title: miR-29a-3p_2

description: Library name: miR-29a-3p_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

value: liver


title: MCD cohort_MCD_Veh_biol rep 3

status: Public on Jul 31 2026

type: SRA

city: Pohang-si

first: Jae

last: Lee

address: 77 Cheongam-ro, Nam-gu

country: South Korea

institute: POSTECH

description: Library name: MCD cohort_MCD_Veh_biol rep 3

library_source: transcriptomic

data_processing:
Raw sequencing reads were quality-checked using FastQC (v0.11.7).
Adapter sequences and low-quality bases were removed using Trimmomatic (v0.38).
Filtered reads reads were aligned to the Mus musculus reference genome (mm10) using HISAT2 (v2.1.0).
Transcript assembly and gene-level quantification were perfomed with StringTie (v2.1.3b).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files contain gene-level raw counts (Entrez Gene IDs) for each sample, with gene symbols annotated.

molecule: polyA RNA

organism: Mus musculus

source_name: liver

extract_protocol:
RNA was isolated from liver tissue using RNeasy Plus Mini Kit (QIAGEN, 74134) according to the manufacturer’s instructions. RNA concentration and integrity (RIN > 7.0) were assessed using 4200 TapeStation System (Agilent).
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) following the manufacturer's protocol.

treatment_protocol: DTMB was orally administered at a dose of 10mg/kg/day.

tag: tissue

tag: strain

tag: Sex

value: male

tag: genotype

value: WT

tag: disease state

value: MASH

tag: batch

value: MCD


title: Nanostring of human20

type: RNA

city: Beijing

first: Junping

last: Zhang

state: Beijing

address: No. 50, Yikesong Road, District Haidian, Beijing

country: China

institute: Sanbo Brain Hospital Capital Medical University

description: MiniBenifit

hyb_protocol: hybridization of 100 ng RNA to a version of the NanoString PanCancer code set for reading on the nCounter platform

scan_protocol: nCounter

data_processing: nSolver Analysis software, IO 360 Data Analysis Service

label: brain glioma

molecule: total RNA

organism: Homo sapiens

source_name: SD/PD

label_protocol: As little as 10 ng with nCounter RNA Low Input Kit and Panel specific primer pools (sold separately)

extract_protocol: The tumor tissue was divided into two parts. MagMAX FFPE RNA Ultra Kit (item No. A31881 ThermoFisher) was used to extract RNA from the tumor tissue, and the RNA was inspected according to relevant quality inspection standards. After the quality inspection was qualified, the RNA sequencing library was constructed

tag: gender


title: AAVS1, RNA-Seq, Donor 3, Condition 2

city: Cambridge

first: Varshini

last: Ramanathan

state: Massachusetts

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

country: USA

institute: Massachusetts Institute of Technology

description: Library name: AAVS1 Con2

library_source: genomic

data_processing:
RNA-seq was aligned using the STAR aligner (v2.7.11b) (7) and deduplicated using samtools markdup (v1.0.1 (v1.44.0) (11).
Count matrices were generated using subread featureCounts (v2.0.6) (10) using the Gencode v45 gene annotation set.
Assembly: hg38
Supplementary files format and content: Count matrices as generated by subread featureCounts (.txt)

molecule: genomic DNA

source_name: CD34+ HSPCs (donor-derived, peripheral blood), differentiated to day 13

growth_protocol: Human CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from mobilized peripheral blood of healthy adult donors were obtained from the Cooperative Center of Excellence in Hematology at the Fred Hutchinson Cancer Research Center. Cryopreserved HSPCs were thawed and cultured in maintenance medium consisting of StemSpan SFEM II (StemCell Technologies) supplemented with CC100 cytokine cocktail (StemCell Technologies), 50 ng/mL human thrombopoietin (TPO; PeproTech), 1% penicillin-streptomycin (Life Technologies), and 1% L-glutamine (Life Technologies). Following the maintenance phase, erythroid differentiation was performed as follows. A basal erythroid medium was prepared using IMDM (Gibco) supplemented with 2% human AB plasma (SeraCare), 3% human AB serum (Life Technologies), 3 U/mL heparin, 10 μg/mL insulin, 200 μg/mL holo-transferrin, and 1% penicillin-streptomycin. During phase I (days 1–7), the basal medium was supplemented with 3 U/mL erythropoietin (EPO), 10 ng/mL human stem cell factor (SCF), and 1 ng/mL interleukin-3 (IL-3). During phase II (days 7–12), cells were cultured in basal medium supplemented with 3 U/mL EPO and 10 ng/mL SCF. During phase III (day 12 onward), cells were cultured in basal medium supplemented with 3 U/mL EPO and 1 mg/mL holo-transferrin. Cells were collected on day 13.

extract_protocol:
RNA extraction was performed from 0.5-1 million cells from each replicate using the Norgen Total RNA Purification Plus Kit plus gDNA removal column.
VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina

treatment_protocol: Genome editing was performed in primary human CD34⁺ hematopoietic stem and progenitor cells (HSPCs) using the 4D-Nucleofector system (Lonza) and the P3 Primary Cell 4D-Nucleofector X Kit S (Lonza). For NFE2 knockout, ribonucleoprotein (RNP) complexes were assembled by combining 100 pmol Cas9 protein (IDT) with 100 pmol chemically modified sgRNA (Synthego) and incubating at room temperature for 15 min. RNP complexes were delivered into CD34⁺ HSPCs using the P3 nucleofection reagent supplemented with Alt-R Cas9 Electroporation Enhancer (IDT) at a 20:1 molar ratio, using program DZ-100. For knockout of cohesin complex components (STAG1, STAG2, and NIPBL), two editing conditions were used to achieve different levels of gene disruption. In condition 1 (Con1), cells were edited using the same procedure described above. In condition 2 (Con2), cells underwent a second round of nucleofection 2 days after the initial editing using the same RNP delivery protocol. Following editing, cells were cultured under erythroid differentiation conditions beginning 3 days after the initial nucleofection. Knockout efficiency was assessed by western blot analysis of protein lysates or by genomic DNA extraction followed by ICE (Inference of CRISPR Edits) analysis.

tag: cell type


title: MCD cohort_MCD_Veh_biol rep 2

description: Library name: MCD cohort_MCD_Veh_biol rep 2


title: S14Ta

city: San Juan

first: Elba

last: Caraballo Rivera

state: Puerto Rico

address: Av. Jose Kiko Custodio

institute: University of Puerto Rico Comprehensive Cancer Center

description: Library name: Sample 28

data_processing:
Quality assessment of the raw FASTQ reads was conducted using FastQC to evaluate data integrity. Adapter trimming and low-quality base removal were performed using Trimmomatic, followed by alignment of the reads to the human reference genome GRCh38 (hg38) using the STAR. Gene-level quantification was carried out using RSEM, and the resulting expression data was imported into R/RStudio.
Assembly: hg38
Supplementary files format and content: rna-seq-normalized-counts_allSamples.csv-CSV file that contains gene-level raw read counts for each RNA-seq sample.
Supplementary files format and content: differential_gene_expression_te_me.csv-CSV file that contains differential gene expression results when comparing early-stage CRC tumors with adjacent mucosal tissue.
Supplementary files format and content: differential_gene_expression_ta_ma.csv-CSV file that contains differential gene expression results when comparing advanced-stage CRC tumors with adjacent mucosal tissue.

source_name: Advanced CRC

growth_protocol: This study was a secondary data analysis and uses previously collected tissue from PRH enrolled in the Puerto Rico Familial Colorectal Cancer Registry (PURIFICAR) IRB #2290034759. Tissue was stored at 80°C

extract_protocol:
RNA was extracted from frozen tumor and adjacent mucosal tissue samples using the Qiagen RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol.  RNA quality and concentration were assessed prior to library preparation using a NanoDrop 2000 (Thermo Fisher Scientific).
RNA-seq libraries were prepared from total RNA using a poly(A)-selected library preparation kit according to the manufacturer’s protocol.

treatment_protocol: No in vitro treatment was applied. Samples represent primary early and advanced CRC tumors and adjacent mucosal tissue collected at the time of surgery.

value: Colorectal

value: Tumor tissue


title: AAVS1, RNA-Seq, Donor 3, Condition 1

description: Library name: AAVS1 Con1

value: CD34+ HSPCs (donor-derived, peripheral blood), differentiated to day 13


title: MCD cohort_MCD_Veh_biol rep 1

description: Library name: MCD cohort_MCD_Veh_biol rep 1


title: Nanostring of human18

description: MiniBenifit

value: female


title: NIPBL-KO, RNA-Seq, Donor 3, Condition 2

description: Library name: NIPBL-KO Con2


title: MCD cohort_ND_Veh_biol rep 4

description: Library name: MCD cohort_ND_Veh_biol rep 4

value: Normal


title: S13Me

description: Library name: Sample 25

source_name: Early CRC

value: Adjacent mucosal tissue


title: NIPBL-KO, RNA-Seq, Donor 3, Condition 1

description: Library name: NIPBL-KO Con1


title: Nanostring of human17

description: MiniBenifit


title: Tab_NT, rep1

city: NANTES

first: Emmanuel

last: SCOTET

state: Loire Atlantique

address: IRS UN, 8 quai Moncousu

country: France

institute: Emmanuel SCOTET

description:
Library name: 73_Tab_NT_1
Tab_NT_1

data_processing:
Base calling was performed directly by sequencing facility using phred-33 standard quality scores
Adapter sequences and low-quality reads were removed using SOAPnuke directly after FASTQ generation by the sequencing facility
Transcript count table from FASTQ files was generated  using subread (2.0.1) by alignment to the human genome (GRCh38) using STAR (2.7.10b) with Ensembl GTF (release 111)
Gene expression changes and statistics were realized using DESeq2 (1.34.0)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes counts after normalization, average expressions by conditions, and results of statistical analysis by DESeq2 (logFC, pval, padj)

