title: MEF_untreated_rep2

description:
Library name: MEF_untreated_rep2
peaks called with macs2 on filtered bam files (see methods)

tag: cell type


title: caSTAT3, day15 (caS3_day15)

status: Public on Feb 19 2026

type: SRA

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

description: Library name: caS3_day15

library_source: transcriptomic

data_processing:
Illumina NovaSeq 6000 was used for base calling.
Sequenced reads were trimmed with low-quality bases using fastp. Read lengths less than 15 nucleotides or a PHRED Quality Score of less than 15 were removed.
The trimmed reads were mapped to the GRCh38 human reference genome using HISAT2 (version 2.2.1).
Read counts for each gene were calculated using featureCounts of the Subread package (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: Calculated raw read counts for individual genes are shown in a tab-delimited text file.

molecule: total RNA

organism: Homo sapiens

source_name: CD8+ T cells

growth_protocol: Human T cells were stimulated on day 0 with K562 cells engineered to express an anti-CD3 monoclonal antibody (clone OKT3)-derived scFv fused to the transmembrane and cytoplasmic domains of CD8α, along with CD80 (K562-OKT3/CD80). On day 2, the stimulated T cells were retrovirally transduced with an anti-mesothelin CAR construct (ss1-28z) alone, or in combination with either constitutively active STAT3 (caSTAT3) or STAT5 (caSTAT5). The CAR-T cells were then expanded in vitro in RPMI medium supplemented with 10% FBS and 100 IU/mL recombinant human IL-2.

extract_protocol:
CD8+ CAR-T cell populaiton was isolated by an MA900 Cell Sorter (Sony). Total RNA was isolated from the purified CD8+ T cells using the Nucleospin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the SMART-Seq mRNA HT LP RNA-seq Library Prep Kit for Illumina according to standard Illumina protocols.

treatment_protocol: Control, caSTAT3, or caSTAT5-expressing CAR-T cells were intravenously infused into NSG mice inoculated with AsPC-1 cells on day 5. Tumor-infiltrating CAR-T cells were harvested between days 17 and 20.

value: CD8+ T cells

tag: treatment

value: CAR and caSTAT3

tag: batch


title: input, sham, aCSF1R 1

city: St Louis

first: Fang

middle: R

last: Zhao

state: MO

country: USA

institute: Washington University in St Louis

description: Library name: sample.1_I

library_source: other

data_processing:
Sequencing data was demultiplexed using Illumina’s DRAGEN and BCLconvert version 4.2.4 software. Reads were then aligned and mapped to the Ensembl release 101 primary assembly with STAR version 2.7.9a. A count matrix containing all expression data was then generated from the number of uniquely aligned unambiguous read using Subread:featureCount version 2.0.3  and isoform expression of known Ensembl transcripts quantified with Salmon version 1.5.2. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
Assembly: Ensembl release 101 primary assembly with STAR version 2.7.9a
Supplementary files format and content: Excel table read counts

molecule: other

organism: Mus musculus

source_name: distal part of small intestine

extract_protocol:
Samples were homogenized using homogenization buffer (50 mM Tris, pH 8.0; 100 mM KCl; 12 mM MgCl2; 1 % Igepal; 1 mg/mL sodium heparin; 100 µg/mL cycloheximide; 0.2 U/µL SUPERaseIn RNase Inhibitor, 2 mM DTT). After centrifugation (10,000 x g; 10 min; 4oC) 25 µg of primary antibody against GFP (rabbit; # AB290; Abcam) was added, and samples were rotated for 1 h at 4 oC. Subsequently, 200 µl of DynabeadsTM Protein G (# 10004D; Invitrogen) were added, and samples were incubated rotating overnight at 4 C. The beads were washed four times with high-salt buffer (50 mM Tris, pH 8.0; 300 mM KCl; 12 mM MgCl2; 1 % Igepal; 100 µg/mL cycloheximide). RNA was extracted and purified with Arcturus PicoPure RNA Isolation Kit (ThermoFisher: Kit0204 - Applied biosystems; 12204-01) according to the manufacturer’s instructions. To prevent contamination with DNA, RNase-Free DNase Set (Qiagen; # 29254) was used according to the manufacturer's instructions.
Library preparation was performed with 1-50 ng of total RNA.  cDNA was prepared using the SeqPlex RNA Amplification Kit (Sigma) per manufacturer's protocol and then fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, an A base was added to the 3' ends, and then Illumina sequencing adapters were ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

tag: tissue

value: distal part of small intestine

tag: genotype

value: Plp1CreERT2 - B6.Cg-Tg(Plp1-cre/ERT)3Pop/J; NuTRAP - B6;129S6-Gt(ROSA)26Sortm2(CAG-NuTRAP)Evdr/J

value: sham


title: MEF_untreated_rep1

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

description:
Library name: MEF_untreated_rep1
peaks called with macs2 on filtered bam files (see methods)

library_source: genomic

data_processing:
Raw reads were processed with bcl2fastq (v 2.19.1), adapters were trimmed with cutadapt (v 2.2.0), reads were mapped to mm10 using bowtie2 (v 2.2.5) (-X 1500 –no-mixed –no-discordant).
chrM and duplicate reads were removed, quality filtering was performed with samtools (v 1.4.1) (-b -f3 -F4 -F8 -q7) and reads in blacklisted regions from (Buenrostro et al, 2013) and (Encode Project Consortium, 2012) were removed.
Peaks were called using macs2 (v 2.2.0) (-f BAMPE, -q 0.001), consensus peaks per condition were defined as peaks present in all 3 biological replicates, these peaks were combined and reads within defined peaks were counted using bedtools, v 2.26.0, coverage  to generate a count table for downstream analysis in R.
References: Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., and Greenleaf, W.J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Meth 10, 1213.; ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74.
Assembly: mm10
Supplementary files format and content: For nascent/ replicated repli-ATAC-seq and matched unreplicated ATAC-seq libraries, processed files contain the mm10 coordinates for loci called as peaks from each condition's merged replicates.

molecule: genomic DNA

source_name: Fibroblasts

growth_protocol: Reprogramming MEFs Mouse embryonic fibroblasts (MEFs) were cultured in MEF media: DMEM (Gibco, 31966021) supplemented with 10% heat-inactivated FCS (GE Hyclone, SV30160.03), 1X Glutamax (Gibco, 35050061), 1X non-essential amino acids (Gibco, 11140050), 55 µM beta-mercaptoethanol (Gibco, 21985023), and 1X penicillin-streptomycin (Gibco, 15140122) and incubated at 37 °C with 5% oxygen.  ESCs to EpiLCs ESC were cultured on 0.1% gelatin in serum free media containing N2B27 (Neurobasal medium and DMEM:F12 (Gibco) supplemented with N2 (made in house), B27 (Gibco),  L-glutamine and 100 μM 2-mercaptoethanol (Sigma)) supplemented with 3 μM Gsk3i (Chir99021: Axon Medchem) and 1μM MEKi (PD0325901: Sigma) and LIF. 24hrs prior to EpiLC induction, MEKi was exchanged with FGFR inhibitor (PD173074 from Sigma-Aldrich) at 250 nM.

extract_protocol:
After the appropriate treatment, cells were trypsinized and collected in media. Samples were then processed and tagmented using TD buffer and TDE1 enzyme (Illumina).
EdU-positive samples were biotinylated via Click-IT (Invitrogen) and purified with Ampure XP beads (Beckman Coulter). Biotinylated products were captured using MyOne Streptavidin T1 beads (Thermo Fisher Scientific), and the unbound fraction (unreplicated/ bulk) in the supernatant from streptavidin pulldown was purified using the MinElute Reaction Cleanup kit (Qiagen). Samples were amplified using NEBNext High-Fidelity 2x PCR Master Mix (NEB) and final libraries were purified using Ampure XP beads.

treatment_protocol: Reprogramming MEFs Reprogramming was induced by seeding 6 x 106 MEFs on 10 cm plates coated with 0.2% gelatin (Sigma, G9391) and culturing in reprogramming media: KnockOut DMEM (Gibco, 10829018) supplemented with 15% heat-inactivated FCS (GE Hyclone, SV30160.03), 1X Glutamax (Gibco, 35050061), 1X non-essential amino acids (Gibco, 11140050), 55 µM beta-mercaptoethanol (Gibco, 21985023), 1X penicillin-streptomycin (Gibco, 15140122), custom-made LIF, 2 µg/mL doxycycline (Sigma, D9891), and 50 µg/mL L-ascorbic acid (Sigma, A4544) incubated at 37 °C with atmospheric oxygen levels. To prevent DNA replication, MEFs were cultured and induced to reprogram as above. 4 hours after reprogramming induction,  aphidicolin (5 µg/mL, Sigma, A0781) was added and both treated and untreated controls were cultured for a further 10 hours before being harvested for ATAC-seq generation.  ESCs to EpiLCs For EpiLC induction 10.000cells/cm2 were plated on fibronectin in N2B27 supplemented with FGF2 (10ng/mL) and Activin A (20ng/mL) both from Peprotech.  EdU Labelling EdU-positive samples were incubated in media containing EdU (20 uM final concentration) for 10 minutes, then either collected for processing (nascent samples) or cultured for 1 hour 50 minutes (total time since label: 2 hours) in media containing 10 uM thymidine before processing.  CellViolet Staining For ATAC-seq in proliferative subpopulations, 5 x 106 MEFs cultured in hypoxic conditions as described above were washed once in 1X PBS, resuspended in 5 mL 1X PBS containing 1X CellTrace Violet dye (Thermo Fisher, C34557), and incubated at 37 °C with atmospheric oxygen levels for 20 minutes in the dark. Labelling was stopped by addition of 10 mL MEF media and further incubation at 37 °C with atmospheric oxygen levels for 5 minutes in the dark. Labelled cells were then divided evenly between two 10 cm plates, one coated as above containing reprogramming media and one uncoated and containing MEF media (uninduced control). Both dishes were incubated at 37 °C with atmospheric oxygen levels for 60 hours before harvesting.

value: Fibroblasts

tag: cell line

value: OKSM reprogramming intermediates from MEFs

value: Col1a1::tetOP-OKSM het; R26-M2rtTA het; Oct4GFP het

tag: timepoint

tag: passages


title: MEF_aphidicolin_rep3

description:
Library name: MEF_aphidicolin_rep3
peaks called with macs2 on filtered bam files (see methods)


title: MEF_aphidicolin_rep2

description:
Library name: MEF_aphidicolin_rep2
peaks called with macs2 on filtered bam files (see methods)


title: caSTAT3, day12 (caS3_day12)

description: Library name: caS3_day12


title: caSTAT5, day12 (caS5_day12)

description: Library name: caS5_day12

value: CAR and caSTAT5


title: enriched, WNV 6dpi, isotype control 16

description: Library name: sample.16

value: WNV


title: MEF_aphidicolin_rep1

description:
Library name: MEF_aphidicolin_rep1
peaks called with macs2 on filtered bam files (see methods)


title: caSTAT3, day13 (caS3_day13)

description: Library name: caS3_day13


title: MEF_36h_mature_bulk_ATAC_rep3

description:
Library name: MEF_36h_mature_bulk_ATAC_rep3
36mB_IPSC.bed

data_processing:
Raw reads were processed with bcl2fastq (v 2.19.1), adapters were trimmed with cutadapt (v 2.2.0), reads were mapped to mm10 using bowtie2 (v 2.2.5) (-X 1500 –no-mixed –no-discordant).
chrM and duplicate reads were removed, quality filtering was performed with samtools (v 1.4.1) (-b -f3 -F4 -F8 -q7) and reads in blacklisted regions from (Buenrostro et al, 2013) and (Encode Project Consortium, 2012) were removed.
Peaks were called using macs2 (v 2.2.0) (-f BAMPE, -q 0.001), consensus peaks per condition were defined as peaks present in all 3 biological replicates, these peaks were combined and reads within defined peaks were counted using bedtools, v 2.26.0, coverage  to generate a count table for downstream analysis in R.
References: Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., and Greenleaf, W.J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Meth 10, 1213.; ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74.
Assembly: mm10
Supplementary files format and content: For CellViolet-sorted ATAC-seq libraries, processed files contain the mm10 coordinates for loci from each condition's consensus peak set which were called as peaks in all three biological replicates.
Supplementary files format and content: For nascent/ replicated repli-ATAC-seq and matched unreplicated ATAC-seq libraries, processed files contain the mm10 coordinates for loci called as peaks from each condition's merged replicates.

