title: Human PBMCs treated with cGAMP replicate3

description: Library name: Human_cGAMP_3

value: Human PBMCs treated with cGAMP


title: naive, ATAC-seq, rep 2

status: Public on Aug 14 2025

type: SRA

city: Halifax

first: Spencer

middle: Gordon

last: Jones

state: NS

address: 5850 College St

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

library_source: genomic

data_processing:
Raw sequence reads were trimmed using trimmomatic (version 0.39) to remove low quality leading and tailing bases (below quality 3).
Trimmed reads were aligned to D. melanogaster genome (dm6) using Bowtie (version 2.4.1), with the very-sensitive settings.
Reads were shifted , +4 bp for the forward strand and -5 bp for the negative strand, to account for the DNA repair nick of the Tn5 transpose. Duplicate reads, as well as reads that aligned to multiple loci, had a low mapping quality (<4), aligned to mitochondrial chromosomes, or scaffolds were removed.
ATAC-seq peaks were identified with macs2 (version 2.1.2), using q<0.01.
Assembly: dm6
Supplementary files format and content: narrowPeak

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Mushroom body

extract_protocol:
Fly heads were obtained from samples of 50-60 flies through flash freezing with liquid nitrogen, followed by vortexing and separation through a series of a sieves. Fly heads were then suspended in homogenization buffer and nuclei released into solution through chemical and physical agitation of the cell membrane. Anti-GFP bound beads were then used to isolate GFP-positive nuclei from the whole head homogenate to represent the mushroom body-specific fraction (MB). DNA was isolated using a Qiagen MinElute Kit.
ATAC-Seq libraries were generated by mixing purified DNA with custom Nextera primers and High-Fidelity PCR Mastermix (NEB) and amplified as per manufacturer's instructions. Final libraries were purified using a Qiagen PCR purification kit.

tag: tissue

value: Mushroom body

tag: genotype

tag: treatment

value: Naive


title: mNPC, nestin cre wt, IgG, rep2

city: Reykjavik

first: Tinna

last: Reynisdottir

state: Ísland

address: Sturlugata 8

country: Iceland

institute: University Of Iceland

data_processing:
Fastq sample files were aligned to the mouse mm10 genome using Bowtie2 (version 2.4.4)
For vizulising H3K4me1 peaks in UCSC, bam files for all samples for each genotype were merged with SAMtools. They were then converted to bigwig files with deepTools (version 3.5.1) and normalized to 1x mouse genome with --normalizeUsing RPGC .
Peaks were called for merged genotypes against the merged IgG samples for each genotype using MACS3 (version 3.0.0)
Differential peak analysis was performed using DESeq2
Assembly: mm10
Supplementary files format and content: bigWig file for each sample
Library strategy: CUT&Run

organism: Mus musculus

source_name: Neuronal progenitor cells

extract_protocol:
CUT&RUN was performed according to CUTANA™ CUT&RUN Protocol (v.1.7 EpiCypher) from 160.000 cells per sample
Library preparation was done using TruSeq RNA CD Index plate (Illumina, 20019792).

tag: cell type

value: Neuronal progenitor cells

tag: cut&run antibody

value: IgG, EpiCypher, 23613-0042

value: nes-cre+/-


title: Human PBMCs treated with cGAMP replicate2

city: Aarhus

first: Soren

last: Paludan

address: CF Møllers Alle 6, Building 1115

department: Biomedicine

country: Denmark

institute: Aarhus university

description: Library name: Human_cGAMP_2

library_source: transcriptomic

data_processing:
To ensure high data quality, Trim Galore was used in paired-end mode to remove low-quality base pairs and adaptor sequences from the libraries. Subsequently, sequencing reads were aligned to their respective reference genomes using the STAR aligner.
Assembly: GCF_000001405.40_GRCh38, GCF_000001635.27_GRCm39, ASM359739v1 and rGopEvg1_v1.p, ASM1834038v1, and bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: Tab-separated count matrix

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
RNA harvested using Rneasy mini plus kit (Qiagen) was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit

value: PBMC


title: Uninfected 1

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description:
Library name: uninfected1
Mock-sorted uninfected BMDMs

data_processing:
fastp (0.20.1) for quality control (trimming and adapter removal, q>=36)
STAR (2.7.3a) was used for indexing the reference genome (Hg38) and aligning the reads
SAMTOOLS (0.1.13) was used to filter out multiply mapped reads
HTSeq (2.0.8) was used to calculate the read counts per gene
Normalisation and differential gene expression analysis was done using DESeq2
Assembly: Reference genome used : Mus Musculus (GRCm38, mm10) , accession number : NCBI:GCA_000001635.8
Supplementary files format and content: tab separated value .tsv files containing raw reads count (raw_counts.tsv) and comparison of genes’ expression for sample pairs

molecule: polyA RNA

source_name: Bone marrow-derived macrophages (BMDMs)

growth_protocol: Bone marrow derived macrophages (BMDMs) were cultured in DMEM medium supplemented with 10% FBS, 2mM L-Glutamine, 1mM sodium pyruvate, 10mM HEPES buffer and 30ng/ul macrophage colony stimulating factor (MCSF) for 6 days.

extract_protocol:
Total RNA was extracted from macrophages and subjected to purification and removal of genomic DNA contamination. Ribosomal RNA was depleted to obtain enriched mRNA for library preparation.
Fragmentation and random priming of samples was done for 10 nanograms of mRNA for each sample. First and second strand cDNA synthesis was carried out using NEBNextUltra Dirctional RNA library prep kit for Illumina according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a highthroughput run on the Illumina NovaSeq6000 sequencer using the paired end sequencing format.

treatment_protocol: MCSF differentiated bone marrow-derived macrophages (BMDMs)  were infected with log phase culture of Mycobacterium tuberculosis H37Rv expressing biosensor Mrx1-roGFP2 at moi 10. After 3 hours, extracellular bacteria were removed by washing thrice with pre-warmed DPBS. Infected cells were incubated for 24 hours at 37 degrees Celcius in 5% CO2. At 24 hours post-infection, infected macrophages were flow sorted using BD FACS Aria into three bins (based on the Mrx1-roGFP2 excitation ratio read-out) viz. macrophages harboring EMSH-reduced (mycothiol redox potential around -300 mV) and those harboring EMSH-oxidized (mycothiol redox potential around -240 mV). For uninfected control, macrophages were cultured parallely and were mock sorted through the flow sorter without infection.

value: Bone marrow-derived macrophages (BMDMs)

value: BMDMs never infected or exposed to Mtb.


title: Old Infected

city: Chicago

first: Justin

last: Richner

address: 835 S. Wolcott AVe

country: USA

institute: University of Illinois Chicago

description:
10x Genomics
integrated_annotated.h5ad

library_source: transcriptomic single cell

data_processing:
Single-cell counts were generated with Cell Ranger (v7.1.0) with default settings and using the 10x mm10 (v1.2.0) reference
Assembly: mm10
Supplementary files format and content: h5 raw droplet counts, h5ad file containing preprocessed and annotated cells

source_name: Lymph node

extract_protocol:
Brachial, axial, and popliteal LNs were harvested from infected mice at 2 days post infection (DPI). Inguinal, brachial, and axial LNs were harvested from naïve mice at this same time point as well. Lymph nodes were digested using an enzymatic solution of collagenase IV, dispase, and DNAse I, from which single cell suspensions were generated . To isolate LNSCs from the lymph node cellular suspensions, cells were subjected to a CD45 magnetic microbead negative selection. The CD45-negative cells were then incubated with biotinylated anti-CD31 and anti-gp38 antibodies, and subjected to a CD31/gp38 magentic microbead positive selection to further enrich for LNSCs that expressed CD31 and/or gp38. The resulting LNSCs were then resupended in DMEM with 10% FBS for further scRNA-seq processing.
Single-cell suspensions of adult and old LNSCs from naïve and infected lymph nodes were filtered, counted, diluted to optimal range using DMEM supplemented with 10% FBS, and loaded into the Chromium Controller  to capture between 5,000 and 10,000 cells per group, depending on sample yield. Samples were then processed using the Chromium Single Cell 3’ Kit v3 or v3.1, per the manufacturer’s user guide. Library quality control was performed using the Qubit fluorometer and the Agilent TapeStation . Libraries were pooled and sequenced on the Illumina NovaSeq 6000 PE.

treatment_protocol: Adult and old mice in the infected group were subcutaneously infected with 4x10^3 FFU/mL of WNV-Kunjin two days prior to LNSC isolation. Remaining mice were left as naïve

tag: strain

tag: age

value: Old (18 months)

value: Lymph node

value: Lymph node stromal cells

tag: infection

value: WNV-Kunjin infection (2 DPI)


title: mNPC, wild-type, H3K4me1, rep1

value: H3K4me1, Abcam, ab8895


title: mNPC, Kmt2a KO, IgG, rep2


title: 19 hours after training, trained, rep 3, MB

data_processing:
Raw sequence reads were trimmed using Trimmomatic (version 0.39), removing low quality leading and tailing bases (below quality 3) and reads below 30 bases.
Trimmed reads were aligned to D. melanogaster genome (dm6) using STAR (version 2.7.5a). Reads were also aligned to C. elegans unc-84 gene (NC_003284.9).
Reads that aligned to multiple loci, or to one loci with >4 mismatches, and genes that mapped to Drosophila rRNA were removed.
Gene counts were obtained using using FeatureCounts from the Rsubread R package (version 2.4.2).
Assembly: dm6
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

molecule: nuclear RNA

extract_protocol:
Fly heads were obtained from samples of 50-60 flies through flash freezing with liquid nitrogen, followed by vortexing and separation through a series of a sieves. Fly heads were then suspended in homogenization buffer and nuclei released into solution through chemical and physical agitation of the cell membrane. Anti-GFP bound beads were then used to isolate GFP-positive nuclei from the whole head (WH) homogenate to represent the mushroom body-specific fraction (MB). RNA was then isolated from MB and WH fractions using a PicoPure RNA Isolation Kit (Invitrogen:KIT0204) according to the manufacturer instructions.
RNA libraries were generated using the Tecan Universal Plus Total RNA-Seq library preparation kit (Tecan: 3061-A01) according to manufacturer instructions.

value: Long-term courtship memory training


title: mNPC, nestin cre wt, IgG, rep1


title: Adult Infected Rep 2

description:
10x Genomics
integrated_annotated.h5ad

value: Adult (8-10 weeks)


title: 19 hours after training, trained, rep 2, WH

source_name: Whole head

value: Whole head


title: PBMCs from human control replicate2

description: Library name: Human_UT_2

value: PBMCs from human control


title: mNPC, nestin cre wt, H3K4me1, rep1


title: Subject 14

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

description:
Library name: Subject 14
Bronchoalveolar lavage cells from healthy adult after LPS exposure

data_processing:
Initial pre-processing of the 10 subjects’ 10X scRNA-seq data, including demultiplexing, alignment to the hg38 human genome, and UMI-based gene expression quantification, was performed using Cell Ranger (version 3.0, 10X Genomics)
Assembly: hg38
Supplementary files format and content: comma separated (.csv) matrix of raw counts. Rows are features and columns are cells.

source_name: Bronchoalveolar lavage cells

extract_protocol:
Enrolled subjects underwent flexible fiberoptic bronchoscopy and bronchoalveolar lavage with serial installation and aspiration of normal saline. Lavage fluid was centrifuged to pellet cells. Cell pellet was resuspended at 1x10^6 cells per ml in PBS containing 0.04% bovine serum albumin.
Single cells were captured using The Chromium Box (10x Genomics, Pleasanton, CA). The Chromium Single Cell 3’ GEM, library, and gel bead kit PN-1000075 were used along with Bead Chip B PN-1000092 for cell capture and library construction. Libraries were sequenced with the Illumina NovaSEQ 6000 sequencer (Illumina, Inc., San Diego, CA) using an S4 flow cell.

