title: HGDMEM-3

description:
Library name: 3RNA-AO-2761-11_S20
Column name in rawcounts_4media_RNAseq.txt: HGDMEM_3

treatment_protocol: For all experiments, 2x105 HepG2 cells were seeded in 6-well plates in EMEM containing 10% heat-inactivated FBS. 24 hours after seeding, wells were washed with PBS and the appropriate media (DMEM-HG, DMEM-LG, Plasmax or EMEM) containing 10% heat-inactivated FBS was added. Media was refreshed after 48 hours and cells were harvested 96 hours after transition to the different media types.

value: HGDMEM


title: CG30020WT_FLAG-ChIP_rep1

status: Public on Jan 08 2026

type: SRA

city: Bunkyo-ku

first: Raku

last: Saito

state: Tokyo-to

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

description: Library name: Sample11

library_source: genomic

data_processing:
Raw sequence reads were trimmed by fastp.
Trimmed reads were mapped to drosophila dm6 (BDGP6) genome by bowtie2.
Uniquely mapped reads were extracted by samtools.
Matrix bigwig files were produced by deeptools.
Peak calling were performed by MACS2.
Assembly: dm6
Supplementary files format and content: general bigwig, narrowPeak file format

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
nc14 (2h10min-2h40min) early embryo for ChIP and adult ovary for RNA-seq
Prepared by manufacturer's protocol of NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: tissue

value: embryo

tag: cell line

value: nc14 embryo

tag: genotype


title: T. turgidum Queule Heat Rep1

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

description: Library name: TA2QUEU

library_source: transcriptomic

data_processing:
Raw sequencing reads were pseudo-aligned and quantified using Kallisto (v0.50.1) with a k-mer size of 31. The following reference transcriptomes were used: Triticum aestivum (IWGSC RefSeq v2.1) , Triticum turgidum (Svevo v1) , and Triticum monococcum (TA10622 v1.1). Differential expression analysis was performed using DESeq2 v1.42 in R.
Assembly: IWGSC RefSeq v2.1 for T.aestivum, Svevo v1 for T.turgidum, TA10622 v1.1 for T.monococcum
Supplementary files format and content: tsv files includes raw counts and tpm

molecule: total RNA

organism: Triticum turgidum

source_name: Wheat grain

growth_protocol: Field experiments were conducted at the Experimental Station of the Universidad Austral de Chile (UACh) in Valdivia (39° 47' S, 73° 14' W), Chile. The crops were grown under typical temperate conditions with supplemental irrigation to prevent water stress. Plots were fertilized with 150 kg/ha N and 300 kg/ha P2O5 at sowing, with an additional 150 kg/ha N during mid-tillering.

extract_protocol:
Total RNA was isolated from complete caryopses (harvested from central spikelets) using a modified CTAB-based protocol. RNA quality was assessed using a Nanoquant Infinite M200 spectrophotometer(A260/A280 ratios between 1.8-2.0)
Illumina RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Sample Prep Kit following the manufacturer's protocol. Unique barcodes were incorporated for multiplexing.

treatment_protocol: Thermal treatments were applied during the early grain-filling period (10-14 days after anthesis) using temperature-controlled polyethylene chambers. The experiment compared a Control (ambient temperature) against a severe Heat Stress treatment (TT2, up to 32°C mean temperature). Grain samples for RNA-seq were collected 3 hours after imposing the heat stress treatment on day 10 after anthesis.