source_name: ab T Cells

extract_protocol:
RNA was extracted by RNeasy Plus Micro Kits (Qiagen)
Messenger RNA-Seq libraries were prepared using a SMART-SeqII combined with transposase-based library construction, libraries were circularized, and sequencing was executed by DNA Nanoballs (DNBTM™) technology

value: ab T Cells

tag: treatment

value: Untreated


title: Nanostring of human16

description: MiniBenifit


title: MCD cohort_ND_Veh_biol rep 3

description: Library name: MCD cohort_ND_Veh_biol rep 3


title: STAG2-KO, RNA-Seq, Donor 3, Condition 2

description: Library name: STAG2-KO Con2


title: S12Ta

description: Library name: Sample 24


title: C57_Bladder_KO_Female3

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

description:
Library name: C57_Bladder_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Transcripts were quantified with Salmon (v1.10.3) in quasi-mapping-based mode.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

source_name: Bladder

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: Bladder

value: Mecp2 KO

value: Female

tag: age

value: 7.5 months

tag: mouse id


title: MCD cohort_ND_Veh_biol rep 2

description: Library name: MCD cohort_ND_Veh_biol rep 2

value: liver


title: S12Ma

description: Library name: Sample 23


title: Nanostring of human15

description: MiniBenifit

value: male


title: MCD cohort_ND_Veh_biol rep 1

description: Library name: MCD cohort_ND_Veh_biol rep 1

value: WT


title: Nanostring of human14

description: MiniBenifit


title: STAG1-KO, RNA-Seq, Donor 3, Condition 2

description: Library name: STAG1-KO Con2


title: S11Te

description: Library name: Sample 22


title: HFD cohort_HFD_DTMB_biol rep 4

description: Library name: HFD cohort_HFD_DTMB_biol rep 4

value: MASLD

value: HFD


title: STAG1-KO, RNA-Seq, Donor 3, Condition 1

description: Library name: STAG1-KO Con1


title: Nanostring of human13

description: MiniBenifit


title: HFD cohort_HFD_DTMB_biol rep 3

description: Library name: HFD cohort_HFD_DTMB_biol rep 3


title: S10Ta

description: Library name: Sample 20

value: Colorectal


title: NFE2-KO, RNA-Seq, Donor 1

description: Library name: NFE2-KO Don1


title: Nanostring of human12

description: MiniBenifit


title: S10Ma

description: Library name: Sample 19


title: HFD cohort_HFD_DTMB_biol rep 2

description: Library name: HFD cohort_HFD_DTMB_biol rep 2


title: Nanostring of human11

description: MiniBenifit


title: S9Ta

description: Library name: Sample 18

value: Tumor tissue


title: AAVS1, RNA-Seq, Donor 2

description: Library name: AAVS1 Don2

value: CD34+ HSPCs (donor-derived, peripheral blood), differentiated to day 13


title: HFD cohort_HFD_DTMB_biol rep 1

description: Library name: HFD cohort_HFD_DTMB_biol rep 1


title: HFD cohort_HFD_Veh_biol rep 4

description: Library name: HFD cohort_HFD_Veh_biol rep 4


title: S9Ma

description: Library name: Sample 17


title: AAVS1, RNA-Seq, Donor 1

description: Library name: AAVS1 Don1


title: Nanostring of human8

description: LongBenifit

source_name: CR/PR

value: female


title: HFD cohort_HFD_Veh_biol rep 3

description: Library name: HFD cohort_HFD_Veh_biol rep 3


title: S8Te

description: Library name: Sample 16


title: STAG2-KO, Clone2

description: Library name: STAG2_Clone2

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired-end reads were aligned with bwa-mem2 (v2.2.1) (flags: -SP) flag to the UCSC hg38 AnalysisSet genome and processed with pairtools (v1.1.2) parse2 (flags: --add-columns mapq --expand --report-position outer --min-mapq 30 --max-insert-size 150). Reads from the same replicate were merged then deduplicated with pairtools dedup (flags: --max-mismatch 1).
Replicate-wise .pairs files were  merged between sequencing runs (pairtools merge) and deduplicated once more (pairtools dedup). Due to sequencing read mismatch between phases, Phase 1, Rep 1 was downsampled using pairtools sample 0.65 to yield comparable read depth to the second replicate.
Final .pairs files were indexed with pairix (v0.3.8), and made into a .cool file with cooler (v0.10.3) cload pairs at 50bp bin size. Finally, .cool files were converted to .mcool files using cooler zoomify with the --balance flag up to 10Mb bin sizes.
Assembly: hg38
Supplementary files format and content: .mcool file contains all valid Micro-C pairs stored in HDF5 format with multiple binsizes

growth_protocol: Isogenic U937 single cell clones with and without STAG2 knockout were used, generated as described in (2). Three WT (Gc1a1, Gc3e1, Gc3e3) and two STAG2-KO (A2f11, A2g4) clones were thawed and cultured in RPMI, 10% fetal bovine serum, and 1% Pen/Strep with glutamine

extract_protocol:
30 million viable cells per genotype were collected (800g, 5min, room temperature), washed with PBS, and recollected. Cells were resuspended in Pierce DSG cross linker (Thermo Fisher #20593 ) at 1x10^6 cells/mL and rotated for 35 minutes at room temperature. Formaldehyde was added dropwise to a final concentration of 1%, and cells were fixed for 10 minutes rotating at room temperature. Tris pH 7.5 was again added dropwise to a final concentration of 0.375M, and cells were quenched for 5 minutes rotating at room temperature. The cells were then collected, washed with cold PBS twice, and aliquoted into 5 million cell pellets. The pellets were snap frozen in liquid nitrogen and stored at -80 °C for Micro-C.
Library preparation was performed with the NEBNext Ultra II kit (New England BioLabs #E7645).

tag: cell line


title: HFD cohort_HFD_Veh_biol rep 2

description: Library name: HFD cohort_HFD_Veh_biol rep 2


title: Nanostring of human7

description: LongBenifit


title: S8Me

description: Library name: Sample 15


title: STAG2-KO, Clone1

description: Library name: STAG2_Clone1


title: HFD cohort_HFD_Veh_biol rep 1

description: Library name: HFD cohort_HFD_Veh_biol rep 1


title: WT, Clone3

description: Library name: WT_Clone3


title: S7Te

description: Library name: Sample 14


title: Nanostring of human6

description: LongBenifit


title: Nanostring of human5

description: LongBenifit


title: WT, Clone2

description: Library name: WT_Clone2


title: S7Me

description: Library name: Sample 13


title: HFD cohort_ND_Veh_biol rep 3

description: Library name: HFD cohort_ND_Veh_biol rep 3

value: Normal


title: HFD cohort_ND_Veh_biol rep 2

description: Library name: HFD cohort_ND_Veh_biol rep 2


title: Nanostring of human4

description: LongBenifit


title: HFD cohort_ND_Veh_biol rep 1

description: Library name: HFD cohort_ND_Veh_biol rep 1


title: WT, Clone1

description: Library name: WT_Clone1


title: S6Me

description: Library name: Sample 11

value: Adjacent mucosal tissue


title: Nanostring of human2

description: LongBenifit


title: S5Te

description: Library name: Sample 10


title: Splenic CD8+ T cells, anti-CD3/CD28 activated, 24-hours, Dusp2-floxed control, mouse 3

city: Rochester

first: Emilia

middle: R

last: Dellacecca

state: MN

address: 200 First Street SW, Kellen Building 02-102

department: Immunology

institute: Mayo Clinic

description: Library name: 119D_R

data_processing:
Raw RNA sequencing paired-end reads were processed through Mayo RNA-Seq bioinformatics pipeline, MAP-Rseq (v3.1.5) to align to genome build mm39.
Variants were called using the RVBoost module from MAPR-seq.
Gene and exon expression quantification were performed using the Subread package to obtain both raw and normalized (FPKM) reads.
FASTQC, MultiQC, and RSEQC tools were used for comprehensive quality control assessment of the aliqned reads.
Assembly: mm39
Supplementary files format and content: Tab-delimited text file including raw counts and FPKM for each sample

source_name: Spleen

growth_protocol: CD8+ T cells were maintained in RPMI 1640 + 10% fetal bovine serum, 20 mM HEPES buffer, and 1X penicillin/streptomycin at 37 degrees Celsius with 5% CO2.

extract_protocol:
Total RNA was isolated with TRIzol Reagent (Invitrogen), prior to inclusion in spin-column based isolation (Zymo Research). 100 ng of total RNA was used for construction of cDNA libraies.
Libraries were prepared with Illumina Stranded mRNA Prep kit following manufacturer's instructions. The concentration and size distribution of the completed libraries were determined with the Agilent TapeStation's D1000 ScreenTape and Qubit fluorometry.

treatment_protocol: CD8+ T cells were activated with anti-CD3/CD28 beads (Gibco) for 24-hours, rested cells were maintained under the same conditions without addition of beads.

value: Spleen

value: CD8+ T cells


title: S5Me

description: Library name: Sample 09


title: Splenic CD8+ T cells, rested, 24-hours, Dusp2 conditional knockout, mouse 3

description: Library name: 119D_A

value: Activated with anti-CD3/CD28


title: MITO (Mitochondrial Matrix) in vitro 4SU+AP+DF (Maxima H) bio rep2

city: Shanghai

first: Jiapeng

last: Liu

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

description:
Library name: HEK-MTS_Target_1112_rep2
Ribosomal RNA Depletion

data_processing:
Quantification of gene expression level. Reference genome and gene model annotation files (v44) were downloaded from genome website directly. Index of the reference genome was built using STAR-2.7.9a and paired-end clean reads were aligned to the reference genome using STAR-2.7.9a.
FeatureCounts was used to count the read numbers mapped to each gene.
Differential expression analysis. Differential expression analysis of two groups (two biological replicates per condition) was performed using the DESeq2 R package (1.42.0).
Assembly: GRCh38

extract_protocol:
RNA was harvested using VeZol Reagent (R411, Vazyme).
RNA libraries for RNA-seq were prepared using Ribo-MagOff rRNA Depletion Kit (N420, Vazyme) and VAHTS Universal V10 RNA-seq Library Prep Kit (NR616, Vazyme) fllowing manufacturer's protocols.

