of plasma was used for the  proteomic assay

hyb_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

data_processing: https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.

label: 5’ fluorophore, photocleavable linker, and biotin

molecule: protein

source_name: EDTA Plasma

extract_protocol: EDTA plasma from whole blood

tag: participant id

tag: time point (days)

value: EDTA Plasma

tag: treatment group (dose)

value: Covid convalescent control (PCR-negative)

tag: bmi (kg/m2)

value: M

tag: race

value: Black


title: Old normal diet replicate 1

description:
Library name: OND_14
colnames in ND_raw_counts.txt: 14_OND_1-146032948/ (25564750.0 total)
ND_raw_counts.txt

tag: tissue


title: Old normal diet replicate 4

description:
Library name: OND_17
colnames in ND_raw_counts.txt: 17_OND_4-146033952/ (29529071.0 total)
ND_raw_counts.txt


title: PETER001_HK2_24H_X1_B46:H21

description: L1000 inferred profile; pert_id: DMSO

source_name: HK2 treated with DMSO 0.5 uM for 24.0 h

tag: cell line

tag: treatment

value: DMSO 0.5 uM


title: PETER001_HK2_6H_X1.A2_B46:A04

tag: duration

tag: plate


title: Old high fat diet replicate 2

description:
Library name: OHFD_11
colnames in HFD_raw_counts.txt: 11-OHFD-2_S11 (31787043.0 total)
HFD_raw_counts.txt

value: HFD


title: Old high fat diet replicate 4

description:
Library name: OHFD_13
colnames in HFD_raw_counts.txt: 13-OHFD-4_S13 (32102637.0 total)
HFD_raw_counts.txt


title: Old normal diet replicate 3

description:
Library name: OND_16
colnames in ND_raw_counts.txt: 16_OND_3-146049909/ (33099890.0 total)
ND_raw_counts.txt


title: F00374593

scan_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

value: F


title: Old high fat diet replicate 3

description:
Library name: OHFD_12
colnames in HFD_raw_counts.txt: 12-OHFD-3_S12 (36100261.0 total)
HFD_raw_counts.txt


title: F14605591

label_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

value: Day 123

tag: delivery

value: SC

value: Mepolizumab (24 mg)

value: Black or African America


title: Old high fat diet replicate 1

description:
Library name: OHFD_10
colnames in HFD_raw_counts.txt: 10-OHFD-1_S10 (36172622.0 total)
HFD_raw_counts.txt


title: Young normal diet replicate 4

description:
Library name: YND_09
colnames in ND_raw_counts.txt: 09_YND_4-146049906/ (32975364.0 total)
ND_raw_counts.txt

value: Young


title: F14605521

value: Day 49


title: F14605566

value: Day 93


title: F14605551

value: Day 63


title: PETER001_HK2_24H_X1_B46:H19

description: L1000 inferred profile; pert_id: DMSO

tag: well


title: PETER001_HK2_24H_X1_B46:H18

description: L1000 inferred profile; pert_id: Darunavir

source_name: HK2 treated with Darunavir 0.1 uM for 24.0 h

value: Darunavir 0.1 uM


title: Young normal diet replicate 3

description:
Library name: YND_08
colnames in ND_raw_counts.txt: 08_YND_3-146047911/ (33094583.0 total)
ND_raw_counts.txt

value: whole liver

value: ND

value: male


title: Young normal diet replicate 2

description:
Library name: YND_07
colnames in ND_raw_counts.txt: 07_YND_2-146042917/ (27517312.0 total)
ND_raw_counts.txt


title: PETER001_HK2_24H_X1_B46:H17


title: Young high fat diet replicate 4

description:
Library name: YHFD_04
colnames in HFD_raw_counts.txt: 04-YHFD-4_S4 (32884182.0 total)
HFD_raw_counts.txt


title: F14604237

value: Day 21

value: EDTA Plasma


title: PETER001_HK2_24H_X1_B46:H16


title: Young high fat diet replicate 5

description:
Library name: YHFD_05
colnames in HFD_raw_counts.txt: 05-YHFD-5_S5 (43021732.0 total)
HFD_raw_counts.txt


title: Young high fat diet replicate 3

description:
Library name: YHFD_03
colnames in HFD_raw_counts.txt: 03-YHFD-3_S3 (33279047.0 total)
HFD_raw_counts.txt


title: Young normal diet replicate 1

description:
Library name: YND_06
colnames in ND_raw_counts.txt: 06_YND_1-146041911/ (25452183.0 total)
ND_raw_counts.txt


title: PETER001_HK2_24H_X1_B46:H15

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir

source_name: HK2 treated with Emtricitabine|Ritonavir 0.1|0.5 uM for 24.0 h

value: Emtricitabine|Ritonavir 0.1|0.5 uM


title: F14340531

description: 55 ul of plasma was used for the  proteomic assay

value: Day 14


title: Young high fat diet replicate 1

description:
Library name: YHFD_01
colnames in HFD_raw_counts.txt: 01-YHFD-1_S1 (45394364.0 total)
HFD_raw_counts.txt

value: HFD


title: Young high fat diet replicate 2

description:
Library name: YHFD_02
colnames in HFD_raw_counts.txt: 02-YHFD-2_S2 (29656204.0 total)
HFD_raw_counts.txt


title: PETER001_HK2_24H_X1_B46:H13


title: PETER001_HK2_24H_X1_B46:H14


title: F14605359

value: Day 28

value: F


title: F14340124-1

value: Day 3

value: SC

value: Mepolizumab (24 mg)


title: H55.1C wild-type cells exposed to sorafenib 12h

city: Ferrara

first: Cristian

last: Bassi

state: Ferrara

address: Via Fossato di Mortara 70

department: Medicina Traslazionale e per la Romagna

country: Italy

institute: Università di Ferrara

description: Library name: SF-SHORT_12h

data_processing:
The obtained sequences were mapped to the mouse genome (GRCm38) using the HISAT2 algorithm 44 and a prebuilt genome index downloadable from the HISAT2 website. Then, StringTie 45 was used to assemble and quantify the transcripts in each sample. Finally, the expressed transcripts were normalized using the “DESeq2” package 46 for R.
Assembly: GRCm38
Supplementary files format and content: The file contains the normalized gene expression data

growth_protocol: All cell lines were propagated and maintained in Iscove’s modified Dulbecco's medium supplemented with 10% fetal bovine serum (FBS), 0.1% gentamicin, and 1% L-glutamine (Sigma‒Aldrich, St. Louis, MO, USA).

extract_protocol:
Total RNA was extracted from frozen liver cells or tissues using a Maxwell RSC instrument (Promega Italia, Milan) and a Maxwell RSC miRNA from a tissue purification kit (#AS1460, Promega) according to the manufacturer's instructions.
RNA quality and integrity were checked by a Bioanalyzer 2100 and Agilent RNA 6000 Nano Kit (No. 5067-1511 Agilent, Santa Clara, CA, USA). RNA-seq libraries were prepared using the Qiagen QIAseq Fast Select rRNA HMR kit (no. 334386, Qiagen Düsseldorf, Germany) for ribosomal RNA depletion and the Qiagen QIAseq stranded total RNA library kit (no. 180745, Qiagen) according to the manufacturer's instructions. RNA sequencing was performed according to the Illumina pipeline on a NextSeq 500 instrument (Illumina, San Diego, CA, USA.) using the NextSeq 500/550 High Output Kit v2.5 150 Cycles (#20024907, Illumina).

treatment_protocol: For in vitro experiments, Sorafenib (S-8599, LC Laboratories, Woburn, MA, USA), SR9009 (1379686-30-2, BOC SCIENCES, NY, USA) were solubilized in dimethyl sulfoxide (DMSO).


title: H55.1C wild-type cells exposed to sorafenib 24h

description: Library name: SF-SHORT_24h


title: H55.1C wild-type cells exposed to sorafenib

description: Library name: H55-SF


title: F14340252

value: Day 7

value: Black or African America


title: F14340014

value: Day 2


title: H55.1C wild-type cells exposed to sorafenib + SR9009

description: Library name: H55_SR-SF


title: F14340124


title: H55.1C wild-type cells exposed to sorafenib 8h

description: Library name: SF-SHORT_8h


title: PETER001_HK2_24H_X1_B46:H11

description: L1000 inferred profile; pert_id: Darunavir|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM for 24.0 h


title: PETER001_HK2_24H_X1_B46:H12

value: Darunavir|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: H55.1C wild-type cells exposed to sorafenib 4h

description: Library name: SF-SHORT_4h


title: F14339575

value: Day 1


title: H55.1C wild-type cells exposed to sorafenib 6h

description: Library name: SF-SHORT_6h


title: H55-RES sorafenib resistant cell-lines, sample 424

description: Library name: H55-RES_424

source_name: Hep55.1C derived cells

value: Hep55.1C derived cells


title: F14056007

value: Day 123

value: IV

value: Reslizumab (0.8 mg/kg)

value: White


title: H55-RES sorafenib resistant cell-lines, sample 423

description: Library name: H55-RES_423


title: H55.1C wild-type cells exposed to sorafenib 2h

description: Library name: SF-SHORT_2h


title: PETER001_HK2_24H_X1_B46:H10


title: PETER001_HK2_24H_X1_B46:H09

description: L1000 inferred profile; pert_id: Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM for 24.0 h


title: H55.1C wild-type sorafenib sensitive cells, sample NT1

description: Library name: H55_NT1


title: PETER001_HK2_24H_X1_B46:H07

value: Ritonavir|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: H55-RES sorafenib resistant cell-lines, sample 422

description: Library name: H55-RES_422


title: F14055982

value: Day 93

value: EDTA Plasma


title: H55-RES sorafenib resistant cell-lines, sample 412

description: Library name: H55-RES_412


title: F14055775

value: Day 28

value: F


title: PETER001_HK2_24H_X1_B46:H08


title: H55.1C wild-type sorafenib sensitive cells, sample NT2

description: Library name: H55_NT2


title: M_liver_10mo_VEH_TGT127_9me3

city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: Sample 51
PI: Aylor

library_source: genomic

data_processing:
Data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore
ChIP-Seq reads were mapped to the mouse genome build UCSC mm10 using bowtie2 and duplicate reads were removed
Peaks were called using MACS2
bigWig files were generated using deeptools v3.5.2
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: liver

extract_protocol:
Chromatin was cross-linked with formaldehyde, the reaction stopped with glycine, and sonicated with a bioruptor to obtain fragment sizes of 100–300 bp for ChIP-seq. ChIP-validated antibodies used were directed against H3K4me3 (Active Motif #39915), H3K4me1 (Abcam ab8895), H3K27ac (Abcam ab4729), H3K27me3 (Active Motif #61017), and H3K9me3 (Active Motif #61013). Immunoprecipitated DNA was recovered and purified using the QIAquick PCR Purification kit (Qiagen)
QIAseq FX DNA library kit or the QIAseq Ultralow Input Library Kit