value: Wheat grain

value: Tetraploid

tag: cell type

value: 10 DAA (3h post-stress)

value: Queule

tag: treatment

value: Heat (TT2)

tag: batch

value: replicate 1


title: RNA-seq of HU-HSA-2 with glucose rep2

city: Sapporo

first: Suzuki

last: Tamami

state: Hokkaido

address: Kita-18-jo, Nishi-9-chome, Kita-ku

department: Department of Clinical Sciences, Faculty of Veterinary

institute: Hokkaido University

description:
Library name: RNA_H2_25mM_48h_2
GeneExpressionMatrixTPM_H2_48h_CF3.tsv

data_processing:
Sequencing reads were mapped to the CanFam3.1 canine reference genome using STAR.
Expression levels were estimated using RSEM. Differential expression was analyzed with edgeR 3.42.0
Assembly: CanFam3.1
Supplementary files format and content: tsv file include TPM count in each sample

molecule: polyA RNA

organism: Canis lupus familiaris

growth_protocol: DMEM as indictaed glucose concentration with 10% fetal bovine serum and penicillin–streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA isolation kit
mRNA-seq libraries were constructed using a NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: w/o 25 mM glucose for 4 or 48 hours

value: with glucose


title: LGDMEM-3

city: Melbourne

first: Kristin

middle: K

last: Brown

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: 3RNA-AO-2761-10_S19
Column name in rawcounts_4media_RNAseq.txt: LGDMEM_3

data_processing:
QC, alignment, and counting were performed in Galaxy.
Sample QC was performed using FastQC (v0.72). Reads were trimmed using Cutadapt (v1.16)
Reads were mapped to human genome assembly (Ensembl hg19, GRCh37) using RNA STAR (v2.7.5b)
Counting was performed using featurecounts (v1.6.3)
Differentially expressed genes were identified using Degust (Limma-Voom v3.40.6)
Assembly: Reads were mapped to human genome assembly (Ensembl hg19, GRCh37)
Supplementary files format and content: Count file generated by featureCounts

organism: Homo sapiens

growth_protocol: HepG2 cells were maintained in EMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1mM sodium pyruvate, and 2 mM glutamine. The cells were grown in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel) as per manufacturer's instructions.
cDNA libraries were prepared using QuantSeq 3' mRNA seq kit (Lexogen).

value: Hepatic cell

value: WT

value: LGDMEM


title: CG30020deltaZAD_FLAG-ChIP_rep2

description: Library name: Sample10


title: CG30020deltaZAD_FLAG-ChIP_rep1

description: Library name: Sample9


title: RNA-seq of HU-HSA-2 with glucose rep1

description:
Library name: RNA_H2_25mM_48h_1
GeneExpressionMatrixTPM_H2_48h_CF3.tsv


title: RNA-seq of HU-HSA-2 without glucose rep3

description:
Library name: RNA_H2_0mM_48h_3
GeneExpressionMatrixTPM_H2_48h_CF3.tsv

value: without glucose


title: T. turgidum Queule Control Rep2

description: Library name: CBQUEU

value: Control

value: replicate 2


title: EMEM-3

description:
Library name: 3RNA-AO-2761-09_S18
Column name in rawcounts_4media_RNAseq.txt: EMEM_3

value: EMEM


title: CG30020_FLAG-ChIP_rep2

description: Library name: Sample8


title: Plasmax-3

description:
Library name: 3RNA-AO-2761-08_S17
Column name in rawcounts_4media_RNAseq.txt: Plasmax_3

value: Plasmax


title: RNA-seq of HU-HSA-2 without glucose rep2

description:
Library name: RNA_H2_0mM_48h_2
GeneExpressionMatrixTPM_H2_48h_CF3.tsv


title: CG2678RA_FLAG-ChIP_rep2

description: Library name: Sample6

value: embryo


title: IFNG -/-_3

city: Columbia

first: John

last: Driver

state: MO

address: 1201 Rollins Street

country: USA

institute: University of Missouri

description: Library name: G0330

library_source: transcriptomic single cell

data_processing:
The gene matrix data was obtained using Cell Ranger (v7.0.1) and Cellbender (v0.2.2).
Assembly: Sscrofa 11.1
Supplementary files format and content: matrix h5 files

organism: Sus scrofa

source_name: endometrial

extract_protocol:
Previously frozen endometrial samples from IFNG–/– recipients and control gilts were used for single-nuclei isolation
Nuclei were loaded into the 10x Chromium system (10x Genomics) using the Single Cell 3′ Reagent Kit v3