treatment_protocol: PRADA metabolic labeling in living cells. Cells stably expressing the indicated PRADA construct were grown to approximately 90% confluency. Cells were then incubated in fresh media containing 100 µM s4U for 5 hrs at 37°C. The media were then replaced with fresh media containing 0.5 mM alkyne phenol and 100 µM s4U for another 30 minutes. To initiate PRADA labeling, a final concentration of 10 mM D-amino acid was added for 30 minutes. The cells were then rinsed with quench solution three times to terminate the labeling reaction. Cells omitting D-amino acid treatment were used as the unlabeled control group. PRADA labeling in mice. 1 × 10^7 HEK-PRADA stable cells in 100 μL PBS were subcutaneously implanted into the hind leg regions of B-NDG mouse. Tumour sizes were measured with calliper and tumour volumes were calculated according to the standard formula (length × width × Height × π/6). For s4U metabolic labeling, s4U was dissolved in 2 mL saline solution and injected intraperitoneally at a dose of 430 mg/kg body weight. 5 hours after injection, tumor-bearing B-NDG mice were anesthetized and intratumorally injected with 1 mL saline solution containing 30 mM alkyne phenol, 100 mM D-Ala, and 100 mM D-Phe. The solution was prepared using non-contact ultrasound-assisted dissolution (<45°C). After 30 minutes, another 1 mL of the solution was injected. After an additional 30 min, the mice were euthanized, and the tissues were collected for subsequent experiments. Mice receiving only 30 mM alkyne phenol in saline solution were used as unlabeled negative controls.

value: a stable clone derivative of the human embryonic kidney (HEK) 293 cell line


title: Nanostring of human1

description: LongBenifit


title: S4Ta

description: Library name: Sample 08


title: MITO (Mitochondrial Matrix) in vitro 4SU+AP+DF (Maxima H) bio rep1

description:
Library name: HEK-MTS_Target_1112_rep1
Ribosomal RNA Depletion


title: S4Ma

description: Library name: Sample 07


title: Splenic CD8+ T cells, anti-CD3/CD28 activated, 24-hours, Dusp2-floxed control, mouse 2

description: Library name: 119A_A

value: Female


title: MITO (Mitochondrial Matrix) in vitro 4SU+AP (Maxima H) bio rep 2

description:
Library name: HEK-MTS_Ctrl_1112_rep2
Ribosomal RNA Depletion


title: S3Ta

description: Library name: Sample 06


title: MITO (Mitochondrial Matrix) in vitro 4SU+AP (Maxima H) bio rep1

description:
Library name: HEK-MTS_Ctrl_1112_rep1
Ribosomal RNA Depletion


title: Splenic CD8+ T cells, rested, 24-hours, Dusp2-floxed control, mouse 1

description: Library name: 116B_R

value: Male


title: S2Ta

description: Library name: Sample 04


title: S2Ma

description: Library name: Sample 03


title: S1Ta

description: Library name: Sample 02


title: Splenic CD8+ T cells, rested, 24-hours, Dusp2 conditional knockout, mouse 1

description: Library name: 116A_R


title: Splenic CD8+ T cells, anti-CD3/CD28 activated, 24-hours, Dusp2 conditional knockout, mouse 1

description: Library name: 116A_A


title: HEK293T Xenograft biol rep 3

description:
Library name: Sample 13
Ribosomal RNA Depletion

library_source: other

molecule: other

source_name: HEK293T Xenograft

value: HEK293T Xenograft


title: S1Ma

description: Library name: Sample 01


title: Splenic CD8+ T cells, rested, 24-hours, Dusp2-floxed control, mouse 2

description: Library name: 119A_R


title: SPF, Lung, immune cells+non-immune cells, irradiation

city: Duarte

first: Jaeho

last: Kim

state: CA

address: 1500 E Duarte Rd

department: RadiationOncology

institute: City of Hope

description: Library name: COHP_58715

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were processed using Cell Ranger count v8.0.1. Libraries were prepared with the 10x Genomics GEM-X 3′ Gene Expression v4 kit, and chemistry was set to automatic detection.
Reads were aligned to the mm10 (2020-A) reference genome, with the include-introns option enabled to retain intronic reads. All other parameters were kept at their default settings.
Assembly: Mm10
Supplementary files format and content: Feature, barcode, matrix

source_name: Lung

growth_protocol: Mice were housed in specific pathogen free (SPF) facility in City of Hope.

extract_protocol:
Lung tissues were harvested from mice and processed into single-cell suspensions using the Mouse Lung Dissociation Kit (Miltenyi Biotec, Cat# 130-095-927) according to the manufacturer’s protocol. Lung tissues were minced and enzymatically digested using the enzyme mix provided in the kit, with mechanical dissociation performed on the gentleMACS Octo Dissociator (Miltenyi Biotec). The resulting cell suspensions were filtered through a 70-µm cell strainer (Fisherbrand, Cat# 22363548) and treated with ACK lysis buffer (Invitrogen, Cat# 00-4333-57) to remove red blood cells.
Libraries were sequenced on the NovaSeq X Series platform using the 10B reagent kit. NovaSeq Control Software v1.2.2.48004 was used for instrument operation, and Illumina BCL Convert v4.2.7 was used to convert base call (BCL) files into FASTQ format. Sequencing targeted approximately 10,000 cells per sample.

treatment_protocol: A focal lung irradiation device was used to selectively irradiate a 7-mm diameter area in the left lung while sparing other thoracic structures to mimic stereotactic body radiation therapy (SBRT). Mice were anesthetized with isoflurane and immobilized on a custom-designed plastic platform where their heads were secured using two pegs to ensure consistent posture. The platform was placed inside an anesthesia chamber, and an acrylic plate with a matching aperture was used to align the irradiation field. Radiation targeting was further verified using lasers to ensure precision and reproducibility. Irradiation was delivered using an Xstrahl CIX3 (Xstrahl, Suwanee, GA) small animal radiation research platform. Radiation was administered at a source-to-surface distance (SSD) of 30 cm, using a 1.0 mm Cu filter and a tube voltage of 300 kV, with a dose rate of 3.1742 Gy/min. Control mice underwent sham irradiation, receiving anesthesia and positioning without radiation exposure.

value: Lung

value: Immune cells + non-immune cells

value: irradiation


title: GCTB

city: chongqing

first: dongyang

last: zhang

address: No. 30, Gaotanyan Zhengjie, Shapingba District

institute: Department of Orthopedics, the First Affiliated Hospital of Army Medical University

description:
Library name: GCTB
Giant cell tumor of bone, distal femoral metaphysis/epiphysis

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hd38
Supplementary files format and content: tab-separated values files and matrix files

source_name: tumor tissue

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: tumor tissue


title: HEK293T Xenograft biol rep 1

description:
Library name: Sample 11
Ribosomal RNA Depletion


title: S3Ma

description: Library name: Sample 05

value: Colorectal


title: HEK293T Xenograft mitochondrion isolation biol rep 2

description:
Library name: Sample 15
Ribosomal RNA Depletion


title: Splenic CD8+ T cells, anti-CD3/CD28 activated, 24-hours, Dusp2-floxed control, mouse 1

description: Library name: 116B_A


title: MITO (Mitochondrial Matrix) in vitro 6SG label biol rep 2

description:
Library name: Sample 10
Ribosomal RNA Depletion


title: SPF, Lung, immune cells+non-immune cells, no-irradiation

description: Library name: COHP_58714

value: WT

value: no-irradiation


title: DAM_Nup153_Replicate4_s_2

city: Dresden

first: Abhinav

last: Soni

state: Saxony

address: Tatzberg 41

department: Nuclear architecture in neural plasticity and aging

country: Germany

institute: German Center for Neurodegenerative Diseases, Dresden

description:
Library name: NEBNext07_s_2
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.

data_processing:
.bw files files were generated using bamCoverage from Deeptools (v3.5.6) or bedgraph files using bedGraphToBigWig from UCSC (PMID: 20639541).
Assembly: mm10
Supplementary files format and content: Processed data files includes .bam files for each samples. In addition normalized and unnormalized bigwig files for DAM-Nup153 are also provided.
Library strategy: DamID-Seq

source_name: Primary cortical neurons

growth_protocol: Embryonic cortices (embryonic day 17.5-19.5) (C57/BL6 mice) from one litter were dissected and pooled together to be processed as a single biological replicate. Dissociated primary cortical neurons were plated in Poly-Dl-Ornithine Hydrobromide coated plates. Cells were maintained in incubators at 37°C with a CO2 concentration of 5%. 30% medium was replaced at DIV4 and DIV8 with Brain Phys Neuronal Culture Medium (STEMCELL Tec), supplemented with 2% SM1-NC (STEMCELL Tec).

extract_protocol:
PCNs were collected in the basal state at DIV13. PCNs were treated with DNAase (Worthington) for 1hr at 37°C. Cells were then scraped from the plates and collected in a 1.5ml tube, pelleted by centrifugation at 300 G, and washed with PBS-PI. Samples were either stored at -80°C or processed directly for DAM-ID seq.
DamID samples were processed according to Marshall et al., Nat Protoc, 2016 (PMID: 27490632) and subjected to Illumina library preparation using the NEBnext Ultra II DNA library preparation chemistry (New England Biolabs, E7645L). The libraries were size-selected with Seramag beads. The resulting libraries were checked for quality and quantified using a Tapestation and Qubit. The final libraries were subjected to 50bp paired-end sequencing on the Illumina NovaSeqX platform. Reads from Dam-only libraries with lower read-depth were pooled into a single Dam-only control for each of the 4 Dam-Nup153 replicates.

