title: HCoF Young replicate 1

city: Suwon-si

first: min jung

last: sung

state: Gyeonggi-do

address: 206, World cup-ro, Yeongtong-gu

country: South Korea

institute: ajou university

description: Library name: HCoF_Young_1

data_processing:
Raw sequencing data are provided as FASTQ files.
Raw sequencing reads were processed using fastp v0.23.1 to remove adapter sequences and low-quality reads.
Filtered reads were aligned to the reference genome using Bowtie2 v2.3.4.3.
PCR duplicate reads were removed using Picard v2.27.5. Reads mapping to mitochondrial DNA or with low mapping quality were filtered using samtools v1.17.
Reads mapping to ENCODE blacklist regions were removed. Tn5 insertion bias was corrected by adjusting read coordinates using the alignmentSieve function from deepTools v3.5.2.
Peak calling was performed using MACS2 v2.2.8. Peaks were annotated using the ChIPseeker R package v1.36.0. Differential chromatin accessibility analysis was conducted using edgeR v3.42.4 with TMM-normalized log2(CPM + 1) values. Motif enrichment analysis was performed using HOMER v4.11.1.
Assembly: Reads were aligned to the human reference genome (GRCh38/hg38).
Supplementary files format and content: Processed data files include ATAC-seq peak files in TSV format listing accessible chromatin regions and genome browser tracks in bigWig format representing normalized chromatin accessibility signals.

source_name: Colon

extract_protocol:
For ATAC-seq, 100,000 fresh cells were washed twice with cold PBS and resuspended in lysis buffer. Cells were incubated on ice for 10 minutes to isolate nuclei, followed by centrifugation at 500 g at 4°C for 10 minutes to remove the supernatant.
ATAC-seq libraries were prepared using the ATAC-Seq Library Prep Kit for Illumina (Active Motif, United States) according to the manufacturer’s instructions. Briefly, isolated nuclei were incubated with Tagmentation Master Mix at 37°C for 30 minutes with shaking at 800 rpm. Tagmented DNA was purified using the DNA purification column provided in the kit. Libraries were amplified by PCR for 10 cycles under the following conditions: 72°C for 10 minutes; 98°C for 30 seconds; followed by cycling at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. Amplified libraries were purified using SPRI beads to remove primer dimers. Library quality and fragment size distribution were assessed using TapeStation HS D5000 Screen Tape (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq XP platform with 150 bp paired-end reads.

value: Colon

value: HCoF

value: Colonic fibroblast

value: Wild type

tag: batch

value: Young


title: HL60-DIMATE-002

status: Public on Jul 01 2026

type: RNA

city: Lyon

first: Céline

last: BAIER

address: 655 Allée des Parcs

country: France

institute: Advanced Biodesign

description: Gene expression after 6hr DIMATE

hyb_protocol: SurePrint G3 human GE 8x60K V2 chips

scan_protocol: Microarrays were  scanned through standard Agilent protocol

data_processing: Data were processed using Feature Extraction software. A multiple test correction was performed a false discovery rate (FDR) of 5% and a fold change of 1,5 were fixed

molecule: total RNA

organism: Homo sapiens

label_protocol: One hundred nanogram of total RNA was labelled using One-Color Microarray-Based Gene Expression Analysis: Low Input Quick Amp (LIQA) labelling protocol

growth_protocol: HL60 grew in 6well plates

extract_protocol: RNA was extracted with Qiagen Protocol, RNeasy Mini kit (Qiagen, France)

treatment_protocol: DIMATE 10µM during 6h

tag: treatment

value: DIMATE

tag: cell line


title: HL60-DIMATE-001

description: Gene expression after 6hr DIMATE


title: Ovis aries, plasma, CTRL, week 7, replicate 3

type: SRA

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

description:
Library name: CTRL_A3
Sequencing internal ID: 31621-003

library_source: transcriptomic

data_processing:
Raw reads (76 nt single-end, AVITI) were demultiplexed by the sequencing provider; UMI barcodes (12 nt) and 3' Illumina P7 adapter were removed using cutadapt v4.9, retaining inserts ≥17 nt.
UMI-aware deduplication was performed by collapsing reads with identical (sequence, UMI) pairs.
Trimmed reads were aligned to extended ovine miRNA hairpin sequences (miRBase v22, Ovis aries) using bowtie v1.3.1; per-miRNA counts (raw and normalized) were obtained with a custom Python counter handling multi-mappers with fractional counting.
Novel miRNA candidate discovery was performed using miRDeep2 v0.1.3 against the Ovis aries reference genome ARS-UI_Ramb_v3.0 (Ensembl).
Differential expression analysis was performed in R using DESeq2 v1.42 with a paired design accounting for repeated measures within individuals (~ group + group:individual + timepoint + group:timepoint).
Assembly: Ovis aries ARS-UI_Ramb_v3.0 (Ensembl release 113); miRBase release 22.1
Supplementary files format and content: GEO_raw_counts_matrix.tsv: tab-delimited matrix of raw read counts per miRNA (rows) per sample (columns); 364 miRNAs (known + novel) x 18 samples.
Supplementary files format and content: Per-sample raw count files (31621-001_counts.tsv to 31621-018_counts.tsv): tab-delimited two-column files (miRNA, count) for each individual sample.

organism: Ovis aries

source_name: plasma

growth_protocol: Twelve Polish Longwool ewes (ovariectomized, with estradiol implants) were housed under standard conditions and randomly assigned to CTRL (n=6, standard diet) or OBESE (n=6, high-fat diet) groups.

extract_protocol:
Total RNA including small RNA was extracted from 200 µL plasma using the QIAseq miRNA Library Kit (QIAGEN). RNA quality and quantity were assessed by Qubit fluorometry and TapeStation analysis.
Small RNA libraries were prepared using QIAseq miRNA Library Kit (QIAGEN) with UMI-based deduplication. Libraries were sequenced on the AVITI platform (Element Biosciences) using 1x76 single-end reads.

treatment_protocol: OBESE animals received a high-fat diet for 14 weeks. Blood samples were collected at week 7 (T1), week 10 (T2) and week 14 (T3). Plasma was isolated by centrifugation and stored at -80°C until use.

tag: animal breed

value: Polish Longwool

tag: tissue

value: plasma

tag: group

value: CTRL

tag: timepoint

value: week 7

tag: Sex

value: female

value: control diet


title: MCF10CA1a_rep2

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

country: USA

institute: University of Vermont

data_processing:
RNA-seq reads were aligned to the hg38 genome using STAR version v2.7.9a using  default parameters.
Raw RNA-seq count data were processed and normalized using edgeR to generate a table of Transcripts Per Million (TPM) values.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including TPM values for each sample

growth_protocol: Cells were grown in DMEM: F12 with 5%  horse serum supplmented with 10mg/ml human insulin + 20ng/ml recombinant hEGF + 100 ng/ml cholera toxin + 0.5 mg/ml hydrocortisone + penicillin/streptomycin and 2 mM glutamine. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was harvested using Directzol  kit (Zymo). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Ultra2 stranded RNA-seq library Prep Kit following manufacturer's protocols.
Stranded RNA-seq libraries

tag: cell type

value: cell line


title: Patient 26 COAD 026

city: Seoul

first: Chungyeop

last: Lee

address: Songpagu Olympicro 43gil

institute: Asan Medical Center

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software. Training cohort and validation cohort normalization were separately conducted.

source_name: Locally Advanced Rectal Cancer

label_protocol: No labeling was performed; digital barcoding system was used (NanoString).

extract_protocol: Total RNA was extracted from pretreatment FFPE biopsy tissues using the RNeasy FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol.

value: rectal cancer

tag: histology

value: Total


title: Muscat Hamburg ovule,day 61 rep1

city: Zhengzhou

first: Yongzhou

last: Li

address: No. 28, Gangwan Road, Guancheng District

country: China

institute: Chinese Academy of Agricultural Sciences Zhengzhou Fruit Research Institute

description:
Library name: SAMPLE 7
MH61-1

data_processing:
sequence reads were obtained by filtering out reads containing adapters, poly-N sequences, and low-quality reads. Transcriptome analysis involved mapping the clean reads to a reference genome (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_030704535.1/)
Gene expression levels were calculated by fragments per kilobase of transcript per million mapped reads (FPKM) values
Assembly: genome assemblies:69
Supplementary files format and content: Excel file includes FPKM values for each saple

organism: Vitis vinifera

source_name: grape  ovule

extract_protocol:
Store to -80 °C with skin retained.RNA extraction and subsequent sequencing were done by metware Biology (Wuhan, China).
RNA library were prepared for sequence using stabdard  illumina nova seq X plus protocol

value: grape  ovule

tag: variety

value: Muscat Hamburg

tag: time

value: day 61


title: MCF10CA1a_rep1


title: HL60-untreated-004

description: Gene expression after 6hr  CTL

value: UNT


title: Muscat Hamburg ovule,day 55 rep2

description:
Library name: SAMPLE 6
MH55-2

value: day 55


title: Ovis aries, plasma, CTRL, week 7, replicate 2

description:
Library name: CTRL_A2
Sequencing internal ID: 31621-002


title: HL60-untreated-003

description: Gene expression after 6hr  CTL


title: MCF10AT1_rep3


title: Ovis aries, plasma, CTRL, week 7, replicate 1

description:
Library name: CTRL_A1
Sequencing internal ID: 31621-001


title: HL60-untreated-002

description: Gene expression after 6hr  CTL


title: Muscat Hamburg ovule,day 55 rep1

description:
Library name: SAMPLE 5
MH55-1


title: MCF10AT1_rep2


title: T26_0232

type: genomic

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie-Institute for Clinical Brain Research

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hypridized to human Infinium MethylationEPIC version 2 array using standard Illumina protocols

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

data_processing:
SeSAMe pipline (v1.24.0)
Average Beta values

label: Cy3 and Cy5

molecule: genomic DNA

source_name: meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from human meningiomas was extracted using QIAamp DNA Blood Mini Kit

value: meningioma


title: Muscat Hamburg ovule,day 45 rep2

description:
Library name: SAMPLE 4
MH45-2

value: day 45


title: HL60-untreated-001

description: Gene expression after 6hr  CTL


title: MCF10AT1_rep1


title: M. extorquens ORS 2060 grown in 2 uM La2Ox3 rep 2

city: Berkeley

first: Nathan

last: Good

state: CA

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: UC-Berkeley

description:
Library name: nodulans_Ox2_expression
oxide growth rep2

data_processing:
HISAT2 - v2.1.0 to align reads
StringTie v2.1.5 to assemble and quantify transcripts
DeSeq v1.20.0 for differential expression analysis
Assembly: GCA_000022085.1
Supplementary files format and content: spreadsheet with gene counts for every gene and every sample

organism: Methylobacterium nodulans ORS 2060

source_name: bacterial cells

growth_protocol: Methylobacterium nodulans ORS 2060 was grown in MP minimal media with 2 uM La2O3 or 2 uM LaCl3, 50 mM methanol, no citrate.

extract_protocol:
RNA was extracted using the Rneasy RNA extraction kit from Qiagen according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed on the Illumina NovaSeq X Plus platform using a 300 cycle flow cell kit to produce 2x150bp paired reads.

value: bacterial cells

tag: genotype

value: WT

value: limiting phosphate methanol + lanthanum growth


title: M. extorquens ORS 2060 grown in 2 uM La2Ox3 rep 1

description:
Library name: nodulans_Ox1_expression
oxide growth rep1


title: Muscat Hamburg ovule,day 45 rep1

description:
Library name: SAMPLE 3
MH45-1


title: MCF10A_rep3


title: Muscat Hamburg ovule,day 35 rep2

description:
Library name: SAMPLE 2
MH35-2

value: day 35


title: M. extorquens ORS 2060 grown in 2 uM LaCl3 rep 2

description:
Library name: nodulans_CL2_expression
chloride growth rep2


title: MCF10A_rep2


title: M. extorquens ORS 2060 grown in 2 uM LaCl3 rep 1

description:
Library name: nodulans_CL1_expression
chloride growth rep1


title: Muscat Hamburg ovule,day 35 rep1

description:
Library name: SAMPLE 1
MH35-1


title: MCF10A_rep1


title: CTR

city: Guangzhou

first: Fang

last: Zheng

address: 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

description: lncRNA expression data

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

source_name: HCC cell line

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of cyanine-3-CTP

growth_protocol: The high metastatic cell line LM9 were infected by lentivirus-CTR and lentivirus-HA-3’-NFYB and lentivirus-HA-5’-NFYB for stably expressing-NFYB cell lines.

