title: snATAC_Brassicacea_flowerbuds1

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

institute: Joint Genome Institute

description: Library name: OCZBU-OCZBW-OCZBX-OCZBY_Alyrata-Athaliana-Boleracea-Crubella_Br4sp-FlwBuds-atac-1

data_processing:
We used the Cell Ranger-ATAC version 2.1.0 count command to filter and map reads to each reference, and generate the fragments file containing a unique ATAC-seq fragment created by two separate transposition events. We then used SnapATAC2 v2.50 to process the fragment files to downstream analyses from cell filtering to cell type annotation. To keep high-quality cells we required a minimum of 3000 fragments per cell and a 3-fold enrichment around the TSS. We separated the data into 500 bp windows across the genome and created a cell by bin count matrix. We used the scrublet algorithm to identify potential doublets and remove them afterwards. We then combined replicates using the MNN-Correct algorithm in SnapATAC2 for batch correction. For visualization purposes we created a UMAP of each atlas. Pseudo-bulk profiles generated from our snATAC-seq data aligned well with published whole-tissue open chromatin profiles (Pearson r2 0.58). We used gene accessibility scores as a proxy for gene expression to annotate cells with cell types from our snRNA-seq atlases. We calculated gene accessibility scores using the ‘pp.make_gene_matrix()’ function in snapATAC2. Briefly, this function assigns genomic bins to nearby genes, counts the transposase insertion events associated with each gene, and creates a matrix of accessibility scores for a particular gene and cell. Using the gene accessibility matrix, we integrated the snATAC-seq and the snRNA-seq datasets selecting the top 1000 most variable genes from our snATAC-seq data. We used scVI integrated in SnapATAC2 to transfer cell type labels from the snRNA-seq atlas to the snATAC-seq atlas. To do this, we trained models using as covariate the batch information, negative binomial distribution (“nb”) as the gene likelihood statistic, and a maximum number of epochs of 1000. After assigning cell type labels, we called peaks using MACS3 integrated into snapATAC2 independently for each cell type. We then merged peaks that were in close proximity (250 bp to either edge) to make comparisons across different cell types possible. To calculate the differentially accessible regions (DARs) we sampled random cells per cell type, excluding the cell type being tested, and combined them to create a background using the regression-based test from snapATAC2 “snap.tl.diff_test()”, to identify regions more likely to be open in a given cell type than the background set of cells. We defined DARs as peaks with an adjusted p< 0.01.
Assembly: Arabidopsis thaliana Col-0 TAIR/Araport via Phytozome
Assembly: Arabidopsis lyrata MN47 Phytozome v2.1
Assembly: Brassica oleracea TO1000DH3 NCBI RefSeq GCF_000695525.1
Assembly: Capsella rubella Monte_Gargano Phytozome v1.1
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Arabidopsis thaliana
Brassica oleracea
Arabidopsis lyrata
Capsella rubella

source_name: floral bud

growth_protocol: A. thaliana, A. lyrata, C. rubella, and B. oleracea seeds were surface sterilized before planting vertically on agar plates containing 3mM Ca(NO3)2, 1.5mM MgSO4, 1.25mM NH4H2PO4, 1mM KCl, and 1x micronutrients (Murashige and Skoog Micronutrient Salts 100x, MSP18-10LT), in 0.8% agar with pH 5.7. The seeds were sterilized by soaking in 75% ethanol for 1 minute and 50% bleach for 5 minutes, 25% bleach with 0.2% Triton X-100 (Sigma-Aldrich 93443) for 4 minutes, then rinsed with sterile water 8 times. After sterilization, seeds in the 2 mL Eppendorf tube were wrapped in aluminum foil and put into a 4°C fridge for cold stratification. Seeds were left in the fridge for 3 days for A. thaliana and C. rubella, or 5 days for A. lyrata. Cold stratification was not needed for efficient germination of B. oleracea seeds. We staggered the planting of different species to account for different germination times of the four plant species, allowing us to harvest seedling root and shoot tissues of plants at the same 5-7 day old growth stage of all species on the same day. A. lyrata was planted on the agar plates 3 days before A. thaliana, C. rubella was planted 1 day after A. thaliana, and B. oleracea seeds without cold stratification were planted 2 days after A. thaliana. The conditions of the growth chamber (Percival Scientific) were set to 16 hours light at 22°C and 8 hours dark at 19°C, with the light turning on at 5am and turning off at 9pm. Root, shoot, and whole seedlings were sampled between 10am and 12pm for all experiments.

extract_protocol:
Freshly harvested samples were used for all snATAC-seq libraries. Nuclei isolation from tissues was performed as follows. Buffer 1 (lysis buffer) consisted of 0.275 M sorbitol (Sigma-Aldrich S6021), 0.1% Triton X-100 (Sigma-Aldrich 93443), 0.01 M MgCl2 (Ambion AM9530G), 1x protease inhibitor cocktail (Sigma-Aldrich 4693132001), 0.3 U/μl RNase inhibitor (Roche 03335399001), and 1 mM DTT (Teknova D9750). Buffer 2 (wash and resuspension buffer) consisted of 1x phosphate buffer saline (without Mg and Ca), 1% BSA, 0.4 U/μl RNase inhibitor, and 1 mM DTT. For isolation of nuclei from mature leaves containing high levels of chloroplasts, an extra modified wash and resuspension buffer (buffer 3) was used to eliminate chloroplasts before the final wash and resuspension step by buffer 2. It consisted of 0.275 M sorbitol, 0.2% Triton X-100, 0.2% NP40 (Thermo Fisher Scientific PI28324), 0.01 M MgCl2, 1x protease inhibitor cocktail, and 1 mM DTT. All nuclei isolation steps were carried out in a cold room at 4°C. For each sample, 20-100 mg fresh or frozen tissue was chopped for 3 minutes using a razor blade on a glass plate with 100-200 μl buffer 1, then transferred to a petri dish with 1.5 mL cold buffer 1 and allowed to rest on ice with gentle shaking for 2 minutes. For multiplexed samples, tissues from different species were weighed separately before being combined and chopped together. The samples were then transferred to a 48-well filter plate (25 μm, 4mL, Agilent, 201003-100), which was pre-wet with 1 mL cold buffer 1 before it was placed on the receiving plate attached to a QIAvac96 (Qiagen). Pressure was maintained below 100 bar during filtration. The filtered nuclei solution was centrifuged at 500x g for 10 minutes at 4°C to pellet the nuclei, after which the supernatant was discarded. For samples with low or no chloroplast content: The pellet was resuspended by gentle flicking and pipetting, washed with 2 mL cold buffer 2, centrifuged at 500x g for 5 minutes, and the supernatant was discarded. For nuclei isolation from mature leaves with high chloroplast content: The pellet was resuspended by gentle flicking and pipetting and 10 mL cold buffer 3 was added, centrifuged at 500x g for 5 minutes, and the supernatant was discarded. The pellet was washed with 2 mL cold buffer 2, centrifuged at 500x g for 10 minutes, and the supernatant was discarded. For both protocols, pellets from the final centrifugation were resuspended in 100 μl cold buffer 2 for snRNA-seq, or cold 1x nuclei buffer (10X Genomics PN-2000207) for snATAC-seq. Nuclei quality and quantity were assessed by flow cytometry and microscopy before continuing to the single nuclei partitioning and barcoding step. A BD Accuri C6 plus flow cytometer was used to analyze the quality and quantity of nuclei stained by propidium iodide (Sigma-Aldrich P4864), added to a final concentration of 50 μg/mL. The stained samples were incubated on ice in darkness for 5-10 min prior to analysis. The analysis was conducted using light-scatter and fluorescence signals produced by a 20 mW laser illumination at 488 nm. Signals corresponding to forward-angle scatter (FSC), 90° side scatter (SSC), and fluorescence were collected. Fluorescence signals (pulse area measurements) were screened using the following filter configurations: (a) FL-2, with a 585/40 nm band-pass filter, and (b) FL-3, with a 670 nm long-pass filter. Threshold levels were set empirically at 80,000 for FSC-H to exclude debris commonly found in plant homogenates. Templates for uni- (FL2-A and number of nuclei) and bi-parametric (FL2-A and FL3-A) frequency distributions were established. Upon identifying the region corresponding to nuclei, data was collected to a total count of 5,000–10,000 nuclei. The flow cytometer was operated at the Slow Flow Rate setting (14 μl sample/minute), with data acquisition for a single sample typically taking 3–5 minutes. Different plant species exhibited varying patterns of somatic endoreduplication within most of their tissues and organs. For example, in young A. thaliana roots and cotyledons, this variation is reflected in the form of multiple clusters within the distribution, corresponding to nuclei forming a 2C, 4C, 8C, 16C, etc., of the endoreduplicative series61. All the nuclei of all the endoreduplicative series were counted and divided by the actual volume analyzed in the flow cytometer to obtain the concentration of the nuclei. An EVOS M5000 microscope was also used for validation of nuclei quality and quantity by analyzing 7 μl diluted nuclei sample stained by 1 µl of diluted SYBR Green dye (Thermo Fisher Scientific S7585 diluted 1:10,000 in water) using a C-Chip Disposable Hemocytometer. For nuclei prepared from fresh tissue samples, most of the nuclei in each sample showed well-resolved edges without obvious evidence of blebbing. In the case of nuclei prepared from frozen samples, where cell debris around the nuclei can interfere with these microscopy observations, nuclei quality was primarily assessed by comparing to fresh nuclei’s distribution and the endoreduplicative series pattern on the flow cytometer.
The nuclei suspension was then diluted to concentration of 700-1000 nuclei/μl using cold buffer 2 for snRNAseq or cold 1x nuclei buffer (10x Genomics PN-2000207) for snATAC-seq. Single nuclei were partitioned and barcoded using a Chromium system (10x Genomics) with the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) for snRNAseq or Chromium Single Cell ATAC Reagent Kits v2 for snATAC-seq. Approximately 20,000 nuclei in total were loaded for single species samples, and up to 60,000 nuclei for multiplexed species samples. Library creation was carried out following the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell or NovaSeq X plus 10B or 25B flow cell, using 2x150 bp paired-end sequencing, targeting 200M fragments per species for RNA-seq samples and 250M fragments per species for mixed-species ATAC-seq samples, with higher coverage for A. thaliana seedling samples (900M fragments and 1800M fragments for root and shoot respectively).

value: floral bud

tag: tissue condition

value: fresh

tag: platform

value: 10X Chromium

tag: number of_multiplexed_species


title: R3_clone38.1

status: Public on Jun 23 2026

type: SRA

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building (CRB)

country: USA

institute: University of Pennsylvania

description: Library name: R3_clone38.1

library_source: genomic

data_processing:
Pipeline overview: data were aligned to human genome assembly hg38 and subsequent analysis was performed with CUT&RUNTools v2.0 (https://github.com/fl-yu/CUT-RUNTools-2.0) using the standard CUT&Tag pipeline.
Read trimming and alignment: reads were trimmed with trimmomatic v0.36 and aligned with bowtie2 v2.4.2. bowtie2 --very-sensitive-local --phred33 -I 10 -X 700
Filtering: unmapped/unpaired reads were filtered out using samtools v1.1 view -bS -h -f 3 -F 4 -F 8
PCR duplicates removal were performed using PICARD: picard.jar MarkDuplicates REMOVE_DUPLICATES=True ASSUME_SORT_ORDER=queryname
Read shift: aligned reads were shifted +4bp and -5bp for positive and negative strand reference genome alignments, respectively, to account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase.
Peak calling: peaks were called using MACS2 v2.2.7.1.
Peak merge: peaks from individual replicates were merged where overlapping.
Track creation: ATACseq bigwig files were generated with deeptools 3.5.1  bamCoverage --normalizeUsing CPM.
Assembly: hg38/GRCh38
Supplementary files format and content: The BED file union_peaks_clean_named.bed contains all ATAC-seq peaks from MACS2 narrow peak calls and were then merged if overlapping.
Supplementary files format and content: The bigwig files *.bw were generated using deeptools bamCoverage with CPM normalisation.