tag: Sex

value: female

value: Bronchoalveolar lavage cells

tag: diagnosis

value: healthy

tag: timepoint

value: day 1 post-LPS


title: 19 hours after training, trained, rep 2, MB

value: Mushroom body


title: Adult Infected Rep 1

description:
10x Genomics
integrated_annotated.h5ad


title: Adult Naïve Rep 1

description:
10x Genomics
integrated_annotated.h5ad

value: Naive


title: Subject 12

description:
Library name: Subject 12
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: male

value: day 2 post-LPS


title: Subject 13

description:
Library name: Subject 13
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: day 5 post-LPS


title: 19 hours after training, trained, rep 1, WH


title: mNPC, nestin cre wt, H3K4me1, rep2

value: Neuronal progenitor cells

value: nes-cre+/-


title: naive, ATAC-seq, rep 1


title: Subject 11

description:
Library name: Subject 11
Bronchoalveolar lavage cells from healthy adult after LPS exposure


title: 19 hours after training, trained, rep 3, WH


title: mNPC, nestin cre Kmt2a KO, H3K4me1, rep3


title: mNPC, nestin cre Kmt2a KO, H3K4me1, rep2


title: 19 hours after training, trained, rep 1, MB


title: mNPC, nestin cre Kmt2a KO, rep 3

description: Sample 12

data_processing:
Raw reads were pseudoaligned to the mouse mm10 reference transcriptome (GRCm38) using Kallisto (version 0.48.0). Aligned data was imported to R and differential expression analysis was performed using DESeq2 (v 1.42.0) on samples containing >10 counts and genes with only one sample containing counts were excluded.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: mNPC

extract_protocol:
mNPCs were harvested in TRIzol™ Reagent (Thermo Fisher Scientific, #15596026) and RNA isolated with Direct-zol™ RNA Microprep kit (Zymo, #R2060).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.

value: mNPC


title: Old Naïve

description:
10x Genomics
integrated_annotated.h5ad

value: Old (18 months)

value: Lymph node

value: Lymph node stromal cells


title: Subject 15

description:
Library name: Subject 15
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: day 3 post-LPS


title: 13 hours after training, trained, rep 3, WH

value: Whole head

value: Long-term courtship memory training


title: Subject 10

description:
Library name: Subject 10
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: Bronchoalveolar lavage cells


title: Human PBMCs treated with cGAMP replicate1

description: Library name: Human_cGAMP_1

value: PBMC

value: Human PBMCs treated with cGAMP


title: mNPC, nestin cre Kmt2a KO, H3K4me1, rep1

value: H3K4me1, Abcam, ab8895


title: mNPC, nestin cre Kmt2a KO, rep 2

description: Sample 11


title: 13 hours after training, trained, rep 3, MB

value: Mushroom body


title: Subject 9

description:
Library name: Subject 9
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: male

value: healthy


title: mNPC, Kmt2a KO, IgG, rep1

value: IgG, EpiCypher, 23613-0042


title: mNPC, nestin cre Kmt2a KO, rep 1

description: Sample 10

value: Neuronal progenitor cells


title: 13 hours after training, trained, rep 2, WH


title: Subject 8

description:
Library name: Subject 8
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: female

value: day 4 post-LPS


title: mNPC, Kmt2a KO, H3K4me1, rep1


title: 13 hours after training, trained, rep 2, MB


title: mNPC, nestin cre Kmt2a KO, IgG, rep1


title: mNPC, nestin cre wt, rep3

description: Sample 9

value: mNPC

value: nes-cre+/-


title: Adult Naïve Rep 2

description:
10x Genomics
integrated_annotated.h5ad

value: Adult (8-10 weeks)

value: Lymph node

value: Lymph node stromal cells

value: Naive


title: mNPC, nestin cre wt, rep 2

description: Sample 8


title: Subject 7

description:
Library name: Subject 7
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: Bronchoalveolar lavage cells

value: day 3 post-LPS


title: 13 hours after training, trained, rep 1, WH

value: Whole head

value: Long-term courtship memory training


title: Subject 6

description:
Library name: Subject 6
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: day 2 post-LPS


title: mNPC, nestin cre wt, rep 1

description: Sample 7


title: Subject 5

description:
Library name: Subject 5
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: day 5 post-LPS


title: 13 hours after training, trained, rep 1, MB

value: Mushroom body


title: 7 hours during training, trained, rep 3, WH


title: mNPC, Kmt2a KO, rep 2

description: Sample 5


title: Subject 4

description:
Library name: Subject 4
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: male

value: healthy


title: 7 hours during training, trained, rep 3, MB


title: Subject 3

description:
Library name: Subject 3
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: day 1 post-LPS


title: mNPC, Kmt2a KO, rep 1

description: Sample 4

value: Neuronal progenitor cells


title: Subject 2

description:
Library name: Subject 2
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: day 4 post-LPS


title: 7 hours during training, trained, rep 2, WH


title: mNPC, wild-type, rep 3

description: Sample 3

value: mNPC


title: SHDAg overexpressing dKO, mock, biological rep 3

type: RNA

city: Heidelberg

first: Angga

last: Prawira

address: Im Neuenheimer Feld 344

department: Molecular Virology

country: Germany

institute: University Hospital Heidelberg

hyb_protocol: hybridisation was done according to manufacturer's instructions

scan_protocol: Cartridges were scanned with GeneChip Scanner 3000 7G System (cartridge) and GeneTitan Multi-channel

data_processing: Data were processed in R/Bioconductor using the robust multiarray analysis (RMA)  of affy library

label: biotin

source_name: 293 dKO-NTCP-SHDAg cells without infection

label_protocol: no labeling of RNA performed

growth_protocol: Cells were cultivated in DMEM+10% FCS+PenStrep at 5% CO2, 90% humidity and 37C temperature

extract_protocol: RNA was extracted using the Macherey-Nagel NucleoSpin RNA isolation kit according to manufacturer's instructions

treatment_protocol: Cells were infected with HDV in the presence of 4% polyethylene glycol 8000 for 1 day and further cultivated for an additional 5 days before RNA extraction.

tag: cell line

value: human embryonic kidney cells


title: mNPC, wild-type, rep 2

description: Sample 2


title: SHDAg overexpressing dKO, HDV infected, biological rep 2

source_name: 293 dKO-NTCP-SHDAg cells with infection


title: 7 hours during training, trained, rep 2, MB


title: Subject 1

description:
Library name: Subject 1
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: female


title: BHLHE40 knockdown, mRNA-derived cDNA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA79258

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (GRCh38) reference genome using HISAT2 ver.2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: inflamed colon

extract_protocol:
Total RNA was extracted from cells using the RNeasy Micro kit (QIAGEN N.V.) according to the enclosed instructions.
A full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio), following the instructions provided with the kit. Then, a NexteraXT DNA Library Preparation Kit (Illumina) was used to prepare the cDNA library.

value: inflamed colon

value: CD4+ T cells


title: 7 hours during training, trained, rep 1, WH


title: 7 hours during training, trained, rep 1, MB


title: RUNX2 knockdown, mRNA-derived cDNA

description: Library name: GA79257


title: HiC-BMAL1KO-Exp2

city: Granada

first: Ivan

middle: Fernández

last: Rengel

address: Avenida de la Ilustración 114

country: Spain

institute: GENyO

description:
Hi-C library - UDI (Unique Dual Index pairs) - knockout replicate 2
KO_balanced.mcool
KO_insulation_table.tsv
KO_100000_eigen1.tsv
KO_50000_eigen1.tsv

data_processing:
mcool: raw reads from biological replicates were aligned, parsed, filtered and merged with TADbit. mcool files of merged replicates were obtained with cooler zoomify at 10kb, 20kb, 50kb, 100kb, 0.5Mb and 1Mb resolutions and ICE balanced default parameters for "cooler balance" command.
insulation_table: raw reads from biological replicates were aligned, parsed, filtered and merged with TADbit. Hi-C data was normalized with cooler balance with default parameters. Interaction matrices at 50kb resolution was then used to generate insultation scores using cooltools with windows set to 150kb and 250kb.
eigen files: raw reads from biological replicates were aligned, parsed, filtered and merged with TADbit. Hi-C data was normalized with cooler using default paramaters. Balanced matrices at 100kb resolution were used to calculate eigen values using cooltools with default parameters.
Assembly: mm10
Supplementary files format and content: mcool: HDF5-based format to organize multidimensional array data and metadata in binary form. It contains data from Hi-C raw and balanced matrices at multiple resolutions.
Supplementary files format and content: insulation_table: tab-delimited text file containing TAD boundaries and insulation scores obtained at 50kb resolution using 150kb and 250kb window sizes.
Supplementary files format and content: eigen files: tab-delimited text file of compartments analysis containing genomic regions of 100Kb and their correspondent eigen values.

source_name: Embryonic

growth_protocol: mESCs were grown in serum-free 2i media: N2B27 supplemented with MEK inhibitor PD0325901 (1µM) (Millipore) and GSK3 inhibitor CHIR99021 (3 µM) (Millipore) in the presence of LIF.  mESCs were cultured feeder-free on 0.1% gelatin-coated dishes at 37 ºC and 5% CO2.

extract_protocol:
mESCs were fixed during 10 minutes in 1% formaldehyde and stored at -80ºC before being lysed and digested with the MboI enzyme overnight. After end-repair and biotynylation, the ends were ligated overnight. Then, ligated fragments were purified with AMPure beads after RNAse A treatment and crosslink reversion with Proteinase K.
DNA was sheared and biotynilated fragments were pulled-down with streptavidine beads. The library was build with the NEBNext End repair (E6050L) and A-tailing (E6053L) modules and, after adapters ligation, DNA was indexed with NEBNext UDI primer pairs ( E6446S) and amplified with 8 PCR cycles.

value: Embryonic

value: mouse embryonic stem cell (mESC)

value: Untreated


title: SHDAg overexpressing dKO, mock, biological rep 1


title: mNPC, Kmt2a KO, rep 3

description: Sample 6


title: mNPC, wild-type, rep 1

description: Sample 1


title: 7 hours after training, trained, rep 3, MB

value: Long-term courtship memory training


title: GM23815, Sendai OSKM, day 10

city: San Diego

first: William

last: Tu

state: CA

address: 5510 Morehouse Dr

institute: Altos Labs

description:
Library name: GM23815_D10
10x Genomics 3' GEX v3.1

data_processing:
Samples were demultiplexed and fastq files were generated from the mkfastq pipeline using Cell Ranger v7.1.0. Fastq files were aligned to the human genome GRCh38 using the count pipeline with intron mode included of Cell Ranger v7.1.0. Count matrices were loaded to create Seurat objects using Seurat v5.0.0. Cells with more than 500 genes and genes detected in at least 5 cells were kept for further processing. Separate samples were merged and normalized using sctransform v2, with regression for percent mitochondrial gene.
Assembly: GRCh38
Supplementary files format and content: h5 files and rds files

source_name: Skin

growth_protocol: Human dermal fibroblasts from a healthy 96-year old male donor (GM00731, Coriell) and a healthy 22-year old male donor (GM23815, Coriell) were cultured in fibroblast medium (Dulbecco’s Modified Eagle Medium (ThermoFisher) with 10% fetal bovine serum (Omega Scientific), 1× non-essential amino acids solution (ThermoFisher), 1× GlutaMAX supplement (ThermoFisher), 0.5× penicillin-streptomycin, and 0.0007% β-mercaptoethanol (Sigma)) in a 5% O2 incubator.

extract_protocol:
Cells were dissociated using TrypLE, filtered through 40-μm cell strainers, resuspended in 0.04% BSA in PBS, counted, and adjusted to 1200 cells/μL. Cells were loaded onto Chromium X on Chromium Next GEM Chip G (10x Genomics).
Libraries were generated using the Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) protocol (10x Genomics) as per manufacturer's instructions.

treatment_protocol: Reprogramming of fibroblasts was conducted using CytoTune-iPS 2.0 Sendai reprogramming kit, according to the manufacturer’s protocol (ThermoFisher). In brief, fibroblasts were seeded at a density of 2-3×105 cells per well of 6-well plates coated with 0.1% gelatin in fibroblast medium. One day after seeding, cells were counted and transduced with Sendai viruses in fibroblast medium at a multiplicity of infection (MOI) of 5:5:3 for SeV-KLF4-OCT4-SOX2, SeV-MYC, and SeV-KLF4, respectively. Fresh medium was replaced every two days. On day 7, cells were dissociated with TrypLE (ThermoFisher) and 1×105 cells per well of 6-well plates were seeded onto plates coated with Vitronectin Recombinant Human Protein, Truncated (ThermoFisher) in fibroblast medium. On day 8, cells were changed to Essential 8 Medium (ThermoFisher).