treatment_protocol: Reprogramming MEFs Reprogramming was induced by seeding 6 x 106 MEFs on 10 cm plates coated with 0.2% gelatin (Sigma, G9391) and culturing in reprogramming media: KnockOut DMEM (Gibco, 10829018) supplemented with 15% heat-inactivated FCS (GE Hyclone, SV30160.03), 1X Glutamax (Gibco, 35050061), 1X non-essential amino acids (Gibco, 11140050), 55 µM beta-mercaptoethanol (Gibco, 21985023), 1X penicillin-streptomycin (Gibco, 15140122), custom-made LIF, 2 µg/mL doxycycline (Sigma, D9891), and 50 µg/mL L-ascorbic acid (Sigma, A4544) incubated at 37 °C with atmospheric oxygen levels.  ESCs to EpiLCs For EpiLC induction 10.000cells/cm2 were plated on fibronectin in N2B27 supplemented with FGF2 (10ng/mL) and Activin A (20ng/mL) both from Peprotech.  EdU Labelling EdU-positive samples were incubated in media containing EdU (20 uM final concentration) for 10 minutes, then either collected for processing (nascent samples) or cultured for 1 hour 50 minutes (total time since label: 2 hours) in media containing 10 uM thymidine before processing.  CellViolet Staining For ATAC-seq in proliferative subpopulations, 5 x 106 MEFs cultured in hypoxic conditions as described above were washed once in 1X PBS, resuspended in 5 mL 1X PBS containing 1X CellTrace Violet dye (Thermo Fisher, C34557), and incubated at 37 °C with atmospheric oxygen levels for 20 minutes in the dark. Labelling was stopped by addition of 10 mL MEF media and further incubation at 37 °C with atmospheric oxygen levels for 5 minutes in the dark. Labelled cells were then divided evenly between two 10 cm plates, one coated as above containing reprogramming media and one uncoated and containing MEF media (uninduced control). Both dishes were incubated at 37 °C with atmospheric oxygen levels for 60 hours before harvesting.


title: Control, day14 (Ct_day14)

description: Library name: Ct_day14

value: CAR


title: MEF_12h_mature_bulk_ATAC_rep3

description:
Library name: MEF_12h_mature_bulk_ATAC_rep3
12mB_IPSC.bed


title: Control, day15 (Ct_day15)

description: Library name: Ct_day15


title: enriched, WNV 6dpi, isotype control 15

description: Library name: sample.15


title: MEF_12h_mature_bulk_ATAC_rep2

description:
Library name: MEF_12h_mature_bulk_ATAC_rep2
12mB_IPSC.bed


title: MEF_36h_mature_bulk_ATAC_rep1

description:
Library name: MEF_36h_mature_bulk_ATAC_rep1
36mB_IPSC.bed


title: input, sham, aCSF1R 2

description: Library name: sample.2_I


title: enriched, WNV 6dpi, isotype control 13

description: Library name: sample.13


title: MEF_36h_mature_bulk_ATAC_rep2

description:
Library name: MEF_36h_mature_bulk_ATAC_rep2
36mB_IPSC.bed


title: Control, day13 (Ct_day13)

description: Library name: Ct_day13


title: MEF_6h_mature_bulk_ATAC_rep3

description:
Library name: MEF_6h_mature_bulk_ATAC_rep3
6mB_IPSC.bed


title: Control, day12 (Ct_day12)

description: Library name: Ct_day12


title: caSTAT5, donor2 (caS5_D4)

description: Library name: caS5_D4

data_processing:
Illumina NovaSeq 6000 was used for base calling.
Sequenced reads were trimmed with low-quality bases using fastp. Read lengths less than 15 nucleotides or a PHRED Quality Score of less than 15 were removed.
The trimmed reads were mapped to the GRCh38 human reference genome using HISAT2 (version 2.2.1).
Read counts for each gene were calculated using featureCounts of the Subread package (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: Raw read counts for each sample and gene were included in a tab-delimited text file.

growth_protocol: Human T cells were stimulated on day 0 with K562 cells engineered to express an anti-CD3 monoclonal antibody (clone OKT3)-derived scFv fused to the transmembrane and cytoplasmic domains of CD8α, along with CD80 (K562-OKT3/CD80). On day 2, the stimulated T cells were retrovirally transduced with an anti-CD19 CAR construct (FMC63-28z) alone, or in combination with either constitutively active STAT3 (caSTAT3) or STAT5 (caSTAT5). The CAR-T cells were then expanded in vitro in RPMI medium supplemented with 10% FBS and 100 IU/mL recombinant human IL-2.

extract_protocol:
CD8+ CAR-T cell populaiton was isolated by an MA900 Cell Sorter (Sony). Total RNA was then extracted from the purified CD8+ T cells using the Nucleospin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina according to standard Illumina protocols.

treatment_protocol: Control, caSTAT3-, or caSTAT5-expressing CAR-T cells were cultured overnight in cytokine-free medium on day6.

value: Donor 2


title: enriched, WNV 6dpi, isotype control 14

description: Library name: sample.14


title: MEF_12h_mature_bulk_ATAC_rep1

description:
Library name: MEF_12h_mature_bulk_ATAC_rep1
12mB_IPSC.bed


title: enriched, WNV 6dpi, aCSF1R 12

description: Library name: sample.12


title: MEF_6h_mature_bulk_ATAC_rep1

description:
Library name: MEF_6h_mature_bulk_ATAC_rep1
6mB_IPSC.bed


title: enriched, WNV 6dpi, aCSF1R 11

description: Library name: sample.11


title: caSTAT3, donor2 (caS3_D4)

description: Library name: caS3_D4


title: EpiLC_48h_bulk_ATAC_rep3

description: Library name: EpiLC_48h_bulk_ATAC_rep3

source_name: Epiblast-like stem cells

value: Epiblast-like stem cells

value: Epi-like cells

value: WT


title: EpiLC_48h_mature_repliATAC_rep3

description: Library name: EpiLC_48h_mature_repliATAC_rep3


title: caSTAT5, donor1 (caS5_D1)

description: Library name: caS5_D1

value: Donor 1


title: EpiLC_48h_nascent_repliATAC_rep3

description: Library name: EpiLC_48h_nascent_repliATAC_rep3


title: MEF_6h_mature_bulk_ATAC_rep2

description:
Library name: MEF_6h_mature_bulk_ATAC_rep2
6mB_IPSC.bed


title: ESC_9h_bulk_ATAC_rep3

description: Library name: ESC_9h_bulk_ATAC_rep3

source_name: Embryonic stem cells

value: Embryonic stem cells

value: EpiLC differentiation intermediates


title: ESC_9h_nascent_repliATAC_rep3

description: Library name: ESC_9h_nascent_repliATAC_rep3


title: ESC_0h_bulk_ATAC_rep3

description: Library name: ESC_0h_bulk_ATAC_rep3

value: ES cells


title: ESC_9h_mature_repliATAC_rep3

description: Library name: ESC_9h_mature_repliATAC_rep3


title: enriched, WNV 6dpi, aCSF1R 9

description: Library name: sample.9

value: distal part of small intestine


title: caSTAT3, donor1 (caS3_D1)

description: Library name: caS3_D1

value: CD8+ T cells

value: CAR and caSTAT3


title: enriched, WNV 6dpi, aCSF1R 10

description: Library name: sample.10

value: Plp1CreERT2 - B6.Cg-Tg(Plp1-cre/ERT)3Pop/J; NuTRAP - B6;129S6-Gt(ROSA)26Sortm2(CAG-NuTRAP)Evdr/J


title: enriched, sham, isotype control 8

description: Library name: sample.8

value: sham


title: ESC_0h_mature_repliATAC_rep3

description: Library name: ESC_0h_mature_repliATAC_rep3


title: enriched, sham, isotype control 6

description: Library name: sample.6


title: enriched, sham, isotype control 7

description: Library name: sample.7


title: EpiLC_48h_bulk_ATAC_rep2

description: Library name: EpiLC_48h_bulk_ATAC_rep2


title: EpiLC_48h_mature_repliATAC_rep2

description: Library name: EpiLC_48h_mature_repliATAC_rep2


title: EpiLC_48h_nascent_repliATAC_rep2

description: Library name: EpiLC_48h_nascent_repliATAC_rep2


title: enriched, sham, isotype control 5

description: Library name: sample.5


title: caSTAT5, donor 3 (caS5_D3)

description: Library name: caS5_D3

data_processing:
Illumina NovaSeq 6000 was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and read lengths less than 20 nucleotides and a PHRED Quality Score of less than 15 were removed using the fastp software.
The trimmed reads were mapped to the GRCh38 human reference genome using HISAT2 (version 2.1.0).
Read counts for each gene were calculated using HTSeq (version 0.11.2).
Assembly: GRCh38
Supplementary files format and content: Raw read counts for each sample and gene were included in a tab-delimited text file.

extract_protocol:
The CD8+ CAR-T cell population was isolated using a FACSAria III cell sorter (BD Biosciences). Total RNA was then extracted from the purified CD8+ T cells using the NucleoSpin RNA Kit (Macherey-Nagel), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the TruSeq Standard mRNA Library Prep kit according to standard Illumina protocols.

treatment_protocol: Control, caSTAT3-, or caSTAT5-expressing CAR-T cells were stimulated with NALM-6 cells on day 6 and subsequently expanded for three days.

value: Donor 3


title: ESC_0h_nascent_repliATAC_rep3

description: Library name: ESC_0h_nascent_repliATAC_rep3


title: caSTAT5, donor 2 (caS5_D2)

description: Library name: caS5_D2


title: ESC_9h_mature_repliATAC_rep2

description: Library name: ESC_9h_mature_repliATAC_rep2


title: enriched, sham, aCSF1R 4

description: Library name: sample.4


title: caSTAT5, donor 1 (caS5_D1)

description: Library name: caS5_D1


title: caSTAT3, donor 3 (caS3_D3)

description: Library name: caS3_D3


title: ESC_0h_bulk_ATAC_rep2

description: Library name: ESC_0h_bulk_ATAC_rep2


title: ESC_0h_mature_repliATAC_rep2

description: Library name: ESC_0h_mature_repliATAC_rep2


title: Control, donor1 (Ct_D1)

description: Library name: Ct_D1


title: EpiLC_48h_bulk_ATAC_rep1

description: Library name: EpiLC_48h_bulk_ATAC_rep1


title: enriched, sham, aCSF1R 3

description: Library name: sample.3


title: caSTAT3, donor 2 (caS3_D2)

description: Library name: caS3_D2


title: enriched, sham, aCSF1R 2

description: Library name: sample.2


title: ESC_0h_nascent_repliATAC_rep2

description: Library name: ESC_0h_nascent_repliATAC_rep2


title: Control, donor2 (Ct_D4)

description: Library name: Ct_D4


title: EpiLC_48h_mature_repliATAC_rep1

description: Library name: EpiLC_48h_mature_repliATAC_rep1


title: ESC_9h_nascent_repliATAC_rep2

description: Library name: ESC_9h_nascent_repliATAC_rep2


title: enriched, sham, aCSF1R 1

description: Library name: sample.1


title: EpiLC_48h_nascent_repliATAC_rep1

description: Library name: EpiLC_48h_nascent_repliATAC_rep1


title: caSTAT3, donor 1 (caS3_D1)

description: Library name: caS3_D1


title: ESC_9h_bulk_ATAC_rep2

description: Library name: ESC_9h_bulk_ATAC_rep2


title: ESC_9h_mature_repliATAC_rep1

description: Library name: ESC_9h_mature_repliATAC_rep1


title: input, WNV, 6 dpi, 6

description: Library name: sample.6WI


title: ESC_9h_bulk_ATAC_rep1

description: Library name: ESC_9h_bulk_ATAC_rep1


title: ESC_9h_nascent_repliATAC_rep1

description: Library name: ESC_9h_nascent_repliATAC_rep1


title: ESC_0h_mature_repliATAC_rep1

description: Library name: ESC_0h_mature_repliATAC_rep1


title: input, WNV, 6 dpi, 4

description: Library name: sample.4WI


title: Control, donor 2 (Ct_D2)

description: Library name: Ct_D2


title: Control, donor 3 (Ct_D3)

