title: hairyroot, slwrky71OX, rep2

city: Utrecht

first: Leonardo

last: Jo

email: l.jo@uu.nl, jo.leonardo85@gmail.com

address: Padualaan 8, Z309

department: Institute of Environment Biology

institute: Utrecht University

data_processing:
We quality trimmed paired-end reads using Trim Galore (version 0.6.6) using default settings. After trimming, we pseudo-aligned the paired reads to the tomato reference transcriptome version ITAG4.1 (Sol Genomics, https://solgenomics.net) using Kallisto (version 0.46.2) with the following parameters: -b 100 . Pseudo-counts were then used for differential expression analysis.  All scripts used for the trimming and alignment can be found in https://github.com/leonardojo/tomato-TF-exodermis-2024.
Assembly: ITAG4.1
Supplementary files format and content: TSV file containing gene pseudocounts (row) from each individual sample (column)

organism: Solanum lycopersicum

source_name: hairy-roots

growth_protocol: We subcultured the hairy roots of lines of the control (empty vector), 35S::MYB41-3xFLAG (SlMYB41-OX), 35S::MYB92-3xFLAG (SlMYB92-OX), 35S::WRKY71-3xFLAG (SlWRKY71-OX), Slmyb41-ko, Slmyb92-ko, Slwrky71-ko(4), and Slwrky71-ko(5) on sterile square Petri dishes (120x120x17 mm, Greiner Bio One) on MS medium (Duchefa Biochemie) supplemented with 3% sucrose, 200 mg/L cefotaxime sodium (Duchefa Biochemie), 1% BD Difco agar (Fisher Scientific), 0.5 g/L MES hydrate (Thermo Fisher Scientific) and grew them at 25°C in the dark. After 9 days of growth, we collected the first cm of 10 root tips for each of the four biological replicates per line and snap-froze them in liquid nitrogen. The samples were collected in 2-ml tubes containing ceramic beads and ground using a tissuelyser (Retsch MM300). The mRNA extraction and library preparation were performed according to the non-strand specific random primer-primed RNAseq library protocol of Townsley et al. (2015). The libraries were pair-end sequenced (75 bp) at Utrecht Sequencing Facility (Utrecht, The Netherlands) using Illumina NextSeq2000.

extract_protocol:
Tissue samples were ground with a tissuelyzer and immediately incubated in 400 μL lysis buffer (LBB: 100 mM Tris-HCl, 1000 mM LiCl, 10 mM EDTA, 1% SDS, 5 mM DTT, Antifoam A) supplemented with 5 μl/ml β-mercaptoethanol before use. The tubes were beat 2 times for 1min at 30 Hz. The samples were incubated at room temperature for 10 min and spun down at 13,000 rpm for 10 min. One uL of 12.5 μM biotin-20nt-dT oligo was mixed into 200 μL of lysate in PCR tubes and incubated  at room temperature for 10 min. Then, we added 20 μL Biolabs® streptavidin magnetic beads per reaction for incubation and left on agitation for 10 min. The mRNA from samples binds the oligo through the polyA tail, and the biotin in the oligo binds the streptavidin on the beads. This allows pulling down only the mRNA and washing the rest of the material off. So, the samples were separated into magnetic bead-bound mRNA and supernatant by 96 well Magwell® magnetic separator. The bead pellets were washed with 200 μl washing buffer series: washing buffer A (WBA; 10 mM Tris-HCl, 150 mM LiCl, 1 mM EDTA, 0.1% SDS), washing buffer B (WBB; 10 mM Tris-HCl, 150 mM LiCl, 1mM EDTA), and low salt buffer LSB (20 mM Tris-HCl,150 mM NaCl, 1 mM EDTA). The mRNA was eluted in 16 uL Tris-HCl with 80°C. These pulldown and washing steps were repeated a second time to remove non-specifically associating rRNA from the samples.
RNA fragmentation was carried out by preparing 10 μL mixtures of 1.5 μl 5X Thermo Scientific RT buffer, 0.5 μl Invitrogen random primers, 8 μl mRNA from the above elution. The mixtures were put into thermocycler for temperature-induced fragmentation and priming of 1st strand of cDNA (25°C 1 sec, 94°C 1.5 min, 4°C 5 min, 4°C hold). We prepared first strand cDNA synthesis master mixture as following: 1.5 μL 5X Thermo Scientific RT buffer, 1.5 μL 0.1 M DTT, 1 μL H2O, 0.5 μL 25 mM dNTPs, 0.5 μL RevertAid H minus reverse transcriptase enzyme (Thermo Fisher Scientific). The mixture was added onto the samples and incubated in thermocycler: 25°C 10 min, 42°C 50 min, 50°C 10 min, 70°C 10 min, 4°C hold. The second strand synthesis, end repair, and A-tailing were performed by adding a 5 μL mixture to the first strand, consisting of 1.5 μL H2O, 0.4 μL 25 mM dNTPs, 1 μL DNA polymerase I (Thermo Fisher Scientific), 0.1 μL RNaseH (NEB), 0.4 μL NEBNext® End Repair Module enzyme mix, 0.2 μL Taq, and 1.4 μL End Repair buffer. This mixture was incubated in a thermocycler following these temperature and time settings: 16°C for 20 min, 20°C for 20 min, 72°C for 20 min, and held at 4°C. Subsequently, the reaction mixture was left at room temperature for 5 minutes with a mix of Beckman® Ampure XP beads at 1.5 times the volume, followed by two washes with 200 μL of 80% ethanol each, until the beads were completely dry. Adapter ligation: the dry beads were mixed with 3 ul of annealed 1 μM universal adapter primers (8 μL of 100 μM each primer was combined with 784 μL of H2O and cooled through the program: 94°C 1 min, (94°C 10 sec) * 60 cycles -1°C /cycle, 20°C 1 min, 4°C hold). Then, 7 μL ligase mixture (5 μL 2X Rapid T4 ligation buffer, 0.25 μL Biolabs® DNA ligase, 1.75 ul H2O) was added and left for 15 min at room temperature. We added 10 μL of 50 mM EDTA and 25 μL Ampure XP Bead Resuspension buffer (15% PEG 8000, 2.5 M NaCl) to each sample, washed with 80% EtOH twice, and eluted the ligated DNA fragments with 20-22 μL 10 mM Tris. After 2 min incubation, we magnetized and transferred the supernatant into fresh tubes. We used 10 μl of cDNA into enrichment mixed containing4 μL 5X Phusion HF buffer (Thermo Fisher Scientific),2.6 μL H2O, 1 μL 2 μM PE1 primer, 1 μl 8 μM each EnrichS1 + S2 primers, 0.2 μl 25 mM dNTPs, and 0.2 μl Phusion Polymerase (Thermo Fisher Scientific). For each sample we used 1 μl of appropriate unique indexed enrichment oligo (Townsley et al., 2015). The mixture was heated in thermocycler with the following program: 98°C 30 sec, (98°C 10 sec, 65°C 30 sec, 72°C 30 sec) *15 cycles, 72°C 5 min, 10°C hold. We cleaned the enriched libraries according to Bailey-Serres lab protocol: 1.1 volume of well-resuspended Ampure beads are mixed well with the samples, followed by washing twice by 200 μl of 80% EtOH and resuspending in 10 μl 10 mM Tris pH 8.0. One μl of the samples were used for quality check by Bioanalyzer High Sensitivity DNA Analysis kit, and we selected cleaned library of 200-350 bps based on the peaks. Libraries were pooled together for sequencing with the same target concentration. A final clean-up was done with 0.8 volumes of Ampure beads and elution to the final target volume.

value: hairy-roots

value: slwrky71 overexpression


title: hairyroot, slwrky71OX, rep3

status: Public on Feb 25 2025

type: SRA

country: Netherlands

library_source: transcriptomic

molecule: polyA RNA

tag: tissue

tag: genotype


title: SSC AgingFX32yo

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

state: California

address: 2700 Stockton Blvd

country: USA

institute: UC Davis

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

library_source: transcriptomic single cell

data_processing:
demultiplexing using bcl2fastq2 2.18 (Illumina)
raw reads were further processed using skewer11 for 3′ quality-trimming, 3′ adaptor-trimming, and removal of degenerate reads (Jiang et al., 2014).
trimmed reads were then mapped to the human genome GRCh38.p13 using STAR 2.4 (Dobin et al., 2013)
When aligning female data the entire Y chromosome was masked, while only the PAR regions on the Y chromosome were masked for male data. If sex was unknown PAR-masking was used.
counts for gene and transcript reads were calculated using RSEM 1.2.21 (Li and Dewey, 2011)
Assembly: hg38
Supplementary files format and content: RSM_gRDS_hSSC.csv = raw gene counts
Supplementary files format and content: Fetal.h5ad = raw gene counts for fetal hSSC analysis
Supplementary files format and content: LineageTree.h5ad = raw gene counts for fetal hSSC lineage tree analysis
Supplementary files format and content: GPPE.h5ad = raw gene counts for growth plate versus periosteal hSSC analysis
Supplementary files format and content: Aging.h5ad = raw gene counts for patient hSSC analysis

molecule: total RNA

organism: Homo sapiens

source_name: Fracture

growth_protocol: freshly purified cells without prior in vitro culture

extract_protocol:
Bone tissue with mechanically and enzymatically digested, stained with antibodies, and cell populations purified via FACS.
SmartSeq2 pipeline (Picelli et al.)
SmartSeq2 single cell RNA sequencing

treatment_protocol: no treatment

tag: cell type

value: SSC

value: Fracture

tag: Sex

value: M

tag: age


title: mESC, Nsd1-KO-1, day 0, biol rep 2

city: New York

first: Jie

last: Li

state: New York

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell Medicine

data_processing:
The fastq files were trimmed using trim-galore 0.6.7 and then aligned to mm39 mouse genome using STAR 2.7.11a. Primary aligned, non-duplicated reads were supplied to featureCounts 2.0.6 for counting read fragments aligned to exons. Raw gene expression counts were further processed with DESeq2 1.42.0. Low-count genes with an average count < 1 were filtered out before downstream analysis.
Differentially expressed genes were defined with a significance cut off of padj<0.01 and |log2FC|>0.58. PCA clustering was performed on VST normalized expression values for top 500 most variable genes. MA plots were generated using the shrunken log2 fold changes, which removed noises associated with low-count genes.
Fuzzy c-means clustering was performed to assign genes to distinct clusters displaying differential gene expression trajectories along differentiation.
Gene Set Enrichment Analysis (GSEA) with H/C2/C5 gene set collections and Gene Ontology (GO) pathway enrichment analysis with the Biological Process annotations was done using the R package clusterProfiler 4.10.0 using a significance cut off of BH-adjusted p values<0.01.
Assembly: mm39
Supplementary files format and content: VST normalized count table

organism: Mus musculus

source_name: mouse blastocyst

growth_protocol: E14 mouse ES cells were cultured in DMEM supplemented with 15% heat-inactivated FBS, 1% NEAA (nonessential amino acids), 0.1mM β-mercaptoethanol, 1% antibiotics, and 1000 U/mL recombinant mouse LIF (leukemia inhibitory factor, Sigma: ESG1107) on top of mitotically inactivated mouse embryonic fibroblast (MEF, Thermo Fisher: A34963) feeder layer in TC-treated dish or plate pre-coated by 0.1% gelatin.

extract_protocol:
Total RNAs were extracted using RNeasy Plus kit (Qiagen: 74136), followed by removal of residual DNAs using Turbo DNA-free kit (Thermo Fisher: AM1907) to ensure purity of RNA sample.
RNA-seq libraries were prepared using TruSeq RNA Library Prep Kit v2 following the kit's protocol.

treatment_protocol: LIF and MEF were removed to induce mESC in vitro differentiation

value: mouse blastocyst

tag: developmental stage

value: mouse embryonic stem cell

tag: treatment

value: LIF and MEF withdrawal

tag: time point

value: 0 day


title: hairyroot, slwrky71OX, rep1


title: MS-5

city: Nan Jing

first: Yizhou

last: Hong

state: Jiang Su

address: No. 639, Longmian Avenue, Jiangning District, Nanjing City

country: China

institute: China Pharmaceutical University

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters。
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using Featurecounts
Assembly: mm10 (mouse)
Supplementary files format and content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: BNST

growth_protocol: The mice were maintained under specific pathogen-free (SPF) conditions at the Center for New Drug Safety Evaluation and Research, China Pharmaceutical University.