value: Skin

value: Fibroblast

value: WT

value: Sendai OSKM, day 10

tag: batch


title: SHDAg overexpressing dKO, HDV infected, biological rep 3


title: Negative control, mRNA-derived cDNA

description: Library name: GA79256


title: HiC-BMAL1KO-Exp1

description:
Hi-C library - UDI (Unique Dual Index pairs) - knockout replicate 1
KO_balanced.mcool
KO_insulation_table.tsv
KO_100000_eigen1.tsv
KO_50000_eigen1.tsv


title: HiC-JM8-Exp2

description:
Hi-C library - UDI (Unique Dual Index pairs) - wildtype replicate 2
WT_balanced.mcool
WT_insulation_table.tsv
WT_100000_eigen1.tsv
WT_50000_eigen1.tsv


title: dKO, HDV infected, biological rep 3

source_name: 293 dKO-NTCP cells with infection


title: SHDAg overexpressing dKO, mock, biological rep 2


title: HiC-JM8-Exp1

description:
Hi-C library - UDI (Unique Dual Index pairs) - wildtype replicate 1
WT_balanced.mcool
WT_insulation_table.tsv
WT_100000_eigen1.tsv
WT_50000_eigen1.tsv


title: dKO, HDV infected, biological rep 2


title: dKO, HDV infected, biological rep 1


title: GM23815, Sendai OSKM, day 3

description:
Library name: GM23815_D3
10x Genomics 3' GEX v3.1

value: Sendai OSKM, day 3


title: 7 hours after training, trained, rep 2, MB

value: Mushroom body


title: 580+

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

data_processing:
Reads were aligned to GRCm39 mouse genome with “Rbowtie2”
counts extracted with featureCounts function from “Rsubread” and gencode annotation release 27 (gencode.vM27.annotation.gtf)
DESeq2 was used to identify genes that were differentially expressed in the 46LCNEC_allo and 57SCLC_allo tumors versus non-tumor lung (Lung). Gene set enrichment analyses were conducted with GSEA (version 4.1.0) software 74, using the DESeq2 normalized count values.
Assembly: GRCm39
Supplementary files format and content: normalized counts

extract_protocol:
Total RNA from back skin derived from Control or GRK2 eKO mice was extracted usingQIAzol reagent (Qiagen) and purified with RNeasy Mini Kit (Qiagen)
RNA sequencing was performed after poly-A selection using Illumina NovaSeq 2x150 bp sequencing.

value: GRK2 eKO


title: 7 hours after training, trained, rep 1, WH

value: Whole head


title: 7 hours after training, trained, rep 2, WH


title: GM23815, Sendai OSKM, day 0

description:
Library name: GM23815_D0
10x Genomics 3' GEX v3.1

value: Sendai OSKM, day 0


title: dKO, mock, biological rep 1

source_name: 293 dKO-NTCP cells without infection

value: human embryonic kidney cells


title: 582+


title: 7 hours after training, trained, rep 3, WH


title: 7 hours after training, trained, rep 1, MB


title: dKO, mock, biological rep 2


title: SHDAg overexpressing dKO, HDV infected, biological rep 1


title: GM00731, Sendai OSKM, day 10

description:
Library name: GM00731_D10
10x Genomics 3' GEX v3.1


title: 82+


title: 4 hours after training, trained, rep 2, WH


title: GM23815, Sendai OSKM, day 7

description:
Library name: GM23815_D7
10x Genomics 3' GEX v3.1

value: Sendai OSKM, day 7


title: SHDAg overexpressing WT, HDV infected, biological rep 3

source_name: 293 WT-NTCP-SHDAg cells with infection


title: 71+


title: GM00731, Sendai OSKM, day 3

description:
Library name: GM00731_D3
10x Genomics 3' GEX v3.1


title: 4 hours after training, trained, rep 2, MB


title: 70+


title: SHDAg overexpressing WT, HDV infected, biological rep 1


title: 4 hours after training, trained, rep 1, WH


title: 4 hours after training, trained, rep 1, MB


title: 83-

value: Control


title: GM00731, Sendai OSKM, day 0

description:
Library name: GM00731_D0
10x Genomics 3' GEX v3.1


title: Ctrl&CD4-6 mix, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA38948

library_source: other

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: vdj_GRCh38_alts_ensembl-4.0.0 and refdata-gex-GRCh38-2020-A
Supplementary files format and content: features.tsv : tab-delimited text file including the information of features (gene and HTO)
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the TCR clonotype information
Supplementary files format and content: genematrix.csv : comma-delimited text files including UMI counts for each feature (gene or HTO) and cell (barcode) conbination
Supplementary files format and content: feature_README.txt : tab-delimited text file including the detail information of HTO
Library strategy: CITE-seq

molecule: protein

source_name: gut

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Hashtag oligonucleotides or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: gut

value: CD4+ CD103+ T cell

tag: disease

value: Crohn's disease and Colorectal cancer

tag: mixed samples

value: Unaffected mucosa of Colorectal  cancer (Ctrl4, Ctrl5, Ctrl6) and Inflammatory mucosa of Crohn's disease (CD4, CD5, CD6)

tag: library type

value: HTO


title: 80-

value: Skin


title: SHDAg overexpressing WT, mock, biological rep 3

source_name: 293 WT-NTCP-SHDAg cells without infection


title: 3.5 hours during training, trained, rep 3, WH

value: Long-term courtship memory training


title: SHDAg overexpressing WT, mock, biological rep 2


title: 78-


title: Ctrl&CD4-6 mix, TCR-derived cDNA

description:
TCR V(D)J segments
GA38947

value: TCR V(D)J


title: 3.5 hours during training, trained, rep 3, MB

source_name: Mushroom body


title: SHDAg overexpressing WT, HDV infected, biological rep 2


title: GM00731, Sendai OSKM, day 7

description:
Library name: GM00731_D7
10x Genomics 3' GEX v3.1

value: Fibroblast

value: WT


title: 124-


title: SHDAg overexpressing WT, mock, biological rep 1


title: Ctrl&CD4-6 mix, mRNA-derived cDNA

description:
poly A RNA
GA38946

value: mRNA


title: Ctrl&CD1-3 mix, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
GA37154

value: Unaffected mucosa of Colorectal  cancer (Ctrl1, Ctrl2, Ctrl3) and Inflammatory mucosa of Crohn's disease (CD1, CD2, CD3)


title: 19-


title: WT, HDV infected, biological rep 3

source_name: 293 WT-NTCP cells with infection


title: WT, HDV infected, biological rep 1


title: 3.5 hours during training, trained, rep 2, MB

value: Mushroom body


title: lymphatic endothelial cells,Red blood cells treatment [RBC3]

city: Shanghai

first: Jinman

last: Chen

address: South of Wanping Road

department: Institute of Spine

country: China

institute: Longhua hospital

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 GRCm39 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: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lymphatic endothelial cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA)
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: lymphatic endothelial cells

value: Red blood cells treatment

tag: time

value: 24 hours


title: Ctrl&CD1-3 mix, TCR-derived cDNA

description:
TCR V(D)J segments
GA37153

tag: tissue


title: 3.5 hours during training, trained, rep 1, WH

value: Whole head

tag: genotype


title: Ctrl&CD1-3 mix, mRNA-derived cDNA

description:
poly A RNA
GA37152

value: gut


title: 3.5 hours during training, trained, rep 1, MB

tag: treatment


title: CD3, HTO-derived cDNA

description: Hashtag oligonucleotide (HTO)

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90, 28+91, or 50+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-6.0.0 or 7.1.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: vdj_GRCh38_alts_ensembl-4.0.0 or -7.0.0, and refdata-gex-GRCh38-2020-A
Supplementary files format and content: features.tsv : tab-delimited text file including the information of features (gene and HTO)
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the TCR clonotype information
Supplementary files format and content: genematrix.csv : comma-delimited text files including UMI counts for each feature (gene or HTO) and cell (barcode) conbination
Library strategy: CITE-seq

tag: cell type

value: CD4+ T cell

value: Crohn's disease

tag: condition

value: Inflammatory mucosa

tag: group

value: CD


title: lymphatic endothelial cells,Red blood cells treatment [RBC1]


title: 1 hour after training, trained, rep 3, WH


title: ssHUDEP, 2-c6, M3814, UNTR, 2

city: Aarhus C

first: Jacob

middle: Giehm

last: Mikkelsen

address: Hoegh-Guldbergs Gade 10

institute: Aarhus University

description: Library name: ssHUDEP-2-c6-M3814-UNTR-2

data_processing:
CRISPResso2
Supplementary files format and content: txt file with alignment output from CRISPResso2

source_name: Human Umbilical cord blood derived

extract_protocol:
Lucigen QuickExtract
TruSeq

value: Human Umbilical cord blood derived

value: Erythroid progenitor cell line


title: WT, mock, biological rep 2

source_name: 293 WT-NTCP cells without infection

value: human embryonic kidney cells


title: WT, mock, biological rep 3


title: CD3, TCR-derived cDNA

description: TCR V(D)J segments

value: TCR V(D)J


title: ssHUDEP, 2-c6, M3814, UNTR, 1

description: Library name: ssHUDEP-2-c6-M3814-UNTR-1


title: lymphatic endothelial cells,Control [CON3]


title: 3.5 hours during training, trained, rep 2, WH

source_name: Whole head

value: Long-term courtship memory training


title: ssHUDEP, 2-c6, UNTR, 2

description: Library name: ssHUDEP-2-c6-UNTR-2


title: lymphatic endothelial cells,Red blood cells treatment [RBC2]


title: dKO, mock, biological rep 3


title: CD3 mRNA-derived cDNA

description: poly A RNA

value: mRNA


title: 1 hour after training, trained, rep 2, WH


title: Ctrl3, HTO-derived cDNA

description: Hashtag oligonucleotide (HTO)

value: Colorectal cancer

value: Unaffected mucosa

value: Ctrl

value: HTO


title: lymphatic endothelial cells,Control [CON2]

value: lymphatic endothelial cells

value: 24 hours


title: WT, HDV infected, biological rep 2


title: lymphatic endothelial cells,Control [CON1]


title: 1 hour after training, trained, rep 2, MB

value: Mushroom body


title: ssHUDEP, 2-c6, UNTR, 1

description: Library name: ssHUDEP-2-c6-UNTR-1


title: ssHUDEP2-c6, sgA, 2

description: Library name: ssHUDEP2-c6-sgA-2


title: Ctrl3, TCR-derived cDNA

description: TCR V(D)J segments

value: gut

value: CD4+ T cell


title: 1 hour after training, trained, rep 1, WH

value: Whole head


title: gonadal fat tissue from adipocyte-specific DNMT1 knockout (AD1KO) mice

city: Atlanta

first: Jia

last: Jing

state: GA

address: Decatur St. SE

department: Biology

institute: Georgia State University

description: Library name: sample 2

data_processing:
The RRBS data analysis including Differentially Methylated Regions (DMRs), methylation rate and pathway analysis were conducted by BGI Bioinformatics Center. The methylation level at each CpG site was determined based on the number of sequences containing methylated CpGs versus the total number of sequences analyzed. For the comparison of DNA methylation rate differences between the HFD- and LFD-fed mice, data were summarized based on genomic features to generate tag density plots around transcription start and termination sites, exon-intron boundaries, CpG islands, and repeat elements and the data were uploaded to University of California Santa Cruz (UCSC) Genome Browser on Mouse (NCBI37/mm9). For RNA-seq, firstly, we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. Then we map those clean reads onto reference genome(mm10), followed with novel gene prediction, SNP & INDEL calling and gene splicing detection. Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations.
Assembly: mm10

source_name: gonadal fat pad

extract_protocol:
For RRBS, genomic DNA from the mouse epididymal white fat was extracted by the phenol-chloroform method and commercially sequenced by Beijing Genomics Institute (BGI) (Shenzhen, China). According to the instruction provided by the company, the genomic DNA was digested with the methylation-insensitive restriction enzyme MspI, ligated to sequencing adaptors, treated with sodium bisulfite, PCR-amplified for library construction and sequenced. For RNA-seq,  white fat pad were removed, flash frozen in liquid nitrogen, and RNA was harvested using Tri-reagent.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using BGISEQ-500.

