title: ICSI-F2_64F1

description: Library name: ICSI-F2_64F1


title: OMP-Ai95-1

status: Public on Apr 21 2026

type: SRA

city: Boston

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

country: USA

institute: Harvard Medical School

description: Library name: OMP-Ai95-1

library_source: transcriptomic single cell

data_processing:
Demultiplexed fastq files were uniformly processed via a custom nextflow pipeline that ran cell ranger (v6), as well as custom post-processing to remove multi-mapping reads (see Tsukahara et al. 2021 PMID: 34879231). All samples (including those in GSE173947) were integrated together to extract (mature) olfactory sensory neurons for downstream analyses.
Assembly: Ensembl GRCm39 version 105 genome, including ectopic genes like GFP and modified GTF file to extend the 3' UTRs for TAAR genes
Supplementary files format and content: All_samples_GEP_usage.csv.gz: usage for each of the gene expression programs described in Tsukahara et al. 2021 (PMID: 34879231) for each cell, for the set of 2.3M mature OSNs identified across all samples, as well as the singularly-expressed olfactory receptor (OR) that was chosen in each mOSN.
Supplementary files format and content: OSN_subtype_hvg_mean.csv.gz: The mean expression of each of the the ~1350 OSN highly-variable genes for each OSN subtype (the set of OSNs singularly expressing a given OR), for the 1100 subtypes detected in our 2.3M integrated OSN dataset
Supplementary files format and content: <sample_name>__filtered_feature_bc_matrix.h5: Raw cell x gene matrix from cell ranger for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: whole olfactory mucosa

extract_protocol:
The main olfactory epithelium was dissected and cleaned up in the Earle’s Balanced Salt Solution (EBSS, pre-treated with carbogen for at least 5 minutes before each use, Worthington), then transferred to a round-bottomed glass dish containing 750 µL of papain solution (one vial of Papain, (Worthington) dissolved in 5 mL of EBSS and then equilibrated 10 minutes at 37 °C) and 100 µL of DNase solution (one vial of DNase-I (Worthington) dissolved in 500 µL of EBSS). Bone was removed from the epithelium under a dissecting microscope and the resultant tissue was placed in a 5 mL tube (Becton Dickinson) with an additional 1.75 mL of Papain solution and 200 µL of DNase-I solution and rocked gently for ~60 minutes at 37 °C. The tissue was then gently triturated with a 5 mL pipette 10-15 times, passed through a 40 µm cell strainer (Becton Dickinson), and washed with 1 mL of Hibernate-A medium containing 10 % Fetal Bovine Serum (FBS, GIBCO). Filtered cells were transferred to a new 5 mL tube and centrifuged 5 minutes at 300 x g. The supernatant was decanted, the cells were washed once with 4 mL Hibernate-A containing 10 % FBS and resuspended in 1 mL Hibernate-A containing 0.2 % FBS. Each of the solutions above contained transcriptional inhibitors (5 µg/mL of Actinomycin D, 10 µg/mL of Anisomycin and 10 µM of Triptolide, all obtained from Sigma) for all experiments. Dissociated cells were stained with propidium iodide (final concentration 1.65 µg/mL), and subject to FACS to remove dead cells and obvious doublets. For GFP-expressing mouse lines , GFP positive and negative cells were sorted separately using a FITC filter. Cells were sorted into Hibernate-A containing 5 % FBS (also include 0.1x of transcriptional inhibitors), centrifuged for 5 minutes at 300 g, and resuspended with PBS. Prepared single cell suspensions were used to prepare single cell RNA-seq library with the chromium single cell gene expression system (chromium single cell 3’ reagents and GEM v3.1 dual index, 10x genomics), using the default protocols provided by 10x genomics. Each of the replicates other than GFP-positive ones was aimed to have 10,000 cells. The expected multiplet rate is ~8.0 %.
Chromium Next GEM Single Cell 3 v3.1: Dual Index. Quantified via Kapa qPCR kit and sequenced via Illumina platform (NovaSeq 6000 or X Plus)

tag: tissue

value: whole olfactory mucosa

tag: strain

tag: Sex

value: male


title: ICSI-F2-pl-63A2

city: Kyoto

first: mito

last: shinohara

state: Kyoto

address: Sakyo-ku, Yoshida Konoe

department: Medicine

country: Japan

institute: Kyoto University

description: Library name: ICSI-F2-pl-63A2

library_source: transcriptomic

data_processing:
Adapter sequences were trimmed from the raw reads using Clip adapter (Galaxy Version 2.5.1). Small RNA analyses were performed using sRNAtoolbox and Galaxy mississippi [2].
Assembly: mm39
Supplementary files format and content: Excel file include raw counts data.

molecule: total RNA

source_name: E13.5 placenta

growth_protocol: C57BL/6 wt females were mated with male ICSI-F1 offspring. Placenta were recovered from pregnant females at E13.5. Control placenta samples were prepared from C57BL/6 wt pregnant females at

extract_protocol:
Placenta tissue were homogenized. Total RNA samples were extracted with miRNeasy mini kit (Quiagen  217084) with treatment with RNase-Free DNase (Quiagen 79254).
RNA integrity was assessed with Bioanalyzer (Agilent Technologies). The library preparation was performed using a NEB Next Multiplex Small RNA Library Prep Set for Illumina (Cat No. E7300) according to the manufacturer’s instructions. Sequencing was performed on an Illumina NovaSeq X plus (51bp single-end).

value: E13.5 placenta

tag: genotype


title: VAT58

city: Los Angeles

first: Kyla

last: Gelev

email: kylagelev@gmail.com, kzg@g.ucla.edu

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

description:
Library name: VAT58
10x Genomics

data_processing:
Alignment was performed against the GRCh38 human genome reference with GENCODE v42 gene annotations using STAR v2.7.10a, with parameter ‘--soloFeatures Gene GeneFull SJ Velocyto’ to accommodate snRNA-seq data.
We used demuxlet v2 via popscle to demultiplex the samples within the batches.
Afterwards, we used DIEM v2.4.1 and DecontX (celda v1.16.1) to remove empty droplets and contaminated reads.
DoubletFinder v2.0.3 was used to remove heterotypic doublets.
Assembly: GRCh38
Supplementary files format and content: Gene counts are found in matrix market file format.
Supplementary files format and content: Barcodes, gene names, and meta data are in tab-separated value formats.

organism: Homo sapiens

source_name: visceral adipose tissue

extract_protocol:
Frozen visceral adipose tissue biopsies were incubated in ice cold lysis buffer (1mL per 100mg), consisting of 10mM Tris-HCl, 10nM NaCl, 3mM MgCl2, 0.1% of IGEPAL, and 0.2 U/μL of RNase inhibitor (Sigma #3335402001). The lysate was immediately run on the gentleMACS dissociator gentleMACS Program 4C_nuclei_1a followed by the gentleMACS Program 4C_nuclei_1b (5 min total). The lysate was then incubated for an additional 10 minutes. The lysate was filtered through MACS 30μm strainer (Miltenyi Biotec #130-110-915) and then centrifuged at 500 x g for 5 minutes at 4°C.  The pellet was re-suspended in 1mL wash buffer consisting of 2.0% BSA, 1X PBS, and 0.2 U/μL of RNase inhibitor (Sigma #3335402001). Following this, the lysate was filtered through another MACS 30μm strainer (Miltenyi Biotec #130-110-915) and centrifuged again at 500 x g for 5 minutes at 4°C. Re-suspension of the pellet was done in 70 uL wash buffer in preparation of library construction.
Libraries were prepared using the 10x Chromium Single Cell 3' Reagent kit v3.1.

value: visceral adipose tissue

tag: cohort

value: Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA)


title: control_64A5

description: Library name: control_64A5

data_processing:
RNAseq
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.2.1), with the GENCODE M23 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-3.4.
The gene expression count matrix was generated using HTSeq (version 2.0.2) with GENCODE M23 annotation gtf file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RawCounts values for each Sample

source_name: brain

growth_protocol: Neonatal brain tissue were prepared from male F2 offspring of C57BL/6 strain produced by natural mating from male ICSI-F1 offspring. Control brain samples were prepared from neonate born by natural mating from wild-type C57BL/6 parents .

extract_protocol:
Neonatal brain tissue were homogenized. Total RNA samples were extracted with miRNeasy mini kit (Quiagen  217084) with treatment with RNase-Free DNase (Quiagen 79254).
The library preparation was performed using a Illumina Stranded mRNA Prep Ligation Kit (Illumina), according to the manufacturer’s instructions.

value: brain

tag: cell type

value: control


title: NewCage2h-2

description: Library name: NewCage2h-2


title: VAT57

description:
Library name: VAT57
10x Genomics


title: ICSI-F2-pl-63A1

description: Library name: ICSI-F2-pl-63A1


title: VAT56

description:
Library name: VAT56
10x Genomics


title: control_63F2

description: Library name: 63F2

data_processing:
RNAseq
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.2.1), with the GENCODE M23 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-3.4.
The gene expression count matrix was generated using HTSeq (version 2.0.2) with GENCODE M23 annotation gtf file.
Assembly: mm10
Supplementary files format and content: Excel file include RawCounts values for each Sample

growth_protocol: ICSI was performed using C57BL/6 epididymal sperm and oocytes. Male ICSI-F2 offspring was mated with wild-type C57BL/6 female, and placentae recovered from pregnant females at E13.5 were examined for gene expression.

extract_protocol:
Placenta tissue were homogenized. Total RNA samples were extracted with miRNeasy mini kit (Quiagen  217084) with treatment with RNase-Free DNase (Quiagen 79254).
The library preparation was performed using a Illumina Stranded mRNA Prep Ligation Kit (Illumina), according to the manufacturer’s instructions.


title: control_63F1

description: Library name: 63F1


title: ICSI-F2-pl-37D8

description: Library name: ICSI-F2-pl-37D8


title: MeCP2KO-eA6h-2

description: Library name: MeCP2KO-eA6h-2

value: MeCP2 KO


title: NewCage2h-1

description: Library name: NewCage2h-1


title: VAT55

description:
Library name: VAT55
10x Genomics


title: control-pl-63F2

description: Library name: control-pl-63F2


title: ICSI_F2_63D2

description: Library name: 63D2


title: control-pl-63F1

description: Library name: control-pl-63F1


title: VAT53

description:
Library name: VAT53
10x Genomics


title: VAT54

description:
Library name: VAT54
10x Genomics


title: control-pl-37B3

description: Library name: contro-pl-37B3


title: MeCP2KO-eA2w-1

description: Library name: MeCP2KO-eA2w-1


title: ICSI_F2_63A2

description: Library name: 63A_2


title: MeCP2KO-eA2h-2

description: Library name: MeCP2KO-eA2h-2


title: control-pl-37B2

description: Library name: contro-pl-37B2


title: VAT52

description:
Library name: VAT52
10x Genomics


title: MeCP2KO-eA2w-2

description: Library name: MeCP2KO-eA2w-2


title: MeCP2KO-eA2h-1

description: Library name: MeCP2KO-eA2h-1


title: control-pl-37A3

description: Library name: contro-pl-37A3


title: ICSI_F2_63A1

description: Library name: 63A_1


title: ICSI_F2_37D8

description: Library name: 37D_8


title: MeCP2KO-eA6h-1

description: Library name: MeCP2KO-eA6h-1


title: VAT51

description:
Library name: VAT51
10x Genomics


title: VAT50

description:
Library name: VAT50
10x Genomics


title: ICSI_F2_63B2

description: Library name: 63B2


title: MHV_12_replicate 2

first: Stephen

middle: Joseph

last: Ross

state: Massachusetts

address: 72 E Concord St

institute: Boston University School of Medicine

description: Library name: Sample 18

data_processing:
FASTQ files obtained from BU, YCGA, or Sequence Read Archive (SRA) available datasets (see table below) were trimmed for Illumina adaptor content using Cutadapt. Trimmed FASTQ files were mapped to the MHV-GP33-GFP [15] or SARS-CoV-2 genome (MN985325) using Hisat2 v2.2.1. Once mapped, .sam and .bam files were processed using samtools. Junction reads were quantified using regtools (-junctions extract) with sorted and indexed .bam files. The resulting .bed files were used to obtain raw chimeric read counts. Reads were normalized by total chimeric reads. Statistical analyses were performed using GraphPad Prism v10.
Assembly: MN985325.1

source_name: Cell line

growth_protocol: L929 cells (mouse connective tissue; ATCC CCL-1) and 17CL-1 cells (mouse fibroblasts; kindly provided by Dr. V. Thiel, Institution of Virology and Immunology, Bern, Switzerland) were maintained in Eagle’s Minimum Essential Medium (EMEM; Corning, NY, USA) supplemented with 10% fetal bovine serum (FBS; R&D Systems, Minneapolis, MN, USA), 2 mM L-glutamine (Thermo Fisher Scientific, Waltham, MA, USA), and either 100 U/mL penicillin-streptomycin (Thermo Fisher Scientific, Waltham, MA, USA) or 100 μg/mL Primocin (Invivogen, San Diego, CA, USA). African green monkey kidney epithelial cells (Vero E6, ATCC CRL-1586) were maintained in Dulbecco’s modified Eagle medium (DMEM, Corning, NY, USA) supplemented with 5% FBS (VWR) and 1% Penicillin-Streptomycin-Glutamine (PSG, Corning, NY, USA). Cells were grown at 37°C and 5% CO2.