value: liver

value: male

value: Vehicle

tag: antibody


title: H55-RES sorafenib resistant cell-lines, sample 191

description: Library name: H55-RES_191


title: F14055967

value: Day 63


title: M_liver_10mo_VEH_TGT163_9me3

description:
Library name: Sample 53
PI: Aylor


title: PETER001_HK2_24H_X1_B46:H06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine

source_name: HK2 treated with Darunavir|Emtricitabine 0.1|0.1 uM for 24.0 h

value: Darunavir|Emtricitabine 0.1|0.1 uM


title: M_liver_10mo_VEH_TGT155_9me3

description:
Library name: Sample 52
PI: Aylor


title: M_liver_10mo_VEH_TGT125_9me3

description:
Library name: Sample 50
PI: Aylor


title: PETER001_HK2_24H_X1_B46:H05


title: M_liver_5mo_VEH_TGT087_9me3

description:
Library name: Sample 48
PI: Aylor


title: M_liver_10mo_VEH_TGT171_9me3

description:
Library name: Sample 54
PI: Aylor


title: F14055937

value: Day 49


title: F14022602

value: Day 7


title: PETER001_HK2_24H_X1_B46:H03

description: L1000 inferred profile; pert_id: Water

source_name: HK2 treated with Water 0.01 uM for 24.0 h

value: Water 0.01 uM


title: F14055755

value: Day 21


title: M_liver_5mo_VEH_TGT024_9me3

description:
Library name: Sample 45
PI: Aylor


title: M_liver_5mo_VEH_TGT086_9me3

description:
Library name: Sample 47
PI: Aylor


title: M_liver_10mo_VEH_TGT115_9me3

description:
Library name: Sample 49
PI: Aylor


title: PETER001_HK2_24H_X1_B46:H01

description: L1000 inferred profile; pert_id: Water


title: F14022474

value: Day 3

value: IV


title: PETER001_HK2_24H_X1_B46:H02

description: L1000 inferred profile; pert_id: Water


title: M_liver_5wk_VEH_TGT176_9me3

description:
Library name: Sample 42
PI: Aylor


title: M_liver_5mo_VEH_TGT019_9me3

description:
Library name: Sample 43
PI: Aylor


title: M_liver_5wk_VEH_TGT071_9me3

description:
Library name: Sample 41
PI: Aylor


title: M_liver_5mo_VEH_TGT085_9me3

description:
Library name: Sample 46
PI: Aylor


title: PETER001_HK2_24H_X1_B46:G20

description: L1000 inferred profile; pert_id: DMSO

value: DMSO 0.5 uM


title: PETER001_HK2_24H_X1_B46:G19

description: L1000 inferred profile; pert_id: DMSO


title: F14022881

value: Day 14

value: Reslizumab (0.8 mg/kg)

value: White


title: M_liver_5wk_VEH_TGT063_9me3

description:
Library name: Sample 39
PI: Aylor


title: F14021925

value: Day 1

value: EDTA Plasma


title: PETER001_HK2_24H_X1_B46:G18

description: L1000 inferred profile; pert_id: Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Tenofovir Alafenamide Fumarate 0.5 uM for 24.0 h

value: Tenofovir Alafenamide Fumarate 0.5 uM


title: F13750383

value: Day 123

value: SC

value: M


title: M_liver_5wk_VEH_TGT065_9me3

description:
Library name: Sample 40
PI: Aylor

value: liver

value: male

value: Vehicle


title: F14022364

value: Day 2

value: F


title: PETER001_HK2_24H_X1_B46:G21

description: L1000 inferred profile; pert_id: DMSO


title: M_liver_5wk_VEH_TGT052_9me3

description:
Library name: Sample 38
PI: Aylor


title: M_liver_5wk_VEH_TGT050_9me3

description:
Library name: Sample 37
PI: Aylor


title: M_liver_10mo_VEH_TGT155_27me3

description:
Library name: Sample 35
PI: Aylor


title: M_liver_10mo_VEH_TGT163_27me3

description:
Library name: Sample 36
PI: Aylor


title: PETER001_HK2_24H_X1_B46:G16


title: F13750358

value: Day 93


title: M_liver_10mo_VEH_TGT127_27me3

description:
Library name: Sample 34
PI: Aylor


title: F13750343

value: Day 63


title: M_liver_5mo_VEH_TGT021_9me3

description:
Library name: Sample 44
PI: Aylor


title: M_liver_10mo_VEH_TGT115_27me3

description:
Library name: Sample 33
PI: Aylor


title: PETER001_HK2_24H_X1_B46:G15

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM for 24.0 h


title: M_liver_5mo_VEH_TGT021_27me3

description:
Library name: Sample 31
PI: Aylor


title: F13750313

value: Day 49


title: F13750151

value: Day 28


title: M_liver_5mo_VEH_TGT086_27me3

description:
Library name: Sample 32
PI: Aylor


title: M_liver_5wk_VEH_TGT176_27me3

description:
Library name: Sample 29
PI: Aylor


title: PETER001_HK2_24H_X1_B46:G14

value: Darunavir|Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1|0.1 uM


title: M_liver_5mo_VEH_TGT019_27me3

description:
Library name: Sample 30
PI: Aylor


title: PETER001_HK2_24H_X1_B46:G12

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM for 24.0 h


title: PETER001_HK2_24H_X1_B46:G13


title: M_liver_5wk_VEH_TGT063_27me3

description:
Library name: Sample 26
PI: Aylor


title: M_liver_5wk_VEH_TGT065_27me3

description:
Library name: Sample 27
PI: Aylor


title: M_liver_5wk_VEH_TGT071_27me3

description:
Library name: Sample 28
PI: Aylor


title: F13679117

value: Day 14

value: White


title: F13678838

value: Day 7

value: EDTA Plasma


title: F13750131

value: Day 21


title: M_liver_5wk_VEH_TGT052_27me3

description:
Library name: Sample 25
PI: Aylor


title: PETER001_HK2_24H_X1_B46:G11

value: Darunavir|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM


title: PETER001_HK2_24H_X1_B46:G09

description: L1000 inferred profile; pert_id: Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM for 24.0 h


title: M_liver_3wk_VEH_7M3V_9me3

description:
Library name: Sample 23
PI: Walker


title: M_liver_3wk_VEH_6M3V_9me3

description:
Library name: Sample 22
PI: Walker


title: M_liver_5wk_VEH_TGT050_27me3

description:
Library name: Sample 24
PI: Aylor


title: M_liver_3wk_VEH_7M3V_27me3

description:
Library name: Sample 20
PI: Walker


title: M_liver_3wk_VEH_4M3V_9me3

description:
Library name: Sample 21
PI: Walker


title: PETER001_HK2_24H_X1_B46:G06

description: L1000 inferred profile; pert_id: Darunavir|Emtricitabine|Ritonavir

source_name: HK2 treated with Darunavir|Emtricitabine|Ritonavir 0.1|0.1|0.5 uM for 24.0 h


title: M_liver_3wk_VEH_6M3V_27me3

description:
Library name: Sample 19
PI: Walker


title: M_liver_3wk_VEH_6M3V_4me3

description:
Library name: Sample 16
PI: Walker


title: F13678710

value: Day 3

value: SC

value: M


title: PETER001_HK2_24H_X1_B46:G07

value: Emtricitabine|Ritonavir|Tenofovir Disoproxil Fumarate 0.1|0.5|0.1 uM


title: F13678600

value: Day 2


title: M_liver_3wk_VEH_7M3V_4me3

description:
Library name: Sample 17
PI: Walker

value: liver

value: male

value: Vehicle


title: PETER001_HK2_24H_X1_B46:G04


title: M_liver_3wk_VEH_4M3V_27me3

description:
Library name: Sample 18
PI: Walker


title: F13678161

value: Day 1


title: F13749980

value: Day 123

value: IV


title: M_liver_3wk_VEH_5M3V_4me3

description:
Library name: Sample 15
PI: Walker


title: F13749955

value: Day 93


title: M_liver_3wk_VEH_3M3V_4me3

description:
Library name: Sample 13
PI: Walker


title: M_liver_3wk_VEH_4M3V_4me3

description:
Library name: Sample 14
PI: Walker


title: PETER001_HK2_24H_X1_B46:G03

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 24.0 h


title: PETER001_HK2_24H_X1_B46:G10


title: M_liver_3wk_VEH_2M3V_4me3

description:
Library name: Sample 12
PI: Walker


title: F13749940

value: Day 63

value: White


title: PETER001_HK2_24H_X1_B46:G02

value: Elvitegravir|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: M_liver_3wk_VEH_1M3V_4me1

description:
Library name: Sample 10
PI: Walker


title: PETER001_HK2_24H_X1_B46:G01


title: M_liver_3wk_VEH_1M3V_4me3

description:
Library name: Sample 11
PI: Walker


title: M_liver_3wk_VEH_3M3V_4me1

description:
Library name: Sample 8
PI: Walker


title: M_liver_3wk_VEH_4M3V_4me1

description:
Library name: Sample 9
PI: Walker


title: PETER001_HK2_24H_X1_B46:F21

description: L1000 inferred profile; pert_id: Wortmannin

source_name: HK2 treated with Wortmannin 5 uM for 24.0 h

value: Wortmannin 5 uM


title: F13749748

source_name: EDTA Plasma

value: Day 28

value: EDTA Plasma


title: PETER001_HK2_24H_X1_B46:F19


title: F13749910

value: Day 49


title: F13749728

value: Day 21

value: M


title: F13677831

value: Day 14


title: M_liver_3wk_VEH_2M3V_4me1

description:
Library name: Sample 7
PI: Walker

value: liver


title: M_liver_3wk_VEH_6M3V_27ac

description:
Library name: Sample 5
PI: Walker

value: male


title: M_liver_3wk_VEH_4M3V_27ac

description:
Library name: Sample 3
PI: Walker

value: Vehicle


title: M_liver_3wk_VEH_5M3V_27ac

description:
Library name: Sample 4
PI: Walker


title: M_liver_3wk_VEH_3M3V_27ac

description:
Library name: Sample 2
PI: Walker


title: PETER001_HK2_24H_X1_B46:F18

description: L1000 inferred profile; pert_id: Bictegravir

source_name: HK2 treated with Bictegravir 0.5 uM for 24.0 h

value: Bictegravir 0.5 uM


title: PETER001_HK2_24H_X1_B46:F17


title: F13677552

value: Day 7


title: M_liver_3wk_VEH_2M3V_27ac

description:
Library name: Sample 1
PI: Walker


title: TAC-operated_NRG_replicate 5

city: Basel

first: Parisa

last: Aghagolzadeh

address: Hebelstrasse 20

country: Switzerland

institute: Basel university

description:
Library name: TAC_NRG_replicate 5
Heart tissue isolated from TAC-operated mice treated with NRG

data_processing:
BRB-seq data was analyzed using Alithea Genomics
Data was normalized by the trimmed mean of M values (TMM)
Assembly: Mouse genome (GRCm39)
Supplementary files format and content: Tab-delimited text file includes TMM normalized values.

source_name: Heart

extract_protocol:
Total RNA was extracted from the frozen tissues with Tri Reagent .
RNA-Seq libraries were prepared using extraction-free, highly multiplexed 3′-end bulk RNA barcoding and sequencing (MERCURIUSTM BRB-seq service).