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen) and prepared into cDNA library according to the standard Illumina RNA-seq instruction.
The cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq2500 by a 2X150 bp run.

treatment_protocol: Chronic restraint stress (CRS)-induced mouse model of anxiety was established.

value: BNST

value: Male

value: Susceptible


title: SSC AgingFX30yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

value: F


title: mESC, WT, day 0, biol rep 2

value: WT


title: MS-3


title: MS-4


title: hairyroot, slwrky71ko5, rep3

value: slwrky71 knockout line 5


title: SSC AgingFX27yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad


title: hairyroot, slwrky71ko5, rep2


title: MS-2


title: SSC AgingFX28yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad


title: MS-1


title: hairyroot, slwrky71ko4, rep3

value: slwrky71 knockout line 4


title: Leukemic spleen, TMX11, H3K4me3

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm39 genome using bwa version 0.7.17. Only uniquely mapping reads with at most two mismatches were retained. In addition, duplicate reads (“PCR duplicates”) were removed using BAMtools (v2.5.2) and Samtools (v1.17).
Peaks were called uing MACS2 v2.7.1 with the significance cut-off q-value <=0.01
Differential peak analysis was performed using edgeR (v 4.20)
bigWig files were generated using deepTools (v 3.5.1).
Assembly: mm39
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Leukemic spleen

growth_protocol: Acly conditional knockout T-ALLs were injected intravenously in sub-lethally Irradiated mice.

extract_protocol:
Leukemic spleens were removed, single-cell suspensions were obtained by pressing them through a 40mm filter, and subsequently subjected to red blood cell lysis. Pellets of 25 million cells were formaldehyde-crosslinked and frozen prior to shipment to Active Motif.
ChIP-seq libraries were obtained using Active Motif-validated antibodies, and subsequently prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were allowed to become overtly leukemic and then treated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection, and leukemic spleens were collected 72h later.

value: Leukemic spleen

value: Leukemic splenocytes

value: Acly-deleted

tag: chip antibody


title: Leukemic spleen, Pooled Input


title: FS-4

value: Female


title: hairyroot, slwrky71ko5, rep1

value: hairy-roots


title: SSC AgingFX18yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

value: SSC

value: Fracture


title: FS-5


title: hairyroot, slwrky71ko4, rep2


title: Leukemic spleen, VEH4, H3K4me3

value: Acly-WT


title: hairyroot, slwrky71ko4, rep1


title: SSC AgingFibrousDysplasia

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

source_name: FD

value: FD


title: SSC AgingPeriost

description:
SmartSeq2
RSM_gRDS_hSSC.csv
GPPE.h5ad

source_name: PeriosteumAdult

value: PeriosteumAdult

value: M


title: hairyroot, slmyb92OX, rep3

value: slmyb92 overexpression


title: FS-3

value: BNST

value: Susceptible


title: SSC FetalPeriost

description:
SmartSeq2
RSM_gRDS_hSSC.csv
GPPE.h5ad

source_name: Periosteum

value: Periosteum

value: not provided

value: fetal


title: mESC, Nsd1-KO-1, day 0, biol rep 1

value: mouse blastocyst

value: mouse embryonic stem cell

value: LIF and MEF withdrawal

value: 0 day


title: FS-2

value: Female


title: Leukemic spleen, VEH4, H3K9Ac

value: Leukemic spleen

value: Leukemic splenocytes


title: mESC, WT, day 0, biol rep 1

value: WT


title: hairyroot, slmyb92OX, rep1

value: hairy-roots


title: SSC FetalTibiaFemur

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Fetal.h5ad

source_name: Tibia Femur

value: SSC

value: Tibia Femur


title: SSC AgingFX25yo

description:
SmartSeq2
RSM_gRDS_hSSC.csv
Aging.h5ad

value: Fracture

value: M


title: NonunionTissue

description:
10x Genomics
NovaSeq6000 partial lane

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: GRCh38.p13
Supplementary files format and content: feature matrix .h5 file and Scanpy python processing notebook
Supplementary files format and content: 10X_Nonunion.h5
Supplementary files format and content: 10X_Nonunion.ipynb

source_name: Nonunion bone tissue

extract_protocol:
Nonunion tissue was mechanically and enzymatically digested, stained with antibodies, and living non-hematopoietic populations purified via FACS. cDNA was prepared according to 10X Genomics manufacturer instructions for 3' v3.1.
10X Genomics

treatment_protocol:
n/a
n/a

value: Nonunion bone tissue

value: 63 years


title: Leukemic spleen, TMX11, H3K27Ac

value: Acly-deleted


title: hairyroot, slmyb92OX, rep2

value: slmyb92 overexpression


title: FS-1

value: BNST

value: Susceptible


title: MC-5

value: Male

value: Control


title: PE_tissue10X

description:
10x Genomics
NovaSeq6000 partial lane

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: GRCh38.p13
Supplementary files format and content: feature matrix .h5 file and Scanpy python processing notebook
Supplementary files format and content: GP.h5
Supplementary files format and content: Barcode_GP.ipynb
Supplementary files format and content: PE.h5
Supplementary files format and content: Barcode_PE.ipynb

source_name: Periosteum long bone

extract_protocol:
Graft tissue generated by skeletal stem cells was mechanically and enzymatically digested, stained with antibodies, and living Venus-expressing populations purified via FACS. cDNA was prepared according to 10X Genomics manufacturer instructions for 3' v3.1.
25% (10ul) of cDNA was used for standard 10X Genomics library preparation protocol. Another 25% was used for clonal barcode amplification. The extra 10 µL of cDNA were amplified using a combination of Partial Read 1 primer  (5’-CTACACGACGCTCTTCCGATCT-3’) and an adaptor-FBP1 (Read 2 primer + barcode recognition site) primer (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCGACCACCGAACGCAACGCACGCA-3’). Barcode amplification was run as recommended for cDNA reaction (10X protocol step 2.2) plus 4 extra cycles. From there the product was handled as per standard protocol starting from the index primer reaction without any fragmentation or ligation steps.

value: skeletal stem cells

value: Periosteum long bone

value: 17 weeks gestation


title: hairyroot, slmyb92ko, rep3

value: slmyb92 knockout


title: hairyroot, slmyb92ko, rep2

value: hairy-roots


title: MC-2


title: MC-3


title: GP_tissue10X

description:
10x Genomics
NovaSeq6000 partial lane

source_name: Growth plate long bone

value: Growth plate long bone


title: Leukemic spleen, TMX11, H3K9Ac

value: Leukemic spleen

value: Leukemic splenocytes


title: Spaceflight immunized mouse 3 - F40

city: Loma Linda

first: Lorelei

last: Hughes

state: CA

address: 11021 Campus

department: Pathology and Human Anatomy

institute: Loma Linda University

data_processing:
Cutadapt and perl scripts in house were used to remove reads with adaptor contamination, low quality bases and undetermined bases
sequence quality verified using FastQC
HISAT2 was used to map the reads
StringTie was used to assemble mapped reads
StringTie and Ballgown were used to estimate expression levels of transcripts
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: heart

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method

value: heart

tag: cell line

value: female

value: 14 weeks

value: Spaceflight Immunized - replicate 3

value: 5 Weeks


title: Spaceflight immunized mouse 2 - F29

value: Spaceflight Immunized - replicate 2


title: MC-4

value: BNST


title: Spaceflight immunized mouse 1 - F28

value: Spaceflight Immunized - replicate 1


title: hairyroot, slmyb41OX, rep3

value: slmyb41 overexpression


title: hairyroot, slmyb92ko, rep1


title: MC-1

value: Male

value: Control


title: H1N1_VDJ

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

country: Germany

institute: Universitätsklinikum Erlangen

description: 10x Genomics

data_processing:
Data was normalized using size factors using DESeq2 and scaled with Scanpy’s log1p function. Scirpy was employed for the analysis of the TCR data.
Both the AD and H1N1 sample contain a pool of 4 different mice. Every hash of the CSP is associated with one mouse per sample. The same hashes are used in both the AD and H1N1 samples, but they are different mice.
Assembly: mm10
Supplementary files format and content: comma separated values format (csv)

source_name: lung

extract_protocol:
Lymphocytes were isolated from lung tissue. First, lungs were cut into small pieces and enzymatically digested in collagenase D (250 U/ml) and DNase I (80 U/ml) diluted in 2 ml R10 medium (RPMI 1640 supplemented with 10 % FCS, 2 mM L-Glutamine, 10 mM HEPES, 50 µM β-mercaptoethanol and 1 % penicillin/streptomycin) for 45 min at 37 °C. Disaggregated lung tissues were passed through 70-μm cell strainers and red blood cells were lysed by resuspension in ammonium-chloride-potassium. Isolated lymphocytes were directly stained in PBS containing 0.5 % BSA and 1mM NaN3.
Library was performed to the manufacter's instruction (Chromium Next GEM Chip K Single Cell Kit, Chromium Next GEM Single-Cell 5′ Kit v2 Kit, Dual Index Kit TT Set A, 5’ Feature Barcode Kit, Chromium Single-Cell Mouse TCR Amplification Kit (all 10x Genomics, CA, USA)). Briefly, for each group, 2x105 barcoded NP147-155-specific CD8+ T cells were sorted. Samples were centrifuged, resuspended, and a master-mix containing RT Reagent B, Poly-dt RT Primer, and RT Enzyme C was added (Chromium Next GEM Single Cell 5’ Reagent Kits v2, 10x Genomics). This master-mix and cell suspension mixture was loaded into Chromium Chip K (10x Genomics) and partitioned into Gel Beads In-Emulsions (GEMs) in a chromium controller (10x Genomics). ScRNA libraries as well as those for scTCR-sequencing were prepared according to the Chromium Next GEM Chip K Single Cell Kit, the Chromium Next GEM Single-Cell 5′ Kit v2 Kit, the Dual Index Kit TT Set A, the 5’ Feature Barcode Kit, and the Chromium Single-Cell Mouse TCR Amplification Kit (all 10x Genomics, CA, USA). The single-cell RNA-seq (scRNA-seq) and VDJ libraries were sequenced by Novogene UK.