extract_protocol:
Total cellular RNA was extracted via TRIzol purification for analysis (SARS-CoV-2).
300 ng to 1 µg of total cellular RNA from rMHV-infected L929 cells or Vero E6 cells infected with rSARS-CoV-2 WT, rSARS-CoV-2 DORF8, rSARS-CoV-2 DORF7a, or rSARS-CoV-2 ORF8 DG was used as a template for reverse transcription and (-) sgRNA library generation using the QuantSeq-Flex kit (Lexogen Inc., Greenland, NH, USA). Libraries were created according to the manufacturer’s instructions. Briefly, primers (see below) which bind to nucleotides 26 to 48 of the SARS-CoV-2 or nucleotides 35 to 54 of the rMHV (-) sgRNA 3′ end leader regions, respectively, were used for first strand synthesis. The template RNA was degraded prior to second strand synthesis using reagents provided in the kit. Libraries were amplified via PCR using QuantSeq-Flex kit reagents. Libraries at a final concentration of 1-2 ng DNA/μL were sent to the Yale Center for Genomic Analysis (YCGA) for sequencing (SARS-CoV-2). 10 μg of total RNA isolated from rMHV-infected cells was treated with DNase I (NEB, Ipswich, MA) according to the manufacturer’s instructions. Total RNA was isolated from the DNase I reaction via acid phenol:chloroform extraction and isopropanol precipitation. Briefly, equal parts of acid phenol and chloroform were added to the DNase I reaction. Tubes were placed on ice and centrifuged at ~12,000 x g at 4°C in a table-top centrifuge. The aqueous phase was transferred to a new tube and precipitated with 40 μL 3 M sodium acetate, 12 μL glycerol, and 1 mL of 100% isopropanol for 1 hour at -20°C. Tubes were centrifuged for 10 minutes at ~20,000 x g. The pellets were washed with 70% ethanol and resuspended in 20 μL of nuclease free H2O. RNA was incubated at 55°C for 15 minutes for homogenization. 1 µg of DNase I treated RNA was spiked with 50 ng of yeast RNA. Samples were submitted to Boston University (BU) Sequencing Core for poly(A) selection, library preparation, and sequencing (MHV).

treatment_protocol: The rSARS-CoV-2 WT and mutant viruses used in this study were generated using the bacterial artificial chromosome (BAC)-based reverse genetic system [16]. The rSARS-CoV-2 WT sequence is based on the SARS-CoV-2 Washington strain (WA1, GenBank: MN985325.1). For the mutant rSARS-CoV-2, mutations were introduced into the intermediate plasmid (pUC57-F1) using site-directed mutagenesis (SDM). The modified F1 fragment was then excised via BsmBI digestion and used to replace the corresponding region in the BAC backbone, following the previously described protocol [17]. The mutant rSARS-CoV-2 was recovered by transfection of Vero E6 cells with the resultant BAC as described previously [17].

tag: cell line

value: Fibroblast

value: WT


title: MeCP2KO-eA-DPG30m-2

description: Library name: MeCP2KO-eA-DPG30m-2


title: control_37B3

description: Library name: 37B_3


title: MHV_12_replicate 1

description: Library name: Sample 17


title: control_37B2

description: Library name: 37B_2


title: MHV_6_replicate 2

description: Library name: Sample 16


title: VAT49

description:
Library name: VAT49
10x Genomics


title: VAT48

description:
Library name: VAT48
10x Genomics


title: control_37A3

description: Library name: 37A_3


title: MeCP2KO-eA-ACE2h-2

description: Library name: MeCP2KO-eA-ACE2h-2


title: MeCP2KO-eA-DPG30m-1

description: Library name: MeCP2KO-eA-DPG30m-1


title: WT_47B_11

description: Library name: WT_47B_11

source_name: E19.5 placenta

growth_protocol: ICSI was performed using C57BL/6 epididymal sperm and oocytes. The ICSI-F2 generation was produced using the sperm of the ICSI-F1 generation via in vitro fertilisation. Placentae recovered by caesarean section at E19.5 were examined for gene expression.

value: E19.5 placenta


title: MeCP2KO-eA-ACE2h-1

description: Library name: MeCP2KO-eA-ACE2h-1


title: MHV_4_replicate 2

description: Library name: Sample 14


title: WT_47B_10

description: Library name: WT_47B_10


title: VAT45

description:
Library name: VAT45
10x Genomics


title: MeCP2KO-cage-2

description: Library name: MeCP2KO-cage-2


title: VAT46

description:
Library name: VAT46
10x Genomics


title: MeCP2KO-cage-1

description: Library name: MeCP2KO-cage-1


title: VAT44

description:
Library name: VAT44
10x Genomics


title: WT_47A_9

description: Library name: WT_47A_9


title: MHV_4_replicate 1

description: Library name: Sample 13


title: VAT47

description:
Library name: VAT47
10x Genomics


title: MeCP2KO-ON-2

description: Library name: MeCP2KO-ON-2


title: WT_47A_10

description: Library name: WT_47A_10


title: MHV_6_replicate 1

description: Library name: Sample 15


title: VAT43

description:
Library name: VAT43
10x Genomics


title: F2_52E_4

description: Library name: F2_52E_4


title: MeCP2KO-NC2h-2

description: Library name: MeCP2KO-NC2h-2


title: VAT42

description:
Library name: VAT42
10x Genomics


title: F2_52D_4

description: Library name: F2_52D_4


title: MeCP2KO-NC2h-1

description: Library name: MeCP2KO-NC2h-1


title: MeCP2KO-ON-1

description: Library name: MeCP2KO-ON-1


title: MCF10, DMSO, rep 1

type: RNA

city: cairo

first: Monica

last: Rostom

state: Cairo

address: first settlement, Banafseg 4

country: Egypt

institute: German University in Cairo

description: Gene expression data from MCF10 treated with DMSO, which is the solvent used for DZH_2 compound

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 17 hr at 45C on GeneChip™ hybridization oven 654. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using the Affymetric GeneChip® Scanner 3000.

data_processing: The data were analyzed with Transcriptome Analysis Software (TAC software, V4.0.2.15, applied Biosystems by ThermoFischer Scientific).

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (GeneChip™ WT PLUS Reagent Kit Pub. No. MAN0018137).

growth_protocol: MDA-MB-231 and MCF10 cells were seeded for 24 hours

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MDA-MB-231 and MCF10 cells weretreated with DZH_2 and/or Maraviroc for 48 hours

tag: treatment

value: DMSO


title: VAT39

description:
Library name: VAT39
10x Genomics


title: F2_52A_4

description: Library name: F2_52A_4


title: VAT41

description:
Library name: VAT41
10x Genomics


title: MeCP2KO-DPG30m-1

description: Library name: MeCP2KO-DPG30m-1


title: VAT40

description:
Library name: VAT40
10x Genomics


title: VAT38

description:
Library name: VAT38
10x Genomics


title: MeCP2KO-ACE2h-2

description: Library name: MeCP2KO-ACE2h-2


title: MeCP2KO-ACE2h-1

description: Library name: MeCP2KO-ACE2h-1


title: F1_51F_2

description: Library name: F1_51F_2


title: F1_51G_2

description: Library name: F1_51G_2


title: F2_52B_4

description: Library name: F2_52B_4


title: MeCP2KO-DPG30m-2

description: Library name: MeCP2KO-DPG30m-2


title: MCF10, DZH_2, IC50, rep 1

description: Gene expression data from MCF10 treated with the IC50 concentration of DZH_2 compound


title: VAT37

description:
Library name: VAT37
10x Genomics


title: VAT36

description:
Library name: VAT36
10x Genomics


title: MDA-MB-231, Untreated, rep 1

description: Gene expression data from untreated MDA-MB-231 cells

value: Untreated


title: F1_51D_2

description: Library name: F1_51D_2


title: MDA-MB-231, ethanol, rep 2

description: Gene expression data from MDA-MB-231 treated with ethanol which is the solvent used for Maraviroc compound

value: Ethanol (MVC solvent)


title: MDA-MB-231, ethanol, rep 1


title: F1_51F_3

description: Library name: F1_51F_3


title: MeCP2-het-2

description: Library name: MeCP2-het-2

value: MeCP2 het

value: female


title: MDA-MB-231, DMSO, rep 1

description: Gene expression data from MDA-MB-231 treated with DMSO, which is the solvent used for DZH_2 compound

value: DMSO (DZH_2 solvent)


title: MCF10, DZH_2, IC20, rep 1

description: Gene expression data from MCF10 treated with the IC20 concentration of DZH_2 compound


title: VAT35

description:
Library name: VAT35
10x Genomics


title: MeCP2-het-1

description: Library name: MeCP2-het-1

value: whole olfactory mucosa


title: MeCP2-WT2

description: Library name: MeCP2-WT2

value: MeCP2 WT

value: male


title: VAT33

description:
Library name: VAT33
10x Genomics

value: visceral adipose tissue


title: MeCP2-WT1

description: Library name: MeCP2-WT1


title: KLF2-OE, biological replicate 1

city: Nanchang

first: Xiaohua

last: Yan

address: No. 1299, Xuefu Avenue, Honggutan

country: China

institute: Nanchang University

description: Library name: HCCLM3_KLF2_rep1

library_source: genomic

data_processing:
ATAC-seq reads were quality-controlled and trimmed from the 3' end until the last base had a quality score > 30 using Trim Galore v0.6.10. Trimmed reads were aligned to the hg38 human reference genome using Bowtie2 v2.5.4 with default parameters. Only uniquely mapping reads with at most two mismatches were retained. Peak calling was performed on the filtered clean reads using MACS2 v2.1.0 with parameters: -g hs --keep-dup all , to identify open chromatin regions (peaks).
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data files include normalized chromatin accessibility signal tracks in bigWig format for each sample.

molecule: genomic DNA

growth_protocol: HCCLM3 cells were maintained as adherent cultures in DMEM supplemented with 10% fetal bovine serum at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Approximately 5 × 10^4 HCCLM3 cells were collected and washed once with cold 1× PBS, followed by centrifugation at 500 × g for 5 min at 4°C. Cell pellets were resuspended in 50 μl pre-chilled nuclei lysis buffer and gently pipetted to release nuclei. Nuclei were collected by centrifugation at 500 × g for 10 min at 4°C, and the supernatant was discarded immediately before transposition.
ATAC-seq libraries were prepared from isolated nuclei using Tn5 transposase. Nuclei were resuspended in transposition reaction mix and incubated at 37°C for 30 min. Transposed DNA was purified using the Qiagen MinElute PCR Purification Kit. Libraries were amplified by PCR using NEBNext High-Fidelity 2× PCR Master Mix for 10–15 cycles and purified again using the Qiagen MinElute PCR Purification Kit. Library concentration was measured using Qubit 4.0, and fragment size distribution was assessed using QSep400. Qualified libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads.

treatment_protocol: Control samples were derived from HCCLM3 cells stably transfected with the empty vector, and experimental samples were derived from HCCLM3 cells stably overexpressing KLF2. Cells were collected under the same culture conditions for ATAC-seq library preparation.

value: Human hepatocellular carcinoma cell

tag: genetic modification

value: stable overexpression of KLF2


title: VAT34

description:
Library name: VAT34
10x Genomics

value: Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA)


title: MeCP2-WT-ACE

description: Library name: MeCP2-WT-ACE


title: MDA-MB-231, DMSO, rep 2

description: Gene Gene expression data from MDA-MB-231 treated with DMSO, which is the solvent used for DZH_2 compound


title: VAT32

description:
Library name: VAT32
10x Genomics


title: VAT31

description:
Library name: VAT31
10x Genomics


title: Vector control, biological replicate 1

description: Library name: HCCLM3_vector_rep1

value: stable transfection with empty vector


title: KLF2-OE, biological replicate 2

description: Library name: HCCLM3_KLF2_rep2


title: Vector control, biological replicate 2

description: Library name: HCCLM3_vector_rep2


title: VAT30

description:
Library name: VAT30
10x Genomics


title: MeCP2-KI2

description: Library name: MeCP2-KI2

value: MeCP2 KI


title: Tumor infiltrated S71 CAR-T cells, 15 days, rep5

city: Nanjing

first: Rongchen

last: Sun

address: Longmian

institute: China Pharmaceutical University

description:
Library name: S71e
S71e

data_processing:
quality control and removal of technical sequences by Cutadapt (V1.9.1)
the reads were aligned to the human reference genome and annotation files using HISAT2 (v.2.2.1)
Gene expression was quantified using HTSeq-counts (v.0.6.1) to estimate gene and isoform.
Assembly: GRCh38
Supplementary files format and content: xlsx files include FPKM values for each sample

source_name: Tumor infiltrated S71 CAR-T

extract_protocol:
RNA from each sample was extracted using RNeasy Mini Kit (Qiagen). 1 μg total RNA was used for subsequent library preparation.
Libraries with different indices were then multiplexed and loaded on an Illumina NovaSeq instrument for sequencing using a 2 × 150 paired-end (PE) configuration according to the manufacturer’s instructions.