extract_protocol: RNA immunoprecipitation was performed using Magna RIP RNA-Binding Protein Immunoprecipitation Kit

treatment_protocol: Lysates of CTR-, HA-3’-NFYB-infected and HA-5’-NFYB-infected LM9 cells were immunoprecipitated using anti-HA primary antibody

value: HCC cell line

tag: transfected with

value: lentivirus-CTR

tag: rip antibody

value: anti-HA primary antibody


title: NT257

status: Public on Jun 30 2026

city: seoul

first: Dakyung

address: 101 Daehakro

institute: University

description: Library name: NT257

data_processing:
RNA sequencing data were processed using RSEM, which employs the STAR aligner to map reads to the GRCh38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: normal

extract_protocol:
To isolate RNA from tumor tissues of patients and PDX models, approximately 5 mm³ of tumor tissue was snap-frozen in liquid nitrogen and homogenized in 1 ml of Tri-RNA Reagent (Favorgen, Cat# FATRR001, Taiwan) using a Biomasher (Takara, Cat# 9791A, Japan). Subsequently, 200 µl of chloroform was added for phase separation, followed by isopropanol precipitation to extract total RNA from the homogenized tissue.
TruSeq RNA

value: normal


title: X257

description: Library name: X257

source_name: xenograft tumor

value: xenograft tumor


title: T257

description: Library name: T257

source_name: primary tumor

value: primary tumor


title: 5’NFYB

description: lncRNA expression data


title: HCoF Young replicate 3

description: Library name: HCoF_Young_3

library_source: genomic

value: Colon

value: HCoF

value: Colonic fibroblast

value: Wild type

value: Young


title: HCoF Old replicate 2

description: Library name: HCoF_Old_2

value: Old


title: 3’NFYB

description: lncRNA expression data


title: CTRL_FEM_6

city: Lausanne

first: Benjamin

last: Rothé

address: Station 19

department: SV

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description: Library name: CTRL_FEM_6

data_processing:
Reads were trimmed to remove ISML (Nextera) adapter sequences.
FASTQ reads were aligned to the mouse mm10 reference genome using STAR (v2.7.10b) (Dobin et al., 2013), and gene-level counts were generated based on annotations from Ensembl release 102.
Assembly: mm10 - Ensembl release 102
Supplementary files format and content: Processed files include a data table of gene counts (by row) for each sample (column) taken from STAR quantMode

organism: Mus musculus

source_name: kidney

extract_protocol:
Kidneys were collected, weighed, and processed according to downstream applications.
Mouse RNA samples were pooled, and Illumina Stranded mRNA Ligation (ISML) libraries were prepared. Libraries were sequenced on the NovaSeq 6000 platform using paired-end 60 bp (PE60) reads, yielding approximately 60 million reads per sample.

treatment_protocol: Mice were maintained in individually ventilated cages. Bicc1lox/lox mice were crossed with KSP1.3/Cre mice (JAX stock #012237). Deletion of Bicc1 in cKO-P8LC1 mice was induced by administering doxycycline (200 mg/kg) in the chow for 10 days.

value: kidney

value: female

value: CTRL


title: CTRL_MALE_5

description: Library name: CTRL_MALE_5

value: male


title: CTRL_MALE_3_CTRL_MALE_7

description: Library name: CTRL_MALE_3_CTRL_MALE_7


title: CTRL_MALE_2_CTRL_MALE_6

description: Library name: CTRL_MALE_2_CTRL_MALE_6


title: CTRL_FEM_4_CTRL_FEM_8

description: Library name: CTRL_FEM_4_CTRL_FEM_8


title: CTRL_MALE_1_CTRL_MALE_4

description: Library name: CTRL_MALE_1_CTRL_MALE_4


title: CTRL_FEM_1_CTRL_FEM_5

description: Library name: CTRL_FEM_1_CTRL_FEM_5


title: cKO-KSP_MALE_3_cKO-KSP_MALE_7

description: Library name: cKO-KSP_MALE_3_cKO-KSP_MALE_7

value: cKO-KSP


title: cKO-KSP_MALE_5

description: Library name: cKO-KSP_MALE_5


title: cKO-KSP_MALE_2_cKO-KSP_MALE_6

description: Library name: cKO-KSP_MALE_2_cKO-KSP_MALE_6


title: cKO-KSP_FEM_1_cKO-KSP_FEM_5

description: Library name: cKO-KSP_FEM_1_cKO-KSP_FEM_5


title: cKO-KSP_FEM_2_cKO-KSP_FEM_4

description: Library name: cKO-KSP_FEM_2_cKO-KSP_FEM_4


title: Ries_1_31_1400_3

city: Brookings

first: Anne

last: Fennell

state: SD

address: Raven Precision Ag Building Box 2100A

department: Agronomy, Horticulture & Plant Science

institute: South Dakota State University

description:
Library name: Ries_1_31_1400_3
Total RNA single illumina

data_processing:
1. Quality Control of Raw Reads- Raw RNA-seq reads were assessed for quality using FastQC, and summary reports across all samples were generated using MultiQC.
2. Adapter Trimming and Filtering- Adapter sequences and low-quality bases were removed using Trimmomatic. Since the data consisted of single-end reads, the TruSeq2 single-end adapter file was used during trimming.
3. Reference Genome Preparation- The Vitis vinifera 12Xv2 reference genome assembly and V2.20 GFF3 annotation file were downloaded and prepared for downstream analysis.
4. Genome Index Generation - Genome indices were generated using STAR to facilitate efficient   alignment of RNA-seq reads.
5. Read Alignment - Trimmed reads were aligned to the Vitis vinifera reference genome using STAR, producing BAM alignment files for each sample.
Assembly: 6. Gene Expression Quantification- Gene-level read counts were generated using featureCounts  with the V2.20 GFF3 annotation file, retaining gene IDs for downstream expression analysis.
Supplementary files format and content: geo_processed_read_counts.csv

source_name: Bud

growth_protocol: Standard commercial vineyard management, Ravines Wine Cellar, Geneva, New York

extract_protocol:
RNA was extracted from 3 bud pooled samples. Tissue was homogenized to powder while frozen then promptly extracted using Sigma Plant Total RNA kits with the addition of 3% PVP40 at the lysis buffer stage.
Poly(A)-selected mRNA-seq library, prepared with a TruSeq-compatible kit, random-hexamer primed, sequenced 1×75 SE on Illumina NextSeq 500/550.

treatment_protocol: Field Conditions

value: Bud

value: total RNA

value: single


title: CTRL_FEM_3_CTRL_FEM_7

description: Library name: CTRL_FEM_3_CTRL_FEM_7


title: cKO-KSP_MALE_1_cKO-KSP_MALE_4

description: Library name: cKO-KSP_MALE_1_cKO-KSP_MALE_4


title: Ries_1_31_1400_2

description:
Library name: Ries_1_31_1400_2
Total RNA single illumina


title: cKO-KSP_FEM_6

description: Library name: cKO-KSP_FEM_6


title: Ries_1_30_1400_2

description:
Library name: Ries_1_30_1400_2
Total RNA single illumina


title: Ries_1_30_1400_3

description:
Library name: Ries_1_30_1400_3
Total RNA single illumina


title: Ries_1_30_1400_1

description:
Library name: Ries_1_30_1400_1
Total RNA single illumina


title: cKO-KSP_FEM_3_cKO-KSP_FEM_7

description: Library name: cKO-KSP_FEM_3_cKO-KSP_FEM_7


title: Ries_1_29_1400_3

description:
Library name: Ries_1_29_1400_3
Total RNA single illumina


title: Ries_1_29_1400_2

description:
Library name: Ries_1_29_1400_2
Total RNA single illumina


title: Ries_1_31_1400_1

description:
Library name: Ries_1_31_1400_1
Total RNA single illumina


title: Ries_1_29_1400_1

description:
Library name: Ries_1_29_1400_1
Total RNA single illumina


title: Ries_1_27_600_3

description:
Library name: Ries_1_27_600_3
Total RNA single illumina


title: Ries_1_28_1400_3

description:
Library name: Ries_1_28_1400_3
Total RNA single illumina


title: Ries_1_28_1400_1

description:
Library name: Ries_1_28_1400_1
Total RNA single illumina


title: Ries_1_27_1400_2

description:
Library name: Ries_1_27_1400_2
Total RNA single illumina


title: Ries_1_27_1400_3

description:
Library name: Ries_1_27_1400_3
Total RNA single illumina


title: Ries_1_28_1400_2

description:
Library name: Ries_1_28_1400_2
Total RNA single illumina


title: Ries_1_27_600_2

description:
Library name: Ries_1_27_600_2
Total RNA single illumina


title: Ries_1_26_600_3

description:
Library name: Ries_1_26_600_3
Total RNA single illumina


title: Ries_1_26_600_1

description:
Library name: Ries_1_26_600_1
Total RNA single illumina


title: Patient 22 COAD 022

description: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software.

value: rectal cancer

value: Near total


title: Ries_1_26_1800_3

description:
Library name: Ries_1_26_1800_3
Total RNA single illumina


title: Ries_1_27_1400_1

description:
Library name: Ries_1_27_1400_1
Total RNA single illumina


title: Ries_1_26_1800_1

description:
Library name: Ries_1_26_1800_1
Total RNA single illumina


title: Ries_1_27_600_1

description:
Library name: Ries_1_27_600_1
Total RNA single illumina


title: Ries_1_26_1800_2

description:
Library name: Ries_1_26_1800_2
Total RNA single illumina


title: Ries_1_26_1400_3

description:
Library name: Ries_1_26_1400_3
Total RNA single illumina


title: Ries_1_26_1400_2

description:
Library name: Ries_1_26_1400_2
Total RNA single illumina


title: hMSC_donor2_ctrl_4h_exp2_rep1

city: Warsaw

first: Alicja

last: Trebinska-Stryjewska

address: gen. S. Kaliskiego 2

department: Institute of Optoelectronics

institute: Military University of Technology

description:
257236328904_2_1
hMCS donor2, control, 4h, experiment 2, replicate 1

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented following the manufacturer's protocol at 60°C for 30 min; fragmentation reaction was stopped by adding 2 × Hi-RPM Hybridization buffer. Fragmented Cy3-labeled cRNA was hybridized to Agilent-072363 SurePrint G3 Human Gene Expression v3 8x60K microarrays for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed following manufacturer's instructions with GE Wash Buffer 1 and 2 (Agilent).

scan_protocol: Microarray slides were scanned immediately after washing with the SureScan Microarray Scanner (Agilent) using the Agilent Microarray Scan Control program version 9.1 with the following settings: resolution of 3 µm; dye channel green; green PMT sensitivity of 100%.

data_processing: Data from scanned images were extracted with the Feature Extraction Software 12.0 using default parameters (protocol: GE1_1200_Jun14, grid: 072363_D_F_20190214) to obtain the background-subtracted and detrended processed signal intensities. Obtained results were further processed with GeneSpring version 14.9, and log2-transformed normalized signal intensities were obtained after normalization by a percentile shift (75th percentile). The baseline was set to the median of all samples.

source_name: hMCS donor2, control, 4h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of Total RNA using the Low Input Quick Amp Labeling Kit, One Color (Agilent) according to manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Addition of RNA Spike-In, One color (Agilent) served as an internal control. Cy3-labeled cRNA quality and quantity were assessed using 2100 Agilent Bioanalyzer (Agilent) and Agilent RNA 6000 Nano Reagent (Agilent).

growth_protocol: Poietics Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC) (Lonza) from two different donors were propagated in MSCGM Mesenchymal Stem Cell Growth Medium BulletKit (Lonza), and antibiotic/antimycotic in 5% carbon dioxide at 37ºC until semi-confluent.

extract_protocol: Immediately, 4 h or 24 h after treatment, cells were trypsinized, harvested, washed twice in ice-cold PBS and centrifuged at 150xg (hMSC donor 1) or 300xg (hMSC donor 2) for 5 min at 4ºC; cell pellets were frozen at -80ºC. Total RNA was isolated from the frozen pellets using the RNeasy Mini Kit (QIAGEN) according to manufacturer's instructions (including on-column DNaseI treatment). RNA was quantified using the QuantiFluor RNA System and Quantus Fluorometer (Promega). RNA quality was assessed with 2100 Agilent Bioanalyzer and Agilent RNA 6000 Nano Reagent. RIN ranged from 9.2 to 10.0.