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary human skin fibroblasts

growth_protocol: Primary human skin fibroblasts were obtained from commercial sources, obtained from neonatal male donors (Cascade Biologics, #C0045C). Cells were cultured in DMEM (ThermoFisher, #11995065),  supplemented with 10% fetal bovine serum (FBS) and 5% penicillin/streptomycin (Invitrogen, #15140122). Cells were passaged every 3-4 days using 0.05% trypsin-EDTA (Invitrogen, #25300054). Cell cultures tested negative for mycoplasma.

extract_protocol:
We performed ATAC sequencing according to the protocol of Corces et al., 2017 (PMID: 28846090). In short, we lysed cells and set up the transposition reaction with the Tn5 transposase at 37 C for 30 minutes. Next, we isolated transposed and adaptor-ligated genomic DNA with the Zymo DNA Clean and Concentrator Kit (Zymo, #D4014).
We amplified the library using custom-made primers (Supplemental Table 2, available on BioRxiv), originally designed by the William Greenleaf lab at Stanford University.

treatment_protocol: Cells used for ATAC-seq analysis were untreated.

tag: cell type

value: human skin fibroblasts

tag: treatment

tag: replicate


title: Patient 1, No Response, Baseline

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description:
Library name: Sample 1
10X Genomics FLEX

library_source: transcriptomic single cell

data_processing:
QC, alignment, demultiplexing, barcode correction, and gene counting were perfomed using 10X Genomics Cell Ranger v10.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Per-sample Cell Ranger BAMs were converted back into demultiplexed FASTQs using 10X Genomics' bamtofastq tool (https://www.10xgenomics.com/support/software/cell-ranger/latest/miscellaneous/cr-bamtofastq).
Assembly: GRCh38
Supplementary files format and content: Cell Ranger Filtered Feature Barcode Matrices (HDF5 Format)

molecule: polyA RNA

source_name: bone marrow mononuclear cells

extract_protocol:
A mononuclear cell layer was isolated from bone marrow aspirates via ficoll and washed with sterile PBS.
Single-cell capture and library construction was performed according to manufacturers instructions (10X Genomics GEM-X Flex Gene Expression v1).

treatment_protocol: Bone marrow samples from AML patients treated with venetoclax (28 days) and oral azacitidine (14 days). Samples are at baseline (prior to treatment), after 4 days of treatment (Day 4) and after 28 days of treatment (Day 28)

tag: tissue

value: bone marrow mononuclear cells

tag: patient

value: Patient 1

tag: response

value: No Response

tag: timepoint

value: Baseline


title: 8037_Avonex_low_72

type: protein

city: Silver Spring

first: Lakshmi Manasa

middle: Sakuntala

last: Chekka

state: Maryland

address: 10903 New Hampshire Avenue

department: DARS, CDER

institute: U.S. FDA

hyb_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

data_processing:
https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.
Read out is relative flourescent units (RFU) which is directly proportional to the amount of target protein in the initial sample, as informed by a standard curve generate for each protein-SOMAmer pair. Raw RFU is normalized as described in the data processing step above.

label: 5’ fluorophore, photocleavable linker, and biotin

molecule: protein

source_name: EDTA plasma

growth_protocol: EDTA Plasma from healthy subjects was collected and stored at -80 degrees centigrade.

extract_protocol: EDTA plasma from whole blood

treatment_protocol: Subjects were randomized between IFNβ-1a (7.5 µg) and pegIFNβ-1a (31.25 µg).

tag: drug group

tag: delivery

value: IM

tag: dose


title: snATAC_Brassicacea_flowerbuds2

description: Library name: OCZBZ-OCZCA-OCZCB-OCZCC_Alyrata-Athaliana-Boleracea-Crubella_Br4sp-FlwBuds-atac-2

library_source: genomic single cell


title: NR1_clone6.1

description: Library name: NR1_clone6.1


title: snATAC_Brassicacea_matureleaf1

description: Library name: OCZBC-OCZBG-OCZBH-OCZBN_Alyrata-Athaliana-Boleracea-Crubella_Br4sp-FreMaLF-atac-1

source_name: seedling leaf

value: seedling leaf


title: 8037_Avonex_low_32

scan_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).


title: 8037_Avonex_low_48

label_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).


title: 8037_Avonex_low_8


title: snATAC_Brassicacea_matureleaf2

description: Library name: OCZBO-OCZBP-OCZBS-OCZBT_Alyrata-Athaliana-Boleracea-Crubella_Br4sp-FreMaLF-atac-2


title: 8037_Avonex_low_16


title: snATAC_Brassicacea_root1

description: Library name: NYZYW-NYZYX-NYZYY-NYZYZ_Alyrata-Athaliana-Boleracea-Crubella_Ath-Aly-Cru-Bol-rt

source_name: seedling root

value: seedling root


title: 8037_Avonex_low_3


title: snATAC_Brassicacea_root2

description: Library name: NZYPS-NZYPT-NZYPU-NZYPW_Alyrata-Athaliana-Boleracea-Crubella_Ath-Aly-Cru-Bol-rt-2


title: snATAC_Brassicacea_shoot

description: Library name: NYZZA-NYZZB-NYZZC-NYZZG_Alyrata-Athaliana-Boleracea-Crubella_Ath-Aly-Cru-Bol-sht

source_name: seedling shoot

value: seedling shoot


title: 8037_Avonex_low_0


title: 8036_Pleg_low_312

value: SC


title: M3

city: Hohhot

first: jiemin

last: wang

address: State Key Laboratory of Reproductive  Regulation and Breeding of Grassland  Livestock

country: China

institute: inner Mongolia university

description: Library name: M3

library_source: transcriptomic

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

molecule: total RNA

source_name: cell culture

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, cell culture were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

treatment_protocol: For the experimental group, PMA-induced THP-1 cells were treated with exosomes derived from A549 lung cancer cells transfected with the METTL3-overexpressing construct (OE-METTL3-Exo). Briefly, A549 cells were transfected with OE-METTL3, and the culture supernatants were collected for exosome isolation. The isolated OE-METTL3-Exo were then co-cultured with PMA-differentiated THP-1 cells. Three biological replicates were performed for this group.

value: cell culture

tag: cell line


title: 8057_Avonex_low_48


title: 8036_Pleg_low_216_repeat


title: M1

description: Library name: M1


title: M2

description: Library name: M2


title: NC3

description: Library name: NC3

treatment_protocol: For the control group, PMA-induced THP-1 cells were treated with exosomes derived from A549 lung cancer cells transfected with the negative control vector (NC-Exo). Briefly, A549 cells were transfected with OE-NC, and the culture supernatants were collected for exosome isolation. The isolated NC-Exo were then co-cultured with PMA-differentiated THP-1 cells. Three biological replicates were performed for this group.

value: OE-NC


title: 8036_Pleg_low_216


title: 8036_Pleg_low_144


title: 8036_Pleg_low_120


title: NC1

description: Library name: NC1


title: 8036_Pleg_low_72


title: 8036_Pleg_low_96


title: NC2

description: Library name: NC2


title: Y_Ctr_2

city: Hangzhou

first: Yicheng

last: Fu

state: Zhejiang

address: Gudun road

institute: Zhejiang hospital

description:
Library name: symbol8
FPKM.Y_Ctr_2

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina Novaseq 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by DEAeq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen) according to the manufacturer’s procedure. 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using novaseq 6000 following manufacturer's protocols.

tag: age

value: Young


title: 8036_Pleg_low_48


title: 8036_Pleg_low_32


title: Y_Ctr_1

description:
Library name: symbol7
FPKM.Y_Ctr_1


title: SD45 Evogliptin

city: La Jolla

first: Brian

middle: A

last: Aguado

state: CA

address: 2880 Torrey Pines Scenic Dr

institute: University of California San Diego

description: Library name: BV6

data_processing:
Quality control using fastqc v0.12.1.
Confirmed adaptor sequence content with fastqc. If adaptor sequence content exceeded <5%, trimmomatic (v0.39) was performed.
Alignment using HISAT2-2.2.1.
Gene counts quantified using featureCounts  using the Sus_scrofa.Sscrofa11.1.111.gtf annotation file.
Assembly: Sus scrofa 11.1 (Ensembl) Sus_scrofa.Sscrofa11.1.dna_sm.toplevel.fa.gz
Supplementary files format and content: Tab delimited text includes raw counts for each sample

organism: Sus scrofa

source_name: Porcine aortic valve

growth_protocol: Valvular interstitial cells (VICs) were seeded onto stiff hydrogels and cultured with Media 199, 1% human serum, antibiotic and antifungal supplements.

extract_protocol:
Total RNA was isolated using Qiagen Rneasy Micro kit, following manufacturer protocol. A minimum of 100 ng of RNA per sample was used for library preparation.
RNA library for RNA-seq was prepared using Illumina's stranded mRNA kit.

treatment_protocol: VICs were treated with either DMSO (vehicle), Evogliptin at 5.4 nM, or Evogliptin at 5.4 nM with 1 ug/mL neutraizing insulin-like growth factor binding protein 2 antibody. After 2 days, VICs were lysed for RNA collection.