treatment_protocol: 15 days after reinfusion of 28Z CAR-T or S71 CAR-T cells into tumor-bearing mice, tumor tissues from five mice per group were dissociated into single-cell suspensions. CD3+ CART cells were enriched using magnetic-activated cell sorting (MACS), and bulk RNA sequencing was performed on the isolated CD3+ tumor-infiltrating CART cells from each mouse.

value: Tumor infiltrated S71 CAR-T

value: Human primary T cell

value: Tumor infiltration for 15 days


title: MDA-MB-231, DZH_2, IC50, rep 2

description: Gene expression data from MDA-MB-231 treated with the IC50 concentration of DZH_2 compound


title: MDA-MB-231, DZH_2, IC50, rep 1


title: MeCP2-KI1

description: Library name: MeCP2-KI1


title: Tumor infiltrated S71 CAR-T cells, 15 days, rep4

description:
Library name: S71d
S71d


title: MDA-MB-231, DZH_2, IC20, rep 2

description: Gene expression data from MDA-MB-231 treated with the IC20 concentration of DZH_2 compound


title: MDA-MB-231, Maraviroc, IC50 rep 2

description: Gene expression data from MDA-MB-231 treated with the IC50 concentration of Maraviroc

value: Maraviroc


title: MDA-MB-231, DZH_2, IC20, rep 1


title: MCF10, Untreated, rep 1

description: Gene expression data from untreated MCF10 cells

value: Untreated


title: VAT29

description:
Library name: VAT29
10x Genomics


title: Tumor infiltrated S71 CAR-T cells, 15 days, rep3

description:
Library name: S71c
S71c


title: MeCP2-KI-ACE

description: Library name: MeCP2-KI-ACE


title: VAT27

description:
Library name: VAT27
10x Genomics


title: VAT28

description:
Library name: VAT28
10x Genomics


title: Tumor infiltrated 28Z CAR-T cells, 15 days, rep5

description:
Library name: 28Ze
28Ze

source_name: Tumor infiltrated 28Z CAR-T

value: Tumor infiltrated 28Z CAR-T


title: MDA-MB-231, Maraviroc, IC50 rep 1


title: Tumor infiltrated S71 CAR-T cells, 15 days, rep1

description:
Library name: S71a
S71a


title: MUS2

description: Library name: MUS2


title: VAT26

description:
Library name: VAT26
10x Genomics


title: VAT25

description:
Library name: VAT25
10x Genomics


title: Tumor infiltrated S71 CAR-T cells, 15 days, rep2

description:
Library name: S71b
S71b


title: MHX2

description: Library name: MHX2


title: MDA-MB-231, Maraviroc, IC20 rep 2

description: Gene expression data from MDA-MB-231 treated with the IC20 concentration of Maraviroc


title: Tumor infiltrated 28Z CAR-T cells, 15 days, rep4

description:
Library name: 28Zd
28Zd


title: MS0_1p2h-2

description: Library name: MS0_1p2h-2


title: MUS1

description: Library name: MUS1


title: MI replicate 2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

hyb_protocol: Labeled fragments were hybridized to Applied Biosystems Clariom S Human Arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization Oven 645

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Macrophages isolated from the blast cells of a 10-year-old male with biphenotypic B-myelomonocytic leukemia treated with 1 µM MI-463

label_protocol: We used the Applied Biosystems GeneChip WT PLUS Reagent Kit (catalog no.: 902280 and 902281) for cDNA synthesis, amplification, cRNA synthesis, second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin according to manufacturer's instructions.

growth_protocol: MV4-11 cultured in Iscove's Modified Dulbecco's Media with 10% FCS and 100 I.U./mL penicillin and 100 μg/mL streptomycin

extract_protocol: RNA was isolated using the Rneasy Mini Kit (Quiagen) according to the manufacturer's instructions.

treatment_protocol: Seeded in 0.5 x 10e6 cells/mL in 2 mL in 12 well-plate and treated with either DMSO or 1 µM MI-463 (volume: 2 µL/mL)

value: Macrophage

value: Peripheral blood

value: Gene fusion:MLL-AFF1; Mutation:FLT3


title: MDA-MB-231, Maraviroc, IC20 rep 1


title: VAT24

description:
Library name: VAT24
10x Genomics


title: MS0_1p2h-1

description: Library name: MS0_1p2h-1

value: whole olfactory mucosa


title: Tumor infiltrated 28Z CAR-T cells, 15 days, rep3

description:
Library name: 28Zc
28Zc


title: MI replicate 4


title: MI replicate 3


title: VAT23

description:
Library name: VAT23
10x Genomics


title: MI replicate 1


title: MHX1

description: Library name: MHX1

value: male


title: Tumor infiltrated 28Z CAR-T cells, 15 days, rep2

description:
Library name: 28Zb
28Zb


title: MI replicate 5


title: Tumor infiltrated 28Z CAR-T cells, 15 days, rep1

description:
Library name: 28Za
28Za


title: M72G-2

description: Library name: M72G-2

value: female


title: VAT20

description:
Library name: VAT20
10x Genomics

value: visceral adipose tissue


title: VAT22

description:
Library name: VAT22
10x Genomics


title: VAT21

description:
Library name: VAT21
10x Genomics


title: M72G-1

description: Library name: M72G-1


title: VAT19

description:
Library name: VAT19
10x Genomics


title: Vehicle replicate 2

source_name: Macrophages isolated from the blast cells of a 10-year-old male with biphenotypic B-myelomonocytic leukemia treated with vehicle (= DMSO)

value: vehicle


title: CD8+ S71 CAR-T cells, coculture with tumor, PBS, 24h, donor 1

description:
Library name: S71a
S71a

source_name: S71 CAR-T

treatment_protocol: Sorted CD8+CAR+ EDB CAR-T cells were manufactured from 3 different donors (donor 1: tumour-bearing patient; donor 2 and donor 3: healthy adult) and starved with serum and all cytokines for 12 h. Each group was treated under different conditions with U87MG-WT for 24 h at E:T=1:1 (EDB-S71 + PBS; EDB-28Z + PBS; EDB-28Z + hIL2; EDB-28Z + hIL15).

value: S71 CAR-T

value: PBS 24h


title: Kir-WT-2

description: Library name: Kir-WT-2


title: VAT18

description:
Library name: VAT18
10x Genomics

value: Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA)


title: CD8+ S71 CAR-T cells, coculture with tumor, PBS, 24h, donor 2

description:
Library name: S71b
S71b


title: Vehicle replicate 1


title: snRNAseq_P14

city: Bonn

first: Mona

last: Malek Mohammadi

address: Venusberg-Campus 1

institute: University Hospital Bonn

description:
Library name: Sample 1
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Renger software 9.0.1
Assembly: Mouse mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Heart

extract_protocol:
Snap frozen tissues were fixed and nuclei were isolated according to the manufacturer's instructions (10x Genomics), followed by Flex single-cell sequencing
Library was constructed according to the manufacturer's instructions (10x Flex), probe set name: Chromium Mouse Transcriptome Probe Set V1.0.1

treatment_protocol: at P0-P1 nTAC or nPAB was performed

value: Heart

tag: tissue type

value: LV and RV

value: cardiac cells

value: no injury, P1nTAC, P1nPAB

tag: age

value: 14 days


title: Kir-WT-1

description: Library name: Kir-WT-1


title: Vehicle replicate 5


title: Vehicle replicate 3


title: CD8+ S71 CAR-T cells, coculture with tumor, PBS, 24h, donor 3

description:
Library name: S71c
S71c

value: Human primary T cell


title: Vehicle replicate 4

value: Macrophage


title: Kdm6b-flox-1

description: Library name: Kdm6b-flox-1


title: Kdm6b-flox-2

description: Library name: Kdm6b-flox-2


title: CD8+ 28Z CAR-T cells, coculture with tumor, IL2, 24h, donor 3

description:
Library name: 28IL2c
28IL2c

source_name: 28Z CAR-T

value: 28Z CAR-T

value: IL2 24h


title: R012_RH

city: Ithaca

first: Erica

last: Secor

state: NY

address: 960 Campus Rd

institute: Cornell University

description:
Sex: MC
Library name: G05_270796_23_RH_10474875_HL3TJBGXV_R1

data_processing:
The quality of the generated FastQ files was checked with the fastqc tool (v.0.12.1). FastQ files were right-end-trimmed by 10 bases and filtered for a minimum Phred quality score of 20 using the BBDuk tool from BBtools (v.39.08).
Processed reads were aligned to the NCBI RefSeq EquCab3.0 reference genome using STAR aligner (v.2.7.11b) with default alignment parameters.23
Aligned read counts were generated using the featureCounts tool from Subread (v.2.0.3).
Assembly: NCBI RefSeq EquCab3.0
Supplementary files format and content: tab delimited text files containing Subread featureCounts output for each sample library

organism: Equus caballus

source_name: Synovial Membrane

extract_protocol:
Tissue samples were pulverized using an automated shaker mill (Spex Certiprep 6750), followed by RNA isolation using the Qiagen RNeasy Mini Kit (Qiagen, Germantown MD).
RNA sequencing (RNA-seq) library preparation was performed by the Cornell University genomics facility using the Lexogen QuantSeq FWD V2 library preparation kit using the manufacturer's protocol (Lexogen GmbH). Sequencing was performed using an Illumina NextSeq 500 instrument (Novogene, Sacramento CA).

value: Synovial Membrane

tag: limb

value: Right Hind

tag: batch


title: VAT17

description:
Library name: VAT17
10x Genomics


title: CD8+ 28Z CAR-T cells, coculture with tumor, IL2, 24h, donor 2

description:
Library name: 28IL2b
28IL2b


title: Kdm6b-cKO-2

description: Library name: Kdm6b-cKO-2

value: whole olfactory mucosa

value: male


title: CD8+ 28Z CAR-T cells, coculture with tumor, IL15, 24h, donor 3

description:
Library name: 28IL15c
28IL15c


title: VAT16

description:
Library name: VAT16
10x Genomics

value: visceral adipose tissue


title: R012_LH

description:
Sex: MC
Library name: C04_270796_23_LH_10474875_HL3TJBGXV_R1

value: Left Hind


title: R011_RH

description:
Sex: MC
Library name: F04_263400_23_RH_10474875_HL3TJBGXV_R1


title: VAT15

description:
Library name: VAT15
10x Genomics


title: Kdm6b-cKO-1

description: Library name: Kdm6b-cKO-1


title: R011_LH

description:
Sex: F
Library name: E05_263400_23_LH_10474875_HL3TJBGXV_R1


title: DPG30m-6

description: Library name: DPG30m-6


title: CD8+ 28Z CAR-T cells, coculture with tumor, IL15, 24h, donor 1

description:
Library name: 28IL15a
28IL15a


title: VAT13

description:
Library name: VAT13
10x Genomics


title: DPG30m-5

description: Library name: DPG30m-5


title: VAT12

description:
Library name: VAT12
10x Genomics


title: CD8+ 28Z CAR-T cells, coculture with tumor, PBS, 24h, donor 3

description:
Library name: 28Zc
28Zc

value: PBS 24h


title: R010_RH

description:
Sex: F
Library name: E04_245886_23_RH_10474875_HL3TJBGXV_R1


title: VAT14

description:
Library name: VAT14
10x Genomics

value: Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA)