treatment_protocol: Human MSC were used for experiments at the fourth or fifth passage, at 80% confluence. Before the exposure, standard hMSC medium in 175 cm2 cell culture flask was replaced with 10 ml of new, warm medium. Cells were exposed to a single high-peak power electromagnetic pulse (peak field: 1 Mv/m, rise time: 3 ns, pulse width: 30 ns, center frequency: 50 MHz). Cells were either harvested immediately after treatment or cultured for another 4 h or 24 h after adding 40 ml of standard hMSC medium. Sham-treated cells were prepared as above, except during exposure they were placed in a Faraday cage (80 dB attenuation for frequencies ranging from 100 kHz to 1 GHz). Control cells were kept in an incubator in standard cell culture conditions before harvesting.

tag: age of the donor

value: 24 years

tag: sex of the donor

value: Female

tag: race/ethnicity of the donor

value: Black

value: Control

value: 4 h


title: Ries_1_25_600_2

description:
Library name: Ries_1_25_600_2
Total RNA single illumina

tag: treatment


title: Ries_1_26_1400_1

description:
Library name: Ries_1_26_1400_1
Total RNA single illumina


title: Ries_1_25_600_1

description:
Library name: Ries_1_25_600_1
Total RNA single illumina


title: Ries_1_25_1800_3

description:
Library name: Ries_1_25_1800_3
Total RNA single illumina


title: Ries_1_25_1800_2

description:
Library name: Ries_1_25_1800_2
Total RNA single illumina


title: Ries_1_25_600_3

description:
Library name: Ries_1_25_600_3
Total RNA single illumina


title: Ries_1_25_1800_1

description:
Library name: Ries_1_25_1800_1
Total RNA single illumina


title: Ries_1_25_1400_3

description:
Library name: Ries_1_25_1400_3
Total RNA single illumina


title: Ries_1_25_1400_1

description:
Library name: Ries_1_25_1400_1
Total RNA single illumina


title: Ries_1_25_1400_2

description:
Library name: Ries_1_25_1400_2
Total RNA single illumina


title: Ries_1_24_600_3

description:
Library name: Ries_1_24_600_3
Total RNA single illumina


title: Ries_1_24_600_2

description:
Library name: Ries_1_24_600_2
Total RNA single illumina


title: Ries_1_24_1800_2

description:
Library name: Ries_1_24_1800_2
Total RNA single illumina


title: Ries_1_24_1800_1

description:
Library name: Ries_1_24_1800_1
Total RNA single illumina


title: Ries_1_24_1400_3

description:
Library name: Ries_1_24_1400_3
Total RNA single illumina


title: Ries_1_24_1400_2

description:
Library name: Ries_1_24_1400_2
Total RNA single illumina


title: Ries_1_24_1400_1

description:
Library name: Ries_1_24_1400_1
Total RNA single illumina


title: Ries_1_23_1800_2

description:
Library name: Ries_1_23_1800_2
Total RNA single illumina


title: Ries_1_23_1800_1

description:
Library name: Ries_1_23_1800_1
Total RNA single illumina


title: Ries_1_23_1400_3

description:
Library name: Ries_1_23_1400_3
Total RNA single illumina


title: Ries_1_23_1400_1

description:
Library name: Ries_1_23_1400_1
Total RNA single illumina


title: Ries_1_23_1400_2

description:
Library name: Ries_1_23_1400_2
Total RNA single illumina


title: Ries_1_22_1400_3

description:
Library name: Ries_1_22_1400_3
Total RNA single illumina


title: Ries_1_22_1400_2

description:
Library name: Ries_1_22_1400_2
Total RNA single illumina


title: Ries_1_21_1400_3

description:
Library name: Ries_1_21_1400_3
Total RNA single illumina


title: Ries_1_22_1400_1

description:
Library name: Ries_1_22_1400_1
Total RNA single illumina


title: Ries_1_26_600_2

description:
Library name: Ries_1_26_600_2
Total RNA single illumina


title: Ries_1_21_1400_1

description:
Library name: Ries_1_21_1400_1
Total RNA single illumina


title: Embryos treated with DMSO vehicle Replicate 1

city: Lexington

first: Jeramiah

middle: James

last: Smith

state: KY

address: 101 Morgan Building

department: Biology

institute: University of Kentucky

description: Library name: DMSO_1

data_processing:
RNA-seq reads were aligned to the reference genome using HISAT2 v2.2.1 (Kim et al. 2019).
Gene expression estimates were obtained from these alignments using StringTie v2.2.3 (Pertea et al. 2015)
Assembly: GCA_040938575.1
Supplementary files format and content: Gene Count matrix from StringTie V2.2.3 in .csv format

molecule: polyA RNA

organism: Ambystoma mexicanum

source_name: St42 embryo

extract_protocol:
RNA was isolated using TRIzol (Invitrogen) and syringe needles for initial tissue disruption, and then following instructions included with a Monarch Total RNA Isolation Kit (NEB).
RNA samples were submitted to a commercial vendor (Novogene) to generate approximately 25-30 million raw reads per sample on an Illumina sequencer.

value: St42 embryo

value: DMSO vehicle


title: Ries_1_20_1400_3

description:
Library name: Ries_1_20_1400_3
Total RNA single illumina


title: Ries_1_20_1400_2

description:
Library name: Ries_1_20_1400_2
Total RNA single illumina


title: Ries_1_20_1400_1

description:
Library name: Ries_1_20_1400_1
Total RNA single illumina


title: Ries_1_19_1400_2

description:
Library name: Ries_1_19_1400_2
Total RNA single illumina


title: Ries_1_19_1400_3

description:
Library name: Ries_1_19_1400_3
Total RNA single illumina


title: Ries_1_19_1400_1

description:
Library name: Ries_1_19_1400_1
Total RNA single illumina


title: Ries_1_18_600_1

description:
Library name: Ries_1_18_600_1
Total RNA single illumina


title: Ries_1_18_600_3

description:
Library name: Ries_1_18_600_3
Total RNA single illumina


title: Ries_1_18_1400_2

description:
Library name: Ries_1_18_1400_2
Total RNA single illumina


title: Ries_1_18_1400_1

description:
Library name: Ries_1_18_1400_1
Total RNA single illumina


title: Ries_1_18_1400_3

description:
Library name: Ries_1_18_1400_3
Total RNA single illumina


title: Ries_1_17_600_3

description:
Library name: Ries_1_17_600_3
Total RNA single illumina


title: Ries_1_17_1800_3

description:
Library name: Ries_1_17_1800_3
Total RNA single illumina


title: Ries_1_17_600_1

description:
Library name: Ries_1_17_600_1
Total RNA single illumina


title: Ries_1_17_600_2

description:
Library name: Ries_1_17_600_2
Total RNA single illumina


title: Ries_1_17_1800_2

description:
Library name: Ries_1_17_1800_2
Total RNA single illumina


title: Ries_1_17_1400_3

description:
Library name: Ries_1_17_1400_3
Total RNA single illumina


title: Ries_1_17_1400_2

description:
Library name: Ries_1_17_1400_2
Total RNA single illumina


title: Ries_1_16_600_1

description:
Library name: Ries_1_16_600_1
Total RNA single illumina


title: Ries_1_16_1800_2

description:
Library name: Ries_1_16_1800_2
Total RNA single illumina


title: Ries_1_16_1800_1

description:
Library name: Ries_1_16_1800_1
Total RNA single illumina


title: Ries_1_16_1400_2

description:
Library name: Ries_1_16_1400_2
Total RNA single illumina


title: Ries_1_16_1400_3

description:
Library name: Ries_1_16_1400_3
Total RNA single illumina


title: Ries_1_16_1400_1

description:
Library name: Ries_1_16_1400_1
Total RNA single illumina


title: Ries_1_15_600_3

description:
Library name: Ries_1_15_600_3
Total RNA single illumina


title: Ries_1_16_1800_3

description:
Library name: Ries_1_16_1800_3
Total RNA single illumina


title: Ries_1_15_600_2

description:
Library name: Ries_1_15_600_2
Total RNA single illumina


title: Ries_1_15_1800_1

description:
Library name: Ries_1_15_1800_1
Total RNA single illumina


title: Ries_1_14_1800_2

description:
Library name: Ries_1_14_1800_2
Total RNA single illumina


title: Ries_1_15_600_1

description:
Library name: Ries_1_15_600_1
Total RNA single illumina


title: Ries_1_15_1800_2

description:
Library name: Ries_1_15_1800_2
Total RNA single illumina


title: Ries_1_15_1400_1

description:
Library name: Ries_1_15_1400_1
Total RNA single illumina


title: Ries_1_14_1800_3

description:
Library name: Ries_1_14_1800_3
Total RNA single illumina


title: Ries_1_15_1400_3

description:
Library name: Ries_1_15_1400_3
Total RNA single illumina


title: Ries_1_14_1800_1

description:
Library name: Ries_1_14_1800_1
Total RNA single illumina


title: Ries_1_14_1400_1

description:
Library name: Ries_1_14_1400_1
Total RNA single illumina


title: Ries_1_14_1400_2

description:
Library name: Ries_1_14_1400_2
Total RNA single illumina


title: Cab_Franc_1_31_1400_2

description:
Library name: Cab_Franc_1_31_1400_2
Total RNA single illumina


title: Cab_Franc_1_30_1400_3

description:
Library name: Cab_Franc_1_30_1400_3
Total RNA single illumina


title: Cab_Franc_1_31_1400_1

description:
Library name: Cab_Franc_1_31_1400_1
Total RNA single illumina


title: Cab_Franc_1_31_1400_3

description:
Library name: Cab_Franc_1_31_1400_3
Total RNA single illumina


title: Cab_Franc_1_29_1400_2

description:
Library name: Cab_Franc_1_29_1400_2
Total RNA single illumina


title: Cab_Franc_1_29_1400_3

description:
Library name: Cab_Franc_1_29_1400_3
Total RNA single illumina


title: Cab_Franc_1_30_1400_1

description:
Library name: Cab_Franc_1_30_1400_1
Total RNA single illumina


title: Cab_Franc_1_29_1400_1

description:
Library name: Cab_Franc_1_29_1400_1
Total RNA single illumina


title: Group1_PND10_125, GEX

city: New York

first: Chrysothemis

last: Brown

state: New York

department: Immuno-Oncology Program

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Group1_PND10_125_mRNA
GEX (3' mRNA) library from lung and medLN of neonatal mice