value: lung

value: Memory T-cells

value: lymphocytes

value: WT

value: intranasal H1N1 infection

tag: library type

value: VDJ


title: hairyroot, slmyb41OX, rep2

value: hairy-roots


title: hairyroot, slmyb41OX, rep1


title: FC-4

value: Female


title: H1N1_GEX

description: 10x Genomics

value: GEX


title: hairyroot, slmyb41ko, rep3

value: slmyb41 knockout


title: FC-3


title: Leukemic spleen, VEH4, H3K27Ac

value: Leukemic spleen

value: Leukemic splenocytes

value: Acly-WT


title: rAd_VDJ

description: 10x Genomics

value: intranasal adenoviral immunization


title: hairyroot, slmyb41ko, rep1


title: FC-2

value: BNST


title: rAd_CSP

description: 10x Genomics

value: CSP


title: sod2_Day8_3

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

description: Library name: Sample 11

data_processing:
Adaptor sequences and low quality score bases (Phred score < 30) were first trimmed using Trimmomatic (Bolger et al., 2014). The resulting reads were aligned to the WBcel235 assembly of the C. elegans reference genome, using STAR (Dobin et al., 2012). Read counts were obtained using HTSeq (Anders et al 2015) with parameters -m intersection-nonempty -stranded=reverse.
Assembly: Caenorhabditis elegans WBcel235
Supplementary files format and content: Tab-separated count values

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: NGM plates, 20 degrees Celsius, OP50 bacteria

extract_protocol:
Trizol
polyA enriched RNA library Illumina

value: Whole worm

value: All

tag: batch


title: FC-1

value: Control


title: rAd_GEX

description: 10x Genomics

value: lung

value: Memory T-cells

value: lymphocytes


title: hairyroot, control, rep2

value: Control (empty vector)


title: H1N1_CSP

description: 10x Genomics

value: WT

value: intranasal H1N1 infection


title: T_2

city: St. Louis

first: Hao

last: Chen

state: MO

address: 4370 Duncan Ave

institute: Washington University School of Medicine in St. Louis

data_processing:
For gene-level analysis, RNA-seq reads were then aligned to the Ensembl GRCm38.101 primary assembly with STAR version 2.7.9a82.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.383. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.084.
For differential intron splicing analysis, LeafCutter v0.2.9 was run with default parameters unless otherwise specified, following the protocol described in Li et al.34 Briefly, fastq files were aligned to GRCm38 (Ensembl GTF release 102) using the STAR aligner, v2.7.9a, with flag “--outSAMstrandField intronMotif”. The resulting BAM files were sorted and indexed using samtools v1.10. Junctions were extracted using regtools v1.0.0, with minimum intron length set to 50. LeafCutter’s `leafcutter_cluster_regtools.py` script was used (with flag “-m 50”) to identify intron clusters and quantify junction usage.
For differential exon usage analysis, DEXSeq v1.34.1 was used35,36. Exon annotation files were produced using the `dexseq_prepare_annotation.py` script with the "--aggregate no" flag. Fastq files were aligned to GRCm38 (Ensembl GTF release 102) using the STAR aligner, v2.7.9a. Initial count tables were generated using DEXSeq’s ` dexseq_count.py` script.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: gene counts as txt format

source_name: the cerebral cortex

growth_protocol: Mice were aged to postnatal day 18.

extract_protocol:
Total RNA from 5 sex and litter-matched pairs (2 pairs of male mice and 3 pairs of female mice) of P18 cortical tissues of Usp7 WT; Trp53+/- and Usp7 cKO; Trp53+/- mice was extracted with RNeasy Plus Mini Kit (QIAGEN) for RNA-seq analysis.
Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers to ensure complete coverage of gene body. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: Usp7 fl/fl mice were crossed with NEX-cre mice to generate Usp7 conditional knockout specifically in glutamatergic neurons, on a genetic background of Trp53+/-

value: the cerebral cortex

value: female

value: Usp7 cKO; Trp53+/-


title: WT_Day8_3

description: Library name: Sample 8


title: CA3 AAV-shRNA(mef2c) 5

growth_protocol: The male mice were maintained under specific pathogen-free (SPF) conditions at the Center for New Drug Safety Evaluation and Research, China Pharmaceutical University.

treatment_protocol: AAV-shRNA(mef2c) or AAV-shRNA(scramble) was infused into the bilateral CA3 of male or female C57BL/6J mice by stereotaxic injection for Mef2c knockdown in CA3 PyNs

tag: strain

value: Male


title: FC-5

value: Female


title: hairyroot, slmyb41ko, rep2

value: hairy-roots

value: slmyb41 knockout


title: sod2_Day8_1

description: Library name: Sample 9


title: hairyroot, control, rep1


title: WT_Day8_2

description: Library name: Sample 7


title: AB5075_control_3

city: Uxbridge

first: Ronan

last: McCarthy

address: Kingston Ln

country: United Kingdom

institute: Brunel University London

description: 37 C, 180 rpm, grown to mid- exponential phase (OD600 0.6 approx.)

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl2fastq (2.20.0.422)
Read mapping was performed with HISAT
Differential expression analysis was performed using R package DESeq.
Read quantification was performed using Subread’s featureCounts functionality.
Read counts were normalized and p values generated using DESeq.
Assembly: NZ_CP008706.1
Supplementary files format and content: Matrix table (tab-delimited file) with raw gene counts for every gene and every sample
Supplementary files format and content: Individual tab-delimited files with normalize counts.

organism: Acinetobacter baumannii AB5075

source_name: mid-exponential phase culture

growth_protocol: A. baumannii AB5075 (6 independent replicates) was inoculated from a pure VIR-O type stock and incubated overnight in LB (37 C, 180 rpm). Then, cultures were diluted in LB (suplemented with 1% saccharin or with a mock treatment) to OD600 0.05 and incubated at 37 C, 180 rpm until reaching mid-exponential phase (OD600 0.6 approx.).

extract_protocol:
Cultures were harvested by centrifugation and washed in RNAlater to preserve RNA integrity. RNA was isolated using athe Qiagen RNAeasy Kit with on-column DNAase digestion (Qiagen). RNA quality was assessed using a Bioanalyzer.
Samples were additionally treated with RNAse-free DNAse (Invitrogen). cDNA library was prepared with Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

treatment_protocol: The treatment (1% saccharin or a water control) was applied as a supplement in the LB medium and was present since the beginning of the growth.

value: mid-exponential phase culture

value: water control


title: CA3 AAV-shRNA(mef2c) 4


title: R4_3


title: R4_2

value: Usp7 WT; Trp53+/-


title: CA3 AAV-shRNA(mef2c) 2


title: R5_3

value: male


title: sod2_Day8_2

description: Library name: Sample 10

value: Whole worm

value: All


title: CA3 AAV-shRNA(mef2c) 1


title: AB5075_control_2


title: WT_Day8_1

description: Library name: Sample 6


title: AB5075_control_1


title: R5_2


title: CA3 AAV-shRNA(scramble) 5

value: AAV-shRNA(scramble)


title: sod2_Day1_2

description: Library name: Sample 5


title: hairyroot, control, rep3

source_name: hairy-roots

value: Control (empty vector)


title: CA3 AAV-shRNA(mef2c) 3


title: AB5075_sac_3

value: WT

value: 1% saccharin


title: L4_1

value: the cerebral cortex


title: CA3 AAV-shRNA(scramble) 4


title: WT_Day1_3

description: Library name: Sample 3


title: AB5075_sac_2


title: CA3 AAV-shRNA(scramble) 3


title: AB5075_sac_1


title: WT_Day1_1

description: Library name: Sample 1


title: L3R3_3


title: CA3 AAV-shRNA(scramble) 1


title: Spinal microglia, WT

description:
Library name: WT
10XGenomics

data_processing:
Raw BCL files from the Illumina NovaSeq 6000 were demultiplexed into paired-end, gzip-compressed FASTQ files for each channel using Cell Ranger’s mkfastq.
Using Cell Ranger’s count, reads were aligned to the mouse reference transcriptome (mm10), and transcript counts quantified for each annotated gene within every cell.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: spinal cord

extract_protocol:
Microglia extracted from mouse lumbar spinal cord after collagenase IV treatment and mechanical dissociation, followed by Percoll gradient and subsequent FACS sorting (CD45lo,CD11b+,CX3CR1+)
10X Chromium Single Cell 3'

value: spinal cord

value: sorted microglia


title: Batch3_iPSC-CMs (isWT7), MM+NP group, day42

status: Public on Feb 24 2025

city: Dresden

first: Mario

last: Schubert

address: Fetscherstraße 74

department: Pharmacology

institute: TU Dresden

description:
Library name: Sample 8
Column name in Raw_counts_all_samples.tsv.gz and Norm_counts_all_samples.tsv.gz: s11__Batch_37_F2_NP

data_processing:
Base-calling software: bcl2fastq2 2.20.0
Quality control: FastQC (http://www.bioinformatics.babraham.ac.uk/) was used to perform a basic quality control
Alignment: Fragments were aligned to the human reference genome hg38 (Ensembl 104 splice sites) using the aligner STAR (2.7.10b).
Gene counts: Counts per gene and sample were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation using featureCounts (v2.0.1).
Normalisation: Normalisation of raw fragments based on library size and testing for differential expression between the different conditions was performed using the DESeq R package (v1.38.3).
Assembly: hg38
Supplementary files format and content: Raw_counts_all_samples.txt: tab-delimited file that contains the raw counts of all samples
Supplementary files format and content: Normalized_counts_all_samples.txt: tab-delimited file that contains the normalized counts of all samples

source_name: Induced pluripotent stem cell-derived cardiomyocyte

extract_protocol:
Cell pellets were lysed in 1 mL TRIzolTM (Thermo Fisher Scientific) and homogenized through continuous pipetting (30x) using a metal syringe. Lysates were centrifuged for 5 min at 12,000 x g at 4°C, the clear supernatant was transferred into a new tube, and 0.2 mL chloroform was added. Samples were mixed thoroughly, incubated for 3 min on ice and centrifuged for 15 min at 4°C and 15,000 x g to separate phases. The upper phase containing the isolated RNA was carefully collected and mixed with doubled volume of 95% ethanol. The solution was loaded on RNA columns of RNeasy isolation kit (Qiagen), RNA was purified according to manufacturer’s protocol, and eluted in RNAse-free water.
mRNA was isolated from an average of 600 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the strand-specific RNA-seq library preparation workflow (Ultra II Directional RNA Library Prep, NEB). Ligation was performed using the NEB Next Adapter from the NEB Next Multiplex Oligos for Illumina Kit. After ligation, the adapters were depleted by XP bead purification (Beckman Coulter), where the bead solution was added to the samples in a ratio of 0.9:1. Unique dual indexing was done during the subsequent PCR enrichment (12 cycles) using amplification primers carrying the same sequence for i7 and i5 index (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two further XP bead purifications (0.9:1), the libraries were quantified using the Fragment Analyzer (Agilent). Libraries were sequenced on an Illumina NovaSeq 6000 in 100 bp paired-end mode with an average of 50 million fragments per library.