value: gonadal fat pad

value: adipocyte-specific Dnmt1 knockout


title: Ctrl3, mRNA-derived cDNA

description: poly A RNA


title: gonadal fat tissue from floxed control (Dnmt1^fl/fl^)

description: Library name: sample 1

value: fl/fl


title: ssHUDEP2-c6, sgA, 1

description: Library name: ssHUDEP2-c6-sgA-1

value: Human Umbilical cord blood derived

value: Erythroid progenitor cell line


title: ssHUDEP2-c6, sg2, 2

description: Library name: ssHUDEP2-c6-sg2-2


title: 1 hour after training, trained, rep 1, MB

value: Long-term courtship memory training


title: CD2, HTO-derived cDNA

description: Hashtag oligonucleotide (HTO)

value: Crohn's disease

value: Inflammatory mucosa

value: CD


title: 1 hour during training, trained, rep 3, WH


title: 1 hour after training, trained, rep 3, MB


title: CD2, TCR-derived cDNA

description: TCR V(D)J segments

value: TCR V(D)J


title: ssHUDEP2-c6, sg2, 1

description: Library name: ssHUDEP2-c6-sg2-1


title: Ctrl2, HTO-derived cDNA

description: Hashtag oligonucleotide (HTO)

value: Colorectal cancer

value: Unaffected mucosa

value: Ctrl

value: HTO


title: WT, mock, biological rep 1

value: human embryonic kidney cells


title: ssHUDEP2-c6, sg1, 2

description: Library name: ssHUDEP2-c6-sg1-2


title: 1 hour during training, trained, rep 2, WH


title: P_Ms_5mo_CRM_5xFAD+PLX5622_M4

city: San Antonio

first: Xianlin

last: Han

state: TX

address: 7703 Floyd Curl Drive

department: Barshop Institute

institute: UT Health San Antonio

hyb_protocol: An aliquot of each sample was diluted to 25ng in 5μL of nuclease-free water and loaded into individual NanoString Hybridization reactions. Each reaction was hybridized for 16 hours at +65C and stored at +4C until use the following morning. Following hybridization, samples were further diluted with 20μL of nuclease-free water. 35μL of each sample was loaded into a NanoString nCounter SPRINT cartridge.

scan_protocol: For quality control assessment, data was imported into nSolver Analysis Software 4.0. Samples were separated into experimental groups and sex based on the ‘JPNSF Sample Information’ table. Background thresholding was applied with a threshold count value of 20. Positive Control Normalization was applied using the geometric mean to compute the normalization factor. CodeSet content Normalization was used as “Standard.” Housekeeping genes of Asb10, Supt7l, and Gusb were excluded from the housekeeping calculation as their average counts were at or below the threshold (100 counts). Fold Change estimation was based on ‘Partitioning by experimental group.’ Group A was used as the baseline for comparisons (Group A vs. B, A vs. C) and False Discovery Rates were calculated for all comparisons.

data_processing: Detailed analysis was performed via nSolver Advanced Analysis Software 2.0.134. Raw data values were imported into Advanced Analysis where housekeeping and normalization steps were applied. Housekeeping genes of Tbp, Asb10, Csnk2a2, Mto1, and Gusb were excluded from housekeeping calculations due to high variance (> 25%). Low count data was omitted. Normalized data was used to complete Fold Change analysis via nSolver Advanced Analysis data analysis software. For differential expression, ‘Experimental Group’ (Group A, B, and C) was assigned as the predictor for the analysis. Group ‘A’ was used for the reference level. Differential expression analysis was performed using Benjamini- Hochberg False Discovery Rate methods.

label_protocol: Extracts were labeled based on the animal groups, IDs, processing dates, and etc.

extract_protocol: RNA from frozen, powdered mouse cerebrum samples was extracted and stored at -80C. After thawing gently on ice, sample concentration was determined using the Qubit RNA BR Assay Kit. Internal sample identifier, original sample identifier, experimental group, extracted RNA concentration, and measured RIN run are listed accordingly. All samples were of sufficient quantity and quality for use on the NanoString nCounter SPRINT. After experimental procedures, the remaining sample RNA was placed in long-term storage at -80C.

value: cerebrum

value: male


title: 1 hour during training, trained, rep 2, MB

value: Mushroom body


title: P_Ms_5mo_CRM_5xFAD+PLX5622_M2


title: ssHUDEP2-c6, M3814, sgA, 2

description: Library name: ssHUDEP2-c6-M3814-sgA-2


title: P_Ms_5mo_CRM_5xFAD+PLX5622_M1


title: Ctrl2, mRNA-derived cDNA

description: poly A RNA

value: gut

value: CD4+ T cell

value: mRNA


title: 1 hour during training, trained, rep 3, MB


title: CD2, mRNA-derived cDNA

description: poly A RNA


title: Ctrl1, HTO-derived cDNA

description: Hashtag oligonucleotide (HTO)


title: ssHUDEP2-c6, M3814, sgA, 1

description: Library name: ssHUDEP2-c6-M3814-sgA-1

value: Human Umbilical cord blood derived

value: Erythroid progenitor cell line


title: 1 hour during training, trained, rep 1, WH

value: Whole head

value: Long-term courtship memory training


title: ssHUDEP2-c6, sg1, 1

description: Library name: ssHUDEP2-c6-sg1-1


title: 1 hour during training, trained, rep 1, MB


title: ssHUDEP2-c6, M3814, sg2, 2

description: Library name: ssHUDEP2-c6-M3814-sg2-2


title: P_Ms_5mo_CRM_5xFAD_M3


title: ssHUDEP2-c6, M3814, sg2, 1

description: Library name: ssHUDEP2-c6-M3814-sg2-1


title: Plantaris, Mut, Control

city: Paris

first: Léa

last: Delivry

address: 24 rue faubourg Saint-Jacques

country: France

institute: Cochin Institute

description:
Library name: MutCtl
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skeletal muscle

extract_protocol:
Control and overload muscles were treated according to the STAR protocol « Extraction and sequencing of single nuclei from murine skeletal muscles », 2021
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Skeletal muscle

value: Control


title: ssHUDEP2-c6, M3814, sg1, 2

description: Library name: ssHUDEP2-c6-M3814-sg1-2


title: Plantaris, Mut, 7OV

description:
Library name: Mut7OV
10x Genomics

value: 7 days overload


title: P_Ms_5mo_CRM_5xFAD_M2


title: ssHUDEP2-c6, M3814, sg1, 1

description: Library name: ssHUDEP2-c6-M3814-sg1-1


title: P_Ms_5mo_CRM_5xFAD_M1


title: P_Ms_5mo_CRM_WT_M4


title: CD1, HTO-derived cDNA

description: Hashtag oligonucleotide (HTO)

value: Crohn's disease

value: Inflammatory mucosa

value: CD


title: Plantaris, mTmG, 21OV

description:
Library name: mTmG21OV
10x Genomics


title: CD1, TCR-derived cDNA

description: TCR V(D)J segments

value: TCR V(D)J


title: P_Ms_5mo_CRM_5xFAD_M4

value: cerebrum


title: CeapinA7-4

city: Stanford

first: Allyssa

last: Bradley

address: 450 Jane Stanford Way

institute: Stanford University

description: Library name: CA7_4

data_processing:
Sequencing data was aligned to Mus_musculus_GCF_000001635.27_GRCm39 using the HISAT2 alignment program (v2.0.4)
Gene expression and normalized reads (in FPKM) were quantified using RSEM software (v1.2.18)
Differential expression analysis between control and drug-treated groups, along with the statistical significance, was determined using the DESeq2 package (v1.4.5)
Sequencing saturation-Perl script is used for sequencing saturation analysis.
Assembly: Integrative Genomics Viewer genome (IGV) browser to view the reads align to the genome
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
Supplementary files format and content: excel file includes FPKM values for each sample

source_name: Retina

extract_protocol:
Cornea and lens were removed and retina was harvested using Rneasy miniplus kit (Quagen)/ >2ug of total RNA eas used for the construction of sequencing libarieis.
DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing preperation - Stranded mRNA library

treatment_protocol: In oxygen-induced retinopathy, mouse pups of both sexes at postnatal day (P) 7 and their nursing mothers were placed in an environment with 75% oxygen (hyperoxia) for five consecutive days. They were then returned to room air at P12. Retinas were collected after 5 days in room air when neovascularization peaks (P17). In chemical injection, Ceapin-A7 (10 μM) was dissolved in sterile-filtered saline with 0.05-0.1% dimethyl sulfide, and saline with 0.05-0.1% dimethyl sulfide was used for PBS control. 1 μL of solution was administered to both eyes by intravitreal injection using 33-guage Hamilton syringe needle.

value: Retina

value: WT


title: CeapinA7-5

description: Library name: CA7_5


title: P_Ms_5mo_CRM_WT_M2

value: male


title: CD1, mRNA-derived cDNA

description: poly A RNA

value: gut

value: CD4+ T cell


title: CD3_scMultiome_GEX

data_processing:
The Gene Expression library was sequenced on NovaSeq 6000 platform in a 50+91, 28+90, or 28+91 base paired-end mode. The ATAC ibrary was sequenced on NovaSeq 6000 platform in a 50+24(index)+49, 50+24(index)+91, or 101+24(index)+101 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger count pipeline (cellranger-arc-2.0.0, 10x Genomics) for alignment to the GRCh38 genome and calculation of a feature-barcode matrix.
For a Gene Expression feature, each element in the matrix is the number of UMIs associated with the corresponding gene and cell (barcode).
For a ATAC Peaks feature, each element in the matrix is the number of cut sites associated with the corresponding genomic region and cell (barcode).
Assembly: refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Supplementary files format and content: filtered_feature_bc_matrix.h5 : HDF5 format file including filtered read counts or number of cut sites for each feature (gene or genomic region) and cell barcode combination
Supplementary files format and content: raw_feature_bc_matrix.h5 : HDF5 format file including raw read counts or number of cut sites for each feature (gene or genomic region) and cell barcode combination
Supplementary files format and content: atac_peak_annotation.tsv: tab-delimited text file including the position and the nearby gene information of called peaks with ATAC-Seq

extract_protocol:
Transposed nuclei were partitioned into droplets by 10x Genomics Chromium Controller. mRNAs with UMIs and cell-barcodes were generated at single-cell level. Transposed DNA fragments with cell-barcodes were also generated at single-cell level.
The single cell Gene Expression library and ATAC ibrary were prepared following the protocol outlined in the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide.

value: CD4-positive T-cell


title: Plantaris, mTmG, Control

description:
Library name: mTmGCtl
10x Genomics

value: 21 days overload


title: P_Ms_5mo_CRM_5xFAD+PLX5622_M3


title: Ctrl1, TCR-derived cDNA

description: TCR V(D)J segments

value: Colorectal cancer

value: Unaffected mucosa

value: Ctrl


title: P_Ms_5mo_CRM_WT_M1


title: CeapinA7-3

description: Library name: CA7_3


title: Plantaris, WT, Control

description:
Library name: WTCtl
10x Genomics

value: Skeletal muscle

value: Control


title: Plantaris, WT, 7OV

description:
Library name: WT7OV
10x Genomics

value: 7 days overload


title: G_Ms_5mo_CRM_FIRE_M3


title: CD3_scMultiome_ATAC

library_source: genomic single cell

value: Crohn's disease


title: CeapinA7-2

description: Library name: CA7_2


title: Plantaris, mTmG, 7OV

description:
Library name: mTmG7OV
10x Genomics


title: G_Ms_5mo_CRM_FIRE_M2


title: Ctrl3_scMultiome_GEX


title: TCF1ΔLEF1Δ, rep3

city: Acton

first: Zhi-Ping

last: Feng

state: ACT

address:
131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University

country: Australia

institute: JCSMR

description:
Library name: sorted peritoneal B-1a cells, TCF1ΔLEF1Δ, rep3
sorted peritoneal B-1a cells, TCF1ΔLEF1Δ

data_processing:
The single end reads of 76bp sequencing from 12 mice were aligned to the mm10 (Ensembl 84) genome using hisat2
The mapped reads were assigned with FeatureCounts  based on genome-build GRCm38.p4 annotation (Mus_musculus.GRCm38.82.chr.gtf)
Differential expression analyses were performed with voom-limma, after quality controls and removal of lowly expressed genes.
Assembly: mm10 (GRCm38) genome
Supplementary files format and content: table delimat text format containing gene x sample table of read count matrix and gene information