title: VAT11

description:
Library name: VAT11
10x Genomics


title: R010_LH

description:
Sex: MC
Library name: A06_245886_23_LH_10474875_HL3TJBGXV_R1


title: CD8+ 28Z CAR-T cells, coculture with tumor, PBS, 24h, donor 2

description:
Library name: 28Zb
28Zb


title: R009_RF

description:
Sex: MC
Library name: B04_349754_RF_10474875_HL3TJBGXV_R1

value: Right Front


title: CD8+ 28Z CAR-T cells, coculture with tumor, IL15, 24h, donor 2

description:
Library name: 28IL15b
28IL15b


title: CD8+ 28Z CAR-T cells, coculture with tumor, PBS, 24h, donor 1

description:
Library name: 28Za
28Za


title: Cnga2-wt-1

description: Library name: Cnga2-wt-1

value: Cnga2 WT

value: female


title: Cnga2-wt-2

description: Library name: Cnga2-wt-2


title: R16_Tumour

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

description: Library name: T3591

data_processing:
RNA-Seq reads were mapped to the human genome (hg19, Genome Reference Consortium) using STAR (v2.7.9a)
Counting of the reads was performed with rsem using the ensembl annotation GRCh37.87
Genes that achieved at least one read count per million reads (cpm) in at least 25% of samples were used to generate an RPKM normalized expression matrix was generated
Assembly: hg19
Supplementary files format and content: comma separated file of log2RPKM gene expression

extract_protocol:
Total RNA was extracted and purified from 100-300μm cryosections from frozen tissue sections using TRI Reagent (Sigma-Aldrich T9424)
mRNA library preparation was performed with RNA-Seq Ribodepletion

value: Tumour


title: VAT10

description:
Library name: VAT10
10x Genomics


title: Cnga2-het-2

description: Library name: Cnga2-het-2

value: Cnga2 KO


title: R009_LF

description:
Sex: MC
Library name: A04_349754_LF_10474875_HL3TJBGXV_R1

value: Left Front


title: VAT9

description:
Library name: VAT9
10x Genomics


title: Cnga2-het-1

description: Library name: Cnga2-het-1


title: R15_Tumour

description: Library name: T4702


title: VAT8

description:
Library name: VAT8
10x Genomics


title: Cd36-KO-2

description: Library name: Cd36-KO-2


title: VAT7

description:
Library name: VAT7
10x Genomics


title: Cd36-KO-1

description: Library name: Cd36-KO-1


title: R008_LF

description:
Sex: F
Library name: C06_257049_22_LF_10474875_HL3TJBGXV_R1


title: R13_Tumour

description: Library name: T4617


title: VAT6

description:
Library name: VAT6
10x Genomics


title: R007_LH

description:
Sex: F
Library name: H06_258365-22_LH_10474875_HL3TJBGXV_R1


title: R12_Tumour

description: Library name: T4580


title: R008_RF

description:
Sex: MC
Library name: G06_257049_22_RF_10474875_HL3TJBGXV_R1


title: CAST_propanoic_acid-1

description: Library name: CAST_propanoic_acid-1

value: CAST/EiJ


title: VAT5

description:
Library name: VAT5
10x Genomics


title: R14_Tumour

description: Library name: T4683


title: CAST_octanoic_acid-3

description: Library name: CAST_octanoic_acid-3


title: R006_LH

description:
Sex: MC
Library name: D05_255884_22_LH_10474875_HL3TJBGXV_R1


title: R10_Tumour

description: Library name: T02429


title: R006_RH

description:
Sex: MC
Library name: H05_255884_22_RH_10474875_HL3TJBGXV_R1


title: CAST_octanoic_acid-2

description: Library name: CAST_octanoic_acid-2


title: R11_Tumour

description: Library name: T02667


title: VAT4

description:
Library name: VAT4
10x Genomics


title: CAST_propanoic_acid-2

description: Library name: CAST_propanoic_acid-2


title: R9_Tumour

description: Library name: T02309


title: R005_RF

description:
Sex: MC
Library name: H04_245826_22_RF_10474875_HL3TJBGXV_R1


title: VAT3

description:
Library name: VAT3
10x Genomics


title: R005_LH

description:
Sex: MC
Library name: B05_245826_22_LH_10474875_HL3TJBGXV_R1


title: R8_Tumour

description: Library name: T03359


title: VAT2

description:
Library name: VAT2
10x Genomics


title: R004_RH

description:
Sex: M
Library name: G04_222616_22_RH_10474875_HL3TJBGXV_R1


title: CAST_heptanoic_acid-2

description: Library name: CAST_heptanoic_acid-2


title: R004_LH

description:
Sex: M
Library name: C05_222516_22_LH_10474875_HL3TJBGXV_R1


title: CAST_heptanoic_acid-1

description: Library name: CAST_heptanoic_acid-1


title: R7_Tumour

description: Library name: T353


title: CAST_octanoic_acid-1

description: Library name: CAST_octanoic_acid-1


title: CAST_butanoic_acid-2

description: Library name: CAST_butanoic_acid-2


title: R003_LF

description:
Sex: MC
Library name: E06_187389_22_LF_10474875_HL3TJBGXV_R1


title: CAST_butanoic_acid-1

description: Library name: CAST_butanoic_acid-1


title: R6_Tumour

description: Library name: T319


title: VAT1

description:
Library name: VAT1
10x Genomics


title: R003_RF

description:
Sex: MC
Library name: A05_187389_22_RF_10474875_HL3TJBGXV_R1


title: R4_Tumour

description: Library name: T074


title: R5_Tumour

description: Library name: T258


title: FCDI_2

city: Shenzhen

first: Yaqian

last: Zhang

state: Guangdong Province

address: Guangming

department: Department of Neurology

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

description:
Library name: Sample5
10x Genomics snRNA-Seq

data_processing:
Cell Ranger(7.1.0) aligns the previously generated FASTQ sequencing data to a reference genome, performs cell and UMI counting, and generates a cell-by-gene expression matrix.
Assembly: GRCh38
Supplementary files format and content: processed data files

source_name: temporal neocortex,epileptogenic

extract_protocol:
Single-nucleus dissociation was performed following the 10x Genomics protocol with optimizations based on laboratory-specific conditions. RNA integrity of each sample was first assessed using an Agilent 2100 Bioanalyzer, and only samples meeting quality criteria were processed further. Brain tissue was sectioned into 1–2 mm³ pieces and transferred to a Dounce homogenizer containing lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20; 0.1% IGEPAL; 2% BSA). The tissue was homogenized to ensure complete lysis and nuclear release. The homogenate was transferred to a centrifuge tube and spun at 4°C for 10 min. The supernatant was removed, and the nuclear pellet was resuspended in ice-cold wash buffer (1× PBS with 1% BSA and 0.2 U/μl RNase inhibitor) to maintain nuclear integrity. A 40 μm cell strainer was used to remove debris and large aggregates. Nuclear concentration and integrity were assessed using a hemocytometer and trypan blue staining. Myelin debris was removed using a myelin removal reagent, followed by additional centrifugation and washing steps to obtain purified nuclei. The final nuclear concentration was adjusted to 700–1200 nuclei/μl for downstream library preparation.
Isolated nuclei were loaded into a 10x Genomics Chromium microfluidic chip and captured using the Chromium Controller. Nuclei were encapsulated with gel beads and reagents to form single-nucleus droplets (Gel Beads-in-Emulsions, GEMs). Within the GEMs, reverse transcription (RT) was performed to generate barcoded cDNA from nuclear mRNA. The cDNA fragments were then amplified via PCR. Library construction was completed using the 10x Genomics Single Cell 3' v3 reagent kit, followed by high-throughput sequencing on the Illumina NextSeq X Plus platform.

value: temporal neocortex,epileptogenic

value: brain tissue cells


title: FCDI_1

description:
Library name: Sample4
10x Genomics snRNA-Seq


title: R3_Tumour

description: Library name: T036


title: CAST_DPG30m-4

description: Library name: CAST_DPG30m-4


title: R002_RH

description:
Sex: MC
Library name: D06_183130_22_RH_10474875_HL3TJBGXV_R1

value: Synovial Membrane


title: FCDI_3

description:
Library name: Sample6
10x Genomics snRNA-Seq


title: R2_Tumour

description: Library name: T034


title: Control_3

description:
Library name: Sample3
10x Genomics snRNA-Seq

source_name: temporal neocortex,nonepileptic

value: temporal neocortex,nonepileptic


title: CAST_DPG30m-3

description: Library name: CAST_DPG30m-3

value: whole olfactory mucosa


title: Control_2

description:
Library name: Sample2
10x Genomics snRNA-Seq


title: R1_Tumour

description: Library name: T219


title: R001_LH

description:
Sex: M
Library name: F05_181928_22_LH_10474875_HL3TJBGXV_R1


title: R002_LH

description:
Sex: MC
Library name: B06_183130_22_LH_10474875_HL3TJBGXV_R1


title: Control_1

description:
Library name: Sample1
10x Genomics snRNA-Seq


title: CAST_DPG30m-1

description: Library name: CAST_DPG30m-1

value: male


title: R001_RH

description:
Sex: M
Library name: F06_181928_22_RH_10474875_HL3TJBGXV_R1

value: Right Hind


title: R20_Tumour

description: Library name: T4091


title: SNDX replicate 6

description: Library name: SNDX_6

data_processing:
ATAC-seq reads were processed using the nf-core/atacseq pipeline (v2.1.2) with default parameters, except for the specification of a read length of 100 bp to match the sequencing protocol.
Reads were aligned to the human reference genome (GRCh38) using BWA-MEM, followed by duplicate removal, filtering, and fragment size estimation.
Peak calling was performed with MACS2 , and consensus peak sets were generated using bedtools.
Assembly: GRCh38
Supplementary files format and content: bigWig, broadPeak
Supplementary files format and content: raw read count per peak in tab delimited file

source_name: Peripheral blood

growth_protocol: MV4-11 were cultured in Iscove's Modified Dulbecco's Media with 10% FCS and 100 I.U./mL penicillin and 100 μg/mL streptomycin

extract_protocol:
Tagmented DNA was isolated from 8 x 10e4 cells following the Omni-ATAC protocol from Corces et al. (2017). No DNAse treatment was performed.
Libraries were prepared following the Omni-ATAC protocol from Corces et al. (2017). Two rounds of double size selection and cleanup of the libraries were done with AMPure XP beads.

treatment_protocol: Cells were seeded in cell culture 12-well plates at a concentration of 0.5 x 10e6 cells/mL in 2 mL and treated with either DMSO or 0.2 µM SNDX-5613 (2 µL/mL). The cells were incubated for 48h. After 48h, the cells were collected and analyzed.

value: Peripheral blood

value: Macrophage

value: Gene fusion:MLL-AFF1; Mutation:FLT3


title: MPD28

city: Fuzhou

first: Pengfei

last: Cha

address: 243xihong road

institute: Fuzhou Dermatology Hospital

description:
Library name: SAMPLE 39
MPD without recurrence

data_processing:
Paired-end sequencing was conducted on an Illumina HiSeq™ 4000 platform (Illumina, Inc., USA). Raw sequencing data were generated in FASTQ format for each sample. Initial quality assessment was performed using FastQC. Adapter contamination and low-quality bases were subsequently removed using Trimmomatic (v0.39) with the following parameters: SLIDINGWINDOW:4:20 MINLEN:36.
Assembly: Cleaned reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 under default settings. Transcript assembly and gene-level abundance estimation were carried out with StringTie based on Ensembl annotations.
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: paget disease

extract_protocol:
Total RNA was isolated using TRIzol® reagent (Thermo Fisher Scientific), followed by purification with RNeasy Mini Kit (Qiagen). Polyadenylated mRNA was enriched by binding to oligo(dT)-coated magnetic beads (Thermo Fisher Scientific) through hybridization to the poly(A) tail, ensuring high-quality mRNA selection for downstream analysis. mRNA was reverse transcribed, amplified, and quality control which were performed by the Sangon Biotech Inc (Shanghai, China). Libraries with insert sizes of 300–500 bp and concentrations ≥10 nM were selected for sequencing.
All subsequent steps, including reverse transcription, amplification and quality control, were conducted by Sangon Biotech Inc. (Shanghai, China). Finally, libraries with an insert size of 300–500 bp and a concentration ≥10 nM were prepared for sequencing.