description: Library name: Ct_D3


title: ESC_0h_nascent_repliATAC_rep1

description: Library name: ESC_0h_nascent_repliATAC_rep1


title: ESC_0h_bulk_ATAC_rep1

description: Library name: ESC_0h_bulk_ATAC_rep1


title: input, WNV, 6 dpi, 1

description: Library name: sample.1WI


title: MEF_60h_Q2_ATAC_rep3

description: Library name: MEF_60h_Q2_ATAC_rep3

value: Fibroblasts

value: OKSM reprogramming intermediates from MEFs

value: Col1a1::tetOP-OKSM het; R26-M2rtTA het; Oct4GFP het


title: MEF_60h_Q4_ATAC_rep3

description: Library name: MEF_60h_Q4_ATAC_rep3


title: MEF_60h_Q3_ATAC_rep3

description: Library name: MEF_60h_Q3_ATAC_rep3


title: hCO_control65D

city: Nankang

first: Yuan-Hsuan

last: Liu

state: Taipei

address: 128, Section 2, Academia Road

department: Research Center for Applied Sciences

country: Taiwan

institute: Academia Sinica

description:
Library name: SAMPLE1
10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were aligned to the GRCh38 human reference genome by the Cell Ranger pipeline v.6.1.2 (10x Genomics) with default parameters to generate the cell-by-gene count matrix.
Assembly: GRCh38
Supplementary files format and content: Matrix files

source_name: human induced pluripotent stem cells (hiPSCs)

extract_protocol:
Cerebral organoids were washed with calcium and magnesium-free DPBS and incubated with Corning Cell Recovery Solution to dissociate the polymerized Matrigel. The collected hCOs were cut into 2 to 4 small pieces using a scalpel and washed with the DPBS several times to remove the potential debris. The pieces of the hCOs were disassociated into single-cell suspension through the Neural Tissue Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, German)
Following the manufacturer’s instruction, the single-cell RNA sequencing (scRNA-seq) libraries were prepared with the Chromium Single Cell 3’ Library & Gel Bead Kit v.3.1 (10x Genomics). The constructed libraries were sequenced following the specific procedures (R1:28 cycles, R2: 91 cycles, and i7 index: 8 cycles) by a sequencing system (NovaSeq 6000, Illumina, San Diego CA).


title: CTMS1_followup8_GEX

city: New York

first: Zachary

last: Sethna

state: NY

address: 417 E 68th Street

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: CTMS1_followup8_GEX
10x Genomics

data_processing:
10x Genomics Cell Ranger Single Cell Software suite (https://support.10xgenomics.com/ single-cell-gene-expression/software/pipelines/latest/what-is-cell- ranger was used to perform sample) was used for demultiplexing, align- ment (hg19), filtering, UMI counting, single-cell 5′ end gene counting, TCR assembly, annotation of paired VDJ and performing quality control using the manufacturer’s parameters.
Assembly: hg19
Supplementary files format and content: TCR sequencing files are .csv, scRNAseq files are .h5

source_name: Human PBMC

extract_protocol:
Bulk T cells from patient-derived PBMCs were purified by fluorescence-activated cell sorting
Single-cell RNA sequencing libraries were pre- pared according to 10x Genomics specifications (Chromium Single Cell V(D)J User Guide PN-1000006, 10x Genomics).

tag: individual

value: Human PBMC


title: input, WNV, 6 dpi, 2

description: Library name: sample.2WI

value: WNV


title: Control, donor 1 (Ct_D1)

description: Library name: Ct_D1

value: CAR


title: MEF_60h_Q1_ATAC_rep3

description: Library name: MEF_60h_Q1_ATAC_rep3


title: MEF_60h_Q4_ATAC_rep2

description: Library name: MEF_60h_Q4_ATAC_rep2


title: MEF_60h_Q3_ATAC_rep2

description: Library name: MEF_60h_Q3_ATAC_rep2


title: hCO_shNGB65D

description:
Library name: SAMPLE2
10x Genomics

value: human induced pluripotent stem cells (hiPSCs)


title: MEF_60h_Q2_ATAC_rep2

description: Library name: MEF_60h_Q2_ATAC_rep2


title: input, sham control 5

description: Library name: sample.5SI


title: CTMS1_followup8_TCR

description:
Library name: CTMS1_followup8_TCR
10x Genomics


title: input, sham control 2

description: Library name: sample.2SI


title: input, sham control 4

description: Library name: sample.4SI


title: input, sham control 1

description: Library name: sample.1SI


title: CTMS1_followup6_GEX

description:
Library name: CTMS1_followup6_GEX
10x Genomics


title: MEF_60h_Q4_ATAC_rep1

description: Library name: MEF_60h_Q4_ATAC_rep1


title: CTMS1_followup6_TCR

description:
Library name: CTMS1_followup6_TCR
10x Genomics


title: MEF_60h_Q1_ATAC_rep1

description: Library name: MEF_60h_Q1_ATAC_rep1


title: MEF_60h_Q3_ATAC_rep1

description: Library name: MEF_60h_Q3_ATAC_rep1


title: MEF_60h_Q1_ATAC_rep2

description: Library name: MEF_60h_Q1_ATAC_rep2


title: CTMS1_mFOL2_GEX

description:
Library name: CTMS1_mFOL2_GEX
10x Genomics


title: MEF_36h_bulk_ATAC_rep3

description: Library name: MEF_36h_bulk_ATAC_rep3


title: MEF_60h_Q2_ATAC_rep1

description: Library name: MEF_60h_Q2_ATAC_rep1


title: MEF_36h_mature_repliATAC_rep3

description: Library name: MEF_36h_mature_repliATAC_rep3


title: enriched, WNV, 6dpi, 6

description: Library name: sample.6W


title: enriched, WNV, 6dpi, 4

description: Library name: sample.4W


title: CTMS1_mFOL2_TCR

description:
Library name: CTMS1_mFOL2_TCR
10x Genomics


title: MEF_36h_nascent_repliATAC_rep3

description: Library name: MEF_36h_nascent_repliATAC_rep3


title: MEF_12h_bulk_ATAC_rep3

description: Library name: MEF_12h_bulk_ATAC_rep3


title: enriched, WNV, 6dpi, 2

description: Library name: sample.2W


title: CTMS1_pcv5_GEX

description:
Library name: CTMS1_pcv5_GEX
10x Genomics


title: MEF_12h_nascent_repliATAC_rep3

description: Library name: MEF_12h_nascent_repliATAC_rep3


title: MEF_6h_bulk_ATAC_rep3

description: Library name: MEF_6h_bulk_ATAC_rep3


title: MEF_12h_mature_repliATAC_rep3

description: Library name: MEF_12h_mature_repliATAC_rep3


title: enriched, sham control 5

description: Library name: sample.5S


title: CTMS1_pcv5_TCR

description:
Library name: CTMS1_pcv5_TCR
10x Genomics


title: enriched, WNV, 6dpi, 1

description: Library name: sample.1W


title: MEF_6h_nascent_repliATAC_rep3

description: Library name: MEF_6h_nascent_repliATAC_rep3


title: MEF_6h_mature_repliATAC_rep3

description: Library name: MEF_6h_mature_repliATAC_rep3


title: CTMS1_pcv1_GEX

description:
Library name: CTMS1_pcv1_GEX
10x Genomics


title: enriched, sham control 4

description: Library name: sample.4S


title: MEF_36h_mature_repliATAC_rep2

description: Library name: MEF_36h_mature_repliATAC_rep2


title: CTMS1_pcv1_TCR

description:
Library name: CTMS1_pcv1_TCR
10x Genomics


title: enriched, sham control 2

description: Library name: sample.2S


title: MEF_12h_bulk_ATAC_rep2

description: Library name: MEF_12h_bulk_ATAC_rep2


title: CTMS1_atezo_GEX

description:
Library name: CTMS1_atezo_GEX
10x Genomics


title: MEF_36h_bulk_ATAC_rep2

description: Library name: MEF_36h_bulk_ATAC_rep2


title: enriched, sham control 1

description: Library name: sample.1S


title: CTMS1_atezo_TCR

description:
Library name: CTMS1_atezo_TCR
10x Genomics


title: MEF_12h_nascent_repliATAC_rep2

description: Library name: MEF_12h_nascent_repliATAC_rep2


title: MEF_12h_mature_repliATAC_rep2

description: Library name: MEF_12h_mature_repliATAC_rep2


title: MEF_6h_bulk_ATAC_rep2

description: Library name: MEF_6h_bulk_ATAC_rep2


title: MEF_6h_mature_repliATAC_rep2

description: Library name: MEF_6h_mature_repliATAC_rep2


title: CTMS1_presurgery_GEX

description:
Library name: CTMS1_presurgery_GEX
10x Genomics


title: WNV, 6dpi, 4

description: Library name: sample.4W

extract_protocol:
Mid and distal regions of small intestines (10-cm tissue measured from cecum) were cut into 5-cm segments, flushed with PBS, and positioned on a glass rod. After creating a shallow incision with fine forceps, the muscularis externa was separated by gently rolling it away with a cotton swab. The muscularis externa and the remaining gut tissue were minced using scissors (0.5 mm pieces) and digested in buffer (RPMI 1640 with 20 mM HEPES (Gibco, # 24020117), 400 U/mL collagenase D, 2.5 U/mL Liberase TM (Roche, # 05401127001), 50 µg/mL DNase I (Roche, # 10104159001) at 37°C on a shaker (140 rpm) for 40 min. Digested tissue was further dissociated using a 1-ml pipette, After filtering through a 70-µm strainer and washing with FACS buffer (PBS supplemented with 2% FBS, 5 mM EDTA, 0.1% NaN3). Cells were sorted using Fluorescent Activated Cell sorting directly into extraction buffer using MACSQuant Tyto Cartridges and a MACSQuant Tyto sorter (ThermoFisher/Applied Biosystems, #12204-01).
Library preparation was performed with 1-50 ng of total RNA.  cDNA was prepared using the SeqPlex RNA Amplification Kit (Sigma) per manufacturer's protocol and then fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, an A base was added to the 3' ends, and then Illumina sequencing adapters were ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Cx3cr1CreERT2 (B6.129P2(C)-Cx3cr1tm2.1(cre/ERT)Jung/J; Ai3 (YFP) (B6.Cg-Gt(ROSA)26Sortm3(CAG-EYFP)Hze/J


title: WNV, 6dpi, 3

description: Library name: sample.3W


title: MEF_36h_bulk_ATAC_rep1

description: Library name: MEF_36h_bulk_ATAC_rep1


title: MEF_36h_nascent_repliATAC_rep2

description: Library name: MEF_36h_nascent_repliATAC_rep2


title: MEF_6h_nascent_repliATAC_rep2

description: Library name: MEF_6h_nascent_repliATAC_rep2


title: MEF_36h_mature_repliATAC_rep1

description: Library name: MEF_36h_mature_repliATAC_rep1


title: WNV, 6dpi, 1

description: Library name: sample.1W


title: MEF_12h_bulk_ATAC_rep1

description: Library name: MEF_12h_bulk_ATAC_rep1


title: RPE, YAP-HA, Y3

city: Ulsan

first: Hyo Kyung

last: Lee

address: UNIST-gil 50

department: Biomedical engineering

country: South Korea

institute: UNIST

data_processing:
Gene expression matrices were generated using Cell Ranger 6.0.1 from 10x Genomics with the mouse genome reference data (mm10).
All raw files were mapped to the human genome reference data (GRCh38) using STAR (version 2.7.3a). After evaluating quality of the raw data by FastQ Screen (version 0.14.1), we calculated TPM (transcripts per millions) using RSEM (RNA-Seq by Expectation-Maximization) (version 1.3.1).
STAR (version 2.7.10b) was used to map the raw sequencing data to the mouse genome reference data (GRCm39). FastQ Screen (version 0.14.1) was used to check the raw data quality. Transcripts per million (TPM) were obtained using RNA-Seq by Expectation-Maximization (RSEM) (version 1.3.1).
Assembly: mm10
Assembly: GRCh38
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: tab-delimited text file includes TPM count for each Sample