source_name: spleen

extract_protocol:
Total RNA was purified from sorted peritoneal B-1a cells (CD19+CD3-B220-CD5+CD23-7AAD-) using the PicoPure RNA isolation kit.
sorted peritoneal B-1a cells (CD19+CD3-B220-CD5+CD23-7AAD-) using the PicoPure RNA isolation kit

value: spleen

value: B cells

value: TCF1 knock out  and LEF1 knock out


title: P_Ms_5mo_CRM_WT_M3

value: cerebrum


title: CeapinA7-1

description: Library name: CA7_1

value: Retina

value: WT


title: PBS_5

description: Library name: PBS-5

value: PBS


title: Ctrl3_scMultiome_ATAC

value: gut


title: TCF1ΔLEF1Δ, rep2

description:
Library name: sorted peritoneal B-1a cells, TCF1ΔLEF1Δ, rep2
sorted peritoneal B-1a cells, TCF1ΔLEF1Δ


title: G_Ms_5mo_CRM_FIRE_M1

value: male


title: CD2_scMultiome_GEX

value: CD4-positive T-cell

value: CD


title: TCF1ΔLEF1Δ, rep1

description:
Library name: sorted peritoneal B-1a cells, TCF1ΔLEF1Δ, rep1
sorted peritoneal B-1a cells, TCF1ΔLEF1Δ


title: PBS_4

description: Library name: PBS-4


title: CD2_scMultiome_ATAC


title: LEF1Δ,  rep2

description:
Library name: sorted peritoneal B-1a cells, LEF1Δ,  rep2
sorted peritoneal B-1a cells, LEF1Δ

value: LEF1 knock out


title: G_Ms_5mo_CRM_FIRE_F3

value: female


title: Ctrl2_scMultiome_GEX

value: Colorectal cancer

value: Ctrl


title: PBS_3

description: Library name: PBS-3


title: LEF1Δ, rep3

description:
Library name: sorted peritoneal B-1a cells, LEF1Δ, rep3
sorted peritoneal B-1a cells, LEF1Δ


title: LEF1Δ, rep1

description:
Library name: sorted peritoneal B-1a cells, LEF1Δ, rep1
sorted peritoneal B-1a cells, LEF1Δ


title: Ctrl2_scMultiome_ATAC


title: PBS_1

description: Library name: PBS-1


title: G_Ms_5mo_CRM_WT_M3


title: PBS_2

description: Library name: PBS-2


title: TCF1Δ, rep3

description:
Library name: sorted peritoneal B-1a cells, TCF1Δ, rep3
sorted peritoneal B-1a cells, TCF1Δ

value: TCF1 knock out


title: G_Ms_5mo_CRM_FIRE_F1


title: Ctrl1_scMultiome_GEX


title: TCF1Δ, rep2

description:
Library name: sorted peritoneal B-1a cells, TCF1Δ, rep2
sorted peritoneal B-1a cells, TCF1Δ


title: Atf6KO_5

description: Library name: Atf6KO-5

value: Atf6 knockout

value: oxygen-induced retinopathy


title: G_Ms_5mo_CRM_WT_M2


title: Ctrl1_scMultiome_ATAC


title: Ctrl2, TCR-derived cDNA

description: TCR V(D)J segments

value: CD4+ T cell

value: Unaffected mucosa

value: TCR V(D)J


title: Atf6KO_4

description: Library name: Atf6KO-4

value: Retina


title: TCF1Δ, rep1

description:
Library name: sorted peritoneal B-1a cells, TCF1Δ, rep1
sorted peritoneal B-1a cells, TCF1Δ

value: spleen

value: B cells


title: Atf6KO_3

description: Library name: Atf6KO-3


title: G_Ms_5mo_CRM_WT_M1

value: cerebrum


title: TCF1WTLEF1WT, rep3

description:
Library name: sorted peritoneal B-1a cells, TCF1WTLEF1WT, rep3
sorted peritoneal B-1a cells, TCF1WTLEF1WT


title: CD1_scMultiome_ATAC

value: gut

value: Crohn's disease


title: Atf6KO_1

description: Library name: Atf6KO-1


title: TCF1WTLEF1WT, rep2

description:
Library name: sorted peritoneal B-1a cells, TCF1WTLEF1WT, rep2
sorted peritoneal B-1a cells, TCF1WTLEF1WT


title: RB_3

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: blood

extract_protocol:
Total RNA was extracted from cells with TRIzol reagent and a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Library preparation was performed using a SMART-Seq mRNA HT LP kit (Takara Bio) according to the manufacturer's instructions.

treatment_protocol: PMA/Ionomycin stimulation

value: blood

value: CD4-positive T-cell

tag: genetic modification

value: RUNX2, BHLHE40

tag: disease state

value: Healthy

value: Female


title: TCF1WTLEF1WT, rep1

description:
Library name: sorted peritoneal B-1a cells, TCF1WTLEF1WT, rep1
sorted peritoneal B-1a cells, TCF1WTLEF1WT


title: G_Ms_5mo_CRM_WT_F2

tag: Sex

value: female


title: RB_2

value: Male


title: G_Ms_5mo_CRM_5xFAD_M3

value: male


title: WT_5

description: Library name: WT-5

value: WT

value: oxygen-induced retinopathy


title: G_Ms_5mo_CRM_WT_F1


title: RNA-CLOCK-KO-R2

data_processing:
Reads quality control performed with FastQC
STAR_v2.5.3a used for aligning sequences to reference genome mm10
featureCounts used to obtain gene expression values
BamCoverage 3.5.1 used to normalize with BPM method and to apply a smoothing of 10 bp.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Bigwig files containing Bins per Million (BPM) with a 10 bp smoothing

source_name: Embryonic

extract_protocol:
Trizol extraction
Truseq stranded mRNA library construction protocol
Strand specific mRNA-seq libraries

value: Embryonic

value: mouse embryonic stem cell (mESC)

value: Clock-/-

value: Untreated


title: RB_1


title: WT_4

description: Library name: WT-4

value: Retina


title: RNA-JM8-R2


title: WT_2

description: Library name: WT-2


title: RNA-CLOCK-KO-R1


title: G_Ms_5mo_CRM_5xFAD_M1

value: cerebrum


title: B_2


title: G_Ms_5mo_CRM_5xFAD_M2


title: B_3


title: WT_3

description: Library name: WT-3


title: G_Ms_5mo_CRM_WT_F3


title: Atf6KO_2

description: Library name: Atf6KO-2

value: Atf6 knockout


title: B_1

value: blood


title: RNA-JM8-R1


title: G_Ms_5mo_CRM_5xFAD_F3


title: FLAG-BMAL1-JM8-Input

data_processing:
Paired-end reads of BMAL, TRIM28, H3K9me3 and their respective Inputs were aligned to the concatenated genome sequence of mouse and human spike-in genomes (mm10 and hg19, respectively) using Bowtie 2 with the “--no-mixed” and “--no-discordant” options . Paired-end reads were aligned to the genome sequence of concatenated mouse using Bowtie 2 for Flag-BMAL1 (mm10).  Reads that were mapped one time or were multi-hits with alignment scores greater than secondary valid alignment scores were keeped as described in Teissandier et al. 2019. Duplicates were removed, samples sorted and files converted to BAMs using SAMTools.
Internal calibration of BMAL, TRIM28 and H3K9me3 samples was performed with a fixed number of spiked-in control cells (human A549 cells – hg19 genome) as described by Fursova et al, 2019. Namely, mm10 aligned reads were separated and randomly subsampled using factors that reflected the total number of spike-in reads in each sample. The downsampling factors were additionally corrected using the ratio of  hg19/mm10 total read counts in corresponding Input samples.
Peak sets were generated with MACS3 using corresponding Input samples for background normalizacion.
BigWigs were generated without subtracting the Input samples using deepTools Suite, without normalization for calibrated samples, and with reads per million (RPM) normalization for the uncalibrated Flag-BMAL1.
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigWig files representing genome bin coverage (bin widths of 10; smooth of 50) of BMAL, TRIM28, H3K9me3 spike-in normalised cChIP-seqs.  bigWig files representing genome bin coverage (bin widths of 10; smooth 50) of Flag-BMAL1 normalized to RPKMs (--normalizeUsing RPKM).

extract_protocol:
ChIP assays were mainly performed as described previously (Gallardo et al, 2022)
ChIP-seq libraries were generated from 1-5 ng of immunoprecipitated DNA with the NEBNext Ultra DNA Library Prep kit for Illumina according to manufacturer’s instructions.


title: R_3

value: CD4-positive T-cell


title: WT_1

description: Library name: WT-1


title: G_Ms_5mo_CRM_5xFAD_F2


title: Aganglionic colonic tissue specimen from HSCR patient 3

city: Jinan

first: Jichang

state: Shandong

address: 107 Wenhua Xi Road

department: Department of Pediatric Surgery

institute: Qilu hospital of Shandong University

description:
Library name: Sample6
X-3

data_processing:
Quality assessment with FastQC (v0.18.0)
Adapters and low-quality reads removed (>5% N bases or >20% bases with Q ≤ 10)
Clean reads aligned to human genome (GRCh38/hg38) using HISAT2 (v2.0.4)
Transcript assembly with StringTie (v1.2.1) and merged with Cuffmerge (v2.2.1)
Gene expression levels quantified as FPKM values using RSEM (v1.2.12)
Assembly: GRCh38
Supplementary files format and content: The processed data file (HSCR_FPKM_matrix.txt) contains gene-level expression values in FPKM units. Rows represent genes identified by Ensembl gene IDs, and columns represent individual samples (paired ganglionic and aganglionic colon tissues from 3 Hirschsprung disease patients). Values are tab-delimited plain text.

organism: Colon

source_name: Homo sapiens

extract_protocol:
Total RNA was extracted from colonic tissue samples using TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and by RNase-free agarose gel electrophoresis.
Eukaryotic mRNA was enriched using Oligo(dT) beads, fragmented into short fragments using fragmentation buffer, and reverse-transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA) with random hexamer primers. The resulting double-stranded cDNA was end-repaired, A-tailed, and ligated to Illumina sequencing adapters. Ligated products were purified using AMPure XP beads (1.0X) and amplified by PCR to generate the final cDNA libraries.

value: Homo sapiens

tag: subject status

value: pediatric patients diagnosed with Hirschsprung disease

value: Aganglionic colonic tissue


title: FLAG-ChIPSeq-FLAG-BMAL1-JM8


title: R_2

value: Healthy


title: Aganglionic colonic tissue specimen from HSCR patient 2

description:
Library name: Sample5
X-2


title: G_Ms_5mo_CRM_5xFAD_F1

value: female


title: G_Ms_5mo_CRM_5xFIRE_M3

value: male


title: R_1

value: Male


title: G_Ms_5mo_CRM_FIRE_F2


title: Aganglionic colonic tissue specimen from HSCR patient 1

description:
Library name: Sample4
X-1


title: H3K9me3-ChIPseq-JM8-Input

value: WT


title: Ganglionic colonic tissue specimen from HSCR patient 3

description:
Library name: Sample3
K-3

value: Ganglionic colonic tissue


title: H3K9me3-ChIPseq-BMAL1KO-Input

value: Embryonic

value: mouse embryonic stem cell (mESC)


title: BMAL1-TRIM28-ChIPseq-BMAL1KO-Input

value: Untreated


title: G_Ms_5mo_CRM_5xFIRE_M2


title: G_Ms_5mo_CRM_5xFIRE_M1


title: C_2

value: control


title: BMAL1-TRIM28-ChIPseq-JM8-Input


title: G_Ms_5mo_CRM_5xFIRE_F2

value: cerebrum


title: G_Ms_5mo_CRM_5xFIRE_F3


title: C_1


title: H3K9me3-ChIPseq-BMAL1KO


title: PBMCs from Carp control replicate3

city: Aarhus

first: Soren

address: CF Møllers Alle 6, Building 1115

institute: Aarhus university

description: Library name: Carp_UT_3

data_processing:
To ensure high data quality, Trim Galore was used in paired-end mode to remove low-quality base pairs and adaptor sequences from the libraries. Subsequently, sequencing reads were aligned to their respective reference genomes using the STAR aligner.
Assembly: GCF_000001405.40_GRCh38, GCF_000001635.27_GRCm39, ASM359739v1 and rGopEvg1_v1.p, ASM1834038v1, and bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: Tab-separated count matrix