treatment_protocol: iPSC-CMs were cultured in lipid-supplemented maturation medium (MM), in MM and on nanopatterned surfaces (MM+NP), or on NP and in MM comibined with electrostimulation (ES)

value: Maturation medium (MM) and nanopatterning (NP)


title: L3_3

value: female


title: CA3 AAV-shRNA(scramble) 2

value: Male


title: WT_Day1_2

description: Library name: Sample 2


title: Spinal microglia, KO

description:
Library name: KO
10XGenomics

value: 4E-BP1 cKO


title: Batch2_iPSC-CMs (iWTD2), MM+NP+ES group, day42

description:
Library name: Sample 6
Column name in Raw_counts_all_samples.tsv.gz and Norm_counts_all_samples.tsv.gz: s6__Batch_7_F2_NP_ES

value: Induced pluripotent stem cell-derived cardiomyocyte

value: Maturation medium (MM), nanopatterning (NP), and electrostimulation (ES)


title: Batch1_iPSC-CMs (iWTD2), MM group, day42

description:
Library name: Sample 1
Column name in Raw_counts_all_samples.tsv.gz and Norm_counts_all_samples.tsv.gz: s1__Batch_5_F2

value: Maturation medium (MM)


title: L1_2

value: Usp7 WT; Trp53+/-


title: Batch2_iPSC-CMs (iWTD2), MM+NP group, day42

description:
Library name: Sample 5
Column name in Raw_counts_all_samples.tsv.gz and Norm_counts_all_samples.tsv.gz: s5__Batch_7_F2_NP


title: Batch3_iPSC-CMs (isWT7), MM+NP+ES group, day42

description:
Library name: Sample 9
Column name in Raw_counts_all_samples.tsv.gz and Norm_counts_all_samples.tsv.gz: s12__Batch_37_F2_NP_ES


title: Batch2_iPSC-CMs (iWTD2), MM group, day42

description:
Library name: Sample 4
Column name in Raw_counts_all_samples.tsv.gz and Norm_counts_all_samples.tsv.gz: s4__Batch_7_F2


title: Monocyte_VOL_EFS8_rep5

city: Rouen

first: Sylvain

last: Fraineau

address: 22 Boulevard Gambetta

country: France

institute: Unversity of Rouen Normandy

description: Library name: EFS_8

data_processing:
Reads were aligned to the human genome build hg38 and the transcript assembly GRCh38 from Ensmbl using Hisat2 version 2.0.541
Assembly: Transcript quantification was performed with feature Counts from the subread package42. Differential analysis, including normalization, was performed with DESeq2 bioconductor package version 1.22.143 using R version 3.5.1.
Supplementary files format and content: gene_fpkm.xls contains FPKM counts far all samples

source_name: Blood

extract_protocol:
total RNA extracted from healthy volunteer (n=5), NCAVD (n=5) and CAVD (n=5) patients using NucleoSpin RNA XS kit (Macherley-Nagel Cat# 740902)
400 ng of total RNA with a concentration >20 ng/ml and a RIN ratio >8 were used for Poly-A mRNA-seq, sequencing length of 150 nt paired end (PE150) with the Illumina NovaSeq 6000

value: Blood

value: Monocyte


title: sod2_Day1_1

description: Library name: Sample 4

value: Whole worm

value: All


title: Monocyte_VOL_EFS6_rep3

description: Library name: EFS_6


title: Monocyte_VOL_EFS7_rep4

description: Library name: EFS_7


title: Batch1_iPSC-CMs (iWTD2), MM+NP group, day42

description:
Library name: Sample 2
Column name in Raw_counts_all_samples.tsv.gz and Norm_counts_all_samples.tsv.gz: s2__Batch_5_F2_NP

value: WT


title: Batch1_iPSC-CMs (iWTD2), MM+NP+ES group, day42

description:
Library name: Sample 3
Column name in Raw_counts_all_samples.tsv.gz and Norm_counts_all_samples.tsv.gz: s3__Batch_5_F2_NP_ES


title: Monocyte_VOL_EFS5_rep2

description: Library name: EFS_5


title: R4_1

value: male

value: Usp7 cKO; Trp53+/-


title: Monocyte_CAVD_TG9_rep5

description: Library name: TG_2_9


title: Monocyte_VOL_EFS4_rep1

description: Library name: EFS_4


title: Monocyte_CAVD_PP8_rep4

description: Library name: PP_2_8


title: Batch3_iPSC-CMs (isWT7), MM group, day42

description:
Library name: Sample 7
Column name in Raw_counts_all_samples.tsv.gz and Norm_counts_all_samples.tsv.gz: s10__Batch_37_F2


title: Monocyte_CAVD_GM10_rep3

description: Library name: GM_2_10


title: Monocyte_CAVD_DS6_rep2

description: Library name: DS_2_6


title: Monocyte_CAVD_BA5_rep1

description: Library name: BA_2_5


title: Monocyte_NCAVD_MG2_rep4

description: Library name: MG_1_2


title: Monocyte_NCAVD_HA7_rep3

description: Library name: HA_1_7


title: Monocyte_NCAVD_DM4_rep2

description: Library name: DM_1_4


title: Monocyte_NCAVD_BM9_rep1

description: Library name: BM_1_9


title: MDA 231-BrM2-831, CRISPR control, rep3

city: Nashville

first: Wendy

middle: E

last: Bindeman

state: TN

address: Preston Research Building 738 2220 Pierce Ave

department: Cancer Biology

institute: Vanderbilt University

description:
Library name: MDA231BrM2_CTL_3
column name in 231_gene_fpkm: WT_C

data_processing:
Raw data reads were processed using in-house perl scripts by Novogene Corporation. Company documentation states that reads containing adaptor contamination, N>10%, and base quality <5 for >50% of reads were removed.
Clean reads were aligned to hg38/mm10 using Hisat2 v2.0.5 with default parameters. Performed by Novogene Corporation.
Mapped reads were quantified using FeatureCounts v1.5.0-p3 with default parameters and counts were normalized using FPKM. Performed by Novogene.
Assembly: hg38, mm10
Supplementary files format and content: .csv files containing FPKM values for each sample

source_name: Breast, derived from metastatic pleural effusion

growth_protocol: 100,000 cells/well were plated in DMEM + 2% FBS for 48h.

extract_protocol:
RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research) and submitted to Novogene Corporation Inc (Sacramento, CA). Subsequent processing was performed by Novogene. Sample quality was re-confirmed by Novogene using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Performed by Novogene Corporation Inc

treatment_protocol: IL13-treated cells were treated with 20ng/mL murine IL13 for 48h in DMEM + 2% FBS

value: epithelial cells

value: untreated


title: MDA 231-BrM2-831, IL13RA2 CRISPR knockout, rep2

description:
Library name: MDA231BrM2_RA2_2
column name in 231_gene_fpkm: RA2_B

value: Breast, derived from metastatic pleural effusion

value: IL13RA2 KO


title: MDA 231-BrM2-831, CRISPR control, rep2

description:
Library name: MDA231BrM2_CTL_2
column name in 231_gene_fpkm: WT_B


title: MDA 231-BrM2-831, IL13RA2 CRISPR knockout, rep1

description:
Library name: MDA231BrM2_RA2_1
column name in 231_gene_fpkm: RA2_A


title: MDA 231-BrM2-831, CRISPR control, rep1

description:
Library name: MDA231BrM2_CTL_1
column name in 231_gene_fpkm: WT_A


title: CaSkiRB3 Sc

city: Chilpancingo

first: Gloria

last: Fernández Tilapa

state: Guerrero

address: Ciudad Universitaria Sur, Av. Lázaro Cárdenas S/N

country: Mexico

institute: Autonomous University of Guerrero

description:
Library name: Sample 12
CaSkiRB3_Sc.bam

data_processing:
The quality of the raw reads was assessed using FastQC (v0.73)
The paired-end fastq files were mapped against the GRCh38 using STAR (v2.7.10b) with default parameters.
Uniquely mapped reads from bam files were used to assess gene counts using FeatureCounts (v2.0.3).
Gene counts were used to conduct differential gene expression analysis using EdgeR (v3.36.0).
Assembly: hg38
Supplementary files format and content: Normalized raw counts in txt format

source_name: cell line

growth_protocol: Human CC cell lines C-33A and CaSki were cultured in DMEM high in glucose, the culture medium was supplemented with 10% fetal bovine serum (FBS). All cells were cultured in a humid atmosphere with 5% CO2, at 37°C.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) reagent according to the manufacturer's protocol.
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 using either dUTP for directional library or dTTP for non-directional library.  For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: cell line

value: Cervical cancer cell line in situ (HPV-negative)

value: transfection


title: CaSkiRB1 Sc

description:
Library name: Sample 10
CaSkiRB1_Sc.bam


title: C33ARB2 Tri

description:
Library name: Sample 2
C33ARB2_Tri.bam


title: C33ARB1 Tri

description:
Library name: Sample 1
C33ARB1_Tri.bam


title: CaSkiRB1 Tri

description:
Library name: Sample 7
CaSkiRB1_Tri.bam


title: C33ARB3 Tri

description:
Library name: Sample 3
C33ARB3_Tri.bam


title: C33ARB1 Sc

description:
Library name: Sample 4
C33ARB1_Sc.bam


title: C33ARB2 Sc

description:
Library name: Sample 5
C33ARB2_Sc.bam


title: CaSkiRB3 Tri

description:
Library name: Sample 9
CaSkiRB3_Tri.bam


title: CaSkiRB2 Tri

description:
Library name: Sample 8
CaSkiRB2_Tri.bam


title: CaSkiRB2 Sc

description:
Library name: Sample 11
CaSkiRB2_Sc.bam


title: Monocyte_NCAVD_PM8_rep5

description: Library name: PM_1_8


title: CPNPIO

city: Berlin

first: Philipp

last: Euskirchen

address: Charitéplatz 1

institute: Charité - Universitätsmedizin Berlin

description:
Library name: CPNPIO.CG
WGBS

data_processing:
Processing of WGBS data from 22 human diffuse glioma samples was erformed using the One Touch Pipeline (OTP) which uses bwa v0.6.1 for alignment and methylCtools v1.0.0 for methylation calling. Plus- and minus-strand methylated allele frequencies at CpG sites were merged using custom scripts. For nanopore sequencing data, raw sequencing data were basecalled using ONT's proprietary software (guppy or dorado) and aligned to hg19 using minimap2. Methylated allele frequencies were extracted using modkit.
Assembly: hg19
Supplementary files format and content: bedMethyl
The BED files adhere to the ENCODE bedMethyl standard outlined in 'Whole-Genome Bisulfite Sequencing Data Standards and Processing Pipeline – ENCODE' (encodeproject.org)
https://www.encodeproject.org/data-standards/wgbs/

source_name: tumor

extract_protocol:
Genomic DNA was extracted from tumor tissue using commercial extraction kits as part of neuropathological routine workup.
WGBS libraries were prepared using a NEBNext Methyl-seq Kit (NEB), and were then sequenced on an Illumina NovaSeq 6000 platform at the BIH Core Unit Genomics over two S4 flow cells in a paired-end setting of 2 x 150 bp. Nanopore libraries were prepared using Rapid Barcoding Kit (ONT) and sequenced on R9 or R10.4.1 flow cells on MinION/GridION or P2 Solo devices.

