title: TrnA-mutant, 25-week-old, 78% mutation load, mtscATAC-seq

first: Guo-shi

last: Chai

state: --- Select One ---

address: No. 600 Dunyu Road, Sandun Town, Xihu District, Hangzhou, Zhejiang PR China

institute: Westlake University

description:
Library name: sample3
10x Genomics

library_source: other

data_processing:
The nuclear mitochondrial DNA segments (NUMTs) were masked in the mm10 genome (PMID: 32788668 and PMID: 36792778). Raw sequencing data were aligned to the modified mm10 reference genome using CellRanger-ATAC (v 2.1.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: small intestine

extract_protocol:
Mouse small intestines were excised and flushed with cold PBS. The tissues were opened longitudinally along the lumen and cut into 1 cm segments. The segments were incubated in cold PBS containing 20 mM EDTA for 1 hour on ice. Following incubation, the supernatant was discarded and replaced with fresh cold PBS. The tubes were then vortexed for 30 seconds to dissociate villi and crypts from the basement membrane. The released villi and crypts were transferred to a new tube and digested with TrypLE (Thermo Fisher Scientific, 12604013) supplemented with 10 mg/mL DNase I (Roche, 10104159001) for 10 minutes at 32°C. The digested cell suspension was sequentially filtered through 70-μm and 40-μm cell strainers. Isolated single IECs were centrifuged and resuspended in cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing 2% fetal bovine serum (FBS). For flow cytometry sorting, cell suspensions were stained on ice for 30 minutes with the following antibodies diluted in cold 2% FBS in DPBS: CD45-APC (1:100, clone 30-F11, BioLegend, 103112), CD31-PE (1:50, clone MEC13.3, BioLegend, 102507), TER-119-Brilliant Violet 510™ (1:50, clone TER-119, BioLegend, 116237), and CD326-APC/Cyanine7 (1:100, clone G8.8, BioLegend, 118217). Following incubation, cells were washed with cold 2% FBS in DPBS, resuspended in the same buffer supplemented with 0.1 μg/mL DAPI (BioLegend, 422801), and filtered through a 40-μm cell strainer. Fluorescence-activated cell sorting was performed using a BD FACSAria™ Fusion instrument, and the sorting strategy was visualized using FlowJo Software.
The mtscATAC-seq libraries were generated using the 10× Chromium Controller and the Chromium Single Cell ATAC Library & Gel Bead Kit (1000390) following the manufacturer’s protocols (CG000496 Rev B and CG000169 Rev E), with a modified mtDNA enrichment method adapted from previous studies(40). Sorted cells were washed with cold DPBS and fixed with 1% formaldehyde (ThermoFisher Scientific, 28906) for 10 minutes at room temperature. Fixation was quenched by adding glycine to a final concentration of 0.125 M. The cells were then washed again with cold DPBS and pelleted by centrifugation at 1,000 × g for 5 minutes at 4°C. The cell pellet was lysed in lysis buffer (10 mM Tris–HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, and 1% BSA) for 3 minutes on ice, followed by addition of cold wash buffer (10 mM Tris–HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, and 1% BSA). After another centrifugation step at 1,000 × g for 5 minutes at 4°C, the supernatant was removed, and the cells were resuspended in 1× nuclei buffer (10× Genomics). Cell concentration was determined using trypan blue exclusion and adjusted for Tn5 tagmentation according to the Chromium Single Cell ATAC Reagent Kit protocol. Following tagmentation, cells were loaded onto a Chromium Next GEM Chip H (1000161), and single-cell gel bead-in-emulsions (GEMs) were generated using the Chromium Controller. Barcoded, tagmented DNA was amplified via PCR after GEM breakage and purified to construct mtscATAC libraries. Library quality and concentration were assessed using the Qubit dsDNA HS Assay Kit (Invitrogen) and the High Sensitivity DNA Kit (Agilent). Libraries were sequenced on the NovaSeq 6000 and NovaSeq X Plus platforms with a 2 × 150 bp paired-end read configuration.

value: small intestine

value: intestinal epithelial cells

value: 78% TrnA mutation load


title: TrnA-mutant, 3-week-old, 79% mutation load, mtscATAC-seq

status: Public on Jul 30 2026

type: SRA

city: Hangzhou

country: China

description:
Library name: sample1
10x Genomics

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

value: 79% TrnA mutation load


title: SJSTS030873_D1

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

country: USA

institute: St. Jude Children's Research Hospital

description:
Library name: SJSTS030873_D1
10X Genomics 3’ RNA kit

library_source: transcriptomic single cell

data_processing:
Aligning and transcript counting were performed using 10x Genomics Cell Ranger version 7
Assembly: Hg38 for patient samples. Combined Hg38 and mm10 for PDX samples
Supplementary files format and content: processed data reflect cell ranger output from the filter_bc_matrix folder, including feature names, cell barcode IDs, and expression count matrix (unnormalized)

molecule: polyA RNA

organism: Homo sapiens

source_name: MRT

extract_protocol:
cells or nuclei were extracting using protocols described in Slyper et al Nat Medicine 2020 (https://doi.org/10.1038/s41591-020-0844-1)
Libraries were generating using the 10x Genomics 3' gene expression kits version 3.1

value: MRT

tag: group

value: Patient

tag: method

value: nucleus

tag: sjid

tag: age

tag: gender

value: male

tag: primary site

value: kidney

tag: sample site

tag: timepoint

value: diagnostic

tag: sample

value: primary

tag: treatment status

value: untreated


title: aortic tissues, TAD, rep3

first: Fan

last: He

address: No.50 Majiaqiao Street

institute: Zhejiang University

description:
Library name: SAMPLE 8
FPKM.TAD3

library_source: transcriptomic

data_processing:
Real-Time Analysis (version 3.4.4) and bcl2fastq (version 2.19 ).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.1).
Trimmed sequence reads were mapped to GRCh38/hg38 using hisat2 with default parameters.
Read count extraction were performed using htseq-count,and normalized counts using FPKM (Fragments Per Kilobase Million).
Assembly: hg38
Supplementary files format and content: Processed data files.xlsx

molecule: total RNA

source_name: aortic tissues

extract_protocol:
RNA was extracted by TRIpure Reagent (BioTeke, Beijing, China), 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina®  following manufacturer's protocols.

value: aortic tissues


title: SJMRT015723_D1

description:
Library name: SJMRT015723_D1
10X Genomics 3’ RNA kit

value: unknown

value: chest wall

value: recurrence

value: metastatic

value: treated


title: aortic tissues, TAD, rep2

description:
Library name: SAMPLE 7
FPKM.TAD2


title: mES, dTAG_DGCR8, DMSO, FLAG, rep1

city: Shanghai

first: ying

last: cai

address: Fudan University, 131 Dong'an Road, Shanghai

institute: Fudan University

description: Library name: mES, dTAG_DGCR8, DMSO, FLAG, rep1

library_source: genomic

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 genome using Bowtie2 (v2.5.1). PCR duplicates were removed using samtools (v1.11) rmdup. Genome coverage bigwig files were generated by deeptools (v2.5.7) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files

molecule: genomic DNA

growth_protocol: E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2.

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

treatment_protocol: dTAG cells were treated with DMSO or 100 nM dTAG for 24 hours.

tag: cell line

value: Embryonic stem cells

tag: treatment

value: DMSO 24h

tag: chip antibody


title: aortic tissues, TAD, rep1

description:
Library name: SAMPLE 6
FPKM.TAD1


title: SJMEL063827_D1

description:
Library name: SJMEL063827_D1
10X Genomics 3’ RNA kit

source_name: MEL

value: MEL

value: female

value: pontine meninges


title: SJMEL030083_D2

description:
Library name: SJMEL030083_D2
10X Genomics 3’ RNA kit

value: Patient

value: nucleus

value: leg


title: aortic tissues, control, rep5

description:
Library name: SAMPLE 5
FPKM.Control5


title: aortic tissues, control, rep4

description:
Library name: SAMPLE 4
FPKM.Control4


title: SJMEL030083_D1

description:
Library name: SJMEL030083_D1
10X Genomics 3’ RNA kit

value: male


title: SJIFS030375_R1

description:
Library name: SJIFS030375_R1
10X Genomics 3’ RNA kit

source_name: IFS

value: IFS

value: thigh

value: primary


title: aortic tissues, control, rep3

description:
Library name: SAMPLE 3
FPKM.Control3

value: aortic tissues


title: SJHGS015726_D2

description:
Library name: SJHGS015726_D2
10X Genomics 3’ RNA kit

source_name: HGS

value: HGS

value: lung

value: recurrent

value: metastasis


title: aortic tissues, control, rep2

description:
Library name: SAMPLE 2
FPKM.Control2


title: SJHGS015726_D1

description:
Library name: SJHGS015726_D1
10X Genomics 3’ RNA kit

value: treated


title: SJOS012409_D1

description:
Library name: SJOS012409_D1
10X Genomics 3’ RNA kit

source_name: OS

value: OS

value: Femur

value: diagnostic


title: aortic tissues, control, rep1

description:
Library name: SAMPLE 1
FPKM.Control1


title: mES, dTAG_DGCR8, dTAG3h, PROseq, rep1

description: Library name: mES, dTAG_DGCR8, dTAG3h, PROseq, rep1

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with “-q 25”, remaining reads were mapped to mouse rDNA database using Bowtie (v2.5.1) with parameter “--very-sensitive-local” to remove rRNA contamination. Unmapped reads were aligned to mm10 genome and hg38 genome respectively, with default parameter. Samtools (v1.11) was used to filter and deduplicate SAM files. The counts of spike-in hg38 reads were used to generate normalization factors for coverage profiles.
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files
Library strategy: PRO-seq

extract_protocol:
RNA was isolated with TRIzol.
Permeabilized cells were subjected to nuclear run-on reactions in the presence of biotin-labeled nucleotides. Biotinylated nascent RNA was extracted, fragmented by base hydrolysis, and enriched using streptavidin magnetic beads. Enriched RNA was ligated with a 3' RNA adaptor using T4 RNA ligase I, followed by another round of streptavidin bead enrichment. The 5' ends were then decapped with RNA 5' Pyrophosphohydrolase (RppH) and repaired with Polynucleotide Kinase (PNK) before ligation to a 5' RNA adaptor with T4 RNA ligase I. Adaptor-ligated RNA was enriched again with streptavidin beads. Reverse transcription (RT) was performed using Superscript IV (Thermo Fisher Scientific) with a custom RT primer. The reverse transcription products were proceeded to library amplification using Phusion polymerase (NEB) for 12-14 cycles. Libraries were sequenced on the Illumina NovaSeq platform in paired-end 60/50 bp cycle runs following the manufacturer's protocols.

treatment_protocol: dTAG Cells were treated with DMSO or dTAG-13 for 3h.

value: Embryonic stem cells

value: dTAG 3h


title: SJHGS012411_D1

description:
Library name: SJHGS012411_D1
10X Genomics 3’ RNA kit

value: Patient

value: nucleus

value: female

value: untreated


title: mES, dTAG_ERH, dTAG3h, TTseq, rep2

description: Library name: mES, dTAG_ERH, dTAG3h, TTseq, rep2

data_processing:
Raw reads were filtered by Trim Galore (v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with “-q 25”, remaining reads were mapped to mouse rDNA database using Bowtie (v2.5.1) with parameter “--very-sensitive-local” to remove rRNA contamination. Unmapped reads were aligned to mm10 genome and hg38 genome respectively, with default parameter. Samtools (v1.11) was used to filter and deduplicate SAM files. The counts of spike-in hg38 reads were used to generate normalization factors for coverage profiles.
Assembly: Genome_build: mm10
Supplementary files format and content: Genome coverage bigwig files

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.


title: IgG_3 (RRBS)