value: paget disease


title: MPD26

description:
Library name: SAMPLE 37
MPD without recurrence


title: SNDX replicate 5

description: Library name: SNDX_5


title: CAST_DPG30m-2

description: Library name: CAST_DPG30m-2

source_name: whole olfactory mucosa


title: Arrb2KO-DPG30m-2

description: Library name: Arrb2KO-DPG30m-2


title: Arrb2KO-ACE2h-2

description: Library name: Arrb2KO-ACE2h-2


title: MPD27

description:
Library name: SAMPLE 38
MPD without recurrence


title: R19_Tumour

description: Library name: T02290


title: MPD25

description:
Library name: SAMPLE 36
MPD without recurrence


title: R18_Tumour

description: Library name: T1740


title: R17_Tumour

description: Library name: T4563


title: SNDX replicate 3

description: Library name: SNDX_3


title: Arrb2KO-DPG30m-1

description: Library name: Arrb2KO-DPG30m-1


title: MPD24

description:
Library name: SAMPLE 35
MPD without recurrence


title: Arrb2KO-ACE2h-1

description: Library name: Arrb2KO-ACE2h-1


title: SNDX replicate 4

description: Library name: SNDX_4


title: S12_Tumour

description: Library name: S1979


title: SNDX replicate 2

description: Library name: SNDX_2


title: 72T4-2

description: Library name: 72T4-2

value: M72 > TAAR4


title: SNDX replicate 1

description: Library name: SNDX_1


title: 72T4-1

description: Library name: 72T4-1


title: S11_Tumour

description: Library name: A3000


title: S9_Adjacent

description: Library name: A2940

value: Adjacent


title: Vehicle replicate 6

description: Library name: Vehicle_6

value: vehicle


title: S7_Adjacent

description: Library name: S2037


title: MPD21

description:
Library name: SAMPLE 32
MPD without recurrence

value: female


title: MPD22

description:
Library name: SAMPLE 33
MPD without recurrence


title: MPD23

description:
Library name: SAMPLE 34
MPD without recurrence


title: 574_Ctl_3

description: Library name: 574_Ctl_3

value: HP1 swap


title: Vehicle replicate 4

description: Library name: Vehicle_4


title: 575_Ctl_4

description: Library name: 575_Ctl_4


title: MPD20

description:
Library name: SAMPLE 31
MPD without recurrence


title: Vehicle replicate 3

description: Library name: Vehicle_3


title: MPD19

description:
Library name: SAMPLE 30
MPD without recurrence


title: Vehicle replicate 5

description: Library name: Vehicle_5


title: S6_Adjacent

description: Library name: A1908


title: 573_HP1_Swap_3

description: Library name: 573_HP1_Swap_3

value: HP1 swap; Foxg1-Cre


title: 571_Ctl_2

description: Library name: 571_Ctl_2


title: S4_Adjacent

description: Library name: S1560


title: Vehicle replicate 2

description: Library name: Vehicle_2


title: S3_Adjacent

description: Library name: S1470


title: MPD17

description:
Library name: SAMPLE 28
MPD without recurrence


title: S1_Adjacent

description: Library name: S1352


title: Vehicle replicate 1

description: Library name: Vehicle_1


title: Adult Kidney input

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

country: France

institute: INEM

description:
Library name: Input38R
BamCoverage in CPM

data_processing:
For quality control FASTQC(version0.11.5) was applied.
Alignments were done with bowtie2(version 2.3.3.1, default-sensitive-local argument) on linux with the mm10 genome reference.
Assembly: mm10 UCSC genome refernce
Supplementary files format and content: Bigwig files were generated using bamCoverage with binSize = 1, Counts Per Million unit
Supplementary files format and content: Peaks were called using GEM version 3.4  https://groups.csail.mit.edu/cgs/gem/, narrowPeak format

source_name: kidney

growth_protocol: All experiments were performed on 60-day-old male wild-type mice. Animals were fed ad libitum and housed in a room with constant ambient temperature and a 12-hour light/12-hour dark cycle.

extract_protocol:
Nuclei were extracted from kidneys with a homogenizer in hypotonic buffer. Chromatin from released nuclei was crosslinked with 1% formaldehyde for 10 min. After quenching and nuclear lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode).
ChIP-seq libraries were prepared using the MicroPlex kit v2 (Diagenode) according to the manufacturer’s protocol. 1ng of immunoprecipitated material was repaired, end-blunted and amplified (10 cycles). The resulting libraries were purified using AMPure XP beads protocol (Beckman Coulter, Indianapolis, IN). Libraries were then normalized and pooled at 2nM and spike-in PhiX Control v3 (Illumina, San Diego, CA) was added. Sequencing was done using a NextSeq 500 instrument (Illumina) in paired-end read mode (2x40 cycles).

value: kidney

value: wildtype

tag: chip antibody

value: HNF1B ( Santa Cruz, sc-22840)


title: 501_HP1_Swap_4

description: Library name: 501_HP1_Swap_4

data_processing:
Demultiplexed fastq files were uniformly processed via a custom nextflow pipeline that ran cell ranger (v6), as well as custom post-processing to remove multi-mapping reads (see Tsukahara et al. 2021 PMID: 34879231). All samples (including those in GSE173947) were integrated together to extract (mature) olfactory sensory neurons for downstream analyses.
Assembly: Ensembl GRCm39 version 105 genome, including ectopic genes like GFP and modified GTF file to extend the 3' UTRs for TAAR genes
Supplementary files format and content: All_samples_GEP_usage.csv.gz: usage for each of the gene expression programs described in Tsukahara et al. 2021 (PMID: 34879231) for each cell, for the set of 2.3M mature OSNs identified across all samples, as well as the singularly-expressed olfactory receptor (OR) that was chosen in each mOSN.
Supplementary files format and content: OSN_subtype_hvg_mean.csv.gz: The mean expression of each of the the ~1350 OSN highly-variable genes for each OSN subtype (the set of OSNs singularly expressing a given OR), for the 1100 subtypes detected in our 2.3M integrated OSN dataset
Supplementary files format and content: <sample_name>__filtered_feature_bc_matrix.h5: Raw cell x gene matrix from cell ranger for each sample

extract_protocol:
The main olfactory epithelium was dissected and cleaned up in the Earle’s Balanced Salt Solution (EBSS, pre-treated with carbogen for at least 5 minutes before each use, Worthington), then transferred to a round-bottomed glass dish containing 750 µL of papain solution (one vial of Papain, (Worthington) dissolved in 5 mL of EBSS and then equilibrated 10 minutes at 37 °C) and 100 µL of DNase solution (one vial of DNase-I (Worthington) dissolved in 500 µL of EBSS). Bone was removed from the epithelium under a dissecting microscope and the resultant tissue was placed in a 5 mL tube (Becton Dickinson) with an additional 1.75 mL of Papain solution and 200 µL of DNase-I solution and rocked gently for ~60 minutes at 37 °C. The tissue was then gently triturated with a 5 mL pipette 10-15 times, passed through a 40 µm cell strainer (Becton Dickinson), and washed with 1 mL of Hibernate-A medium containing 10 % Fetal Bovine Serum (FBS, GIBCO). Filtered cells were transferred to a new 5 mL tube and centrifuged 5 minutes at 300 x g. The supernatant was decanted, the cells were washed once with 4 mL Hibernate-A containing 10 % FBS and resuspended in 1 mL Hibernate-A containing 0.2 % FBS. Each of the solutions above contained transcriptional inhibitors (5 µg/mL of Actinomycin D, 10 µg/mL of Anisomycin and 10 µM of Triptolide, all obtained from Sigma) for all experiments. Dissociated cells were stained with propidium iodide (final concentration 1.65 µg/mL), and subject to FACS to remove dead cells and obvious doublets. For GFP-expressing mouse lines , GFP positive and negative cells were sorted separately using a FITC filter. Cells were sorted into Hibernate-A containing 5 % FBS (also include 0.1x of transcriptional inhibitors), centrifuged for 5 minutes at 300 g, and resuspended with PBS. Prepared single cell suspensions were used to prepare single cell RNA-seq library with the chromium single cell gene expression system (chromium single cell 3’ reagents and GEM v3.1 dual index, 10x genomics), using the default protocols provided by 10x genomics. Each of the replicates other than GFP-positive ones was aimed to have 10,000 cells. The expected multiplet rate is ~8.0 %.
Chromium Next GEM Single Cell 3 v3.1: Dual Index. Quantified via Kapa qPCR kit and sequenced via Illumina platform (NovaSeq 6000 or X Plus)


title: 568_HP1_Swap_2

description: Library name: 568_HP1_Swap_2


title: T12_Tumour

description: Library name: T1979

value: Tumour


title: T13_Tumour

description: Library name: T1940


title: 4MA0_1p2h-1

description: Library name: 4MA0_1p2h-1

value: whole olfactory mucosa


title: 4MA0_1p2h-2

description: Library name: 4MA0_1p2h-2

value: male


title: Adult Kidney rep3

description:
Library name: IP38R1
BamCoverage in CPM


title: T11_Tumour

description: Library name: T3000


title: Adult Kidney rep4

description:
Library name: IP47R1
BamCoverage in CPM


title: 496_Ctl_1

description: Library name: 496_Ctl_1


title: MPD16

description:
Library name: SAMPLE 27
MPD without recurrence


title: MPD15

description:
Library name: SAMPLE 26
MPD with recurrence


title: MPD13

description:
Library name: SAMPLE 24
MPD without recurrence


title: T9_Tumour

description: Library name: T2940


title: Adult Kidney rep2

description:
Library name: IP47L
BamCoverage in CPM


title: Adult Kidney rep1

description:
Library name: IP39L
BamCoverage in CPM


title: MPD14

description:
Library name: SAMPLE 25
MPD without recurrence


title: H3K27me3 CUT&Tag Seq of mouse HSPCs, IgG

city: Chengdu

first: Yiman

last: Peng

state: Sichuan

address: No.1, Keyuan 4th Road, Gaopeng Avenue, Chengdu, Sichuan, China

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University

institute: Sichuan University

description:
Library name: H3K27me3_IgG
IgG.bw

data_processing:
After quality control by fastp standard workflow, Bowtie2 (RRID: SCR_016368) was used for mouse genome (mm10) index construction and clean reads alignments. SAMtools was performed to convert sam files into sorted bam files. Normalized bw files were generated by DeepTools with "bamCoverage -p 30 --normalizeUsing BPM --binSize 50 -b" option. MACS3 was performed for peak calling. Data normalization and difference comparison were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak
Library strategy: CUT&Tag

source_name: HSPC

growth_protocol: mouse cKit+ HSPCs and AML cells were cultured at 37 °C with 7.5% CO2 in BCM medium [45% IMDM + 45% DMEM + 10% FBS + 50 × 10-6 M β-mercaptoethanol + penicillin (100 U mL-1)/streptomycin (0.1 mg mL-1)] supplemented with 10% stem cell medium (SCM) including mIL-3 (10 ng mL-1, Cat# 403-ML; R&D Systems), mIL-6 (10 ng mL-1, Cat# 406-ML; R&D Systems), and mSCF (50 ng mL-1, Cat# 455-MC; R&D Systems)

extract_protocol: The CUT&Tag assay was performed using a NovoNGS CUT&Tag 2.0 High-Sensitivity kit (Novoprotein Scientific, N259-YH01-01A).

value: HSPC

value: WT


title: T8_Tumour

description: Library name: T2066


title: MPD12

description:
Library name: SAMPLE 23
MPD without recurrence


title: 494_HP1_Swap_1

description: Library name: 494_HP1_Swap_1


title: Exp2, Splenic B cells, Day42, scRNAseq, HTO

city: Melbourne

first: Oliver

middle: Philip

last: Skinner

state: VIC

address: 792 Elizabeth Street

department: Microbiology and Immunology

country: Australia

institute: Peter Doherty Institute, University of Melbourne

description:
Library name: Experiment2_Day42_HTO
10X Genomics
experiment2.RDS

library_source: other

data_processing:
For both the experiment 1 (days 0-14) and experiment 2 (days 10-42), the transcriptome of splenic B cells was aligned using Cell Ranger 3.1.0 (10X Genomics) against mouse genome v2020-A (10X Genomics). Hashtag demultiplexing and pre-processing of the data was performed using R version 4.2.0 and Seurat version 4
Assembly: mm10
Supplementary files format and content: tsv file of BCR contig annotations for Experiment 1 and Experiment 2. RDS Seurat objects of demultiplexed, merged data for Experiment 1, Experiment 2 and integrated Seurat object of both Experiments. csv files of Experiment 1 and Experiment 2 detailing HTO's in each sample.

molecule: protein

source_name: Spleen

extract_protocol:
Spleens were harvested from mice and homogenised through 70µM cell strainers. RBCs were lysed using Pharm Lyse (BD) for 3 minutes at room temperature and then single cell suspensions washed twice in 1x PBS. Samples were then incubated with Fc receptor-blocking antibodies (BD) for 20 minutes on ice, followed by incubation with titrated monoclonal fluorescently conjugated antibodies and TotalSeq-C (BioLegend) mouse hashtags for 20 minutes on ice. Cells were washed twice and resuspended with propidium iodide (1:500 dilution) in PBS 2% BSA. For experiment 1, samples from five individual mouse replicates were pooled together for each timepoint. Note, for timepoint day 4 post infection, there were four separately infected mice with one uninfected naive sample pooled in. Live, TCRβ negative, CD19+, B220int-hi cells were sorted using a FACS Aria III (BD) into a 2% BSA/PBS buffer. For experiment 2, samples from seven individual mice (three for PcAS, three for PcAS+drug and one uninfected) were pooled together for each timepoint. Live, TCRβ negative, CD19+, B220int-hi, IgDlo cells were sorted using a FACS Aria III (BD) into a 2% BSA/PBS buffer. For each sample, a small number of IgDhi naive cells were spiked in to assist in removal of batch effects for downstream scRNAseq analysis.
After sorting, cells were loaded onto the chromium controller and using the Chromium GEM-X Single Cell 5' Kits v3 (Catalogue #1000695;10X Genomics), cDNA-sequencing libraries were prepared as per manufacturer's instructions.