value: tumor

tag: tumor type

value: Glioblastoma, IDH-mutant


title: QNFJRV

description:
Library name: QNFJRV.CG
WGBS

value: Glioblastoma, IDH-wildtype


title: KPJYDW

description:
Library name: KPJYDW.CG
WGBS


title: WFVZUC

description:
Library name: WFVZUC.CG
WGBS

value: Anaplastic astrocytoma, IDH-mutant


title: QOALZB

description:
Library name: QOALZB.CG
WGBS


title: MDA 231-BrM2-831, IL13RA2 CRISPR knockout, rep3

description:
Library name: MDA231BrM2_RA2_3
column name in 231_gene_fpkm: RA2_C


title: TAVEZE

description:
Library name: TAVEZE.CG
WGBS


title: FUMNZK

description:
Library name: FUMNZK.CG
WGBS


title: MROEUC

description:
Library name: MROEUC.CG
WGBS


title: VRYGDG

description:
Library name: VRYGDG.CG
WGBS


title: HVDQQY

description:
Library name: HVDQQY.CG
WGBS


title: NYYWJB

description:
Library name: NYYWJB.CG
WGBS


title: C33ARB3 Sc

description:
Library name: Sample 6
C33ARB3_Sc.bam


title: ORGTMD

description:
Library name: ORGTMD.CG
WGBS


title: BXENRT

description:
Library name: BXENRT.CG
WGBS


title: FRMWFW

description:
Library name: FRMWFW.CG
WGBS


title: VZGQQT

description:
Library name: VZGQQT.CG
WGBS


title: WFSDGP

description:
Library name: WFSDGP.CG
WGBS


title: HYXIOL

description:
Library name: HYXIOL.CG
WGBS


title: CZDZHX

description:
Library name: CZDZHX.CG
WGBS


title: GYRMKE

description:
Library name: GYRMKE.CG
WGBS


title: XPORAE

description:
Library name: XPORAE.CG
WGBS

value: Diffuse astrocytoma, IDH-mutant


title: Input-ChIP-seq_THP-1_SVI_6h_2025

city: Athens

first: Marios

last: Agelopoulos

state: Attica

address: 4 Soranou Ephessiou Str

department: Center of Basic Research

country: Greece

institute: Biomedical Research Foundation Academy of Athens

description:
Library name: Input-ChIP-seq_THP-1_SVI_6h_2025
ATCC, TIB-202™

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control steps (QC) were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.72+galaxy1).
Adaptors’ contaminants and low-quality reads, were trimmed, and thus excluded from the downstream analyses, by the application of Trim Galore (Galaxy Version 0.6.7+galaxy0). Trimmed sequencing reads were mapped to the reference human (hg19) or mouse (mm9) genome by the application of the Bowtie2 software (Galaxy Version 2.4.2+galaxy0), with “very sensitive end to end” parameters (Langmead and Salzberg, 2012). The input data were utilized as controls.
Duplicate reads were eliminated using the RmDup tool (Galaxy Version 2.0.1) of the SAMtools package (Li et al., 2009). Samples were normalized to the same sequencing depth using the Downsample SAM/BAM (Galaxy Version 2.18.2.1) tool from Picard.
Peaks were called by MACS2 callpeak algorithm (Galaxy Version 2.1.1.20160309.6) following the above outlined parameters: (a) band width=150 bp, (b) lower mfold=5, (c) upper mfold=50, and (d) q value=0.05 (Feng et al., 2012).
Peaks detected in unplaced contigs (chrUn, chrM) and in ENCODE hg19 and mm9 blacklisted regions were excluded from the downstream analyses (Amemiya HM, et al., Sci Rep. 2019). Reads that mapped within peaks were tallied using bedtools' MultiCovBed tool (Galaxy Version 2.30.0) (Quinlan and Hall, 2010).
Assembly: hg19 (Homo sapiens), mm9 (Mus musculus)
Supplementary files format and content: bigwig files including RPKM normalized signal and BED files of total peaks

growth_protocol: Human and mouse cells were cultured under optimum conditions according to the manufacturer’s instructions. A549 cells (ATCC, CCL-185™) and NIH/3T3 cells (ATCC, CRL-1658™) were grown in DMEM medium (Sigma-Aldrich). THP-1 cells (ATCC, TIB-202™) were grown in RPMI 1640 medium (Sigma-Aldrich). Culture media for A549 and NIH/3T3 cells were supplemented with 1% Pen-Strep (Gibco) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Gibco,  Biowest). For THP-1 cells the culture medium was supplemented with 1% Pen-Strep (Gibco), 20% v/v heat-inactivated Fetal Bovine Serum (FBS) (Gibco, Biowest), and 2-mercaptoethanol to a final concentration of 0.05 mM. All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
ChIP-seq assays on human and mouse cells were carried out based on published protocols (Agelopoulos et al 2014; Agelopoulos et al 2012; Agelopoulos and Thanos 2006) with modifications. Cells were fixed in 1% formaldehyde (F8775, Sigma-Aldrich), for 30 minutes at room temperature, followed by quenching of the reaction by 0.125M Glycine. Cell pellets were diluted in 15 ml Buffer I [10 mM Tris-Cl pH 8.0, 10 mM EDTA, 0.25% Triton X-100] and incubated for 10 minutes on ice, followed by centrifugation at 3,500 rpm for 5 minutes at 4 °C and aspiration. Pellets were diluted in 15 ml Buffer II [10 mM Tris-Cl pH 8.0, 200 mM NaCl, 1 mM EDTA] and incubated for 10 minutes on ice, followed by centrifugation at 3,500 rpm for 5 minutes at 4 °C and aspiration. Pellets were diluted in sonication Buffer [10 mM Tris-Cl pH 8.0, 1 mM EDTA] and chromatin filaments were sheared to a range of 200-2,000 bp using a Covaris S220 Sonicator , followed by two sequential steps of 2,000 rpm and 12,000 rpm centrifugation, for 8 minutes at 4 °C, to avoid trapping of chromatin by the cell debris.
Multiplexed-DNA-libraries were prepared according to a published protocol (Ford et al., 2014) with modifications. The NEBNext Multiplex Oligos for illumina (Index Primers Set 1 and 2) (E7335S and E7500S, illumina) were used to produce compatible ends to the DNA fragments.

treatment_protocol: Cell cultures were grown at 85–95% confluence and subjected to mock-infection (control; 0h) or Sendai-Virus-infection (Cantell strain, Charles River lab., 2000 HA units/ml) for 3 or 6 hrs, prior to proceeding in downstream examinations. Sendai Virus was supplied directly in the culture medium at a ratio of 1/10 (v/v).

value: Monocytes

value: Sendai Virus Cantell strain, Charles River lab

tag: time

value: 6 hrs


title: Input-ChIP-seq_THP-1_SVI_0h_2025

description:
Library name: Input-ChIP-seq_THP-1_SVI_0h_2025
ATCC, TIB-202™

value: 0 hrs (naïve)


title: H3K27ac-ChIP-seq_A549_SVI_0h_2025

description:
Library name: H3K27ac-ChIP-seq_A549_SVI_0h_2025
ATCC, CCL-185™

value: Lung cells

value: H3K27ac (CST;Cell Signaling Technology,#8173)


title: IRF3-ChIP-seq_A549_SVI_0h_2025

description:
Library name: IRF3-ChIP-seq_A549_SVI_0h_2025
ATCC, CCL-185™

value: IRF3 (CST;Cell Signaling Technology,#4302S)


title: H3K27ac-ChIP-seq_THP-1_SVI_6h_2025

description:
Library name: H3K27ac-ChIP-seq_THP-1_SVI_6h_2025
ATCC, TIB-202™


title: IRF3-ChIP-seq_A549_SVI_6h_2025

description:
Library name: IRF3-ChIP-seq_A549_SVI_6h_2025
ATCC, CCL-185™


title: H3K27ac-ChIP-seq_A549_SVI_6h_2025

description:
Library name: H3K27ac-ChIP-seq_A549_SVI_6h_2025
ATCC, CCL-185™


title: Input-ChIP-seq_A549_SVI_6h_2025

description:
Library name: Input-ChIP-seq_A549_SVI_6h_2025
ATCC, CCL-185™


title: STD_Cas9

city: Aarhus

first: Jacob

middle: Giehm

last: Mikkelsen

address: Hoegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

description: Library name: STD_Cas9

data_processing:
bwa alignment, sorting, indexing and BLENDER2
Assembly: GRCh38
Supplementary files format and content: Processed data files are .txt output of the BLENDER2 pipeline

extract_protocol:
Nuclear extraction
DISCOVER-seq


title: HiFi_Cas9

description: Library name: HiFi_Cas9


title: H3K27ac-ChIP-seq_THP-1_SVI_0h_2025

description:
Library name: H3K27ac-ChIP-seq_THP-1_SVI_0h_2025
ATCC, TIB-202™


title: Cal51 Fenofibrate plus Ezetimibe_2

city: Jinan

first: Fabao

last: Liu

state: Shandong

address: #44 wenhua xi road

institute: Shandong university

description: Library name: Sample 17

data_processing:
Using the Ubuntu 20.04.2.0 LTS system
Raw data  of fastq format were firstly processed through fastp software（Version: 0.20.0+dfsg-1build1）
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The reads numbers mapped to each gene were counted using featureCounts v1.5.0-p3.
Assembly: hg38
Supplementary files format and content: Tab_delimited text file includes FPKM value for each sample

extract_protocol:
Total RNA was harvested by SPARKeasy Cellular RNA Extraction Kit (SparkJade).
RNA libraries for RNA seq were prepared using SMARTER mRNA-seq library Prep Kit following manufactor's protocols.