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: Library name: BLRB009

data_processing:
RRBS FASTQ files were aligned to the in silico bisulfite converted genome (mm10) using Bismark with the Bowtie2 option. Binary Alignment Map (BAM) files were parsed to derive DNA methylation calls that were collapsed to the CpG level using custom R scripts that made use of the ‘Rsamtools’ and ‘data.table’ packages (available upon request).
Data were summarized for CpGs that were covered at 10x in all samples and CpGs that were covered at 10x by all groups
Assembly: mm10
Supplementary files format and content: Count matrix of methylated and unmethylated reads for each CpG covered by a minimum of 10 reads within each group. For each CpG there is the chromosome location and for each sample there are three columns of data containing the sample name followed by the following extensions: ".meth", % of reads methylated; ".u", number of reads unmethylated; ".m", number of reads methylated.

source_name: Spleen

extract_protocol:
Spleen and dLN from influenza infected mice were homogenized, red blood cells lysed with ACK Lysis buffer (150mM NH4Cl, 10mM KHCO3 and 0.5M EDTA (pH 7.3)). Lymphocytes from influenza infected mice were stained for cell sorting.
For each sample, DNA was harvested from 1,000-2,000 cells using Zymo Quick-DNA Microprep Kit (Zymo Research, D302;). The DNA was split at a 60:40 ratio and digested overnight with Mspl (New England BioLabs, R0106S) and Taql (New England BioLabs, R0149S) respectively to yield various sized sticky end fragments. The digested DNA fragments were combined, purified, and size selected using AMPure XP beads (Beckman Coulter, A63881). Lambda (λ) DNA (New England BioLabs, N3011S), CpG Methyltransferase New England BioLabs, M0226S) and ΦX174 RF I (PhiX) DNA (New England BioLabs, N3021S) were spiked in as bisulfite conversion internal controls. A-tailing, end repair, and methylated sequencing adaptor ligation was performed using the KAPA Hyper Prep Kit (KAPA Biosystems, KK850). Purified adaptor ligated genomic DNA was treated with sodium bisulfite to convert unmethylated cytosines to uracils with the EpiTech Bisulfite Kit (Qiagen, 5912). Bisulfite converted DNA was then PCR amplified (KAPA Biosystems, KK2802) with dual indexing Illumina compatible primers.

treatment_protocol: C57BL/6J mice were infected with 15000 vfu influenza A/PR8/34. At 14 days post infection, the spleen and mediastinal-lung draining lymph node (dLN) from 5 mice were pooled into 1 sample for analysis.

value: Spleen

value: Antibody secreting cell

tag: cell sorting_markers

tag: asc isotype

value: IgG

tag: mouse pool


title: SJOS010929_D1

description:
Library name: SJOS010929_D1
10X Genomics 3’ RNA kit

tag: tissue

value: male

value: primary


title: SJHGS012410_D1

description:
Library name: SJHGS012410_D1
10X Genomics 3’ RNA kit

value: HGS

tag: group

value: unknown

value: lung

value: diagnosis


title: IgA_3 (RRBS)

description: Library name: BLRB007

tag: cell type

value: IgA


title: IgM_3 (RRBS)

description: Library name: BLRB008

value: IgM


title: SJHB030622_D1

description:
Library name: SJHB030622_D1
10X Genomics 3’ RNA kit

source_name: HB

value: HB

tag: method

tag: sjid

value: liver

value: diagnostic

value: metastasis

value: treated


title: IgM_2 (RRBS)

description: Library name: BLRB005


title: SJGCT030372_D1

description:
Library name: SJGCT030372_D1
10X Genomics 3’ RNA kit

source_name: GCT

value: GCT

value: Patient

value: nucleus

tag: age

tag: gender

value: testes

value: untreated


title: SJEWS063834_A2

description:
Library name: SJEWS063834_A2
10X Genomics 3’ RNA kit

source_name: EWS

value: EWS

value: female

tag: primary site

tag: sample site

value: recurrence


title: IgG_2 (RRBS)

description: Library name: BLRB006

value: Spleen

value: Antibody secreting cell

value: IgG


title: SJGIST030657_D1

description:
Library name: SJGIST030657_D1
10X Genomics 3’ RNA kit

source_name: GIST

value: GIST

value: male

value: stomach

tag: timepoint

tag: sample

value: primary


title: SJOS001116_M2

description:
Library name: SJOS001116_M2
10X Genomics 3’ RNA kit

value: OS

value: unknown

value: Lung

value: metastasis

tag: treatment status


title: IgA_2 (RRBS)

description: Library name: BLRB004

value: IgA


title: SJEWS063834_A1

description:
Library name: SJEWS063834_A1
10X Genomics 3’ RNA kit

value: Patient

value: nucleus

value: chest wall


title: IgG_1 (RRBS)

description: Library name: BLRB003


title: IgM_1 (RRBS)

description: Library name: BLRB002

value: IgM


title: SJEWS063829_D1

description:
Library name: SJEWS063829_D1
10X Genomics 3’ RNA kit

value: EWS

value: female

value: femur

value: diagnosis

value: treated


title: SJEWS063826_D1

description:
Library name: SJEWS063826_D1
10X Genomics 3’ RNA kit

value: male

value: rib

value: axilla

value: recurrence

value: untreated


title: IgA_1 (RRBS)

description: Library name: BLRB001

value: Spleen

value: Antibody secreting cell


title: SJEWS049193_D2

description:
Library name: SJEWS049193_D2
10X Genomics 3’ RNA kit

value: ilium

value: lung

value: metastasis


title: IgG_3 (ATAC-seq)

description: Library name: BLA009

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie
bigWig files were normalized to reads per million and generated using GenomicRanges and bedGraphToBigWig function from the UCSC genome browser
Assembly: mm10
Supplementary files format and content: reads per million normalized bigWig files

extract_protocol:
Spleen and dLN from influenza infected mice were homogenized, red blood cells lysed with ACK Lysis buffer (150mM NH4Cl, 10mM KHCO3 and 0.5M EDTA (pH 7.3)). Lymphocytes from influenza infected mice were stained for cell sorting.
For each sample, 5,000 cells were sorted into culture media and transposition was performed. Briefly, cells were resuspended in 12.5 μl 2x TD Buffer, 2.5 μl Tn5, 2.5 μl 1% Tween-20, 2.5 μl 0.2% Digitonin, and 5 μl H2O and incubated at 37C for 1 hr. Cells were then lysed with the addition of 2 μl 10 mg/ml Proteinase-K, 23 μl Tagmentation Clean-up buffer (326 mM NaCl, 109 mM EDTA, 0.63% SDS), and incubated at 40°C for 30 min. Tagmented DNA was purified and size selected for small fragments using AMPure XP beads (Beckman Coulter, A63881) and PCR amplified (Roche, KK2602) with dual indexing Illumina primers (Illumina, FC-131- 2004) ) to generate a sequencing library. Final libraries were again purified and size selected using AMPureXP beads, quantitated by QuBit (Life Technologies, Q33231).

value: IgG


title: IgM_3 (ATAC-seq)

description: Library name: BLA008

value: IgM


title: SJEWS001321_D2

description:
Library name: SJEWS001321_D2
10X Genomics 3’ RNA kit

value: EWS

value: Patient

value: nucleus

value: tibia

value: primary


title: SJEWS049193_D1

description:
Library name: SJEWS049193_D1
10X Genomics 3’ RNA kit

value: male

value: treated


title: SJSTS046147_R1

description:
Library name: SJSTS046147_R1
10X Genomics 3’ RNA kit

source_name: EPSARC

value: EPSARC

value: spine

value: diagnostic


title: IgG_2 (ATAC-seq)

description: Library name: BLA006

value: Spleen


title: IgA_3 (ATAC-seq)

description: Library name: BLA007

value: Antibody secreting cell

value: IgA


title: SJUESL030381_D1

description:
Library name: SJUESL030381_D1
10X Genomics 3’ RNA kit

source_name: EMBSARC

value: EMBSARC

value: female

value: liver

value: untreated


title: IgM_2 (ATAC-seq)

description: Library name: BLA005

value: IgM


title: SJDSRCT049192_R1

description:
Library name: SJDSRCT049192_R1
10X Genomics 3’ RNA kit

source_name: DSRCT

value: DSRCT

value: Patient

value: abdominopelvic

value: recurrence

value: metastatic


title: IgA_2 (ATAC-seq)

description: Library name: BLA004


title: SJDSRCT049192_D1

description:
Library name: SJDSRCT049192_D1
10X Genomics 3’ RNA kit

value: nucleus

value: male

value: primary

value: treated


title: SJDSRCT046151_D1

description:
Library name: SJDSRCT046151_D1
10X Genomics 3’ RNA kit

value: pelvis

value: diagnostic


title: IgM_1 (ATAC-seq)

description: Library name: BLA002

value: Spleen

value: Antibody secreting cell


title: IgA_1 (ATAC-seq)

description: Library name: BLA001

value: IgA


title: SJCCS030604_R1

description:
Library name: SJCCS030604_R1
10X Genomics 3’ RNA kit

source_name: CCSST

value: CCSST

value: female

value: thumb


title: IgA_3 (RNA-seq)

description: Library name: BLA009

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the GENCODE v27 reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: tab delimited text file of RPKM normalized read counts for each gene

extract_protocol:
Spleen and dLN from influenza infected mice were homogenized, red blood cells lysed with ACK Lysis buffer (150mM NH4Cl, 10mM KHCO3 and 0.5M EDTA (pH 7.3)). Lymphocytes from influenza infected mice were stained for cell sorting.
For each sample, 1,000 cells were sorted into RLT buffer (Qiagen 79216) containing 1% 2-Mercaptoethanol. RNA was isolated using Zymo Quick-RNA MicroPrep Kit (Zymo Research, R1051). Synthesis of cDNA was performed using SMART-Seq v4 Ultra Low Input RNA Kit (634894; Takara Bio) kit. Final libraries were generated using 200 pg of cDNA as input for the NexteraXT kit (Illumina, FC-131-1024) with 12 cycles of PCR amplification.


title: IgG_1 (ATAC-seq)

description: Library name: BLA003

value: IgG


title: SJCCS030167_D3

description:
Library name: SJCCS030167_D3
10X Genomics 3’ RNA kit

source_name: CCSK

value: CCSK

value: Patient

value: kidney


title: IgG_3 (RNA-seq)

description: Library name: BLA008


title: SJACT030812_D2

description:
Library name: SJACT030812_D2
10X Genomics 3’ RNA kit

source_name: ACT

value: ACT

value: Abdomen

value: Distal pancreas

value: untreated


title: IgM_3 (RNA-seq)

description: Library name: BLA007

value: IgM


title: SJACT030812_D1

description:
Library name: SJACT030812_D1
10X Genomics 3’ RNA kit

value: nucleus

value: male

value: Adrenal mass

value: primary


title: IgA_2 (RNA-seq)

description: Library name: BLA006

value: Spleen

value: Antibody secreting cell

value: IgA


title: SJACT030686_D1

description:
Library name: SJACT030686_D1
10X Genomics 3’ RNA kit

value: unknown

value: not collected

value: Abdominal mass


title: IgG_2 (RNA-seq)

description: Library name: BLA005

value: IgG


title: Sample Line 11 HTO

city: Pittsburgh

first: Amr

middle: H

last: Sawalha

state: PA

address: 530 45th Street

department: Department of Pediatrics

institute: University of Pittsburgh

description:
Library name: Sawalha_043024_3-1_3Pv4_FBHTO_S22
10x Genomics

data_processing:
Sequencing reads were aligned to the GRCh38 human reference genome using the Cell Ranger pipeline v8.0.1 from 10x Genomics. The resulting count matrices were imported into Seurat v5.0 for downstream analysis. Quality control included removal of cells with fewer than 400 detected genes, cells with more than 10% mitochondrial reads, and genes detected in fewer than 3 cells. Doublets were identified and removed using DoubletFinder. Filtered count matrices were normalized and variance-stabilized using SCTransform v2 with regression of mitochondrial content. Dimensionality reduction was performed using PCA followed by UMAP, and cell types were annotated using canonical marker expression and reference mapping to the Monaco Immune Database through SingleR.
Assembly: GRCh38
Supplementary files format and content: comma-separated values files and .h5 files containing demultiplexed scRNA-seq samples
Supplementary files format and content: The All.merged6_SCT_FLT_clean.rds contains the processed single-cell Seurat object to facilitate interpretation of the dataset together with the previously submitted raw FASTQ files and demultiplexed data.