treatment_protocol: Plasmodium infection with 1x10^5 infected RBCs (Plasmodium chabaudi chabaudi AS strain - PcAS)

value: Spleen

value: 6-12 weeks

value: B cells

value: Uninfected + Plasmodium infection + Plasmodium infection with anti-malarials


title: MPD11

description:
Library name: SAMPLE 22
MPD without recurrence

value: paget disease


title: T7_Tumour

description: Library name: T2037


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shAbcb8&shKmt2c rep3

description:
Library name: H3K27me3_shAbcb8_shKmt2c_rep3
combine_all_H3k27me3_shAbcb8_shMll3.bw

value: shAbcb8; shKmt2c


title: MPD10

description:
Library name: SAMPLE 21
MPD without recurrence

value: female


title: T6_Tumour

description: Library name: T1908


title: MPD9

description:
Library name: SAMPLE 20
MPD without recurrence


title: T5_Tumour

description: Library name: T1686


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shAbcb8&shKmt2c rep1

description:
Library name: H3K27me3_shAbcb8_shKmt2c_rep1
combine_all_H3k27me3_shAbcb8_shMll3.bw


title: Exp2, Splenic B cells, Day42, scRNAseq, mRNA

description:
Library name: Experiment2_Day42_GEX
10X Genomics
experiment2.RDS


title: T4_Tumour

description: Library name: T1560


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shAbcb8 rep3

description:
Library name: H3K27me3_shAbcb8_rep3
combine_all_H3K27me3_shAbcb8.bw


title: Exp2, Splenic B cells, Day35, scRNAseq, HTO

description:
Library name: Experiment2_Day35_HTO
10X Genomics
experiment2.RDS


title: MPD8

description:
Library name: SAMPLE 19
MPD without recurrence


title: Exp2, Splenic B cells, Day42, scRNAseq, BCR

description:
Library name: Experiment2_Day42_VDJ
10X Genomics
Experiment_2_bcr_processed_data.tsv
experiment2.RDS


title: T3_Tumour

description: Library name: T1470


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shAbcb8 rep2

description:
Library name: H3K27me3_shAbcb8_rep2
combine_all_H3K27me3_shAbcb8.bw


title: Exp2, Splenic B cells, Day35, scRNAseq, BCR

description:
Library name: Experiment2_Day35_VDJ
10X Genomics
Experiment_2_bcr_processed_data.tsv
experiment2.RDS


title: MPD7

description:
Library name: SAMPLE 18
MPD without recurrence


title: MPD6

description:
Library name: SAMPLE 17
MPD with recurrence


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shAbcb8&shKmt2c rep2

description:
Library name: H3K27me3_shAbcb8_shKmt2c_rep2
combine_all_H3k27me3_shAbcb8_shMll3.bw


title: Exp2, Splenic B cells, Day35, scRNAseq, mRNA

description:
Library name: Experiment2_Day35_GEX
10X Genomics
experiment2.RDS


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shAbcb8 rep1

description:
Library name: H3K27me3_shAbcb8_rep1
combine_all_H3K27me3_shAbcb8.bw


title: T1_Tumour

description: Library name: T1352


title: Exp2, Splenic B cells, Day28, scRNAseq, HTO

description:
Library name: Experiment2_Day28_HTO
10X Genomics
experiment2.RDS


title: MPD5

description:
Library name: SAMPLE 16
MPD without recurrence


title: MPD4

description:
Library name: SAMPLE 15
MPD without recurrence


title: T2_Tumour

description: Library name: T1360


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shKmt2c rep3

description:
Library name: H3K27me3_shKmt2c_rep3
combine_all_H3k27me3_shMll3.bw


title: CUT and Tag for IgG in iPSCs, Replicate 2

first: James

middle: H.

last: Holt

state: London

address: Blizard Institute

department: Blizard Institute

description: Library name: IgG R2

data_processing:
read were de-multiplexed by Novogene UK Co., Ltd. (Cambridge).
Assembly: hg38
Supplementary files format and content: genome coverage in bigwig format
Library strategy: CUT&Tag

growth_protocol: iPSCs cultured in mTeSR media, supplemented with ROCK inhibitor upon passaging.

extract_protocol: EpiCypher® CUTANA™ Direct-to-PCR CUT & Tag Protocol version 1.7

value: iPSC


title: Exp2, Splenic B cells, Day28, scRNAseq, BCR

description:
Library name: Experiment2_Day28_VDJ
10X Genomics
Experiment_2_bcr_processed_data.tsv
experiment2.RDS


title: MPD3

description:
Library name: SAMPLE 14
MPD with recurrence


title: CUT and Tag for IgG in iPSCs, Replicate 1

description: Library name: IgG R1


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shKmt2c rep2

description:
Library name: H3K27me3_shKmt2c_rep2
combine_all_H3k27me3_shMll3.bw


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shKmt2c rep1

description:
Library name: H3K27me3_shKmt2c_rep1
combine_all_H3k27me3_shMll3.bw


title: MPD2

description:
Library name: SAMPLE 13
MPD with recurrence


title: MPD1

description:
Library name: SAMPLE 12
MPD without recurrence


title: Exp2, Splenic B cells, Day21, scRNAseq, BCR

description:
Library name: Experiment2_Day21_VDJ
10X Genomics
Experiment_2_bcr_processed_data.tsv
experiment2.RDS


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shRen rep3

description:
Library name: H3K27me3_shRen_rep3
combine_all_H3K27me3_shRen.bw

value: shRen


title: CUT and Tag for H3K9me3 in iPSCs, Replicate 2

description: Library name: H3K9me3 R2


title: Exp2, Splenic B cells, Day21, scRNAseq, mRNA

description:
Library name: Experiment2_Day21_GEX
10X Genomics
experiment2.RDS


title: CUT and Tag for H3K9me3 in iPSCs, Replicate 1

description: Library name: H3K9me3 R1


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shRen rep2

description:
Library name: H3K27me3_shRen_rep2
combine_all_H3K27me3_shRen.bw


title: Exp2, Splenic B cells, Day28, scRNAseq, mRNA

description:
Library name: Experiment2_Day28_GEX
10X Genomics
experiment2.RDS


title: Exp2, Splenic B cells, Day21, scRNAseq, HTO

description:
Library name: Experiment2_Day21_HTO
10X Genomics
experiment2.RDS


title: EMPD11

description:
Library name: SAMPLE 11
EMPD with recurrence


title: H3K27me3 CUT&Tag Seq of mouse HSPCs with shRen rep1

description:
Library name: H3K27me3_shRen_rep1
combine_all_H3K27me3_shRen.bw


title: Exp2, Splenic B cells, Day14, scRNAseq, HTO

description:
Library name: Experiment2_Day14_HTO
10X Genomics
experiment2.RDS


title: EMPD10

description:
Library name: SAMPLE 10
EMPD with recurrence


title: CUT and Tag for H3K27ac in iPSCs, Replicate 1

description: Library name: H3K27ac R1


title: MPD18

description:
Library name: SAMPLE 29
MPD without recurrence


title: CUT and Tag for H3K27ac in iPSCs, Replicate 2

description: Library name: H3K27ac R2


title: Exp2, Splenic B cells, Day14, scRNAseq, BCR

description:
Library name: Experiment2_Day14_VDJ
10X Genomics
Experiment_2_bcr_processed_data.tsv
experiment2.RDS


title: mouse HSPCs with shAbcb8 rep2, treated with FAS, batch4

description:
Library name: 4_RNAseq_shAbcb8_FAS_rep2
batch4_RNASeq_raw_counts.csv

data_processing:
For RNA-Seq, after removing the adapters, ploy-N, and low-quality reads, clean data were aligned against the reference mouse genome (mm10) using STAR_2.7.10b. Following this, raw counts were normalized and significance scores as well as log2-fold change values were calculated using the DESeq2 (v1.26.0).
Assembly: mm10
Supplementary files format and content: csv files include raw counts and DESeq2 normalized data of RNAseq.

growth_protocol: For Utx KO/WT samples, WBM cells were freshly isolated from Utxf/f and Utxf/f; Mx1-Cre mice, and then HSPCs were sorted with mouse CD117 magnetic microbeads. Primary mouse cells were cultured in BCM medium (50% IMDM+50% DMEM+10% FBS+5% PS+0.34% BME) with 10% Stem Cell Medium (SCM) including 10% FBS, IL3 (10ng/mL; 1:1000), IL6 (10ng/mL; 1:500), and SCF (50ng/mL; 1:1000). For other RNA-Seq samples, mouse cKit+ HSPCs and AML cells were cultured at 37 °C with 7.5% CO2 in BCM medium [45% IMDM + 45% DMEM + 10% FBS + 50 × 10-6 M β-mercaptoethanol + penicillin (100 U mL-1)/streptomycin (0.1 mg mL-1)] supplemented with 10% stem cell medium (SCM) including mIL-3 (10 ng mL-1, Cat# 403-ML; R&D Systems), mIL-6 (10 ng mL-1, Cat# 406-ML; R&D Systems), and mSCF (50 ng mL-1, Cat# 455-MC; R&D Systems)

extract_protocol:
RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kits (NEB, E7770) according to the manufacturer's protocol.
RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kits (NEB, E7770) according to the manufacturer's protocol.

value: FAS


title: CUT and Tag for MPP8 in iPSCs, Replicate 2

description: Library name: MPP8 R2


title: EMPD8

description:
Library name: SAMPLE 8
EMPD without recurrence


title: CUT and Tag for MPP8 in iPSCs, Replicate 1

description: Library name: MPP8 R1


title: Exp2, Splenic B cells, Day10, scRNAseq, HTO

description:
Library name: Experiment2_Day10_HTO
10X Genomics
experiment2.RDS


title: EMPD7

description:
Library name: SAMPLE 7
EMPD without recurrence


title: mouse HSPCs with shAbcb8 rep3, treated with FAS, batch4

description:
Library name: 4_RNAseq_shAbcb8_FAS_rep3
batch4_RNASeq_raw_counts.csv


title: EMPD9

description:
Library name: SAMPLE 9
EMPD without recurrence


title: mouse HSPCs with shAbcb8 rep3, treated with vehicle, batch4

description:
Library name: 4_RNAseq_shAbcb8_Veh_rep3
batch4_RNASeq_raw_counts.csv


title: iPSCs treated with shControl, Replicate 4

description: Library name: shCtrl R4

data_processing:
read were de-multiplexed by Novogene UK Co., Ltd. (Cambridge).
Assembly: hg38
Supplementary files format and content: count tables in tsv format.

source_name: iPSC

extract_protocol:
RNeasy mini kit
Samples were processed using a 150bp paired-end ribosomal-RNA depleted total RNA-seq pipeline by Novogene UK Co., Ltd. (Cambridge).