data_processing:
Single-cell RNA-seq FASTQ files were aligned to mm10 (Cell Ranger mouse reference genome mm10-2020-A) and counted by Cell Ranger v8.0.1 with default parameters. HTO sequencing data were aligned to the HTO barcodes, and UMIs were counted for each cell using CITE-seq-Count. Samples were then demultiplexed using the SHARP v0.1.3 pipeline. The singlet barcodes were further filtered based on the number of RNA-seq transcripts (>400 and <22,000), the number of detected genes (>400 and <8,000), and the fraction of mitochondrial transcripts (<8%). Following quality control filtering, raw counts were library-size normalized and log-transformed (‘log-normalized’ expression values) using Scanpy v1.10.3. A nearest-neighbor graph was constructed using the top 50 principal components (PCs) with 30 nearest neighbors. Clustering was performed using PhenoGraph (k = 30, clustering_algo = ‘louvain’). Cell clustering was visualized using UMAP, computed from the nearest neighbor graph built by PhenoGraph.
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger processed output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Output files for hashtag: Group1_124_PND10_HTO_barcodes.tsv.gz, Group1_124_PND10_HTO_features.tsv.gz, Group1_124_PND10_HTO_matrix.mtx.gz Group2_124_PND10_HTO_barcodes.tsv.gz, Group2_124_PND10_HTO_features.tsv.gz, Group2_124_PND10_HTO_matrix.mtx.gz Group3_124_PND10_HTO_barcodes.tsv.gz, Group3_124_PND10_HTO_features.tsv.gz, Group3_124_PND10_HTO_matrix.mtx.gz Group4_124_PND10_HTO_barcodes.tsv.gz, Group4_124_PND10_HTO_features.tsv.gz, Group4_124_PND10_HTO_matrix.mtx.gz Group1_125_PND10_HTO_barcodes.tsv.gz, Group1_125_PND10_HTO_features.tsv.gz, Group1_125_PND10_HTO_matrix.mtx.gz Group2_125_PND10_HTO_barcodes.tsv.gz, Group2_125_PND10_HTO_features.tsv.gz, Group2_125_PND10_HTO_matrix.mtx.gz Group3_125_PND10_HTO_barcodes.tsv.gz, Group3_125_PND10_HTO_features.tsv.gz, Group3_125_PND10_HTO_matrix.mtx.gz Group4_125_PND10_HTO_barcodes.tsv.gz, Group4_125_PND10_HTO_features.tsv.gz, Group4_125_PND10_HTO_matrix.mtx.gz, Group1_124_5DPI_HTO_barcodes.tsv.gz, Group1_124_5DPI_HTO_features.tsv.gz, Group1_124_5DPI_HTO_matrix.mtx.gz Group2_124_5DPI_HTO_barcodes.tsv.gz, Group2_124_5DPI_HTO_features.tsv.gz, Group2_124_5DPI_HTO_matrix.mtx.gz Group3_124_5DPI_HTO_barcodes.tsv.gz, Group3_124_5DPI_HTO_features.tsv.gz, Group3_124_5DPI_HTO_matrix.mtx.gz Group4_124_5DPI_HTO_barcodes.tsv.gz, Group4_124_5DPI_HTO_features.tsv.gz, Group4_124_5DPI_HTO_matrix.mtx.gz Group1_125_5DPI_HTO_barcodes.tsv.gz, Group1_125_5DPI_HTO_features.tsv.gz, Group1_125_5DPI_HTO_matrix.mtx.gz Group2_125_5DPI_HTO_barcodes.tsv.gz, Group2_125_5DPI_HTO_features.tsv.gz, Group2_125_5DPI_HTO_matrix.mtx.gz Group3_125_5DPI_HTO_barcodes.tsv.gz, Group3_125_5DPI_HTO_features.tsv.gz, Group3_125_5DPI_HTO_matrix.mtx.gz Group4_125_5DPI_HTO_barcodes.tsv.gz, Group4_125_5DPI_HTO_features.tsv.gz, Group4_125_5DPI_HTO_matrix.mtx.gz
Supplementary files format and content: Analysis results from Scanpy including pheno louvain clusters, celltype annotations, treatment groups and UMAP
Library strategy: CITE-seq

source_name: Lung and medLN

extract_protocol:
For single cell RNA seq of stem-like progenitors, pre-DCs and differentiated-DCs, lung and mediastinal lymph nodes from OPN+/+ or OPN-/- reared neonates treated with D-PLA were pooled from six biological replicates. Cells were incubated with 𝛼-CD16/32-BV605 in PBS-2% FBS for 20 min at 4°C to block binding to Fc receptors. Cell surface antigens were then stained for 30 mins at 4°C in PBS-2% FBS. Cells from distinct tissues were ‘stained’ with BioLegend TotalSeq B oligo-conjugated antibodies consisting of a pool of antibodies directed against CD45 (BioLegend; Clone 30-F11) and H2 MHC Class I alloantigens (BioLegend; clone M1/42). Immediately prior to fluorescent-assisted cell sorting (FACS), cells were resuspended in sorting buffer with SYTOX blue (Invitrogen; Cat# S34857) for dead cell exclusion. Live, lineage (CD3, CD19, NK1.1, Siglec-F, TCRβ, TCR𝛾𝛿)- singlets were then sort purified into six distinct populations: cDCs (CD11chi MHCII+ B220-), pDCs (CD11clo/int B220+ SiglecH+), pre-cDCs (CD11chi MHCII- CD135+ CD172a-), MDP/CDPs (CD11c- MHCII- cKIT+ SCA1- CD135+), LMPP/CMPs (CD34+ cKIT+ CD127- SCA1+/- CD16/32-) and CLPs (CD34- cKIT+ CD127+ Flt3+). Cells were sorted into cRPMI (Gibco; Cat# 11875093), each of the sort populations were counted and then pooled together to a final concentration of ~1600 cells per µL according to 10X Genomics guidelines for optimal cell recovery.
Single Cell Gene Expression was performed on a Chromium X (10X Genomics) following the user guide manual for Chromium GEM-X Single Cell 3’ Reagent Kit V4 (CG000732; Rev B). Briefly, cell viability was confirmed >90% with 0.5% (v/v) Trypan Blue (Sigma-Aldrich; Cat# T8154) staining and hemocytometer quantification. Cells were then captured in gel bead emulsions (GEMs). Following reverse transcription and cell barcoding, the GEMs were broken and cDNA purified using Dynabeads MyOne SILANE (Invitrogen; Cat# 37002D) followed by PCR amplifications as instructed by the manual. ~240,000 cells were targeted in total. Cells from different tissues and replicates were multiplexed together on one lane of 10X Chromium X using Hash Tag Oligonucleotides - HTO following a previously described protocol (Stoeckius et al., 2018). The final 3’ Gene Expression and cell surface protein libraries were loaded in a ratio of 9:1 and sequenced on an Illumina NextSeq 2000 (2 x P3 Flow Cell 1200mil reads) platform (Read 1 – 28 cycles, i7 index – 10 cycles, i5 index – 10 cycles, Read 2 – 90 cycles).

value: Lung and medLN

value: Lymphocytes

tag: age

value: post-natal day 10

tag: host strain

tag: foster mother_strain

value: PBS

tag: infection

value: uninfected

tag: library type

value: mRNA


title: T26_0220

tag: tissue

value: meningioma


title: T26_0035


title: Cab_Franc_1_28_1400_1

description:
Library name: Cab_Franc_1_28_1400_1
Total RNA single illumina

value: Bud

value: total RNA

value: single


title: Cab_Franc_1_28_1400_2

description:
Library name: Cab_Franc_1_28_1400_2
Total RNA single illumina


title: hMSC_donor2_sham_24h_exp1_rep1

description:
257236328897_1_3
hMCS donor2, sham, 24h, experiment 1, replicate 1

source_name: hMCS donor2, sham, 24h

tag: cell line

value: Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC)

value: 24 years

value: Sham-exposed


title: Cab_Franc_1_30_1400_2

description:
Library name: Cab_Franc_1_30_1400_2
Total RNA single illumina


title: hMSC_donor1_sham_24h_exp1_rep2

description:
257236328901_1_3
hMSC donor1, sham, 24h, experiment 1, replicate 2

source_name: hMSC donor1, sham, 24h

value: 22 years

value: Male

value: Hispanic/Latino


title: Cab_Franc_1_27_600_3

description:
Library name: Cab_Franc_1_27_600_3
Total RNA single illumina


title: Cab_Franc_1_27_600_1

description:
Library name: Cab_Franc_1_27_600_1
Total RNA single illumina


title: Cab_Franc_1_27_600_2

description:
Library name: Cab_Franc_1_27_600_2
Total RNA single illumina


title: Cab_Franc_1_27_1400_2

description:
Library name: Cab_Franc_1_27_1400_2
Total RNA single illumina


title: Cab_Franc_1_27_1400_1

description:
Library name: Cab_Franc_1_27_1400_1
Total RNA single illumina


title: Cab_Franc_1_27_1400_3

description:
Library name: Cab_Franc_1_27_1400_3
Total RNA single illumina


title: Cab_Franc_1_26_600_3

description:
Library name: Cab_Franc_1_26_600_3
Total RNA single illumina


title: Cab_Franc_1_26_600_1

description:
Library name: Cab_Franc_1_26_600_1
Total RNA single illumina


title: Cab_Franc_1_26_600_2

description:
Library name: Cab_Franc_1_26_600_2
Total RNA single illumina


title: Cab_Franc_1_26_1800_3

description:
Library name: Cab_Franc_1_26_1800_3
Total RNA single illumina


title: Cab_Franc_1_26_1800_2

description:
Library name: Cab_Franc_1_26_1800_2
Total RNA single illumina


title: Cab_Franc_1_26_1800_1

description:
Library name: Cab_Franc_1_26_1800_1
Total RNA single illumina


title: Cab_Franc_1_26_1400_2

description:
Library name: Cab_Franc_1_26_1400_2
Total RNA single illumina


title: Cab_Franc_1_26_1400_1

description:
Library name: Cab_Franc_1_26_1400_1
Total RNA single illumina


title: Cab_Franc_1_25_600_2

description:
Library name: Cab_Franc_1_25_600_2
Total RNA single illumina


title: Cab_Franc_1_25_600_1

description:
Library name: Cab_Franc_1_25_600_1
Total RNA single illumina


title: Cab_Franc_1_25_1800_1

description:
Library name: Cab_Franc_1_25_1800_1
Total RNA single illumina


title: Cab_Franc_1_25_1800_3

description:
Library name: Cab_Franc_1_25_1800_3
Total RNA single illumina


title: Cab_Franc_1_25_1800_2

description:
Library name: Cab_Franc_1_25_1800_2
Total RNA single illumina


title: Cab_Franc_1_25_1400_2

description:
Library name: Cab_Franc_1_25_1400_2
Total RNA single illumina


title: Cab_Franc_1_25_1400_3

description:
Library name: Cab_Franc_1_25_1400_3
Total RNA single illumina


title: Cab_Franc_1_24_600_3

description:
Library name: Cab_Franc_1_24_600_3
Total RNA single illumina


title: Cab_Franc_1_24_600_2

description:
Library name: Cab_Franc_1_24_600_2
Total RNA single illumina


title: Cab_Franc_1_24_1800_3

description:
Library name: Cab_Franc_1_24_1800_3
Total RNA single illumina


title: Cab_Franc_1_24_1800_2

description:
Library name: Cab_Franc_1_24_1800_2
Total RNA single illumina


title: Cab_Franc_1_24_1800_1

description:
Library name: Cab_Franc_1_24_1800_1
Total RNA single illumina


title: Cab_Franc_1_24_1400_3

description:
Library name: Cab_Franc_1_24_1400_3
Total RNA single illumina


title: Cab_Franc_1_24_1400_2

description:
Library name: Cab_Franc_1_24_1400_2
Total RNA single illumina


title: Cab_Franc_1_23_1800_3

description:
Library name: Cab_Franc_1_23_1800_3
Total RNA single illumina


title: Cab_Franc_1_23_1800_2

description:
Library name: Cab_Franc_1_23_1800_2
Total RNA single illumina


title: Cab_Franc_1_23_1800_1

description:
Library name: Cab_Franc_1_23_1800_1
Total RNA single illumina


title: Cab_Franc_1_23_1400_3

description:
Library name: Cab_Franc_1_23_1400_3
Total RNA single illumina


title: Cab_Franc_1_23_1400_1

description:
Library name: Cab_Franc_1_23_1400_1
Total RNA single illumina


title: Cab_Franc_1_22_1400_3

description:
Library name: Cab_Franc_1_22_1400_3
Total RNA single illumina


title: Cab_Franc_1_22_1400_2

description:
Library name: Cab_Franc_1_22_1400_2
Total RNA single illumina


title: Cab_Franc_1_22_1400_1

description:
Library name: Cab_Franc_1_22_1400_1
Total RNA single illumina


title: Cab_Franc_1_21_1400_3

description:
Library name: Cab_Franc_1_21_1400_3
Total RNA single illumina


title: hMSC_donor2_HPEM_0h_exp1_rep2

description:
257236328898_1_2
hMCS donor2, HPEM, 0h, experiment 1, replicate 2

source_name: hMCS donor2, HPEM, 0h

value: Female

value: Black

value: Exposed to a high power electromagnetic pulse (HPEM), 1 MV/m

value: 0 h


title: hMSC_donor2_HPEM_0h_exp1_rep1

description:
257236328897_1_2
hMCS donor2, HPEM, 0h, experiment 1, replicate 1


title: Cab_Franc_1_21_1400_1

description:
Library name: Cab_Franc_1_21_1400_1
Total RNA single illumina


title: Cab_Franc_1_20_1400_1

description:
Library name: Cab_Franc_1_20_1400_1
Total RNA single illumina


title: SK-N-BE(2) cells, NUDT21 knockdown, replicate 1

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

description: Library name: Sample 1

data_processing:
Filtering: Only read 2 was used to determine PAS sites. Raw reads were trimmed to remove adapters, low-quality bases with a score below 20, more than 3 consecutive "G"s at the end of the sequence, as well as "N"s and all subsequent sequences. Reads containing no less than 30% of the bases with a quality score below 20 were filtered out. Processed reads with a remaining length greater than 20 were retained.
Removing poly(A) tract: To remove poly(A) tract, we first search for at least 8 consecutive A's from the end of the reads. If more than 2 consecutive non-A bases are encountered, the poly(A) tract and all subsequent bases are removed, retaining only those reads with a length of 12 bases or more. Next, we scan for A's starting from the 5' end of the reads; if more than 9 consecutive A's are present, the poly(A) tract and all subsequent bases are removed, with reads of 12 bases or longer retained.
Alignment: These two sets of processed reads above are then simultaneously aligned to hg38 genome and Gencode.v45 using HISAT2. For reads that align successfully under both conditions, priority is given to the alignment result corresponding to the read with a poly(A) tract at the end.
Assembly: hg38
Supplementary files format and content: BigWig files containing read coverage normalized to CPM (read count per million)