source_name: peripheral blood

extract_protocol:
Peripheral blood samples were collected into EDTA-coated tubes and processed within 2 hours of venipuncture. Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Paque density gradient centrifugation and washed twice with phosphate-buffered saline (PBS). No red blood cell lysis step was required. Cells were resuspended in freezing media composed of 90% fetal bovine serum (FBS) and 10% dimethyl sulfoxide (DMSO), aliquoted at 5 × 10⁶ cells per vial, and frozen. Cells were later thawed, washed, and assessed for viability, with >85% viability required before downstream single-cell processing.
TotalSeq B hashtag antibodies were used for sample multiplexing in pools of 4 to 6 samples. Single-cell suspensions were loaded onto the 10x Genomics Chromium Controller for droplet encapsulation and library construction using the Chromium Next GEM Single Cell 3′ v4 HT kit, following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform with a mean sequencing depth of over 11,000 reads per cell.

value: peripheral blood

value: PBMC


title: Sample Line 11

description:
Library name: Sawalha_043024_3-1_3Pv4_GEX_S11
10x Genomics


title: Sample Line 10 HTO

description:
Library name: Sawalha_043024_3_3Pv4_FBHTO_S21
10x Genomics


title: IgA_1 (RNA-seq)

description: Library name: BLA003


title: IgG_1 (RNA-seq)

description: Library name: BLA002


title: IgM_2 (RNA-seq)

description: Library name: BLA004


title: SJDSRCT030722_D1

description:
Library name: SJDSRCT030722_D1
10X Genomics 3’ RNA kit

value: DSRCT

value: Patient

value: thigh

value: diagnostic

value: metastatic

value: treated


title: Sample Line 10

description:
Library name: Sawalha_043024_3_3Pv4_GEX_S10
10x Genomics


title: IgM_1 (RNA-seq)

description: Library name: BLA001

value: IgM


title: Sample Line 9 HTO

description:
Library name: Sawalha_043024_2_3Pv4_FBHTO_S20
10x Genomics


title: Alveoar AT2 cells isolated from WT mice fed with regular chow 2

city: Houston

first: Tingting

last: Mills

state: Texas

address: 6431 Fannin

institute: The University of Texas Health Science Center at Houston

description: Library name: G5_2

data_processing:
Illumina bcl2fastq was used for conversion into Fastq files.
Trimmotatic (version 0.39) was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads were mapped to mouse genome GRCm38/mm10 with STAR (2.7.1a) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools  (1.7) (Li et al. 2009).
The University of California, Santa Cruz (UCSC) known canonical gene set (55,421) were used for annotation, and the reads mapped to the exons were quantified using analyzeRNA.pl script in the Homer software  (v4.11) (Heinz et al. 2010) with an option of –rpkm or -noadj for FPKM or raw read counts, respectively
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include raw read counts and FPKM values for each Sample.

source_name: Lung

growth_protocol: Primary lung alveolar epithelial type 2 cells are cultured in epithelial growth medium (DMEM with 10% FBS and 1% penicillin-streptomycin antibiotics) at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
RNA were extracted using the RNAeasy mini plus kit (Qiagen).
Regular Poly-A Tail Library Preparation

treatment_protocol: Mice were fed with standard chow alone or standard chow supplemented with 0.1% NOB (10 mg/kg b.w.) beginning at weaning (postnatal day 25) and continued for 20 weeks.

value: Lung

tag: cell line

value: Primary cells

tag: genotype

value: Wildtype

tag: treatment

value: Regular chow


title: Alveoar AT2 cells isolated from WT mice fed with regular chow 1

description: Library name: G5_1


title: Sample Line 8 HTO

description:
Library name: Sawalha_043024_1_3Pv4_FBHTO_S19
10x Genomics


title: Alveoar AT2 cells isolated from Cry1/2 dKO mice fed with regular chow 2

description: Library name: G2_2

value: Cry1/2 dKO


title: Alveoar AT2 cells isolated from Cry1/2 dKO mice fed with regular chow 1

description: Library name: G2_1


title: Alveoar AT2 cells isolated from Cry1/2 dKO mice fed with Nobiletin 2

description: Library name: G1_2

value: Nobiletin Chow


title: Sample Line 7 HTO

description:
Library name: Sawalha_042424_3_3Pv4_FBHTO_S18
10x Genomics


title: Alveoar AT2 cells isolated from Cry1/2 dKO mice fed with Nobiletin 1

description: Library name: G1_1


title: Sample Line 7

description:
Library name: Sawalha_042424_3_3Pv4_GEX_S7
10x Genomics


title: Sample Line 6 HTO

description:
Library name: Sawalha_042424_2_3Pv4_FBHTO_S17
10x Genomics


title: BAL cells from 2 WT mice receiving WT Bone marrow 3

description: Library name: S9394_BAL

data_processing:
Illumina bcl2fastq was used for conversion into Fastq files.
Trimmotatic (version 0.39) was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads were mapped to mouse genome GRCm39/mm39 with STAR (2.7.4a) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools  (1.7) (Li et al. 2009).
The University of California, Santa Cruz (UCSC) known canonical gene set (55,416) were used for annotation, and the reads mapped to the exons were quantified using analyzeRNA.pl script in the Homer software  (v4.11) (Heinz et al. 2010) with an option of –rpkm or -noadj for FPKM or raw read counts, respectively
Assembly: GRCm39/mm39
Supplementary files format and content: Tab-delimited text files include raw read counts and FPKM values for each Sample.

source_name: Primary Cells

growth_protocol: Cells are not cultured

treatment_protocol: CD45.1 recipient mice were lethally irradiated with two doses of 500 RAD delivered 3 hours apart. Bone marrow cells were freshly isolated from Cry1/2 double-knockout (dKO) or age- and sex-matched wild-type (WT) donor mice, and 3.5 × 10⁶ total BM cells were retro-orbitally injected into the irradiated CD45.1 recipients to establish hematopoietic chimeras.

value: Immue Cells


title: Sample Line 6

description:
Library name: Sawalha_042424_2_3Pv4_GEX_S6
10x Genomics


title: BAL cells from 3 WT mice receiving WT Bone marrow 2

description: Library name: S91_92_BAL


title: Sample Line 5 HTO

description:
Library name: Sawalha_042424_1_3Pv4_FBHTO_S16
10x Genomics


title: BAL cells from 3 WT mice receiving WT Bone marrow

description: Library name: S888990_BAL


title: Sample Line 5

description:
Library name: Sawalha_042424_1_3Pv4_GEX_S5
10x Genomics


title: Sample Line 4 HTO

description:
Library name: Sawalha_042324_3_3Pv4_FBHTO_S15
10x Genomics


title: Sample Line 8

description:
Library name: Sawalha_043024_1_3Pv4_GEX_S8
10x Genomics


title: BAL cells from 2 WT mice receiving Cry1/2 dKO Bone marrow 3

description: Library name: S8687_BAL


title: BAL cells from 3 WT mice receiving Cry1/2 dKO Bone marrow

description: Library name: S80_81_82BAL


title: BAL cells from 3 WT mice receiving Cry1/2 dKO Bone marrow 2

description: Library name: S838485_BAL


title: Sample Line 3 HTO

description:
Library name: Sawalha_042324_2_3Pv4_FBHTO_S14
10x Genomics


title: Sample Line 4

description:
Library name: Sawalha_042324_3_3Pv4_GEX_S4
10x Genomics


title: ND_rep2

city: Nanjing

first: Jiashuo

last: Li

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

description: Library name: ND_rep2

data_processing:
The raw bisulfite sequencing reads were trimmed to remove adaptors and low-quality bases by using trim_galore (v0.6.10) (parameters: -q 20 --phred33 --length 30 --stringency 3 --paired --clip_R1 10 --clip_R2 10). Next, Bismark (v0.24.2) was used to map clean reads to GRCm38/GRCh38 with single-end alignment mode (parameters: --non_directional --bowtie2 --bam --single_end). PCR duplicates were removed using deduplicate_bismark with default parameters. And only the high-quality reads (MAPQ > 10) were retained for further analysis. DNA methylation level estimation. The DNA methylation level of each cytosine site in the reference genome sequence was calculated as the percentage of reads supporting C (methylated). Unless otherwise specified, the DNA methylation level of CpG sites in a given sample or region refers to the average methylation level across that sample or region. Owing to the low number of input cells, CpG sites with read depths ≥1 were included for methylation analysis. For DNA methylation pattern profiling, the whole genome was divided into consecutive 20-kb windows, and the average methylation level within each bin was calculated. Principal component analysis (PCA) of methylation data was performed using methylKit (v1.30.0). Differentially methylated regions (DMRs) calling. Differential methylation analysis was performed using metilene (v0.2.6) with default parameters, and differentially methylated regions (DMRs) were annotated using ChIPseeker (v1.36.0).
Assembly: GRCh38,GRCm39
Supplementary files format and content: BigWig including CG sites methylation values for each sample

source_name: oocyte

extract_protocol:
Collect 15 mouse oocytes/one human oocyte for cell lysis.
Whole-genome bisulfite sequencing (WGBS) was performed on mouse oocytes using 15 oocytes as input, whereas Enzymatic Methyl-seq (EM-seq) was applied to human oocytes starting from a single cell due to its high efficiency with minimal input. Library preparation and sequencing: Mouse metaphase II (MII) oocytes (n = 15 per replicate, two biological replicates per group) were used for WGBS. Briefly, cells were lysed in buffer (10 mM Tris-HCl, pH 7.4, 2% SDS), and genomic DNA was extracted and digested with proteinase K. Purified DNA was subjected to bisulfite conversion using the EZ DNA Methylation-Gold Kit (ZYMO, D5008), followed by purification with Agencourt AMPure XP beads (Beckman). The converted DNA was end-repaired and dA-tailed, then ligated to Illumina sequencing adapters. Libraries were amplified for 13 cycles using Illumina universal PCR primer and indexed primers. For human samples, individual oocytes were lysed and genomic DNA were fragmented to ~ 300 bp using a DNA fragmentation device (Shanghai Jingxin, DNA Fragmentation Model 26A). Libraries were constructed using the NEBNext® Enzymatic Methyl-seq kit (NEB, E7120 L) and the Unique Dual Index Primer pairs (NEB, E7140L). Unmethylated lambda phage DNA and CpG-methylated plasmid pUC19 DNA were included as negative and positive controls. For single-oocyte libraries, amplification was performed for 18 cycles. Libraries were purified using the DNA Clean & Concentrator-5 kit (ZYMO, D4013). Finally, equimolar amounts of libraries were pooled and subjected to paired-end sequencing on an Illumina NovaSeq 6000 platform.