value: Primary cortical neurons

value: LV treatment from DIV8 to DIV13 in basal state primary cortical neurons


title: MITO (Mitochondrial Matrix) in vitro 6SG label biol rep 1

description:
Library name: Sample 9
Ribosomal RNA Depletion


title: DAM_Nup153_Replicate4_s_1

description:
Library name: NEBNext07_s_1
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: HEK293T Xenograft mitochondrion isolation biol rep 1

description:
Library name: Sample 14
Ribosomal RNA Depletion


title: MITO (Mitochondrial Matrix) in vitro 6SG unlabel biol rep 2

description:
Library name: Sample 8
Ribosomal RNA Depletion


title: DAM_Nup153_Replicate3_s_2

description:
Library name: NEBNext27_s_2
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: DAM_Nup153_Replicate3_s_1

description:
Library name: NEBNext27_s_1
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: MITO (Mitochondrial Matrix) in vitro 6SG unlabel biol rep 1

description:
Library name: Sample 7
Ribosomal RNA Depletion


title: MITO (Mitochondrial Matrix) in vitro 4SU+AP

description:
Library name: Sample 6
Ribosomal RNA Depletion


title: DAM_Nup153_Replicate2_s_2

description:
Library name: NEBNext25_s_2
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: MITO (Mitochondrial Matrix) in vitro 4SU+AP+DF

description:
Library name: Sample 5
Ribosomal RNA Depletion


title: DAM_Nup153_Replicate2_s_1

description:
Library name: NEBNext25_s_1
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: MITO (Mitochondrial Matrix) in vitro 4SU+BP

description:
Library name: Sample 3
Ribosomal RNA Depletion


title: MCD cohort_MCD_Veh_biol rep 4

description: Library name: MCD cohort_MCD_Veh_biol rep 4

value: liver

value: male

value: MASH

value: MCD


title: DAM_Nup153_Replicate1_s_2

description:
Library name: NEBNext13_s_2
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: MITO (Mitochondrial Matrix) in vitro 4SU+BP+DF

description:
Library name: Sample 2
Ribosomal RNA Depletion

value: a stable clone derivative of the human embryonic kidney (HEK) 293 cell line


title: Lung, SAM24463986:scRNA-seq

city: South San Francisco

first: David

last: Garfield

address: 1 DNA Way

department: Center of Excellence for Computational Sciences

institute: Genentech

description:
Library name: SAM24463986
10x genomics

data_processing:
After processing with the 10x chromium, the resulting libraries were sequenced on an Illumnia NovaSeq machine with the resulting images being processed to Fastq files using the bcl2fastq program following standard process. Fastq files were then aligned to hg38 (IGIS4) using CellRanger 9.0 with the include introns option set to True. To remove ambient RNA contamination frequently seen in scRNA-seq data that include AT2 cells, we further processed the CellRanger alignments using CellBender v 0.3.0 using default settings. Initial QC filtering as well as batch integration and clustering were performed in R using the scran.chan package (##). In brief, cells were initially removed from any sample if they were outside three median absolute deviations in terms of total number of reads, number of features detected, or fraction of reads mapping to mitochondrial genes. Upon visual inspection of the results, we did an additional filtering round, removing cells with fewer than 3162 total reads, 1000 genes, or more than 20% mitochondrial reads. Following QC filtering, read counts were log transformed and size factors were calculated using the function logNormCounts.chan with batch set to Sample. To perform downstream PCA and batch integration, we selected the top 2000 most highly variable genes using the modelGeneVar.chan function with batch set to Sample followed by Principal Component Analysis on these genes using sample-weighted PCA in the function runPCA.chan. Batch correction of these PCs was then performed using fastMNN (## ) as implemented in mnnCorrect.chan with neighborhood parameter k set to 15 and otherwise default parameters.  To identify clusters in our data, and to generate tSNE and UMAP embeddings, we processed our fastMNN corrected PCs using the runAllDownstream function from scran.chan using default parameters including  k = 10, number of neighbors = 10, and method set to “multilevel” (Louvain) for clustering. Markers per cluster were calculated using the scoreMarkers function with markers ranked by AUC. Clusters were then given approximate cell type names based on the expression of these marker as well as visual inspection of key marker genes.
Assembly: hg38, IGIS4
Supplementary files format and content: matrix format and tab-delimited files

growth_protocol: 5000 AT2 cells isolated from normal or IPF lungs were mixed with 50000 MRC5 fibroblasts, embedded in Growth Factor Reduced Matrigel, plated on the upper trans-well chamber and allowed to solidify at 37°C for 10 min. 500 uL of TEC plus supplemented with 10uM of Y-27632 was added to the bottom chamber and cultures for 14 days.

extract_protocol:
Matrigel embedded alveolospheres in co-culture with fibroblasts were incubated with Dispase at 37°C for 1h, and dissociated into single cells by TrypLE enzyme for 2 min. Trypsin was inactivated with TEC+ media.
After processing with the 10x chromium, the resulting libraries were sequenced on an Illumnia NovaSeq machine with the resulting images being processed to Fastq files using the bcl2fastq program following standard process.

treatment_protocol: Cells were treated with 0.54 mM Pirfenidone, 1 uM Nintedanib, 10 uM TGFBi (SB-341542), 10 ng/ml hPTN, 2 uM uPAi (BC11 hydrobromide) or 50 nM LIFi (EC359) for 14 days.

tag: disease

value: Fibrosis Pulmonary

value: TGFB inhibitors


title: HEK293T Xenograft biol rep 2

description:
Library name: Sample 12
Ribosomal RNA Depletion

value: HEK293T Xenograft


title: Lung, SAM24463985:scRNA-seq

description:
Library name: SAM24463985
10x genomics

value: Lung

value: Nintedanib


title: DAM_Nup153_Replicate1_s_1

description:
Library name: NEBNext13_s_1
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: Nanostring of human19

description: MiniBenifit

value: female


title: S13Te

description: Library name: Sample 26

value: Tumor tissue


title: S14Ma

description: Library name: Sample 27

value: Colorectal

value: Adjacent mucosal tissue


title: DAM_only_control_Replicate4_s2

description:
Library name: NEBNext12_s_2
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: MITO (Mitochondrial Matrix) in vitro 4SU+BP+H2O2

description:
Library name: Sample 1
Ribosomal RNA Depletion


title: Lung, SAM24463984:scRNA-seq

description:
Library name: SAM24463984
10x genomics

value: Pirfenidone


title: DAM_only_control_Replicate4_s1

description:
Library name: NEBNext12_s_1
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.

value: Primary cortical neurons


title: ld_3

city: nanyang

first: Kai

last: Li

state: henan

address: No. 80, Changjiang Road

institute: Nanyang Institute of Technology

description:
Library name: sample 12
0.5 μM parimifasor, LN229 group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

treatment_protocol: A549 cells were collected 48 hours after siRNA transfection for RNA extraction and transcriptome sequencing. The experimental group was transfected with siRNA targeting BAP18, while the control group was transfected with non-specific siRNA. Each group had three biological replicates.


title: Lung, SAM24463983:scRNA-seq

description:
Library name: SAM24463983
10x genomics

value: Control


title: hiPSC-CM, omicron BA.1 , rep2

city: Hong Kong

first: Maxwell

last: Kwok

address: The Chinese University of Hong Kong, Shatin

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
#Preprocessing: All fastq files were QC'd initially with FastQC (v0.11.9). All files satisfied most QC criteria and therefore trimming was deemed not necessary.
#Alignment: Alignments were performed with STAR (v2.7.9a). A combined genome index of Human (Gencode v39) and the SARS-CoV-2 genome (NCBI Accession ID:NC_045512.2) was used in aligning reads to both the human and viral genomes. Read counts were generated through the in-built counting software of STAR (with arguement --quantMode GeneCounts). Additional parameters specified at the alignment stage included (--outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0)
Assembly: Human (Gencode v39) and the SARS-CoV-2 genome (NCBI Accession ID:NC_045512.2)
Supplementary files format and content: Raw counts of sequencing reads in .csv

source_name: hiPSC-CM

extract_protocol:
Total RNA was harvested using ReliaPrep RNA Miniprep (Promega) following manufacturer's protocols.
500ng of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using TruSeq RNA Kit following manufacturer's protocols.

value: hiPSC-CM


title: NC_3

city: Nanjing

first: Huichen

last: Song

state: Jiangsu

address: Qixia District, Xianlin Road No.163

institute: Nanjing university

description: Library name: NC_3

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver


title: ld_2

description:
Library name: sample 11
0.5 μM parimifasor, LN229 group, replicate biosample 2


title: ld_1

description:
Library name: sample 10
0.5 μM parimifasor, LN229 group, replicate biosample 1


title: DAM_only_control_Replicate3_s2

description:
Library name: NEBNext08_s_2
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.