treatment_protocol: cells were transduced with lentiviral vectors on day 0, selected for 24h with puromycin on day 1 before harvesting on day 4

value: sh Control


title: Exp2, Splenic B cells, Day10, scRNAseq, BCR

description:
Library name: Experiment2_Day10_VDJ
10X Genomics
Experiment_2_bcr_processed_data.tsv
experiment2.RDS


title: mouse HSPCs with shAbcb8 rep2, treated with vehicle, batch4

description:
Library name: 4_RNAseq_shAbcb8_Veh_rep2
batch4_RNASeq_raw_counts.csv


title: Exp2, Splenic B cells, Day14, scRNAseq, mRNA

description:
Library name: Experiment2_Day14_GEX
10X Genomics
experiment2.RDS


title: iPSCs treated with shControl, Replicate 2

description: Library name: shCtrl R2


title: EMPD6

description:
Library name: SAMPLE 6
EMPD with recurrence


title: Exp2, Splenic B cells, Day10, scRNAseq, mRNA

description:
Library name: Experiment2_Day10_GEX
10X Genomics
experiment2.RDS


title: EMPD5

description:
Library name: SAMPLE 5
EMPD without recurrence


title: EMPD4

description:
Library name: SAMPLE 4
EMPD without recurrence


title: iPSCs treated with shControl, Replicate 3

description: Library name: shCtrl R3


title: mouse HSPCs with shAbcb8 rep1, treated with vehicle, batch4

description:
Library name: 4_RNAseq_shAbcb8_Veh_rep1
batch4_RNASeq_raw_counts.csv


title: Exp1, Splenic B cells, Day14, scRNAseq, HTO

description:
Library name: Experiment1_Day14_HTO
10X Genomics
experiment1.RDS

value: Plasmodium infection


title: mouse HSPCs with shAbcb8 rep1, treated with FAS, batch4

description:
Library name: 4_RNAseq_shAbcb8_FAS_rep1
batch4_RNASeq_raw_counts.csv


title: EMPD3

description:
Library name: SAMPLE 3
EMPD with recurrence


title: iPSCs treated with shMPP8, Replicate 3

description: Library name: shMPP8 R3

value: sh MPP8


title: iPSCs treated with shMPP8, Replicate 2

description: Library name: shMPP8 R2


title: mouse HSPCs with shRen rep2, treated with FAS, batch4

description:
Library name: 4_RNAseq_shRen_FAS_rep2
batch4_RNASeq_raw_counts.csv


title: iPSCs treated with shMPP8, Replicate 4

description: Library name: shMPP8 R4


title: EMPD2

description:
Library name: SAMPLE 2
EMPD without recurrence


title: Exp1, Splenic B cells, Day14, scRNAseq, BCR

description:
Library name: Experiment1_Day14_VDJ
10X Genomics
Experiment_1_bcr_processed_data.tsv
experiment1.RDS


title: mouse HSPCs with shRen rep1, treated with FAS, batch4

description:
Library name: 4_RNAseq_shRen_FAS_rep1
batch4_RNASeq_raw_counts.csv


title: Exp1, Splenic B cells, Day14, scRNAseq, mRNA

description:
Library name: Experiment1_Day14_GEX
10X Genomics
experiment1.RDS


title: VAT11

description:
Library name: VAT11
10x Genomics

data_processing:
Sequence reads were aligned to the GRCh38 human genome reference with Gencode v42 gene annotations using STAR v2.7.10a, with parameter ‘--soloFeatures Gene GeneFull SJ Velocyto’.
Following alignment, we removed empty droplets and contaminated reads with DIEM v2.4.1 and DecontX (celda v1.16.1).
Heterotypic doublets were removed using DoubletFinder v2.0.3.
Assembly: GRCh38
Supplementary files format and content: Gene counts are found in matrix market file format.
Supplementary files format and content: Barcodes, gene names, and meta data are in tab-separated value formats.

source_name: visceral adipose tissue

extract_protocol:
Frozen visceral adipose tissue biopsies were minced over dry ice and incubated in 3mL ice cold lysis buffer. Lysis buffer consisted of 10mM Tris-HCl, 10nM NaCl, 3mM MgCl2, 0.1% of IGEPAL, and 0.2 U/μL of RNase inhibitor (Sigma #3335402001). Following a 15 minute incubation period, lysate was filtered through MACS 30μm strainer (Miltenyi Biotec #130-110-915) and centrifuged at 500 x g for 5 minutes at 4°C. The pellet was then re-suspended with 1mL wash buffer. Wash buffer consisted of 2.0% BSA, 1X PBS, and 0.2 U/μL of RNase inhibitor (Sigma #3335402001). Lysate was filtered through another MACS 30μm strainer (Miltenyi Biotec #130-110-915) and centrifuged at 500 x g for 5 minutes at 4°C. Pellet was then re-suspended in 70 uL wash buffer for library construction.
Libraries were prepared using the 10x Chromium Single Cell 3' Reagent kit v3.1.

value: visceral adipose tissue

value: Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA)


title: EMPD1

description:
Library name: SAMPLE 1
EMPD without recurrence

value: male


title: mouse HSPCs with shRen rep2, treated with vehicle, batch4

description:
Library name: 4_RNAseq_shRen_Veh_rep2
batch4_RNASeq_raw_counts.csv

value: HSPC


title: VAT10

description:
Library name: VAT10
10x Genomics


title: mouse HSPCs with shRen rep1, treated with vehicle, batch4

description:
Library name: 4_RNAseq_shRen_Veh_rep1
batch4_RNASeq_raw_counts.csv


title: mouse HSPCs with shRen rep3, treated with vehicle, batch4

description:
Library name: 4_RNAseq_shRen_Veh_rep3
batch4_RNASeq_raw_counts.csv


title: OVCAR5 Pt-R OA n3

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

description: Library name: AMI-6

data_processing:
Fastq files were pre-analyzed using FastQC (0.11.5)
Reads were aligned to the ENSEMBL human genome GRCh38 (release 91) using STAR (2.5.2)
BAM files from STAR alignment were sorted by name using Samtools (1.6)
HTSeq-count (anaconda 3.6) was used to generate raw counts for each BAM file
Assembly: GRCh38
Supplementary files format and content: counts

source_name: cell line

growth_protocol: OVCAR5 Pt-S and Pt-R cells were cultured in RPMI 1640 (Corning), 10% fetal bovine serum (FBS) (Corning), 1% penicillin/streptomycin (Sigma), and 1X GlutaMAX (Gibco). The cell lines were grown in a humidified atmosphere, 5% CO2, and 37°C.

extract_protocol:
The RNA was extracted using the QIAGEN RNeasy Mini Kit according to manufacturer's instructions. The RNA was quantified using a NanoDrop 3300 Fluorospectrometer.
The RNA-sequencing (RNA-seq) libraries were prepared from 1 μg of total RNA of OVCAR5 Pt-S/Pt-R, starvation and supplementation with 50 uM OA/PA. Libraries were generated using the NEBNext Ultra II RNA library prep kit for Illumina (#E7770S, New England Biolabs, Inc.). Library preparation was performed accoding to manufacter's protocol.

treatment_protocol: The cells were first cultured under starvation (induced by reducing the level of Fetal Bovine Serum from 10% down to 1%) for 24 h, and then supplemented with 50 uM OA or PA for further 24 h.

value: cell line

value: High grade serous ovarian cancer

value: Platinum-resistant

value: OA


title: VAT9

description:
Library name: VAT9
10x Genomics


title: OVCAR5 Pt-R OA n2

description: Library name: AMI-5


title: mouse HSPCs with shAbcb8_shKmt2c rep3, batch2

description:
Library name: 2_RNAseq_shAbcb8_shKmt2c_rep3
batch2_RNASeq_raw_counts.csv


title: Exp1, Splenic B cells, Day10, scRNAseq, HTO

description:
Library name: Experiment1_Day10_HTO
10X Genomics
experiment1.RDS

value: Spleen

value: 6-12 weeks

value: B cells


title: Exp1, Splenic B cells, Day10, scRNAseq, BCR

description:
Library name: Experiment1_Day10_VDJ
10X Genomics
Experiment_1_bcr_processed_data.tsv
experiment1.RDS

value: female


title: OVCAR5 Pt-R OA n1

description: Library name: AMI-4


title: VAT8

description:
Library name: VAT8
10x Genomics


title: OVCAR5 Pt-R control n3

description: Library name: AMI-3

value: control (starvation)


title: Exp1, Splenic B cells, Day7, scRNAseq, BCR

description:
Library name: Experiment1_Day7_VDJ
10X Genomics
Experiment_1_bcr_processed_data.tsv
experiment1.RDS


title: VAT6

description:
Library name: VAT6
10x Genomics


title: VAT7

description:
Library name: VAT7
10x Genomics


title: Exp1, Splenic B cells, Day10, scRNAseq, mRNA

description:
Library name: Experiment1_Day10_GEX
10X Genomics
experiment1.RDS


title: Exp1, Splenic B cells, Day7, scRNAseq, mRNA

description:
Library name: Experiment1_Day7_GEX
10X Genomics
experiment1.RDS


title: Exp1, Splenic B cells, Day7, scRNAseq, HTO

description:
Library name: Experiment1_Day7_HTO
10X Genomics
experiment1.RDS


title: mouse HSPCs with shAbcb8 rep3, batch2

description:
Library name: 2_RNAseq_shAbcb8_rep3
batch2_RNASeq_raw_counts.csv


title: mouse HSPCs with shAbcb8_shKmt2c rep2, batch2

description:
Library name: 2_RNAseq_shAbcb8_shKmt2c_rep2
batch2_RNASeq_raw_counts.csv

value: shAbcb8; shKmt2c


title: VAT5

description:
Library name: VAT5
10x Genomics


title: OVCAR5 Pt-R control n2

description: Library name: AMI-2


title: Exp1, Splenic B cells, Day4, scRNAseq, HTO

description:
Library name: Experiment1_Day4_HTO
10X Genomics
experiment1.RDS

value: Uninfected + Plasmodium infection


title: mouse HSPCs with shAbcb8_shKmt2c rep1, batch2

description:
Library name: 2_RNAseq_shAbcb8_shKmt2c_rep1
batch2_RNASeq_raw_counts.csv


title: mouse HSPCs with shAbcb8 rep2, batch2

description:
Library name: 2_RNAseq_shAbcb8_rep2
batch2_RNASeq_raw_counts.csv


title: OVCAR5 Pt-R control n1

description: Library name: AMI-1


title: Exp1, Splenic B cells, Day4, scRNAseq, BCR

description:
Library name: Experiment1_Day4_VDJ
10X Genomics
Experiment_1_bcr_processed_data.tsv
experiment1.RDS


title: VAT4

description:
Library name: VAT4
10x Genomics


title: mouse HSPCs with shAbcb8 rep1, batch2

description:
Library name: 2_RNAseq_shAbcb8_rep1
batch2_RNASeq_raw_counts.csv


title: VAT3

description:
Library name: VAT3
10x Genomics


title: OVCAR5 Pt-S PA n3

description: Library name: PA3

value: Platinum-sensitive

value: PA


title: mouse HSPCs with shKmt2c rep3, batch2

description:
Library name: 2_RNAseq_shKmt2c_rep3
batch2_RNASeq_raw_counts.csv


title: OVCAR5 Pt-S PA n2

description: Library name: PA2


title: mouse HSPCs with shKmt2c rep2, batch2

description:
Library name: 2_RNAseq_shKmt2c_rep2
batch2_RNASeq_raw_counts.csv


title: OVCAR5 Pt-S PA n1

description: Library name: PA1


title: GnhomieZ-WT

city: Princeton

first: Wenfan

last: Ke

state: New Jersey

address: 119 Lewis Thomas Laboratory

department: Department of Molecular Biology

institute: Princeton University

description: Library name: GnhomieZ-WT

data_processing:
MicroC data for D. melanogaster were aligned to custom genomes edited from the Berkeley Drosophila Genome Project (BDGP) Release 6 reference assembly (dos Santos et al. 2015) with BWA-MEM (Li and Durbin 2009) using parameters -S -P -5 -M.  Briefly, the custom genomes are created by inserting the transgenic sequence into the –142kb integration site, as predicted from perfect integration.  The resultant BAM files were parsed, sorted, de-duplicated, filtered, and split with Pairtools (https://github.com/mirnylab/pairtools).  We removed pairs where only half of the pair could be mapped, or where the MAPQ score was less than three.  The resultant files were indexed with Pairix (https://github.com/4dn-dcic/pairix).  The files from replicates were merged with Pairtools before generating 100bp contact matrices using Cooler (Abdennur and Mirny 2020).  Finally, balancing and Mcool file generation was performed with Cooler’s Zoomify tool.
Assembly: dm6
Supplementary files format and content: mcool files generated by cooler for visualizing 3D genome organization

organism: Drosophila melanogaster

source_name: whole embryo, st14

growth_protocol: Embryos were collected on yeasted apple juice plates in population cages for 4 hours, incubated for 12 hours at 25℃, then subjected to fixation

extract_protocol:
Embryos were dechorionated for 2 mins in 3% sodium hypochlorite, rinsed with deionized water, and transferred to glass vials containing 5 mL PBST (0.1% Triton-X100 in PBS), 7.5 mL n-heptane, and 1.5mL fresh 16% formaldehyde.  Crosslinking was carried out at room temperature for exactly 15 mins on an orbital shaker at 250rpm, followed by addition of 3.7 mL 2M Tris-HCl pH7.5 and shaking for 5 mins to quench the reaction.  Embryos were washed twice with 15 mL PBST and subjected to secondary crosslinking.  Secondary crosslinking was done in 10mL of freshly prepared 3mM final DSG and ESG in PBST for 45 mins at room temperature with passive mixing.  The reaction was quenched by addition of 3.7mL 2M Tris-HCl pH7.5 for 5 mins, washed twice with PBST, snap-frozen, and stored at -80℃ until library construction.
Details of the MicroC procedure were described previously (Ke et al. 2024).  Micro-C libraries were prepared as previously described (Batut et al. 2022) with the following modifications:  50uL of 12-16hr embryos were used for each biological `replicate.  60U of MNase were used for each reaction to digest chromatin to a mononucleosome:dinucleosome ratio of 4.  Libraries were barcoded, pooled, and subjected to paired-end sequencing on an Illumina Novaseq S1 100 nt Flowcell (read length 50 bases per mate, 6-base index read).Libraries were barcoded, pooled and subjected to paired-end sequencing on an Illumina Novaseq S1 100 nt Flowcell (read length 50 bases per mate, 8-base index read)