value: oocyte


title: Sample Line 3

description:
Library name: Sawalha_042324_2_3Pv4_GEX_S3
10x Genomics

value: peripheral blood


title: ND_rep1

description: Library name: ND_rep1


title: Sample Line 2 HTO

description:
Library name: Sawalha_042324_1_3Pv4_FBHTO_S13
10x Genomics

value: PBMC


title: Sample Line 2

description:
Library name: Sawalha_042324_1_3Pv4_GEX_S2
10x Genomics


title: HFD_rep1

description: Library name: HFD_rep1


title: Sample Line 1 HTO

description:
Library name: Sawalha_041824_3Pv4_FBHTO_S12
10x Genomics


title: Sample Line 1

description:
Library name: Sawalha_041824_3Pv4_GEX_S1
10x Genomics


title: TeloHAEC, PA supplied, Estradiol supplied 4

city: Chongqing

first: Qing

middle: Rex

last: Lyu

state: Chongqing

address: #118 Xingguang Avenue

department: Affiliated Chongqing General Hospital

institute: Chongqing University

description: Library name: PA_Es_4

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp (v 0.20.1) a n d the low quality reads were removed to obtain the clean reads.
Assembly: The clean reads were mapped to the reference genome using HISAT22 (v2.1.0).
Supplementary files format and content: FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4 (v 0.11.2).

source_name: Telo-HAEC

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer ’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Telo-HAEC

value: endothelial cell

value: WT

value: PA-supplied


title: batch41-BN-control-3weeks

city: Los Angeles

first: Victoria

last: Ho

state: CA

address: 710 Westwood Plz

institute: University of California, Los Angeles

description:
Library name: 41BN
10x Genomics

data_processing:
Cell Ranger (v7.1.0) count was used to generate gene-count matrices. SoupX (v1.6.2) adjustCounts (roundToInt=TRUE) was used to remove ambient RNA contamination. ScDblFinder (v1.22.0) was used to remove doublets. Additional quality control: nFeature_RNA > 200, nCount_RNA > 500, percent.mt < 5%; genes kept if expressed in ≥3 cells. Samples were merged and filtered using Seurat (v5.3.0).
Assembly: GRCm39 (mm10)
Supplementary files format and content: All samples were merged and used to create tab separated values files and matrix file

source_name: dorsal hippocampus

extract_protocol:
Following at least 12 hours of seizure-freedom on EEG, pilocarpine-treated and control littermates were processed in batches. Mice were anesthetized with isofluorane and decapitated. Brains were quickly removed and bilateral hippocampi were dissected on ice. Each hippocampus was bisected and the dorsal half was snap frozen and stored at -80 C for nuclei isolation at a later date. Nuclei were isolated from frozen tissue by Dounce homogenization in 0.1% NP-40 and purification on a discontinuous iodixanol gradient.
Single-cell libraries were prepared using the Chromium Single Cell 3' Reagent Kit v3 (10x Genomics) according to the manufacturer's protocol.

treatment_protocol: Six week old wildtype mice received intraperitoneal injections of a weight-based dose of pilocarpine to induce status epilepticus (SE). Controls received saline. One week prior to tissue collection, skull screws were implanted for EEG monitoring. Tissue was collected at 3- and 6-weeks post-SE.

value: dorsal hippocampus

tag: Sex

value: male

tag: strain

value: control

tag: batch


title: HFD_rep2

description: Library name: HFD_rep2

tag: tissue


title: batch41-AL-epilepsy-3weeks

description:
Library name: 41AL
10x Genomics

value: pilocarpine


title: TeloHAEC, PA supplied, Estradiol supplied 3

description: Library name: PA_Es_3

tag: cell type


title: batch41-BR-control-3weeks

description:
Library name: 41BR
10x Genomics


title: TeloHAEC, PA supplied, Estradiol supplied 2

description: Library name: PA_Es_2


title: batch41-AB-epilepsy-3weeks

description:
Library name: 41AB
10x Genomics


title: batch40-6-BR-control-6weeks

description:
Library name: 40BR
10x Genomics


title: TeloHAEC, PA supplied, Estradiol supplied 1

description: Library name: PA_Es_1


title: TeloHAEC, PA supplied, Control 4

description: Library name: PA_Con_4

value: Control


title: batch40-6-BL-control-6weeks

description:
Library name: 40BL
10x Genomics


title: TeloHAEC, PA supplied, Control 3

description: Library name: PA_Con_3


title: TeloHAEC, PA supplied, Control 2

description: Library name: PA_Con_2


title: batch40-3-BN-control-3weeks

description:
Library name: 40BN
10x Genomics


title: batch40-3-BB-control-3weeks

description:
Library name: 40BB
10x Genomics


title: batch40-6-AR-epilepsy-6weeks

description:
Library name: 40AR
10x Genomics


title: batch40-6-AB-epilepsy-6weeks

description:
Library name: 40AB
10x Genomics


title: TeloHAEC, PA supplied, Control 1

description: Library name: PA_Con_1


title: batch40-3-A1R-epilepsy-3weeks

description:
Library name: 40A1R
10x Genomics


title: Healthy control 4

first: Kathryn

last: Torok

email: TRH107@pitt.edu, kst7@pitt.edu

address: 4401  Penn Ave

description: Library name: H4

data_processing:
Step 1: Raw FASTQ files were aligned to the human genome (GRCh38 v44/Ensembl110 annotation) using Cell Ranger 8.0.1. In the first step, PBMC libraries were demultiplexed using the cellranger multi function.
Step 2: In the second step, alignment for all samples’ RNA and ADT reads was executed with cellranger multi.
Step 3: Cell Ranger output was transformed into counts matrices in R 4.4.1 with the Read10X() function from Seurat 5.3.0.
Step 4: QC filtering, normalization and scaling, batch correction, dimension reductiond & cell type annotation with Seurat 5.3.0
Assembly: GRCh38
Supplementary files format and content: seurat object
Library strategy: CITE-seq

source_name: PBMC

extract_protocol:
Cells are isolated from up to six 25um sections cut from rehydrated FFPE blocks using the xylene and GentleMACS OctoDissociator section of the Sample Preparation from FFPE Tissue Sections for GEM-X Flex Gene Expression protocol. Cell yield and quality is checked using NucSpot 470 stain on a Revvity Cellometer Ascend automated cell counter. If cells will not be barcoded immediately, they are stored in Long Term Storage Buffer at -80C.
Fixed cells are first hybridized with Probe Barcodes. Using a microfluidic chip, the hybridized samples are then partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs). A pool of ~737,000 10x GEM Barcodes (also referred to as 10x Barcodes) is sampled separately to index the contents of each partition. Up to 16 samples may be equally pooled in each GEM reaction using uniquely barcoded probe sets for generation of one library. Final libraries are checked for size on the Agilent Tapestation and concentration using the Invitrogen Qubit 2.0. Libraries are then sequenced on a NovaSeq X Plus sequencer.

value: blood


title: Healthy control 3

description: Library name: H3


title: Healthy control 2

description: Library name: H2


title: batch40-3-A1L-epilepsy-3weeks

description:
Library name: 40A1L
10x Genomics


title: batch35-BN-control-6weeks

description:
Library name: 35BN
10x Genomics


title: batch35-BB-control-6weeks

description:
Library name: 35BB
10x Genomics


title: Healthy control 1

description: Library name: H1


title: batch35-A2R-epilepsy-6weeks

description:
Library name: 35A2R
10x Genomics


title: Sample 594, 6 months post ASCT

description: Library name: 594_6mo

value: jSSc


title: Sample 594, pre-ASCT

description: Library name: 594_baseline


title: batch35-A1N-epilepsy-6weeks

description:
Library name: 35A1N
10x Genomics


title: Sample 594, 24 months post ASCT

description: Library name: 594_24mo


title: Sample Line 9

description:
Library name: Sawalha_043024_2_3Pv4_GEX_S9
10x Genomics


title: Sample 594, 12 months post ASCT

description: Library name: 594_12mo


title: batch29-AR-epilepsy-3weeks

description:
Library name: 29AR
10x Genomics


title: batch29-BL-control-3weeks

description:
Library name: 29BL
10x Genomics


title: Sample 591, pre-ASCT

description: Library name: 591_baseline


title: batch29-AN-epilepsy-3weeks

description:
Library name: 29AN
10x Genomics


title: batch28-AR-epilepsy-3weeks

description:
Library name: 28AR
10x Genomics


title: Sample 515, pre -ASCT

description: Library name: 515_baseline


title: Sample 591, 6 months post ASCT

description: Library name: 591_6mo


title: batch28-BB-control-3weeks

description:
Library name: 28BB
10x Genomics


title: batch28-BN-control-3weeks

description:
Library name: 28BN
10x Genomics


title: Sample 591, 12 months post ASCT

description: Library name: 591_12mo


title: Sample 591, 24 months post ASCT

description: Library name: 591_24mo


title: Sample 515, 24 months post ASCT

description: Library name: 515_24mo


title: batch28-AL-epilepsy-3weeks

description:
Library name: 28AL
10x Genomics


title: Sample 515, 6 months post ASCT

description: Library name: 515_6mo


title: batch27-BB-control-6weeks

description:
Library name: 27BB
10x Genomics


title: batch27-BN-control-6weeks

description:
Library name: 27BN
10x Genomics


title: MCF7 FAH ABE 3

city: Boston

first: Jonathan

middle: David

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

description: Library name: B6

data_processing:
Raw sequencing reads were aligned to a reference transcriptome generated from the Ensembl v104 human transcriptome with salmon v1.4.0 using options “--seqBias --useVBOpt --gcBias --posBias --numBootstraps 30 --validateMappings”.
Assembly: hg38
Supplementary files format and content: ".sf files from salmon v1.4.0. The columns represent the following: Name: the name of the target transcript provided in the input transcript database (FASTA file). Length: the length of the target transcript in nucleotides. EffectiveLength: the computed effective length of the target transcript. TPM: the estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). NumReads: the estimate of the number of reads mapping to each transcript that was quantified."

growth_protocol: MCF7 cells were maintained in DMEM high glucose supplemented with 10% FBS and pen/strep in humidified incubator at 37 degrees

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen)
mRNA-seq library preparation was performed by Novogene using poly-T oligo magnetic beads to enrich mRNA, followed by fragmentation, cDNA synthesis, end repair, A-tailing, adapter ligation, and PCR amplification using  NEBNext Ultra RNA Library Prep Kits for Illumina.

treatment_protocol: 200 nM abemaciclib for 3 days

value: Breast cancer cells

value: FAH WT

value: Abemaciclib


title: batch27-AL-epilepsy-6weeks

description:
Library name: 27AL
10x Genomics


title: batch25-BR-control-6weeks

description:
Library name: 25BR
10x Genomics


title: MCF7 FAH ABE 2

description: Library name: B5


title: batch25-BL-control-6weeks

description:
Library name: 25BL
10x Genomics


title: batch27-AR-epilepsy-6weeks

description:
Library name: 27AR
10x Genomics


title: MCF7 FAH DMSO 3

description: Library name: B3

value: Vehicle


title: MCF7 FAH DMSO 2

description: Library name: B2


title: MCF7 FAH ABE 1

description: Library name: B4


title: batch25-AN-epilepsy-6weeks

description:
Library name: 25AN
10x Genomics


title: MCF7 FAH DMSO 1

description: Library name: B1


title: MCF7 EV ABE 3

description: Library name: A6

value: EV control


title: batch25-AB-epilepsy-6weeks

description:
Library name: 25AB
10x Genomics


title: spleen tissue under chronic bleeding

city: Singapore

first: Rui

last: Yokomori

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

description: Library name: C BLD SP

data_processing:
Raw data were processed using Cell Ranger v7.0.0 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated files and matrix files

source_name: spleen

growth_protocol: Live cells were isolated from spleens under chronic PHZ and BLD treatment.

extract_protocol:
Cells were washed, and processed using the 10x Genomics Chromium controller and Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 following manufacturer's instructions.
Single-cell libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) by Novogene. Sequencing was performed on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads (PE150) by Novogene.

treatment_protocol: C57BL/6 mice were subjected to PHZ injection or bleeding every 3 days for one month to induce chronic anemia.