source_name: eye

extract_protocol:
RPE cells were carefully dissociated using a papain solution (20 U/ml) supplemented with DNase-I (2000 U/ml) in Earle’s balanced salt solution (EBSS) and incubated in a water bath at 37 °C for 30 minutes. The dissociated single RPE cell pellet was washed with PBS and collected after centrifugation at 1200 RPM for 3 min. The RPE samples were then filtered through a 30 µm cell strainer (Miltenyi Biotech, Cat. #130-098-458) and washed twice with cold Ca²⁺- and Mg²⁺-free 0.04% BSA/PBS at 300g for 5 minutes at 4°C. The samples were gently resuspended in cold Ca²⁺- and Mg²⁺-free 0.04% BSA/PBS and counted using a LUNA-FX7™ Automated Fluorescence Cell Counter (Logos Biosystems) after acridine orange (AO) and propidium iodide (PI) staining (Logos Biosystems, Cat. #F23001).
Cells were harvested after 5 days and total RNA was isolated using QIAzol Lysis Reagent (QIAZEN). Total RNA concentration was measured using the Quant-IT RiboGreen Assay (Invitrogen, #R11490). To assess RNA integrity, samples were analyzed using the TapeStation RNA ScreenTape system (Agilent, #5067-5576) and only RNA samples with an RNA Integrity Number (RIN) greater than 7.0 were selected for RNA library preparation. For each sample, 1 µg of total RNA was used to construct libraries using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-2101). Poly-A mRNA was isolated using poly-T coated magnetic beads and fragmented at high temperatures in the presence of divalent cations.
The eyeballs were trimmed to remove surrounding muscle and anterior segments were dissected. After carefully removing the retina, lysis buffer was gently applied to the eye cup and RNA was extracted following the manufacturer’s instructions for the RNeasy Mini Kit (QIAGEN).
scRNA-seq libraries were prepared using the 10x Chromium Controller and Next GEM Single Cell 5’ Reagent v2 kits (10x Genomics, PN-1000244), following the 10x Chromium Single Cell 5’ v2 protocol. Cell suspension with a target recovery of 10,000 cells was combined with a reverse transcription master mix and loaded onto a Single Cell K-Chip (10x Genomics, PN-1000286) together with single cell 5′ gel beads and partitioning oil to generate gel beads-in-emulsion (GEMs), in which RNA transcripts from individual cells were uniquely barcoded and reverse transcribed. The resulting barcoded full-length cDNA was amplified by PCR, and for 5’ Gene Expression Library preparation, the cDNA underwent enzymatic fragmentation, end repair, A-tailing, adapter ligation, and index PCR. The purified libraries were quantified by the qPCR Qualification Protocol Guide (KAPA), evaluated for quality with the Agilent 4200 TapeStation (Agilent Technologies), and sequenced on the Illumina HiSeq platform (Illumina).
cDNA library was generated from the fragmented RNA with SuperScript II reverse transcriptase (Invitrogen, 18064014). Quantification of the prepared libraries was performed using the KAPA Library Quantification Kit for Illumina platforms according to the manufacturer's protocol (KAPA BIOSYSTEMS, #KK4854). Library quality was assessed using the TapeStation D1000 ScreenTape (Agilent, #5067-5582). The indexed libraries were then sequenced on an Illumina NovaSeqX platform (Illumina) with paired-end 2×100 bp reads performed by Macrogen Incorporated.
The sequencing library was then constructed using the SMARTer Stranded RNA-Seq Kit according to the manufacturer’s instructions. Library quantification, quality assessment, and sequencing on Illumina NovaSeqX platform were performed as described above.

value: eye

value: RPE

tag: condition

value: cells with overexpression of YAP-HA


title: WNV, 6dpi, 2

description: Library name: sample.2W

value: distal part of small intestine


title: sham control 4

description: Library name: sample.4S


title: MEF_12h_nascent_repliATAC_rep1

description: Library name: MEF_12h_nascent_repliATAC_rep1


title: CTMS1_presurgery_TCR

description:
Library name: CTMS1_presurgery_TCR
10x Genomics


title: RPE, YAP-HA, Y1


title: MEF_6h_nascent_repliATAC_rep1

description: Library name: MEF_6h_nascent_repliATAC_rep1


title: sham control 3

description: Library name: sample.3S


title: RPE, YAP-HA, Y2


title: sham control 2

description: Library name: sample.2S


title: WT-IgG-T2

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

description: Library name: WT-IgG-T2

data_processing:
scRNA-seq data from 10x Genomics is processed using the Cell Ranger pipeline, which aligns reads to a reference genome, identifies cell barcodes and UMIs, and generates a gene expression matrix. Quality control filters low-quality cells and doublets, normalization adjusts for sequencing depth, and dimensionality reduction and clustering identify and annotate cell types for downstream analysis.
Assembly: Mouse mm10
Supplementary files format and content: gzip compressed tab delimited value files and matrix files

source_name: 344SQ parental (WT)

growth_protocol: Cells are grown at 37oC, 5% CO2 in RPMI media with 10% FBS. The cells were confirmed to be mycoplasma negative prior to implantation into mice.

extract_protocol:
Tumors were excised and processed into single cells first by physical mincing, then enzymatic digestion with collagenase + hyalaronidase + DNAse. Single cell suspension was washed 2x, stained with Sytox Blue and FACS sorted for viable cells.
The library construction step of scRNA-seq using 10x Genomics begins with encapsulating individual cells into droplets along with barcoded beads using a microfluidic platform. Cells are lysed, and their RNA binds to barcoded oligonucleotides, ensuring each transcript is tagged with a unique cell barcode and UMI. The captured RNA is reverse transcribed into barcoded cDNA, which is then amplified via PCR. The cDNA is fragmented, end-repaired, A-tailed, and ligated with sequencing adapters. Sample indices are added if multiplexing is required. Finally, the libraries are quality-checked for fragment size and concentration before being sequenced on a high-throughput platform of Illumina.

treatment_protocol: IgG antibody treatment weekly by intraperitoneal injection (200ug/mouse)

value: 344SQ parental (WT)

value: lung cancer

value: IgG antibody

tag: time point

value: 6 weeks


title: MEF_12h_mature_repliATAC_rep1

description: Library name: MEF_12h_mature_repliATAC_rep1


title: MEF_36h_nascent_repliATAC_rep1

description: Library name: MEF_36h_nascent_repliATAC_rep1


title: sham control 1

description: Library name: sample.1S

value: sham


title: RPE, 1.5 kPa, S3

value: cultured on 1.5 kPa


title: MEF_6h_mature_repliATAC_rep1

description: Library name: MEF_6h_mature_repliATAC_rep1

value: Fibroblasts

value: OKSM reprogramming intermediates from MEFs


title: MEF_6h_bulk_ATAC_rep1

description: Library name: MEF_6h_bulk_ATAC_rep1

value: Col1a1::tetOP-OKSM het; R26-M2rtTA het; Oct4GFP het


title: 140P-IgG-T2

description: Library name: 140P-IgG-T2


title: RPE, 1.5 kPa, S2


title: SampleB, HTO, ADT

first: Sneha

last: Mitra

address: 1275 York Avenue

description:
Library name: SampleB_HTO_ADT
CITE-seq feature barcode library containing both anitbody-derived tags (ADT) and hashtag-oligonucleotides; read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
CITE-seq files were demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files: NFIL3KO-D0-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D0-B_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D14-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D14-B_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D7-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D7-B_sample_filtered_feature_bc_matrix.h5, WT-D0-A_sample_filtered_feature_bc_matrix.h5, WT-D0-B_sample_filtered_feature_bc_matrix.h5, WT-D14-A_sample_filtered_feature_bc_matrix.h5, WT-D14-B_sample_filtered_feature_bc_matrix.h5, WT-D7-A_sample_filtered_feature_bc_matrix.h5, WT-D7-B_sample_filtered_feature_bc_matrix.h5,
Supplementary files format and content: Cellranger output files: NFIL3KO-D0-A_airr_rearrangement.tsv,   WT-D0-A_airr_rearrangement.tsv, NFIL3KO-D0-B_airr_rearrangement.tsv,   WT-D0-B_airr_rearrangement.tsv, NFIL3KO-D14-A_airr_rearrangement.tsv,  WT-D14-A_airr_rearrangement.tsv, NFIL3KO-D14-B_airr_rearrangement.tsv,  WT-D14-B_airr_rearrangement.tsv, NFIL3KO-D7-A_airr_rearrangement.tsv,   WT-D7-A_airr_rearrangement.tsv, NFIL3KO-D7-B_airr_rearrangement.tsv,   WT-D7-B_airr_rearrangement.tsv

molecule: protein

source_name: spleen

extract_protocol:
1 million cells per condition were stained in cell staining buffer containing cell hashing antibodies for 30 minutes at 4°C. 3ml cell staining buffer was added and centrifuged at 400g for 5 mins. Repeated wash two more times for a total of three washes. Cells were resuspended in 500 μl of cell staining buffer and slowly filtered through a 40 μM cell strainer. Cell concentration and viability were verified and loaded on the 10X Chromium Next GEM Chip K Kit. Libraries were prepared according to manufacturer’s protocol (5’V2 kit, 10x Genomics) and sequenced on a NovaSeq X System using the 10B 100C kit (Illumina).
Libaries construction for both scRNA, CITE, scTCR followed manufacturer protocols (10X genomics).

value: spleen

value: T-cell

tag: library type

value: HTO/ADT

value: B

tag: hto/adt

value: TotalSeq C


title: RPE, 1.5 kPa, S1

value: eye

value: RPE


title: Gene expression B-lineage cells from MM9

city: Pamplona

first: Carmen

last: González

state: Navarra

address: Av. de Pío XII, 55

country: Spain

institute: University of Navarra

description: Library name: MM9_gex

data_processing:
Demultiplexing, alignment and different kit aggregation/correction, as well as gene counts and BCR reconstruction were performed with the Cell Ranger Software Suite (version 7.0, 10X Genomics), using default parameters and the GRCh38/hg38 reference genome. Downstream analyses were performed in R version 4.1.1 with Seurat package version 5.2.1 unless specified below. Matrices with filtered unique molecular identifier (UMI) counts from all cases were merged in a single Seurat-object, onto the BCR dataset was added.
Data processing was performed using Cell Ranger v7.0.0, starting with cellranger mkfastq for raw data conversion, followed by cellranger multi for alignment and analysis, and concluded with cellranger aggr for aggregating data across multiple samples
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: Contains a list of barcode identifiers (unique cell IDs) used in the experiment, with each line representing an individual cell's barcode.
Supplementary files format and content: features.tsv.gz: Contains a list of features (genes or transcripts) detected in the cells, with each line representing an individual feature in the experiment.
Supplementary files format and content: matrix.mtx.gz: A sparse matrix containing gene expression counts per cell, where rows correspond to features (genes) and columns to cells, with values representing the number of reads for each gene in each cell.

source_name: Bone Marrow

extract_protocol:
EDTA-anticoagulated BM aspirates were stained with the following combination of monoclonal antibodies prior to FACS: CD3-FITC, CD19-PeCy7, CD38-APCH7, CD45-V500, CD56-PE, CD138-V450, CD300e-APC and 7-AAD-PerCP (viability). For scRNA/BCR-seq studies, CD19+veCD138-ve B cells and CD138+ve PC (independently of CD19 expression) were sorted into 100 µL of Lysis/Binding Buffer (Thermo Fisher Scientific, Waltham, MA). Cells were isolated in a FACSAria IIb flow cytometer (Becton Dickinson Biosciences [BDB], San Jose, CA) and sorted into 100 µL of Lysis/Binding Buffer (Thermo Fisher Scientific, Waltham, MA) for subsequent sequencing studies.
scRNA/BCR-seq was performed using 10X Genomics Single Cell 5′ Solution v1 and v2 following the manufacturer’s protocol (10X Genomics, CA, USA). Libraries were sequenced in a NextSeq550 (Illumina, CA, USA) for gene expression and BCR data.