value: Porcine aortic valve

value: Aortic valvular interstitial cell

tag: serum sample

value: Evogliptin


title: Y_Ctr_3

description:
Library name: symbol9
FPKM.Y_Ctr_3


title: OLD_Ctr_3

description:
Library name: symbol6
FPKM.OLD_Ctr_3

value: Old


title: 8036_Pleg_low_8


title: OLD_Ctr_2

description:
Library name: symbol5
FPKM.OLD_Ctr_2


title: SD26 Evogliptin

description: Library name: BV4


title: OLD_Ctr_1

description:
Library name: symbol4
FPKM.OLD_Ctr_1


title: SD30 Evogliptin

description: Library name: BV5


title: 8036_Pleg_low_3


title: Crocin3

description:
Library name: symbol3
FPKM.Crocin3

value: Crocin


title: 8036_Pleg_low_0


title: Crocin2

description:
Library name: symbol2
FPKM.Crocin2


title: 8032_Pleg_low_312


title: Crocin1

description:
Library name: symbol1
FPKM.Crocin1


title: 8032_Pleg_low_216


title: 8032_Pleg_low_144


title: 8032_Pleg_low_120


title: Patient 3 Infiltrating zone

city: Beijing

first: Cao

last: Yuchen

address: Thirty-three Badachu Road, Shijingshan District, Beijing, P.R. China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Library name: 240816044
GEXSCOPE

data_processing:
Raw sequencing reads were processed using fastQC and fastp for quality control. Poly-A tails and adapter sequences were trimmed using cutadapt. Reads were aligned to the human reference genome GRCh38 (Ensembl release 99) using STAR. Gene expression counts and UMI counts were quantified using FeatureCounts. An expression matrix was generated for downstream analysis. Cell quality control and clustering: Cells were filtered based on: gene counts per cell (200–5000), UMI counts (<30,000), and mitochondrial content (<20–30%). After filtering, 128,678 high-quality cells were retained. Data normalization and scaling were performed using Seurat v3.1.2 (NormalizeData and ScaleData). The top 2000 variable genes were selected for PCA. Batch effects were corrected using Harmony v1.0. Clustering was performed with the Louvain algorithm (resolution = 1.2) in Seurat, followed by UMAP visualization. Downstream analysis: Differentially expressed genes were identified using Seurat FindMarkers (Wilcoxon test, avg_logFC > 0.25, adj. p < 0.05). Cell type annotation was based on canonical markers and SynEcoSys database. Pathway enrichment was performed with clusterProfiler (GO and KEGG). Trajectory analysis used Monocle2/3 and CytoTRACE. Cell-cell interactions were analyzed with CellPhoneDB v2.1.0.
Assembly: GRCh38 (Ensembl release 99)
Supplementary files format and content: Processed data files format and content: Filtered gene expression count matrices in 10x Genomics-compatible Market Exchange (MEX) format: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene IDs), and matrix.mtx.gz (UMI counts). Additional processed files include Seurat RDS objects containing normalized data, metadata (zone, cluster, cell type), UMAP coordinates, and downstream analysis results (DEGs, pseudotime, cell-cell interactions).
Supplementary files format and content: Processed data files format and content: The processed data include gene expression count matrices (UMI counts) generated from Singleron GEXSCOPE scRNA-seq. Files are provided as:  barcodes.tsv.gz: Cell barcodes features.tsv.gz: Gene features (gene IDs/symbols) matrix.mtx.gz: Sparse UMI count matrix (Matrix Market Exchange format, 10x Genomics compatible)  Additional processed files:  Combined Seurat object files (.rds) containing normalized data, scaled data, PCA, Harmony-corrected embeddings, UMAP coordinates, cluster identities, cell type annotations, and sample/zone metadata (Infiltrating zone vs Hypercellular zone). Tab-delimited files (.tsv.gz) of differentially expressed genes (DEGs), cluster marker genes, and pathway analysis results.

source_name: keloid

growth_protocol: Not applicable. Samples were primary human keloid tissues obtained directly from surgical excision.

extract_protocol:
issue dissociation and single-cell suspension preparation: Keloid samples were preserved in GEXSCOPE tissue preservation solution and transferred to the laboratory under cold conditions. Samples were washed three times with Hanks Balanced Salt Solution (HBSS), cut into 1-2 mm fragments, and digested in 2 ml GEXSCOPE tissue dissociation solution (Singleron Bio, Nanjing, China). After digestion, the mixture was filtered, centrifuged, and the pellet resuspended in PBS. Cell viability and concentration were assessed using trypan blue staining and Countstar Rigel fluorescence cell counter. Single-cell RNA library construction and sequencing: Single-cell suspensions (2×10^5 cells/mL) were loaded onto microwell chips using the Singleron Matrix Single Cell Processing System. scRNA-seq libraries were constructed with GEXSCOPE Single Cell RNA Library Kits (Singleron) following the manufacturer’s protocol. Libraries were sequenced on Illumina NovaSeq 6000 with 150 bp paired-end reads.
Single-cell suspensions (2×10⁵ cells/mL in PBS) were loaded onto microwell chips using the Singleron Matrix® Single Cell Processing System. scRNA-seq libraries were constructed according to the manufacturer’s protocol using the GEXSCOPE® Single Cell RNA Library Kits (Singleron Bio, Nanjing, China). Individual libraries were quantified, diluted to 4 nM, pooled, and sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

treatment_protocol: No treatment was administered. None of the patients had received any topical or intralesional treatment (including corticosteroid injections, 5-fluorouracil, laser therapy, cryotherapy, or radiotherapy) targeting the keloid lesions prior to surgical excision.

value: keloid

value: None of the enrolled patients had received any topical or intralesional treatment (including corticosteroid injections, 10-fluorouracil, laser therapy, cryotherapy, or radiotherapy) targeting the keloid lesions prior to surgical excision

tag: batch


title: Patient 4 Infiltrating zone

description:
Library name: 241011061
GEXSCOPE

value: None of the enrolled patients had received any topical or intralesional treatment (including corticosteroid injections, 12-fluorouracil, laser therapy, cryotherapy, or radiotherapy) targeting the keloid lesions prior to surgical excision


title: Patient 4Hypercellular zone

description:
Library name: 241011060
GEXSCOPE

value: None of the enrolled patients had received any topical or intralesional treatment (including corticosteroid injections, 11-fluorouracil, laser therapy, cryotherapy, or radiotherapy) targeting the keloid lesions prior to surgical excision


title: 8036_Pleg_low_16


title: Patient 3 Hypercellular zone

description:
Library name: 240816045
GEXSCOPE

value: None of the enrolled patients had received any topical or intralesional treatment (including corticosteroid injections, 9-fluorouracil, laser therapy, cryotherapy, or radiotherapy) targeting the keloid lesions prior to surgical excision


title: 8032_Pleg_low_96


title: 8032_Pleg_low_48


title: Patient 2 Infiltrating zone

description:
Library name: 240807018
GEXSCOPE

value: None of the enrolled patients had received any topical or intralesional treatment (including corticosteroid injections, 8-fluorouracil, laser therapy, cryotherapy, or radiotherapy) targeting the keloid lesions prior to surgical excision


title: 8032_Pleg_low_72


title: 8032_Pleg_low_32


title: 8032_Pleg_low_16


title: Patient 1 Infiltrating zone

description:
Library name: 240717031
GEXSCOPE

value: None of the enrolled patients had received any topical or intralesional treatment (including corticosteroid injections, 6-fluorouracil, laser therapy, cryotherapy, or radiotherapy) targeting the keloid lesions prior to surgical excision


title: 8032_Pleg_low_3


title: 8032_Pleg_low_0


title: Sorted T CD4 AIM+ cells, LC11713, Long COVID

city: Santiago

first: Adolfo

middle: Alexis

last: Rojas-Hidalgo

address: OLIVOS 1007

country: Chile

institute: Universidad de Chile

description:
Library name: LC11713-AIM
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)

data_processing:
Initial data processing used CellRanger v7.1.0 (10x Genomics) for demultiplexing and alignment to human reference genome GRCh38.
Assembly: GRCh38
Supplementary files format and content: Expression matrix files of single-cell RNA sequencing experiments in HDF5 format (.h5)

source_name: PBMCs

extract_protocol:
Whole blood was collected from participants in heparin or EDTA-coated tubes, with processing initiated within four hours of collection. PBMCs were isolated from heparin tubes using Ficoll gradient separation and cryopreserved in cell freezing medium (90% heat-inactivated fetal bovine serum with 10% DMSO) until further use. CD4+ T cells were evaluated using an activation-induced marker (AIM) assay. Briefly, cryopreserved PBMCs were thawed, washed and cultured for 24 hours at 37°C and 5% CO2 with SARS-CoV-2 MPs containing spike and non-spike epitopes (1μg/mL), DMSO (negative control), or staphylococcal enterotoxin B (1μg/mL, positive control). Cells were pre-incubated with anti-human CD40 blocking antibody (0.5μg/mL) for 15 minutes prior to stimulation. Following stimulation, cells were stained with fluorochrome-conjugated antibodies, and CD16 and analyzed on a FACSAria IIu cell sorter (BD Biosciences). CD4+ T cells were classified into naïve (CCR7+CD45RA+), central memory (CCR7+CD45RA−), effector memory (CCR7−CD45RA−), and terminally differentiated effector memory (CCR7−CD45RA+) subsets. AIM+ cells were identified as OX40+41BB+. Three populations (naive, total memory, and AIM+) were sorted for subsequent single-cell RNA sequencing, with viability confirmed before experiments.
For sorted cells, indexed V(D)J, 5' Feature Barcode, and GEX libraries were prepared using the Chromium Next GEM Single Cell 5' v2 Dual Index kit with Feature Barcoding (10x Genomics). Pools of cells of the same subtype from five to seven individuals were obtained following the Cell Multiplexing Oligo Labeling protocol. Libraries were sequenced on Illumina NovaSeq platform.

value: PBMCs

value: T-cell

tag: Sex

value: male

tag: severity

value: Moderate


title: 8030_Avonex_low_144

value: IM


title: Sorted T CD4 AIM+ cells, LC11638, Long COVID

description:
Library name: LC11638-AIM
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: Sorted T CD4 AIM+ cells, LC11837, Recovered control

description:
Library name: LC11837-AIM
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)

value: Severe


title: 8030_Avonex_low_120


title: 8030_Avonex_low_72


title: Sorted T CD4 AIM+ cells, LC11780, Long COVID

description:
Library name: LC11780-AIM
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)

value: female


title: Sorted T CD4 AIM+ cells, LC11720, Long COVID

description:
Library name: LC11720-AIM
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: Sorted T CD4 AIM+ cells, LC11703, Recovered control

description:
Library name: LC11703-AIM
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: 8030_Avonex_low_32_repeat


title: Sorted T CD4 AIM+ cells, LC11900, Recovered control

description:
Library name: LC11900-AIM
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: 8032_Pleg_low_8

value: SC


title: 8030_Avonex_low_32


title: 8030_Avonex_low_8


title: Sorted T CD4 naive cells, LC11713, Long COVID

description:
Library name: LC11713-Naive
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: 8030_Avonex_low_0


title: Sorted T CD4 naive cells, LC11638, Long COVID

description:
Library name: LC11638-Naive
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: 8030_Avonex_low_3


title: 8030_Avonex_low_16


title: Sorted T CD4 naive cells, LC11837, Recovered control

description:
Library name: LC11837-Naive
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: Sorted T CD4 naive cells, LC11710, Long COVID

description:
Library name: LC11710-Naive
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: 8027_Avonex_low_144


title: Sorted T CD4 naive cells, LC11780, Long COVID

description:
Library name: LC11780-Naive
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: 8027_Avonex_low_120


title: Sorted T CD4 naive cells, LC11720, Long COVID

description:
Library name: LC11720-Naive
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: 8027_Avonex_low_96


title: 8027_Avonex_low_48


title: 8027_Avonex_low_32


title: Sorted T CD4 naive cells, LC11900, Recovered control

description:
Library name: LC11900-Naive
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: 8027_Avonex_low_16


title: Sorted T CD4 memory cells, LC11780, Long COVID

description:
Library name: LC11780-Memory
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: 8027_Avonex_low_8


title: Sorted T CD4 memory cells, LC11720, Long COVID

description:
Library name: LC11720-Memory
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: Sorted T CD4 memory cells, LC11703, Recovered control

description:
Library name: LC11703-Memory
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: Sorted T CD4 naive cells, LC11373, Recovered control

description:
Library name: LC11373-Naive
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: 8027_Avonex_low_3


title: 8027_Avonex_low_0


title: 8023_Pleg_low_312


title: Sorted T CD4 memory cells, LC11900, Recovered control

description:
Library name: LC11900-Memory
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)


title: BD3

city: Wuxi

first: qin

last: chu

address: Department of Respiratory, The Affiliated Wuxi People’s Hospital of Nanjing Medical University

department: Department of Respiratory

description:
Library name: BD3
Human airway epithelial cells, control cells treated with house dust mite (HDM).