treatment_protocol: Male C57BL/6NRj mice underwent sham or transverse aortic constriction (TAC) surgery.

value: Heart

tag: cell type

value: left ventricle

tag: strain

tag: batch


title: PETER001_HK2_24H_X1_B46:F16


title: TAC-operated_NRG_replicate 4

description:
Library name: TAC_NRG_replicate 4
Heart tissue isolated from TAC-operated mice treated with NRG

tag: Sex


title: TAC-operated_NRG_replicate 3

description:
Library name: TAC_NRG_replicate 3
Heart tissue isolated from TAC-operated mice treated with NRG


title: PETER001_HK2_24H_X1_B46:F15

description: L1000 inferred profile; pert_id: Elvitegravir

source_name: HK2 treated with Elvitegravir 0.1 uM for 24.0 h

value: Elvitegravir 0.1 uM


title: F13677314

description: 55 ul of plasma was used for the  proteomic assay

tag: participant id

value: Day 2

value: IV

tag: age

value: White


title: F13677424

tag: time point (days)

value: Day 3

tag: treatment group (dose)


title: TAC-operated_NRG_replicate 2

description:
Library name: TAC_NRG_replicate 2
Heart tissue isolated from TAC-operated mice treated with NRG


title: F13676875

value: Day 1

value: EDTA Plasma

tag: bmi (kg/m2)

tag: race


title: TAC-operated_NRG_replicate 1

description:
Library name: TAC_NRG_replicate 1
Heart tissue isolated from TAC-operated mice treated with NRG

tag: tissue


title: TAC-operated_Saline_replicate 5

description:
Library name: TAC_Saline_replicate 5
Heart tissue isolated from TAC-operated mice treated with saline

tag: treatment


title: TAC-operated_Saline_replicate 4

description:
Library name: TAC_Saline_replicate 4
Heart tissue isolated from TAC-operated mice treated with saline


title: TAC-operated_Saline_replicate 3

description:
Library name: TAC_Saline_replicate 3
Heart tissue isolated from TAC-operated mice treated with saline


title: PETER001_HK2_24H_X1_B46:F13

tag: cell line

tag: duration


title: PETER001_HK2_24H_X1_B46:F14

tag: plate


title: PETER001_HK2_24H_X1_B46:F12

description: L1000 inferred profile; pert_id: Elvitegravir|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Elvitegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 24.0 h

tag: well


title: TAC-operated_Saline_replicate 2

description:
Library name: TAC_Saline_replicate 2
Heart tissue isolated from TAC-operated mice treated with saline


title: F13387439

value: Day 93

tag: delivery

value: Reslizumab (0.8 mg/kg)


title: sham-operated_Saline_replicate 5

description:
Library name: Sham_Saline_replicate 5
Heart tissue isolated from sham-operated mice treated with saline

tag: cell type


title: PETER001_HK2_24H_X1_B46:F11

value: Elvitegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: F13387464

value: Day 123

value: M


title: sham-operated_Saline_replicate 4

description:
Library name: Sham_Saline_replicate 4
Heart tissue isolated from sham-operated mice treated with saline

value: male

tag: strain


title: sham-operated_Saline_replicate 3

description:
Library name: Sham_Saline_replicate 3
Heart tissue isolated from sham-operated mice treated with saline

tag: batch


title: TAC-operated_Saline_replicate 1

description:
Library name: TAC_Saline_replicate 1
Heart tissue isolated from TAC-operated mice treated with saline

tag: Sex


title: F13387424

tag: participant id

value: Day 63


title: F13387394

value: Day 49

tag: age


title: PETER001_HK2_24H_X1_B46:F10


title: RM-1 tumors treated with RP-6306

description:
Library name: RP-6306
10X Genomics

source_name: RM-1 tumors

extract_protocol:
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol,10x Genomics). RNA libraries were prepared for sequencing using standard Illumina protocols

value: RM-1 tumors

value: prostate cancer cell line

tag: genotype

value: WT


title: M_liver_3wk_VEH_7M3V_27ac

description:
Library name: Sample 6
PI: Walker

value: liver

value: Vehicle

tag: antibody


title: sham-operated_Saline_replicate 2

description:
Library name: Sham_Saline_replicate 2
Heart tissue isolated from sham-operated mice treated with saline

value: Heart

value: left ventricle


title: sham-operated_Saline_replicate 1

description:
Library name: Sham_Saline_replicate 1
Heart tissue isolated from sham-operated mice treated with saline


title: F13387232

tag: time point (days)

value: Day 28

value: IV

tag: treatment group (dose)

tag: bmi (kg/m2)

value: White


title: RM-1 tumors treated with vehicle

description:
Library name: vehicle
10X Genomics

tag: tissue

tag: treatment

value: vehicle


title: F13359171

value: Day 14

value: EDTA Plasma

value: Reslizumab (0.8 mg/kg)

tag: race


title: PETER001_HK2_24H_X1_B46:F09

description: L1000 inferred profile; pert_id: Darunavir|Ritonavir

source_name: HK2 treated with Darunavir|Ritonavir 0.1|0.5 uM for 24.0 h

tag: cell line

value: Darunavir|Ritonavir 0.1|0.5 uM

tag: duration

tag: plate


title: PETER001_HK2_24H_X1_B46:F07

tag: well


title: F13387212

value: Day 21

tag: delivery

value: M


title: Wild type, NMDA, Input, rep2

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
All ChIP reads in FASTQ format were aligned to the GRCm38.p6.101 mouse genome using Bowtie2 (v 2.4.4) and removed redundant reads.
Peak calling was carried out using MACS2 (ver 2.2.6) with “–nomodel -f AUTO -p 0.001” options.
After confirmed the consistency between each replicate, we pooled extended reads and generated the bigwig track for visualization with IGV (ver.2.8.7).
Assembly: GRCm38.p6.101
Supplementary files format and content: Bigwig, coverage with bin size 50bp

source_name: Retina

growth_protocol: Control male C57BL/6J mice were also purchased from the Jackson Laboratory. Mice are kept in a 12-hour light-dark cycle with free access to water and mice food

extract_protocol:
Retinal tissue samples were cross-linked with 1% paraformaldehyde for 10 minutes at 23°C and quenching with glycine. The samples were homogenized in SDS lysis buffer, and chromatin was sheared using a bioruptor sonicator (Diagenode) at high power for 45 cycles.
The TruSeq ChIP Library Preparation Kit (Set A, IP-202-1012, Set B, IP-202-1024, Illumina, CA, USA) was used to create the ChIP-seq library. 5 μg of input and ChIP-enriched DNA were end-repaired, A-tailed, and ligated with TruSeq index adapters before being amplified. The Illumina NextSeq 500 platform was used for paired-end sequencing of all ChIP libraries.

treatment_protocol: Intravitreal injections were performed under a microscope with a microsyringe and a 30-gauge needle. In control experiments, eyes (n = 6 retinas each; 3 independent experiments) were pretreated by injecting 1 μL of 1X PBS (pH 7.4), and in experimental groups, eyes (n = 6 retinas each; 3 independent experiments) were treated by injecting 1 μL of 40 mM NMDA (Sigma; corresponding to 40 nmoles) prepared in PBS.

value: Retina

tag: strain

value: Wild type

value: NMDA

tag: read length


title: PETER001_HK2_24H_X1_B46:F05

description: L1000 inferred profile; pert_id: Dolutegravir|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Dolutegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 24.0 h


title: Wild type, NMDA, PAX6 ChIP, rep2


title: Wild type, PBS, Input, rep2

value: PBS


title: Wild type, NMDA, Input, rep1


title: PETER001_HK2_24H_X1_B46:F06

value: Dolutegravir|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: F13358892

tag: participant id

value: Day 7

tag: Sex


title: Wild type, NMDA, PAX6 ChIP, rep1

tag: genotype


title: Wild type, PBS, PAX6 ChIP, rep2


title: PETER001_HK2_24H_X1_B46:F03

description: L1000 inferred profile; pert_id: Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM for 24.0 h


title: Wild type, PBS, Input, rep1


title: F13358654

description: 55 ul of plasma was used for the  proteomic assay

value: Day 2

tag: age


title: Wild type, PBS, PAX6 ChIP, rep1


title: PETER001_HK2_24H_X1_B46:F04


title: SCLC_JSJ

city: Guangzhou

first: Guodi

last: Cai

state: Guangdong Province

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-Sen university

description:
Library name: S_JSJ
10x Genomics

data_processing:
We merged and integrated this public dataset with our data following the Scanpy workflow. Firstly, we applied the log1pCP10K normalization on the raw counts and selected highly variable genes. Next, we regressed out the effects of the total count per cell and the percentage of mitochondrial gene count. Then, the first 50 principal components were calculated and sample-level batch effects were removed using the Harmony package. Utilizing a graph-based cluster method, we finally acquired unsupervised cell clusters based on the top 10 principal components and annotated the clusters referring to the expression patterns of literature-derived marker genes.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
Tissues were placed in MACS Tissue Storage Solution (Miltenyi Biotec) until processing.
The BD Rhapsody system was used to capture the transcriptomic information of the sample-derived single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across > 200,000 microwells by a limitingdilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with each cell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected in a single tube for reverse transcription and ExoI digestion. Each cDNA was tagged at the 5′-end (i.e., the 3′-end of an mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole-transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow, including random priming and extension (RPE), RPE amplification PCR, and WTA index PCR. The libraries were quantified using a High-Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2200 and the Qubit High-Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed using an Illumina sequencer (San Diego, CA, USA) on a 150-bp paired-end run.