value: endometrial

value: IFNG -/-


title: CG30020_FLAG-ChIP_rep1

description: Library name: Sample7

value: nc14 embryo


title: RNA-seq of HU-HSA-2 without glucose rep1

description:
Library name: RNA_H2_0mM_48h_1
GeneExpressionMatrixTPM_H2_48h_CF3.tsv


title: EMEM-2

description:
Library name: 3RNA-AO-2761-05_S14
Column name in rawcounts_4media_RNAseq.txt: EMEM_2


title: SKOV-3 cisplatin-resistant, KDM5B knockout, H3K4me3 (ChIP)

city: Incheon

first: So Hee

last: Kwon

address: 85, Songdogwahak-ro, Yeonsu-gu

department: Pharmacy

country: South Korea

institute: Yonsei University

description: Library name: SKOV-3 CDDP KDM5B KO, ChIP

data_processing:
ChIP-Seq data processing entailed the trimming of adapter sequences from both ends (10 bp) using Trim Galore (version 0.6.7).
Subsequent alignment of the trimmed reads to the human reference genome GRCh38 was achieved using bwa (version 0.7.18).
Only mappings with a quality score above 10 were retained and organized using SAMtools (version 1.15.1), after which duplicates were removed utilizing the Picard toolkit (MarkDuplicates version 3.2.0-1).
Peaks calling for H3K4me3 were conducted with MACS3 (version 3.0.3), excluding regions within ENCODE Blacklist areas.
Peaks were annotated with ChIPseeker (version 1.38.0) and visualized using deepTools Toolkit (version 3.5.5).
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: SKOV-3 and SKOV-3 CDDP were cultured in RMPI medium supplemented with 10% FBS and 1% penicillin-streptomycin. All cells were incubated in humidified chambers with temeperature maintained at 37 ℃with 5% CO2.

extract_protocol:
Prior to cell lysis, cells were cross-linked with 1% formaldehyde for 7 minutes at 37°C to preserve protein-DNA complexes. Cells were lysed and chromatin was sheared to an average size of 200 bp to 500 bp using sonication for 5 min at 20% amplitude.
DNAs were amplified and subjected to DNA library construction using Illumina DNA Prep Kit (Illumina, Inc., San Diego, CA, USA) following the manufacturer’s instructions. The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (#KK4854, KAPA BIOSYSTEMS) and qualified using the D5000 Screen Tape (Agilent Technologies, Waldbronn, Germany).

value: epithelial ovarian adenocarcinoma

value: KDM5B knockout

tag: drug resistance

value: cisplatin

tag: chip antibody

value: H3K4me3 (Millipore, ABE305)


title: LGDMEM-2

description:
Library name: 3RNA-AO-2761-06_S15
Column name in rawcounts_4media_RNAseq.txt: LGDMEM_2


title: SKOV-3 cisplatin-resistant, KDM5B knockout, H3K4me3 (Input)

description: Library name: SKOV-3 CDDP KDM5B KO, Input

value: Rabbit IgG Control (GenScript, A01008)


title: CG2678RA_FLAG-ChIP_rep1

description: Library name: Sample5


title: HGDMEM-2

description:
Library name: 3RNA-AO-2761-07_S16
Column name in rawcounts_4media_RNAseq.txt: HGDMEM_2

value: Hepatic cell

value: HGDMEM


title: control_4

description: Library name: s971

value: control


title: Plasmax-2

description:
Library name: 3RNA-AO-2761-04_S13
Column name in rawcounts_4media_RNAseq.txt: Plasmax_2

value: WT


title: CG17361_FLAG-ChIP_rep2

description: Library name: Sample4


title: HGDMEM-1

description:
Library name: 3RNA-AO-2761-03_S12
Column name in rawcounts_4media_RNAseq.txt: HGDMEM_1


title: CG17361_FLAG-ChIP_rep1

description: Library name: Sample3


title: SKOV-3 cisplatin-resistant, H3K4me3 (Input)