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count for each Sample

source_name: Human airway epithelial cells

extract_protocol:
Total RNA was extracted from cultured CAFs using TRIzol reagent. Subsequently, small RNA fragments (18-30 nt) were enriched and purified via denaturing polyacrylamide gel electrophoresis to isolate high-quality miRNAs for sequencing.
Purified miRNAs were sequentially ligated to 3' and 5' adapters. The ligated products were reverse-transcribed into cDNA and amplified by PCR. The final cDNA library was purified and validated for quality prior to sequencing.

value: airway epithelial cells

value: Human airway epithelial cells


title: W12_PBMC_G2_HTO

status: Public on Jun 24 2026

first: Patrick

last: Madden

address: 9420 Athena Circle

department: Center for Vaccine Innovation

institute: La Jolla Institute for Immunology

description:
Library name: W12_PBMC_G2_HTO
HTO 5' mRNA library

library_source: other

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: CITE-seq

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
N332-GT5 epitope-specific B cells were isolated from peripheral blood samples collected from rhesus macaques immunized with N332-GT5 and subsequent heterologous boost immunizations. Probes for each boost immunogen were included in flow cytometry staining for each respective Group, allowing determination of the proportion of N332-GT5 epitope-specific cells cross-binding the boost immunogen (N332-GT5++KO– Boost++). Thawed cells were incubated with both N332-GT5 KO and Boost KO probes for twenty minutes at 4°C. Following that, cells were sequentially incubated with the combined Booster WT probes for fifteen minutes at 4°C and then with the combined N332-GT5 WT probes for thirty minutes at 4°C. A master mix of surface staining antibodies was added next, with 2 μg per 5 million cells of anti-human Total-Seq-C hashtag antibodies (Biolegend) following the surface staining, and incubated for thirty minutes at 4°C. Cells were then washed twice and prepared for sorting on BD FACSymphony S6 (BD Biosciences). Epitope-specific B cells were sorted at all time points.Once sorted, epitope-specific PBMC and LN FNA B cells were washed with PBS and loaded onto a Chromium chip and controller following the manufacturers protocol (10X Genomics).  Indexed V(D)J, Feature Barcode, and Gene Expression libraries were prepared following the 10X Genomics protocol with the Feature Barcoding Kit (10X Genomics) and sequenced on a NovaSeq 6000 (Illumina).
Libraries were constructed according to the manufacturer's protocol using the Chromium Next GEM Single Cell 5’ Reagent Kit v3.

value: PBMC

value: B cells

value: Protein immunized


title: 8023_Pleg_low_144


title: BD2

institute: The Affiliated Wuxi People’s Hospital of Nanjing Medical University

description:
Library name: BD2
Human airway epithelial cells, control cells treated with house dust mite (HDM).


title: 8023_Pleg_low_120


title: Jejunum, KO saline day 7, mouse 42295

type: RNA

city: Odense

first: Mark

last: Burton

address: J.B. Winsløvsvej 4

department: Clinical Genetics

country: Denmark

institute: Odense University Hospital

description: Jejunum; one array per animal.

hyb_protocol: Hybridisation, washing and staining were performed automatically on the Affymetrix GeneTitan instrument according to the manufacturer's protocol for the Mouse Transcriptome Array 1.0 (fluidics/staining protocol FS450_0001).

scan_protocol: Arrays were scanned automatically in the Affymetrix GeneTitan instrument.

data_processing: CEL files were summarised at gene (transcript-cluster) level using Signal Space Transformation RMA (SST-RMA) in the Affymetrix Expression Console / Transcriptome Analysis Console (TAC) v3.0; the accompanying matrix contains log2 SST-RMA signal. Differential expression was assessed by ANOVA in TAC v3.0 (FDR < 0.05).

label: biotin

organism: Mus musculus

source_name: jejunum

label_protocol: Biotinylated sense-strand cDNA targets were prepared from total RNA using the Affymetrix GeneChip WT PLUS reagent kit according to the manufacturer's protocol.

growth_protocol: Adult 10-12-week-old female Sftpd-/- (KO) mice, backcrossed >10 generations onto the C57BL/6N background, and Sftpd+/+ (WT) littermates were bred in-house. Genotypes were confirmed by DNA PCR.

extract_protocol: Total RNA was isolated from jejunum using TRIzol (Invitrogen) per the manufacturer's instructions; quantity/purity assessed by NanoDrop (all A260/280 >= 1.8) and integrity verified on an Agilent 2100 Bioanalyzer (RNA 6000 Nano kit).

treatment_protocol: At day 0 mice received a single intraperitoneal injection of doxorubicin 20 mg/kg (Doxorubicin Accord) or an equal volume of isotonic saline, and were sacrificed on day 3 or day 7. The small intestine was removed and the jejunum (middle segment) was sampled.

tag: genotype

value: Sftpd-/- (knockout)

tag: agent

value: isotonic saline (vehicle)

tag: time

value: day 7


title: BD1

description:
Library name: BD1
Human airway epithelial cells, control cells treated with house dust mite (HDM).

tag: cell type

tag: treatment


title: HK3

description:
Library name: HK3
Human immortalized epidermal cells, TMPRSS4 knockout cells treated with TNFα + IFNγ.

source_name: Human immortalized epidermal cells

value: Human immortalized epidermal cells


title: 8023_Pleg_low_72


title: HK2

description:
Library name: HK2
Human immortalized epidermal cells, TMPRSS4 knockout cells treated with TNFα + IFNγ.


title: 8023_Pleg_low_32


title: 8023_Pleg_low_16


title: BK3

description:
Library name: BK3
Human airway epithelial cells, TMPRSS4 knockout cells treated with house dust mite (HDM)


title: HK1

description:
Library name: HK1
Human immortalized epidermal cells, TMPRSS4 knockout cells treated with TNFα + IFNγ.


title: 8023_Pleg_low_8


title: BK1

description:
Library name: BK1
Human airway epithelial cells, TMPRSS4 knockout cells treated with house dust mite (HDM)


title: 8023_Pleg_low_3


title: HD3

description:
Library name: HD3
Human immortalized epidermal cells, control cells treated with TNFα + IFNγ.

value: control cells treated with TNFα + IFNγ


title: 8023_Pleg_low_0


title: 8019_Avonex_low_120


title: THP1_24h_3

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
Library name: THP1_24h_3
THP-1 IACS 24 h relicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCh38/hg38 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for all 18 samples

source_name: AML cell line

extract_protocol:
Five million AML cells were plated and treated with DMSO or 50 nM IACS-010759 for 8 or 24 h for three independent replicates. Total RNA was isolated using a RNeasy kit (Qiagen) with the on-column DNA digest following the manufacturer’s protocol.
RNA sequencing libraries for each sample were prepared with 1 ug total RNA by using the TruSeq RNA Sample Prep v2 Kit (Illumina) per the manufacturer’s instructions, and sequencing was completed on the Illumina NovaSeq 6000.

tag: tissue

value: AML cell line

value: IACS 24 h


title: 8019_Avonex_low_96


title: THP1_8h_3

description:
Library name: THP1_8h_3
THP-1 IACS 8 h replicate 3

value: IACS 8 h


title: 8019_Avonex_low_72

value: IM


title: THP1_Ctrl_3

description:
Library name: THP1_Ctrl_3
THP-1 DMSO replicate 3

value: DMSO


title: 8019_Avonex_low_48


title: THP1_24h_2

description:
Library name: THP1_24h_2
THP-1 IACS 24 h relicate 2


title: 8019_Avonex_low_32


title: HD1

description:
Library name: HD1
Human immortalized epidermal cells, control cells treated with TNFα + IFNγ.


title: POND-hLIN28A_hESC_rep-1

first: Yangming

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

institute: Peking University

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7) (https://github.com/FelixKrueger/TrimGalore) to eliminate low-quality reads and trim adapter sequences.
Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) combined with ERCC spike-in sequences (https://assets.thermofisher.cn/TFS-Assets/LSG/manuals/ERCC92.zip) by STAR (v2.7.10a) using the GENCODE (Human v40 or Mouse vM25) transcript annotation as transcriptome guide, with parameters: --outFilterMismatchNoverLmax 0.04.
The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
For RBP POND-seq data, raw counts were normalized to counts per million (CPM) using ERCC spike-ins, and RBP targets were defined as transcripts with CPM >= 50, log2foldchange > 2, and adjusted P-value < 0.05 in RBP-POND versus control (EPN24 or EPN24-GFP) samples by DESeq2 (v1.36.0).
The POND-seq data for mutated RBPs were also quantified using absolute quantification based on ERCC spike-in controls. The total CPM of wild-type RBP-POND were set to 1,000,000, and the CPM of mutated RBPs-POND were calculated relative to that of wild-type RBP. For transcriptome analysis with PABPC1-POND-seq and RNA-seq, raw counts were normalized to transcripts per million (TPM) as gene expression level.
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawCounts, csv files include DESeq2 results

molecule: cytoplasmic RNA

source_name: H1 human embryonic stem cells

growth_protocol: HEK293T, Huh-7, and A549 cells were cultured at 37°C under 5% CO2 in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% FBS (PANSera), penicillin (100 U/ml) and streptomycin (100 µg/ml). V6.5 mouse ESCs were grown on gelatin-coated dish at 37°C under 5% CO2, in KnockOutTM DMEM (Gibco) supplemented with 15% FBS (Hyclone), nonessential amino acids, 2-mercaptoethanol, and 1,000 units/ml lymphocyte inhibitory factor. H1 Human ESCs were grown in mTeSRTM (STEMCELL Technologies) on Matrigel-coated dish at 37°C under 5% CO2.

extract_protocol:
Cell supernatant was clariﬁed by centrifugation at 3,000 g for 5 minutes, then filtrated through a cellulose acetate ﬁlter with 0.45 μm pore size (Corning). 200 μl of supernatant was mixed with 800 μl TRIzol reagent (Magen) and 1 μl diluted External RNA Controls Consortium (ERCC) synthetic spike-in RNAs (ThermoFisher). RNA was extracted and dissolved in 15-20 μl nuclease-free water.
For POND-seq, 5 μl RNA was used for library construction with modified VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). Typically, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) for fragmentation at 85℃ for 6 min. For ribosomal depletion, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) and 0.7 μl FastSelect reagent (Vazyme) for fragmentation at 85℃ for 6 min. Then 8 μl fragmentated RNA was used for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (16-18 cycles) according to the manufacture’s instruction manual. The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene, China) or DNBSEQ-T7 platform (GenePlus, China). For FMR1 mutation screening, library construction was completed with VNL-96P (Vazyme) automated library preparation workstation. Briefly, 4 μl RNA was mixed with 4 μl 2×Prime buffer V2 (Vazyme) and 1 μl FastSelect reagent (Vazyme) for fragmentation at 85°C for 6 min. Then 8 μl fragmentated RNA was adopted for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (17 cycles) according to VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). The NGS sequencing was performed on DNBSEQ-T7 platform (GenePlus). For cellular RNA-seq, the total RNA of HEK293T, Huh-7 and A549 were extracted with TRIzol reagent (Magen) and dissolved in nuclease-free water. 500 ng total RNA was used for library construction with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene) or DNBSEQ-T7 platform (GenePlus).