value: whole embryo, st14

value: GnhomieZ-WT


title: ZhomieG-deltaN

description: Library name: ZhomieG-deltaN

value: ZhomieG-deltaN


title: mouse HSPCs with shKmt2c rep1, batch2

description:
Library name: 2_RNAseq_shKmt2c_rep1
batch2_RNASeq_raw_counts.csv

value: HSPC


title: VAT1

first: Kyla

last: Gelev

address: 695 Charles E. Young Drive South

description:
Library name: VAT1
10x Genomics

value: visceral adipose tissue

value: Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA)


title: FCDI_2

description:
Library name: Sample4
10x Genomics Spatial transcriptome sequencing

data_processing:
Space Ranger(2.1.1)  was used to decode spatial barcodes, align the reads to the human GRCh38 reference genome, and generate a gene expression count matrix annotated with spatial coordinates.
Assembly: GRCh38
Supplementary files format and content: processed data files
Library strategy: Spatial Transcriptomics

extract_protocol:
Tissue sections were first quality-checked, and only those meeting the criteria proceeded to further processing. OCT-embedded tissue blocks were cryosectioned at a thickness of 10 μm using a Leica CM1950 cryostat under controlled conditions (-20°C). Sections were fixed with methanol and subjected to hematoxylin and eosin (H&E) staining to visualize tissue architecture, allowing selection of optimal sections. Tissue permeabilization was optimized using the 10x Genomics Visium Spatial Tissue Optimization slides and reagent kits. High-resolution imaging was performed using a Nikon ECLIPSE Ti fluorescence microscope to determine the optimal permeabilization time for tissue sections.
Tissue sections were placed within the capture area of the spatial gene expression slide. After H&E staining, tissue morphology was examined under a brightfield microscope, followed by permeabilization to release cellular mRNA. The mRNA or probes hybridized with oligonucleotides containing spatial barcodes on the spots. Reverse transcription was performed within the capture area to generate barcoded cDNA, which was subsequently amplified. The cDNA was fragmented to an appropriate size (200–300 bp) using the 10x Genomics reagent kit. High-quality libraries were obtained through PCR amplification and assessed using an Agilent 2100 Bioanalyzer. The final libraries were sequenced on the Illumina NovaSeq 6000 platform for high-throughput analysis.

value: temporal neocortex,epileptogenic

value: brain tissue cells


title: ZhomieG-WT

description: Library name: ZhomieG-WT

value: ZhomieG-WT


city: Guangzhou

first: Shen

last: Weishan

state: Guangdong

address: 58 Zhongshan 2nd Road

department: cirtical care medicine

institute: The First Affiliated Hospital, Sun Yat-sen University (FAH-SYSU)

description:
Library name: DMSO_uninfected_3
Uninfected BV2 cells treated with DMSO, rep3.

data_processing:
All clean data were mapped to the mouse genome mm10 using HISAT2 v2.1.0 with default parameters and BAM files were sorted by Samtools 1.9. Reads counts were summarized using the feature Counts program as part of the Subread package release 2.0.0 (http://subread.sourceforge.net/) .
Assembly: mm10
Supplementary files format and content: BV2_HSV1_BulkRNAseq.xlsx

extract_protocol:
Total RNA was extracted from BV2 cells using TRIzol reagent
sequencing was conducted by Annoroad Gene Technology Corporation (Beijing). Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed. NA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlus™ Real-Time PCR System (Library valid concentration＞10 nM). The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions.

value: wild-type

value: Uninfected treated with DMSO


title: mouse HSPCs with shRen rep3, batch2

description:
Library name: 2_RNAseq_shRen_rep3
batch2_RNASeq_raw_counts.csv

value: shRen


title: OVCAR5 Pt-S OA n3

description: Library name: OA3

value: cell line

value: High grade serous ovarian cancer

value: OA


title: OVCAR5 Pt-S OA n1

description: Library name: OA1

value: Platinum-sensitive


title: OVCAR5 Pt-S OA n2

description: Library name: OA2


title: mouse HSPCs with shRen rep2, batch2

description:
Library name: 2_RNAseq_shRen_rep2
batch2_RNASeq_raw_counts.csv


title: FCDI_1

description:
Library name: Sample3
10x Genomics Spatial transcriptome sequencing


title: Exp1, Splenic B cells, Day4, scRNAseq, mRNA

description:
Library name: Experiment1_Day4_GEX
10X Genomics
experiment1.RDS

value: Spleen

value: 6-12 weeks

value: B cells

value: Uninfected + Plasmodium infection

value: female


title: GnhomieZ-delN

description: Library name: GnhomieZ-delN

value: whole embryo, st14

value: GnhomieZ-delN


title: mouse HSPCs with shRen rep1, batch2

description:
Library name: 2_RNAseq_shRen_rep1
batch2_RNASeq_raw_counts.csv

value: HSPC


title: VAT2

institute: University of California, Los Angeles

description:
Library name: VAT2
10x Genomics

value: visceral adipose tissue

value: Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA)


title: mouse HSPCs with shAbcb8_1022 rep3, batch1

description:
Library name: 1_RNAseq_shA1022_rep3
batch1_RNASeq_raw_counts.csv


title: OVCAR5 Pt-S control n3

description: Library name: C3

value: control (starvation)


title: Control_3

description:
Library name: Sample2
10x Genomics Spatial transcriptome sequencing

value: temporal neocortex,nonepileptic

value: brain tissue cells


title: iMGL derived from minor allele hiPSC treated with vehicle (replicate3)

city: Daegu

first: Jichang

last: Yu

address: 333, Techno jungang-daero

department: Department of Brain Sciences

country: South Korea

institute: DGIST

description: Library name: MinorControl3

data_processing:
Raw FASTQ files were quality checked using FastQC. Reads were aligned to the GRCh38.99 human reference genome using HISAT2. Aligned reads were quantified at the gene level using featureCounts. Differential expression analysis was performed using DESeq2 in R. Genes with adjusted p < 0.05 were considered significantly differentially expressed.
Assembly: GRCh38.99 (Ensembl release 99)
Supplementary files format and content: Processed data file is a tab-delimited text file containing FPKM values for each gene across all samples. Rows represent genes and columns represent individual samples.

source_name: brain

extract_protocol:
Cells were lysed using QIAzol Lysis Reagent (QIAGEN) for the extraction of RNA. The lysates were separated into an aqueous phase containing RNAs using chloroform (Daejung) and centrifuged at 12,000 rpm for 15 mins at 4°C in RNase-free condition. The RNA pellets were washed with RNase-free 75% ethanol, air-dried, and suspended in RNase-free water.
Total RNA concentration was measured using Quant-IT RiboGreen (Invitrogen, #R11490), and RNA integrity was assessed using Agilent TapeStation RNA ScreenTape (#5067-5576). Only samples with RIN > 7.0 were used. Libraries were constructed using 1 µg of total RNA per sample with the Illumina TruSeq Stranded mRNA Library Prep Kit (#20020595). Poly-A containing mRNA was purified using poly-T magnetic beads, fragmented, and reverse-transcribed using SuperScript II reverse transcriptase (Invitrogen, #18064014). Second-strand cDNA synthesis was carried out using DNA Polymerase I, RNase H, and dUTP. The cDNA fragments were end-repaired, A-tailed, adapter-ligated, and PCR-amplified. Libraries were quantified using the KAPA Library Quantification Kit.

value: brain

value: hiPSC

value: Microglia


description:
Library name: DMSO_uninfected_2
Uninfected BV2 cells treated with DMSO, rep2.

value: wild-type

value: Uninfected treated with DMSO


title: OVCAR5 Pt-S control n2

description: Library name: C2

value: cell line

value: High grade serous ovarian cancer

value: Platinum-sensitive


description:
Library name: DMSO_HSV_3
BV2 cells infected with HSV-1 (MOI=1)  for 24 hours and treated with DMSO, rep3


description:
Library name: DMSO_uninfected_1
Uninfected BV2 cells treated with DMSO, rep1.


title: OVCAR5 Pt-S control n1

description: Library name: C1


title: mouse HSPCs with shAbcb8_1022 rep2, batch1

description:
Library name: 1_RNAseq_shA1022_rep2
batch1_RNASeq_raw_counts.csv


title: iMGL derived from minor allele hiPSC treated with vehicle (replicate2)

description: Library name: MinorControl2


title: Control_2

description:
Library name: Sample1
10x Genomics Spatial transcriptome sequencing


title: mouse HSPCs with shAbcb8_322 rep2, batch1

description:
Library name: 1_RNAseq_shA322_rep2
batch1_RNASeq_raw_counts.csv


title: mouse HSPCs with shAbcb8_1022 rep1, batch1

description:
Library name: 1_RNAseq_shA1022_rep1
batch1_RNASeq_raw_counts.csv


title: mouse HSPCs with shAbcb8_322 rep3, batch1

description:
Library name: 1_RNAseq_shA322_rep3
batch1_RNASeq_raw_counts.csv


description:
Library name: DMSO_HSV_1
BV2 cells infected with HSV-1 (MOI=1)  for 24 hours and treated with DMSO, rep1


description:
Library name: CFZ_uninfected_3
Uninfected BV2 cells treated with 30 nM CFZ, rep3

value: Uninfected treated with 30 nM CFZ


title: Human Coronary Smooth Muscle Cells, H3K27ac ChIP-Seq input

city: Singapore

first: Roger

last: Foo

address: 14 Medical Drive, MD6

country: Singapore

institute: National University of Singapore

description: Library name: HCASMC H3K27ac ChIP-Seq input

data_processing:
Paired-end sequencing reads were aligned to human genome (hg38) using BWA mem version 0.7.5
Reads were deduplicated using Picard MarkDuplicates function and aligned mapped reads in BAM file were used as input for peak-calling using Dfilter to identify significant H3K27ac peaks using the following setting: -ks=60, -bs=100, -Ipvalue=8.
Bigwig tracks were normalized for sequencing depths and the sum of normalized binned tag-count represents the peak height
Assembly: hg38
Supplementary files format and content: Peak call files for respective samples (Except inputs)
Supplementary files format and content: bigwig tracks for samples (Except inputs)

source_name: HCASMC

growth_protocol: human healthy coronary artery smooth muscle cells (HCASMC) (Thermo Scientific, Product code C-017-5C, Lot. 1689414) are cultured in human vascular smooth muscle (VSMC) basal medium (Gibco, M231500), in Smooth Muscle Growth Supplement (SMGS) (Gibco, S00725) and 1% penicillin/streptomycin. human healthy coronary artery endothelial cells (HCAEC) (ATCC, Product code PCS-100-020, Lot 62382179) are cultured in Endothelial Cell Growth medium MV2 (PromoCell, C-22022).

extract_protocol:
Cells were crosslinked with 1% Formaldehyde for 10 min at room temperature and quenched with glycine (125mM) for 5 min. The cells were rinsed twice with cold 1XPBS and sonicated in nuclei lysis buffer.
Library preparation was performed on the eluted ChIP DNA using the NEB Ultra II library preparation kit, according to the manufacturer’s protocol. 10 PCR cycles were performed using indexed primers and the library of DNA fragments with sizes between 300 to 500 bp was selected using the Omega MagBind NGS cleanup Magnetic beads (Omega M1378). The libraries were sent for paired end sequencing with at least 50 million read pairs at 2 x 151 bp read length on the illumina HiSeq 4000 platform.

value: Heart

value: Smooth Muscle Cells

value: anti-H3K27ac (Abcam, ab4729)


title: iMGL derived from major allele hiPSC treated with vehicle (replicate3)

description: Library name: MajorContorl3


title: Human Coronary Endothelial Cells, H3K27ac ChIP-Seq input

description: Library name: HCAEC H3K27ac ChIP-Seq input

source_name: HCAEC

value: Endothelial


title: Human Coronary Endothelial Cells, H3K27ac ChIP-Seq Rep 1

description: Library name: HCAEC H3K27ac ChIP-Seq Replicate 1


title: iMGL derived from major allele hiPSC treated with vehicle (replicate2)

description: Library name: MajorControl2


title: mouse HSPCs with shAbcb8_322 rep1, batch1

description:
Library name: 1_RNAseq_shA322_rep1
batch1_RNASeq_raw_counts.csv

value: HSPC


description:
Library name: DMSO_HSV_2
BV2 cells infected with HSV-1 (MOI=1)  for 24 hours and treated with DMSO, rep2


title: Human Coronary Smooth Muscle Cells, H3K27ac ChIP-Seq Rep 2

description: Library name: HCASMC H3K27ac ChIP-Seq Replicate 2