value: Breast cancer cell line


title: Cal51 Fenofibrate plus Ezetimibe_3

description: Library name: Sample 18


title: FPEBBN

description:
Library name: FPEBBN.CG
WGBS


title: Cal51 Fenofibrate plus Ezetimibe_1

description: Library name: Sample 16


title: Cal51 Ezetimibe_2

description: Library name: Sample 14


title: SMFPSD

description:
Library name: SMFPSD.CG
WGBS


title: Cal51 Fenofibrate_2

description: Library name: Sample 11


title: Cal51 Ezetimibe_3

description: Library name: Sample 15


title: Cal51 Ezetimibe_1

description: Library name: Sample 13


title: Cal51 Fenofibrate_3

description: Library name: Sample 12


title: Cal51 Fenofibrate_1

description: Library name: Sample 10


title: Cal51 PKM2 KO_3

description: Library name: Sample 6


title: Cal51 PKM2 KO_1

description: Library name: Sample 4


title: Cal51 DMSO_1

description: Library name: Sample 7


title: Cal51 PKM2 KO_2

description: Library name: Sample 5


title: Input-ChIP-seq_A549_SVI_0h_2025

description:
Library name: Input-ChIP-seq_A549_SVI_0h_2025
ATCC, CCL-185™


title: Cal51 DMSO_2

description: Library name: Sample 8


title: Mock

description: Library name: Mock


title: RIF_8_Glandular CD56

city: Liverpool

first: Jamie

last: Soul

address: Crown St

department: ISMIB

institute: University of Liverpool

description: Library name: DSP-1005990008601-E-H11

data_processing:
FASTQ files generated upon sequencing were converted to Digital Count Conversion (DCC) files using the NanoString Technologies pipeline (GeoMx® NGS Pipeline). Through the pipeline, individual probe alignment was performed using identification of read tag sequences (RTS), and duplicate counts of probes generated during the library preparation polymerase chain reaction were removed through evaluation of the probe unique molecular identifier (UMI) sequences.
Assembly: hg38
Supplementary files format and content: DCC files
Library strategy: Spatial Transcriptomics

source_name: endometrium

extract_protocol:
Paraffin-embedded human endometrial biopsies were sectioned and mounted on slides and sent (on dry ice) to the NanoString Technology Access Platform (TAP) for GeoMx digital spatial profiling analysis. Briefly, NanoString GeoMx DSP uses a pool of ~20,000 transcript-specific RNA probes, links each of the probes to a unique, probe specific barcode through a UV cleavable linker. The probe pool was hybridized to target mRNAs on tissue slides (overnight), and slides were then stained using fluorophore-labelled antibodies (“morphology markers”; here CD45, CD56, PanCK, and DNA) and imaged on the GeoMx profiler platform. A total of 3-4 regions of interest (ROIs) were selected per skin tissue sample, and UV light was applied to release and collect the DSP barcodes from selected ROIs.
Libraries constructed using NanoString NGS readout protocol where Illumina i5 and i7 dual indexing primers were added to the oligonucleotide tags during PCR to uniquely index each AOI.

value: endometrium

tag: patient

tag: slide

tag: region of_interest_id

tag: segment

value: Glandular CD56

tag: disease

value: recurrent implanation failure (RIF)


title: RIF_8_Glandular PanCK

description: Library name: DSP-1005990008601-E-H10

tag: tissue

value: Glandular PanCK


title: RIF_8_Luminal Stroma

description: Library name: DSP-1005990008601-E-H09

value: Luminal Stroma


title: Cal51 Control_1

description: Library name: Sample 1

tag: cell type


title: RIF_8_Glandular Stroma

description: Library name: DSP-1005990008601-E-H12

value: Glandular Stroma


title: Cal51 DMSO_3

description: Library name: Sample 9


title: Cal51 Control_2

description: Library name: Sample 2


title: RIF_8_Luminal PanCK

description: Library name: DSP-1005990008601-E-H07

value: Luminal PanCK


title: Cal51 Control_3

description: Library name: Sample 3


title: RIF_8_Luminal CD45

description: Library name: DSP-1005990008601-E-H08

value: Luminal CD45


title: RIF_7_Glandular Stroma

description: Library name: DSP-1005990008601-E-H06


title: RIF_7_Luminal Stroma

description: Library name: DSP-1005990008601-E-H03


title: RIF_7_Luminal CD45

description: Library name: DSP-1005990008601-E-H02


title: RIF_7_Glandular CD56

description: Library name: DSP-1005990008601-E-H05


title: RIF_7_Glandular PanCK

description: Library name: DSP-1005990008601-E-H04


title: RIF_7_Luminal PanCK

description: Library name: DSP-1005990008601-E-H01


title: RIF_6_Luminal Stroma

description: Library name: DSP-1005990008601-E-G09


title: RIF_6_Luminal CD45

description: Library name: DSP-1005990008601-E-G08


title: RIF_6_Glandular PanCK

description: Library name: DSP-1005990008601-E-G10


title: RIF_6_Glandular CD56

description: Library name: DSP-1005990008601-E-G11


title: RIF_5_Glandular CD56

description: Library name: DSP-1005990008601-E-G05


title: RIF_5_Luminal CD45

description: Library name: DSP-1005990008601-E-G02


title: RIF_5_Luminal PanCK

description: Library name: DSP-1005990008601-E-G01


title: RIF_5_Glandular PanCK

description: Library name: DSP-1005990008601-E-G04


title: RIF_5_Glandular Stroma

description: Library name: DSP-1005990008601-E-G06


title: RIF_5_Luminal Stroma

description: Library name: DSP-1005990008601-E-G03


title: RIF_4_Glandular Stroma

description: Library name: DSP-1005990008601-E-F12


title: RIF_4_Glandular CD56

description: Library name: DSP-1005990008601-E-F11


title: RIF_3_Glandular Stroma

description: Library name: DSP-1005990008601-E-F06


title: RIF_4_Glandular PanCK

description: Library name: DSP-1005990008601-E-F10


title: RIF_4_Luminal PanCK

description: Library name: DSP-1005990008601-E-F07


title: RIF_3_Glandular CD56

description: Library name: DSP-1005990008601-E-F05


title: RIF_3_Luminal PanCK

description: Library name: DSP-1005990008601-E-F01


title: RIF_4_Luminal Stroma

description: Library name: DSP-1005990008601-E-F09


title: RIF_4_Luminal CD45

description: Library name: DSP-1005990008601-E-F08


title: RIF_3_Glandular PanCK

description: Library name: DSP-1005990008601-E-F04


title: RIF_6_Glandular Stroma

description: Library name: DSP-1005990008601-E-G12


title: RIF_3_Luminal Stroma

description: Library name: DSP-1005990008601-E-F03


title: RIF_6_Luminal PanCK

description: Library name: DSP-1005990008601-E-G07


title: RIF_3_Luminal CD45

description: Library name: DSP-1005990008601-E-F02


title: RIF_2_Glandular CD56

description: Library name: DSP-1005990008601-E-E11


title: RIF_2_Glandular Stroma

description: Library name: DSP-1005990008601-E-E12


title: RIF_2_Luminal Stroma

description: Library name: DSP-1005990008601-E-E09


title: RIF_2_Luminal CD45

description: Library name: DSP-1005990008601-E-E08


title: RIF_2_Luminal PanCK

description: Library name: DSP-1005990008601-E-E07


title: RIF_2_Glandular PanCK

description: Library name: DSP-1005990008601-E-E10


title: RIF_1_Glandular CD56

description: Library name: DSP-1005990008601-E-E05


title: RIF_1_Glandular PanCK

description: Library name: DSP-1005990008601-E-E04


title: RIF_1_Glandular Stroma

description: Library name: DSP-1005990008601-E-E06


title: RIF_1_Luminal Stroma

description: Library name: DSP-1005990008601-E-E03


title: RIF_1_Luminal CD45

description: Library name: DSP-1005990008601-E-E02


title: Control_8_Luminal Stroma

description: Library name: DSP-1005990008601-E-D09

value: Control


title: Control_8_Glandular Stroma

description: Library name: DSP-1005990008601-E-D12


title: RIF_1_Luminal PanCK

description: Library name: DSP-1005990008601-E-E01


title: Control_8_Luminal PanCK

description: Library name: DSP-1005990008601-E-D07


title: Control_8_Luminal CD45

description: Library name: DSP-1005990008601-E-D08


title: Control_8_Glandular CD56

description: Library name: DSP-1005990008601-E-D11


title: Control_7_Glandular CD56

description: Library name: DSP-1005990008601-E-D05


title: Control_8_Glandular PanCK

description: Library name: DSP-1005990008601-E-D10


title: Control_7_Glandular Stroma

description: Library name: DSP-1005990008601-E-D06


title: Control_6_Luminal PanCK

description: Library name: DSP-1005990008601-E-C07


title: Control_6_Luminal CD45

description: Library name: DSP-1005990008601-E-C08


title: Control_7_Glandular PanCK

description: Library name: DSP-1005990008601-E-D04


title: Control_6_Glandular CD56

description: Library name: DSP-1005990008601-E-C11


title: Control_5_Glandular PanCK

description: Library name: DSP-1005990008601-E-C04


title: Control_7_Luminal CD45

description: Library name: DSP-1005990008601-E-D02


title: Control_5_Luminal Stroma

description: Library name: DSP-1005990008601-E-C03


title: Control_7_Luminal PanCK

description: Library name: DSP-1005990008601-E-D01


title: Control_6_Glandular Stroma

description: Library name: DSP-1005990008601-E-C12


title: Control_7_Luminal Stroma

description: Library name: DSP-1005990008601-E-D03


title: Control_5_Glandular CD56

description: Library name: DSP-1005990008601-E-C05


title: Control_5_Glandular Stroma

description: Library name: DSP-1005990008601-E-C06


title: Control_6_Glandular PanCK

description: Library name: DSP-1005990008601-E-C10


title: Control_6_Luminal Stroma

description: Library name: DSP-1005990008601-E-C09


title: Control_4_Glandular Stroma

description: Library name: DSP-1005990008601-E-C01


title: Control_4_Luminal CD45

description: Library name: DSP-1005990008601-E-B09


title: Control_4_Glandular CD56

description: Library name: DSP-1005990008601-E-B12


title: Control_4_Luminal PanCK

description: Library name: DSP-1005990008601-E-B08


title: Control_3_Glandular Stroma

description: Library name: DSP-1005990008601-E-B07


title: Control_3_Glandular CD56

description: Library name: DSP-1005990008601-E-B06


title: Control_3_Glandular PanCK

description: Library name: DSP-1005990008601-E-B05


title: Control_3_Luminal CD45

description: Library name: DSP-1005990008601-E-B03


title: Control_3_Luminal Stroma

description: Library name: DSP-1005990008601-E-B04


title: Control_3_Luminal PanCK

description: Library name: DSP-1005990008601-E-B02


title: Control_5_Luminal PanCK

description: Library name: DSP-1005990008601-E-C02


title: Control_2_Glandular PanCK

description: Library name: DSP-1005990008601-E-A11


title: Control_2_Luminal CD45

description: Library name: DSP-1005990008601-E-A06


title: Control_1_Glandular Stroma

description: Library name: DSP-1005990008601-E-A10


title: Tfh, RA_A2, scRNAseq

city: Columbus

first: Hsin-Jung Joyce

last: Wu

state: Ohio

address: 480 Medical Center Drive

department: Department of Internal Medicine

institute: The Ohio State University

description: 10x Genomics

data_processing:
The demultiplexing, barcoding processing and gene counting were made by using Cell Ranger. The annotation, gene counts filtering and DESeq2 normalization were done by using R and Seurat.
Assembly: hg38
Supplementary files format and content: gz files include features, barcodes, and matrix