value: multiple myeloma (MM)

value: Bone Marrow

value: B-lineage cells


title: SampleA, HTO, ADT

description:
Library name: SampleA_HTO_ADT
CITE-seq feature barcode library containing both anitbody-derived tags (ADT) and hashtag-oligonucleotides; read1 contains cell barcode and UMI; read2 contains transcript sequence

value: A


title: Gene expression B-lineage cells from MM8

description: Library name: MM8_gex


title: RPE, plastic, P3

value: cultured on plastic


title: BRC from B-lineage cells from MM9

description: Library name: MM9_vdj

data_processing:
Demultiplexing, alignment and different kit aggregation/correction, as well as gene counts and BCR reconstruction were performed with the Cell Ranger Software Suite (version 7.0, 10X Genomics), using default parameters and the GRCh38/hg38 reference genome. Downstream analyses were performed in R version 4.1.1 with Seurat package version 5.2.1 unless specified below. Matrices with filtered unique molecular identifier (UMI) counts from all cases were merged in a single Seurat-object, onto the BCR dataset was added.
Data processing was performed using Cell Ranger v7.0.0, starting with cellranger mkfastq for raw data conversion, followed by cellranger multi for alignment and analysis, and concluded with cellranger aggr for aggregating data across multiple samples
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: Contains a list of barcode identifiers (unique cell IDs) used in the experiment, with each line representing an individual cell's barcode.
Supplementary files format and content: features.tsv.gz: Contains a list of features (genes or transcripts) detected in the cells, with each line representing an individual feature in the experiment.
Supplementary files format and content: matrix.mtx.gz: A sparse matrix containing gene expression counts per cell, where rows correspond to features (genes) and columns to cells, with values representing the number of reads for each gene in each cell.
Library strategy: BCR-Seq


title: WT-IgG-T1

description: Library name: WT-IgG-T1

value: 344SQ parental (WT)

value: lung cancer

value: IgG antibody

value: 4 weeks


title: SampleB, TCR

description:
Library name: SampleB_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
CITE-seq files were demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files: NFIL3KO-D0-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D0-B_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D14-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D14-B_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D7-A_sample_filtered_feature_bc_matrix.h5, NFIL3KO-D7-B_sample_filtered_feature_bc_matrix.h5, WT-D0-A_sample_filtered_feature_bc_matrix.h5, WT-D0-B_sample_filtered_feature_bc_matrix.h5, WT-D14-A_sample_filtered_feature_bc_matrix.h5, WT-D14-B_sample_filtered_feature_bc_matrix.h5, WT-D7-A_sample_filtered_feature_bc_matrix.h5, WT-D7-B_sample_filtered_feature_bc_matrix.h5,
Supplementary files format and content: Cellranger output files: NFIL3KO-D0-A_airr_rearrangement.tsv,   WT-D0-A_airr_rearrangement.tsv, NFIL3KO-D0-B_airr_rearrangement.tsv,   WT-D0-B_airr_rearrangement.tsv, NFIL3KO-D14-A_airr_rearrangement.tsv,  WT-D14-A_airr_rearrangement.tsv, NFIL3KO-D14-B_airr_rearrangement.tsv,  WT-D14-B_airr_rearrangement.tsv, NFIL3KO-D7-A_airr_rearrangement.tsv,   WT-D7-A_airr_rearrangement.tsv, NFIL3KO-D7-B_airr_rearrangement.tsv,   WT-D7-B_airr_rearrangement.tsv
Library strategy: TCR-seq

value: VDJ


title: 140P-IgG-T1

description: Library name: 140P-IgG-T1


title: Gene expression B-lineage cells from MM7

description: Library name: MM7_gex


title: BRC from B-lineage cells from MM7

description: Library name: MM7_vdj


title: Gene expression B-lineage cells from MM6

description: Library name: MM6_gex


title: RPE, plastic, P1


title: BRC from B-lineage cells from MM6

description: Library name: MM6_vdj


title: RPE, plastic, P2


title: Ed1-cl1, isogenic, SHANK3 point mutation

city: São Paulo

first: Victor

middle: Hugo

last: Calegari de Toledo

state: SP

address: R. do Matão, 303 - Butantã

department: Genética

country: Brazil

institute: Universidade de São Paulo

data_processing:
Reads were trimmed and quality-filtered using Trimmomatic (Bolger et al., 2014). Sequences were aligned to the reference human genome (hg38) using STAR with reduced spurious junctions (‘--outFilterType BySJout’) and extra alignment score for junctions of 1 (‘--sjdbScore 1’), generating a BAM file aligned to transcriptome (Dobin et al., 2013). Read counts per gene were summarized using RSEM, calculating read start position distribution (‘--estimate-rspd’) to better estimate transcripts (Li and Dewey, 2011).
tximport (version 1.10.1) was employed to aggregate transcript abundances into gene-level counts. Genes with low counts level were filtered out (gene count > 10 for at least the number of samples for the smallest group, i.e. 6 samples).
Assembly: GRCh38 primary assembly
Supplementary files format and content: Raw counts imported by tximport

source_name: cultured neural cells

extract_protocol:
Total RNA from all 60 days of neuron cultures was isolated using NucleoSpin TriPrep (Macherey-Nagel).
The RNA library was made with the ribosomal RNA depletion method using Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research) according to the manufacturer’s instructions.

value: cultured neural cells

value: neural cells

value: SHANK3 point mutation

value: neuron differentiation


title: BRC from B-lineage cells from MM8

description: Library name: MM8_vdj


title: Gene expression B-lineage cells from MM5

description: Library name: MM5_gex


title: SampleB, CAR-T-cells, GEX

description:
Library name: SampleB_RNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

molecule: polyA RNA

value: spleen

value: T-cell

value: mRNA

value: B


title: BRC from B-lineage cells from MM5

description: Library name: MM5_vdj

value: multiple myeloma (MM)

value: Bone Marrow


title: SampleA, TCR

description:
Library name: SampleA_tcr
VDJ library: read1 contains cell barcode and UMI; read2 contains transcript sequence

value: A


title: C6-cl3, control

value: control


title: BRC from B-lineage cells from MM3

description: Library name: MM3_vdj

value: B-lineage cells


title: Gene expression B-lineage cells from MM3

description: Library name: MM3_gex


title: C7-cl3, control


title: SampleA, CAR-T-cells, GEX

description:
Library name: SampleA_RNA
5' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Gene expression B-lineage cells from MM4

description: Library name: MM4_gex


title: Male Mouse B cells IFNAR1+/+, LCMV CL13, day 14

city: Laval

first: Alain

last: Lamarre

state: Quebec

address: 531 Boul des Prairies,

department: Immunology virology

country: Canada

institute: Centre Armand-Frappier Santé Biotechnologie de l'INRS

description:
Library name: VDJ_MaleIFNAR1flox
BCR repertoire analysis

data_processing:
Analyses were performed using the Immcantation framework  (www.immcantation.org), executed in R via Docker, followed by further processing in RStudio. V(D)J gene annotations from CellRanger (v8.0.0) outputs were reassigned through alignment to the IMGT GENE-DB reference database (vdj_GRCm38_alts_ensembl-7.1.0) using IgBLAST and Change-O, implemented within the Docker-based Immcantation environment.  BCR data were integrated with previously demultiplexed GEX data, allowing traceability of each sequence to its experimental condition and mouse of origin. Only productive sequences were retained, and barcodes associated with multiple heavy chains were excluded to ensure one productive heavy chain per cell.
Assembly: V(D)J data were processed using the 10x Genomics VDJ reference vdj_GRCm38_alts_ensembl-7.1.0.
Supplementary files format and content: For V(D)J data, the processed file is filtered_contig.fastq, containing assembled and annotated V(D)J sequences per cell barcode, generated using the Cell Ranger VDJ pipeline.

extract_protocol:
Mice were euthanized by CO₂ exposure followed by cervical dislocation. After spleen collection, mechanical dissociation and cell count, cell suspensions were adjusted to a concentration of 10⁸ cells/mL. B cells were then enriched by depleting non-B lymphocytes using the EasySep™ Mouse Biotin Positive Selection Kit II (Stemcell, Canada) and the following biotinylated antibodies: anti-CD4 (1/250), anti-CD4 (1/400), anti-CD8 (1/400), anti-TER119 (1/300), anti-CD49b (1/300), anti-CD11c (1/300), anti-CD11b (1/400), and anti-Ly6G (1/400). Next, we followed the Cell Surface Protein Labeling for Single-Cell RNA Sequencing Protocol (10X Genomics), using the following anti-mouse TotalSeq™ barcoded antibodies (BioLegend, USA): TotalSeq™-C0301, barcode: ACCCACCAGTAAGAC; TotalSeq™-C0302, barcode: GGTCGAGAGCATTCA; TotalSeq™-C0303, barcode: CTTGCCGCATGTCAT; TotalSeq™-C0304, barcode: AAAGCATTCTTCACG. 4 animals per experimental group were individually stained with the above barcoded-antibodies and for each experimental condition, TotalSeq™-C0301 was pooled with TotalSeq™-C0302, and TotalSeq™-C0303 was pooled with TotalSeq™-C0304, resulting in two tubes per condition.In the MalesVSV and FemellesMB1cre groups, one mouse per group was lost before processing. To maintain consistency in the number of cells analyzed per condition, we duplicated the same enriched B cell sample from one individual within each affected group. Thus, two technical replicates originating from the same mouse were used in these groups, each contributing approximately 10,000 cells for single-cell RNA sequencing. Approximately 10,000 multiplexed enriched B cells per sample were processed for single-cell RNA sequencing (scRNA-seq).
Libraries were prepared using the Chromium Next GEM Single Cell 5' Reagent Kit v2 (10X Genomics, CG000330 Rev F) for 5' gene expression, BCR V(D)J repertoire sequencing, and cell surface protein detection, according to the manufacturer’s protocol.

treatment_protocol: Mice were infected intravenously with either LCMV Clone 13 or VSV. Six hours post-infection, they were immunized intraperitoneally with NP-CGG.

tag: time

value: Day 14

value: B cells

tag: strain

tag: Sex

value: Male

value: LCMV CL13+ NP-CGG


title: C4-cl1, control

value: cultured neural cells


title: C5-cl1, control

value: neural cells


title: Gene expression B-lineage cells from MM2

description: Library name: MM2_gex


title: BRC from B-lineage cells from MM11

description: Library name: MM11_vdj


title: Female Mouse B cells IFNAR1+/+, LCMV CL13, day 14

description:
Library name: VDJ_FemaleIFNAR1flox
BCR repertoire analysis

value: Female


title: Male Mouse B cells IFNAR1-/-, LCMV CL13, day 14

description:
Library name: VDJ_MaleMB1cre
BCR repertoire analysis. In MaleMB1cre groups, one mouse was lost during the experimental procedure. To ensure equal cell input across all conditions, a single mouse sample was duplicated, resulting in two technical replicates derived from the same animal.


title: C3-cl1, control

value: neuron differentiation


title: BRC from B-lineage cells from MM4

description: Library name: MM4_vdj


title: BRC from B-lineage cells from MM1

description: Library name: MM1_vdj


title: C2-cl1, control


title: Male Mouse B cells IFNAR1+/+, VSV, day 14

description:
Library name: VDJ_MaleVSV
BCR repertoire analysis

value: spleen

value: VSV+ NP-CGG


title: Gene expression B-lineage cells from MM1

description: Library name: MM1_gex


title: Gene expression B-lineage cells from MM10

description: Library name: MM10_gex


title: BRC from B-lineage cells from MM2

description: Library name: MM2_vdj


title: Female Mouse B cells IFNAR1-/-, LCMV CL13, day 14

description:
Library name: VDJ_FemaleMB1cre
BCR repertoire analysis


title: Female Mouse B cells IFNAR1+/+, VSV, day 14

description:
Library name: VDJ_FemaleVSV
BCR repertoire analysis. In FemellesVSV groups, one mouse was lost during the experimental procedure. To ensure equal cell input across all conditions, a single mouse sample was duplicated, resulting in two technical replicates derived from the same animal.


title: C1-cl1, control


title: Gene expression B-lineage cells from HA3

description: Library name: HA3_gex

value: healthy adult (HA)


title: BRC from B-lineage cells from HA3

description: Library name: HA3_vdj


title: Male Mouse B cells IFNAR1+/+, LCMV CL13, day 14 - CSP

description:
Library name: CSP_MaleIFNAR1flox
cell surface protein using TotalSeq-C antibodies

data_processing:
Gene expression data were aligned to the GRCm39-2024-A mouse reference genome using CellRanger v8.0.0. Samples were demultiplexed using TotalSeq barcodes and processed in Seurat v5.1.0 with R v4.4.2. Quality filtering was applied (nFeature_RNA > 1400, nCount_RNA > 2500, percent.mt < 5%). SCTransform was used for normalization and dataset integration. 30 PCs were used for PCA, followed by UMAP and clustering (resolution = 0.8).
Assembly: Gene expression (GEX) data were aligned to the mouse genome reference GRCm39-2024-A
Supplementary files format and content: For gene expression (GEX), the processed data include matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz files (filtered feature-barcode matrix from Cell Ranger output).