value: Lymph node


title: F13358764

tag: time point (days)

value: Day 3

value: IV


title: SCLC_LLF

description:
Library name: S_LLF
10x Genomics


title: F13386255

value: Day 123

value: SC

tag: treatment group (dose)

value: Mepolizumab (24 mg)

value: F

value: Black or African America


title: SCLC_HGY

description:
Library name: S_HGY
10x Genomics


title: SCLC_LQG

description:
Library name: S_LQG
10x Genomics


title: PETER001_HK2_24H_X1_B46:F01

value: Cobicistat|Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.1|0.5 uM


title: T_SCLC_ZXF

description:
Library name: T_ZXF
10x Genomics


title: F13358215

value: Day 1

value: EDTA Plasma

value: Reslizumab (0.8 mg/kg)

tag: bmi (kg/m2)

value: M

value: White


title: PETER001_HK2_24H_X1_B46:F02


title: PETER001_HK2_24H_X1_B46:E21

description: L1000 inferred profile; pert_id: Rapamycin

source_name: HK2 treated with Rapamycin 5 uM for 24.0 h

value: Rapamycin 5 uM


title: T_SCLC_HSP

description:
Library name: T_HSP
10x Genomics

tag: tissue


title: PETER001_HK2_24H_X1_B46:E20

tag: treatment


title: Pool2.2 HTO

city: Hannover

first: Jenni

last: Fleischauer

address: Carl-Neuberg-Strasse 1

department: Institute of Experimental Hematology

country: Germany

institute: Hannover Medical School

description:
Library name: N4024
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
The 10X Genomics CellRanger analysis pipeline set (v7.0.0) was used with default parameters. Briefly, BCL files were demultiplexed into FASTQ files by cellranger mkfastq using the respective sample sheet with utilized 10X barcodes. The cellranger count pipeline was used to align read data to the reference genome provided by 10X Genomics (Human reference dataset refdata-gex-GRCh38-2020-A), counting aligned reads per gene, and calculating clustering and summary statistics. Subsequently, outputs from cellranger count of all samples were aggregated, normalized to the same sequencing depth, and the feature-barcode matrices were recomputed by cellranger aggr. Simultaneously, feature barcoding data was processed during the cellranger count step with a feature reference build according to the specification of TotalSeq™-B antibodies. The output from cellranger count was demultiplexed to retrieve values for each previously pooled sample. Demultiplexing with hashtag oligos was performed using a Seurat (v.4.0.0) based workflow developed in a collaboration of Dresden-concept Genome Center (TU Dresden) and Research Core Unit Genomics (Hannover Medical School) (https://github.com/ktrns/scrnaseq).
Assembly: Human hg38
Supplementary files format and content: Cellranger output files: N3917_barcodes.tsv.gz, N3917_features.tsv.gz, N3917_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: N3918_barcodes.tsv.gz, N3918_features.tsv.gz, N3918_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: N6178_barcodes.tsv.gz, N6178_features.tsv.gz, N6178_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: N6179_barcodes.tsv.gz, N6179_features.tsv.gz, N6179_matrix.mtx.gz
Supplementary files format and content: Cellranger output files: N6180_barcodes.tsv.gz, N6180_features.tsv.gz, N6180_matrix.mtx.gz

source_name: Umbilical cord blood

growth_protocol: Human umbilical cord blood (UCB)-derived hematopoietic stem and progenitor cells (HSPCs) were purified for CD34+CD38-CD45RA- cells and seeded for expansion. The basal medium contains the cytokines SCF, FLT3-L, TPO, and IL-3 in StemSpan SFEM medium. To enhance HSPC expansion, the small molecules A83-01, pomalidomide, and UM171 were added. HSPCs were expanded in most experiments for 7 days, but extended expansion for 14 days was also evaluated.

extract_protocol:
Uncultivated cells were thawed on the day of the run. The expanded HSPCs were harvested directly from culture. Cells were washed with PBS and prepared for Hashtag Oligo (HTO) antibody staining. Therefore, 1x10^6 cells were resuspended in FACS buffer (PBS with 2% FCS, 2 mM EDTA) containing Fc receptor blocking solution for 15 min at 4°C. Then, cells were stained with 0.1 µg antibody/10^6 cells for 30 min at 4°C. Afterwards, the cells were washed 3x with FACS buffer. BioLegend recommends using 5-ml tubes and centrifugation in swing-bucket centrifuges. To exclude dead cells during FACS, we resuspended the cells in FACS buffer with 0.2 µg/ml DAPI. Before the sort, the cells were filtered through a 40-µM cell strainer. We sorted DAPI-negative cells using the FACSAria Fusion cell sorter with a 100-µm nozzle. We started sorting the uncultivated cells (the lowest cell number) and sorted equivalent cell numbers of the other conditions into one tube. Usually, one pool contained five HTO-labelled samples.
Library preparation for single-cell mRNA seq was performed according to the Chromium NextGEM Single Cell 3ʹ Reagent Kits v3.1 CellSurfaceProtein User Guide (Manual Part Number CG000206 Rev D, 10x Genomics).

treatment_protocol: Human UCB-derived HSPC expansion with APU compounds

value: Umbilical cord blood

tag: library type

value: HTO

tag: hto


title: F13386230

value: Day 93

tag: race


title: Pool1 HTO

description:
Library name: N4023
Hashtag-derived oligonucleotide (HTO)


title: F13386215

value: Day 63


title: PETER001_HK2_24H_X1_B46:E19

tag: cell line

tag: duration

tag: plate


title: ERa-High-RepC

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

description: Library name: Sample16

data_processing:
Data were processed using an adapted pipeline from Hoffman et al., eLife, 2018 (PMID: 29792595)
Assembly: hg38
Supplementary files format and content: bigWig: read coverage
Library strategy: CUT&Tag

source_name: Cell Line

growth_protocol: MCF7 cells were cultured in DMEM supplemented with 10% FBS, 1% Pen/Strep and 1% L-Glutamine and hormone depleted in Phenol-red free DMEM supplemented with 10% Charcoal-stripped FBS, 1% Pen/Strep and 1% L-Glutamine.

extract_protocol:
Fresh nuclei were extracted  according to the Bench top CUT&Tag V.3 protocol (PMID: 31036827)
Extracted DNA was PCR amplified using unique primer sets (Nextera XT v2 Full Set (N7-S5).

treatment_protocol: MCF7 cells were hormone depleted for 72 hours before Estrogen stimulation using 1nM E2 for 48 hours of treatment.

value: Cell Line

tag: cell type

value: ER+ Breast Cancer

value: 48h 1nM E2 TFF1high


title: T_SCLC_ZFY

description:
Library name: T_ZFY
10x Genomics

value: Lymph node


title: ERa-Low-RepC

description: Library name: Sample15


title: ERa-High-RepB

description: Library name: Sample14


title: PETER001_HK2_24H_X1_B46:E17

description: L1000 inferred profile; pert_id: Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Tenofovir Disoproxil Fumarate 0.1 uM for 24.0 h

value: Tenofovir Disoproxil Fumarate 0.1 uM

tag: well


title: F13386023

tag: participant id

value: Day 28

tag: delivery

value: SC

value: Mepolizumab (24 mg)

value: F

value: Black or African America


title: F13386185

value: Day 49

value: EDTA Plasma

tag: Sex


title: ERa-High-RepA

description: Library name: Sample12


title: ERa-Low-RepA

description: Library name: Sample11


title: F13386003

value: Day 21

tag: age


title: PETER001_HK2_24H_X1_B46:E16


title: ERa-Low-RepB

description: Library name: Sample13


title: PETER001_HK2_24H_X1_B46:E15

description: L1000 inferred profile; pert_id: Cobicistat

source_name: HK2 treated with Cobicistat 0.1 uM for 24.0 h

value: Cobicistat 0.1 uM


title: Treated-2

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

description: Library name: Treated2

data_processing:
Base-call data was processed and demultiplexed with Bcl2fastq2 (v2.20).
Adapter sequences were eliminated using skewer v.0.2.2
Duplicates were removed with Samtools (v0.1.19)
Sequences aligned to the hg38 reference genome using the BWA algorithm (mem mode; default settings). Sequencing reads were processed as matched pairs, and only uniquely mapped reads with a mapping quality ³ 1 were retained for subsequent analysis. To generate genome-wide coverage data, the alignments were extended in silico to a fixed length of 200 base pairs, and assigned to 32-base pair bins along the genome. BigWig files were created using deeptools (v3.5.1)
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: cell line

growth_protocol: Human breast epithelial cells, MCF10A, were cultured in DMEM/F12 media supplemented with 5% horse serum, 1X penicillin-streptomycin, 20 ng/mL EGF, 0.5 ug/mL hydrocortisone, 100 ng/mL cholera toxin, and 10 μg/mL insulin. Cells were mainted in humidified incubator at 37C with 5% CO2.

extract_protocol:
MCF10A cells (empty plasmid vector, H2B variants expressing cells, or transformed cells with EMT-inducing cytokines) were grown to 70-90% confluency, cryopreserved in DMEM/F12 media containing 50% horse serum, and sent to ActiveMotif (Carlsbad, CA) for ATAC sequencing. 10^5 cells were resuspended in lysis buffer, then centrifiuged to collect nuclei from which genomic DNA was obatined.
Libraries used for ATAC-sequencing were prepared using the Illumina Nextera Library Prep Kit.DNA fragments were then purified with a Qiagen MinElute PCR purification kit. After 10 PCR cycles amplification of the tagged DNA fragments, the amplified products were purified with Beckman Coulter Agencourt AMPure SPRI beads. For quantification, the KAPA Library Quantification Kit was used.
ATAC-seq libraries were prepared using the Illumina Nextera Library Prep Kit, and the resulting DNA fragments purified with a Qiagen MinElute PCR purification kit. Tagged DNA fragments were amplified through 10 PCR cycles, and amplified products purified

treatment_protocol: MCF10A cells were electroporated with either constructs stably expressing mRNA of H2B variants under their own promoter or empy vector control constructs.

value: cell line

value: breast epithelial

tag: genotype

value: WT

value: TNFalpha and TGFB


title: Treated-1

description: Library name: Treated1


title: Treated-3

description: Library name: Treated3


title: H2BO-2xHA-3

description: Library name: H2BO3

value: H2BO-2xHA mRNA overexpression

value: nucleofection


title: F13352741

source_name: EDTA Plasma

tag: time point (days)

value: Day 14

tag: treatment group (dose)


title: PETER001_HK2_24H_X1_B46:E14


title: H2BO-2xHA-2

description: Library name: H2BO2

tag: tissue


title: F13352334

value: Day 3

tag: bmi (kg/m2)


title: PETER001_HK2_24H_X1_B46:E13

tag: treatment


title: H2BO-2xHA-1

description: Library name: H2BO1


title: H2BH-2xHA-2

description: Library name: H2BH2

value: H2BH-2xHA mRNA overexpression


title: PETER001_HK2_24H_X1_B46:E12

description: L1000 inferred profile; pert_id: Bictegravir|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Bictegravir|Tenofovir Alafenamide Fumarate 0.5|0.5 uM for 24.0 h


title: F13352462

value: Day 7

value: SC


title: H2BH-2xHA-1

description: Library name: H2BH1


title: PETER001_HK2_24H_X1_B46:E11

value: Bictegravir|Tenofovir Alafenamide Fumarate 0.5|0.5 uM


title: F13351785

value: Day 1

value: Mepolizumab (24 mg)

value: F

value: Black or African America


title: H2BC-2xHA-2

description: Library name: H2BC2

value: H2BC-2xHA mRNA overexpression


title: H2BC-2xHA-3

description: Library name: H2BC3

value: cell line


title: EV-3

description: Library name: EV3

value: breast epithelial

value: Empty vector control


title: PETER001_HK2_24H_X1_B46:E10


title: F13385076

value: Day 123

value: EDTA Plasma

value: IV

value: Reslizumab (0.8 mg/kg)

value: M

value: White


title: H2BC-2xHA-1

description: Library name: H2BC1

value: nucleofection


title: EV-2

description: Library name: EV2


title: EV-1

description: Library name: EV1


title: F13352224

value: Day 2

value: SC


title: PETER001_HK2_24H_X1_B46:E09

description: L1000 inferred profile; pert_id: Bictegravir|Emtricitabine

source_name: HK2 treated with Bictegravir|Emtricitabine 0.5|0.1 uM for 24.0 h

value: Bictegravir|Emtricitabine 0.5|0.1 uM


title: F13385036

value: Day 63


title: H3K27me3-Low-RepC

value: Cell Line

value: ER+ Breast Cancer

value: 48h 1nM E2 TFF1high


title: F13385051

value: Day 93


title: PETER001_HK2_24H_X1_B46:E08


title: H3K27me3-High-RepC


title: PETER001_HK2_24H_X1_B46:E07


title: H3K27me3-High-RepB


title: H3K27me3-Low-RepB


title: F13385006

value: Day 49


title: FishOil_TBI4

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

description: Library name: Sample_14-4

data_processing:
The reads were aligned with STAR (version 2.5.2a), and genes annotated in Gencode vM16 were quantified with featureCounts (v1.4.3-p1).
Assembly: mm10
Supplementary files format and content: Tab-separated file with raw read counts per gene

source_name: Brain

extract_protocol:
Total RNA was isolated using the Zymo Miniprep Plus Kit. A total of 500 ng of RNA was used for library preparation.
RNA-seq libraries were prepared using the TruSeq Stranded kit according to the manufacturer’s instructions. Samples were sequenced on an Illumina NovaSeq 6000 platform with 2 × 100 bp paired-end reads.