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01).
For each sample, 5 μg of total RNA was treated with RQ1 DNase (M6101,Promega, USA) to remove DNA, fragmented RNAs were used for PAS-seq library preparation. mRNAs were captured with mRNA Capture Beads kit （N401,Vazyme,Chian）. Fragmented mRNAs were used for directional PAS-seq library preparation by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (KK8544, Roche, USA). Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726, Roche, USA). After purification of ligation product and size fractioning to 300-500 bp, the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq Xplus system for 150 nt paired-end sequencing.

tag: cell type

value: Neuroblastoma cells

value: NUDT21 knockdown


title: Cab_Franc_1_19_1400_3

description:
Library name: Cab_Franc_1_19_1400_3
Total RNA single illumina


title: naive CD8 donor 2

city: Atlanta

first: Donald

last: McGuire

state: GA

address: 1462 Clifton Road room 412

institute: Emory University School of Medicine

description: Library name: p24118-s011_595-CD8-N

data_processing:
Samples were alligned to Hg38 using Hisat2 and processed into bam files using samtools 1.13.  Count data was obtained using featurecout from the subread package.  Splicing of the PTPRC gene was done using a coustom python script using the pysam package
Assembly: Hg38
Supplementary files format and content: CSV(comma seperated values)

source_name: PBMC

extract_protocol:
1,000-10,000 T cells were flow sorted based on CD45RA and CCR7 expression into RPMI supplemented with 10% FBS.  RNA was then obtained use Qiagen DNA/RNA mini allprep kit.
cDNA libraries prepared using TakaraBio's SMART-Seq v4 Ultra Low Input RNA Kit with Illumina's Nextera XT DNA Library Preparation Kit

value: PBMC

value: CD45RA+ CCR7+ CD8+ CD3+


title: Cab_Franc_1_19_1400_1

description:
Library name: Cab_Franc_1_19_1400_1
Total RNA single illumina

value: Bud


title: Cab_Franc_1_19_1400_2

description:
Library name: Cab_Franc_1_19_1400_2
Total RNA single illumina

value: total RNA


title: Cab_Franc_1_18_600_3

description:
Library name: Cab_Franc_1_18_600_3
Total RNA single illumina

value: single


title: Cab_Franc_1_18_600_2

description:
Library name: Cab_Franc_1_18_600_2
Total RNA single illumina


title: Cab_Franc_1_18_600_1

description:
Library name: Cab_Franc_1_18_600_1
Total RNA single illumina


title: Cab_Franc_1_18_1400_3

description:
Library name: Cab_Franc_1_18_1400_3
Total RNA single illumina


title: Cab_Franc_1_18_1400_2

description:
Library name: Cab_Franc_1_18_1400_2
Total RNA single illumina


title: Cab_Franc_1_18_1400_1

description:
Library name: Cab_Franc_1_18_1400_1
Total RNA single illumina


title: Cab_Franc_1_17_600_2

description:
Library name: Cab_Franc_1_17_600_2
Total RNA single illumina


title: Cab_Franc_1_17_600_3

description:
Library name: Cab_Franc_1_17_600_3
Total RNA single illumina


title: Cab_Franc_1_17_600_1

description:
Library name: Cab_Franc_1_17_600_1
Total RNA single illumina


title: Cab_Franc_1_17_1800_3

description:
Library name: Cab_Franc_1_17_1800_3
Total RNA single illumina


title: Cab_Franc_1_17_1800_2

description:
Library name: Cab_Franc_1_17_1800_2
Total RNA single illumina


title: Cab_Franc_1_17_1800_1

description:
Library name: Cab_Franc_1_17_1800_1
Total RNA single illumina


title: Cab_Franc_1_17_1400_3

description:
Library name: Cab_Franc_1_17_1400_3
Total RNA single illumina


title: Cab_Franc_1_17_1400_2

description:
Library name: Cab_Franc_1_17_1400_2
Total RNA single illumina


title: Cab_Franc_1_16_600_3

description:
Library name: Cab_Franc_1_16_600_3
Total RNA single illumina


title: Cab_Franc_1_16_600_1

description:
Library name: Cab_Franc_1_16_600_1
Total RNA single illumina


title: Cab_Franc_1_16_1800_3

description:
Library name: Cab_Franc_1_16_1800_3
Total RNA single illumina


title: Cab_Franc_1_16_1400_3

description:
Library name: Cab_Franc_1_16_1400_3
Total RNA single illumina


title: Cab_Franc_1_16_1400_1

description:
Library name: Cab_Franc_1_16_1400_1
Total RNA single illumina


title: Cab_Franc_1_15_600_3

description:
Library name: Cab_Franc_1_15_600_3
Total RNA single illumina


title: Cab_Franc_1_15_600_2

description:
Library name: Cab_Franc_1_15_600_2
Total RNA single illumina


title: Cab_Franc_1_15_600_1

description:
Library name: Cab_Franc_1_15_600_1
Total RNA single illumina


title: Cab_Franc_1_15_1800_3

description:
Library name: Cab_Franc_1_15_1800_3
Total RNA single illumina


title: Cab_Franc_1_15_1800_2

description:
Library name: Cab_Franc_1_15_1800_2
Total RNA single illumina


title: Cab_Franc_1_15_1800_1

description:
Library name: Cab_Franc_1_15_1800_1
Total RNA single illumina


title: Cab_Franc_1_15_1400_3

description:
Library name: Cab_Franc_1_15_1400_3
Total RNA single illumina


title: Cab_Franc_1_15_1400_2

description:
Library name: Cab_Franc_1_15_1400_2
Total RNA single illumina


title: Cab_Franc_1_15_1400_1

description:
Library name: Cab_Franc_1_15_1400_1
Total RNA single illumina


title: Cab_Franc_1_14_1800_3

description:
Library name: Cab_Franc_1_14_1800_3
Total RNA single illumina


title: Cab_Franc_1_14_1800_2

description:
Library name: Cab_Franc_1_14_1800_2
Total RNA single illumina


title: Cab_Franc_1_14_1800_1

description:
Library name: Cab_Franc_1_14_1800_1
Total RNA single illumina


title: Cab_Franc_1_26_1400_3

description:
Library name: Cab_Franc_1_26_1400_3
Total RNA single illumina


title: Cab_Franc_1_14_1400_3

description:
Library name: Cab_Franc_1_14_1400_3
Total RNA single illumina


title: Cab_Franc_1_25_1400_1

description:
Library name: Cab_Franc_1_25_1400_1
Total RNA single illumina


title: Cab_Franc_1_25_600_3

description:
Library name: Cab_Franc_1_25_600_3
Total RNA single illumina


title: Cab_Franc_1_14_1400_2

description:
Library name: Cab_Franc_1_14_1400_2
Total RNA single illumina


title: Cab_Franc_1_14_1400_1

description:
Library name: Cab_Franc_1_14_1400_1
Total RNA single illumina


title: Cab_Franc_1_24_600_1

description:
Library name: Cab_Franc_1_24_600_1
Total RNA single illumina


title: Cab_Franc_1_24_1400_1

description:
Library name: Cab_Franc_1_24_1400_1
Total RNA single illumina


title: mouse lung (PND56), ozone, rep2

status: Public on Jun 26 2026

city: Taiyuan

first: Xiaoyun

last: Wu

state: Shanxi

address: Wucheng Road 92, Xiaodian District

institute: Shanxi University

description: Library name: Sample 11

data_processing:
Qualified libraries were sequenced on an Illumina NovaSeq6000 platform with paired-end 150 bp reads (PE150). Clean reads were aligned to the mouse reference genome (GRCm38) via HISAT2 v2.0.4 with default parameters. Gene expression levels were quantified as fragments per kilobase of exon per million mapped reads (FPKM).
Assembly: mouse reference genome (GRCm38)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lung

growth_protocol: BALB/c mice (7- to 8-week-old, Beijing Vital River Laboratory Animal Technology Co., Ltd.) were acclimatized for one week under controlled conditions (12-hour light/dark cycle, 22 ± 2°C, 50% relative humidity) with ad libitum access to food and water.

extract_protocol:
Total RNA was extracted using the MJzol Animal RNA Isolation Kit (Majorbio), purified with RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN), and quantified via Agilent 2100 Bioanalyzer.
Libraries were constructed through fragmentation, cDNA synthesis, end repair, and Illumina adapter ligation, followed by size selection using an Agilent 4200 TapeStation (Agilent Technologies).

treatment_protocol: For timed pregnancy, male and female mice were co-housed at a 1:1 ratio, and vaginal plug detection was used to designate embryonic day 0.5 (E0.5). Pregnant mice were randomly assigned to control or O3-exposed groups (0.5 ppm, 4 hours/day). O3 exposure began at E9.5, with O3 generated via ultraviolet light irradiation and precisely controlled by mass flow controllers, continuously monitored using calibrated O3 analyzers (TONGLIN OZONE). Pregnant dams were allowed to give birth naturally. Some of the offspring were euthanized at PND14 and PND56, and lung tissues were collected for transcriptomic sequencing and bioinformatics analysis. To minimize the birth effect as much as possible, fetal samples were systematically and randomly distributed among different biological duplications of birth.

value: lung

value: WT

value: ozone (0.5 ppm)

tag: batch


title: mouse lung (PND56), ozone, rep3

description: Library name: Sample 12


title: mouse lung (PND56), ozone, rep1

description: Library name: Sample 10


title: mouse lung (PND56), control, rep3

description: Library name: Sample 9

value: filtered air


title: mouse lung (PND56), control, rep1

description: Library name: Sample 7


title: Cab_Franc_1_23_1400_2

description:
Library name: Cab_Franc_1_23_1400_2
Total RNA single illumina


title: mouse lung (PND14), ozone, rep3

description: Library name: Sample 6


title: mouse lung (PND14), ozone, rep1

description: Library name: Sample 4


title: mouse lung (PND14), ozone, rep2

description: Library name: Sample 5


title: mouse lung (PND14), control, rep3

description: Library name: Sample 3


title: mouse lung (PND14), control, rep2

description: Library name: Sample 2


title: Cab_Franc_1_21_1400_2

description:
Library name: Cab_Franc_1_21_1400_2
Total RNA single illumina


title: mouse lung (PND14), control, rep1

description: Library name: Sample 1


title: PD-NC4 C2Y DNMTi neg ctrl T2T

city: Pittsburgh

first: Megan

last: Mahlke

state: Pennsylvania

address: 5115 Centre Ave

institute: UPMC

description:
Library name: PD-NC4 C2Y DNMTi neg ctrl T2T
This data was aligned to the T2T CHM13 v2.0 assembly.