value: LV treatment from DIV8 to DIV13 in basal state primary cortical neurons


title: Lung, SAM24463982:scRNA-seq

description:
Library name: SAM24463982
10x genomics

value: Control D0


title: STAG2-KO, RNA-Seq, Donor 3, Condition 1

description: Library name: STAG2-KO Con1

value: CD34+ HSPCs (donor-derived, peripheral blood), differentiated to day 13


title: DAM_only_control_Replicate3_s1

description:
Library name: NEBNext08_s_1
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: Lung, SAM24444436:scRNA-seq

description:
Library name: SAM24444436
10x genomics

source_name: lung

value: lung

value: Normal


title: lc_3

description:
Library name: sample 9
0.2% DMSO, LN229 group, replicate biosample 3


title: DAM_only_control_Replicate2_s2

description:
Library name: NEBNext03_s_2
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: Lung, SAM24444435:scRNA-seq

description:
Library name: SAM24444435
10x genomics


title: S11Me

description: Library name: Sample 21


title: lc_2

description:
Library name: sample 8
0.2% DMSO, LN229 group, replicate biosample 2


title: NFE2-KO, RNA-Seq, Donor 2

description: Library name: NFE2-KO Don2


title: lc_1

description:
Library name: sample 7
0.2% DMSO, LN229 group, replicate biosample 1


title: DAM_only_control_Replicate2_s1

description:
Library name: NEBNext03_s_1
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: DAM_only_control_Replicate1_s2

description:
Library name: NEBNext01_s_2
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: Lung, SAM24444434:scRNA-seq

description:
Library name: SAM24444434
10x genomics


title: kd_3

description:
Library name: sample 6
0.5 μM parimifasor, KYSE140 group, replicate biosample 3


title: Lung, SAM24439427:scRNA-seq

description:
Library name: SAM24439427
10x genomics


title: DAM_only_control_Replicate1_s1

description:
Library name: NEBNext01_s_1
DAM sample collected from basal state primary cortical neurons  DIV13.Sample was sequenced on Illumina NovaSeq X in 50bp paired-end mode.


title: kd_2

description:
Library name: sample 5
0.5 μM parimifasor, KYSE140 group, replicate biosample 2


title: Nanostring of human10

description: MiniBenifit

value: male


title: Lung, SAM24444433:scRNA-seq

description:
Library name: SAM24444433
10x genomics

value: Lung


title: dCLNs,CD4,1,scRNAseq [vdj_t]

city: Rehovot

first: Michal

last: Schwartz

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

description: 10x Genomics

data_processing:
Samples were demultiplexed using mkfastq, and gene expression count matrices were created using multi from the 10x Genomics Cell Ranger Software Suite (version 6.0.1). UMI counts were uploaded into the R environment with the read10x function and converted into a Seurat object using CreateSeuratObject function. Demultiplexing with hashtag oligos (HTOs also called cell hashing) was performed using the Seurat R package, as previously described (Stoeckius, M. et al. Genome Biol. 19, 224. 2018).  Downstream analysis was performed using the Seurat R package (version 4.1.0).
Quality control was performed by including cells expressing less than 3009 genes and less than 10129.5 UMIs.  Cells with more than 443 genes, more than 744 UMIs and less than 7.4% mitochondrial genes were also included.  Cells expressing hemoglobin genes (Hbb-bt, Hbb-bs, Hbb-bh1, Hbb-bh2, Hbb-y, Hba-x, Hba-a1, Hba-a2, Hbq1b, Hbq1a) were removed. Cells having UMI counts higher than 5000 and expressing a combination of either Cd3e and Cd79a or Cd3e and Ms4a1, were also removed, since they represent potential doublets. The lincRNA genes AY036118 and Gm42418 were removed from the analysis since they represent rRNA contamination75. Normalization, scaling, and selection of variable genes out of the expression matrix were performed using SCTransform. Principal Component Analysis was performed, and the first 30 principal components were chosen based on the heatmap and elbow plots for downstream analysis. A KNN graph depicting the Euclidian distance of cells in PCA space was constructed using FindNeighbors and then the Louvain algorithm was implemented to group cells together using the function FindClusters (selected resolution was 1.2). Clusters were given a general annotation of either T-cells or B-cells based on the expression of canonical gene markers Cd3e, Cd4, Cd8a (T cells) and CD79a, CD79b (B cells). T cell and B cell clusters were sub-clustered for separate analysis using the same clustering parameters as the original dataset. Clusters were then merged based on the gene expression pattern resulting in 9 clusters for both T cells and B cells compartments. T cells clusters were annotated based on the expression of gene markers manually, while B cells clusters were given a generic annotation based on the cluster separation. Analysis of differentially expressed genes between conditions was performed using the FindMarkerGenes function.
For BCRs and TCRs analysis, samples were demultiplexed using mkfastq, and reads were aligned to the reference genome to assemble BCRs and TCRs followed by creation of expression count matrices using multi from the 10x Genomics Cell Ranger Software Suite (version 6.0.1). Downstream analysis was performed following the Immcantation framework recommendations.
IgBLAST was used to perform germline V(D)J annotation utilizing Ig reference specific for C57BL/6 strain of Mus musculus. IgBLAST results are parsed into AIRR format for downstream analysis. Productive BCR heavy chain sequences were subsetted, and then only cells with one heavy chain sequence paired with at least one light chain sequence were kept. TCRs were selected for having one TRB chain, and the TRA chain with the highest UMI count was kept in cells with multiple TRA chains.
BCRs and TCRs with two or more identical CDR3 regions in one sample were considered clonally expanded. Information about BCR and TCR clonality was added to the Seurat gene expression analysis by adjusting the metadata. After pre-processing there were 15019 cells with paired heavy and light BCR chains of which 13726 had matching gene expression data. There were 8776 cells with paired TRA and TRB chains for TCRs of which 7788 had matching gene expression data.
Assembly: Mouse (mm10) 2020-A (from 10x Genomics)
Supplementary files format and content: Filtered contig igblast db passed output

source_name: deep cervical lymph node

extract_protocol:
Females 10–11-month-old mice were i.p. administered a lethal dose of ketamine (100 mg/mL)/xylazine (10 mg/mL), intracardially injected with 10 µl of heparin sodium and transcardially perfused with ice-cold 1x PBS. The dCLNs, sCLNs and iLNs were harvested and placed into a 0.4 ml enzymatic mix [100 µg/ml Liberase TL (Roche) and 20 µg/ml DNase I (Roche) in sterile freshly opened IMDM (Sigma)] in a 24-well plate on ice. The tissues were mechanically dissociated using sterile 1 ml syringe plungers on ice and incubated at 37°C for 10 minutes with frequent agitation. The enzymatic reaction was stopped by placing the plate on ice and adding ice-cold RPMI (Biological Industries) supplemented with 10% FBS (Gibco) and 2 mM EDTA (Biological Industries). Samples were then filtered through a 100 µm filter and centrifuged at 450 x g for 6 minutes. The supernatant was aspirated and BioLegend cell staining buffer was used to wash and resuspend the cells. Cell count was evaluated using an automated cell counter (TC20, Bio-Rad). From each sample, 2*106 cells were transferred into new tubes and washed with 1 ml of BioLegend cell staining buffer. After aspiration of the supernatant, the residual contents of each sample were resuspended and incubated with 0.5 µl TruStain FcX PLUS (anti-mouse CD16/32, BioLegend) blocking reagent at 4°C for 10 minutes. Cell hashing was performed by incubating at 4°C for 30 minutes 0.5 µg of anti-mouse Totalseq-C 001, 002, 003 or 004 hashtags (oligo-tagged antibodies from BioLegend). Next, three washes with 3.5 ml of BioLegend cell staining buffer were performed. The cells were then resuspended with 1x PBS supplemented with 1% bovine serum albumin (BSA, Sigma), and cell viability was evaluated using Trypan blue and an automated cell counter (TC20, Bio-Rad). Only samples with cellular viability higher than 87% were used. The single cell suspension from the different tubes were finally combined into composite samples containing an equal number of cells from each original sample.
Up to 17,500 cells from each composite sample (final concentration ~1000 cells/μl) were loaded onto a 10x Genomics Chromium platform for gel beads-in-emulsion (GEM) partitioning and cDNA generation. Gene Expression (GEX), V(D)J (TCR and BCR) and Cell Surface Protein library from the same samples were then constructed using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein and Immune Receptor Mapping. Libraries were sequenced on the NovaSeq 6000 (Illumina), achieving library depths of ~22,200-36,800 mean reads per cell for GEX, ~13,100-26,400 reads per cell for TCR, ~10,900-26,500 mean reads per cell for BCR, and ~4,400-8,400 mean reads per cell for feature barcodes (cell hashing).

value: deep cervical lymph node

value: immune cells

value: WT


title: dCLNs,CD4,2,scRNAseq [vdj_t]

description: 10x Genomics


title: kd_1

description:
Library name: sample 4
0.5 μM parimifasor, KYSE140 group, replicate biosample 1


title: Lung, SAM24439426:scRNA-seq

description:
Library name: SAM24439426
10x genomics


title: Lung, SAM24439425:scRNA-seq

description:
Library name: SAM24439425
10x genomics


title: Nanostring of human9

description: LongBenifit


title: kc_3

description:
Library name: sample 3
0.2% DMSO, KYSE140 group, replicate biosample 3


title: Lung, SAM24438944:scRNA-seq

description:
Library name: SAM24438944
10x genomics


title: dCLNs,CD4,2,scRNAseq [GEX]