value: H1 human embryonic stem cells


title: ICH5

city: shanghai

first: Zuopeng

last: Su

address: 170 Xinsong Road, Xinzhuang Town, Minhang District,

department: Department of Neurosurgery,

institute: Minhang Hospital, Fudan University

description:
Library name: sample 5
Hypertension with cerebral hemorrhage group (ICH group),rep5

data_processing:
The raw reads were preprocessed and filtered using Trimmomatic  with the following steps:Removal of P7 and P5 adapter sequences (sequences provided above),trimming of bases with quality scores <20,discarding reads shorter than 50 bp and singleton reads.
Clean reads after quality control were aligned to the reference genome GRCh38.p13 using HISAT2 to acquire mapping positions.
Alignment outputs from HISAT2 were analyzed using htseq-count (v0.6.0)  to quantify read counts per transcript.
Alternative splice events that occurred in the samples were identified by Multivariate Analysis of Transcript Splicing (MATS, http://rnaseq-mats.sourceforge.net/).
Assembly: GRCh38
Supplementary files format and content: expression.xlsx

source_name: Peripheral Blood

extract_protocol:
RNA was harvested using TIANSeq mRNA Capture Kit (TIANGEN Biotech).
Libraries were constructed using the TIANSeq Fast RNA Library Prep Kit for Illumina (TIANGEN Biotech).

value: Peripheral Blood

value: Peripheral Blood Mononuclear Cells

tag: sample group


title: THP1_Ctrl_2

description:
Library name: THP1_Ctrl_2
THP-1 DMSO replicate 2


title: THP1_8h_2

description:
Library name: THP1_8h_2
THP-1 IACS 8 h replicate 2


title: THP1_24h_1

description:
Library name: THP1_24h_1
THP-1 IACS 24 h relicate 1


title: 8019_Avonex_low_3

tag: timepoint


title: THP1_8h_1

description:
Library name: THP1_8h_1
THP-1 IACS 8 h replicate 1


title: ABA48hS2

first: Sharon

last: Greenblum

institute: DOE Joint Genome Institute

description: Library name: NTPTP

data_processing:
raw data are paired-end interleaved fastq files
BBTools v38.96 bbduk.sh was used to filter raw reads for 1) removal of artifact sequence, RNA spike-in reads, PhiX reads, and reads containing any N, 2) quality trimming with method set at Q6, and 3) removal of reads with <50 bases
Filtered reads from each library were aligned to the A. thaliana TAIR10 reference genome using HISAT2 v2.2.1127
featureCounts was used to generate raw gene counts using Araport 11 gene annotations. Only primary hits assigned to the reverse strand were included (-s 2 -p --primary options)
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: counts.txt: tab-separated matrix containing read counts for each gene (rows) in each library (columns)

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: seeds were sterilized, then planted on nylon mesh in agar plates containing 3mM Ca(NO3)2, 1.5mM MgSO4, 1.25mM NH4H2PO4, 1mM KCl, and 1x micronutrients (Murashige and Skoog Micronutrient Salts 100x, MSP18-10LT), in 0.8% agar with pH 5.7. Seeds were sown on plates at a density of 3 rows per plate with ~30 plants per row and plates were placed vertically in a growth chamber under conditions of 16 h light at 22°C, 8 h dark at 19°C

extract_protocol:
mRNA was isolated from an input of 1000 ng of total RNA with oligo dT magnetic beads and fragmented to 300 bp - 400 bp with divalent cations at a high temperature.
Using TruSeq stranded mRNA kit (Illumina), the fragmented mRNA was reverse transcribed to create the first strand of cDNA with random hexamers and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) followed by second strand synthesis. The double stranded cDNA fragments were treated with A-tailing, ligation with NEXTFLEX UDI Barcodes (PerkinElmer) and enriched using 8.0 cycles of PCR. Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell, using 2x150 bp paired-end sequencing.

treatment_protocol: On the 5th day, the nylon mesh and plants were transferred using forceps to agar plates containing either 2 μM ABA, 150 μM SA, or the standard growth medium without added hormones as a negative control. Samples were collected at time points of 0, 1, 2, 4, 7, 24, and 48 hours, separating root and shoot tissues with a single razor blade cut at the time of collection.

value: shoot

tag: strain

value: ABA

tag: replicate


title: THP1_Ctrl_1

description:
Library name: THP1_Ctrl_1
THP-1 DMSO replicate 1


title: 8015_Pleg_low_312

tag: drug group

tag: delivery

value: SC

tag: dose


title: MV411_24h_3

description:
Library name: MV411_24h_3
MV4-11 IACS 24 h relicate 3

tag: cell line


title: 8015_Pleg_low_216


title: POND-EPN_forPUM2&YTHDF2_rep-2

source_name: HEK293T cell line

value: HEK293T cell line


title: MV411_8h_3

description:
Library name: MV411_8h_3
MV4-11 IACS 8 h replicate 3


title: 8015_Pleg_low_144

source_name: EDTA plasma


title: 8015_Pleg_low_120


title: MV411_24h_2

description:
Library name: MV411_24h_2
MV4-11 IACS 24 h relicate 2


title: 8015_Pleg_low_96


title: MV411_8h_2

description:
Library name: MV411_8h_2
MV4-11 IACS 8 h replicate 2


title: MV411_Ctrl_2

description:
Library name: MV411_Ctrl_2
MV4-11 DMSO replicate 2


title: 8015_Pleg_low_32


title: MV411_8h_1

description:
Library name: MV411_8h_1
MV4-11 IACS 8 h replicate 1


title: 8015_Pleg_low_16


title: MV411_Ctrl_1

description:
Library name: MV411_Ctrl_1
MV4-11 DMSO replicate 1


title: hnrnpa1 KO 3, 30 hpf

city: Munich

first: Bettina

last: Schmid

address: Feodor-Lynen-Str. 17

country: Germany

institute: DZNE

description: Library name: MUC5480

data_processing:
The STAR aligner (v 2.4.2a) (Dobin et al.,2013) with default parameter settings (except one: -twopassMode =Basic) was used for split-read alignment against the zebrafish genome assembly GRCz11 (Ensembl release 91) and Ensembl gene annotation (both downloaded from Ensembl).
To quantify the number of reads mapping to annotated genes we use HTSeq-count (v0.6.0) with default parameter settings (Anders et al., 2015).
FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values are calculated using custom scripts. The output of HTSeq-count was then used as input for the R Bioconductor package DESeq2 (Love et al., 2014) which was used for differential expression analysis following the standard workflow (https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html).
Assembly: zebrafish genome assembly GRCz11 (Ensembl release 91)
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: all.fpkms.xlsx

organism: Danio rerio

source_name: whole larvae

growth_protocol: at 28°C in E3 medium

extract_protocol:
RNA was isolated from whole-cell lysates using the AllPrep RNA Kit (Qiagen)
1 ug of RNA was poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (Illumina). End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the Low Throughput protocol of the TruSeq RNA Sample Prep Guide (Illumina).

treatment_protocol: comparison of hnrnpa1 knockout versus wildtype control

value: whole larvae

tag: developmental stage

value: embryo 30hpf

value: hnrnpa1 knockout


title: ICH6

description:
Library name: sample 6
Hypertension with cerebral hemorrhage group (ICH group),rep6


title: 8015_Pleg_low_8


title: 8019_Avonex_low_16


title: 8015_Pleg_low_3


title: DNA from Wilms Tumor 11

city: Caserta

first: Abu

last: Saadat

state: Caserta

address: Via Vivaldi, 43

department: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies

country: Italy

institute: Università degli Studi della Campania Luigi Vanvitelli

description:
Library name: WT11
Column name in normalized_counts_All_Samples.csv: WT11

data_processing:
The obtained reads were assessed for quality using FastQC and trimmed for adapter sequences using Trimmomatic (v0.39) in PE mode and ‘MINLEN’ parameter set to 50. Only the good quality reads were considered for alignment to the human reference genome (hg19) using STAR (v2.7.4a) with ‘outFilterMultimapNmax’ to 1. UMI-Tools utility was employed in PE mode to remove the duplicate reads. The filtered reads were then assigned to genes using ‘featureCount’ function from Subread package (v2.0.1).
The expression data were processed using CPM filtering implemented in NOIseq (v2.38.0) with default parameters. The filtered data was normalised using upperquartile normalisation from the EDAseq package (v2.28.0).
Assembly: hg19
Supplementary files format and content: csv file containing upper quartile normalized counts for all samples

source_name: Kidney

extract_protocol:
Total RNA was extracted from fast-frozen samples of Wilms Tumors (WTs) and adjacent non-neoplastic kidneys (NNKs) using Trizol protocol.
Sequencing libraries were prepared using Ovation SoLo RNA-seq Library Preparation kit (Tecan Genomics, Redwood city, CA) as per the manufacturares instruction manual (library type: fr-secondstrand).

value: Kidney

tag: Sex

value: Female

tag: batch

value: C


title: 8019_Avonex_low_8


title: DNA from Wilms Tumor 28

description:
Library name: WT28
Column name in normalized_counts_All_Samples.csv: WT28

value: Male


title: 8019_Avonex_low_0


title: 8015_Pleg_low_0


title: 8013_Pleg_low_312


title: DNA from Wilms Tumor 30

description:
Library name: WT30
Column name in normalized_counts_All_Samples.csv: WT30


title: Carotid body bifurcation_wildtype control_3

city: Storrs

first: Daniel

last: Mulkey

state: Connecticut

address: 69 North Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

description: Library name: Sample 3

data_processing:
Raw data were trimmed with Trimmomatic v0.38
Trimmed data were aligned to the reference with hisat2 v2.2.1
Gene counts were generated with htseq-count v0.13.5
Assembly: GRCm39
Supplementary files format and content: column 1 = gene name, column 2 = count

source_name: Bilateral carotid body bifurcations

extract_protocol:
RNA was harvested using TRIzol reagent
Total RNA samples were prepared for mRNA sequencing using the Illumina Stranded mRNA Ligation Sample Preparation kit following the manufacturer’s protocol (Illumina, San Diego, CA, USA). Libraries were sequenced on the NovaSeq 6000, version 1.5 chemistry.