value: spleen

value: chronic Bleeding


title: spleen tissue under chronic PHZ

description: Library name: C PHZ SP

value: chronic PHZ


title: MCF7 EV DMSO 2

description: Library name: A2


title: MCF7 EV ABE 2

description: Library name: A5


title: MCF7 EV DMSO 3

description: Library name: A3


title: CHIPseq.Lap2alphaKO.LaminA.E1.16cycles

city: Vienna

first: Roland

last: Foisner

address: Dr.-Bohr-Gasse 9

country: Austria

institute: Max Perutz Labs, Medical University of Vienna

description:
Library name: CHIPseq.Lap2alphaKO.LaminA.E1.16cycles
Illumina NovaSeq SP

data_processing:
Reads were mapped to the reference genome using NextGenMap v0.5.5 using default settings
Mapped reads were filtered for a minimum mapping quality of 10 using samtools view -q 10
log2ratio files between the ChIP and Input samples were generated using bamCompare from deepTools with the settings --operation log2 --binSize 10
Peaks were called using two different programs, with MACS2 v2.1.4 using settings callpeak --nomodel -g mm -p 1e-1 --extsize 200, and with SPP v1.14 with default settings. Peak regions that are common in both MACS2 and SPP peaks were extracted for each sample using bedtools intersect. To optimize these peak intersections for the regions with maximum CHIPseq signal, HOMER v4.11.1 was used, by first running makeTagDirectory on all mapped read  files of all samples, then by running  getPeakTags -center on the peak files. Resulting peak sets were used to be combined for 16 and 20 sonication cycles of the same samples using bedtools merge.
Assembly: GRCm38
Supplementary files format and content: The bigwig (bw) files contain the log2ratio values across the genome for each sample.
Supplementary files format and content: The bed files contain the peaks for each sample.

source_name: mouse dermal fibroblast

growth_protocol: DMEM supplemented with 10% fetal calf serum, 100 U/ml penicillin and 100 μg/ml streptomycin; cultured at 37°C and 5% CO2

extract_protocol:
Cells were subjected to dual crosslinkin using 2mM DSG and 1% v/v formaldehyde. Fixation was quenched and followed by washing and cell lysis. Chromatin was sonicated using the Bioruptor PICO sonicator by Diagenode.
Libraries were prepared by the Next Generation Sequencing facility at the Vienna Biocenter Core Facilities, Vienna, Austria, using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina and unique NEB adaptors. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: mouse dermal fibroblast

value: Lap2alpha KO


title: MCF7 EV ABE 1

description: Library name: A4


title: MCF7 EV DMSO 1

description: Library name: A1


title: CHIPseq.Lap2alphaKO.LaminA.E1.20cycles

description:
Library name: CHIPseq.Lap2alphaKO.LaminA.E1.20cycles
Illumina NovaSeq SP


title: T47D KO ABE_4

description: Library name: LD7LS6_16

data_processing:
FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1, Read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp, Alignment to the appropriate reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, Coordinate sorting of BAM files using samtools v1.22.1, UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0.
Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RSeQC v5.0.4 and Qualimap v2.3, Generation of comprehensive QC report using MultiQC v1.32.
Gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes cpm for each sample

growth_protocol: T47D cells were maintained in DMEM high glucose supplemented with 10% FBS and pen/strep in humidified incubator at 37 degrees

extract_protocol:
Cells submitted to Plasmidsaurus for extraction
RNA-seq libraries were generated by converting mRNA into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation and library indexing and amplification.

treatment_protocol: 500 nM Abemaciclib for 3 days

value: FAH Knockout


title: CHIPseq.Lap2alphaKO.LaminA.3A6.16cycles

description:
Library name: CHIPseq.Lap2alphaKO.LaminA.3A6.16cycles
Illumina NovaSeq SP


title: CHIPseq.Lap2alphaKO.LaminA.3A6.20cycles

description:
Library name: CHIPseq.Lap2alphaKO.LaminA.3A6.20cycles
Illumina NovaSeq SP


title: T47D KO ABE_3

description: Library name: LD7LS6_15


title: CHIPseq.Lap2alphaKO.INPUT.16cycles

description:
Library name: CHIPseq.Lap2alphaKO.INPUT.16cycles
Illumina NovaSeq SP


title: CHIPseq.Lap2alphaKO.INPUT.20cycles

description:
Library name: CHIPseq.Lap2alphaKO.INPUT.20cycles
Illumina NovaSeq SP


title: T47D KO ABE_1

description: Library name: LD7LS6_13


title: T47D KO ABE_2

description: Library name: LD7LS6_14


title: T47D KO DMSO_4

description: Library name: LD7LS6_12


title: CHIPseq.Lap2alphaKO.CHD4.16cycles

description:
Library name: CHIPseq.Lap2alphaKO.CHD4.16cycles
Illumina NovaSeq SP


title: CHIPseq.Lap2alphaKO.CHD4.20cycles

description:
Library name: CHIPseq.Lap2alphaKO.CHD4.20cycles
Illumina NovaSeq SP


title: T47D KO DMSO_3

description: Library name: LD7LS6_11


title: T47D KO DMSO_1

description: Library name: LD7LS6_9


title: CHIPseq.Lap2alphaKO.BRG1.20cycles

description:
Library name: CHIPseq.Lap2alphaKO.BRG1.20cycles
Illumina NovaSeq SP


title: T47D KO DMSO_2

description: Library name: LD7LS6_10


title: CHIPseq.Lap2alphaKO.BRG1.16cycles

description:
Library name: CHIPseq.Lap2alphaKO.BRG1.16cycles
Illumina NovaSeq SP


title: CHIPseq.WT.Lap2alpha.1H11.20cycles

description:
Library name: CHIPseq.WT.Lap2alpha.1H11.20cycles
Illumina NovaSeq SP

value: WT


title: T47D Cntr ABE_4

description: Library name: LD7LS6_8

value: control guide


title: CHIPseq.WT.LaminA.E1.20cycles

description:
Library name: CHIPseq.WT.LaminA.E1.20cycles
Illumina NovaSeq SP


title: CHIPseq.WT.Lap2alpha.1H11.16cycles

description:
Library name: CHIPseq.WT.Lap2alpha.1H11.16cycles
Illumina NovaSeq SP


title: T47D Cntr ABE_2

description: Library name: LD7LS6_6


title: CHIPseq.WT.LaminA.E1.16cycles

description:
Library name: CHIPseq.WT.LaminA.E1.16cycles
Illumina NovaSeq SP


title: T47D Cntr ABE_3

description: Library name: LD7LS6_7


title: T47D Cntr ABE_1

description: Library name: LD7LS6_5


title: CHIPseq.WT.LaminA.3A6.20cycles

description:
Library name: CHIPseq.WT.LaminA.3A6.20cycles
Illumina NovaSeq SP


title: T47D Cntr DMSO_4

description: Library name: LD7LS6_4


title: CHIPseq.WT.LaminA.3A6.16cycles

description:
Library name: CHIPseq.WT.LaminA.3A6.16cycles
Illumina NovaSeq SP


title: CHIPseq.WT.INPUT.20cycles

description:
Library name: CHIPseq.WT.INPUT.20cycles
Illumina NovaSeq SP


title: T47D Cntr DMSO_2

description: Library name: LD7LS6_2


title: T47D Cntr DMSO_3

description: Library name: LD7LS6_3


title: CHIPseq.WT.INPUT.16cycles

description:
Library name: CHIPseq.WT.INPUT.16cycles
Illumina NovaSeq SP


title: CHIPseq.WT.CHD4.16cycles

description:
Library name: CHIPseq.WT.CHD4.16cycles
Illumina NovaSeq SP


title: T47D Cntr DMSO_1

description: Library name: LD7LS6_1


title: CHIPseq.WT.CHD4.20cycles

description:
Library name: CHIPseq.WT.CHD4.20cycles
Illumina NovaSeq SP


title: CHIPseq.WT.BRG1.20cycles

description:
Library name: CHIPseq.WT.BRG1.20cycles
Illumina NovaSeq SP


title: 10642_Granule-neuron-of-cerebellum_UMBN6114_SCA3

city: Tallinn

first: Kert

last: Mätlik

address: Akadeemia tee 15

department: Department of Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

description: Library name: 10642

data_processing:
Sequence and transcript coordinates for human hg38 UCSC genome and gene models were retrieved from the BSgenome.Hsapiens.UCSC.hg38 Bioconductor package (version 1.62.0) and TxDb.Hsapiens.UCSC.hg38.knownGene (version 3.4.0) Bioconductor libraries respectively. FANSseq reads were aligned to the genome using Rsubread's subjunc method (version 1.30.6). Aligned reads were exported as bigWigs normalized to reads per million using the rtracklayer package (version 1.54.0). Aligned reads in genes were counted using the featurecounts function within the Rsubread package against gene exons.
Assembly: BSgenome.Hsapiens.UCSC.hg38
Supplementary files format and content: BigWig files, Counts files

molecule: nuclear RNA

source_name: Cerebellum (vermis)

extract_protocol:
RNA extraction was carried out with AllPrep DNA/RNA FFPE Kit (Qiagen, #80234) as described in Pressl C., et al, Curr Protoc. 2024 (PMID: 39651942).
RNA-seq libraries were prepared with Revelo™ RNA-Seq High Sensitivity library preparation kit (Tecan, cat. no. 30201359) as described in Pressl C., et al, Curr Protoc. 2024 (PMID: 39651942), and were pooled for sequencing on NovaSeq6000 (SP 2 x 150bp).

treatment_protocol: Nuclei were isolated from fresh-frozen post-mortem human cerebellum, labeled with cell type-specific probes and separated by FACS as described by Mätlik K et al. 2024 (PMID: 38291334).

value: Cerebellum (vermis)

value: Granule neuron of cerebellum


title: 10882_Granule-neuron-of-cerebellum_UMBN5777_SCA3

description: Library name: 10882


title: 14159_Purkinje_UMich1832_SCA3

description: Library name: 14159

value: Purkinje


title: 10625_Granule-neuron-of-cerebellum_UMich1602_SCA3

description: Library name: 10625


title: CHIPseq.WT.BRG1.16cycles

description:
Library name: CHIPseq.WT.BRG1.16cycles
Illumina NovaSeq SP


title: Lymph node, EV treated, replicate 2

first: Xia

last: Yang

address: 610 Charles E. Young Drive East

description:
Library name: EV2
10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were all done using the Cell Ranger software version 7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
Lymph nodes were harvested from experimental and control animals and immediately placed in cold, sterile PBS supplemented with 2% FBS to maintain cell viability during processing. The lymph nodes were mechanically disrupted and passed through a 70 µm cell strainer to obtain a single-cell suspension. The filter was rinsed with additional media to maximize cell recovery. The resulting cell suspension was stained with trypan blue and counted using a hemocytometer. Only samples with high viability (typically >80%) were selected for single-cell sequencing.
Library construction was performed according to the 10x 3′single-cell RNA-seq V3.1 manufacter’s protocol. Briefly, the master mix which contained the single cell suspensions of immune cells, partitioning oil and gel beads were loaded into the Chromium Next GEM Chip G to generate the gel bead-in-emulsions (GEMs). Primer containing an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode are mixed with the cell lysate and reverse transcription reagents to obtain barcoded cDNA from the poly-A RNA in the GEMs. The resulting pooled barcoded cDNA was then cleaned up with the provided DynaBeads then amplified by PCR. The fragments were then size selected using SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Wild-type C57BL/6 mice were subcutaneously injected with a total of 100 µg of iPSC Evs.