description: 10x Genomics

data_processing:
Samples were demultiplexed using mkfastq, and gene expression count matrices were created using multi from the 10x Genomics Cell Ranger Software Suite (version 6.0.1). UMI counts were uploaded into the R environment with the read10x function and converted into a Seurat object using CreateSeuratObject function. Demultiplexing with hashtag oligos (HTOs also called cell hashing) was performed using the Seurat R package, as previously described (Stoeckius, M. et al. Genome Biol. 19, 224. 2018).  Downstream analysis was performed using the Seurat R package (version 4.1.0).
Quality control was performed by including cells expressing less than 3009 genes and less than 10129.5 UMIs.  Cells with more than 443 genes, more than 744 UMIs and less than 7.4% mitochondrial genes were also included.  Cells expressing hemoglobin genes (Hbb-bt, Hbb-bs, Hbb-bh1, Hbb-bh2, Hbb-y, Hba-x, Hba-a1, Hba-a2, Hbq1b, Hbq1a) were removed. Cells having UMI counts higher than 5000 and expressing a combination of either Cd3e and Cd79a or Cd3e and Ms4a1, were also removed, since they represent potential doublets. The lincRNA genes AY036118 and Gm42418 were removed from the analysis since they represent rRNA contamination75. Normalization, scaling, and selection of variable genes out of the expression matrix were performed using SCTransform. Principal Component Analysis was performed, and the first 30 principal components were chosen based on the heatmap and elbow plots for downstream analysis. A KNN graph depicting the Euclidian distance of cells in PCA space was constructed using FindNeighbors and then the Louvain algorithm was implemented to group cells together using the function FindClusters (selected resolution was 1.2). Clusters were given a general annotation of either T-cells or B-cells based on the expression of canonical gene markers Cd3e, Cd4, Cd8a (T cells) and CD79a, CD79b (B cells). T cell and B cell clusters were sub-clustered for separate analysis using the same clustering parameters as the original dataset. Clusters were then merged based on the gene expression pattern resulting in 9 clusters for both T cells and B cells compartments. T cells clusters were annotated based on the expression of gene markers manually, while B cells clusters were given a generic annotation based on the cluster separation. Analysis of differentially expressed genes between conditions was performed using the FindMarkerGenes function.
For BCRs and TCRs analysis, samples were demultiplexed using mkfastq, and reads were aligned to the reference genome to assemble BCRs and TCRs followed by creation of expression count matrices using multi from the 10x Genomics Cell Ranger Software Suite (version 6.0.1). Downstream analysis was performed following the Immcantation framework recommendations.
IgBLAST was used to perform germline V(D)J annotation utilizing Ig reference specific for C57BL/6 strain of Mus musculus. IgBLAST results are parsed into AIRR format for downstream analysis. Productive BCR heavy chain sequences were subsetted, and then only cells with one heavy chain sequence paired with at least one light chain sequence were kept. TCRs were selected for having one TRB chain, and the TRA chain with the highest UMI count was kept in cells with multiple TRA chains.
BCRs and TCRs with two or more identical CDR3 regions in one sample were considered clonally expanded. Information about BCR and TCR clonality was added to the Seurat gene expression analysis by adjusting the metadata. After pre-processing there were 15019 cells with paired heavy and light BCR chains of which 13726 had matching gene expression data. There were 8776 cells with paired TRA and TRB chains for TCRs of which 7788 had matching gene expression data.
Assembly: Mouse (mm10) 2020-A (from 10x Genomics)
Supplementary files format and content: Barcodes (tsv.gz), features (tsv.gz) and matrix (mtx.gz) gzipped files, which logically make up the count matrix


title: kc_2

description:
Library name: sample 2
0.2% DMSO, KYSE140 group, replicate biosample 2


title: Lung, SAM24434754:scRNA-seq

description:
Library name: SAM24434754
10x genomics

value: Fibrosis Pulmonary


title: dCLNs,CD4,1,scRNAseq [GEX]

description: 10x Genomics


title: MITO (Mitochondrial Matrix) in vivo label biol rep 2

description:
Library name: Sample 8
Ribosomal RNA Depletion

data_processing:
Quantification of gene expression level. Reference genome and gene model annotation files (v44) were downloaded from genome website directly. Index of the reference genome was built using STAR-2.7.9a and paired-end clean reads were aligned to the reference genome using STAR-2.7.9a.
FeatureCounts was used to count the read numbers mapped to each gene.
Differential expression analysis. Differential expression analysis of two groups (two biological replicates per condition) was performed using the DESeq2 R package (1.42.0).
Assembly: GRCh38
Supplementary files format and content: Processed data files are not required to be uploaded to GEO.

value: HEK293T Xenograft

value: a stable clone derivative of the human embryonic kidney (HEK) 293 cell line


title: kc_1

description:
Library name: sample 1
0.2% DMSO, KYSE140 group, replicate biosample 1


title: dCLNs,CD4,2,scRNAseq

description: 10x Genomics


title: dCLNs,CD4,1,scRNAseq

description: 10x Genomics


title: Lung, SAM24429968:scRNA-seq

description:
Library name: SAM24429968
10x genomics

value: Nintedanib


title: Lung, SAM24429969:scRNA-seq

description:
Library name: SAM24429969
10x genomics

value: Pirfenidone


title: MITO (Mitochondrial Matrix) in vivo label biol rep 1

description:
Library name: Sample 7
Ribosomal RNA Depletion


title: E-A14 cell line_rep2

city: LYON

first: Amélien

last: SANLAVILLE

address: 28 Rue Laennec

institute: Cancer Research Center of Lyon

description:
Gene expression data from E-A14 tumor cell line
Sample56

data_processing:
Image analysis and base calling resulted in .bcl files, which were converted into .fastq files with the CASAVA1.8.2 software.
Sequencing reads were mapped to the Mus musculus genome sequence and transcriptome annotations (as provided by GENCODE release M9) and converted to gene counts using STAR (Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21, 2013).
All statistical calculations were performed in R programming language (v. 3.5.3). DESeq2 (v. 1.22.2; Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550, 2014) was used to normalize raw counts
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Mammary tumor cells

growth_protocol: Her2-expressing E-A14 mouse mammary tumor cells were implanted into the fourth mammary fat pad of 6-8 week old FVB/N mice.

extract_protocol:
Tumors were collected at growth end-point (20 days post-injection of E-A14 tumor cells in CD4/CD8-depleted mice versus 47 days post-injection in control mice) and enzymatically digested in 10mg.mL-1 collagenase and 0.2mg.mL-1 DNAse I for 30min at 37°C. Red blood cells were then lysed 5min with Pharmlyse Buffer (BD Biosciences) at room temperature. These cells were labeled with fluorescence-conjugated CD90, CD105, CD45, Her2 and EpCAM antibodies and Zombie Fixable Viability Dye. Her2+EpCAM+ and Her2+EpCAM- cells were sorted by a FACSAria III cell sorter (BD Biosciences) after exclusion of dead cells, CD90(+), CD105(+) and CD45(+) cells. Total RNA was extracted from sorted cells and also from single cell suspensions of two replicates of in vitro cultured E-A14 tumor cells stabilized in RLT buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Micro Kit (Qiagen). The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories) was used to generate first strand cDNA from 0.1 to 1.0 ng total-RNA. Double stranded cDNA was amplified by LD PCR (10, 12 or 14 cycles) and purified via magnetic bead clean-up.
Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina). The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on a HiSeq 1000 instrument using the indexed, 50 cycles single-read protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide.

treatment_protocol: Mice were depleted both for CD4 and CD8 T cells, via twice per week intraperitoneal injection of 100µg anti-CD4 and 100µg anti-CD8a antibodies, or injected twice per week with 100µg of rat IgG2a and 100µg of rat IgG2b as control. Both treatments started 2 weeks before tumor implantation and were maintained all along tumor growth.

value: E-A14 tumor cells

value: FVB/N

value: In vitro cell culture

tag: cell selection method

value: N/A (cell culture suspension)

tag: collection time points

value: N/A (E-A14 injected cells)


title: Lung, SAM24429967:scRNA-seq

description:
Library name: SAM24429967
10x genomics

value: Control


title: MITO (Mitochondrial Matrix) in vivo unlabel biol rep 2

description:
Library name: Sample 6
Ribosomal RNA Depletion


title: E-A14 cell line_rep1

description:
Gene expression data from E-A14 tumor cell line
Sample55


title: MITO (Mitochondrial Matrix) in vivo unlabel biol rep 1

description:
Library name: Sample 5
Ribosomal RNA Depletion


title: Lung, SAM24429211:scRNA-seq

description:
Library name: SAM24429211
10x genomics

value: Control D0


title: Mac_PiKO_IL

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

description:
Library name: Sample 8
10X Genomics

data_processing:
Reads were processed using the 10X Genomics Cell Ranger Single Cell 2.0.0 pipeline.
Assembly: Human GRCh38
Supplementary files format and content: An integrated RDS object that contains all individual samples.

source_name: Myeloid cell

extract_protocol:
10X Single Cell 3' GEM kit v3.1
mRNA stranded

value: Myeloid cell

value: PINK1 KO

value: treated


title: Her2(+)EpCAM(-) mammary tumor cells - IgG control-depleted  - Day47_rep5

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample47

value: tumor cells isolated from E-A14 tumors

value: Rat IgG2a and Rat IgG2b double depletion

value: cell sorting based on Her2-positive and EpCAM-negative expression

value: 47 days after E-A14 tumor cell injection


title: Her2(+)EpCAM(-) mammary tumor cells - IgG control-depleted  - Day47_rep6

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample48


title: Mac_WT_IL

description:
Library name: Sample 7
10X Genomics

value: WT


title: MITO (Mitochondrial Matrix) in vitro label biol rep 1

description:
Library name: Sample 3
Ribosomal RNA Depletion

value: a stable clone derivative of the human embryonic kidney (HEK) 293 cell line


title: MITO (Mitochondrial Matrix) in vitro unlabel biol rep 2

description:
Library name: Sample 2
Ribosomal RNA Depletion


title: Her2(+)EpCAM(-) mammary tumor cells - IgG control-depleted  - Day47_rep4

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample46


title: Mac_WT_NS

description:
Library name: Sample 5
10X Genomics

value: non-treated


title: MITO (Mitochondrial Matrix) in vitro unlabel biol rep 1

description:
Library name: Sample 1
Ribosomal RNA Depletion


title: Her2(+)EpCAM(-) mammary tumor cells - IgG control-depleted  - Day47_rep3

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample45


title: Her2(+)EpCAM(-) mammary tumor cells - IgG control-depleted  - Day47_rep1

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample43


title: Her2(+)EpCAM(-) mammary tumor cells - IgG control-depleted  - Day47_rep2

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample44


title: Mono_WT_IL

description:
Library name: Sample 3
10X Genomics


title: Largemouth bass Gill, 24h post-challenge, AhFc, biological replicate 3 [29R3G]

city: Auburn

first: Timothy

middle: James

last: Bruce

state: AL

address: 203 Swingle Hall

department: School of Fisheries, Aquaculture and Aquatic Sciences

institute: Auburn University

description:
Library name: 29R3G
A. hydrophila + F. columnare coinfection; 24h post-challenge; Gill; EXCLUDED from DESeq2 model — gDNA contamination (mapping rate <25%)
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