value: Bilateral carotid body bifurcations

tag: postnatal day

tag: genotype

tag: diurnal cycle

value: dark cycle


title: Carotid body bifurcation_wildtype control_2

description: Library name: Sample 2


title: DNA from Wilms Tumor 43

description:
Library name: WT43
Column name in normalized_counts_All_Samples.csv: WT43

value: B


title: 8013_Pleg_low_216


title: DNA from Wilms Tumor 9

description:
Library name: WT9
Column name in normalized_counts_All_Samples.csv: WT9


title: 8013_Pleg_low_144


title: 8013_Pleg_low_120


title: DNA from Wilms Tumor 41

description:
Library name: WT41
Column name in normalized_counts_All_Samples.csv: WT41


title: DNA from Wilms Tumor 40

description:
Library name: WT40
Column name in normalized_counts_All_Samples.csv: WT40


title: 8013_Pleg_low_96


title: DNA from Wilms Tumor 39

description:
Library name: WT39
Column name in normalized_counts_All_Samples.csv: WT39


title: 8013_Pleg_low_48


title: MV411_Ctrl_3

description:
Library name: MV411_Ctrl_3
MV4-11 DMSO replicate 3

value: AML cell line

value: DMSO


title: 8013_Pleg_low_72


title: DNA from Wilms Tumor 27

description:
Library name: WT27
Column name in normalized_counts_All_Samples.csv: WT27

value: A


title: DNA from Wilms Tumor 24

description:
Library name: WT24
Column name in normalized_counts_All_Samples.csv: WT24


title: 8013_Pleg_low_32


title: 8013_Pleg_low_16


title: DNA from Wilms Tumor 23

description:
Library name: WT23
Column name in normalized_counts_All_Samples.csv: WT23


title: DNA from Wilms Tumor 19

description:
Library name: WT19
Column name in normalized_counts_All_Samples.csv: WT19


title: 8015_Pleg_low_72


title: 8013_Pleg_low_8


title: 8013_Pleg_low_3


title: DNA from Wilms Tumor 18

description:
Library name: WT18
Column name in normalized_counts_All_Samples.csv: WT18


title: 8013_Pleg_low_0


title: DNA from Wilms Tumor 8

description:
Library name: WT8
Column name in normalized_counts_All_Samples.csv: WT8


title: DNA from Wilms Tumor 7

description:
Library name: WT7
Column name in normalized_counts_All_Samples.csv: WT7


title: DNA from Wilms Tumor 6

description:
Library name: WT6
Column name in normalized_counts_All_Samples.csv: WT6


title: 8009_Avonex_low_144

value: IM


title: 8015_Pleg_low_48


title: 8009_Avonex_low_120


title: MV411_24h_1

description:
Library name: MV411_24h_1
MV4-11 IACS 24 h relicate 1

value: IACS 24 h


title: 8009_Avonex_low_72


title: DNA from Wilms Tumor 29

description:
Library name: WT29
Column name in normalized_counts_All_Samples.csv: WT29


title: DNA from Wilms Tumor 31

description:
Library name: WT31
Column name in normalized_counts_All_Samples.csv: WT31


title: 8009_Avonex_low_48


title: DNA from Wilms Tumor 48

description:
Library name: WT48
Column name in normalized_counts_All_Samples.csv: WT48


title: 8009_Avonex_low_96


title: 8009_Avonex_low_32


title: DNA from Wilms Tumor 32

description:
Library name: WT32
Column name in normalized_counts_All_Samples.csv: WT32


title: DNA from Wilms Tumor 26

description:
Library name: WT26
Column name in normalized_counts_All_Samples.csv: WT26


title: 8009_Avonex_low_16


title: DNA from Wilms Tumor 25

description:
Library name: WT25
Column name in normalized_counts_All_Samples.csv: WT25


title: 8009_Avonex_low_8


title: 8009_Avonex_low_3


title: DNA from Non neoplastic kidney control 30

description:
Library name: NNK30
Column name in normalized_counts_All_Samples.csv: NNK30


title: DNA from Non neoplastic kidney control 28

description:
Library name: NNK28
Column name in normalized_counts_All_Samples.csv: NNK28


title: DNA from Non neoplastic kidney control 11

description:
Library name: NNK11
Column name in normalized_counts_All_Samples.csv: NNK11


title: 8009_Avonex_low_0


title: 8004_Avonex_low_120


title: DNA from Non neoplastic kidney control 43

description:
Library name: NNK43
Column name in normalized_counts_All_Samples.csv: NNK43


title: 8004_Avonex_low_144


title: 8004_Avonex_low_96


title: DNA from Non neoplastic kidney control 9

description:
Library name: NNK9
Column name in normalized_counts_All_Samples.csv: NNK9


title: DNA from Non neoplastic kidney control 42

description:
Library name: NNK42
Column name in normalized_counts_All_Samples.csv: NNK42


title: 8004_Avonex_low_72


title: 8004_Avonex_low_48


title: 8004_Avonex_low_32


title: DNA from Non neoplastic kidney control 39

description:
Library name: NNK39
Column name in normalized_counts_All_Samples.csv: NNK39


title: DNA from Non neoplastic kidney control 40

description:
Library name: NNK40
Column name in normalized_counts_All_Samples.csv: NNK40


title: DNA from Non neoplastic kidney control 33

description:
Library name: NNK33
Column name in normalized_counts_All_Samples.csv: NNK33


title: DNA from Non neoplastic kidney control 27

description:
Library name: NNK27
Column name in normalized_counts_All_Samples.csv: NNK27


title: 8004_Avonex_low_8


title: DNA from Non neoplastic kidney control 24

description:
Library name: NNK24
Column name in normalized_counts_All_Samples.csv: NNK24


title: 8004_Avonex_low_16


title: 8004_Avonex_low_3


title: DNA from Non neoplastic kidney control 19

description:
Library name: NNK19
Column name in normalized_counts_All_Samples.csv: NNK19


title: 8004_Avonex_low_0_repeat


title: DNA from Non neoplastic kidney control 18

description:
Library name: NNK18
Column name in normalized_counts_All_Samples.csv: NNK18


title: 8004_Avonex_low_0


title: DNA from Non neoplastic kidney control 16

description:
Library name: NNK16
Column name in normalized_counts_All_Samples.csv: NNK16


title: DNA from Non neoplastic kidney control 8

description:
Library name: NNK8
Column name in normalized_counts_All_Samples.csv: NNK8


title: 8003_Pleg_low_312

value: SC


title: 8003_Pleg_low_216


title: DNA from Non neoplastic kidney control 7

description:
Library name: NNK7
Column name in normalized_counts_All_Samples.csv: NNK7


title: Patient 1 Hypercellular zone

description:
Library name: 240717033
GEXSCOPE

value: keloid

value: None of the enrolled patients had received any topical or intralesional treatment (including corticosteroid injections, 5-fluorouracil, laser therapy, cryotherapy, or radiotherapy) targeting the keloid lesions prior to surgical excision


title: DNA from Non neoplastic kidney control 6

description:
Library name: NNK6
Column name in normalized_counts_All_Samples.csv: NNK6


title: 8003_Pleg_low_144


title: 8003_Pleg_low_96


title: 8003_Pleg_low_120


title: DNA from Non neoplastic kidney control 48

description:
Library name: NNK48
Column name in normalized_counts_All_Samples.csv: NNK48


title: DNA from Non neoplastic kidney control 29

description:
Library name: NNK29
Column name in normalized_counts_All_Samples.csv: NNK29


title: 8003_Pleg_low_72


title: 8003_Pleg_low_48


title: DNA from Non neoplastic kidney control 32

description:
Library name: NNK32
Column name in normalized_counts_All_Samples.csv: NNK32


title: DNA from Non neoplastic kidney control 31

description:
Library name: NNK31
Column name in normalized_counts_All_Samples.csv: NNK31


title: DNA from Non neoplastic kidney control 26

description:
Library name: NNK26
Column name in normalized_counts_All_Samples.csv: NNK26


title: 8003_Pleg_low_32


title: 8003_Pleg_low_16


title: DNA from Non neoplastic kidney control 25

description:
Library name: NNK25
Column name in normalized_counts_All_Samples.csv: NNK25


title: 8003_Pleg_low_3


title: PT10M, KCit, GROUND, MALE, replicate 6

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Library name: S_144

data_processing:
FASTQ files were aligned to the Gencode GRCh38 v45 genome using HiSat2 and coordinate sorted using samtools
Counts/gene were summarized using the Bioconductor Rsubread package, using the Ensembl GRCh38 release 97 data.
Assembly: Ensembl GRCh38 release 97
Supplementary files format and content: Text file with genes in rows and samples in columns

source_name: Primary PTEC cell culture

growth_protocol: In brief, proximal tubule epithelial cells were isolated from whole human donor kidneys (not suitable for transplantation) obtained from Novabiosis (Durham, NC), cryopreserved, and commercially shipped on dry ice to Kennedy Space Center (KSC) where they were cultured and seeded onto 10-15 triplex (TSC) devices per donor to achieve ≥8 fully confluent TSCs per donor. The TSC devices were maintained within the pneumatic Kidney Chip Perfusion Platform system (KCPP) at a flow rate of 1 mL min-1. The integration and operation of the KCPP has been described previously.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004) and converted to cDNA with 20 the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, 634891).
Sequencing libraries were constructed using the SMARTer ThruPlex DNA-Seq Kit (Takara, R400676) and sequenced on a NovaSeq 6000 instrument (Illumina, San Diego, CA).

treatment_protocol: Cultures were incubated for 3-7 days in a standard laboratory incubator prior to transfer to KCPP. Kidney MPS devices were subjected to 1g (control) or microgravity conditions (CRS-22, KSC launch 17:29 UTC, 06/03/21 and ISSNL docking at 09:09 UTC, 06/05/21) for 7 days before media exchange to control (unsupplemented media) or treatment media containing either 1000 µg ml-1 COM crystals or 1000 µg ml-1 COM crystals + 250 µm KCit (potassium citrate tribasic monohydrate, Sigma, St. Louis, MO). The cassettes containing control or treatment media were inverted 4 times to evenly distribute COM microcrystals prior to initiating flow. Exposure to COM crystals and KCit in the ground-based laboratories at KSC or at the ISSNL was performed as previously described12. Upon completion of the test phase, the KCPP was flushed with RNAlater at a flow rate of 10 mL min-1 for 2 h before being placed in ultracold stowage (ISSNL) or -80o C freezer (KSC). ISSNL samples were returned to earth (undocking at 14:45 UTC, 08/08/21) and shipped to the laboratory at UW.

value: Primary PTEC cell culture

tag: cell type

value: PTEC

tag: gravity

value: 1 ng/ml Calcium Oxalate + 250 µM Potassium Citrate


title: 8003_Pleg_low_8

first: Lakshmi Manasa

institute: U.S. FDA

data_processing:
https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.
Read out is relative flourescent units (RFU) which is directly proportional to the amount of target protein in the initial sample, as informed by a standard curve generate for each protein-SOMAmer pair. Raw RFU is normalized as described in the data processing step above.

extract_protocol: EDTA plasma from whole blood


title: PT10M, KCit, GROUND, MALE, replicate 5

description: Library name: S_143

tag: tissue

tag: treatment


title: 8003_Pleg_low_0

tag: timepoint


title: PT10M, KCit, GROUND, MALE, replicate 4

description: Library name: S_142


title: Covid-19 covalescent plasma 1 low

value: Covid-19 covalescent plasma


title: PT9M, KCit, GROUND, MALE, replicate 3

description: Library name: S_141


title: Covid-19 covalescent plasma 2 low


title: PT9M, KCit, GROUND, MALE, replicate 2

description: Library name: S_140


title: PT9M, KCit, GROUND, MALE, replicate 1

description: Library name: S_139


title: 8083_Avonex_intermed_120

treatment_protocol: Subjects were randomized between IFNβ-1a (15 µg) and pegIFNβ-1a (62.5 µg).