description: Library name: SKOV-3 CDDP, Input


title: IFNG -/-_2

description: Library name: G0299


title: T. turgidum Queule Control Rep3

description: Library name: CCQUEU

value: Wheat grain

value: Tetraploid

value: 10 DAA (3h post-stress)

value: Queule

value: Control

value: replicate 3


title: control_3

description: Library name: G0359

value: endometrial


title: SKOV-3 parental, H3K4me3 (Input)

description: Library name: SKOV-3, Input


title: LGDMEM-1

description:
Library name: 3RNA-AO-2761-02_S11
Column name in rawcounts_4media_RNAseq.txt: LGDMEM_1

value: LGDMEM


title: T. turgidum Queule Control Rep1

description: Library name: CAQUEU

value: replicate 1


title: SKOV-3 cisplatin-resistant, H3K4me3 (ChIP)

description: Library name: SKOV-3 CDDP, ChIP

value: epithelial ovarian adenocarcinoma


title: EMEM-1

description:
Library name: 3RNA-AO-2761-01_S10
Column name in rawcounts_4media_RNAseq.txt: EMEM_1

value: EMEM


title: BEAF32_FLAG-ChIP_rep2

description: Library name: Sample2

value: embryo

value: nc14 embryo


title: control_2

description: Library name: s920


title: control_1

description: Library name: s0029


title: Plasmax-1

description:
Library name: 3RNA-AO-2761-12_S21
Column name in rawcounts_4media_RNAseq.txt: Plasmax_1

value: Hepatic cell

value: Plasmax


title: IFNG -/-_1

description: Library name: G0290

value: IFNG -/-


title: BEAF32_FLAG-ChIP_rep1

description: Library name: Sample1


title: PAH_sensitive_+PAH_DNA

status: Public on Jan 07 2026

city: Saint Paul

first: Caren

last: Weinhouse

state: Minnesota

address: 1988 Fitch Ave

institute: Oregon H

description:
Library name: KCERSE
R9.4.1. minion flow cell using a SQK-LSK-110 kit

data_processing:
Raw ONT signal data were basecalled using doroado under the super accurate 5mCG_5hmCG mode for downstream analysis
Assembly: de novo genome assembly (PRJNA1381666/SAMN54117932)
Supplementary files format and content: Minion Sequencing: sample.m.bed, sample_merged.output.vcf, sample.comparison.DMRs.txt

organism: Fundulus heteroclitus

extract_protocol:
Genomic DNA was extracted using a Qiagen DNEasy Blood and Tissue Minikit
Genomic DNA was prepped following the Oxford Nanopore MinION Instrument manufacturers protocol using the SQK-LSK-110 kit. https://nanoporetech.com/document/genomic-dna-by-ligation-sqk-lsk110

value: PAH exposed


title: NCI-H660 neuroendocrine prostate cancer replicate 1

city: Toon

first: RYUTA

last: WATANABE

address: 454 Shitsukawa

institute: Ehime University Hospital

description:
Library name: H660_1
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line

data_processing:
Raw sequencing reads were generated as 150 bp paired-end reads on a DNBSEQ-T7RS platform.
Transcript-level abundance was quantified using Salmon with alignment-free quasi-mapping to the human reference transcriptome.
Transcript-level abundance estimates were imported into R using the tximport package to generate gene-level count matrices.
Differential expression analysis and normalization were performed using DESeq2.
Variance-stabilizing transformation (VST) was applied to normalized count data for downstream analyses, including principal component analysis, sample distance calculations, and data visualization.
Assembly: GRCh38 (human reference genome)
Supplementary files format and content: Processed files are provided in tab-delimited text format and contain gene identifiers and corresponding expression values for each sample.

source_name: Prostate

growth_protocol: LNCaP and C4-2 cells were cultured at 37 °C with 5% CO₂ in RPMI-1640 medium supplemented with 10% fetal bovine serum, penicillin (20 U/mL), and streptomycin (100 µg/mL). NCI-H660 cells were maintained as a suspension culture in DMEM/F-12 (1:1) medium supplemented with 5% fetal bovine serum, GlutaMAX (1×), ITS-G supplement (1×), hydrocortisone (10 nM), and β-estradiol (10 nM).