title: P14-cl1, SHANK3 point mutation

value: SHANK3 point mutation


title: Gene expression B-lineage cells from MM11

description: Library name: MM11_gex

value: multiple myeloma (MM)


title: Gene expression B-lineage cells from HA2

description: Library name: HA2_gex

value: Bone Marrow


title: BRC from B-lineage cells from HA1

description: Library name: HA1_vdj


title: BRC from B-lineage cells from MM10

description: Library name: MM10_vdj


title: P11-cl1, SHANK3 point mutation


title: Male Mouse B cells IFNAR1+/+, LCMV CL13, day 14 - GEX

description:
Library name: GEX_MaleIFNAR1flox
Gene expression analysis using 10x Genomics 5' scRNA-seq.


title: P12-cl1, SHANK3 point mutation


title: BRC from B-lineage cells from AL5

description: Library name: AL5_vdj

value: light-chain amyloidosis (AL)


title: Gene expression B-lineage cells from AL5

description: Library name: AL5_gex


title: Female Mouse B cells IFNAR1+/+, LCMV CL13, day 14 - CSP

description:
Library name: CSP_FemaleIFNAR1flox
cell surface protein using TotalSeq-C antibodies


title: P9-cl1, SHANK3 deletion

value: SHANK3 deletion


title: Gene expression B-lineage cells from HA1

description: Library name: HA1_gex

value: B-lineage cells


title: BRC from B-lineage cells from HA2

description: Library name: HA2_vdj


title: Female Mouse B cells IFNAR1+/+, LCMV CL13, day 14 - GEX

description:
Library name: GEX_FemaleIFNAR1flox
Gene expression analysis using 10x Genomics 5' scRNA-seq.

value: Day 14


title: BRC from B-lineage cells from AL4

description: Library name: AL4_vdj


title: P6-cl2, SHANK3 deletion


title: Gene expression B-lineage cells from AL4

description: Library name: AL4_gex


title: Male Mouse B cells IFNAR1-/-, LCMV CL13, day 14 - CSP

description:
Library name: CSP_MaleMB1cre
cell surface protein using TotalSeq-C antibodies. In MaleMB1cre groups, one mouse was lost during the experimental procedure. To ensure equal cell input across all conditions, a single mouse sample was duplicated, resulting in two technical replicates derived from the same animal.

value: B cells


title: Gene expression B-lineage cells from AL3

description: Library name: AL3_gex


title: BRC from B-lineage cells from AL3

description: Library name: AL3_vdj


title: BRC from B-lineage cells from AL2

description: Library name: AL2_vdj


title: P5-cl1, SHANK3 deletion


title: Gene expression B-lineage cells from AL2

description: Library name: AL2_gex


title: Female Mouse B cells IFNAR1-/-, LCMV CL13, day 14 - CSP

description:
Library name: CSP_FemaleMB1cre
cell surface protein using TotalSeq-C antibodies


title: Male Mouse B cells IFNAR1-/-, LCMV CL13, day 14 - GEX

description:
Library name: GEX_MaleMB1cre
Gene expression analysis using 10x Genomics 5' scRNA-seq.In MaleMB1cre groups, one mouse was lost during the experimental procedure. To ensure equal cell input across all conditions, a single mouse sample was duplicated, resulting in two technical replicates derived from the same animal.

value: Male


title: Gene expression from B-lineage cells from AL1

description: Library name: AL1_gex


title: BRC from B-lineage cells from AL1

description: Library name: AL1_vdj


title: P4-cl1, SHANK3 deletion


title: T3_200days_rep3_scRNA

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust St.

department: Ophthalmology

institute: University of Pittsburgh

description:
Library name: T3_200days_rep3
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

data_processing:
Single cell RNA-seq: Sequencing results were processed through the Cell Ranger 3.1.0 pipeline (10x Genomics) with default parameters. Seurat V4 was used to perform downstream analysis following the standard pipeline.
Assembly: GRCh38
Supplementary files format and content: Cell-by-gene count matrix for all the samples as csv
Supplementary files format and content: Metadata for the cell-by-gene count matrix as csv

source_name: Retinal Organoid

extract_protocol:
Papain dissociation to prepare single cell suspension
scRNA-Seq following 10x Genomics 3' version 3 capture guideline

value: Retinal Organoid

value: H7 ESCs

tag: age

value: ~200 days

value: mRNA


title: P2.2-cl6, SHANK3 deletion

value: cultured neural cells

tag: cell type

value: neural cells

value: neuron differentiation


title: Female Mouse B cells IFNAR1-/-, LCMV CL13, day 14 - GEX

description:
Library name: GEX_FemaleMB1cre
Gene expression analysis using 10x Genomics 5' scRNA-seq.

value: spleen

value: Female

tag: treatment

value: LCMV CL13+ NP-CGG


title: T3_200days_rep2_scRNA

description:
Library name: T3_200days_rep2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: T3_10days_rep1_scRNA

description:
Library name: T3_10days_rep1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: P1-cl1, SHANK3 deletion


title: T3_200days_rep1_scRNA

description:
Library name: T3_200days_rep1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: Male Mouse B cells IFNAR1+/+, VSV, day 14 - GEX

description:
Library name: GEX_MaleVSV
Gene expression analysis using 10x Genomics 5' scRNA-seq.

value: VSV+ NP-CGG


title: T3_10days_rep2_scRNA

description:
Library name: T3_10days_rep2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: SKMAFG3

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

data_processing:
Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1).
Processed raw reads were then aligned to human genome GRCh38 using STAR (v2.7.7a).
Gene expression was evaluated as read count at gene level with RSEM (v1.3.0) and Gencode gene model v30.
Gene express data were then normalized and differential expression between experimental groups were evaluated using DEseq2.
Assembly: GRCh38
Supplementary files format and content: gene/transcript reads count file, text format

source_name: Melanoma

growth_protocol: Cell lines were cultured in RPMI containing 5% FBS at 37˚C in a humidified atmosphere containing 5% CO2

extract_protocol:
Total RNA was isolated using Qiagen mIRNease kit
Library preparation was performed by NEBNext® Ultra™ RNA Library Prep Kit for Illumina® which is for non-stranded libraries.

value: Melanoma

value: Cancer

value: overexpressing MAFG


title: Male Mouse B cells IFNAR1+/+, VSV, day 14 - CSP

description:
Library name: CSP_MaleVSV
cell surface protein using TotalSeq-C antibodies

value: Day 14


title: Control_rep2_scRNA

description:
Library name: Control_rep2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: Control


title: P2-cl5, SHANK3 deletion

value: SHANK3 deletion


title: CSPFemale Mouse B cells IFNAR1+/+, VSV, day 14 - CSP

description:
Library name: CSP_FemaleVSV
cell surface protein using TotalSeq-C antibodies. In FemellesVSV groups, one mouse was lost during the experimental procedure. To ensure equal cell input across all conditions, a single mouse sample was duplicated, resulting in two technical replicates derived from the same animal.

value: B cells


title: SKMAFG2


title: Control_rep1_scRNA

description:
Library name: Control_rep1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: Retinal Organoid

value: H7 ESCs


title: Col0.X57.3

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

description: Library name: Col0.X57.3

data_processing:
Quality analysis of raw and clean reads with FastQC
Adaptor and low-quality trimming with cutadapt
Mapping and read counting with STAR
Assembly: TAIR10 genome assembly and Araport11 annotation
Supplementary files format and content: Text file with tab-separated fields containing read counts per gene for each sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Col-0 5-day-old Arabidopsis thaliana seedlings gron in liquid MS supplemented with 1% sucrose.

extract_protocol:
Total RNA was extracted from approximately 4 mg of ground, freeze-dried Arabidopsis tissue using the PureLink™ RNA Mini Kit (Thermo), following the manufacturer’s instructions.
RNA-seq libraries were prepared by BGI Genomics, following the protocol described on their website (https://www.bgi.com/global/science-detail/transcriptome-sequencing).

treatment_protocol: LS liquid medium was removed and replaced with fresh medium containing either 100 µM X57 or 0.05% DMSO and seedlings were incubated for 5h.

value: seedling

tag: ecotype


title: Col0.DMSO.3

description: Library name: Col0.DMSO.3

tag: tissue


title: SKMAFG1


title: Female Mouse B cells IFNAR1+/+, VSV, day 14 - GEX

description:
Library name: Gex_FemaleVSV
Gene expression analysis using 10x Genomics 5' scRNA-seq. In FemellesVSV groups, one mouse was lost during the experimental procedure. To ensure equal cell input across all conditions, a single mouse sample was duplicated, resulting in two technical replicates derived from the same animal.

tag: genotype


title: Col0.DMSO.2

description: Library name: Col0.DMSO.2


title: Col0.X57.1

description: Library name: Col0.X57.1


title: Col0.X57.4

description: Library name: Col0.X57.4


title: SKGFP3

tag: cell line

value: overexpressing GFP


title: SKGFP2


title: ChIP_YMEP_H3K27ac_rep2

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description: Library name: Sample 64

data_processing:
cutadapt
BWA-mem alignment
deepTools, normalized 10M reads
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: Bone marrow

extract_protocol:
ChIP-seq was performed as described previously with Chromatin Immunoprecipitation (ChIP) Assay Kit (17-295, Millipore). 10,000 sorted cells were crosslinked with 1% formaldehyde (F8775, Sigma-Aldrich) at room temperature (RT) for 10 min
Libraries were prepared with TruSeq Nano DNA Low Throughput Library Prep Kit (20015964, Illumina) according to manufacturer's instructions.

value: Bone marrow

value: MEP

value: WT

tag: batch

tag: antibody


title: Col0.DMSO.1

description: Library name: Col0.DMSO.1


title: KO, Ang II-1 (H3k4me3 ChIP)

city: Beijing

first: ying

last: zhao

state: Beijing

address: 167, Beilishi Road, Xicheng District, Beijing

country: China

institute: Fuwai Hospital, Chinese Academy of Medical Sciences

description: Library name: KO, Ang II-1 (H3k4me3 ChIP)

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Supplementary files format and content: peak text files

source_name: Primary

growth_protocol: Primary vsmc were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), then incubated at 37 ℃ in a 5% CO2 incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Ang II (1uM), 24h

value: Primary

value: Smooth Muscle Cells

value: CSE KO

value: Ang II


title: ChIP_YMEP_H3K4me3_rep2

description: Library name: Sample 61


title: KO, Ang II-2 (H3k4me3 ChIP)

description: Library name: KO, Ang II-2 (H3k4me3 ChIP)


title: A375MAFG3

value: Melanoma

value: Cancer


title: KO, Ang II-3 (H3k4me3 ChIP)

description: Library name: KO, Ang II-3 (H3k4me3 ChIP)


title: ChIP_YMEP_H3K36me3_rep2

description: Library name: Sample 63


title: SKGFP1


title: KO, Ang II-2 (H3k4me3 Input)

description: Library name: KO, Ang II-2 (H3k4me3 Input)


title: ChIP_YMEP_H3K36me3_rep1

description: Library name: Sample 59


title: ChIP_YMEP_H3K27me3_rep2

description: Library name: Sample 62


title: KO, Ang II-3 (H3k4me3 Input)

description: Library name: KO, Ang II-3 (H3k4me3 Input)


title: ChIP_YMEP_H3K27me3_rep1

description: Library name: Sample 58


title: KO, Ang II-1 (H3k4me3 Input)

description: Library name: KO, Ang II-1 (H3k4me3 Input)


title: ChIP_YGMP_H3K27ac_rep2

description: Library name: Sample 56

value: GMP


title: A375MAFG2

value: overexpressing MAFG


title: ChIP_YMEP_H3K27ac_rep1

description: Library name: Sample 60


title: A375GFP3


title: ChIP_YGMP_H3K4me3_rep2

description: Library name: Sample 53


title: WT, Ang II-3 (H3k4me3 ChIP)

description: Library name: WT, Ang II-3 (H3k4me3 ChIP)

value: CSE WT


title: WT, Ang II-2 (H3k4me3 ChIP)

description: Library name: WT, Ang II-2 (H3k4me3 ChIP)


title: ChIP_YGMP_H3K36me3_rep2

description: Library name: Sample 55


title: ChIP_YGMP_H3K27ac_rep1

description: Library name: Sample 52


title: ChIP_YGMP_H3K36me3_rep1

description: Library name: Sample 51


title: A375MAFG1


title: ChIP_YMEP_H3K4me3_rep1

description: Library name: Sample 57


title: WT, Ang II-1 (H3k4me3 ChIP)