value: Brain

value: WT

value: FO High Fat Diet + rlmTBI


title: H3K27me3-Low-RepA


title: H3K27me3-High-RepA


title: F13384844

value: Day 28

value: EDTA Plasma

value: IV


title: PETER001_HK2_24H_X1_B46:E06

description: L1000 inferred profile; pert_id: Emtricitabine|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 24.0 h


title: PETER001_HK2_24H_X1_B46:E05

value: Emtricitabine|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: FishOil_Sham4

description: Library name: Sample_13-4

value: FO High Fat Diet + Sham


title: FishOil_TBI3

description: Library name: Sample_14-1


title: F13143125

value: Day 14

value: Reslizumab (0.8 mg/kg)

value: M

value: White


title: FishOil_Sham3

description: Library name: Sample_13-1


title: PETER001_HK2_24H_X1_B46:E04


title: PETER001_HK2_24H_X1_B46:E03

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir|Emtricitabine

source_name: HK2 treated with Cobicistat|Elvitegravir|Emtricitabine 0.1|0.1|0.1 uM for 24.0 h


title: Purified_Sham4

description: Library name: Sample_10-2

value: Purified Diet + Sham


title: F13384824

value: Day 21


title: Purified_Sham3

description: Library name: Sample_10-1


title: FishOil_Sham2

description: Library name: Sample_9-5


title: PETER001_HK2_24H_X1_B46:E01


title: Purified_TBI4

description: Library name: Sample_5-4

value: Purified Diet + rlmTBI


title: F13142608

value: Day 2


title: FishOil_TBI2

description: Library name: Sample_11-4


title: PETER001_HK2_24H_X1_B46:E02


title: PETER001_HK2_24H_X1_B46:D21

description: L1000 inferred profile; pert_id: Vorinostat

source_name: HK2 treated with Vorinostat 5 uM for 24.0 h

value: Vorinostat 5 uM


title: F13142718

value: Day 3


title: Purified_TBI2

description: Library name: Sample_4-5

value: Brain

value: WT


title: Purified_Sham2

description: Library name: Sample_7-5


title: Purified_TBI3

description: Library name: Sample_5-3


title: F13142169

value: Day 1


title: Sp5C region brain tissue, IS6

city: Beijing

first: Lu

last: Liu

address: No. 23, Hutong Street, Art Gallery, Dongcheng District

institute: Beijing Hospital of Traditional Chinese Medicine, Capital Medical University

data_processing:
(1) The raw sequencing data included a small proportion of reads containing sequencing adapters or reads of low sequencing quality. To ensure the quality and reliability of downstream data analysis, we filtered the raw data as follows:
- removal of Adapter Reads: reads containing adapter sequences were removed.
- removal of Reads with Ambiguous Bases: reads containing "N" bases (indicating unidentified bases) were discarded.
- removal of Low-Quality Reads: reads with low-quality bases, where more than 50% of the read bases had a Qphred score ? 20, were removed.
(2) The reference genome used for alignment was mm10. Bowtie was employed to map the length-filtered sRNA reads to the reference genome, enabling analysis of small RNA distribution across the reference sequence. The subsequent sRNA classification was performed based on these mapped sRNA reads.
(3) The read counts for each gene were obtained using the HTSeq tool, providing the initial count values.
Assembly: mm10
Supplementary files format and content: Text file containing the count data file, listing the read counts per miRNA sequence for each sample

source_name: Sp5C, Brain

extract_protocol:
Small-RNA sequencing was conducted by a commercial service (CNKINGBIO, China). To ensure the quality of the extracted RNA, firstly, RNA degradation and contamination were monitored using 1% agarose gels. The purity of the RNA was then evaluated with a NanoPhotometer spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using the Qubit RNA Assay Kit on a Qubit 2.0 Fluorometer (Life Technologies, CA, USA). Finally, the integrity of the RNA was assessed with the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using Small RNA Library Prep Set (NEB, USA).
After pooling different libraries based on effective concentration and target data output requirements, Illumina SE50 sequencing was performed. A sequencing-by-synthesis method was used. DNA polymerase, adapter primers, and four types of dNTPs with base-specific fluorescent labels were added to the reaction system (similar to the Sanger sequencing method). The 3'-OH groups of these dNTPs are chemically protected, allowing only one dNTP to be added per cycle. After a dNTP is incorporated into the synthesis strand, all unused free dNTPs and DNA polymerase are washed away. Next, a buffer required to excite fluorescence is added, fluorescence signals are activated by laser, and optical equipment records the fluorescence signals. The computer then converts the optical signals into sequencing bases. After fluorescence signal recording is completed, chemical reagents are added to quench the fluorescence and remove the 3'-OH protection group of the dNTP, allowing the next cycle of the sequencing reaction to proceed.

value: Sp5C, Brain

value: Migraine Mouse Model


title: PETER001_HK2_24H_X1_B46:D20


title: PETER001_HK2_24H_X1_B46:D19


title: Sp5C region brain tissue, Con8

value: control


title: Sp5C region brain tissue, IS7


title: PETER001_HK2_24H_X1_B46:D18

description: L1000 inferred profile; pert_id: Efavirenz

source_name: HK2 treated with Efavirenz 0.5 uM for 24.0 h

value: Efavirenz 0.5 uM


title: F13384603

value: Day 49

value: EDTA Plasma

value: IV


title: F13384648

value: Day 93

value: Reslizumab (0.8 mg/kg)

value: M

value: White


title: F13142846

value: Day 7


title: PETER001_HK2_24H_X1_B46:D17


title: shATGL-2

city: Chongqing

first: x

last: q

address: 76 Linjiang Road, Chongqing

institute: Department of Hematology, The Second  Affiliated Hospital, Chongqing Medical  University

description:
Library name: Sample5
A2

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
Total RNA was extracted with miRNeasy Kit (QIAGEN).
The mRNA was reverse-transcribed and amplified according to the method Geo-seq, then the library was constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) according to the manufacturer’s instruction.

treatment_protocol: Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.

value: shATGL


title: F13384673

value: Day 123


title: shATGL-3

description:
Library name: Sample6
A3


title: Sp5C region brain tissue, Con5


title: Sp5C region brain tissue, Con4


title: F13384633

value: Day 63


title: Sp5C region brain tissue,  IS1


title: shATGL-1

description:
Library name: Sample4
A1


title: F13384441

value: Day 28


title: shNC-3

description:
Library name: Sample3
NC3

value: shNC


title: shNC-2

description:
Library name: Sample2
NC2


title: shNC-1

description:
Library name: Sample1
NC1


title: PETER001_HK2_24H_X1_B46:D15

description: L1000 inferred profile; pert_id: Cobicistat|Tenofovir Alafenamide Fumarate

source_name: HK2 treated with Cobicistat|Tenofovir Alafenamide Fumarate 0.1|0.5 uM for 24.0 h

extract_protocol: After treatment, cells were lysed using the TCL Buffer (Qiagen, cat. no. 1031576) and incubated for 30 minutes at 37°C. The lysates were then stored at -80°C. RNA was extracted by the Broad Institute, according to their protocol.


title: PETER001_HK2_24H_X1_B46:D16


title: PETER001_HK2_24H_X1_B46:D14

value: Cobicistat|Tenofovir Alafenamide Fumarate 0.1|0.5 uM


title: F13384421

value: Day 21


title: U2, lung rabbit

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

description: Library name: U2

data_processing:
Demultiplexing was done (bcl2fastq2 v3.8.4).
Raw sequences were processed using BBMap's BBDuk tool (version 36.20) for quality trimming, adapter trimming, and filtering of reads. The parameters used were as follows: minimum length of 40, right trim quality of 20, kmer trim right, and trimming of the leftmost 11 bases. The 'tbo' option was used to trim adapters based on pair overlap detection, and the 'tpe' option was used to trim both reads to the same length.
Kallisto software (version 0.45.0) was used for quantifying transcript abundance from RNA against Oryctolagus cuniculus cDNA reference transcriptome (OryCun2.0) from the Ensembl database, v110.
Differential expression analysis was performed using the DESeq2 R package with the Wald test and the p-values have been adjusted with the Benjamini-Hochberg procedure.
Differentially expressed genes have been defined as genes with adjusted p-values smaller than 0.1.
Assembly: Oryctolagus cuniculus cDNA reference transcriptome (OryCun2.0) from the Ensembl database, v110.
Supplementary files format and content: .csv files that include raw counts

organism: Oryctolagus cuniculus

source_name: lung

growth_protocol: A piece of lung tissue was collected and immediately frozen at -80°C before RNA extraction

extract_protocol:
Rabbit lungs were extracted with the Monarch Total RNA Miniprep kit (New England Biolabs) by following manufacturer's instructions.
From total RNA (300 ng/sample), selection of poly-A RNA was performed with the NEBNext Poly(A) mRNA magnetic isolation module (NEB) according to the manufacturer's protocol. Then, libraries were performed with the NEBNext Ultra II Directional RNA library prep kit (NEB) according to manufacturer's protocol. Libraries were paired-end sequenced (2 x 100 base pairs) on a NextSeq2000 device (Illumina), with a minimal read depth of 15 million reads.

treatment_protocol: Male rabbits underwent protective mechanical ventilation and received an injection of LPS (3 ng/kg) to mimic the effects of an initial infectious challenge and associated immune alterations. Twenty-four hours later, they were inoculated intratracheally with an Enterobacter aerogenes strain to induce VAP. Rabbits (10/group) were randomly assigned to receive either human umbilical cord-derived MSCs (3.10^6/kg, intravenous) or sodium chloride, 4 hours after the Enterobacter challenge. All animales were treated with an antibiotic (cefepime).

value: lung

value: MSCs+cefepim


title: U1, lung rabbit

description: Library name: U1

value: cefepim


title: T1, lung rabbit

description: Library name: T1


title: F13141432

value: Day 3

value: EDTA Plasma


title: PETER001_HK2_24H_X1_B46:D13

city: New York

first: Avi

last: Ma'ayan

address: One Gustave L. Levy Place, Box 1603

institute: Icahn School of Medicine at Mount Sinai

data_processing: The data was normalized relative to the expression of 80 invariant landmark control genes. The expression of additional genes was inferred via a linear model trained on thousands of Affymetrix gene expression datasets from the gene expression omnibus (GEO). In this study, we utilized the L1000 data with the 12,328 measured and inferred mRNAs.