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

organism: Micropterus salmoides

source_name: Gill

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

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

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

value: Gill

tag: sample group


title: Mono_PiKO_IL

description:
Library name: Sample 4
10X Genomics


title: Her2(+)EpCAM(+) mammary tumor cells - IgG control-depleted  - Day47_rep6

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample42

value: FVB/N

value: cell sorting based on Her2-positive and EpCAM-positive expression


title: Her2(+)EpCAM(+) mammary tumor cells - IgG control-depleted  - Day47_rep5

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample41


title: Largemouth bass Spleen, 24h post-challenge, Ah, biological replicate 2 [25T2S]

description:
Library name: 25T2S
Aeromonas hydrophila single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen

value: Aeromonas hydrophila single infection


title: Mono_WT_NS

description:
Library name: Sample 1
10X Genomics


title: Her2(+)EpCAM(+) mammary tumor cells - IgG control-depleted  - Day47_rep4

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample40


title: AATD Patient 4

city: Gainesville

first: Nazli

last: Khodayari

state: FL

department: Pulmonary Medicine

institute: University of Florida

description: Library name: TEMOCON_S7

data_processing:
FREYA
Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic
Trimmed sequence reads were mapped to hg38 using HiSat2
Read count extraction and processing was performed using FeatureCounts
Assembly: GRCh38.109
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: plasma

extract_protocol:
Total RNA was extracted from PMN samples using the RNeasy Plus Universal Mini Kit (Qiagen, Germantown, MD) according to the manufacturer’s protocol.
). Sequencing libraries were prepared using the Illumina RNA-Seq Library Prep Set for low-input RNA, following the manufacturer’s guidelines. Libraries were quantified using qPCR and assessed for fragment size distribution using the Agilent Bioanalyzer before pooling.

value: plasma

value: Female

tag: race

value: Unknown

tag: pathology

value: ZZ


title: Largemouth bass Gill, 24h post-challenge, Ah, biological replicate 3 [25T3G]

description:
Library name: 25T3G
Aeromonas hydrophila single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

tag: tissue


title: AATD Patient 3

description: Library name: KELOBAN_S6

tag: Sex


title: Her2(+)EpCAM(+) mammary tumor cells - IgG control-depleted  - Day47_rep3

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample39

tag: strain


title: Largemouth bass Gill, 24h post-challenge, Ah, biological replicate 2 [25T2G]

description:
Library name: 25T2G
Aeromonas hydrophila single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: AATD Patient 1

description: Library name: GREMINJA_S5

value: Male

tag: genotype


title: Her2(+)EpCAM(+) mammary tumor cells - IgG control-depleted  - Day47_rep1

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample37

value: tumor cells isolated from E-A14 tumors


title: Largemouth bass Spleen, 24h post-challenge, AhFc, biological replicate 3 [29R3S]

description:
Library name: 29R3S
A. hydrophila + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Her2(+)EpCAM(-) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep6

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample12

value: CD4 and CD8 double depletion

value: 20 days after E-A14 tumor cell injection


title: Her2(+)EpCAM(-) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep5

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample11

value: cell sorting based on Her2-positive and EpCAM-negative expression


title: Largemouth bass Spleen, 24h post-challenge, AhFc, biological replicate 1 [29R1S]

description:
Library name: 29R1S
A. hydrophila + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Her2(+)EpCAM(-) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep4

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample10


title: Healthy Control 3

description: Library name: MUUBIE_S11

value: MM


title: Healthy Control 2

description: Library name: JELOCION_S3


title: Largemouth bass Gill, 24h post-challenge, AhFc, biological replicate 2 [29R2G]

description:
Library name: 29R2G
A. hydrophila + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Her2(+)EpCAM(-) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep3

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample09


title: Sample_Rat_HN_Dend28

city: Philadelphia

first: Junhyong

state: PA

address: 433 South University Ave

department: Biology

institute: University of Pennsylvania

description: Library name: Rat_HN_Dend28

data_processing:
We combined the Ensembl genes annotations (downloaded from Ensembl Genome Browser, Dec. 2015) and UCSC genes annotations (downloaded from UCSC, Dec. 2015) to quantify reads with VERSE using options “-s 1 -z 3 --nonemptyModified”
We combined the Ensembl genes annotations (downloaded from Ensembl Genome Browser, Dec. 2015) and UCSC genes annotations (downloaded from UCSC, Dec. 2015) to quantify reads with VERSE using options “-s 1 -z 3 --nonemptyModified” (Zhu et al. 2016, doi:https://doi.org/10.1101/053306)
Assembly: rn6
Supplementary files format and content: *.verse.exon.cnts.txt: tab delimited text files containing raw gene counts.

organism: Rattus norvegicus

source_name: hippocampus

growth_protocol: Hippocampal neurons from embryonic day 18 (E18) rat (Sprague Dawley) were cultured as described in (Buchhalter and Dichter 1991) for 15 days.

extract_protocol:
A micropipette was used to aspirate the soma, which was deposited into a tube containing first strand synthesis buffer and RNase inhibitor and placed on ice. A separate micropipette was used to aspirate the dendrites, which were deposited into a separate tube as above. Samples underwent first strand synthesis within 30 minutes of collection. Poly-adenylated RNA was amplified using three rounds of the aRNA in vitro transcription-based amplification method, as described in (Morris, Singh, and Eberwine 2011). The quality and quantity of the amplified RNA was verified using a Bioanalyzer RNA assay.
Sequencing libraries were prepared using a modified Illumina TruSeq Stranded kit protocol, we ommited that the initial poly-A capture step as the aRNA amplification procedure already selects for poly-adenylated RNA. Samples were sequenced on a  NextSeq (75bp paired-end) to an average depth of 30 million reads.

value: hippocampus

value: pyramidal neurons

value: wildtype

value: Sprague Dawley

tag: rounds of_arna_amplification

tag: cell compartment

value: Dendrites


title: Her2(+)EpCAM(-) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep2

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample08

tag: cell type

value: FVB/N


title: Largemouth bass Spleen, 24h post-challenge, AhFc, biological replicate 3 [29Q3S]

description:
Library name: 29Q3S
A. hydrophila + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen

tag: treatment


title: Her2(+)EpCAM(-) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep1

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample07


title: Sample_Rat_HN_Soma28

description: Library name: Rat_HN_Soma28

value: Soma


title: Largemouth bass Spleen, 24h post-challenge, AhFc, biological replicate 2 [29Q2S]

description:
Library name: 29Q2S
A. hydrophila + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Largemouth bass Spleen, 24h post-challenge, AhFc, biological replicate 1 [29Q1S]

description:
Library name: 29Q1S
A. hydrophila + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Sample_Rat_HN_Soma27

description: Library name: Rat_HN_Soma27


title: Largemouth bass Gill, 24h post-challenge, AhFc, biological replicate 3 [29Q3G]

description:
Library name: 29Q3G
A. hydrophila + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: Sample_Rat_HN_Dend26

description: Library name: Rat_HN_Dend26


title: Her2(+)EpCAM(+) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep3

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample03

value: cell sorting based on Her2-positive and EpCAM-positive expression


title: AATD Patient 2

description: Library name: MEGABON_S1

value: plasma

value: Female

value: Unknown

value: Liver Disease

tag: age

value: ZZ


title: Largemouth bass Gill, 24h post-challenge, AhFc, biological replicate 1 [29Q1G]

description:
Library name: 29Q1G
A. hydrophila + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Sample_Rat_HN_Soma26

description: Library name: Rat_HN_Soma26


title: Her2(+)EpCAM(+) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep2

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample02

value: tumor cells isolated from E-A14 tumors

value: CD4 and CD8 double depletion

value: 20 days after E-A14 tumor cell injection


title: Largemouth bass Spleen, 24h post-challenge, AvFc, biological replicate 3 [28P3S]

description:
Library name: 28P3S
A. veronii + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: A. veronii + F. columnare coinfection


title: Sample_Rat_HN_Dend25

description: Library name: Rat_HN_Dend25

value: hippocampus

value: pyramidal neurons

value: wildtype


title: Her2(+)EpCAM(+) mammary tumor cells - CD4 and CD8-depleted  - Day20_rep1

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample01

value: FVB/N


title: Sample_Rat_HN_Soma25

description: Library name: Rat_HN_Soma25

value: Sprague Dawley


title: Largemouth bass Spleen, 24h post-challenge, AvFc, biological replicate 2 [28P2S]

description:
Library name: 28P2S
A. veronii + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen


title: Sample_Rat_HN_Dend23

description: Library name: Rat_HN_Dend23

value: Dendrites


title: Largemouth bass Spleen, 24h post-challenge, AvFc, biological replicate 1 [28P1S]

description:
Library name: 28P1S
A. veronii + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Sample_Rat_HN_Soma23

description: Library name: Rat_HN_Soma23

value: Soma


title: Largemouth bass Gill, 24h post-challenge, AvFc, biological replicate 3 [28P3G]

description:
Library name: 28P3G
A. veronii + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: PRMT1 OV_Replicate1

first: George

last: Burslem

address: 422 Curie Blvd., 1013 Stellar-Chance Bldg.

description: Library name: Sample 4

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted
Assembly: Reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Supplementary files format and content: TPM_Values.csv

source_name: epithelial

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% FBS, 100 U of penicillin, and 100 mg/mL streptomycin. Cells were cultured in a humidified CO2 incubator, 5% CO2 at a temperature of 37oC.