source_name: Peripheral blood

extract_protocol:
To characterize the Tfh cells, CD4+ T cells were enriched from the peripheral blood mononuclear cell (PBMC) by positive selection using CD4 microbeads (Miltenyi Biotec). Enriched CD4+ T cells were then stained with Abs against CD4, CD3, CD25, CXCR5, and PD-1, and then sorted for Tfh cells, defining as CD4+CD3+CD25−CXCR5+PD-1+. After sorting, cells were suspended in DPBS. Single cells were separated into droplet emulsions according to manufacturer’s instructions (10x Genomics). scRNA-seq was performed according to manufacturer’s instructions (10x Genomics).
10x Genomics library construction kit (Cat # 1000190)

value: Peripheral blood

value: follicular helper T cells

tag: patient diagnosis

value: rheumatoid arthritis


title: Control_1_Glandular PanCK

description: Library name: DSP-1005990008601-E-A08


title: Tfh, HC_A5, scRNAseq

description: 10x Genomics

value: healthy


title: Control_1_Luminal CD45

description: Library name: DSP-1005990008601-E-A03


title: Control_1_Glandular CD56

description: Library name: DSP-1005990008601-E-A09


title: Control_4_Glandular PanCK

description: Library name: DSP-1005990008601-E-B11


title: Tfh, RA_A4, scRNAseq

description: 10x Genomics


title: Tfh, RA_A6, scRNAseq

description: 10x Genomics


title: Tfh, HC_A3, scRNAseq

description: 10x Genomics


title: Tfh, HC_A1, scRNAseq

description: 10x Genomics


title: Control_4_Luminal Stroma

description: Library name: DSP-1005990008601-E-B10


title: Control_2_Luminal PanCK

description: Library name: DSP-1005990008601-E-A05


title: Control_1_Luminal PanCK

description: Library name: DSP-1005990008601-E-A02


title: Control_2_Luminal Stroma

description: Library name: DSP-1005990008601-E-A07


title: preterm intestinal organoid (GA27), EV42 treated, rep2

city: Pohang

first: Jihyun

last: Kim

address: Pohang 37673

country: South Korea

institute: Pohang University of Science and Technology

data_processing:
Trimgalore v0.6.10 (cutadapt v4.7, fastqc v0.12.1), STAR (v2.7.10b), RSEM (v1.3.1)
RNA-seq reads were pre-processed with Trimgalore v0.6.10 (cutadapt v4.7, fastqc v0.12.1).
Trimmed sequence reads were aligned to ensemble GRCh38 reference using STAR (v2.7.10b)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene id, transcript id, length, effective length, expected count, TPM and FPKM values for each sample

source_name: small intestine

growth_protocol: Crypt-laden Matrigel was dispensed onto 48-well culture plates and following solidification of Matrigel droplets, the crypts were overlaid with the following medium: Advanced Dulbecco’s Modified Eagle’s Medium/F12 (Thermon Fisher Scientific) supplemented with penicillin/streptomycin, 10mM HEPES, 2mM GlutaMAX, 1× B-27 Supplement (Thermo Fisher Scientific), 10 nM gastrin I (Sigma-Aldrich), 1 mM N-acetylcysteine (FUJIFILM Wako Pure Chemical), and the niche factors of 100 ng/ml recombinant mouse Noggin (PeproTech), 50 ng/ml recombinant mouse EGF (Thermo Fisher Scientific), 10% R-spondin1 conditioned medium, 500 nM A83-01 (Tocris), 100 ng/mL human Wnt-3α (R&D), which was replaced every 2–3 days with passage 1:3 every 7 days. We added 10 μM Y-27632 (Sigma-aldrich) for the first 2 days after passaging to prevent anoikis.

extract_protocol:
RNA was harvested using Rneasy Micro Kit (Qiagen), and 1.0μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold kit as described in TruSeq Stranded Total RNA Reference Guide (1000000040499 v00).

treatment_protocol: Preterm intestinal organoid was treated with MSCs-derived EVs for 7 days

value: small intestine

value: intestinal organoid

value: epithelial cell

tag: treatment


title: Control_2_Glandular Stroma

description: Library name: DSP-1005990008601-E-B01


title: Control_2_Glandular CD56

description: Library name: DSP-1005990008601-E-A12


title: preterm intestinal organoid (GA27), EV39 treated, rep3


title: Control_1_Luminal Stroma

description: Library name: DSP-1005990008601-E-A04


title: preterm intestinal organoid (GA27), EV42 treated, rep3


title: preterm intestinal organoid (GA27), EV42 treated, rep1


title: preterm intestinal organoid (GA27), EV39 treated, rep2


title: preterm intestinal organoid (GA27), EV39 treated, rep1


title: preterm intestinal organoid (GA27), non-treated, rep3

value: NT


title: preterm intestinal organoid (GA27), non-treated, rep2


title: preterm intestinal organoid (GA27), non-treated, rep1


title: Tibialis anterior, fetus, F2, rep 2

city: Helsinki

first: Marco

last: Savarese

address: Topeliuksenkatu 20

department: Samfundet Folkhälsan i svenska Finland r.f.

country: Finland

institute: Folkhälsan Research Center

description:
sample_70
Raw data for sample_70 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

data_processing:
Paired end reads were mapped to Human genome (GRCH38, GENCODE v39) using the splice aware alignment software STAR. All parameters were left as their default settings except for --outSAMattributes that was set to ALL, --sjdbScore to 1, --limitOutSJcollapsed to 2000000, and --outMultimapperOrder to Random. Furthermore, for a more sensitive exon junction processing (that leads to increased read counts for the exon junctions), the software was run in 2-pass mode by setting the --twopassMode parameter to Basic.
The summarization methods "ExEx" and "ExSkip" supported by IntEREst were used to count the fragments that span the up/and downstream introns, and skip exons.
For the summarization, the paired reads mapping to coordinates of a single gene was considerd only (to ignore the reads mapping to fusion genes). Furthermore, the strandness was set to "reverse" and the junction reads (i.e. split reads) were only considered.
The gender of the samples were rechecked and inferred (for those who the information was missing) by measuring and comparing a ratio (r), i.e. the number of reads that map to chrY, to the number of reads that map to chrX. A cutoff of 0.05 was applied (For Male samples r>0.05).
In addition to the read count information for the samples listed in this study, the read counts have been measured for four ENCODE samples with accession numbers ENCFF001RMW (fetal heart tissues, 19 weeks female), ENCFF001ROG (fetal skeletal muscle tissues, 22 weeks male), ENCFF001RPA (fetal heart tissue, 28 weeks female) and ENCFF001RPE (fetal skeletal muscle tissue, 19 weeks female).
Assembly: GRCh38/GENCODE 39
Supplementary files format and content: Tab delimited text file that includes the coordinates and annotations of the exons as well as two measurement for each exon in each sample, namely the exon junction read count (i.e. column names ending with "_ee") and exon skipping read count (i.e. columns ending with "_es"). In addition to the read count information for the samples listed in this study, the read counts have been measured for four ENCODE samples with accession numbers ENCFF001RMW (fetal heart tissues, 19 weeks female), ENCFF001ROG (fetal skeletal muscle tissues, 22 weeks male), ENCFF001RPA (fetal heart tissue, 28 weeks female) and ENCFF001RPE (fetal skeletal muscle tissue, 19 weeks female).
Supplementary files format and content: Tab delimited text file that includes the coordinates and annotations of the introns as well as Intron spanning read count measurement for each intron in each sample (i.e. column names end with "_is"). In addition to the read count information for the samples listed in this study, the read counts have been measured for four ENCODE samples with accession numbers ENCFF001RMW (fetal heart tissues, 19 weeks female), ENCFF001ROG (fetal skeletal muscle tissues, 22 weeks male), ENCFF001RPA (fetal heart tissue, 28 weeks female) and ENCFF001RPE (fetal skeletal muscle tissue, 19 weeks female).
Supplementary files format and content: Tab delimited text file that includes gene level read counts.

source_name: FETAL MUSCLE, Tibialis anterior, Male

extract_protocol:
For prenatal analysis, a trained fetal pathologist collected fetal skeletal muscles (n=20) and fetal heart muscles (n=2) from 2 different fetuses, without muscle pathology, obtained from voluntary termination of pregnancy (TOP).For postnatal analysis, we collected sample biopsies from an internal cohort of 41 individuals. RNA was extracted with Qiagen RNeasy Plus Universal Mini Kit, processed with Illumina Ribo-Zero Plus rRNA Depletion Kit and sequenced using NovaSeq 6000 (Illumina).
RNA was extracted with Qiagen RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Total RNAseq libraries were prepared using the Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina, Palo Alto, CA, USA) at the Oxford Genomics Center, Welcome Trust Institute, Oxford, United Kingdom and Novogene. Sequencing was performed on NovaSeq 6000 (Illumina), generating over 80 million 150bp-long reads per sample.