title: S2, lung rabbit

description: Library name: S2


title: F13141839

value: Day 14

value: IV


title: R2, lung rabbit

description: Library name: R2


title: S1, lung rabbit

description: Library name: S1


title: R1, lung rabbit

description: Library name: R1


title: T2, lung rabbit

description: Library name: T2


title: F13141560

value: Reslizumab (0.8 mg/kg)

value: M


title: PETER001_HK2_24H_X1_B46:D11

description: L1000 inferred profile; pert_id: Efavirenz|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Efavirenz|Tenofovir Disoproxil Fumarate 0.5|0.1 uM for 24.0 h


title: PETER001_HK2_24H_X1_B46:D12

value: Efavirenz|Tenofovir Disoproxil Fumarate 0.5|0.1 uM


title: Q2, lung rabbit

description: Library name: Q2


title: F13140883

value: Day 1

value: White


title: F13141322

value: Day 2


title: PETER001_HK2_24H_X1_B46:D09

description: L1000 inferred profile; pert_id: Emtricitabine|Tenofovir Disoproxil Fumarate

source_name: HK2 treated with Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1 uM for 24.0 h


title: P2, lung rabbit

description: Library name: P2


title: O1, lung rabbit

description: Library name: O1


title: O2, lung rabbit

description: Library name: O2


title: Q1, lung rabbit

description: Library name: Q1


title: PETER001_HK2_24H_X1_B46:D10


title: P1, lung rabbit

description: Library name: P1


title: PETER001_HK2_24H_X1_B46:D07

value: Emtricitabine|Tenofovir Disoproxil Fumarate 0.1|0.1 uM


title: M2, lung rabbit

description: Library name: M2


title: F12993872

value: Day 93

value: SC

value: Mepolizumab (24 mg)

value: Black or African America


title: PETER001_HK2_24H_X1_B46:D08


title: F12993897

value: Day 123


title: M1, lung rabbit

description: Library name: M1

value: lung

value: cefepim


title: N1, lung rabbit

description: Library name: N1

value: MSCs+cefepim


title: PETER001_HK2_24H_X1_B46:D06

description: L1000 inferred profile; pert_id: Efavirenz|Emtricitabine

source_name: HK2 treated with Efavirenz|Emtricitabine 0.5|0.1 uM for 24.0 h

value: Efavirenz|Emtricitabine 0.5|0.1 uM


title: L2, lung rabbit

description: Library name: L2


title: F12993645-1

value: Day 21

value: EDTA Plasma


title: L1, lung rabbit

description: Library name: L1


title: N2, lung rabbit

description: Library name: N2


title: PETER001_HK2_24H_X1_B46:D05


title: Skin, unenriched, rerioXnigrofasciatus, rep5

city: Eugene

first: John

last: Postlethwait

state: OR

address: 1210 University Of Oregon

department: Biology

institute: University of Oregon

description: Library name: Dni5S

data_processing:
We mapped each of the 48 libraries against combined references containing both parental genomes  (BBMap v38.57 with parameters: k=13, maxindel=100000, minid=0.76, ambiguous=best) to distinguish parental alleles in hybrid samples. Only a single best mapping location was retained for each read.
The 48 sequencing libraries  were split into two species-specific sublibraries. One sublibrary (denoted "Drerio") contained all reads that aligned best to the maternal D. rerio genome. The other sublibrary ("Dother" to denote the other Danio species) contained all reads that aligned best to the genome of the paternal species used to generate the hybrid.
We remapped each sublibrary to the D. rerio genome (BBMap v38.57 with parameters: k=13, maxindel=100000, minid=0.76, ambiguous=best) to utilize the available high quality GRCz11 gene annotations.
Gene expression was quantified using featureCounts (Rsubread v2.18). To mitigate the possibility of mapping bias toward the D. rerio reference in regions with poor sequence conservation, we excluded reads mapping to 3’ and 5’ untranslated regions. These feature counts are included in the processed data files DrerioAlleleCounts.csv and PaternalAllelelCounts.csv.
Statistical analysis was performed using DESeq2 (v1.44.0), filtering genes with less than 1 normalized count per sample (retaining 24,672 of 29,005 genes).
Assembly: GRCz11
Supplementary files format and content: DrerioAlleleCounts.csv quantifies the expression of the maternal D. rerio alleles for each gene.
Supplementary files format and content: PaternalAlleleCounts.csv quantifies the expression of the alleles from the paternal species used to generate each hybrid.

organism: Danio rerio x Danio nigrofasciatus

source_name: Whole skin

extract_protocol:
Takara Bio SMART-seq2 RNA-seq kit
Nextera paired-end library preps

value: Whole skin

value: Unenriched

tag: batch


title: F12993827

value: Day 49

value: M

tag: race


title: F12993857

value: Day 63


title: PETER001_HK2_24H_X1_B46:D04

tag: cell line


title: Skin, unenriched, rerioXnigrofasciatus, rep4

description: Library name: Dni4S


title: Skin, xanthophore-enriched, rerioXnigrofasciatus, rep4

description: Library name: Dni4X

value: Xanthophore-enriched


title: Skin, unenriched, rerioXnigrofasciatus, rep3

description: Library name: Dni3S


title: Skin, xanthophore-enriched, rerioXnigrofasciatus, rep5

description: Library name: Dni5X


title: PETER001_HK2_24H_X1_B46:D01

tag: duration


title: Skin, melanophore-enriched, rerioXnigrofasciatus, rep4

description: Library name: Dni4M

value: Melanophore-enriched


title: Skin, xanthophore-enriched, rerioXnigrofasciatus, rep3

description: Library name: Dni3X


title: PETER001_HK2_24H_X1_B46:D03

tag: plate


title: PETER001_HK2_24H_X1_B46:D02


title: Skin, melanophore-enriched, rerioXnigrofasciatus, rep5

description: Library name: Dni5M


title: F12616425

value: Day 14

value: SC


title: Skin, melanophore-enriched, rerioXnigrofasciatus, rep3

description: Library name: Dni3M


title: Skin, iridophore-enriched, rerioXnigrofasciatus, rep4

description: Library name: Dni4I

value: Iridophore-enriched


title: F12993645

value: Mepolizumab (24 mg)

value: Black or African America


title: F12616018

value: Day 3


title: F12616146

value: Day 7


title: Skin, iridophore-enriched, rerioXnigrofasciatus, rep5

description: Library name: Dni5I


title: PETER001_HK2_24H_X1_B46:C21

description: L1000 inferred profile; pert_id: Genistein

source_name: HK2 treated with Genistein 5 uM for 24.0 h

value: Genistein 5 uM


title: F12615908

description: 55 ul of plasma was used for the  proteomic assay

value: Day 2


title: F12615469

value: Day 1

value: EDTA Plasma


title: Skin, iridophore-enriched, rerioXnigrofasciatus, rep3

description: Library name: Dni3I

value: Whole skin


title: F12483292

value: Day 123


title: PETER001_HK2_24H_X1_B46:C20


title: PETER001_HK2_24H_X1_B46:C19


title: Skin, unenriched, rerioXkyathit, rep3

description: Library name: Dky3S

organism: Danio rerio x Danio kyathit

value: Unenriched


title: Skin, unenriched, rerioXkyathit, rep5

description: Library name: Dky5S


title: PETER001_HK2_24H_X1_B46:C18

description: L1000 inferred profile; pert_id: Emtricitabine

source_name: HK2 treated with Emtricitabine 0.1 uM for 24.0 h

value: Emtricitabine 0.1 uM


title: Skin, unenriched, rerioXkyathit, rep4

description: Library name: Dky4S


title: PETER001_HK2_24H_X1_B46:C17


title: Skin, xanthophore-enriched, rerioXkyathit, rep4

description: Library name: Dky4X

value: Xanthophore-enriched


title: Skin, xanthophore-enriched, rerioXkyathit, rep3

description: Library name: Dky3X


title: Skin, xanthophore-enriched, rerioXkyathit, rep5

description: Library name: Dky5X


title: F12483267

source_name: EDTA Plasma

value: Day 93

value: M


title: F12483252

value: Day 63

value: SC


title: PETER001_HK2_24H_X1_B46:C16


title: Skin, melanophore-enriched, rerioXkyathit, rep3

description: Library name: Dky3M

value: Melanophore-enriched


title: Skin, melanophore-enriched, rerioXkyathit, rep5

description: Library name: Dky5M


title: Skin, melanophore-enriched, rerioXkyathit, rep4

description: Library name: Dky4M


title: F12483060

value: Day 28

value: Black or African America


title: F12483222

value: Day 49


title: F12483040

value: Day 21


title: PETER001_HK2_24H_X1_B46:C15

description: L1000 inferred profile; pert_id: Elvitegravir|Emtricitabine

source_name: HK2 treated with Elvitegravir|Emtricitabine 0.1|0.1 uM for 24.0 h

value: Elvitegravir|Emtricitabine 0.1|0.1 uM


title: Skin, iridophore-enriched, rerioXkyathit, rep5

description: Library name: Dky5I

value: Iridophore-enriched


title: Skin, iridophore-enriched, rerioXkyathit, rep4

description: Library name: Dky4I


title: PETER001_HK2_24H_X1_B46:C14


title: Skin, iridophore-enriched, rerioXkyathit, rep3

description: Library name: Dky3I


title: PATU8902 spheroids, IgG-pulldown_n1 (control)

status: Public on Feb 15 2026

city: Manhattan

first: Mohamad

last: Assi

address: 550 1st Ave

department: Radiation Oncology

institute: NYU Medical Center

data_processing:
Data quality control was performed using FastQC
Mapping onto human genome and peak calling were performed using BWA and MACS, respectively
functional analysis of peak-associated genes and pathway analysis were performed with GOSeq/topGO, Bioconductor and KOBAS
Assembly: hg38
Supplementary files format and content: Data are submitted as bigwig files for each sample

source_name: Cell line

growth_protocol: DMEM 10% FBS, 1% Pen/Strep with 3% Matrigel for 3 days in ultralow attachment plates

extract_protocol:
SimpleChIP® Enzymatic Chromatin IP Kit (9003S, Cell signaling Tech)
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Cell line

tag: cell type

value: Pancreatic cancer cells


title: Pool 1 HTO

description:
Library name: N6181
Hashtag-derived oligonucleotide (HTO)

source_name: Umbilical cord blood

value: Umbilical cord blood

tag: library type

value: HTO

tag: hto


title: Pool 2 HTO

description:
Library name: N6182
Hashtag-derived oligonucleotide (HTO)


title: Pool 3 HTO

description:
Library name: N6183
Hashtag-derived oligonucleotide (HTO)