organism: Cyprinus carpio

source_name: PBMC

extract_protocol:
RNA harvested using Rneasy mini plus kit (Qiagen) was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit

value: PBMC

value: PBMCs from Carp control


title: CD1_scMultiome_GEX

value: gut

value: CD4-positive T-cell

value: Crohn's disease

value: CD


title: G_Ms_5mo_CRM_5xFIRE_F1


title: PBMCs from Turtle control replicate3

description: Library name: ccTurtle_UT_3

organism: Chelonoidis carbonarius

value: PBMCs from Turtle control


title: Ganglionic colonic tissue specimen from HSCR patient 1

description:
Library name: Sample1
K-1

value: Homo sapiens

value: pediatric patients diagnosed with Hirschsprung disease


title: PBMCs from Chicken control replicate3

description: Library name: Chicken_UT_3

organism: Gallus gallus

value: PBMCs from Chicken control


title: PBMCs from Carp control replicate2

description: Library name: Carp_UT_2


title: PBMCs from Chicken control replicate2

description: Library name: Chicken_UT_2


title: PBMCs from Turtle control replicate2

description: Library name: ccTurtle_UT_2


title: PBMCs from Carp control replicate1

description: Library name: Carp_UT_1


title: PBMCs from Turtle control replicate1

description: Library name: ccTurtle_UT_1


title: PBMCs from Chicken control replicate1

description: Library name: Chicken_UT_1


title: C_3

value: blood

value: Healthy

value: Female


title: Ganglionic colonic tissue specimen from HSCR patient 2

description:
Library name: Sample2
K-2

value: Ganglionic colonic tissue


title: Carp PBMCs treated with cGAMP replicate3

description: Library name: Carp_cGAMP_3

value: Carp PBMCs treated with cGAMP


title: Chicken PBMCs treated with cGAMP replicate3

description: Library name: Chicken_cGAMP_3

value: Chicken PBMCs treated with cGAMP


title: Turtle PBMCs treated with cGAMP replicate3

description: Library name: ccTurtle_cGAMP_3

value: Turtle PBMCs treated with cGAMP


title: Turtle PBMCs treated with cGAMP replicate2

description: Library name: ccTurtle_cGAMP_2

value: PBMC


title: Carp PBMCs treated with cGAMP replicate2

description: Library name: Carp_cGAMP_2


title: BMAL1-ChIPseq-BMAL1KO

value: Embryonic

value: mouse embryonic stem cell (mESC)

value: Untreated


title: BMAL1-ChIPseq-JM8

value: WT


title: Chicken PBMCs treated with cGAMP replicate2

description: Library name: Chicken_cGAMP_2


title: Carp PBMCs treated with cGAMP replicate1

description: Library name: Carp_cGAMP_1


title: Lung_PBS_6

status: Public on Aug 13 2025

city: New York

first: Dusan

last: Bogunovic

address: 650 W 168th Street

department: Pediatrics

institute: Columbia University

description: Library name: Sample 20

data_processing:
FASTQ files were uploaded to BaseSpace (Illumina) and sequence reads were trimmed for adaptor sequence and low-quality reads (<q15) using fastp.
Sequences were aligned to t the Mesocricetus auratus (MesAur1.0 assembly) reference genome with the RNA-Seq Alignment (STAR) module.
Assembly: MesAur1.0 assembly
Supplementary files format and content: csv file includes filtered, unnormalized gene-level count matrix for each sample

organism: Mesocricetus auratus

source_name: Lung

extract_protocol:
Total RNA was extracted using RNeasy spin columns (QIAGEN 74104) following manufacturer’s instructions.
RNA sequencing libraries were prepared and sequenced by Azenta Life Sciences.

treatment_protocol: Syrian golden hamsters were treated with PBS, modGFP or modISG10 formulations intranasally on day -1 and evaluated 4 days following SARS-CoV2 infection

value: Lung

value: mock treated, SARS-CoV2 infected


title: Lung_modGFP_5

description: Library name: Sample 18

value: modGFP treated, SARS-CoV2 infected


title: Lung_modGFP_6

description: Library name: Sample 19


title: Lung_modGFP_4

description: Library name: Sample 17


title: H3K9me3-ChIPseq-JM8


title: Lung_modGFP_7

description: Library name: Sample 21


title: TRIM28-ChIPseq-BMAL1KO


title: TRIM28-ChIPseq-JM8


title: Lung_PBS_5

description: Library name: Sample 15


title: Lung_PBS_4

description: Library name: Sample 13


title: Lung_modGFP_3

description: Library name: Sample 9


title: Lung_PBS_2

description: Library name: Sample 11


title: Lung_modISG10_7

description: Library name: Sample 14

value: modISG10 treated, SARS-CoV2 infected


title: Lung_modISG10_5

description: Library name: Sample 8


title: Lung_modISG10_6

description: Library name: Sample 10


title: Lung_modGFP_2

description: Library name: Sample 7


title: Lung_modISG10_4

description: Library name: Sample 5


title: Lung_modISG10_3

description: Library name: Sample 4


title: Lung_modGFP_1

description: Library name: Sample 6


title: Chicken PBMCs treated with cGAMP replicate1

last: Paludan

description: Library name: Chicken_cGAMP_1


title: Turtle PBMCs treated with cGAMP replicate1

description: Library name: ccTurtle_cGAMP_1


title: Lung_modISG10_1

description: Library name: Sample 2


title: Lung_modISG10_2

description: Library name: Sample 3


title: right brain, Day 0, open-field, fish 22E4

city: University Park

first: Jason

last: Keagy

state: PA

address: 410 Forest Resources Bldg

department: Ecosystem Science and Management

institute: Penn State University

description:
Library name: 3B8_22E4
3'TagSeq

data_processing:
We conducted quality control checks using fastqc (v0.11.8).
Next, reads were aligned to the Gasterosteus aculeatus Ensembl BROAD S1 draft genome (version 92) using STAR (v2.2.3a) with alignment rates of 70.43±1.55%
We used htseq (v0.9.1) to count gene transcripts.
Assembly: Gasterosteus aculeatus Ensembl BROAD S1 draft genome (version 92)
Supplementary files format and content: Tab deliminated text file containing raw read counts with samples in columns and genes in rows. Each sample has six columns corresponding to the six lanes of sequencing.

organism: Gasterosteus aculeatus

source_name: right brain

extract_protocol:
Each subject was killed by rapid cervical dissection and the brain was immediately dissected under a microscope in a Sylgaard 184-lined petri-dish. Half of the brain was placed in RNAlater, stored at 4C overnight, and transferred to -20C until RNA extraction. We extracted RNA using Macherey-Nagel NucleoSpin 96 RNA kits with an Eppendorf EpMotion 5075v liquid-handling robot.
242 samples (1.5 μg of RNA in 37.5 μl of RNase-free water) were sent to the Genomic Sequencing and Analysis Facility (GSAF) at the University of Texas at Austin for 3’Tag-seq library preparation and sequencing (6 lanes of Illumina HiSeq 2500, 100 nt reads).