description: Library name: WT, Ang II-1 (H3k4me3 ChIP)


title: ChIP_YGMP_H3K27me3_rep1

description: Library name: Sample 50


title: WMpLMAFG3


title: A375GFP2


title: A375GFP1


title: ChIP_YGMP_H3K4me3_rep1

description: Library name: Sample 49


title: ChIP_YCMP_H3K4me3_rep2

description: Library name: Sample 45

value: CMP


title: ChIP_YCMP_H3K27ac_rep2

description: Library name: Sample 48


title: WMpLMAFG2


title: ChIP_YCMP_H3K36me3_rep2

description: Library name: Sample 47


title: WT, Ang II-1 (H3k4me3 Input)

description: Library name: WT, Ang II-1 (H3k4me3 Input)


title: WT, Ang II-2 (H3k4me3 Input)

description: Library name: WT, Ang II-2 (H3k4me3 Input)


title: ChIP_YGMP_H3K27me3_rep2

description: Library name: Sample 54


title: ChIP_YCMP_H3K27me3_rep2

description: Library name: Sample 46


title: WMpLMAFG1


title: WT, Ang II-3 (H3k4me3 Input)

description: Library name: WT, Ang II-3 (H3k4me3 Input)


title: ChIP_YCMP_H3K27ac_rep1

description: Library name: Sample 44


title: ChIP_YCMP_H3K36me3_rep1

description: Library name: Sample 43


title: ChIP_YCMP_H3K4me3_rep1

description: Library name: Sample 41


title: KO, Ang II-1 (H3k9ac ChIP)

description: Library name: KO, Ang II-1 (H3k9ac ChIP)


title: KO, Ang II-2 (H3k9ac ChIP)

description: Library name: KO, Ang II-2 (H3k9ac ChIP)


title: RNA-seq, Hetero, mature CD8 SP thymocytes, rep.3

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

institute: RIKEN Yokohama

description: Library name: WRPW, rep.3

data_processing:
Adapter sequences were trimmed from the reads by Cutadapt (v4.0)
Mapping to the mm10 genome using HISAT2 (v2.2.1)
Mapping reads on each gene were counted using featureCounts (v2.0.8)
Differential gene expression analysis was conduncted using edgeR (v3.36.0)
Assembly: mm10
Supplementary files format and content: tabular file including counts of each transcript

source_name: Thymus

extract_protocol:
Total RNA was extracted from FACS-purified mature CD8 SP thymocytes using RNeasy Mini kit (Qiagen). RNA integrity number was evaluated using an Agilent 2100 Bioanalyzer with the RNA 6000 Pico Kit (Agiletn), and samples with RNA integrity number > 8 were used for library preparation.
RNA-seq libraries were constructed from 10 ng of total RNA using the NEBNext RNA Library Prep Kit for Illumina (NEB).

value: Thymus

value: Mature CD8 SP thymocytes

value: Runx3 +/WRPW


title: RNA-seq, Hetero, mature CD8 SP thymocytes, rep.1

description: Library name: WRPW, rep.1


title: ChIP_YCMP_H3K27me3_rep1

description: Library name: Sample 42


title: RNA-seq, Hetero, mature CD8 SP thymocytes, rep.2

description: Library name: WRPW, rep.2


title: KO, Ang II-3 (H3k9ac Input)

description: Library name: KO, Ang II-3 (H3k9ac Input)


title: KO, Ang II-3 (H3k9ac ChIP)

description: Library name: KO, Ang II-3 (H3k9ac ChIP)


title: WMpLGFP3

value: overexpressing GFP


title: 164-TMGM-3

data_processing:
Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1).
Processed raw reads were then aligned to human genome GRCh38 using STAR (v2.7.7a).
Gene expression was evaluated as read count at gene level with RSEM (v1.3.0) and Gencode gene model v30.
Gene express data were then normalized and differential expression between experimental groups were evaluated using DEseq2.
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt: tab-delimited files include raw counts for each sample
Supplementary files format and content: TPM_counts.txt: tab-delimited files include TPM values for each sample

growth_protocol: Cells were grown in RPMI with 5% Fetal Bovine Serum  and 1% Penicillin-Streptomycin

extract_protocol:
RNA was isolated using Qiagen mIRNease kit
Library preparation was performed by NEBNext® Ultra™ RNA Library Prep Kit for Illumina® which is for non-stranded libraries.

value: overexpressing T-MGM


title: WMpLGFP2


title: RNA-seq, Wt, mature CD8 SP thymocytes, rep.1

description: Library name: WT, rep.1

value: Runx3 +/+


title: H3K27me3-ChIP, Runx3 +/WRPW

data_processing:
Sequencing data was analyzed on Galaxy platform (https://usegalaxy.org/)
Mapping to the mm10 genome using bowtie2 (v2.5.3)
Removing reads with low mapping quality (MAPQ<30), and duplicated reads using filter (v2.5.2) and MarkDuplicates (v3.1.1.0)
Piling up fragments using MACS2 (v.2.2.9.1) with defalt setting
Converting bedgraph into bigwig files using Convert BedGraph to BigWig (v1.0.1)
Assembly: mm10
Supplementary files format and content: bigwig files: read coverage across the whole genome (fragment pileup per million reads)

extract_protocol:
Freshly isolated thymocytes were cross-linked with 1% formaldehyde. Nuclei were isolated from the cells using lysis buffer and chromatin DNA was fragmented by sonication. The lysate was incubated with rabbit anti-mouse Runx3 (Cell Signaling Technology, D6E2), anti-H3k4me3 (Cell Signaling Technology, C42D8), or anti-H3K27me3 (Cell Signaling Technology, C36B11) antibodies pre-bound to Dynabeads® M-280 Sheep anti-Rabbit IgG overnight at 4 degree C. Chromatin DNA was eluted from Dynabeads and reverse-crosslinked. Samples were treated with RNase A and Proteinase K, and DNA was purified by phenol/Chroroform/Isoamylalcohol treatment and echanol precipitation.
Purified DNA was subjected to the re-sonication with a Covaris S220 to produce DNA fragments with an average size of 200 bp, and was used for library preparation with NEBNext ChIP-seq Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (New England BioLabs). Sequencing was performed by genomics facility at RIKEN IMS with Illumina HiSeq 2500.

value: Mature CD8 SP

tag: chip antibody

value: C36B11, CST


title: 164-TMGM-2


title: KO, Ang II-1 (H3k9ac Input)

description: Library name: KO, Ang II-1 (H3k9ac Input)

value: Primary

value: Smooth Muscle Cells


title: H3K4me3-ChIP, Runx3 +/WRPW

value: C42D8, CST


title: H3K4me3-ChIP, Runx3 +/+


title: H3K27me3-ChIP, Runx3 +/+


title: KO, Ang II-2 (H3k9ac Input)

description: Library name: KO, Ang II-2 (H3k9ac Input)

value: CSE KO

value: Ang II


title: WT, Ang II-3 (H3k9ac ChIP)

description: Library name: WT, Ang II-3 (H3k9ac ChIP)


title: Runx3-ChIP, Runx3 +/WRPW, rep.2

value: D6E2, CST


title: 164-TMGM-1

value: Melanoma

value: Cancer


title: WMpLGFP1


title: 164-GFP-3


title: RNA-seq, Wt, mature CD8 SP thymocytes, rep.2

description: Library name: WT, rep.2


title: Runx3-ChIP, Runx3 +/WRPW, rep.1


title: 164-GFP-2


title: Runx3-ChIP, Runx3 +/+, rep.1


title: Old HSC H3K27ac rep2

description: ChIP-sequencing

data_processing:
cutadapt
BWA-mem alignment
Assembly: mm10
Supplementary files format and content: text file

source_name: Hematopoietic stem cell

extract_protocol:
none provided by the submitter
ChIP-seq pipeline

value: Old


title: Runx3-ChIP, Runx3 +/+, rep.2

value: Thymus


title: WT, Ang II-2 (H3k9ac ChIP)

description: Library name: WT, Ang II-2 (H3k9ac ChIP)

value: CSE WT


title: Young HSC H3K27ac rep2

description: ChIP-sequencing

value: Young


title: WT, Ang II-3 (H3k9ac Input)

description: Library name: WT, Ang II-3 (H3k9ac Input)


title: Young HSC H3K27ac rep1

description: ChIP-sequencing


title: Old HSC H3K36me3 rep2

description: ChIP-sequencing


title: Thalamus, VLP, OCD, Pair 9, HUID 13125

first: Susanne

last: Ahmari

state: PA

address: 450 Technology Dr Suite 223

department: Psychiatry

description: S2 flow cell

data_processing:
CLC Genomics Workbench v 22.0.1
Sequence reads were mapped to GRCh38.106 using CLC Genomics Workbench. Mapping parameters: mismatch cost = 2, insertion or deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8
Read count extraction and normalization was performed using CLC Genomics Workbench
Assembly: GRCh38.p13
Assembly: Ensemble Archive Release v106
Supplementary files format and content: comma-separated values files include raw and normalized (TPM, RPKM) counts for each sample

source_name: Thalamus

extract_protocol:
RNA was extracted using an RNeasy Plus Micro kit (Qiagen)
RNA libraries for RNAseq were generated using Illumina TruSeq Stranded Total RNA kit following manufacturer protocols

value: Thalamus

tag: nucleus

value: VLP

tag: hemisphere

value: right

tag: diagnosis group

value: OCD

tag: subject id

tag: subject pair

value: Pair 9


title: 164-GFP-1

value: overexpressing GFP


title: Thalamus, VLP, CON, Pair 9, HUID 1637

description: S2 flow cell

value: CON

value: HUID 1637


title: KO, Ang II-3 (H3k9me3 ChIP)

description: Library name: KO, Ang II-3 (H3k9me3 ChIP)

value: Primary

value: Smooth Muscle Cells

value: CSE KO


title: WT, Ang II-1 (H3k9ac Input)

description: Library name: WT, Ang II-1 (H3k9ac Input)

value: Ang II


title: KO, Ang II-2 (H3k9me3 ChIP)

description: Library name: KO, Ang II-2 (H3k9me3 ChIP)


title: Old HSC H3K27ac rep1

description: ChIP-sequencing


title: Young HSC H3K36me3 rep2

description: ChIP-sequencing


title: Young HSC H3K27me3 rep2

description: ChIP-sequencing


title: Young HSC H3K36me3 rep1

description: ChIP-sequencing


title: Young HSC H3K4me3 rep2

description: ChIP-sequencing


title: Young HSC H3K27me3 rep1

description: ChIP-sequencing


title: Thalamus, VLP, CON, Pair 8, HUID 13237

description: S2 flow cell

value: Pair 8


title: Thalamus, VLP, OCD, Pair 7, HUID 13022

description: S2 flow cell

value: Pair 7


title: Young HSC H3K4me3 rep1

description: ChIP-sequencing

extract_protocol: none provided by the submitter


title: Old HSC H3K36me3 rep1

description: ChIP-sequencing

value: Old


title: Old HSC ATACseq 7

description: ATAC-sequencing

extract_protocol:
The engineered hyperactive Tn5 transposase that is preloaded with DNA adapters thus removing the need for a separate annealing step.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols


title: KO, Ang II-1 (H3k9me3 ChIP)

description: Library name: KO, Ang II-1 (H3k9me3 ChIP)


title: Thalamus, VLP, CON, Pair 7, HUID 1083

description: S2 flow cell

value: HUID 1083


title: WT, Ang II-1 (H3k9ac ChIP)

description: Library name: WT, Ang II-1 (H3k9ac ChIP)

value: CSE WT


title: KO, Ang II-3 (H3k9me3 Input)

description: Library name: KO, Ang II-3 (H3k9me3 Input)


title: Old HSC ATACseq 5

description: ATAC-sequencing


title: Thalamus, VLP, OCD, Pair 6, HUID 13051

description: S2 flow cell

value: Thalamus

value: Pair 6


title: Old HSC ATACseq 8

description: ATAC-sequencing


title: Young HSC ATACseq 4

description: ATAC-sequencing

value: Young


title: Young HSC ATACseq 3

description: ATAC-sequencing


title: KO, Ang II-1 (H3k9me3 Input)

description: Library name: KO, Ang II-1 (H3k9me3 Input)