extract_protocol:
Total RNA was extracted from cultured cells using standard phenol–chloroform–based or column-based extraction methods according to the manufacturer’s instructions. RNA quality and integrity were assessed prior to library preparation.
RNA sequencing libraries were prepared from poly(A)-selected RNA using the MGIEasy Fast RNA Library Prep Set according to the manufacturer’s protocol.

treatment_protocol: To model androgen receptor (AR) suppression, cells were cultured under untreated conditions, androgen deprivation using charcoal-stripped serum, or long-term exposure to bicalutamide or enzalutamide. Drug concentrations were gradually increased in a stepwise manner based on cell viability and recovery of proliferation. Cells were allowed to resume stable growth at each concentration before further dose escalation.

value: Prostate

value: neuroendocrine prostate cancer cell line

value: wild type

value: NT


title: NCI-H660 neuroendocrine prostate cancer replicate 2

description:
Library name: H660_2
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: PAH_tolerant_control_DNA

description:
Library name: RPClean
R9.4.1. minion flow cell using a SQK-LSK-110 kit

value: Control


title: PAH_sensitive_control_DNA

description:
Library name: KCClean
R9.4.1. minion flow cell using a SQK-LSK-110 kit


title: C4-2 enzalutamide replicate 2

description:
Library name: C4-2_ENZ_2
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line

source_name: Bone

value: Bone

value: prostate cancer cell line

value: Enzalutamide


title: C4-2 bicalutamide replicate 3

description:
Library name: C4-2_Bic_3
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line

value: Bicalutamide


title: NCI-H660 neuroendocrine prostate cancer replicate 3

description:
Library name: H660_3
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: PAH_tolerant_+PAH_DNA

description:
Library name: RPERSE
R9.4.1. minion flow cell using a SQK-LSK-110 kit


title: C4-2 enzalutamide replicate 3

description:
Library name: C4-2_ENZ_3
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: C4-2 enzalutamide replicate 1

description:
Library name: C4-2_ENZ_1
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: C4-2 bicalutamide replicate 2

description:
Library name: C4-2_Bic_2
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: C4-2 bicalutamide replicate 1

description:
Library name: C4-2_Bic_1
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: C4-2 charcoal-stripped serum replicate 3

description:
Library name: C4-2_CS_3
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line

value: CS(charcoal stripped medium)


title: C4-2 charcoal-stripped serum replicate 1

description:
Library name: C4-2_CS_1
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: C4-2 untreated replicate 2

description:
Library name: C4-2_NT_2
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: C4-2 untreated replicate 3

description:
Library name: C4-2_NT_3
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: C4-2 untreated replicate 1

description:
Library name: C4-2_NT_1
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: LNCaP enzalutamide replicate 2

description:
Library name: LNCaP_ENZ_2
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line

source_name: Lymph node

value: Lymph node

value: LNCaP


title: LNCaP biculutamide replicate 2

description:
Library name: LNCaP_Bic_2
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: C4-2 charcoal-stripped serum replicate 2

description:
Library name: C4-2_CS_2
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: LNCaP biculutamide replicate 3

description:
Library name: LNCaP_Bic_3
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: LNCaP enzalutamide replicate 1

description:
Library name: LNCaP_ENZ_1
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: SKOV-3 parental, H3K4me3 (ChIP)

description: Library name: SKOV-3, ChIP

value: epithelial ovarian adenocarcinoma

value: WT

value: H3K4me3 (Millipore, ABE305)


title: LNCaP charcoal-stripped serum replicate 2

description:
Library name: LNCaP_CS_2
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: LNCaP biculutamide replicate 1

description:
Library name: LNCaP_Bic_1
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: LNCaP charcoal-stripped serum replicate 1