title: PETER001_HK2_24H_X1_B46:C13

tag: well


title: PETER001_HK2_24H_X1_B46:C12

description: L1000 inferred profile; pert_id: Abacavir|Emtricitabine

source_name: HK2 treated with Abacavir|Emtricitabine 0.5|0.1 uM for 24.0 h

value: Abacavir|Emtricitabine 0.5|0.1 uM


title: Pool 3

description:
Library name: N6180
total RNA

value: mRNA


title: F12466283

extract_protocol: EDTA plasma from whole blood

tag: participant id

value: Day 14

value: EDTA Plasma

tag: delivery

tag: Sex


title: PETER001_HK2_24H_X1_B46:C11


title: F12466004

tag: time point (days)

value: Day 7

tag: age

value: M


title: ./pt3_IR

city: Los Angeles

first: Ivan

middle: Alexander

last: Salladay-Perez

address: 615 Charles E Young Dr S

department: Department of Microbiology Immunology and Molecular Genetics

institute: University of California, Los Angeles

description: Library name: sample9

data_processing:
Roughly 100 M high quality reads were sequenced per sample using a Novaseq x Plus (Illumina). Raw data in FASTAq format was filtered for adapter sequences or low-quality sequences using SOAPnuke. Reads were aligned to the mm10 reference genome using STAR.
Assembly: Aligned reads were processed using TopHat and a counts matrix was generated using FeatureCounts.
Supplementary files format and content: Raw reads were processed using the latest version of base R commands as of May 2025 (4.5.0)

source_name: PBMCs

growth_protocol: BMDMs used in experiments were derived from bone marrow extracted from the femurs of euthanized mice (6-12 weeks old male C57BL/6J) by mortar and pestle. Femurs were placed in the mortar and were washed with 70% ethanol to sterilize followed by two washes with complete RPMI (cRPMI; standard RPMI (Corning) supplemented with 10% fetal calf serum, penicillin-streptomycin solution (Corning), 1mM sodium pyruvate solution (Corning), 2 mM L-Glutamine solution (Corning), 10nM HEPES buffer (Corning), and 50μM 2-mercaptoethanol). After washing, 10 ml of cRPMI was added to the mortar and the femur bones were gently crushed. The resulting media was collected and filtered through a 70μm filter and placed in a conical tube. The filtered supernatant was centrifuged at 100 g (150 RCF) for 5 minutes. Cells were resuspended, counted and plated at a density of 3E6 cells/10 cm dish in 10 ml of macrophage growth media (cRPMI containing 25% M-CSF containing L929 conditioned media (made in house)). Cells were left to grow for 7 days to differentiate and were supplemented with 5 ml of macrophage growth media on day 5. On day 7, BMDMs (yielding 10-12x106 cells/10cm dish) were lifted off the plate using cold PBS containing 5mM EDTA. BMDMs were counted and replated in macrophage growth media overnight prior to experiments

extract_protocol:
human pbmc cell-culture experiments, RNA was isolated using RNA STAT 60 (Amsbio) as per the manufacturer’s protocol. ~ 2000 ng of RNA was converted to complementary DNA using a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
Mouse BMDM were lysed with RNA STAT 60 (Amsbio) and ~50 ng per uL of RNA was submitted to the UCLA’s Technology Center for Genomics & Bioinformatics (TCGB) core for library preparation and 2x100 paired-end sequencing.

treatment_protocol: On the day of experiments, macrophage growth media was replaced with cRPMI 6 hours prior to stimulation to remove M-CSF.  DNA damaged cells were left in culture for 10 days and media components were replaced every 2-3 days. As a negative control, a mock irradiated or drug treated condition was cultured in parallel and required passing every 2-3 days. All senescent macrophage experiments were performed 10-13 days post DNA damage.

tag: tissue

value: PBMCs

value: Primary

value: Macrophage

value: Sen(IR)


title: ./pt3_DOXO

description: Library name: sample8

value: Sen(Dox)


title: Pool 1

description:
Library name: N6178
total RNA


title: ./pt3_CTRL

description: Library name: sample7

value: Passage Control


title: Pool 2

description:
Library name: N6179
total RNA


title: PETER001_HK2_24H_X1_B46:C10


title: F12465766

city: Silver Spring

first: Paula

last: Hyland

address: 10903 New Hampshire Avenue

institute: FDA

data_processing: https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.

value: Day 2

value: SC

tag: treatment group (dose)

tag: bmi (kg/m2)

value: Black or African America


title: PETER001_HK2_24H_X1_B46:C09

description: L1000 inferred profile; pert_id: Dolutegravir|Emtricitabine

source_name: HK2 treated with Dolutegravir|Emtricitabine 0.1|0.1 uM for 24.0 h

tag: treatment

value: Dolutegravir|Emtricitabine 0.1|0.1 uM


title: ./pt2_IR

description: Library name: sample6

tag: batch


title: F12465876

value: Day 3

tag: race


title: ./pt2_DOXO

description: Library name: sample5

tag: cell line


title: F12465327

value: Day 1


title: F12482889

value: Day 123

value: IV

value: Reslizumab (0.8 mg/kg)


title: ./pt2_CTRL

description: Library name: sample4


title: ./pt1_IR

description: Library name: sample3


title: PETER001_HK2_24H_X1_B46:C08

tag: duration

tag: plate


title: F12482864

value: Day 93

value: EDTA Plasma


title: ./pt1_DOXO

description: Library name: sample2

value: PBMCs

tag: cell type


title: PETER001_HK2_24H_X1_B46:C07


title: ./pt1_CTRL

description: Library name: sample1

value: Primary


title: PETER001_HK2_24H_X1_B46:C05

description: L1000 inferred profile; pert_id: Abacavir|Dolutegravir

source_name: HK2 treated with Abacavir|Dolutegravir 0.5|0.1 uM for 24.0 h

value: Abacavir|Dolutegravir 0.5|0.1 uM


title: Hela, shSRSF1, HMBA, 2 hours, Input

city: Xiamen

first: Min

address: Xiamen University-Xiang'an Campus, Xiang'an District

department: School of Life Sciences

institute: Xiamen University

description: Library name: shSRSF1_HMBA,  Input

data_processing:
Paired-end 150bp reads were mapped to the hg38 reference genome using Bowtie2 (v2.4.5). Potential PCR duplicates were removed with MarkDuplicates (Picard Tools). Pol II peaks were called using MACS (v3.0.3) with default parameters. Genes were annotated using HOMER (v5.1) with the hg38 v7.0 genome annotation.
Assembly: hg38
Supplementary files format and content: bigwig for each sample

source_name: Cervical

growth_protocol: HeLa cells were maintained in high-glucose DMEM medium (Basalmedia, L110KJ) supplemented with 10% FBS (Cell-Box, AUS-01S-02) and 1xPSK (Solarbio, IR9189) at 37°C with 5% CO2..

extract_protocol:
Cells crosslinked with 1% formaldehyde (Pierce, 28908) were subjected to low-salt buffer (75 mM KCl, 0.5% NP-40, 10 mM HEPES pH 7.9, 1.5 mM MgCl₂, 1 mM DTT, 0.5 mM PMSF, and 1×protease inhibitor cocktail) to remove chromatin-free RNA and proteins. Isolated nuclei were incubated with Micrococcal Nuclease (MNase, Beyotime, D7201S) at a ratio of 1 Unit per 10 μg DNA to digest genomic DNA to the optimal length (1–2 nucleosomes). For ChIP, 5 μg anti-Rpb1 antibody (ABclonal, A21980) was used per 15 μg digested DNA according to the manufacturer’s instructions.
DNA libraries were constructed using Hieff NGS DNA Library Prep Kit (Yeasen, 13577) following the manufacturer’s protocols, and sequenced on the NovaSeq X Plus platform (Novogene Co. Ltd., Beijing, China).

treatment_protocol: Cells at ~70% confluence were treated with or without 10 mM HMBA (MCE, HY-124284) for 2 hours.

value: Cervical

value: Hela

value: Adenocarcinoma Cells

tag: genotype

value: SRSF1 knockdown

value: HMBA

tag: chip antibody


title: PETER001_HK2_24H_X1_B46:C06

tag: well


title: Hela, shSRSF1, HMBA, 2 hours, ChIP

description: Library name: shSRSF1_HMBA, ChIP

value: Rpb1 (ABclonal, A21980)


title: Hela, shSRSF1, ChIP

description: Library name: shSRSF1, ChIP

value: untreated


title: F12482849

tag: participant id

value: Day 63

tag: delivery

value: M

value: Black or African America


title: PETER001_HK2_24H_X1_B46:C04


title: Hela, shSRSF1, Input

description: Library name: shSRSF1, Input


title: Hela, shGFP, HMBA, 2 hours, ChIP

description: Library name: shGFP_HMBA, ChIP

value: GFP knockdown


title: PETER001_HK2_24H_X1_B46:C03

description: L1000 inferred profile; pert_id: DMSO

source_name: HK2 treated with DMSO 0.5 uM for 24.0 h

value: DMSO 0.5 uM


title: Hela, shGFP, HMBA, 2 hours, Input

description: Library name: shGFP_HMBA,  Input


title: Hela, shGFP, Input

description: Library name: shGFP, Input


title: F12461139

tag: time point (days)

value: Day 14

value: IV

value: Reslizumab (0.8 mg/kg)

tag: Sex


title: F12482819

value: Day 49

tag: tissue

value: EDTA Plasma

tag: age


title: F12482657

value: Day 28

tag: treatment group (dose)

tag: bmi (kg/m2)


title: F12482637

value: Day 21


title: PETER001_HK2_24H_X1_B46:C02

description: L1000 inferred profile; pert_id: DMSO

tag: treatment


title: VHD_scPrint2_Slide2D1-HE

city: Portland

first: Luiz

middle: E

last: Bertassoni

address: 2720 S Moody Ave

department: Knight Cancer Institute

institute: Oregon Health and Science University

description:
Library name: VHD_scPrint2_Slide2D1
Fixed in place, no embedding or sectioning. Spatial transcriptomic sequencing. Visium HD library.

data_processing:
Raw FASTQ files were processed using the 10x Genomics Space Ranger 3.1.3 pipeline to generate the spatial gene expression matrix, filtered and raw feature matrices, image-linked outputs, spatial metadata, and quality control metrics. Sequences were aligned to the Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A reference transcriptome and the refdata-gex-GRCh38-2020-A reference genome using Space Ranger v3.1.3 default settings.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: image of tissue and spots
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: _HE.tif: full resolution HE image
Supplementary files format and content: _Cytassist.tif: image from CytAssist during probe transfer
Supplementary files format and content: _LoupeAlignment.json: Manual alignment of H&E image and detected transfer
Supplementary files format and content: _IF.tif: live cell image with transduced reporters to aid annotation
Library strategy: Spatial Transcriptomics

source_name: Engineered in vitro model

growth_protocol: A combination of MCF10A, MCF7, and primary human fibroblasts cells were single-cell bioprinted onto a collagen coated glass microscope slide either in a patterened or randomly deposited arrangement. The cells were cultured in M87 media for 24 hours before being fixed with 4% PFA and permeabilized with 100% methanol. The Visium HD spatial transcriptomics protocol was then followed to generate the data deposited here. Complete protocol for sample preparation through library preparation can be found at: Helms HR and Bertassoni LE. Single-cell spatial transcriptomic profiling of cultured cells and engineered tissues without embedding or sectioning. STAR Protocols. 2025. DOI: 10.1016/j.xpro.2025.104074

extract_protocol:
Cells were fixed and place and permeabilized with 100% methanol. The sample was not embedded or sectioned.
Visium HD Spatial Gene Expression (10x Genomics) library was constructed according to manufacturer's instruction.