title: Old HSC ATACseq 6

description: ATAC-sequencing


title: Thalamus, VLP, OCD, Pair 8, HUID 13173

description: S2 flow cell

value: VLP

value: right

value: OCD


title: Thalamus, VLP, CON, Pair 6, HUID 1391

description: S2 flow cell

value: CON

value: HUID 1391


title: WT, Ang II-2 (H3k9ac Input)

description: Library name: WT, Ang II-2 (H3k9ac Input)

value: Primary


title: Young HSC ATACseq 2

description: ATAC-sequencing

data_processing:
cutadapt
BWA-mem alignment
macs2 peak-calling
Assembly: mm10
Supplementary files format and content: text file


title: WT, Ang II-3 (H3k9me3 ChIP)

description: Library name: WT, Ang II-3 (H3k9me3 ChIP)

value: Smooth Muscle Cells


title: Thalamus, VLP, OCD, Pair 5, HUID 1785

description: S2 flow cell

value: HUID 1785

value: Pair 5


title: WT, Ang II-2 (H3k9me3 ChIP)

description: Library name: WT, Ang II-2 (H3k9me3 ChIP)

value: Ang II


title: Old HSC RNAseq 5

description: RNA-sequencing

data_processing:
cutadapt
STAR alignment (RNA-seq)
Assembly: mm10
Supplementary files format and content: text file

extract_protocol:
RNA was purified with TRIzol TM Reagent (Invitrogen, 15596026) and Direct-zol RNA microprep (Zymo R2060)
RNA-seq libraries were constructed using SMARTer Standard total RNA-seq kit v2


title: Old HSC RNAseq 4

description: RNA-sequencing


title: Old HSC RNAseq 7

description: RNA-sequencing


title: Old HSC RNAseq 6

description: RNA-sequencing


title: WT, Ang II-1 (H3k9me3 ChIP)

description: Library name: WT, Ang II-1 (H3k9me3 ChIP)


title: Thalamus, VLP, OCD, Pair 4, HUID 1505

description: S2 flow cell

value: HUID 1505

value: Pair 4


title: Thalamus, VLP, CON, Pair 4, HUID 1092

description: S2 flow cell

value: HUID 1092


title: Thalamus, VLP, CON, Pair 5, HUID 1543

description: S2 flow cell

value: HUID 1543


title: KO, Ang II-2 (H3k9me3 Input)

description: Library name: KO, Ang II-2 (H3k9me3 Input)

value: CSE KO


title: WT, Ang II-3 (H3k9me3 Input)

description: Library name: WT, Ang II-3 (H3k9me3 Input)

value: CSE WT


title: Old HSC RNAseq 2

description: RNA-sequencing

value: Old


title: Old HSC RNAseq 3

description: RNA-sequencing


title: Young HSC ATACseq 1

description: ATAC-sequencing

value: Young


title: Thalamus, VLP, OCD, Pair 3, HUID 1435

description: S2 flow cell

value: Thalamus

value: VLP

value: right

value: HUID 1435

value: Pair 3


title: Old HSC RNAseq 1

description: RNA-sequencing


title: Old HSC RNAseq 8

description: RNA-sequencing


title: Young HSC RNAseq 3

description: RNA-sequencing


title: Thalamus, VLP, CON, Pair 3, HUID 13032

description: S2 flow cell

value: CON


title: WT, Ang II-2 (H3k9me3 Input)

description: Library name: WT, Ang II-2 (H3k9me3 Input)

value: Primary

value: Smooth Muscle Cells


title: Young HSC RNAseq 4

description: RNA-sequencing


title: WT, Ang II-1 (H3k9me3 Input)

description: Library name: WT, Ang II-1 (H3k9me3 Input)

value: Ang II


title: Young HSC RNAseq 2

description: RNA-sequencing

data_processing:
cutadapt
STAR alignment (RNA-seq)
featureCount, gene-level extraction (RNA-seq)
Assembly: mm10
Supplementary files format and content: text file


title: Young HSC RNAseq 1

description: RNA-sequencing


title: scRNA-seq of Ixodes scapularis adult female salivary glands group 5 replicate 2

city: Hamilton

first: Lucas

last: Tirloni

state: MT

address: 903 S 4th Street

department: LB

institute: NIAID

description:
Library name: SCL_G5_2
10x Genomics

data_processing:
The raw sequencing data were demultiplexed and processed using the Cell Ranger Software Suite (10x Genomics). Cell Ranger (v7.0.1) was used to perform sample demultiplexing, barcode processing,  and alignments, as well as counting of single-cell barcode and unique molecular identifier (UMI) gene counting. The 'cellranger count' function was applied for alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting. The genome of Ixodes scapularis reference genome (ASM1692078v2) was used as the reference genome for the alignment.  Following generation of gene-cell matrices from Cell Ranger, further analysis was performed using Seurat v4.3, an R package for analysis of single cell RNAseq data. Sample-specific low-quality cells were excluded based on a threshold set at three median absolute deviations (MAD) from the median of the overall cell population, applied to both UMI and feature counts. Quality control was not applied to exclude cells with high mitochondrial gene content, because mitochondrial genes were expected to be upregulated in feeding groups.  The gene expression matrix was then normalized and scaled. Variable features were identified using the 'vst' method in the 'FindVariableFeatures' function. Dimensionality reduction was performed using principal component analysis (PCA). The most significant principal components were selected for downstream analyses. Based on these components, shared nearest neighbor (SNN) graph-based clustering was performed. Clusters were visualized using Uniform Manifold Approximation and Projection (UMAP). For each cluster, differential gene expression was performed to identify cluster-specific marker genes. These markers were used to annotate cell clusters based on known marker genes for cell types.
Assembly: Ixodes scapularis reference genome (ASM1692078v2)
Supplementary files format and content: *filtered_feature_bc_matrix.zip

organism: Ixodes scapularis

source_name: salivary glands

extract_protocol:
The Ixodes scapularis ticks used in this study were obtained from the tick-rearing facility at Oklahoma State University (Stillwater, OK, USA). Prior to infestation, unfed ticks were maintained at 21°C and 85% relative humidity. One day before feeding, female ticks were paired with males to allow mating. Adult ticks were placed on the outer ear of four naïve female New Zealand rabbits, restricted by orthopedic stockinets that were glued in place. A total of 20 female and 20 male ticks (40 ticks per ear, 80 ticks per rabbit) were allowed to attach. To classify ticks by blood-feeding index, partially fed ticks were collected from the host based on engorgement size, sorted by weight, and divided into biological triplicates: an unfed group (UF) (15 females per replicate, weighing 1.6 mg in average), group G2 (5 females per replicate, weighing 7.2 mg in average), and group G5 (4 females per replicate, weighting 41.5 mg in average). After removal from the host, ticks were rinsed sequentially with 1% bleach, nuclease-free water, 70% ethanol, and a final rinse with nuclease-free water. Ticks were dissected within two hours of removal. Salivary glands (SGs) were isolated and stored in fresh, ice-cold, nuclease-free HBSS buffer (Invitrogen, Carlsbad, CA, USA). To prepare a single-cell suspension, the salivary glands were dissociated following a mechanical and enzymatic protocol. The resulting cell suspension was filtered through a 40 µm Flowmi cell strainer and centrifuged at 600 rcf for five minutes to pellet the cells. The pellet was then resuspended in an appropriate volume of HBSS media to achieve the target cell concentration. Cell counting and viability were assessed using trypan blue staining and a Neubauer chamber for visualization.
The single cell suspensions were loaded (7,000 cells) onto a Chromium Controller for GEM (Gel Bead-In-EMulsion) generation in triplicate for three groups and barcoding using the Chromium Single Cell 3’ Reagent Kits according to the manufacturer's protocol (10x Genomics). After cDNA synthesis, amplification, and library construction, the libraries were sequenced by the Illumina NovaSeq 6000 System.

value: salivary glands

tag: group

value: female


title: scRNA-seq of Ixodes scapularis adult female salivary glands group 5 replicate 3

description:
Library name: SCL_G5_3
10x Genomics

value: group G5 (4 females per replicate, weighting 41.5 mg in average)

tag: Sex


title: IMG Kdm5b KOp rep 3

first: Jessica

last: Wohlfahrt

state: FL

address: 4202 E Fowler Ave

institute: University of South Florida

description: Library name: Z3

data_processing:
Results were analyzed by the Zymo bioinformatics team using the Zymo Research RNA-Seq pipeline (v2.1.0) adapted from nf-core/rnaseq pipeline (v1.4.2) and built using Nextflow (v21.10.5) to provide differentially expressed genes, normalized counts, and data visualizations.
Sequences were quality controlled with FastQC (v0.11.9), trimmed by Trim Galore! (v0.6.6), and aligned to the reference genome by STAR (v2.6.1d).
SAMtools (v1.9) was used to filter and index BAM file and quality control of the library was ensured by RSeQC (v4.0.0) as well as QualiMap (v2.2.2-dev).
Picard tools (v2.23.9) was used to mark duplicate reads, and a complexity estimate of the library was completed using Preseq (v2.0.3). Additional quality control was completed at this stage using dupRadar (v1.18.0).
Alignment to genes was completed using featureCounts (v2.0.1) and UCSC genome browser RepeatMasker rRNA tracks for rRNA genes.
DESeq2 (v1.28.0) was used to determine differential expression of genes with enrichment analysis by g:Profiler python API (v1.0.0). Data visualization and quality control were completed using MultiQC (v1.9).
Assembly: GRCm39
Supplementary files format and content: Microsoft Excel Worksheet includes normalized counts for each sample

source_name: IMG

growth_protocol: Both wildtype (WT) and the Kdm5b knockout pool (KOp) cells of an adult-derived mouse microglia cell line (IMG, Sigma-Aldrich, SCC134) were grown in triplicate in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 U/mL streptomycin at 37°C and 5% CO2.

extract_protocol:
500ng RNA was extracted and purified by the Zymo Research Total RNA-Seq Service using the KingFisher Flex (Thermo) with the Quick-RNA MagBead kit (R2132, Zymo) and the RNA Clean & Concentrator MagBead kit (R1081, Zymo).
RNA libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (R3000, Zymo Research) following the manufacturer’s instructions (v1.3.0). D1000 ScreenTape Assay on TapeStation (Agilent) was used to confirm library construction.

value: IMG

value: microglia

value: Kdm5b KO pool


title: scRNA-seq of Ixodes scapularis adult female salivary glands group 5 replicate 1

description:
Library name: SCL_G5_1
10x Genomics


title: IMG Kdm5b KOp rep 2

description: Library name: Z2


title: scRNA-seq of Ixodes scapularis adult female salivary glands group 2 replicate 3

description:
Library name: SCL_G2_3
10x Genomics

value: group G2 (5 females per replicate, weighing 7.2 mg in average)


title: Thalamus, VLP, OCD, Pair 2, HUID 1424

description: S2 flow cell

value: OCD

value: HUID 1424

value: Pair 2


title: Thalamus, VLP, CON, Pair 2, HUID 1293

description: S2 flow cell

value: Thalamus

value: VLP

value: right

value: HUID 1293


title: Thalamus, VLP, OCD, Pair 11, HUID 13169

description: S2 flow cell

value: Pair 11


title: IMG Kdm5b KOp rep 1

description: Library name: Z1


title: scRNA-seq of Ixodes scapularis adult female salivary glands group unfed replicate 2

description:
Library name: SCL_UF_2
10x Genomics

value: unfed group (UF) (15 females per replicate, weighing 1.6 mg in average)


title: IMG WT rep 3

description: Library name: WT3

value: wild-type


title: scRNA-seq of Ixodes scapularis adult female salivary glands group unfed replicate 1

description:
Library name: SCL_UF_1
10x Genomics

value: salivary glands


title: Thalamus, VLP, CON, Pair 11, HUID 1834

description: S2 flow cell

value: CON

value: HUID 1834


title: scRNA-seq of Ixodes scapularis adult female salivary glands group 2 replicate 1

description:
Library name: SCL_G2_1
10x Genomics

value: female


title: Thalamus, VLP, OCD, Pair 10, HUID 13154

description: S2 flow cell

value: Pair 10


title: scRNA-seq of Ixodes scapularis adult female salivary glands group unfed replicate 3

description:
Library name: SCL_UF_3
10x Genomics


title: Thalamus, VLP, CON, Pair 10, HUID 1282

description: S2 flow cell

value: HUID 1282