description:
Library name: LNCaP_CS_1
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: LNCaP untreated replicate 3

description:
Library name: LNCaP_NT_3
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: LNCaP charcoal-stripped serum replicate 3

description:
Library name: LNCaP_CS_3
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: LNCaP untreated replicate 2

description:
Library name: LNCaP_NT_2
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: PBS-1

city: HANGZHOU

first: xiaohan

last: song

address: No.1 XIANGSHAN ROAD

country: China

institute: University of the Chinese Academy of Sciences Hangzhou Institute for Advanced Study

description:
Library name: Sample 4
PBS-1

data_processing:
Raw FASTQ files were quality checked using FastQC (v0.11.9) Alignment to hg38 was performed using Bowtie2 (v2.4.4). Peaks were called using MACS3 (v3.0.0b1). Peaks were annotated to nearest genes (ChIPseeker v1.34.1).
Assembly: hg38
Supplementary files format and content: Expressed_genes_FPKM_annotation.xlsx (RNA-Seq data, including FPKM values for sample 1-6)

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in DMEM supplemented containing 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in an incubator containing 5% CO2 at 37 oC with suitable humidity.

extract_protocol:
For RNA-seq analysis, total RNA was extracted using the TransZol Up High Performance RNA Extraction Kit (ET111-01-V2, TransGen Biotech)
For RNA-seq analysis, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations

treatment_protocol: HEK293T cells were treated with or without 20 mM oxamate for 24 h

value: HEK293T cells

value: human embryonic kidney cells


title: LNCaP enzalutamide replicate 3

description:
Library name: LNCaP_ENZ_3
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line


title: PBS-3

description:
Library name: Sample 6
PBS-3


title: oxamate-1

description:
Library name: Sample 1
oxamate-1

value: oxamate treated


title: oxamate-3

description:
Library name: Sample 3
oxamate-3


title: Ecoli_T30_S0.5_A1000_6h_2

city: Girona

first: Marie

last: Rescan

address: c/ Emili Grahit,101 (edifici H2O- ICRA)

department: Water Quality

country: Spain

institute: ICRA

description: Library name: 8bp-UDP0094

data_processing:
Reads from the first and second lanes were merged
Sequences quality was checked using FastQC and MultiQC. Trimmomatic was used for adapter removal (Nextera), trimming of the 3 first three bases with medium quality, and a sliding window of 5 bases was used to remove all reads with an average score quality below 25 in the window. T
The cleaned reads were aligned and mapped to the E. coli K12 MG1665 reference genome (NCBI GCF_904425475.1) using HiSat2 with parameters optimized for bacterial genomes (non-spliced alignment and retaining up to 200 alignments per read to handle repetitive regions).
SAM files were converted to BAM format, sorted, and indexed using SamTools.
Assembly: Read counting was performed using FADU.
Supplementary files format and content: tab delimited file include raw counts (column counts) for each sample

molecule: cytoplasmic RNA

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: 24 isogenic populations of Esherichia coli K12 MG1665 were grown in BHI broth from an initial density around 10^8.

extract_protocol:
NA was extracted and purified using the RNeasy (R) Protect Bacteria Mini Kit (Qiagen) following the protocol for enzymatic lysis and Proteinase K digestion of bacteria
Samples were sent to the National Center for Genomic Analysis (CNAG, Barcelona, Spain) for library preparation with the Ribo-Zero Plus Microbiome Depletion kit for rRNA removal

treatment_protocol: They exposed to all combination of two concentrations of atythromycin (0 vs. 1 µg/mL), two temperature (30 and 25 °C) and two salinities (0.085 and 0.585 M, for 6 hours

value: bacterial cell

tag: salinity treatment

tag: temperature treatment

tag: antibiotics treatment

tag: time

tag: replicate


title: Ecoli_T30_S0_A0_6h_1

description: Library name: 8bp-UDP0091


title: Ecoli_T30_S0.5_A0_6h_3

description: Library name: 8bp-UDP0088


title: Ecoli_T30_S0.5_A1000_6h_1

description: Library name: 8bp-UDP0090


title: LNCaP untreated replicate 1

description:
Library name: LNCaP_NT_1
Bulk RNA sequencing of AR inhibitor–treated prostate cancer cell line