data_processing:
aligned to PD-NC4 or T2T assembly with Bwa, Peak calling with MACS2
Assembly: T2T CHM13 v 2.0 (GCF_009914755.1), PD-NC4 Chr4 assembly (https://www.biorxiv.org/content/10.64898/2025.12.23.696241v1.full)
Supplementary files format and content: bigwig, CENP-A read pileup
Library strategy: CUT&Run

extract_protocol:
ChIP-seq or CUT&RUN antibody-directed DNA isolation
NEB Next Ultra II

value: fibroblast

value: Decitabine


title: PD-NC4 C2Y DNMTi ctrl rep 2  T2T & PDNC4

description:
Library name: PD-NC4 C2Y DNMTi ctrl rep 2
This data was aligned to the T2T CHM13 v2.0 assembly.
This data was also aligned to the PDNC4 chromosome 4 assembly.
PD-NC4 C2Y DNMTi ctrl rep 2 T2T
PD-NC4 C2Y DNMTi ctrl rep 2 PDNC4


title: Cab_Franc_1_20_1400_3

description:
Library name: Cab_Franc_1_20_1400_3
Total RNA single illumina


title: PD-NC4 C2Y DNMTi ctrl rep 1  T2T & PDNC4

description:
Library name: PD-NC4 C2Y DNMTi ctrl rep 1
This data was aligned to the T2T CHM13 v2.0 assembly.
This data was also aligned to the PDNC4 chromosome 4 assembly.
PD-NC4 C2Y DNMTi ctrl rep 1 T2T
PD-NC4 C2Y DNMTi ctrl rep 1 PDNC4


title: PD-NC4 C2Y DNMTi 0.025 rep 2  T2T & PDNC4

description:
Library name: PD-NC4 C2Y DNMTi 0.025 rep 2
This data was aligned to the T2T CHM13 v2.0 assembly.
This data was also aligned to the PDNC4 chromosome 4 assembly.
PD-NC4 C2Y DNMTi 0.025 rep 2 T2T
PD-NC4 C2Y DNMTi 0.025 rep 2 PDNC4


title: PD-NC4 C2Y DNMTi 0.025 rep 1  T2T & PDNC4

description:
Library name: PD-NC4 C2Y DNMTi 0.025 rep 1
This data was aligned to the T2T CHM13 v2.0 assembly.
This data was also aligned to the PDNC4 chromosome 4 assembly.
PD-NC4 C2Y DNMTi 0.025 rep 1 T2T
PD-NC4 C2Y DNMTi 0.025 rep 1 PDNC4


title: Cab_Franc_1_20_1400_2

description:
Library name: Cab_Franc_1_20_1400_2
Total RNA single illumina


title: PD-NC4 C2Y DNMTi 0.05 rep 2  T2T & PDNC4

description:
Library name: PD-NC4 C2Y DNMTi 0.05 rep 2
This data was aligned to the T2T CHM13 v2.0 assembly.
This data was also aligned to the PDNC4 chromosome 4 assembly.
PD-NC4 C2Y DNMTi 0.05 rep 2 T2T
PD-NC4 C2Y DNMTi 0.05 rep 2 PDNC4


title: PD-NC4 C2Y DNMTi 0.01 rep 2  T2T & PDNC4

description:
Library name: PD-NC4 C2Y DNMTi 0.01 rep 2
This data was aligned to the T2T CHM13 v2.0 assembly.
This data was also aligned to the PDNC4 chromosome 4 assembly.
PD-NC4 C2Y DNMTi 0.01 rep 2 T2T
PD-NC4 C2Y DNMTi 0.01 rep 2 PDNC4


title: PD-NC4 C2Y DNMTi 0.01 rep 1  T2T & PDNC4

description:
Library name: PD-NC4 C2Y DNMTi 0.01 rep 1
This data was aligned to the T2T CHM13 v2.0 assembly.
This data was also aligned to the PDNC4 chromosome 4 assembly.
PD-NC4 C2Y DNMTi 0.01 rep 1 T2T
PD-NC4 C2Y DNMTi 0.01 rep 1 PDNC4


title: BBB clone G7

description:
Library name: BBB clone G7
This data was aligned to the PDNC4 chromosome 4 assembly.

source_name: BBB

value: BBB

value: lymphocyte


title: PD-NC4 C2Y DNMTi 0.05 rep 1  T2T & PDNC4

description:
Library name: PD-NC4 C2Y DNMTi 0.05 rep 1
This data was aligned to the T2T CHM13 v2.0 assembly.
This data was also aligned to the PDNC4 chromosome 4 assembly.
PD-NC4 C2Y DNMTi 0.05 rep 1 T2T
PD-NC4 C2Y DNMTi 0.05 rep 1 PDNC4


title: BBB clone G8

description:
Library name: BBB clone G8
This data was aligned to the PDNC4 chromosome 4 assembly.


title: BBB clone H2

description:
Library name: BBB clone H2
This data was aligned to the PDNC4 chromosome 4 assembly.


title: BBB Parental

description:
Library name: BBB Parental
This data was aligned to the PDNC4 chromosome 4 assembly.


title: MN12_GEX

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

description: Patient 12 single-cell RNAseq

library_source: transcriptomic single cell

data_processing:
Patient samples were analyzed using Cell Ranger version 3.1.0 (10x Genomics) to obtain the UMI counts for GEX. The number of barcode mismatches was set to be 0 to minimize the demultiplexing error. The ADT libraries were quantified by CITE-seq-Count (https://github.com/Hoohm/CITE-seq-Count) with 15000 expected cells, and cells with overlapping cell barcodes (CB) in GEX results were included in the multimodal analysis.
Assembly: Single-cell cellranger used the pre-built GRCh38 in the pipeline.
Supplementary files format and content: Single-cell processed data contain the gene and protein expression matrices with cell barcodes.

source_name: Bone marrow

growth_protocol: Bone marrow (BM) aspirate was collected from 12 AML patients with known abnormalities on chr7 according to cytogenetics studies

extract_protocol:
Bone marrow mononuclear cells (BMMCs) were purified from BM aspirate using density centrifugation, cryopreserved, and stored in liquid nitrogen.
The 10x Genomics 3’v2 Single Cell Profiling platform was used for scRNAseq. After staining and cell concentration adjustment, cells were loaded onto a Chromium Chip A with master mix, gel beads, and partitioning oil according to manufacturer’s instructions. Desired number of captured cells was 3000-4000. Reverse transcription (RT) of mRNA into barcoded first strand cDNA was performed on the emulsion by incubating at 53°C for 45 min in an Eppendorf Mastercycler X50a. After RT, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE. At this stage, cDNA was amplified by PCR (98°C for 45 seconds; 13 cycles of 98°C for 20 sec, 67°C for 30 sec, 72°C for 1 min; 72°C for 1 min). Additional primers were added to ensure adequate amplification of oligo tags to later generate antibody-derived tag (ADT) sequencing libraries. Amplified cDNA was mixed with 0.6X SPRIselect magnetic beads (Beckman Coulter); after magnetic separation, supernatant was transferred for ADT library generation, and the remaining pellet was used for constructing the gene expression (GEX) library. Concentration of amplified cDNA was measured at a 1:10 dilution with a High Sensitivity (HS)-D5000 chip on an Agilent Tapestation.  For the GEX library, 50ng of amplified cDNA was carried forward for library construction. Fragmentation, end-repair, and A-tailing was performed (32°C for 5 min; 65°C for 30 min), followed by double-sided size selection using SPRIselect beads. Adaptor ligation (20°C for 15 min), cleanup with SPRIselect beads, and PCR amplification with sample indexing primers (98C for 45 seconds, 14 cycles of 90C for 20 sec, 54C for 30 sec, 72°C for 20 sec; 72°C for 1 min) were performed in that order. A final double size-selection was again done using SPRIselect beads. To make ADT libraries, sample index PCR using unique indices was performed with the transferred supernatant taken immediately after initial cDNA amplification (98°C for 45 seconds; 9 cycles of 98°C for 20 sec, 54°C for 30 sec, 72°C for 20 sec; 72°C for 1 min) using Kapa HiFi Hotstart Readymix (Kapa), followed by a single sided size selection cleanup with SPRIselect beads.

treatment_protocol: No treatment

value: Bone marrow

tag: disease

value: Acute Myeloid Leukemia (AML) with Abnormalities on Chromosome 7

value: mRNA


title: IMS13q clone C8

description:
Library name: IMS13q clone C8
This data was aligned to the PDNC4 chromosome 4 assembly.


title: IMS13q clone C1

description:
Library name: IMS13q clone C1
This data was aligned to the PDNC4 chromosome 4 assembly.


title: IMS13q clone E8

description:
Library name: IMS13q clone E8
This data was aligned to the PDNC4 chromosome 4 assembly.


title: IMS13q clone B8

description:
Library name: IMS13q clone B8
This data was aligned to the PDNC4 chromosome 4 assembly.


title: IMS13q clone B2

description:
Library name: IMS13q clone B2
This data was aligned to the PDNC4 chromosome 4 assembly.


title: IMS13q clone B7

description:
Library name: IMS13q clone B7
This data was aligned to the PDNC4 chromosome 4 assembly.


title: IMS13q clone B4

description:
Library name: IMS13q clone B4
This data was aligned to the PDNC4 chromosome 4 assembly.


title: IMS13q clone A4

description:
Library name: IMS13q clone A4
This data was aligned to the PDNC4 chromosome 4 assembly.


title: IMS13q clone A3

description:
Library name: IMS13q clone A3
This data was aligned to the PDNC4 chromosome 4 assembly.


title: IMS13q clone Parental

description:
Library name: IMS13q clone Parental
This data was aligned to the PDNC4 chromosome 4 assembly.


title: PD-NC4 clone C1 12mo

description:
Library name: PD-NC4 clone C1 12mo
This data was aligned to the PDNC4 chromosome 4 assembly.

data_processing:
aligned to PD-NC4 or T2T assembly with Bwa, Peak calling with MACS2
Assembly: T2T CHM13 v 2.0 (GCF_009914755.1), PD-NC4 Chr4 assembly (https://www.biorxiv.org/content/10.64898/2025.12.23.696241v1.full)
Supplementary files format and content: bigwig, CENP-A read pileup


title: PD-NC4 Parental

description:
Library name: PD-NC4 Parental
This data was aligned to the PDNC4 chromosome 4 assembly.


title: 99_SF

status: Public on Jun 23 2026

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

description: Library name: 99SF

data_processing:
Adapter trimming and quality filtering with cutadapt (3' adapter TGGAATTCTC, 5' adapter GATCGTCGGACT; minimum read length 17 nt; Phred quality cutoff Q30).
Trimmed reads were analysed with the miND (miRNA NGS Data analysis) pipeline and mapped against the Equus caballus reference genome (EquCab3.0) and miRBase release 22.1 mature miRNA sequences.
Mature miRNA expression was quantified as raw read counts per miRNA.
Differential expression analysis was performed with edgeR.
Assembly: EquCab3.0 (Equus caballus); miRBase release 22.1
Supplementary files format and content: Tab-delimited text file P90_miRNA_raw_counts.tsv: first column = mature miRNA name (miRBase v22.1, eca- prefix), remaining columns = samples (serum and synovial fluid); values = raw read counts per miRNA.

organism: Equus caballus

source_name: Synovial fluid

extract_protocol:
RNA extraction using miRNeasy Serum/Plasma Advanced Kit (Qiagen)
Small RNA libraries were prepared with the TriLink CleanTag Small RNA Library Prep Kit according to the manufacturer's instructions, followed by PCR amplification and size selection.

value: Synovial fluid

tag: disease state

value: Control


title: 95_SF

description: Library name: 95SF


title: 93_SF

description: Library name: 93SF


title: 8_SF

description: Library name: 8SF

value: OA


title: 89_SF

description: Library name: 89SF


title: 87_SF

description: Library name: 87SF


title: 4_SF

description: Library name: 4SF


title: 3_SF

description: Library name: 3SF


title: mouse lung (PND56), control, rep2

description: Library name: Sample 8

tag: genotype


title: 33_SF

description: Library name: 33SF


title: 2_SF

description: Library name: 2SF


title: 27_SF

description: Library name: 27SF


title: Cab_Franc_1_17_1400_1

description:
Library name: Cab_Franc_1_17_1400_1
Total RNA single illumina

value: Bud


title: 102_SF

description: Library name: 102SF


title: 1_SF

description: Library name: 1SF


title: Cab_Franc_1_16_600_2

description:
Library name: Cab_Franc_1_16_600_2
Total RNA single illumina

value: total RNA


title: 95_Serum

description: Library name: 95

source_name: Serum

value: Serum


title: 93_Serum

description: Library name: 93


title: 89_Serum

description: Library name: 89


title: 99_Serum

description: Library name: 99


title: Cab_Franc_1_16_1800_2

description:
Library name: Cab_Franc_1_16_1800_2
Total RNA single illumina

value: single


title: 87_Serum

description: Library name: 87


title: 4_Serum

description: Library name: 4


title: Cab_Franc_1_16_1800_1

description:
Library name: Cab_Franc_1_16_1800_1
Total RNA single illumina


title: 8_Serum

description: Library name: 8


title: 3_Serum

description: Library name: 3


title: 2_Serum

description: Library name: 2


title: 27_Serum

description: Library name: 27


title: 33_Serum

description: Library name: 33


title: 1_Serum

description: Library name: 1


title: 102_Serum

description: Library name: 102


title: Cab_Franc_1_16_1400_2

description:
Library name: Cab_Franc_1_16_1400_2
Total RNA single illumina


title: Patient 33 - TD 3

status: Public on Jun 18 2026

city: Davis

first: Madison

middle: W.