value: Engineered in vitro model

value: MCF10A, MCF7

value: Human Mammary Fibroblasts (HMF)

tag: batch


title: Hela, shGFP, ChIP

description: Library name: shGFP, ChIP

value: Cervical

tag: cell line

value: Hela

value: Adenocarcinoma Cells

value: Rpb1 (ABclonal, A21980)


title: F12460860

value: Day 7

value: M

tag: race

value: Black or African America


title: VHD_scPrint2_Slide1A1-HE

description:
Library name: VHD_scPrint2_Slide1A1
Fixed in place, no embedding or sectioning. Spatial transcriptomic sequencing. Visium HD library.


title: CG-OSC-L lot 90

first: Christian

last: Kramme

state: New York

address: 450 E 29th Street, Fl 5, Suite 506

institute: Gameto, Inc.

description:
Library name: GTO_101_GC_002
10X Genomics

data_processing:
First bcl2fastq was used to generate the fastq files. Next, a reference genome was generated using split-pipe and the Homo sapiens GRCh38 file, also using STAR and Samtools.
Then, split-pipe was run to process and align the files against the reference genome. The resulting files were generated in an mtx matrix format.
Finally, the files were combined, and an Anndata object was made in h5ad file format. For the analysis, cells with less than 200 genes were filtered out, as well as genes found in less than 3 cells.
Cell counts were normalized to 10,000 Unique molecular identifiers (UMIs) per sample and log (ln) plus 1 transformed. Principal component analysis was performed using the Scanpy package (v1.9.6) based on 30 PCA components, and using PCA results, nearest neighbor analysis was performed using n_neighbors = 20. Batch correction was performed using Scanpy’s ComBat method. The number of components used for batch correction was 30 and the data was then transformed using the Uniform Manifold Approximation and Projection (UMAP) method. Clusters were formed using the Leiden method with a resolution of 0.25 for the complete dataset (containing all lots described in the manuscript), and projected into the subsetted objects.
At first, 15 Leiden clusters were identified. Thereafter, clusters were combined based on biological similarities, which resulted in nine final clusters: Early GC I, Early GC II, Early GC III, GC I, GC II, GC III, Atresia/luteolysis, Mitochondrial gene enriched (Atresia/luteolysis), and Ribosomal gene enriched (Atresia/luteolysis). The marker genes per cluster, as well as certain granulosa cell markers (GJA1, MDK, BBX, HES4, PBX3, YBX3, BMPR2, CD46, COL4A1, COL4A2, LAMC1, ITGAV, and ITGB1), were analyzed to identify cluster cell types. Dot plots and feature plots were generated to assess the expression levels of certain genes per cluster or per sample. Based on downstream analysis, clusters 0 and 5 were subsetted from the original object and they were re-clustered using the Leiden method at a higher resolution of 0.3. Subclusters were combined based on biological similarities. Once all the subgroups were identified, the subclusters resulting from cluster 0 and cluster 5 were merged with the original object. Gene signatures based on genes in the folliculogenesis stage were also analyzed and used in predicting cluster identification. Signature scores for the RUO-OSC-M subset were generated for two groups: Antral and Pre-Ovulatory genes. Based on the final object, 4 more subsets were generated: (1) a RUO-OSC-M object consisting of the following lots: lot 6, lot 7, lot 8, lot 29, lot 48, and lot 56; (2) a RUO-OSC-L object consisting of lot 77 and lot 86; and (3) a CG-OSC-L object consisting of lot 88 and lot 90. UMAPs of all the subsets were generated with the cluster names from the original object.
Assembly: hg38

source_name: hiPSC-derived

extract_protocol:
scRNA-seq was performed to establish comparability between resultant OSCs that were generated under various differentiation conditions, as well as evaluate the consistency of different batches generated using the same condition. OSCs were cryopreserved in CryoStor CS10 (StemCell Technologies) prior to being processed for single-cell RNA sequencing by Genewiz (Azenta). Cells were loaded onto a Chromium Single Cell Chip (10x Genomics) and processed through the Chromium Controller to generate single-cell gel beads in emulsion.
scRNA-seq libraries were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit (10x Genomics). Target cell recovery was estimated to be 3,000 cells per sample. Files were generated following a split-set analysis workflow.

treatment_protocol: Process development for OSC differentiation protocol

value: hiPSC-derived

value: CG-hiPSC

value: ovarian support cells

tag: xf or_not

value: XF

tag: matrix

value: Laminin (L)

value: Lot 90


title: PETER001_HK2_24H_X1_B46:C01

description: L1000 inferred profile; pert_id: DMSO

value: DMSO 0.5 uM

tag: duration

tag: plate


title: PETER001_HK2_24H_X1_B46:B21

description: L1000 inferred profile; pert_id: Water

source_name: HK2 treated with Water 0.01 uM for 24.0 h

value: Water 0.01 uM

tag: well


title: CG-OSC-L lot 88

description:
Library name: GTO_101_GC_001
10X Genomics

tag: cell type

value: Lot 88


title: F12460732

tag: participant id

value: Day 3

value: EDTA Plasma

tag: delivery

value: IV

value: Reslizumab (0.8 mg/kg)


title: PETER001_HK2_24H_X1_B46:B20

description: L1000 inferred profile; pert_id: Water


title: PETER001_HK2_24H_X1_B46:B19

description: L1000 inferred profile; pert_id: Water


title: RUO-OSC-L lot 86

description:
Library name: GC3_Batch_26
10X Genomics

value: RUO-OSC

value: Lot 86


title: RUO-OSC-L lot 77

description:
Library name: GC3_Batch_24
10X Genomics

value: Lot 77


title: F12460622

tag: time point (days)

value: Day 2

tag: Sex

value: M

value: Black or African America


title: RUO-OSC-V lot 49

description:
Library name: GC3_GC_Batch_12_2D_XF
10X Genomics

tag: tissue

value: hiPSC-derived

value: ovarian support cells

value: Vitronectin (V)

value: Lot 49


title: RUO-OSC-M lot 56

description:
Library name: GC3_GC_Batch_15_2D_LD
10X Genomics

value: non-XF

value: Matrigel (M)

value: Lot 56


title: RUO-OSC-V lot 41

description:
Library name: GC3_GC_Batch_10_2D_XF
10X Genomics

value: XF

value: Lot 41


title: RUO-OSC-V lot 57

description:
Library name: GC3_Batch_16
10X Genomics

value: Lot 57


title: F12460183

value: Day 1

value: EDTA Plasma

value: IV

tag: treatment group (dose)

value: Reslizumab (0.8 mg/kg)

tag: age


title: PETER001_HK2_24H_X1_B46:B18

description: L1000 inferred profile; pert_id: Dolutegravir

source_name: HK2 treated with Dolutegravir 0.1 uM for 24.0 h

tag: treatment

value: Dolutegravir 0.1 uM


title: RUO-OSC-M lot 48

description:
Library name: GC3_GC_Batch_11_2D
10X Genomics

value: RUO-OSC

tag: batch

value: Lot 48


title: RUO-OSC-M lot 8

description:
Library name: GC3_GC_Batch_IV_2D
10X Genomics

value: hiPSC-derived

tag: cell line

value: Lot 8


title: PETER001_HK2_24H_X1_B46:B17


title: RUO-OSC-M lot 7

description:
Library name: GC3_GC_Batch_III_2D
10X Genomics

value: ovarian support cells

value: Lot 7


title: RUO-OSC-M lot 29

description:
Library name: GC3_GC_Batch_5_2D
10X Genomics

value: non-XF

value: Lot 29


title: F12383679

description: 55 ul of plasma was used for the  proteomic assay

value: Day 123

value: SC

value: Mepolizumab (24 mg)

tag: bmi (kg/m2)

value: M

tag: race

value: White


title: F12383639

value: Day 63

value: EDTA Plasma


title: PETER001_HK2_24H_X1_B46:B16


title: F12383654

value: Day 93


title: T24 cells, shMED8, rep3

city: Shenzhen

first: Haiyu

last: Zhang

institute: Shenzhen Second People’s Hospital

description:
Library name: Sample6
Column name in Row_counts_all_Samples.txt: Sample6

data_processing:
To get high quality clean reads, reads were further filtered by fastp (https://github.com/OpenGene/fastp,version 0.20.1).
Then, sequences were mapped to the human reference genome (GRCh38) using HISAT2 (https://daehwankimlab.github.io/hisat2/,version 2.2.1).
The mapped reads of each sample were assembled and merged using StringTie (https://github.com/gpertea/stringtie, version 2.0.4).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: cell line

extract_protocol:
Total RNA was harvested using Trizol reagent (5301100，SIMGEN).
RNA libraries for RNA sequencing were prepared using standard IIIumina protocols.

value: cell line

value: bladder cancer cells

tag: genotype


title: RUO-OSC-M lot 6

description:
Library name: GC3_GC_Batch_II_2D
10X Genomics

value: RUO-OSC

tag: xf or_not

tag: matrix

value: Matrigel (M)

value: Lot 6


title: F12383609

value: Day 49


title: T24 cells, shMED8, rep1

description:
Library name: Sample4
Column name in Row_counts_all_Samples.txt: Sample4


title: PETER001_HK2_24H_X1_B46:B15

description: L1000 inferred profile; pert_id: Cobicistat|Elvitegravir

source_name: HK2 treated with Cobicistat|Elvitegravir 0.1|0.1 uM for 24.0 h

value: Cobicistat|Elvitegravir 0.1|0.1 uM

tag: duration

tag: plate

tag: well


title: T24 cells, shMED8, rep2

description:
Library name: Sample5
Column name in Row_counts_all_Samples.txt: Sample5

tag: cell type


title: PETER001_HK2_24H_X1_B46:B14


title: HEK293 cells treated with 12micromolar of  ncpCUL1-ASO-R3

city: Bryan

first: Irtisha

last: Singh

state: Texas

address: 8447 John Sharp Pkwy MREB 2

institute: Texas A&M University

description: Library name: H_CU_M3

data_processing:
Reads were aligned to the hg38 genome using STAR
Gene-level quantification was performed using RefSeq annotations
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: K562 cells were treted  in 1% FBS with IMDM contaning media, KMS34 cells were treated in 7.5% FBS  in RPMI, 10% FBS in DMEM High Glucose.

extract_protocol:
RNA was extracted using Trizol method
Non-Directional, Poly-A Selection

treatment_protocol: Cells were treated with scaramble(12micromolar) or ncpCUL1-ASO (12micromolar) for 44hr.

value: human embryonic kidney

value: Wild Type

value: 12uM of ncpCUL1-ASO for 44h