extract_protocol:
Performed by Azenta following best in class methods for mRNA enrichment by polyA selection, mRNA Fragmentation and Random Priming
Performed by Azenta following best in class methods for first and second strand cDNA synthesis followed by end repair, 5'phosphorylation and dA-tailing. Finally, adaptor ligation, PCR enrichment and Sequencing were performed.

treatment_protocol: In PRMT1 overexpression condations cells were transfected with PCDNA3 contaning PRMT1 as an incert, Transfection was done using PolyJet

value: epithelial

value: Kidney

value: PRMT1 OV

value: PRMT1 overexpression


title: Sample_Rat_HN_Dend22

description: Library name: Rat_HN_Dend22


title: FVB_Thymus_OE_rep1

first: Xiaoping

description:
Library name: FVB_Thymus_OE_rep1_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Transcripts were quantified with Salmon (v1.10.3) in quasi-mapping-based mode.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

source_name: Thymus

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: Thymus

value: MECP2 OE

value: FVB/NJ

value: Male

value: 8 weeks

tag: mouse id


title: PRMT1 OV_Replicate3

description: Library name: Sample 6

tag: cell line


title: MITO (Mitochondrial Matrix) in vitro label biol rep 2

description:
Library name: Sample 4
Ribosomal RNA Depletion

value: a stable clone derivative of the human embryonic kidney (HEK) 293 cell line


title: Largemouth bass Gill, 24h post-challenge, AvFc, biological replicate 2 [28P2G]

description:
Library name: 28P2G
A. veronii + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: A. veronii + F. columnare coinfection


title: Mac_PiKO_NS

description:
Library name: Sample 6
10X Genomics

value: Myeloid cell

value: PINK1 KO

value: non-treated


title: Largemouth bass Spleen, 24h post-challenge, Ah, biological replicate 3 [25T3S]

description:
Library name: 25T3S
Aeromonas hydrophila single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen

value: Aeromonas hydrophila single infection


title: Mock_Replicate3

description: Library name: Sample 3

value: WT

value: Vector Control


title: Sample_Rat_HN_Soma22

description: Library name: Rat_HN_Soma22

value: hippocampus

value: pyramidal neurons

value: wildtype

value: Sprague Dawley

value: Soma


title: PRMT1 OV_Replicate2

description: Library name: Sample 5

value: epithelial

value: Kidney

value: PRMT1 OV

value: PRMT1 overexpression


title: Mono_PiKO_NS

description:
Library name: Sample 2
10X Genomics


title: Largemouth bass Gill, 24h post-challenge, AvFc, biological replicate 1 [28P1G]

description:
Library name: 28P1G
A. veronii + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill

value: A. veronii + F. columnare coinfection


title: Largemouth bass Spleen, 24h post-challenge, Ah, biological replicate 1 [25T1S]

description:
Library name: 25T1S
Aeromonas hydrophila single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Sample_Rat_HN_Dend21

description: Library name: Rat_HN_Dend21

value: Dendrites


title: Largemouth bass Gill, 24h post-challenge, Ah, biological replicate 1 [25T1G]

description:
Library name: 25T1G
Aeromonas hydrophila single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Mock_Replicate1

description: Library name: Sample 1


title: Largemouth bass Spleen, 24h post-challenge, AvFc, biological replicate 3 [28O3S]

description:
Library name: 28O3S
A. veronii + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Her2(+)EpCAM(+) mammary tumor cells - IgG control-depleted  - Day47_rep2

description:
Gene expression data from tumor cells, isolated from mouse mammary tumors grown after E-A14 tumor cell line injection in mice
Sample38

value: tumor cells isolated from E-A14 tumors

value: FVB/N

value: Rat IgG2a and Rat IgG2b double depletion

value: cell sorting based on Her2-positive and EpCAM-positive expression

value: 47 days after E-A14 tumor cell injection


title: Largemouth bass Spleen, 24h post-challenge, AvFc, biological replicate 2 [28O2S]

description:
Library name: 28O2S
A. veronii + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen


title: Sample_Rat_HN_Dend20

description: Library name: Rat_HN_Dend20

value: hippocampus

value: pyramidal neurons


title: Healthy Control 4

description: Library name: NCUR2_S10

value: plasma

value: Female

value: Unknown

value: MM


title: PC3 cells, sh-FOSB_3

city: Guangzhou

first: Jun

last: Huang

state: Dr.

address: the Fifth Affiliated Hospital, Southern Medical University, 566 Congcheng Avenue, Conghua District, Guangzhou 510900, P.R. China

department: Department of Urology

description: Library name: Sample 12

data_processing:
The processed reads were then aligned to the human reference genome (hg19/GRCh37) using Bowtie 2 (v2.1.0).
Gene expression levels (read counts) were quantified using RSEM (v1.2.15)
Gene expression normalization was performed according to the trimmed mean of M values (TMM) method implemented in the edgeR package (v3.21)
Assembly: GRCh38
Supplementary files format and content: Microsoft excel file includes raw counts for each sanple

source_name: prostate cancer

growth_protocol: In all, 1 × 107 OE-NC, OE-FOSB, sh-NC, or sh-FOSB cells were collected.

extract_protocol:
the samples were snap-frozen in liquid nitrogen and shipped on dry ice to Kidio Biotechnology (Guangzhou, China) for RNA sequencing. Briefly, total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany), which included an on-column DNase I digestion step. RNA integrity was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
Library preparation and paired-end sequencing were performed on an Illumina HiSeq 4000 platform by Novogene (Beijing, China). The raw sequencing reads underwent quality control using FastQC (v0.18.0).

treatment_protocol: suspended and centrifuged at 1000 × g for 5 min and washed twice with PBS.

value: prostate cancer

value: FOSB knockdown

value: Knockdown of FOSB in PC3 cells


title: Largemouth bass Spleen, 24h post-challenge, AvFc, biological replicate 1 [28O1S]

description:
Library name: 28O1S
A. veronii + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: A. veronii + F. columnare coinfection


title: Sample_Rat_HN_Soma20

description: Library name: Rat_HN_Soma20

value: wildtype

value: Sprague Dawley

value: Soma


title: Largemouth bass Gill, 24h post-challenge, AvFc, biological replicate 3 [28O3G]

description:
Library name: 28O3G
A. veronii + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: PC3 cells, sh-FOSB_2

institute: the Fifth Affiliated Hospital, Southern Medical University

description: Library name: Sample 11


title: Largemouth bass Spleen, 24h post-challenge, AhFc, biological replicate 2 [29R2S]

description:
Library name: 29R2S
A. hydrophila + F. columnare coinfection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Healthy Control 1

description: Library name: TAFFZ42_S4


title: Sample_Rat_HN_Dend18

description: Library name: Rat_HN_Dend18

value: Dendrites


title: Largemouth bass Gill, 24h post-challenge, AhFc, biological replicate 1 [29R1G]

description:
Library name: 29R1G
A. hydrophila + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: PC3 cells, sh-FOSB_1

description: Library name: Sample 10


title: Largemouth bass Gill, 24h post-challenge, AvFc, biological replicate 2 [28O2G]

description:
Library name: 28O2G
A. veronii + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Mock_Replicate2

description: Library name: Sample 2

value: epithelial

value: Kidney

value: WT

value: Vector Control


title: PC3 cells, sh-NC_3

description: Library name: Sample 9

value: negative control


title: Sample_Rat_HN_Soma18

description: Library name: Rat_HN_Soma18

value: hippocampus

value: pyramidal neurons


title: Largemouth bass Gill, 24h post-challenge, AvFc, biological replicate 1 [28O1G]

description:
Library name: 28O1G
A. veronii + F. columnare coinfection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: PC3 cells, sh-NC_2

description: Library name: Sample 8


title: Sample_Rat_HN_Soma21

description: Library name: Rat_HN_Soma21


title: Largemouth bass Spleen, 24h post-challenge, Fc, biological replicate 3 [27N3S]

description:
Library name: 27N3S
Flavobacterium columnare single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen


title: PC3 cells, sh-NC_1

description: Library name: Sample 7

value: prostate cancer


title: 22RV1 cells, OE-FOSB_3

description: Library name: Sample 6

value: FOSB overexpressing

value: FOSB overexpression in 22Rv1 cells


title: Largemouth bass Spleen, 24h post-challenge, Fc, biological replicate 1 [27N1S]

description:
Library name: 27N1S
Flavobacterium columnare single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Sample_Rat_HN_Soma15

description: Library name: Rat_HN_Soma15


title: 22RV1 cells, OE-FOSB_2

description: Library name: Sample 5


title: Sample_Rat_HN_Dend15

description: Library name: Rat_HN_Dend15


title: Sample_Rat_HN_Dend14

description: Library name: Rat_HN_Dend14


title: Sample_Rat_HN_Soma14

description: Library name: Rat_HN_Soma14


title: Largemouth bass Gill, 24h post-challenge, Fc, biological replicate 3 [27N3G]

description:
Library name: 27N3G
Flavobacterium columnare single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: 22RV1 cells, OE-FOSB_1

description: Library name: Sample 4


title: 22RV1 cells, OE-NC_3

description: Library name: Sample 3


title: Largemouth bass Gill, 24h post-challenge, Fc, biological replicate 2 [27N2G]

description:
Library name: 27N2G
Flavobacterium columnare single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Sample_Rat_HN_Dend13

description: Library name: Rat_HN_Dend13


title: Sample_Rat_HN_Soma13

description: Library name: Rat_HN_Soma13


title: 22RV1 cells, OE-NC_2

description: Library name: Sample 2


title: Largemouth bass Gill, 24h post-challenge, Fc, biological replicate 1 [27N1G]

description:
Library name: 27N1G
Flavobacterium columnare single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Largemouth bass Spleen, 24h post-challenge, Fc, biological replicate 3 [27M3S]

description:
Library name: 27M3S
Flavobacterium columnare single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: 22RV1 cells, OE-NC_1

description: Library name: Sample 1