value: right brain

value: Day 0

value: open-field

value: female


title: left brain, Day 0, open-field, fish 04E7

description:
Library name: 3C8_04E7
3'TagSeq

source_name: left brain

value: left brain


title: left brain, Day 0, baseline, fish 11C8

description:
Library name: 3D8_11C8
3'TagSeq

value: baseline

value: male


title: left brain, Day 10, baseline, fish 35C6

description:
Library name: 3F7_35C6
3'TagSeq

value: Day 10


title: right brain, Day 0, baseline, fish 32C5

description:
Library name: 3H7_32C5
3'TagSeq


title: right brain, Day 10, open-field, fish 07E1

description:
Library name: 3G7_07E1
3'TagSeq


title: right brain, Day 10, baseline, fish 31C6

description:
Library name: 3E7_31C6
3'TagSeq


title: left brain, Day 10, open-field, fish 26E5

description:
Library name: 3A8_26E5
3'TagSeq


title: right brain, Day 0, open-field, fish 32E5

description:
Library name: 3D7_32E5
3'TagSeq


title: left brain, Day 10, baseline, fish 20C2

description:
Library name: 3C7_20C2
3'TagSeq


title: left brain, Day 0, open-field, fish 11E5

description:
Library name: 3A7_11E5
3'TagSeq


title: Lung_modISG10_8

description: Library name: Sample 16


title: right brain, Day 10, baseline, fish 17C5

description:
Library name: 3B7_17C5
3'TagSeq


title: right brain, Day 10, open-field, fish 27E9

description:
Library name: 3E6_27E9
3'TagSeq


title: right brain, Day 0, baseline, fish 22C1

description:
Library name: 3D6_22C1
3'TagSeq


title: Lung_PBS_3

description: Library name: Sample 12


title: Lung_PBS_1

description: Library name: Sample 1


title: left brain, Day 0, baseline, fish 32C3

description:
Library name: 3F6_32C3
3'TagSeq


title: right brain, Day 0, baseline, fish 30C11

description:
Library name: 3F5_30C11
3'TagSeq


title: left brain, Day 0, open-field, fish 32E6

description:
Library name: 3G5_32E6
3'TagSeq


title: right brain, Day 10, open-field, fish 35E3

description:
Library name: 3E5_35E3
3'TagSeq


title: left brain, Day 10, open-field, fish 26E2

description:
Library name: 3C5_26E2
3'TagSeq


title: right brain, Day 0, open-field, fish 11E6

description:
Library name: 3H5_11E6
3'TagSeq


title: Ctrl1, mRNA-derived cDNA

description: poly A RNA

source_name: gut

value: gut

value: CD4+ T cell

value: Colorectal cancer

value: Unaffected mucosa

value: Ctrl

value: mRNA


title: right brain, Day 10, baseline, fish 19C4

description:
Library name: 3D5_19C4
3'TagSeq


title: left brain, Day 0, open-field, fish 22E6

description:
Library name: 3H4_22E6
3'TagSeq


title: right brain, Day 0, baseline, fish 25C3

description:
Library name: 3B5_25C3
3'TagSeq


title: right brain, Day 0, open-field, fish 04E6

description:
Library name: 3A5_04E6
3'TagSeq


title: right brain, Day 0, baseline, fish 30C5

description:
Library name: 3H6_30C5
3'TagSeq


title: left brain, Day 10, baseline, fish 17C4

description:
Library name: 3F4_17C4
3'TagSeq


title: left brain, Day 10, baseline, fish 31C4

description:
Library name: 3D4_31C4
3'TagSeq


title: right brain, Day 10, baseline, fish 26C6

description:
Library name: 3E4_26C6
3'TagSeq


title: left brain, Day 0, baseline, fish 11C2

description:
Library name: 3G4_11C2
3'TagSeq


title: right brain, Day 0, open-field, fish 25E1

description:
Library name: 3C4_25E1
3'TagSeq


title: right brain, Day 10, open-field, fish 19E4

description:
Library name: 3B4_19E4
3'TagSeq


title: left brain, Day 0, baseline, fish 32C6

description:
Library name: 3G3_32C6
3'TagSeq


title: right brain, Day 0, open-field, fish 30E9

description:
Library name: 3H3_30E9
3'TagSeq


title: right brain, Day 10, open-field, fish 31E6

description:
Library name: 3G6_31E6
3'TagSeq


title: left brain, Day 0, open-field, fish 40E6

description:
Library name: 3C6_40E6
3'TagSeq


title: right brain, Day 10, baseline, fish 07C5

description:
Library name: 3A4_07C5
3'TagSeq


title: left brain, Day 10, open-field, fish 20E4

description:
Library name: 3D3_20E4
3'TagSeq


title: right brain, Day 0, baseline, fish 40C2

description:
Library name: 3F3_40C2
3'TagSeq


title: left brain, Day 0, baseline, fish 39C8

description:
Library name: 3A3_39C8
3'TagSeq


title: right brain, Day 10, open-field, fish 20E8

description:
Library name: 3A6_20E8
3'TagSeq


title: left brain, Day 10, open-field, fish 31E5

description:
Library name: 3F2_31E5
3'TagSeq


title: right brain, Day 0, open-field, fish 04E8

description:
Library name: 3H2_04E8
3'TagSeq


title: left brain, Day 0, open-field, fish 25E7

description:
Library name: 3B3_25E7
3'TagSeq


title: right brain, Day 10, open-field, fish 17E8

description:
Library name: 3C2_17E8
3'TagSeq


title: left brain, Day 10, open-field, fish 17E6

description:
Library name: 3B6_17E6
3'TagSeq


title: left brain, Day 10, baseline, fish 27C11

description:
Library name: 3D2_27C11
3'TagSeq


title: right brain, Day 0, baseline, fish 11C6

description:
Library name: 3B2_11C6
3'TagSeq


title: left brain, Day 10, open-field, fish 26E7

description:
Library name: 3C3_26E7
3'TagSeq


title: right brain, Day 0, open-field, fish 40E4

description:
Library name: 3E2_40E4
3'TagSeq


title: right brain, Day 0, baseline, fish 04C6

description:
Library name: 3A2_04C6
3'TagSeq


title: left brain, Day 10, open-field, fish 27E12

description:
Library name: 3H1_27E12
3'TagSeq


title: left brain, Day 10, baseline, fish 26C7

description:
Library name: 3G1_26C7
3'TagSeq


title: left brain, Day 0, baseline, fish 30C10

description:
Library name: 3C1_30C10
3'TagSeq


title: right brain, Day 10, baseline, fish 19C8

description:
Library name: 3E1_19C8
3'TagSeq


title: left brain, Day 0, open-field, fish 32E3

description:
Library name: 3D1_32E3
3'TagSeq


title: right brain, Day 0, open-field, fish 22E2

description:
Library name: 3E3_22E2
3'TagSeq


title: right brain, Day 0, baseline, fish 25C1

description:
Library name: 3F1_25C1
3'TagSeq


title: left brain, Day 10, open-field, fish 35E2

description:
Library name: 3A1_35E2
3'TagSeq


title: right brain, Day 10, baseline, fish 31C8

description:
Library name: 3B1_31C8
3'TagSeq


title: right brain, Day 10, baseline, fish 27C14

description:
Library name: 2A12_27C14
3'TagSeq


title: left brain, Day 0, baseline, fish 40C8

description:
Library name: 2C12_40C8
3'TagSeq


title: right brain, Day 0, open-field, fish 39E7

description:
Library name: 2F11_39E7
3'TagSeq


title: right brain, Day 10, open-field, fish 07E3

description:
Library name: 2G11_07E3
3'TagSeq


title: right brain, Day 10, baseline, fish 20C1

description:
Library name: 2B12_20C1
3'TagSeq


title: left brain, Day 10, open-field, fish 35E6

description:
Library name: 2H11_35E6
3'TagSeq


title: right brain, Day 10, baseline, fish 20C3

description:
Library name: 3G2_20C3
3'TagSeq


title: right brain, Day 10, open-field, fish 17E1

description:
Library name: 2D11_17E1
3'TagSeq


title: left brain, Day 10, open-field, fish 19E3

description:
Library name: 2B11_19E3
3'TagSeq


title: left brain, Day 0, baseline, fish 25C7

description:
Library name: 2A11_25C7
3'TagSeq


title: left brain, Day 0, open-field, fish 04E2

description:
Library name: 2C11_04E2
3'TagSeq


title: left brain, Day 0, open-field, fish 32E1

description:
Library name: 2G10_32E1
3'TagSeq


title: left brain, Day 0, open-field, fish 30E10

description:
Library name: 2H10_30E10
3'TagSeq


title: right brain, Day 10, baseline, fish 35C3

description:
Library name: 2E10_35C3
3'TagSeq


title: right brain, Day 10, baseline, fish 07C1

description:
Library name: 2F10_07C1
3'TagSeq


title: right brain, Day 0, baseline, fish 30C9

description:
Library name: 2D10_30C9
3'TagSeq


title: left brain, Day 0, baseline, fish 39C2

description:
Library name: 2B10_39C2
3'TagSeq


title: right brain, Day 10, open-field, fish 31E3

description:
Library name: 2A10_31E3
3'TagSeq


title: left brain, Day 10, open-field, fish 20E7

description:
Library name: 2G9_20E7
3'TagSeq


title: left brain, Day 0, baseline, fish 04C2

description:
Library name: 2H9_04C2
3'TagSeq


title: right brain, Day 0, open-field, fish 30E7

description:
Library name: 2F9_30E7
3'TagSeq


title: left brain, Day 10, baseline, fish 35C2

description:
Library name: 2C9_35C2
3'TagSeq


title: right brain, Day 10, open-field, fish 27E14

description:
Library name: 2B9_27E14
3'TagSeq


title: right brain, Day 10, open-field, fish 20E6

description:
Library name: 2E9_20E6
3'TagSeq


title: left brain, Day 10, open-field, fish 26E4

description:
Library name: 2H8_26E4
3'TagSeq


title: left brain, Day 0, open-field, fish 11E2

description:
Library name: 2D8_11E2
3'TagSeq


title: left brain, Day 0, baseline, fish 22C8

description:
Library name: 2A8_22C8
3'TagSeq


title: right brain, Day 10, open-field, fish 19E1

description:
Library name: 2A9_19E1
3'TagSeq


title: left brain, Day 0, baseline, fish 30C8

description:
Library name: 2B8_30C8
3'TagSeq


title: left brain, Day 10, open-field, fish 07E2

description:
Library name: 2E8_07E2
3'TagSeq


title: right brain, Day 0, baseline, fish 39C1

description:
Library name: 2D9_39C1
3'TagSeq


title: right brain, Day 10, baseline, fish 26C1

description:
Library name: 2H7_26C1
3'TagSeq


title: right brain, Day 10, baseline, fish 31C1

description:
Library name: 2E11_31C1
3'TagSeq


title: right brain, Day 10, baseline, fish 17C8

description:
Library name: 2C8_17C8
3'TagSeq


title: right brain, Day 10, open-field, fish 27E10

description:
Library name: 2C10_27E10
3'TagSeq


title: left brain, Day 10, baseline, fish 31C5

description:
Library name: 2G7_31C5
3'TagSeq


title: left brain, Day 10, baseline, fish 19C5

description:
Library name: 2E7_19C5
3'TagSeq


title: right brain, Day 0, open-field, fish 22E7

description:
Library name: 2D7_22E7
3'TagSeq


title: left brain, Day 10, baseline, fish 07C8

description:
Library name: 2G6_07C8
3'TagSeq


title: right brain, Day 10, open-field, fish 35E5

description:
Library name: 2F6_35E5
3'TagSeq


title: left brain, Day 10, open-field, fish 17E7

description:
Library name: 2B7_17E7
3'TagSeq


title: left brain, Day 10, baseline, fish 07C4

description:
Library name: 2F7_07C4
3'TagSeq


title: right brain, Day 0, baseline, fish 32C4

description:
Library name: 2E6_32C4
3'TagSeq


title: right brain, Day 0, baseline, fish 40C7

description:
Library name: 2C7_40C7
3'TagSeq


title: left brain, Day 0, open-field, fish 39E8

description:
Library name: 2D6_39E8
3'TagSeq


title: left brain, Day 10, open-field, fish 31E2

description:
Library name: 2A7_31E2
3'TagSeq


title: right brain, Day 10, open-field, fish 17E2

description:
Library name: 2C6_17E2
3'TagSeq


title: right brain, Day 0, baseline, fish 11C7

description:
Library name: 2G8_11C7
3'TagSeq


title: right brain, Day 0, baseline, fish 30C7

description:
Library name: 2A6_30C7
3'TagSeq


title: left brain, Day 0, baseline, fish 04C7

description:
Library name: 2H6_04C7
3'TagSeq


title: left brain, Day 0, baseline, fish 11C3

description:
Library name: 2G5_11C3
3'TagSeq


title: left brain, Day 10, baseline, fish 20C5

description:
Library name: 2F8_20C5
3'TagSeq


title: left brain, Day 0, baseline, fish 22C3

description:
Library name: 2H5_22C3
3'TagSeq


title: left brain, Day 0, open-field, fish 30E8

description:
Library name: 2F5_30E8
3'TagSeq


title: right brain, Day 10, baseline, fish 27C10

description:
Library name: 2E5_27C10
3'TagSeq


title: left brain, Day 0, open-field, fish 40E1

description:
Library name: 2G4_40E1
3'TagSeq


title: right brain, Day 0, open-field, fish 32E7

description:
Library name: 2C5_32E7
3'TagSeq


title: left brain, Day 0, open-field, fish 25E2

description:
Library name: 2H4_25E2
3'TagSeq


title: left brain, Day 10, open-field, fish 19E5

description:
Library name: 2B4_19E5
3'TagSeq


title: right brain, Day 10, baseline, fish 35C5

description:
Library name: 2B5_35C5
3'TagSeq


title: right brain, Day 0, open-field, fish 11E7

description:
Library name: 2F4_11E7
3'TagSeq


title: right brain, Day 10, open-field, fish 20E3

description:
Library name: 2G3_20E3
3'TagSeq


title: right brain, Day 10, baseline, fish 27C9

description:
Library name: 2F3_27C9
3'TagSeq


title: right brain, Day 0, baseline, fish 22C4

description:
Library name: 2E3_22C4
3'TagSeq


title: left brain, Day 10, open-field, fish 27E11

description:
Library name: 2D4_27E11
3'TagSeq


title: right brain, Day 0, baseline, fish 04C4

description:
Library name: 2H3_04C4
3'TagSeq


title: right brain, Day 10, baseline, fish 26C3

description:
Library name: 2E4_26C3
3'TagSeq


title: right brain, Day 0, baseline, fish 25C6

description:
Library name: 2D3_25C6
3'TagSeq


title: left brain, Day 0, open-field, fish 22E8

description:
Library name: 2C4_22E8
3'TagSeq


title: left brain, Day 10, baseline, fish 17C7

description:
Library name: 2A4_17C7
3'TagSeq


title: left brain, Day 0, baseline, fish 32C1

description:
Library name: 2C3_32C1