value: FETAL MUSCLE, Tibialis anterior, Male


title: Vastus lateralis, fetus, F2, rep 2

description:
sample_71
Raw data for sample_71 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Vastus lateralis, Male

value: FETAL MUSCLE, Vastus lateralis, Male


title: Sartorius muscle, fetus, F2, rep 2

description:
sample_69
Raw data for sample_69 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Sartorius muscle, Male

value: FETAL MUSCLE, Sartorius muscle, Male


title: Soleus muscle, fetus, F2, rep 2

description:
sample_68
Raw data for sample_68 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Soleus muscle, Male

value: FETAL MUSCLE, Soleus muscle, Male


title: Biceps femoris, fetus, F2, rep 2

description:
sample_62
Raw data for sample_62 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Biceps femoris, Male

value: FETAL MUSCLE, Biceps femoris, Male


title: Rectus femoris, fetus, F2, rep 2

description:
sample_66
Raw data for sample_66 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Rectus femoris, Male

value: FETAL MUSCLE, Rectus femoris, Male


title: Semimemembranosus muscle, fetus, F2, rep 2

description:
sample_67
Raw data for sample_67 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Smooth (soft) muscle, Male


title: Gastrocnemius medialis, fetus, F2, rep 2

description:
sample_64
Raw data for sample_64 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Gastrocnemius medialis, Male


title: Cardiac muscle, fetus, F2, rep 1

description:
sample_65
Raw data for sample_65 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL HEART, Cardiac muscle, Male

value: FETAL HEART, Cardiac muscle, Male


title: Semimemembranosus muscle, fetus, F1, rep 1

description:
sample_58
Raw data for sample_58 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Smooth (soft) muscle, Female


title: Vastus lateralis, fetus, F1, rep 1

description:
sample_61
Raw data for sample_61 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Vastus lateralis, Female

value: FETAL MUSCLE, Vastus lateralis, Female


title: Gastrocnemius lateralis, fetus, F2, rep 2

description:
sample_63
Raw data for sample_63 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Gastrocnemius lateralis, Male


title: Tibialis anterior, fetus, F1, rep 1

description:
sample_60
Raw data for sample_60 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Tibialis anterior, Female

value: FETAL MUSCLE, Tibialis anterior, Female


title: gastrocnemius lateralis, fetus, F1, rep 1

description:
sample_54
Raw data for sample_54 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, gastrocnemius lateralis, Female


title: Skeletal muscle, postnatal, rep 45

description:
sample_52
Raw data for sample_52 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: POSTNATAL MUSCLE, Female

value: POSTNATAL MUSCLE, Female


title: Biceps femoris, fetus, F1, rep 1

description:
sample_53
Raw data for sample_53 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Biceps femoris, Female

value: FETAL MUSCLE, Biceps femoris, Female


title: Skeletal muscle, postnatal, rep 42

description:
sample_49
Raw data for sample_49 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: POSTNATAL MUSCLE, Male

value: POSTNATAL MUSCLE, Male


title: Rectus femoris, fetus, F1, rep 1

description:
sample_56
Raw data for sample_56 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Rectus femoris, Female

value: FETAL MUSCLE, Rectus femoris, Female


title: gastrocnemius medialis, fetus, F1, rep 1

description:
sample_55
Raw data for sample_55 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, gastrocnemius medialis, Female


title: Skeletal muscle, postnatal, rep 43

description:
sample_50
Raw data for sample_50 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Sartorius muscle, fetus, F1, rep 1

description:
sample_59
Raw data for sample_59 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Sartorius muscle, Female

value: FETAL MUSCLE, Sartorius muscle, Female


title: Cardiac muscle, postnatal, rep 7

description:
sample_48
Raw data for sample_48 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: POSTNATAL HEART, Male (inferred)

value: POSTNATAL HEART, Male (inferred)


title: Skeletal muscle, postnatal, rep 44

description:
sample_51
Raw data for sample_51 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Soleus muscle, fetus, F1, rep 1

description:
sample_57
Raw data for sample_57 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: FETAL MUSCLE, Skeletal, Female

value: FETAL MUSCLE, Skeletal, Female


title: Cardiac muscle, postnatal, rep 5

description:
sample_46
Raw data for sample_46 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Cardiac muscle, postnatal, rep 4

description:
sample_45
Raw data for sample_45 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: POSTNATAL HEART, Female (inferred)

value: POSTNATAL HEART, Female (inferred)


title: Cardiac muscle, postnatal, rep 3

description:
sample_44
Raw data for sample_44 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Cardiac muscle, postnatal, rep 2

description:
sample_43
Raw data for sample_43 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Cardiac muscle, postnatal, rep 1

description:
sample_42
Raw data for sample_42 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 41

description:
sample_41
Raw data for sample_41 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: POSTNATAL MUSCLE, Male (inferred)

value: POSTNATAL MUSCLE, Male (inferred)


title: Skeletal muscle, postnatal, rep 40

description:
sample_40
Raw data for sample_40 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .

source_name: POSTNATAL MUSCLE, Female (inferred)

value: POSTNATAL MUSCLE, Female (inferred)


title: Skeletal muscle, postnatal, rep 38

description:
sample_38
Raw data for sample_38 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 37

description:
sample_37
Raw data for sample_37 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 27

description:
sample_27
Raw data for sample_27 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 33

description:
sample_33
Raw data for sample_33 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 23

description:
sample_23
Raw data for sample_23 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 17

description:
sample_17
Raw data for sample_17 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Cardiac muscle, postnatal, rep 6

description:
sample_47
Raw data for sample_47 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 26

description:
sample_26
Raw data for sample_26 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 24

description:
sample_24
Raw data for sample_24 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 15

description:
sample_15
Raw data for sample_15 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 18

description:
sample_18
Raw data for sample_18 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 20

description:
sample_20
Raw data for sample_20 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 25

description:
sample_25
Raw data for sample_25 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 12

description:
sample_12
Raw data for sample_12 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 21

description:
sample_21
Raw data for sample_21 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 30

description:
sample_30
Raw data for sample_30 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 29

description:
sample_29
Raw data for sample_29 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 28

description:
sample_28
Raw data for sample_28 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 31

description:
sample_31
Raw data for sample_31 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 22

description:
sample_22
Raw data for sample_22 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 32

description:
sample_32
Raw data for sample_32 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 19

description:
sample_19
Raw data for sample_19 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 16

description:
sample_16
Raw data for sample_16 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 14

description:
sample_14
Raw data for sample_14 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 13

description:
sample_13
Raw data for sample_13 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 11

description:
sample_11
Raw data for sample_11 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 9

description:
sample_9
Raw data for sample_9 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 39

description:
sample_39
Raw data for sample_39 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 10

description:
sample_10
Raw data for sample_10 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 36

description:
sample_36
Raw data for sample_36 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 35

description:
sample_35
Raw data for sample_35 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 34

description:
sample_34
Raw data for sample_34 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 5

description:
sample_5
Raw data for sample_5 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 7

description:
sample_7
Raw data for sample_7 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 8

description:
sample_8
Raw data for sample_8 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 6

description:
sample_6
Raw data for sample_6 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 4

description:
sample_4
Raw data for sample_4 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: B Cells, IL-35 producing replicate 3

city: Bethesda

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

data_processing:
Differentially expressed genes and corresponding adjusted p-values were determined using DEseq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw transcript level counts for each sample

source_name: Blood

growth_protocol: PBMC was isolated by Ficoll-Paque density gradient centrifugation using the Lymphocyte Separation Medium (Corning, VA, USA).

extract_protocol:
Total RNA was isolated from human B cells using RNeasy plus mini kit (Qiagen)
mRNA was isolated by oligo-dT beads, and a library was prepared using the standard Illumina library protocol (kit: RS-122-2101 TruSeq Stranded mRNA LT Sample prep kit)

treatment_protocol: B cells were isolated from single cell suspension of PBMC using Human B-cell isolation kit (Miltenyi Biotec, Cat# 130-091-151) and were stimulated with 2µM human CpG and 5ug/mL anti-CD40 for 72h.

value: Blood

value: B cells

value: 2microM human CpG and 5ug/mL anti-CD40 for 72h


title: Skeletal muscle, postnatal, rep 1

description:
sample_1
Raw data for sample_1 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: B Cells, Control replicate 3

value: Control


title: Skeletal muscle, postnatal, rep 3

description:
sample_3
Raw data for sample_3 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: Skeletal muscle, postnatal, rep 2

description:
sample_2
Raw data for sample_2 is not availalbe due to GDPR. For any further enquiries regarding the studied samples please contact marco.savarese@helsinki.fi .


title: B Cells, IL-35 producing replicate 2


title: RNA-seq_MRC5_SVI_3h_exp1_2023

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control (QC) steps were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.74+galaxy0).
Processed sequencing reads were mapped to the reference human (hg19) or mouse (mm9) genome by the HISAT2 alignment tool (Galaxy Version 2.2.1+galaxy1) under “single-end”, “stranded” and “reverse” options.
RNA integrity was measured by the Transcript Integrity Number tool (Galaxy Version 5.0.1+galaxy2). The enrichment of RNA-sequencing reads within gene bodies was examined using Gene Body Coverage (ΒΑΜ) tool.
Calculation of sequencing reads that are mapped into genes was performed with the htseq-count tool (Galaxy Version 0.9.1+galaxy1), in “union” mode, with “stranded”, “reverse”, and “minimum alignment quality 1” and “–nonunique All" options.
Assembly: hg19 (Homo sapiens), mm9 (Mus musculus)
Supplementary files format and content: bigwig files including RPKM normalized signal

source_name: MRC-5 (ATCC, CCL-171)

growth_protocol: Human and mouse cells were cultured under optimum conditions according to the manufacturer’s instructions. MRC-5 cells (ATCC, CCL-171™) and NIH/3T3 cells (ATCC, CRL-1658™) were grown in DMEM medium (Sigma-Aldrich). All culture media were supplemented with 1% Pen-Strep (Biowest) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Biowest). All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
Total RNA was extracted from cells using the Monarch Total RNA Miniprep Kit (T2010S, NEB) that includes treatment with DNase I for 15 minutes at 37°C to remove any DNA remnants.
RNA quality was evaluated at the Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies). RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) for Illumina following the manufacturer's instructions. Samples were subjected to beads-purification (NEBNext Sample Purification Beads, E7767L), and the quality of the isolated libraries was evaluated at the Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies).

treatment_protocol: Cell cultures were grown at 85–95% confluence and subjected to mock-infection (control; 0h) or Sendai-Virus-infection (Cantell strain, Charles River lab., 2000 HA units/ml) for 3, or 6 (MRC-5 cells) or 7 hrs (NIH/3T3 cells), prior to proceeding in downstream examinations. Sendai Virus was supplied directly in the culture medium at a ratio of 1/10 (v/v).

value: MRC-5 (ATCC, CCL-171)

value: Lung Fibroblasts

value: Sendai Virus Cantell strain, Charles River lab

value: 3 hrs


title: B Cells, IL-35 producing replicate 1


title: RNA-seq_MRC5_SVI_3h_exp2_2023


title: ACHN-sgzccHc8-repeat2

city: Shanghai

first: Jianxiu

last: Yu

address: No. 280, Chongqing South Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
For RNA-seq data, paired-end reads were harvested from illumina Novaseq 6000 sequencer, and were quality controlled by Q30.
3’ adaptor-trimming and low quality reads were removing by cutadapt software (v1.9.3).
The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes.
Assembly: hg19
Supplementary files format and content: Excel file includes lncRNA expression profiling
Supplementary files format and content: Excel file includes mRNA expression profiling

source_name: ACHN

extract_protocol:
RNA was extracted from total cell lysates.
Total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.

value: ACHN

tag: genotype


title: RNA-seq_MRC5_SVI_0h_exp1_2023

value: 0 hrs (naive)


title: RNA-seq_MRC5_SVI_6h_exp2_2023

value: 6 hrs