value: Lymph node

value: wildtype

value: EV treated

tag: treatment duration


title: Lymph node, EV treated, replicate 1

description:
Library name: EV1
10x Genomics


title: Lymph node, Control, replicate 2

description:
Library name: Control 2
10x Genomics

value: No treatment


title: 10258_Purkinje_UMich1602_SCA3

description: Library name: 10258


title: 10624_Granule-neuron-of-cerebellum_UMBN5856_SCA3

description: Library name: 10624


title: 9855_Purkinje_UMBN5856_SCA3

description: Library name: 9855


title: P2

city: Xiamen

first: Lingjuan

last: Zhang

address: Xiangan South Street

institute: Xiamen University

data_processing:
The raw sequencing data was demultiplexed and aligned to the reference genome mm10-1.2.0 using Cell Ranger v3.0.2 pipiline(10x Genomics).
The generated raw gene expression matrix was converted into Seurat objects using the R package Seurat v4.4.
To remove doublets and poor-quality nucleus, we utilized the following procedures to control for nucleus quality: >400 genes/nucleus, <6500 genes/nucleus; <29,000 unique molecular identifiers(UMIs)； and <10% mitochondrial
After low quality nucleus and outliers were discarded, 16481 nucleus from P2 skin were used for downstream analysis.
Unsupervised clustering and gene expression were visualized with the Seurat 4.4 on R studio, and assignment of cell clusters was based on expression of validated marker genes.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: dorsal skin

extract_protocol:
To isolate single-nuclei, fresh skin tissues were preserved by snap freezing in liquid nitrogen, transferred to a dounce homogenizer, grinded into a homogenate in lysis buffer. Nuclei were extracted by repeated washes with nuclear resuspension buffer and sucrose cushion buffer, then isolated nuclei were further purified by DAPI staining and sorting.Live single cells or single nuclei were loaded on a 10x Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs).
Single-cell or single-nuclei libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. cDNA libraries were sequenced on an Illumina Novaseq6000 platform (Illumina).

value: dorsal skin


title: Lymph node, Control, replicate 1

description:
Library name: Control 1
10x Genomics


title: genomic DNA of sample F204_CD8

type: genomic

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

description: Smoker CD15 genomic DNA

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and MethylationEPIC Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The raw IDAT files of 450K and EPIC methylation arrays were read into R with the minfi package separately; the combineArrays function in minfi was utilized to combine the two arrays’ data together based on their common CpG sites. Then, the data was preprocessed with background and dye bias correction using the preprocess Noob method.  DNA methylation data were filtered based on these criteria: any samples having more than 5% probes that failed array QC standards, all CpG probes on the X and Y chromosomes, probes containing SNPs with a minor allele frequency ≥ 1% (in EUR or AFR populations of the 1000 Genomes Project) within 5 nucleotides to the CpG site, and probes failing QC standards. We also removed 43,254 probes reported to hybridize to one or more non-target sites in the genome.

label: Cy5 and Cy3

source_name: Blood

label_protocol: 500 ng of DNA was bisulfite converted using the EZ-DNA Methylation kit (Zymo Research)

extract_protocol: Nucleated DNA from cells was collected after sucrose-induced osmotic lysis of cells followed by phenol-chloroform extraction and DNA was stored in Tris-EDTA buffer at -20°C.

value: Blood

value: NS


title: 9787_Purkinje_UMBN5777_SCA3

description: Library name: 9787


title: genomic DNA of sample F207_CD8

description: Smoker CD15 genomic DNA


title: 7382_Oligodendrocyte_BEB19051_CTRL

description: Library name: 7382

source_name: Cerebellum

value: Cerebellum

value: Oligodendrocyte


title: 7380_Microglia_BEB19051_CTRL

description: Library name: 7380

value: Microglia


title: 7381_Astrocyte_BEB19051_CTRL

description: Library name: 7381

value: Astrocyte


title: PANC-1 TP53-KO, Ferroptocide, 2797

status: Public on Jul 31 2026

city: Verona

first: Alessandra

last: Fiore

state: VR

address: Str. le Grazie, 8

country: Italy

institute: University of Verona

description:
Library name: Sample 2797
Column name in raw_counts.csv: 2797

data_processing:
Base calling was performed using Illumina Real-Time Analysis (RTA) software v3.10.30 on an Illumina NextSeq 2000 platform.
Demultiplexing and FASTQ file generation were performed using Illumina bcl-convert v3.10.12 with dual-index barcodes (Index1 and Index2), allowing up to one mismatch per index; FASTQ files were compressed in gzip format.
Sequencing generated single-end reads of 76 bp with dual 8 bp index reads.
Reads were processed using the DRAGEN RNA pipeline v3.10.12 to generate BAM alignments and gene-level read counts.
Read alignment was performed against the human reference genome hg38 using the alt-aware reference bundle (hg38_alt_aware). A raw (unnormalized) gene-level read count matrix was generated by aggregating DRAGEN RNA outputs across all samples.
Assembly: GRCh38 (hg38), alt-aware reference genome.
Supplementary files format and content: raw_counts.csv: CSV file (comma-separated values) containing a raw, unnormalized gene-level read count matrix (rows = genes, columns = samples).
Supplementary files format and content: sample.txt: comma-separated file containing sample metadata describing sample identifiers, cell line, genotype (TP53 wild-type or TP53 knockout), treatment (DMSO, Erastin, RSL3, Ferroptocide).

source_name: PANC-1 TP53-KO

growth_protocol: PANC-1 and TP53 KO PANC-1 cells were maintaned in RPMI-1640 supplemented with 10% FBS and antibiotics in humified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Venlo, Netherland, Cat. No. 74104) according to the manufactures’ instructions. The RNA was eluted in RNAse-free water and stored at – 80° C until quantification.
RNA-seq library preparation was performed starting from 1,000 ng high-quality total RNA using the “TruSeq Stranded mRNA library prep kit” (Illumina, San Diego, USA).

treatment_protocol: PANC-1 and TP53 KO PANC-1 cells were treated with RSL3 (0.5 μM) for 6 hours to induce ferroptosis

value: PANC-1 TP53-KO

value: TP53 knockout

value: Ferroptocide

value: single sequencing run


title: genomic DNA of sample F196_CD56

description: Smoker CD15 genomic DNA

value: SM


title: genomic DNA of sample F223_CD56

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F176_CD56

description: Smoker CD15 genomic DNA


title: 7379_Granule-neuron-of-cerebellum_BEB19051_CTRL

description: Library name: 7379

value: Granule neuron of cerebellum


title: COCs, control, biol rep 1, 12h

city: Chicago

first: Caroline

middle: Elisabeth

last: Kratka

state: IL

address: 303 East Superior Street

department: OBGYN

institute: Northwestern University

description:
Library name: Sample 6
S12h_CTL_T1_S6

data_processing:
Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt (Martin, 2011).
Trimmed reads were aligned to the Mus musculus genome (mm39) using STAR (Dobin et al., 2013).
Read counts for each gene were calculated using htseq-count (Anders et al., 2015) in conjunction with a gene annotation file for mm39 obtained from Ensembl (http://useast.ensembl.org/index.html).
Assembly: mm39
Supplementary files format and content: a count matrix that contains all samples

source_name: Ovary

growth_protocol: Mouse cumulus-oocyte-complexes (COCs) were cultured in ⍺-MEM (Thermo Fisher) supplemented with 5% (v/v) fetal bovine serum (Thermo Fisher), 20 mM HEPES buffer (Sigma), 0.25 mM pyruvate (Sigma), and 0.02% (v/v) mouse epidermal growth factor (Sigma) for 0h, 4h, 8h, or 12h at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using the RNeasy micro kit (Qiagen).
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit following manufacturer's protocols without modifications.

treatment_protocol: COCs were treated with 10 µM proprotein convertase inhibitor (PCI) or DMSO (1/2000) control.

value: Ovary

value: cumulus-oocyte-complexes (COCs)

value: WT

value: None (DMSO control)

tag: time


title: Largemouth bass Spleen, 0h post-challenge, Pre, biological replicate 10

city: Auburn

first: Timothy

middle: James

last: Bruce

state: AL

address: 203 Swingle Hall

department: School of Fisheries, Aquaculture and Aquatic Sciences

institute: Auburn University

description:
Library name: 00S9S
Pre-challenge baseline (0h); 0h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

data_processing:
Raw reads assessed with FastQC/MultiQC; trimmed with fastp (Q20, 50 bp minimum length). Mean retention 97.9% across 7.1 billion reads.
Transcript quantification with Salmon (decoy-aware index GCF_014851395.1, k=31, --libType A, 30 bootstraps, seqBias/gcBias/posBias corrections). Mean mapping rate 82.84%.
Gene-level import with tximeta (lengthScaledTPM), rounded for DESeq2. Pre-filter: rowSums(counts>=10)>=2. Gill: 23,561 genes; Spleen: 22,152 genes.
DESeq2 differential expression: ~group design, reference=t0_Pre, ashr LFC shrinkage. 72 pairwise contrasts (36/tissue). Significance: padj<0.05, |log2FC|>=1 (BH correction).
Annotation: org.Msalmoides.eg.db v1.0.0 (NCBI RefSeq GFF3 + ZFIN GO GAF 2026-04-01 + OrthoDB v12.2 Actinopterygii). 68.9% of genes annotated with at least one GO term.
Please note that the three samples (11B3G, 15J2G, 29R3G) were intentionally excluded from the processed data files due to gDNA contamination, as indicated by mapping rates below 25% (21.4%, 20.9%, and 15.9%, respectively). These samples failed quality control and were not included in the DESeq2 model or any downstream analyses. Their raw FASTQ files are deposited for transparency and completeness, but they do not appear in the processed count matrices (raw_counts_gill.csv, vst_normalized_counts_gill.csv, DESeq2_all_contrasts_gill.csv) for this reason.
Assembly: GCF_014851395.1 (ASM1485139v1, Micropterus salmoides, NCBI RefSeq)
Supplementary files format and content: raw_counts_gill.csv / raw_counts_spleen.csv: CSV, raw gene count matrix (genes x samples); rows=NCBI gene IDs, columns=sample IDs.
Supplementary files format and content: vst_normalized_counts_gill.csv / vst_normalized_counts_spleen.csv: CSV, VST-normalized expression values from DESeq2.
Supplementary files format and content: DESeq2_all_contrasts_gill.csv / DESeq2_all_contrasts_spleen.csv: CSV, annotated DESeq2 results (gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, gene_symbol, contrast) for all 36 contrasts per tissue.
Supplementary files format and content: Stage5_DEG_summary.tsv: TSV, summary of significant DEGs (up/down/total) per contrast.
Supplementary files format and content: Msalmoides_master_annotation_GO.tsv: TSV, master gene annotation for GCF_014851395.1 (gene_id, gene_symbol, drerio_symbol, GO terms, ortholog information).

organism: Micropterus salmoides

source_name: Spleen

growth_protocol: Largemouth bass were maintained in recirculating freshwater systems prior to challenge.

extract_protocol:
Total RNA was extracted from DNA/RNA Shield-preserved tissue at Azenta Inc. RNA quality assessed by TapeStation
Paired-end RNA-Seq libraries prepared from polyA-selected RNA using NEBNext Ultra II. Libraries sequenced on Illumina NovaSeq X (paired-end, 150 bp)

treatment_protocol: Fish were challenged by immersion with Aeromonas veronii, Aeromonas hydrophila, Flavobacterium columnare, or coinfections, or mock-challenged. Gill and spleen were dissected at 0h, 12h, and 24h post-challenge and preserved in DNA/RNA Shield (Zymo Research, Inc.).