3'TagSeq


title: left brain, Day 10, open-field, fish 31E7

description:
Library name: 2B6_31E7
3'TagSeq


title: left brain, Day 0, baseline, fish 11C5

description:
Library name: 2F2_11C5
3'TagSeq


title: right brain, Day 0, open-field, fish 39E6

description:
Library name: 2A3_39E6
3'TagSeq


title: left brain, Day 0, baseline, fish 40C3

description:
Library name: 2D5_40C3
3'TagSeq


title: right brain, Day 0, open-field, fish 40E5

description:
Library name: 2G2_40E5
3'TagSeq


title: right brain, Day 0, open-field, fish 11E4

description:
Library name: 2B3_11E4
3'TagSeq


title: right brain, Day 0, open-field, fish 25E8

description:
Library name: 2E2_25E8
3'TagSeq


title: right brain, Day 10, baseline, fish 19C1

description:
Library name: 2H2_19C1
3'TagSeq


title: left brain, Day 10, baseline, fish 20C7

description:
Library name: 2D2_20C7
3'TagSeq


title: left brain, Day 10, open-field, fish 35E8

description:
Library name: 2B2_35E8
3'TagSeq


title: right brain, Day 10, baseline, fish 26C8

description:
Library name: 2C2_26C8
3'TagSeq


title: right brain, Day 10, open-field, fish 31E8

description:
Library name: 2G1_31E8
3'TagSeq


title: left brain, Day 10, open-field, fish 17E3

description:
Library name: 2F1_17E3
3'TagSeq


title: left brain, Day 0, open-field, fish 32E8

description:
Library name: 2H1_32E8
3'TagSeq


title: right brain, Day 10, open-field, fish 26E6

description:
Library name: 2A5_26E6
3'TagSeq


title: right brain, Day 0, baseline, fish 39C4

description:
Library name: 2C1_39C4
3'TagSeq


title: right brain, Day 0, open-field, fish 04E1

description:
Library name: 2E1_04E1
3'TagSeq


title: right brain, Day 0, baseline, fish 40C4

description:
Library name: 2A1_40C4
3'TagSeq


title: right brain, Day 10, open-field, fish 27E13

description:
Library name: 2D1_27E13
3'TagSeq


title: right brain, Day 10, open-field, fish 26E3

description:
Library name: 2B1_26E3
3'TagSeq


title: left brain, Day 10, baseline, fish 35C8

description:
Library name: 1C12_35C8
3'TagSeq


title: right brain, Day 10, open-field, fish 19E8

description:
Library name: 1E11_19E8
3'TagSeq


title: left brain, Day 0, open-field, fish 04E3

description:
Library name: 1B12_04E3
3'TagSeq


title: right brain, Day 0, baseline, fish 11C4

description:
Library name: 1A12_11C4
3'TagSeq


title: right brain, Day 10, open-field, fish 31E1

description:
Library name: 1B11_31E1
3'TagSeq


title: right brain, Day 0, baseline, fish 39C7

description:
Library name: 1G11_39C7
3'TagSeq


title: right brain, Day 0, baseline, fish 04C1

description:
Library name: 1C11_04C1
3'TagSeq


title: right brain, Day 0, baseline, fish 40C5

description:
Library name: 1H10_40C5
3'TagSeq


title: left brain, Day 0, open-field, fish 39E5

description:
Library name: 1E10_39E5
3'TagSeq


title: right brain, Day 10, open-field, fish 26E8

description:
Library name: 1F10_26E8
3'TagSeq


title: left brain, Day 0, baseline, fish 25C2

description:
Library name: 1D10_25C2
3'TagSeq


title: left brain, Day 0, baseline, fish 25C4

description:
Library name: 1C10_25C4
3'TagSeq


title: right brain, Day 0, open-field, fish 32E4

description:
Library name: 1A11_32E4
3'TagSeq


title: left brain, Day 0, baseline, fish 22C5

description:
Library name: 1B10_22C5
3'TagSeq


title: left brain, Day 10, baseline, fish 07C6

description:
Library name: 1H9_07C6
3'TagSeq


title: left brain, Day 10, baseline, fish 17C3

description:
Library name: 2A2_17C3
3'TagSeq


title: left brain, Day 10, baseline, fish 31C2

description:
Library name: 1F9_31C2
3'TagSeq


title: left brain, Day 0, open-field, fish 11E8

description:
Library name: 1A10_11E8
3'TagSeq


title: right brain, Day 10, baseline, fish 17C2

description:
Library name: 1E9_17C2
3'TagSeq


title: left brain, Day 0, baseline, fish 32C8

description:
Library name: 1G9_32C8
3'TagSeq


title: right brain, Day 0, open-field, fish 04E4

description:
Library name: 1D9_04E4
3'TagSeq


title: left brain, Day 10, baseline, fish 27C12

description:
Library name: 1F11_27C12
3'TagSeq


title: left brain, Day 0, open-field, fish 40E3

description:
Library name: 1A9_40E3
3'TagSeq


title: right brain, Day 10, open-field, fish 07E5

description:
Library name: 1D11_07E5
3'TagSeq


title: right brain, Day 10, baseline, fish 27C13

description:
Library name: 1H8_27C13
3'TagSeq


title: right brain, Day 10, open-field, fish 07E7

description:
Library name: 1C9_07E7
3'TagSeq


title: right brain, Day 0, open-field, fish 11E1

description:
Library name: 1E8_11E1
3'TagSeq


title: right brain, Day 10, open-field, fish 20E1

description:
Library name: 1F8_20E1
3'TagSeq


title: left brain, Day 0, open-field, fish 22E3

description:
Library name: 1H11_22E3
3'TagSeq


title: right brain, Day 10, baseline, fish 35C1

description:
Library name: 1A8_35C1
3'TagSeq


title: right brain, Day 10, open-field, fish 19E6

description:
Library name: 1B8_19E6
3'TagSeq


title: right brain, Day 0, open-field, fish 30E11

description:
Library name: 1G8_30E11
3'TagSeq


title: left brain, Day 10, baseline, fish 17C6

description:
Library name: 1C8_17C6
3'TagSeq


title: left brain, Day 0, baseline, fish 39C3

description:
Library name: 1H7_39C3
3'TagSeq


title: right brain, Day 0, open-field, fish 25E3

description:
Library name: 1G10_25E3
3'TagSeq


title: right brain, Day 0, baseline, fish 04C8

description:
Library name: 1G7_04C8
3'TagSeq


title: right brain, Day 10, open-field, fish 26E1

description:
Library name: 1D7_26E1
3'TagSeq


title: right brain, Day 10, baseline, fish 31C3

description:
Library name: 1B7_31C3
3'TagSeq


title: right brain, Day 0, baseline, fish 22C7

description:
Library name: 1E7_22C7
3'TagSeq


title: left brain, Day 0, open-field, fish 25E4

description:
Library name: 1A7_25E4
3'TagSeq


title: left brain, Day 10, open-field, fish 31E4

description:
Library name: 1D8_31E4
3'TagSeq


title: left brain, Day 0, baseline, fish 40C1

description:
Library name: 1F7_40C1
3'TagSeq


title: left brain, Day 10, open-field, fish 17E4

description:
Library name: 1C7_17E4
3'TagSeq


title: right brain, Day 0, baseline, fish 11C1

description:
Library name: 1H6_11C1
3'TagSeq


title: right brain, Day 10, baseline, fish 07C7

description:
Library name: 1G6_07C7
3'TagSeq


title: right brain, Day 0, baseline, fish 22C2

description:
Library name: 1E6_22C2
3'TagSeq


title: left brain, Day 10, baseline, fish 26C5

description:
Library name: 1B9_26C5
3'TagSeq


title: left brain, Day 0, open-field, fish 30E6

description:
Library name: 1D6_30E6
3'TagSeq


title: left brain, Day 0, open-field, fish 11E3

description:
Library name: 1C6_11E3
3'TagSeq


title: left brain, Day 10, open-field, fish 20E5

description:
Library name: 1B6_20E5
3'TagSeq


title: right brain, Day 10, baseline, fish 19C6

description:
Library name: 1A6_19C6
3'TagSeq


title: left brain, Day 0, baseline, fish 11C9

description:
Library name: 1E5_11C9
3'TagSeq


title: left brain, Day 10, open-field, fish 19E2

description:
Library name: 1G5_19E2
3'TagSeq


title: right brain, Day 10, baseline, fish 20C6

description:
Library name: 1F5_20C6
3'TagSeq


title: right brain, Day 0, open-field, fish 22E1

description:
Library name: 1C5_22E1
3'TagSeq


title: left brain, Day 0, baseline, fish 04C3

description:
Library name: 1D5_04C3
3'TagSeq


title: right brain, Day 0, baseline, fish 39C6

description:
Library name: 1A5_39C6
3'TagSeq


title: left brain, Day 0, baseline, fish 40C6

description:
Library name: 1H4_40C6
3'TagSeq


title: left brain, Day 10, open-field, fish 07E4

description:
Library name: 1B5_07E4
3'TagSeq


title: right brain, Day 10, baseline, fish 35C7

description:
Library name: 1F4_35C7
3'TagSeq


title: right brain, Day 10, baseline, fish 07C3

description:
Library name: 1G3_07C3
3'TagSeq


title: right brain, Day 0, open-field, fish 40E7

description:
Library name: 1E4_40E7
3'TagSeq


title: left brain, Day 10, baseline, fish 26C2

description:
Library name: 1C4_26C2
3'TagSeq


title: left brain, Day 0, open-field, fish 39E2

description:
Library name: 1D4_39E2
3'TagSeq


title: right brain, Day 10, baseline, fish 17C1

description:
Library name: 1B4_17C1
3'TagSeq


title: right brain, Day 0, open-field, fish 32E2

description:
Library name: 1F6_32E2
3'TagSeq


title: left brain, Day 0, baseline, fish 30C12

description:
Library name: 1A4_30C12
3'TagSeq


title: left brain, Day 0, baseline, fish 04C5

description:
Library name: 1C3_04C5
3'TagSeq


title: left brain, Day 10, open-field, fish 07E6

description:
Library name: 1H3_07E6
3'TagSeq


title: left brain, Day 10, baseline, fish 19C7

description:
Library name: 1F3_19C7
3'TagSeq


title: left brain, Day 0, open-field, fish 39E3

description:
Library name: 1B3_39E3
3'TagSeq


title: left brain, Day 0, open-field, fish 22E5

description:
Library name: 1H2_22E5
3'TagSeq


title: left brain, Day 0, open-field, fish 04E5

description:
Library name: 1E2_04E5
3'TagSeq


title: left brain, Day 0, baseline, fish 30C6

description:
Library name: 1A3_30C6
3'TagSeq


title: left brain, Day 0, baseline, fish 39C5

description:
Library name: 1G2_39C5
3'TagSeq


title: right brain, Day 10, open-field, fish 35E1

description:
Library name: 1F2_35E1
3'TagSeq


title: right brain, Day 10, baseline, fish 20C8

description:
Library name: 1D2_20C8
3'TagSeq


title: left brain, Day 10, baseline, fish 26C4

description:
Library name: 1C2_26C4
3'TagSeq


title: left brain, Day 0, baseline, fish 25C5

description:
Library name: 1B2_25C5
3'TagSeq


title: left brain, Day 0, open-field, fish 40E8

description:
Library name: 1A2_40E8
3'TagSeq


title: right brain, Day 0, baseline, fish 32C2

description:
Library name: 1G1_32C2
3'TagSeq


title: left brain, Day 10, open-field, fish 35E4

description:
Library name: 1H5_35E4
3'TagSeq


title: left brain, Day 0, open-field, fish 11E9

description:
Library name: 1F1_11E9
3'TagSeq


title: right brain, Day 0, open-field, fish 30E5

description:
Library name: 1H1_30E5
3'TagSeq


title: right brain, Day 0, baseline, fish 25C8

description:
Library name: 1G4_25C8
3'TagSeq


title: left brain, Day 10, open-field, fish 07E8

description:
Library name: 1D1_07E8
3'TagSeq


title: right brain, Day 10, open-field, fish 17E5

description:
Library name: 1E3_17E5
3'TagSeq


title: right brain, Day 0, open-field, fish 25E6

description:
Library name: 1D3_25E6
3'TagSeq


title: left brain, Day 0, baseline, fish 22C6

description:
Library name: 1C1_22C6
3'TagSeq


title: left brain, Day 10, open-field, fish 19E7

description:
Library name: 1E1_19E7
3'TagSeq


title: left brain, Day 10, baseline, fish 35C4

description:
Library name: 1A1_35C4
3'TagSeq


title: Non-transfected T cells stimulated with CD22 protein coated beads for 4 hours replicate3

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description: Library name: 4hrCD22BstiNTF_Rep3

data_processing:
RNA sequencing reads were aligned to hg19 build of human genome using STAR-2.5.2a
The aligned reads were quantified using feature counts function from the Subread package
Merged counts for all the samples are normalized and analyzed using R package DESeq2 for identifying differentially expressed genes between groups of interest
Assembly: hg19
Supplementary files format and content: Merged counts file
Supplementary files format and content: Normalized counts file

source_name: Primary Human T cells

growth_protocol: Primary human T cells were activated with anti-CD3/28 coated beads, transduced with either CD19.BBζ, CD19.28ζ, or both vectors, and expanded for 7-9 days to generate CARTs

extract_protocol:
non-transfected (NTF), CD19.BBζ-CD19.28ζ, CD19.BBζ and CD19.28ζ CAR T cells after incubation with CD19 protein coated beads, CD22.BBζ-CD22.28ζ, CD22.BBζ and CD22.28ζ CAR T cells after CD22 protein coated beads , and STD CD19.BBζ-CD19.28ζ, MTDs CD19.28ζ-CD22.BBζ and CD19.BBζ-CD22.28ζ after CD19&CD22 protein coated beads ,All stimulations were for 4 hours
All the replicates for the 4hr stimulated cells were extracted for RNA and libraries were created for transcriptional analysis

treatment_protocol: T cells were electroporated with various CAR RNA and one day later CAR T cells were stimulated with CD19 , CD22 ,or CD19&CD22  protein coated beads

value: Primary Human T cells


title: Non-transfected T cells stimulated with CD22 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD22BstiNTF_Rep2


title: CD22.28ζ CAR T cells stimulated with CD22 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD22Bsti110_Rep3


title: CD22.28ζ CAR T cells stimulated with CD22 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD22Bsti110_Rep1


title: CD22.28ζ CAR T cells stimulated with CD22 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD22Bsti110_Rep2


title: CD22.BBζ-CD22.28ζ CAR T cells stimulated with CD22 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD22Bsti109-110_Rep3