last: Stewart

state: California

address: 2121 Glacier Drive, Apt 56

institute: University of California, Davis

description:
Library name: SHC033
10X genomics

data_processing:
Raw sequencing data was first preprocessed through htstream v1.3.3
Sequence alignment, fileting, barcode and UMI counting was done using Cell Ranger v6.0.1
Assembly: GRCh38-3.0.0 (Human)
Supplementary files format and content: hirearchical data files (h5)
Supplementary files format and content: comma separated values (CSV)

source_name: Gracilis muscle

extract_protocol:
Muscle tissues were minced into 2-5 mm pieces and transferred into a gentleMACS™ C Tube containing 2.5 ml of DMEM (Gibco™ 11965092) and enzymes from the Skeletal Muscle Dissociation Kit (Miltenyi Biotec). The tube containing minced muscle tissues was placed in a MACSmix™ Tube Rotator and set for two intervals of 30-min continuous rotation at 37°C for enzyme digestion. Speed of rotation was set at approximately 12 rpm. After each incubation interval, the tube was placed in a gentleMACS™ Dissociator for mechanical disruption using the program “m_muscle_01”. The dissociated muscle tissue solution was filtered through a 70 μm filter. Red blood cell lysis was performed according to the manufacturer’s protocol, and the solution was filtered through a 40 μm cell strainer. To reduce debris in the single cell solution, Debris Removal Solution (Miltenyi Biotec) was applied, and centrifugation steps were performed to separate debris and dead cells from healthy single cells. Finally, single cells were resuspended in 1 ml of freezing solution made of 90% FBS and 10% DMSO. The cryotubes containing single cells were slowly cooled at a freezing rate of -1°C per minute in a -80°C freezer, and they were moved into a liquid nitrogen dewar for storage.
All 10 single cell suspensions were thawed rapidly and re-filtered with 40 μm Flowmi® Cell Strainers prior to submitting samples for sequencing at the UC Davis DNA Technologies & Expression Analysis Core. During quality control, three samples each were selected from the CP group and the TD group based on cell viability and cell concentration to yield a recovery of 2,000 - 10,000 cells per sample. The sequencing libraries were prepared using the Chromium Single Cell 3' reagent V3.1 kit (10X Genomics) in accordance with the manufacturer’s protocol. High Sensitivity DNA Assay was performed to ensure the cDNA quality. The cDNA libraries were pooled and sequenced on one NovaSeq S4 lane using the NovaSeq 6000 System (Illumina) to produce 100 to 350 million reads per library, targeting a sequencing depth of 40,000 reads per cell.

value: Gracilis muscle

value: TD


title: Patient 30 - CP 3

description:
Library name: SHC030
10X genomics

value: CP


title: Patient 28 - TD 1

description:
Library name: SHC028
10X genomics


title: Patient 29 - TD 2

description:
Library name: SHC029
10X genomics


title: Patient 21 - CP 1

description:
Library name: SHC21
10X genomics


title: Donor50

status: Public on Jun 14 2026

city: Dalian

first: Xuehong

last: Zhang

state: Liaoning

address: No. 9 West Section Lvshun South Road, Dalian 116044, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description: Library name: Sample298

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 27, GRCh38).
The Gene abundances are given as Reads Per Kilobase per Million mapped reads (RPKM) with “cuffnorm” command using the Cufflinks package.
Assembly: human GRCh38
Supplementary files format and content: Excel file includes FPKM values for all Samples

source_name: Bone Marrow

extract_protocol:
Total RNA of mononucleated cells of bone marrow or peripheral blood samples from AML patients and healthy donors were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