value: Spleen

value: Pre-challenge baseline (0h)

tag: sample group


title: genomic DNA of sample F200_CD8

description: Smoker CD15 genomic DNA

value: Blood

value: NS


title: 9522_Purkinje_UMBN6114_SCA3

description: Library name: 9522

value: Cerebellum (vermis)

value: Purkinje


title: genomic DNA of sample F214_CD56

description: Smoker CD15 genomic DNA


title: PANC-1 TP53-KO, DMSO, 2798

description:
Library name: Sample 2798
Column name in raw_counts.csv: 2798

value: DMSO


title: placenta DNA, BSAFE, female 22

city: Davis

first: Logan

middle: Allan

last: Williams

address: 1275 Med Sci Dr

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Library name: SW096

data_processing:
Raw sequencing files were preprocessed, aligned to hg38, and used to generate cytosine reports with Epigenerator.In short, Epigenerator provides a user-friendly means of generating cytosine reports from fastq files by applying the FASTQ_Me and CpG_Me workflows in tandem. Merged reads were trimmed of adaptors, corrected for potential methylation bias at the 5’ and 3’ ends, and aligned to hg38. The aligned reads were then deduplicated and CpG methylation was extracted with to generate cytosine reports for further analysis.
Assembly: hg38
Supplementary files format and content: cytosine reports, genome-wide CpG count matrices

source_name: Placenta

extract_protocol:
Placenta samples underwent DNA isolation via the Gentra Puregene kit (Qiagen, Hilden, Germany) by following recommended procedures and quantified with the Qubit DNA Assay Kit (ThermoFisher Scientific, Q32851).
DNA was sheared by sonication, bisulfite-converted with the EZ DNA Methylation Gold kit (Zymo, Irvine, CA, USA) and made into sequencing libraries via the xGen Methyl Seq Library Prep kit (IDT, Coralville, IA, USA). Libraries were made with indexed PCR primers and underwent 7 cycles of amplification before being pooled and sequenced for 150bp paired end reads on 4 lanes of the NovaSeq 6000 S4 (San Diego, CA, USA)  by the DNA Technologies Core at the University of California, Davis (Davis, CA, USA).

treatment_protocol: Placental samples were frozen at -80C within 4 hours of birth and stored until time of isolation.

value: Placenta

value: F

tag: project

value: BSAFE

tag: pm25mass avg_prec

tag: pm25mass avg_preg

tag: pm25tracer5 avg_prec

tag: pm25tracer5 avg_preg

tag: pm25tracer10 avg_prec

tag: pm25tracer10 avg_preg

tag: wf pm25_avg_prec

tag: wf pm25_avg_preg

tag: nonwf pm25_avg_prec

tag: nonwf pm25_avg_preg

tag: pregfire any

value: Wildfire Exposed


title: placenta DNA, MARBLES, female 17

description: Library name: SW090

tag: tissue

tag: Sex

value: MARBLES


title: genomic DNA of sample F207_CD56

description: Smoker CD15 genomic DNA

tag: cell type

tag: treatment


title: placenta DNA, MARBLES, male 28

description: Library name: SW089

value: M


title: genomic DNA of sample F176_CD4

description: Smoker CD15 genomic DNA

value: SM


title: genomic DNA of sample F200_CD56

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, female 21

description: Library name: SW084


title: genomic DNA of sample F213_CD56

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, male 18

description: Library name: SW085


title: placenta DNA, BSAFE, female 18

description: Library name: SW081


title: genomic DNA of sample F196_CD4

description: Smoker CD15 genomic DNA


title: placenta DNA, MARBLES, male 27

description: Library name: SW080


title: placenta DNA, BSAFE, female 20

description: Library name: SW083


title: placenta DNA, BSAFE, female 19

description: Library name: SW082


title: genomic DNA of sample F204_CD56

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F093_CD4

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, male 17

description: Library name: SW079


title: genomic DNA of sample F223_CD4

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F214_CD4

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F213_CD4

description: Smoker CD15 genomic DNA


title: placenta DNA, MARBLES, male 26

description: Library name: SW077


title: genomic DNA of sample F207_CD4

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F204_CD4

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, male 15

description: Library name: SW075


title: genomic DNA of sample F200_CD4

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, male 16

description: Library name: SW078


title: placenta DNA, MARBLES, male 25

description: Library name: SW076


title: genomic DNA of sample F176_CD19

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F223_CD19

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F196_CD19

description: Smoker CD15 genomic DNA


title: placenta DNA, MARBLES, male 24

description: Library name: SW071


title: genomic DNA of sample F213_CD19

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, male 14

description: Library name: SW072


title: placenta DNA, BSAFE, female 16

description: Library name: SW073


title: placenta DNA, BSAFE, female 17

description: Library name: SW074


title: placenta DNA, BSAFE, female 15

description: Library name: SW070


title: Peripheral blood from patient with delayed puberty [206909030005_R08C01]

city: London

first: Sasha

last: Howard

address: JVSC Charterhouse Square

department: Endocrinology

country: United Kingdom

institute: Queen Mary University London

hyb_protocol: Sequencing using the Illumina Infinium Methylation EPIC array BeadChip (850K) was carried out by the Epigenomic Services from Diagenode (Cat nr. G02090000).

scan_protocol: Standard Ilumina protocol

data_processing:
A pipeline following that of Barrett et al (Barrett et al. 2022) was used for a second round of quality control and normalisation of the samples. Quality control, annotation of CpG sites and differential methylation analysis was undertaken in R Studio using the dmpFinder function from the minfi package along with bumphunter.
*processed value definition: Average Beta

label: Cy3 and Cy5

source_name: Peripheral blood

label_protocol: Standard Ilumina protocol

extract_protocol: Genomic DNA was isolated from peripheral blood leukocytes from all patients and family members using standard procedures

value: Peripheral blood

tag: sample group

value: patient with delayed puberty


title: genomic DNA of sample F214_CD19

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F207_CD19

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, female 14

description: Library name: SW069

tag: project


title: placenta DNA, BSAFE, female 13

description: Library name: SW068

tag: pm25mass avg_prec


title: genomic DNA of sample F200_CD19

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F204_CD19

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, male 13

description: Library name: SW067

tag: pm25mass avg_preg


title: genomic DNA of sample F176_CD15

description: Smoker CD15 genomic DNA


title: placenta DNA, MARBLES, male 23

description: Library name: SW066

tag: pm25tracer5 avg_prec


title: placenta DNA, MARBLES, male 22

description: Library name: SW065

tag: pm25tracer5 avg_preg


title: genomic DNA of sample F223_CD15

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F196_CD15

description: Smoker CD15 genomic DNA


title: placenta DNA, MARBLES, female 16

description: Library name: SW064

tag: pm25tracer10 avg_prec


title: genomic DNA of sample F213_CD15

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F207_CD15

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F214_CD15

description: Smoker CD15 genomic DNA


title: placenta DNA, MARBLES, male 20

description: Library name: SW061

tag: pm25tracer10 avg_preg

value: Control


title: placenta DNA, MARBLES, male 21

description: Library name: SW062

tag: wf pm25_avg_prec


title: placenta DNA, MARBLES, female 15

description: Library name: SW063

tag: wf pm25_avg_preg


title: placenta DNA, BSAFE, female 12

description: Library name: SW059

tag: nonwf pm25_avg_prec


title: genomic DNA of sample F204_CD15

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F200_CD15

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, male 12

description: Library name: SW058

tag: nonwf pm25_avg_preg


title: genomic DNA of sample F196_CD14

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, female 11

description: Library name: SW055

tag: pregfire any


title: genomic DNA of sample F214_CD14

description: Smoker CD15 genomic DNA

tag: tissue


title: genomic DNA of sample F223_CD14

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F176_CD14

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F207_CD14

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F204_CD14

description: Smoker CD15 genomic DNA


title: placenta DNA, MARBLES, male 17

description: Library name: SW051

tag: Sex


title: genomic DNA of sample F213_CD14

description: Smoker CD15 genomic DNA

tag: cell type


title: placenta DNA, BSAFE, male 11

description: Library name: SW056


title: placenta DNA, BSAFE, male 10

description: Library name: SW054


title: placenta DNA, MARBLES, male 18

description: Library name: SW052


title: placenta DNA, BSAFE, male 9

description: Library name: SW053


title: placenta DNA, MARBLES, male 16

description: Library name: SW050


title: genomic DNA of sample F200_CD14

description: Smoker CD15 genomic DNA

tag: treatment


title: placenta DNA, MARBLES, male 14

description: Library name: SW048


title: genomic DNA of sample F170_CD56

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F101_CD19

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F151_CD14

description: Smoker CD15 genomic DNA


title: placenta DNA, MARBLES, female 14

description: Library name: SW047


title: genomic DNA of sample F196_WB

description: Smoker CD15 genomic DNA

value: WB


title: genomic DNA of sample F196_CD8

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F005_WB

description: Smoker CD15 genomic DNA


title: genomic DNA of sample F176_CD8

description: Smoker CD15 genomic DNA


title: placenta DNA, MARBLES, female 13

description: Library name: SW045


title: genomic DNA of sample F223_CD8

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, male 8

description: Library name: SW041


title: placenta DNA, MARBLES, male 13

description: Library name: SW044


title: placenta DNA, BSAFE, female 8

description: Library name: SW040


title: genomic DNA of sample F214_CD8

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, female 9

description: Library name: SW042


title: genomic DNA of sample F213_CD8

description: Smoker CD15 genomic DNA


title: placenta DNA, BSAFE, male 7

description: Library name: SW039


title: placenta DNA, MARBLES, male 19

description: Library name: SW057


title: placenta DNA, BSAFE, female 7

description: Library name: SW038


title: placenta DNA, BSAFE, female 6

description: Library name: SW037


title: cKO-6w

city: beijing

first: lijiao

last: deng

state: beijing

address: taipingroad

institute: beijing Institute of Basic Medical Sciences

description:
Library name: SAMPLE-2
10×Genomics

data_processing:
Sequencing data from 10x genomics was processed with CellRanger software (version 6.1.0) with default mapping arguments.
Assembly: mm10
Supplementary files format and content: mtx
Supplementary files format and content: filtered_feature_bc_matrix

source_name: Bone marrow

extract_protocol:
6 weeks after  adult Rack1(F/F) and Rack1(F/F;Mx1-Cre) mice injected with poly(I:C), BM cells were flushed out of the BM cavity of both femurs using a 5 mL syringe with ice-cold PBS, followed by filtration through a 70-µm strainer. BM cells were stained with PE-conjugated antibody against c-Kit and FITC-conjugated antibodies against CD3, B220, CD11b, Gr-1, and Ter-119 in PBS containing 2% FBS for 30 min on ice in the dark. Samples were washed once in staining buffer. Then, the cells were incubated with anti-PE microbeads and all c-Kit+ cells were enriched using an MS column. After that, Lin−/lowcKit+ DAPI- BM singlets were sorted by FACS and subjected to scRNA-seq.
Libraries were produced with a Chromium system (10×Genomics, PN120263) following the manufacture’s instruction (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/technical-note-assay-scheme-and-configuration-of-chromium-single-cell-3-v2-libraries)

value: Bone marrow

value: Lin-/lowcKit+ hematopoietic cells

tag: genotype

value: Rack1(F/F; Mx1-Cre)

value: 6 weeks after single intraperitoneal injection of 10 mg/kg poly(I:C)


title: placenta DNA, BSAFE, male 6

description: Library name: SW036

tag: project


title: cWT-6w

description:
Library name: SAMPLE-1
10×Genomics


title: cKO-12day

description:
Library name: SAMPLE-2
10×Genomics

extract_protocol:
12 days after  adult Rack1(F/F) and Rack1(F/F;Mx1-Cre) mice injected with poly(I:C), BM cells were flushed out of the BM cavity of both femurs using a 5 mL syringe with ice-cold PBS, followed by filtration through a 70-µm strainer. BM cells were stained with PE-conjugated antibody against c-Kit and FITC-conjugated antibodies against CD3, B220, CD11b, Gr-1, and Ter-119 in PBS containing 2% FBS for 30 min on ice in the dark. Samples were washed once in staining buffer. Then, the cells were incubated with anti-PE microbeads and all c-Kit+ cells were enriched using an MS column. After that, Lin−/lowcKit+ DAPI- BM singlets were sorted by FACS and subjected to scRNA-seq.
Libraries were produced with a Chromium system (10×Genomics, PN120263) following the manufacture’s instruction (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/technical-note-assay-scheme-and-configuration-of-chromium-single-cell-3-v2-libraries)