value: 15 μg


title: 8083_Avonex_intermed_144


title: 8083_Avonex_intermed_96


title: PT8F, KCit, GROUND, FEMALE, replicate 2

description: Library name: S_137


title: PT8F, KCit, GROUND, FEMALE, replicate 3

description: Library name: S_138


title: 8083_Avonex_intermed_72


title: PT8F, KCit, GROUND, FEMALE, replicate 1

description: Library name: S_136


title: 8083_Avonex_intermed_48


title: 8083_Avonex_intermed_32


title: PT10M, CaOx, GROUND, MALE, replicate 6

description: Library name: S_135

value: 1 ng/ml Calcium Oxalate


title: 8083_Avonex_intermed_16


title: PT10M, CaOx, GROUND, MALE, replicate 5

description: Library name: S_134


title: PT10M, CaOx, GROUND, MALE, replicate 4

description: Library name: S_133


title: Sorted T CD4 memory cells, LC11837, Recovered control

description:
Library name: LC11837-Memory
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)

value: PBMCs

value: T-cell

tag: age

value: male

tag: severity

value: Severe


title: 8083_Avonex_intermed_8

tag: drug group


title: 8083_Avonex_intermed_0

tag: delivery


title: PT9M, CaOx, GROUND, MALE, replicate 3

description: Library name: S_132


title: PT9M, CaOx, GROUND, MALE, replicate 2

description: Library name: S_131


title: 8083_Avonex_intermed_3

tag: dose


title: PT9M, CaOx, GROUND, MALE, replicate 1

description: Library name: S_130


title: 8081_Pleg_intermed_312_repeat


title: PT8F, CaOx, GROUND, FEMALE, replicate 3

description: Library name: S_129


title: PT8F, CaOx, GROUND, FEMALE, replicate 2

description: Library name: S_128


title: 8081_Pleg_intermed_216


title: 8081_Pleg_intermed_312


title: PT8F, CaOx, GROUND, FEMALE, replicate 1

description: Library name: S_127


title: 8081_Pleg_intermed_144


title: PT10M, Control, GROUND, MALE, replicate 6

description: Library name: S_126

value: Control


title: PT10M, Control, GROUND, MALE, replicate 5

description: Library name: S_125


title: PT10M, Control, GROUND, MALE, replicate 4

description: Library name: S_124


title: 8081_Pleg_intermed_120


title: Sorted T CD4 memory cells, LC11373, Recovered control

description:
Library name: LC11373-Memory
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)

value: Moderate


title: 8081_Pleg_intermed_72


title: PT9M, Control, GROUND, MALE, replicate 3

description: Library name: S_123


title: 8081_Pleg_intermed_96


title: 8081_Pleg_intermed_48


title: 8023_Pleg_low_216


title: 8081_Pleg_intermed_32


title: PT9M, Control, GROUND, MALE, replicate 2

description: Library name: S_122


title: PT9M, Control, GROUND, MALE, replicate 1

description: Library name: S_121


title: PT8F, Control, GROUND, FEMALE, replicate 3

description: Library name: S_120


title: 8081_Pleg_intermed_8


title: 8081_Pleg_intermed_16


title: 8081_Pleg_intermed_3


title: PT8F, Control, GROUND, FEMALE, replicate 2

description: Library name: S_119


title: 8081_Pleg_intermed_0


title: PT8F, Control, GROUND, FEMALE, replicate 1

description: Library name: S_118


title: PT6F, KCit, GROUND, FEMALE, replicate 6

description: Library name: S_117


title: 8076_Pleg_intermed_312


title: 8076_Pleg_intermed_216


title: 8076_Pleg_intermed_144


title: PT6F, KCit, GROUND, FEMALE, replicate 5

description: Library name: S_116


title: PT6F, KCit, GROUND, FEMALE, replicate 4

description: Library name: S_115


title: 8076_Pleg_intermed_120


title: PT6F, CaOx, GROUND, FEMALE, replicate 6

description: Library name: S_114


title: PT6F, CaOx, GROUND, FEMALE, replicate 5

description: Library name: S_113


title: 8076_Pleg_intermed_96


title: 8076_Pleg_intermed_72


title: PT6F, CaOx, GROUND, FEMALE, replicate 4

description: Library name: S_112


title: PT6F, Control, GROUND, FEMALE, replicate 6

description: Library name: S_111


title: 8076_Pleg_intermed_48


title: PT6F, Control, GROUND, FEMALE, replicate 5

description: Library name: S_110


title: 8076_Pleg_intermed_32


title: PT6F, Control, GROUND, FEMALE, replicate 4

description: Library name: S_109


title: 8076_Pleg_intermed_16


title: 8076_Pleg_intermed_8


title: PT7M, KCit, GROUND, MALE, replicate 6

description: Library name: S_108


title: PT7M, KCit, GROUND, MALE, replicate 5

description: Library name: S_107


title: 8076_Pleg_intermed_3


title: PT7M, KCit, GROUND, MALE, replicate 4

description: Library name: S_106


title: 8076_Pleg_intermed_0


title: PT6F, KCit, GROUND, FEMALE, replicate 2

description: Library name: S_104


title: 8074_Avonex_intermed_120

value: IM


title: PT6F, KCit, GROUND, FEMALE, replicate 3

description: Library name: S_105


title: 8074_Avonex_intermed_96


title: PT6F, KCit, GROUND, FEMALE, replicate 1

description: Library name: S_103


title: 8074_Avonex_intermed_48


title: 8074_Avonex_intermed_72


title: PT7M, KCit, GROUND, MALE, replicate 3

description: Library name: S_102


title: PT7M, KCit, GROUND, MALE, replicate 2

description: Library name: S_101


title: PT7M, KCit, GROUND, MALE, replicate 1

description: Library name: S_100


title: 8074_Avonex_intermed_32


title: 8074_Avonex_intermed_16


title: PT7M, CaOx, GROUND, MALE, replicate 2

description: Library name: S_98


title: 8074_Avonex_intermed_8


title: 8074_Avonex_intermed_3


title: PT7M, CaOx, GROUND, MALE, replicate 3

description: Library name: S_99


title: PT7M, CaOx, GROUND, MALE, replicate 1

description: Library name: S_97


title: 8074_Avonex_intermed_144


title: PT6F, CaOx, GROUND, FEMALE, replicate 3

description: Library name: S_96


title: PT6F, CaOx, GROUND, FEMALE, replicate 2

description: Library name: S_95


title: 8065_Avonex_intermed_144


title: PT6F, CaOx, GROUND, FEMALE, replicate 1

description: Library name: S_94


title: TMA2_07_1_CD11c

city: Rotterdam

first: Anneloes

last: van Krimpen

state: Zuid-Holland

address: Doctor Molewaterplein 40

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus MC

data_processing:
Fastq to DCC file conversion was performed using the GeoMxNGSPipeline (local installation), which includes trimming, stitching, alignment and deduplication of the reads.
The resulting counts were normalized using Q3 normalization and DEGs were calculated using a linear mixed model (LMM) as implemented by the GeomxTools v3.10.0 R-package.
Some samples were excluded from our downstream analyses due to low quality. We chose to include the raw files of these samples, but they are excluded from our processed data files.
Assembly: Hg38
Supplementary files format and content: counts_raw.txt files contain non-normalized counts per samples
Supplementary files format and content: counts_Q3norm.txt contain Q3-normalized counts per sample
Library strategy: Spatial Transcriptomics

source_name: Lymph node

extract_protocol:
Digital Spatial Profiling using the GeoMx Whole Transcriptome Atlas (WTA) (Nanostring Technologies, Seattle, WA, United States) was performed following manufacturer’s instructions. In brief, TMA tissue was stained for SYTO 13 (Nanostring Technologies), CD11c-Alexa Fluor 647 (Abcam), CD8a-Alexa Fluor 594 (Biolegend), and CD68-Alexa Fluor 532 (Novus Biologicals), and incubated overnight with GeoMx WTA probes. Within the paracortex, regions where CD11c+ and CD68+, and CD8+ cells co-localized were selected. From these regions, WTA probes from CD11c+, CD8+, and CD68+ cells were collected separately and sequenced using the Illumina Nextseq2000 sequencer. Paired-end clusters were generated, producing reads 26 bases in length.
Nanostring GeoMx DSP NGS Readout library prep