value: Bone Marrow

tag: disease stage

value: Healthy Donor


title: Donor48

description: Library name: Sample296


title: Donor49

description: Library name: Sample297


title: Donor47

description: Library name: Sample295


title: Donor46

description: Library name: Sample294


title: Donor45

description: Library name: Sample293


title: Donor44

description: Library name: Sample292


title: Donor43

description: Library name: Sample291


title: Donor42

description: Library name: Sample290


title: Donor41

description: Library name: Sample289


title: Donor40

description: Library name: Sample288


title: Donor39

description: Library name: Sample287


title: Donor37

description: Library name: Sample285


title: Donor36

description: Library name: Sample284


title: Donor38

description: Library name: Sample286


title: Donor34

description: Library name: Sample282


title: Donor32

description: Library name: Sample280


title: Donor35

description: Library name: Sample283


title: Donor31

description: Library name: Sample279


title: Donor30

description: Library name: Sample278


title: Donor28

description: Library name: Sample276


title: Donor27

description: Library name: Sample275


title: Donor29

description: Library name: Sample277


title: Donor33

description: Library name: Sample281


title: Donor25

description: Library name: Sample273


title: Donor24

description: Library name: Sample272


title: Donor23

description: Library name: Sample271


title: Donor26

description: Library name: Sample274


title: Donor22

description: Library name: Sample270


title: Donor21

description: Library name: Sample269


title: Donor20

description: Library name: Sample268


title: Donor19

description: Library name: Sample267


title: Ries_1_24_600_1

description:
Library name: Ries_1_24_600_1
Total RNA single illumina


title: Donor18

description: Library name: Sample266


title: Donor17

description: Library name: Sample265


title: Donor16

description: Library name: Sample264


title: Donor15

description: Library name: Sample263


title: Donor13

description: Library name: Sample261


title: Donor11

description: Library name: Sample259


title: Donor12

description: Library name: Sample260


title: Donor14

description: Library name: Sample262


title: Ries_1_23_1800_3

description:
Library name: Ries_1_23_1800_3
Total RNA single illumina


title: Donor10

description: Library name: Sample258


title: Donor7

description: Library name: Sample255


title: Donor8

description: Library name: Sample256


title: Donor9

description: Library name: Sample257


title: Donor6

description: Library name: Sample254


title: Donor5

description: Library name: Sample253


title: Donor4

description: Library name: Sample252


title: Donor3

description: Library name: Sample251


title: Donor2

description: Library name: Sample250


title: AML248

description: Library name: Sample248

value: AML


title: Ries_1_21_1400_2

description:
Library name: Ries_1_21_1400_2
Total RNA single illumina


title: Donor1

description: Library name: Sample249


title: AML247

description: Library name: Sample247


title: AML246

description: Library name: Sample246


title: AML245

description: Library name: Sample245


title: AML243

description: Library name: Sample243


title: AML244

description: Library name: Sample244


title: AML242

description: Library name: Sample242


title: AML240

description: Library name: Sample240


title: AML241

description: Library name: Sample241


title: AML239

description: Library name: Sample239


title: AML238

description: Library name: Sample238


title: AML237

description: Library name: Sample237


title: AML236

description: Library name: Sample236


title: AML234

description: Library name: Sample234


title: AML235

description: Library name: Sample235


title: AML233

description: Library name: Sample233


title: AML231

description: Library name: Sample231


title: AML232

description: Library name: Sample232


title: AML230

description: Library name: Sample230


title: AML229

description: Library name: Sample229


title: AML228

description: Library name: Sample228


title: AML227

description: Library name: Sample227


title: AML226

description: Library name: Sample226


title: AML224

description: Library name: Sample224


title: AML225

description: Library name: Sample225


title: AML223

description: Library name: Sample223


title: AML221

description: Library name: Sample221


title: AML222

description: Library name: Sample222


title: AML219

description: Library name: Sample219


title: AML220

description: Library name: Sample220


title: AML218

description: Library name: Sample218


title: Patient 27 - CP 2

description:
Library name: SHC027
10X genomics


title: AML216

description: Library name: Sample216


title: AML215

description: Library name: Sample215


title: AML217

description: Library name: Sample217


title: AML214

description: Library name: Sample214


title: AML213

description: Library name: Sample213


title: AML211

description: Library name: Sample211


title: AML210

description: Library name: Sample210


title: AML209

description: Library name: Sample209


title: AML205

description: Library name: Sample205


title: AML208

description: Library name: Sample208


title: AML203

description: Library name: Sample203


title: AML202

description: Library name: Sample202


title: AML207

description: Library name: Sample207


title: AML200

description: Library name: Sample200


title: AML198

description: Library name: Sample198


title: AML197

description: Library name: Sample197


title: AML196

description: Library name: Sample196


title: AML194

description: Library name: Sample194


title: AML193

description: Library name: Sample193


title: AML192

description: Library name: Sample192


title: AML191

description: Library name: Sample191


title: Ries_1_15_1400_2

description:
Library name: Ries_1_15_1400_2
Total RNA single illumina


title: AML190

description: Library name: Sample190


title: AML188

description: Library name: Sample188


title: AML187

description: Library name: Sample187


title: AML185

description: Library name: Sample185


title: AML184

description: Library name: Sample184


title: AML186

description: Library name: Sample186


title: AML183

description: Library name: Sample183


title: AML181

description: Library name: Sample181


title: AML180

description: Library name: Sample180


title: AML182

description: Library name: Sample182


title: AML177

description: Library name: Sample177


title: AML175

description: Library name: Sample175


title: AML178

description: Library name: Sample178


title: AML174

description: Library name: Sample174


title: AML173

description: Library name: Sample173


title: AML172

description: Library name: Sample172


title: AML171

description: Library name: Sample171


title: AML169

description: Library name: Sample169


title: AML170

description: Library name: Sample170


title: AML168

description: Library name: Sample168


title: AML166

description: Library name: Sample166


title: AML165

description: Library name: Sample165


title: AML164

description: Library name: Sample164


title: AML162

description: Library name: Sample162


title: AML163

description: Library name: Sample163


title: AML160

description: Library name: Sample160


title: AML161

description: Library name: Sample161


title: AML158

description: Library name: Sample158


title: AML157

description: Library name: Sample157


title: AML156

description: Library name: Sample156


title: AML159

description: Library name: Sample159


title: AML154

description: Library name: Sample154


title: AML152

description: Library name: Sample152


title: AML153

description: Library name: Sample153


title: AML149

description: Library name: Sample149


title: AML150

description: Library name: Sample150


title: AML148

description: Library name: Sample148


title: AML147

description: Library name: Sample147


title: AML145

description: Library name: Sample145


title: AML146

description: Library name: Sample146


title: AML144

description: Library name: Sample144


title: AML143

description: Library name: Sample143


title: AML142

description: Library name: Sample142


title: AML141

description: Library name: Sample141


title: AML140

description: Library name: Sample140


title: AML139

description: Library name: Sample139


title: AML138

description: Library name: Sample138


title: AML137

description: Library name: Sample137


title: AML136

description: Library name: Sample136


title: AML135

description: Library name: Sample135


title: AML134

description: Library name: Sample134


title: AML133

description: Library name: Sample133


title: AML132

description: Library name: Sample132


title: AML131

description: Library name: Sample131


title: AML130

description: Library name: Sample130


title: AML129

description: Library name: Sample129


title: AML128

description: Library name: Sample128


title: AML127

description: Library name: Sample127


title: AML126

description: Library name: Sample126


title: AML125

description: Library name: Sample125


title: AML121

description: Library name: Sample121


title: AML120

description: Library name: Sample120


title: AML122

description: Library name: Sample122


title: AML119

description: Library name: Sample119


title: AML118

description: Library name: Sample118


title: AML115

description: Library name: Sample115


title: AML113

description: Library name: Sample113


title: AML114

description: Library name: Sample114


title: AML112

description: Library name: Sample112


title: AML108

description: Library name: Sample108


title: AML107

description: Library name: Sample107


title: AML105

description: Library name: Sample105


title: AML111

description: Library name: Sample111


title: AML109

description: Library name: Sample109


title: AML110

description: Library name: Sample110


title: AML212

description: Library name: Sample212


title: AML103

description: Library name: Sample103


title: AML204

description: Library name: Sample204


title: AML206

description: Library name: Sample206


title: AML199

description: Library name: Sample199


title: AML102

description: Library name: Sample102


title: AML101

description: Library name: Sample101


title: AML100

description: Library name: Sample100


title: AML99

description: Library name: Sample99


title: AML98

description: Library name: Sample98


title: AML97

description: Library name: Sample97


title: AML96

description: Library name: Sample96


title: AML95

description: Library name: Sample95


title: AML94

description: Library name: Sample94


title: AML92

description: Library name: Sample92


title: AML89

description: Library name: Sample89


title: AML86

description: Library name: Sample86


title: AML85

description: Library name: Sample85


title: AML83

description: Library name: Sample83


title: AML82

description: Library name: Sample82


title: AML90

description: Library name: Sample90


title: AML88

description: Library name: Sample88


title: AML123

description: Library name: Sample123


title: AML87

description: Library name: Sample87


title: AML117

description: Library name: Sample117


title: AML80

description: Library name: Sample80


title: AML77

description: Library name: Sample77


title: AML78

description: Library name: Sample78


title: AML76

description: Library name: Sample76


title: AML75

description: Library name: Sample75


title: AML73

description: Library name: Sample73


title: AML74

description: Library name: Sample74


title: AML72

description: Library name: Sample72


title: AML71

description: Library name: Sample71


title: AML68

description: Library name: Sample68


title: AML67

description: Library name: Sample67


title: AML66

description: Library name: Sample66


title: AML64

description: Library name: Sample64


title: AML79

description: Library name: Sample79


title: AML63

description: Library name: Sample63


title: AML62

description: Library name: Sample62


title: AML61

description: Library name: Sample61


title: AML60

description: Library name: Sample60


title: AML70

description: Library name: Sample70


title: AML59

description: Library name: Sample59


title: AML69

description: Library name: Sample69


title: AML91

description: Library name: Sample91


title: AML93

description: Library name: Sample93


title: AML58

description: Library name: Sample58


title: AML57

description: Library name: Sample57


title: AML56

description: Library name: Sample56


title: AML55

description: Library name: Sample55


title: AML65

description: Library name: Sample65


title: AML54

description: Library name: Sample54


title: AML53

description: Library name: Sample53


title: AML52

description: Library name: Sample52


title: AML51

description: Library name: Sample51


title: AML50

description: Library name: Sample50


title: AML49

description: Library name: Sample49


title: AML48

description: Library name: Sample48


title: AML84

description: Library name: Sample84


title: AML47

description: Library name: Sample47


title: AML46

description: Library name: Sample46


title: AML43

description: Library name: Sample43


title: AML45

description: Library name: Sample45


title: AML42

description: Library name: Sample42


title: AML44

description: Library name: Sample44


title: AML41

description: Library name: Sample41


title: AML40

description: Library name: Sample40


title: AML201

description: Library name: Sample201


title: AML39

description: Library name: Sample39


title: AML38

description: Library name: Sample38


title: AML37

description: Library name: Sample37


title: AML35

description: Library name: Sample35


title: AML36

description: Library name: Sample36


title: AML34

description: Library name: Sample34


title: AML33

description: Library name: Sample33


title: AML32

description: Library name: Sample32


title: AML31

description: Library name: Sample31


title: AML30

description: Library name: Sample30


title: AML179

description: Library name: Sample179


title: Ries_1_24_1800_3

description:
Library name: Ries_1_24_1800_3
Total RNA single illumina


title: AML29

description: Library name: Sample29


title: AML28

description: Library name: Sample28


title: AML81

description: Library name: Sample81


title: AML27

description: Library name: Sample27


title: AML25

description: Library name: Sample25


title: AML26

description: Library name: Sample26


title: AML24

description: Library name: Sample24


title: AML23

description: Library name: Sample23


title: AML22

description: Library name: Sample22


title: AML167

description: Library name: Sample167


title: AML21

description: Library name: Sample21


title: AML19

description: Library name: Sample19


title: AML20

description: Library name: Sample20


title: AML15

description: Library name: Sample15


title: AML17

description: Library name: Sample17


title: AML16

description: Library name: Sample16


title: AML14

description: Library name: Sample14


title: AML18

description: Library name: Sample18


title: AML13

description: Library name: Sample13


title: AML12

description: Library name: Sample12


title: AML11

description: Library name: Sample11


title: AML9

description: Library name: Sample9


title: AML10

description: Library name: Sample10


title: AML7

description: Library name: Sample7


title: AML8

description: Library name: Sample8


title: AML6

description: Library name: Sample6


title: AML5

description: Library name: Sample5


title: AML3

description: Library name: Sample3


title: AML2

description: Library name: Sample2


title: AML1

description: Library name: Sample1


title: AML4

description: Library name: Sample4


title: Ries_1_17_1800_1

description:
Library name: Ries_1_17_1800_1
Total RNA single illumina


title: KAS_CTRL_rep2_P35

status: Public on Jun 09 2026

city: Shanghai

first: Jiang

last: Yamei

address: Songhu Road

institute: Fudan University

description: Library name: KAS_CTRL_rep2

data_processing:
For analyzing ChIP-seq and KAS-seq data, we used the ENCODE ChIP-seq pipeline (v2.2.1, https://github.com/ENCODE-DCC/chip-seq-pipeline2). Raw reads were cleaned by Cutadapt (v2.5) (Kechin et al., 2017). After removing adapters, clean reads were aligned against the mouse mm10 genome using bwa (v0.7.17) (Li and Durbin, 2009). Then, sam files were converted to bam files using samtools (v1.9) (Li et al., 2009). PCR duplicates were removed using Picard (v2.20.7) (https://broadinstitute.github.io/picard/). Histone ChIP-seq peaks (such as H2A.Z and histone marks) and KAS-seq peaks were called using MACS2 (v2.2.4) (Zhang et al., 2008), while transcription factor ChIP-seq peaks (such as A-MYB) were called using the R packages spp (v1.15.5) (https://github.com/hms-dbmi/spp). The conservative narrow peaks were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: testis

extract_protocol: For KAS-seq, pachytene cells were labeled with N3-kethoxal, and DNA was isolated using the DNA Clean and Concentrator kit (Zymo, D4013) and subjected to library construction using Q5 high-fidelity DNA polymerase (New England Biolabs, M0544S). Genomic DNA was fragmented using Tn5 transposase and subjected to library construction.

value: testis

value: pachytene spermatocytes

value: CTRL


title: Ries_1_17_1400_1

description:
Library name: Ries_1_17_1400_1
Total RNA single illumina


title: Ries_1_18_600_2

description:
Library name: Ries_1_18_600_2
Total RNA single illumina


title: KAS_CTRL_rep1_P35

description: Library name: KAS_CTRL_rep1


title: Lateral Septum single-nucleus RNA-seq, Female Proestrus Threat-Naive, Replicate 2

status: Public on Jun 07 2026

city: Birmingham

first: Elizabeth

middle: Kathleen

last: Lucas

state: AL

department: Psychiatry and Behavioral Neurobiology

institute: University of Alabama at Birmingham

description:
Library name: snRNA_Naive_rep2
single-nucleus 3' gene expression RNA-seq; female; proestrus

data_processing:
Raw sequencing data were processed with CellRanger-ARC v7.0.0 using the refdata-gex-mm10-2020-A mouse reference to produce raw and filtered feature-barcode matrices.
Background RNA contamination was estimated and corrected with SoupX v1.6.2. Low-quality nuclei were removed if mitochondrial transcripts exceeded 5%. Likely doublets were identified with scDblFinder v1.20.2.
Initial clustering used Seurat v5.2.1. Cluster markers and reference-based annotations were assigned using MapMyCells with the Allen Institute/10x Genomics CCN20230722 Whole Mouse Brain taxonomy.
Leiden clustering used cosine metric, k = 45, resolution 0.8; UMAP used spread 1.1 and min.dist 0.2. Biologically identical clusters were merged manually.
Differential expression was calculated with scvi-tools v1.3.3 using mode = change, delta = 0.25, and 5,000 Monte Carlo samples. FDR <= 0.05 was considered significant.
Assembly: mm10; 10x Genomics refdata-gex-mm10-2020-A
Supplementary files format and content: 10x H5 feature-barcode matrices; AnnData H5AD object containing pooled/integrated processed expression data, annotations, and embeddings; CSV analysis tables; and plain-text file-structure summaries.
Supplementary files format and content: Shared study-level processed files are listed in the STUDY supplementary file field; sample-specific raw/filtered Cell Ranger matrices, summaries, and post-QC matrices are listed in the SAMPLES processed data file columns.

source_name: lateral septum

growth_protocol: Adult C57BL/6J female mice were maintained until assignment to threat-conditioned or threat-naive control groups for the ovarian hormone cycle/proestrus study.

extract_protocol:
C57BL/6J female mice (The Jackson Laboratory Strain #000664; RRID: IMSR_JAX:000664) in proestrus were assigned to threat-conditioned or threat-naive control groups. Five minutes after exiting the conditioning chamber, mice were anesthetized and euthanized by rapid decapitation. Brains were removed, sectioned at 1 mm, and 1.25 mm punches of the lateral septum were collected, snap-frozen, and stored at -80 C. Lateral septum punches were pooled by experimental group before nuclei isolation. Nuclei were isolated using detergent-based lysis, filtered through a 35 um filter, washed, and resuspended in Hibernate AB. Nuclei were stained with 7-AAD, and singlets were sorted by flow cytometry.
Suspensions were processed using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform. Gene expression libraries were prepared using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10x Genomics Cat #1000121) and sequenced on an Illumina NovaSeq 6000 using v1.5 chemistry (28 10 10 90 cycles), targeting >50,000 reads per nucleus. The linked SRA RNA-seq runs are paired-end.

treatment_protocol: Threat conditioning consisted of six co-terminating pairings of a 20 s auditory conditioned stimulus (5 kHz, 75 dB) with a 2 s, 0.5 mA foot shock following a 240 s baseline period; inter-trial intervals were 100 s. Naive controls remained in the home cage.

value: lateral septum

value: threat-naive

value: replicate 2


title: KAS_KO_rep2_P35

description: Library name: KAS_KO_rep2


title: KAS_KO_rep1_P35

description: Library name: KAS_KO_rep1


title: Lateral Septum single-nucleus RNA-seq, Female Proestrus Threat-Naive, Replicate 1

description:
Library name: snRNA_Naive_rep1
single-nucleus 3' gene expression RNA-seq; female; proestrus

value: replicate 1


title: Lateral Septum single-nucleus RNA-seq, Female Proestrus Threat-Trained, Replicate 2

description:
Library name: snRNA_Threat_rep2
single-nucleus 3' gene expression RNA-seq; female; proestrus

value: threat-conditioned


title: Lateral Septum single-nucleus RNA-seq, Female Proestrus Threat-Trained, Replicate 1

description:
Library name: snRNA_Threat_rep1
single-nucleus 3' gene expression RNA-seq; female; proestrus


title: SFFFM_Rox_M1002

status: Public on Jun 01 2026

city: Nashville

first: Abraham

middle: Scott

last: McCall

state: TN

department: Medicine

institute: Vanderbilt University medical Center

description: Library name: 11001_4

data_processing:
Cellranger v9.0.1 with demultiplexing
Doublet calling - scDblFinder
Data integration/annotation -> Seurat, Harmony
Assembly: GRCh38-2020-A
Supplementary files format and content: h5 filtered matrix

source_name: lung organoid

growth_protocol: Primary CD326+ enriched human declined donor were cultured under serum-free feeder free conditions in domed matrigel culture the replated in technical triplicate for each condition for sequencing.

extract_protocol:
Cultured alveolar organoid under indicated experimental conditions were liberated from matrigel using Dispase (2mg/ml), rinsed, trypsinized, and quenched with ACF free trypsin inhibitor,  to generate a single cell suspension then fixed per 10X FLEX protocol, counted and pooled for 10X FLEX library preperation.
Chromium Human Transcriptome Probe Set v1.1.0

value: lung organoid

value: primary

value: epithelial


title: ADM_Veh

description: Library name: 11001_5

value: ADM/DMSO


title: ADM_Rox_M1002

description: Library name: 11001_8


title: SFFFM_Rox_PT-2385

description: Library name: 11001_3


title: ADM_Rox

description: Library name: 11001_6

value: ADM/Roxadustat


title: ADM_Rox_PT-2385

description: Library name: 11001_7


title: SFFFM_Veh

description: Library name: 11001_1

value: SFFFM/DMSO