value: 12days after single intraperitoneal injection of 10 mg/kg poly(I:C)


title: placenta DNA, MARBLES, female 12

description: Library name: SW035

tag: pm25mass avg_prec


title: placenta DNA, BSAFE, female 5

description: Library name: SW034

tag: pm25mass avg_preg


title: KA17_SF_time_OP8_iPAAG

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: Library name: KA17_SF_OP8

data_processing:
Differential analysis for comparisons between iPAAG treated and operated untreated controls was computed using Limma (Linear modeling and empirical Bayes) Voom (Mean–variance modeling) method (limma v3.62.2) longitudinal analysis with baseline (week 2 operated joints) with TMM normalization and duplicate Correlation() (block = patient) to estimate within-patient correlation
Fastp v0.23.2 was used to trim adapters and low-quality reads, STAR version 2.7.10b was used for alignment to Equus caballus EquCab3.0, annotated with Ensembl 113 and feature counts Version 2.0.1 was used to quantify reads.
Assembly: Equus caballus EquCab3.0
Supplementary files format and content: voom_logCPM_normalized_SF.csv

organism: Equus caballus

source_name: synovial fluid

growth_protocol: Synovial fluid samples (≥ 3 mL) were obtained at baseline (pre surgery) and every two weeks throughout study duration until end term (0, 2, 4, 6, 8, 10). To obtain synovial fluid samples, horses were sedated, and joints were aseptically prepared in routine fashion as described for treatment administration. Synovial fluid samples were collected under sterile conditions during routine arthrocentesis. Approximately 3 to 7 mL of synovial fluid were placed in a 15 mL conical tube and placed on ice for transport to the laboratory for processing.

extract_protocol:
The fluid was digested with 0.3 mg/mL hyaluronidase (Sigma, St. Louis, MO, USA) by incubation in a bead bath for 15 minutes at 37 ºC. Next the sample was centrifuged at 750 x g for 10 minutes at 8 ºC. The remaining cell pellet was washed with PBS and centrifuged at 500 x g for 10 minutes at 8 ºC. The cell pellet was resuspended in about 1 to 2 mL of PBS and transferred into a 2 mL microcentrifuge tube. The sample was then centrifuged for 500 x g for 15 minutes. The supernatant was discarded, and the cells were lysed in RLT buffer (Qiagen, Germantown, MD, USA) with 1% ß-Mercaptoethanol (BME; EMD Millipore Corp, Billerica, MA, USA) and stored at -80 ºC until RNA extraction.
Library preparation was conducted on synovial fluid samples using the SMARTer® Stranded Total RNA-Seq Kit -Pico input (Takara Bio USA, Inc.)

treatment_protocol: Treatment – Horses (n=8/group) were randomly assigned to receive either intra-articular 2.5% injectable polyacrylamide hydrogel (Arthramid®, Contura Vet, Franklin, TN, USA) injection (2 mL) or phosphate buffered saline (2 mL) injection. Briefly, horses were sedated with detomidine hydrochloride 0.01 mg/kg and butorphanol tartrate 0.01 mg/kg intravenously. The previously operated middle carpal joint was aseptically prepared in routine fashion and injected intra-articularly at day 14 of the study.

value: synovial fluid

value: SF cells


title: cWT-12day

description:
Library name: SAMPLE-1
10×Genomics


title: KA17_SF_time_OP6_iPAAG

description: Library name: KA17_SF_OP6


title: KA17_SF_time_OP4_iPAAG

description: Library name: KA17_SF_OP4


title: placenta DNA, MARBLES, female 11

description: Library name: SW033

value: Placenta

value: F

tag: pm25tracer5 avg_prec


title: placenta DNA, BSAFE, female 4

description: Library name: SW032

value: BSAFE

tag: pm25tracer5 avg_preg

value: Wildfire Exposed


title: placenta DNA, MARBLES, male 15

description: Library name: SW049

value: M

value: MARBLES

tag: pm25tracer10 avg_prec


title: placenta DNA, BSAFE, male 5

description: Library name: SW031

tag: pm25tracer10 avg_preg


title: KA17_SF_time_OP2_iPAAG

description: Library name: KA17_SF_OP2


title: placenta DNA, MARBLES, female 10

description: Library name: SW030

tag: wf pm25_avg_prec


title: KA17_SF_time_OP10_iPAAG

description: Library name: KA17_SF_OP10


title: placenta DNA, BSAFE, male 4

description: Library name: SW029

tag: wf pm25_avg_preg


title: KA17_SF_time_OP0_iPAAG

description: Library name: KA17_SF_OP0


title: KA16_SF_time_OP8_Control

description: Library name: KA16_SF_OP8


title: placenta DNA, BSAFE, male 3

description: Library name: SW028

tag: nonwf pm25_avg_prec


title: KA16_SF_time_OP4_Control

description: Library name: KA16_SF_OP4


title: placenta DNA, BSAFE, male 1

description: Library name: SW025

tag: nonwf pm25_avg_preg


title: KA16_SF_time_OP6_Control

description: Library name: KA16_SF_OP6


title: placenta DNA, BSAFE, male 2

description: Library name: SW026

tag: pregfire any


title: KA16_SF_time_OP10_Control

description: Library name: KA16_SF_OP10

tag: tissue


title: placenta DNA, BSAFE, female 2

description: Library name: SW024

tag: Sex


title: KA16_SF_time_OP0_Control

description: Library name: KA16_SF_OP0

tag: cell type


title: placenta DNA, BSAFE, female 1

description: Library name: SW023


title: placenta DNA, MARBLES, male 12

description: Library name: SW022


title: KA15_SF_time_OP6_Control

description: Library name: KA15_SF_OP6


title: placenta DNA, MARBLES, female 9

description: Library name: SW021


title: KA15_SF_time_OP8_Control

description: Library name: KA15_SF_OP8


title: placenta DNA, MARBLES, male 11

description: Library name: SW020


title: KA15_SF_time_OP4_Control

description: Library name: KA15_SF_OP4


title: KA15_SF_time_OP2_Control

description: Library name: KA15_SF_OP2


title: placenta DNA, MARBLES, male 8

description: Library name: SW017


title: KA14_SF_time_OP6_iPAAG

description: Library name: KA14_SF_OP6


title: KA15_SF_time_OP0_Control

description: Library name: KA15_SF_OP0


title: placenta DNA, MARBLES, female 8

description: Library name: SW016


title: placenta DNA, MARBLES, female 7

description: Library name: SW015


title: placenta DNA, MARBLES, female 6

description: Library name: SW014


title: placenta DNA, MARBLES, male 7

description: Library name: SW013


title: KA14_SF_time_OP2_iPAAG

description: Library name: KA14_SF_OP2


title: KA14_SF_time_OP10_iPAAG

description: Library name: KA14_SF_OP10


title: placenta DNA, MARBLES, female 5

description: Library name: SW012


title: placenta DNA, MARBLES, male 6

description: Library name: SW010


title: KA13_SF_time_OP6_Control

description: Library name: KA13_SF_OP6


title: placenta DNA, MARBLES, female 4

description: Library name: SW009


title: KA13_SF_time_OP4_Control

description: Library name: KA13_SF_OP4


title: KA15_SF_time_OP10_Control

description: Library name: KA15_SF_OP10


title: placenta DNA, MARBLES, male 5

description: Library name: SW008


title: placenta DNA, MARBLES, male 4

description: Library name: SW007


title: placenta DNA, BSAFE, female 10

description: Library name: SW043


title: KA13_SF_time_OP2_Control

description: Library name: KA13_SF_OP2


title: KA13_SF_time_OP10_Control

description: Library name: KA13_SF_OP10


title: placenta DNA, MARBLES, female 2

description: Library name: SW005


title: KA13_SF_time_OP0_Control

description: Library name: KA13_SF_OP0


title: placenta DNA, MARBLES, female 3

description: Library name: SW006


title: placenta DNA, MARBLES, male 3

description: Library name: SW004


title: KA12_SF_time_OP8_iPAAG

description: Library name: KA12_SF_OP8


title: placenta DNA, MARBLES, male 2

description: Library name: SW003


title: placenta DNA, MARBLES, male 1

description: Library name: SW002


title: KA12_SF_time_OP6_iPAAG

description: Library name: KA12_SF_OP6


title: placenta DNA, MARBLES, female 1

description: Library name: SW001


title: KA12_SF_time_OP4_iPAAG

description: Library name: KA12_SF_OP4


title: KA12_SF_time_OP2_iPAAG

description: Library name: KA12_SF_OP2


title: LCA__UT LCA_UT_3

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

description:
Library name: LCA_UT_3
dr_ciliopathy_treatments_cts.csv.gz

data_processing:
fastp fastq trimming
decoy aware salmon index
salmon quant --index  --libType A --seqBias --gcBias             --validateMappings
tximport into R (4.4)
gencode.v47.primary_assembly.annotation.gtf.gz
Assembly: GRCh38.primary_assembly.genome.fa.gz
Supplementary files format and content: counts, csv

source_name: RPE

growth_protocol: All human samples were collected under an IRB-approved protocol at NEI (protocol #11-E1- 0245). Cells isolated from donor tissue were reprogrammed using Sendai virus-mediated delivery (CytoTune, LifeTechnologies) of the four Yamanaka factors (c-MYC, KLF4, OCT4, SOX2) following the manufacturer's recommendations. For differentiation, iPSCs were seeded onto vitronectin (ThermoFisher) coated T75 flasks followed by guided protocol. Triphasic developmentally guided protocol to generate retinal pigment epithelium from induced pluripotent stem cells, Sharma et. al. 2022

extract_protocol:
RNA was isolated from RPE monolayer 5 weeks post-seeding on transwells, using RNA extraction kit, Macherey&Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were collected after 5 weeks of maturation on transwell inserts. Samples were either untreated or treated after 4days of seeding with Pioglitazone and 6days of seeding with Galunisetib.

value: RPE

tag: cell line

value: iRPE

tag: treatment

value: UT


title: LCA__UT LCA_UT_2

description:
Library name: LCA_UT_2
dr_ciliopathy_treatments_cts.csv.gz


title: KA12_SF_time_OP0_iPAAG

description: Library name: KA12_SF_OP0


title: LCA__UT LCA_UT_1

description:
Library name: LCA_UT_1
dr_ciliopathy_treatments_cts.csv.gz


title: KA11_SF_time_OP6_Control

description: Library name: KA11_SF_OP6


title: LCA__PIO LCA_PIO_3

description:
Library name: LCA_PIO_3
dr_ciliopathy_treatments_cts.csv.gz

value: PIO


title: KA11_SF_time_OP8_Control

description: Library name: KA11_SF_OP8


title: KA11_SF_time_OP2_Control

description: Library name: KA11_SF_OP2


title: KA16_SF_time_OP2_Control

description: Library name: KA16_SF_OP2


title: placenta DNA, BSAFE, female 3

description: Library name: SW027

tag: project


title: LCA__PIO LCA_PIO_1

description:
Library name: LCA_PIO_1
dr_ciliopathy_treatments_cts.csv.gz


title: LCA__GAL LCA_GAL_3

description:
Library name: LCA_GAL_3
dr_ciliopathy_treatments_cts.csv.gz

value: GAL


title: KA11_SF_time_OP10_Control

description: Library name: KA11_SF_OP10


title: KA11_SF_time_OP0_Control

description: Library name: KA11_SF_OP0


title: KA10_SF_time_OP8_Control

description: Library name: KA10_SF_OP8


title: KA10_SF_time_OP6_Control

description: Library name: KA10_SF_OP6