value: Lymph node

tag: disease state

value: Disease-free


title: 8074_Avonex_intermed_0

last: Chekka

address: 10903 New Hampshire Avenue


title: TMA2_07_1_CD8a


title: 8065_Avonex_intermed_120


title: TMA2_07_1_CD68


title: PT5F, CaOx, GROUND, FEMALE, replicate 3

description: Library name: S_93


title: TMA2_06_1_CD11c


title: 8065_Avonex_intermed_96


title: PT5F, CaOx, GROUND, FEMALE, replicate 2

description: Library name: S_92


title: 8065_Avonex_intermed_72


title: TMA2_06_1_CD68


title: TMA2_05_1_CD11c


title: TMA2_06_1_CD8a


title: PT5F, CaOx, GROUND, FEMALE, replicate 1

description: Library name: S_91


title: TMA2_05_1_CD8a


title: PT7M, Control, GROUND, MALE, replicate 3

description: Library name: S_90


title: 8065_Avonex_intermed_48


title: TMA2_05_1_CD68


title: TMA2_04_1_CD11c


title: TMA2_04_1_CD8a


title: PT7M, Control, GROUND, MALE, replicate 2

description: Library name: S_89


title: 8065_Avonex_intermed_16_repeat


title: TMA2_04_1_CD68


title: TMA2_03_1_CD11c


title: TMA2_03_1_CD8a


title: 8065_Avonex_intermed_16


title: TMA2_03_1_CD68


title: PT6F, Control, GROUND, FEMALE, replicate 3

description: Library name: S_87


title: 8065_Avonex_intermed_8


title: PT7M, Control, GROUND, MALE, replicate 1

description: Library name: S_88


title: TMA2_02_1_CD11c


title: TMA2_02_1_CD8a


title: PT6F, Control, GROUND, FEMALE, replicate 2

description: Library name: S_86


title: 8065_Avonex_intermed_32


title: 8065_Avonex_intermed_3


title: PT6F, Control, GROUND, FEMALE, replicate 1

description: Library name: S_85


title: TMA2_01_1_CD8a

value: Recurrence


title: TMA2_01_1_CD11c


title: 8065_Avonex_intermed_0


title: TMA2_02_1_CD68


title: TMA2_01_1_CD68


title: 8063_Pleg_intermed_312

value: SC


title: PT5F, Control, GROUND, FEMALE, replicate 3

description: Library name: S_84

value: Primary PTEC cell culture


title: TMA1_16_1_CD11c


title: TMA1_16_1_CD68


title: PT5F, Control, GROUND, FEMALE, replicate 2

description: Library name: EVT_28B

value: PTEC


title: TMA1_16_1_CD8a


title: 8063_Pleg_intermed_216


title: PT5F, Control, GROUND, FEMALE, replicate 1

description: Library name: EVT_28A


title: TMA1_15_1_CD11c


title: TMA1_15_1_CD8a


title: 8063_Pleg_intermed_144


title: PT10M, KCit, GROUND, MALE, replicate 3

description: Library name: EVT_27C

value: 1 ng/ml Calcium Oxalate + 250 µM Potassium Citrate


title: TMA1_14_1_CD11c


title: TMA1_15_1_CD68


title: TMA1_14_1_CD8a


title: 8063_Pleg_intermed_120


title: 8063_Pleg_intermed_96


title: PT10M, KCit, GROUND, MALE, replicate 1

description: Library name: EVT_27A


title: TMA1_13_1_CD11c


title: PT10M, KCit, GROUND, MALE, replicate 2

description: Library name: EVT_27B


title: TMA1_13_1_CD8a


title: TMA1_14_1_CD68


title: 8063_Pleg_intermed_72


title: PT10M, CaOx, GROUND, MALE, replicate 3

description: Library name: EVT_26C


title: TMA1_12_1_CD11c


title: 8063_Pleg_intermed_48


title: TMA1_12_1_CD8a


title: PT10M, CaOx, GROUND, MALE, replicate 2

description: Library name: EVT_26B


title: TMA1_12_1_CD68


title: PT10M, CaOx, GROUND, MALE, replicate 1

description: Library name: EVT_26A


title: 8063_Pleg_intermed_16


title: TMA1_11_1_CD11c


title: TMA1_11_1_CD8a


title: 8063_Pleg_intermed_32


title: TMA1_11_1_CD68


title: TMA1_13_1_CD68


title: PT10M, Control, GROUND, MALE, replicate 3

description: Library name: EVT_25C


title: TMA1_10_2_CD11c


title: 8063_Pleg_intermed_8


title: TMA1_10_2_CD8a


title: PT10M, Control, GROUND, MALE, replicate 2

description: Library name: EVT_25B


title: TMA1_10_2_CD68


title: TMA1_10_1_CD11c


title: 8063_Pleg_intermed_3


title: PT10M, Control, GROUND, MALE, replicate 1

description: Library name: EVT_25A


title: 8063_Pleg_intermed_0


title: TMA1_10_1_CD8a


title: TMA1_09_1_CD11c


title: TMA1_10_1_CD68


title: PT10M, KCit, FLIGHT, MALE, replicate 5

description: Library name: S_71

value: microgravity


title: PT10M, KCit, FLIGHT, MALE, replicate 6

description: Library name: S_72


title: TMA1_09_1_CD8a


title: 8058_Pleg_intermed_216


title: TMA1_09_1_CD68


title: 8058_Pleg_intermed_312


title: TMA1_08_1_CD11c


title: PT10M, KCit, FLIGHT, MALE, replicate 4

description: Library name: S_70


title: TMA1_08_1_CD8a


title: 8058_Pleg_intermed_144


title: TMA1_08_1_CD68


title: PT9M, KCit, FLIGHT, MALE, replicate 3

description: Library name: S_69


title: TMA1_07_1_CD11c


title: 8058_Pleg_intermed_120


title: 8058_Pleg_intermed_96


title: TMA1_06_1_CD11c


title: TMA1_07_1_CD8a


title: TMA1_07_1_CD68


title: 8058_Pleg_intermed_72


title: TMA1_06_1_CD8a


title: PT9M, KCit, FLIGHT, MALE, replicate 2

description: Library name: S_68


title: PT9M, KCit, FLIGHT, MALE, replicate 1

description: Library name: S_67


title: TMA1_06_1_CD68


title: PT8F, KCit, FLIGHT, FEMALE, replicate 3

description: Library name: S_66


title: TMA1_04_1_CD11c


title: 8058_Pleg_intermed_48


title: PT8F, KCit, FLIGHT, FEMALE, replicate 2

description: Library name: S_65


title: TMA1_04_1_CD68


title: 8058_Pleg_intermed_32


title: TMA1_04_1_CD8a


title: TMA1_03_1_CD11c


title: TMA1_03_1_CD8a


title: PT8F, KCit, FLIGHT, FEMALE, replicate 1

description: Library name: S_64


title: 8058_Pleg_intermed_16


title: TMA1_03_1_CD68


title: PT10M, CaOx, FLIGHT, MALE, replicate 6

description: Library name: S_63


title: 8058_Pleg_intermed_8


title: TMA1_02_1_CD11c


title: TMA1_02_1_CD8a


title: PT10M, CaOx, FLIGHT, MALE, replicate 5

description: Library name: S_62


title: TMA1_02_1_CD68


title: 8058_Pleg_intermed_3


title: TMA1_01_1_CD11c


title: 8058_Pleg_intermed_0


title: TMA1_01_1_CD8a


title: PT10M, CaOx, FLIGHT, MALE, replicate 4

description: Library name: S_61


title: TMA1_01_1_CD68


title: Oxygenation_3

city: Minato-ku

first: Yoshiki

last: Kuse

address: Shirokanedai 4-6-1

country: Japan

institute: The University of Tokyo

description: Library name: SAMPLE7

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary files format and content: Comma-delimited text files include RPM values for each sample.

source_name: Organoid

extract_protocol:
Human iPSC-liver tissue was dissected by surgical scissors and pipetting with lysis buffer was carried out a few minutes. RNA was extracted with PureLink™ RNA Mini Scale Kit (Thermo Fishcer Scientific).
RNA libraries were prepared using total RNA with an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific).

value: Organoid

tag: cell line

value: hiPSC

value: HEP, EC, MC


title: PT9M, CaOx, FLIGHT, MALE, replicate 3

description: Library name: S_60

value: 1 ng/ml Calcium Oxalate


title: Oxygenation_2

description: Library name: SAMPLE6


title: 8052_Pleg_intermed_312


title: Control_4

description: Library name: SAMPLE4


title: PT9M, CaOx, FLIGHT, MALE, replicate 2

description: Library name: S_59


title: 8052_Pleg_intermed_216


title: PT9M, CaOx, FLIGHT, MALE, replicate 1

description: Library name: S_58


title: Oxygenation_1

description: Library name: SAMPLE5


title: Control_3

description: Library name: SAMPLE3


title: 8052_Pleg_intermed_144


title: Control_2

description: Library name: SAMPLE2


title: 8052_Pleg_intermed_120_repeat


title: Control_1

description: Library name: SAMPLE1


title: PT8F, CaOx, FLIGHT, FEMALE, replicate 2

description: Library name: S_56


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array16

city: Cambridge

first: Neva

middle: Cherniavsky

last: Durand

state: MA

address: 75 Ames St

institute: Broad Institute

description: Library name: array16_mRNA

data_processing:
Demultiplexed fastqs were aligned with STAR solo
Assembly: hg38
Supplementary files format and content: Raw STAR solo outputs: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Dial-up transcript enrichment from single-cell WTA libraries was performed using a two-step PCR strategy. Target-specific primers for p16, p15, p14, and ANRIL were combined with a CA-SMART reverse primer to selectively amplify transcripts of interest while retaining cell barcodes and UMIs from the Seq-Well protocol. Amplified products underwent bead cleanup, followed by biotin pull-down (Dynabeads™ kilobaseBINDER™ Kit, Thermo 60101) to enrich the targeted transcripts, which were then eluted for downstream processing. See Methods section of the paper for further details.  WI-38 fibroblasts (ATCC CCL-75) were transduced with pooled CRISPRa libraries (771 gRNAs targeting 175 regions plus 83 controls; designed by the Broad Genetic Perturbation Platform) using a three-vector system (CROP-sgRNA-MS2, lenti dCAS-VP64_Blast, lentiMPH v2). Viral transductions were performed in HEK293FT cells and applied to WI-38 cells with polybrene. After 4–8 days, cells were harvested for single-cell RNA-seq.
Dial-up transcripts were subjected to a second PCR to add Illumina sequencing adapters (P5, P7), dual indices (i5, i7), and sequencing primer binding sites. Amplified libraries were purified with a 0.9X bead cleanup and eluted in 1X TE. Final libraries were sequenced on an Illumina NextSeq 500 using a 75-cycle kit with custom read 1 and custom i5 primers (20 cycles read 1 for cell barcode + UMI, 56 cycles read 2 for transcript sequence, and 2 × 8-bp index reads). See Methods section of the paper.  Single-cell RNA-seq was performed using Seq-Well (Gierahn et al. 2017; Aicher et al. 2019). Cells were loaded onto microwell arrays preloaded with poly-T capture beads, sealed with a semipermeable membrane, lysed, and mRNAs hybridized to beads. Reverse transcription, second-strand synthesis, and whole-transcriptome amplification were performed on-bead. Libraries were prepared via tagmentation (Illumina) and sequenced on an Illumina platform. for further details

value: fibroblast


title: PT8F, CaOx, FLIGHT, FEMALE, replicate 3

description: Library name: S_57


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array15

description: Library name: array15_mRNA


title: PT8F, CaOx, FLIGHT, FEMALE, replicate 1

description: Library name: S_55


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array15

description: Library name: array15_dial-up_CROP

data_processing:
Demultiplexed fastqs were aligned with STAR solo
Assembly: hg38
Supplementary files format and content: Raw STAR solo outputs: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CRISPR Screen


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array16

description: Library name: array16_dial-up_CROP


title: PT10M, Control, FLIGHT, MALE, replicate 6

description: Library name: S_54


title: 8052_Pleg_intermed_96

city: Silver Spring


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array14

description: Library name: array14_mRNA


title: 8052_Pleg_intermed_72


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array14

description: Library name: array14_dial-up_CROP


title: PT10M, Control, FLIGHT, MALE, replicate 5

description: Library name: S_53


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array13

description: Library name: array13_mRNA


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array13

description: Library name: array13_dial-up_CROP


title: PT10M, Control, FLIGHT, MALE, replicate 4

description: Library name: S_52


title: 8052_Pleg_intermed_32


title: 8052_Pleg_intermed_48


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array11

description: Library name: array11_mRNA


title: PT9M, Control, FLIGHT, MALE, replicate 3

description: Library name: S_51


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array12

description: Library name: array12_mRNA


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array12

description: Library name: array12_dial-up_CROP


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array11

description: Library name: array11_dial-up_CROP


title: 8052_Pleg_intermed_16


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array10

description: Library name: array10_mRNA


title: 8052_Pleg_intermed_120


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array10

description: Library name: array10_dial-up_CROP


title: 8052_Pleg_intermed_8


title: PT9M, Control, FLIGHT, MALE, replicate 1

description: Library name: S_49


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array9

description: Library name: array9_mRNA


title: PT9M, Control, FLIGHT, MALE, replicate 2

description: Library name: S_50


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array9

description: Library name: array9_dial-up_CROP


title: PT8F, Control, FLIGHT, FEMALE, replicate 3

description: Library name: S_48


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array8

description: Library name: array8_mRNA


title: 8052_Pleg_intermed_0


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array8

description: Library name: array8_dial-up_CROP


title: PT8F, Control, FLIGHT, FEMALE, replicate 2

description: Library name: S_47


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array7

description: Library name: array7_mRNA


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array7

description: Library name: array7_dial-up_CROP


title: 8052_Pleg_intermed_3


title: 8051_Avonex_intermed_144

value: 15 μg


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array6

description: Library name: array6_mRNA


title: 8051_Avonex_intermed_120


title: PT8F, Control, FLIGHT, FEMALE, replicate 1

description: Library name: S_46

value: Control


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array5

description: Library name: array5_mRNA


title: PT6F, KCit, FLIGHT, FEMALE, replicate 6

description: Library name: S_45


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array6

description: Library name: array6_dial-up_CROP


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array4

description: Library name: array4_mRNA


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array5

description: Library name: array5_dial-up_CROP


title: PT6F, KCit, FLIGHT, FEMALE, replicate 5

description: Library name: S_44


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array4

description: Library name: array4_dial-up_CROP


title: 8051_Avonex_intermed_72


title: PT6F, KCit, FLIGHT, FEMALE, replicate 4

description: Library name: S_43


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array3

description: Library name: array3_mRNA


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array3

description: Library name: array3_dial-up_CROP


title: 8051_Avonex_intermed_48


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array2

description: Library name: array2_mRNA


title: PT6F, CaOx, FLIGHT, FEMALE, replicate 6

description: Library name: S_42


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array2

description: Library name: array2_dial-up_CROP


title: CRISPRa screen mRNA scRNA-seq, WI-38 fibroblasts, array1

description: Library name: array1_mRNA


title: PT6F, CaOx, FLIGHT, FEMALE, replicate 5

description: Library name: S_41


title: CRISPRa screen and dial-up scRNA-seq, WI-38 fibroblasts, array1

description: Library name: array1_dial-up_CROP