value: wild type


title: PBS-2

description:
Library name: Sample 5
PBS-2


title: Ecoli_T30_S0_A1000_6h_2

description: Library name: 8bp-UDP0093


title: Nerve cells co-cultured with Vegf siRNA transfected IVD cells, sample 2

city: St. Louis

first: Simon

last: Tang

address: 425 S. Euclid Ave, Campus Box 8233, Tang Lab, Washington University School of Medicine

department: Orthopaedic Surgery

institute: Washington University in St. Louis

description: Library name: NervesVegfa2_LIB042641.genome_accepted_hits.bam

data_processing:
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: RNA-seq reads were aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1
Supplementary files format and content: tab delimined text file for each sample

growth_protocol: Human intervertebral disc (IVD) cells were isolated from the IVD tissue of eight patients removed during elective discectomy surgeries. IVD cells were isolated from the tissue and cultured in monolayer in F-12 medium with 10% FBS and 1% P/S. HMEC-1 were cultured in MCDB 131 medium containing 10 ng/mL epidermal growth factor, 500 mg/mL hydrocortisone, 1% P/S, 2 mM L-Glutamine and supplemented with 10% FBS.SH-SY5Y human neuroblastoma cell line was cultured in a 1:1 mixture of Eagle’s Minimum Essential Medium and Ham’s F12 medium, supplemented with 10% FBS and 1% P/S.

extract_protocol:
Post co-culture experiments, HMEC-1 or SH-SY5Y cells were lysed with TRIzol reagent and the total RNA was extracted with a Direct-zol RNA MicroPrep Kit.
Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol

treatment_protocol: IVD cells were plated and 1 ng/mL of IL-1β was added to the stimulate the cells for 24 hours. IL-1β was removed and cells were then transfected with Control, Scrambled siRNA (Scram) or VEGF siRNA (Vegfa)for 24 hours. Next, the IL-1β stimulated and siRNA transfected IVD cells were co-cultured with either SH-SY5Y neuronal cells (Nerves) for 48 hours or HMEC-1 endothelial cells (Endo) for 24 hours.

value: Neuronal


title: Ecoli_T30_S0_A1000_6h_1

description: Library name: 8bp-UDP0086


title: Nerve cells co-cultured with Scrambled siRNA transfected IVD cells, sample 3

description: Library name: NervesScram3_LIB042646.genome_accepted_hits.bam


title: Nerve cells co-cultured with Scrambled siRNA transfected IVD cells, sample 2

description: Library name: NervesScram2_LIB042642.genome_accepted_hits.bam


title: Ecoli_T25_S0.5_A1000_6h_3

description: Library name: 8bp-UDP0085


title: Nerve cells co-cultured with Vegf siRNA transfected IVD cells, sample 1

description: Library name: NervesVegfa1_LIB042637.genome_accepted_hits.bam


title: oxamate-2

description:
Library name: Sample 2
oxamate-2


title: Nerve cells co-cultured with Vegf siRNA transfected IVD cells, sample 3

description: Library name: NervesVegfa3_LIB042645.genome_accepted_hits.bam


title: Ecoli_T25_S0_A0_6h_3

description: Library name: 8bp-UDP0081


title: Ecoli_T30_S0.5_A0_6h_2

description: Library name: 8bp-UDP0092


title: Naive nerve cells (not co-cultured), sample 2

description: Library name: NervesNaive2_LIB042640.genome_accepted_hits.bam


title: Ecoli_T30_S0.5_A1000_6h_3

description: Library name: 8bp-UDP0087


title: Nerve cells co-cultured with Scrambled siRNA transfected IVD cells, sample 1

description: Library name: NervesScram1_LIB042638.genome_accepted_hits.bam


title: Ecoli_T25_S0.5_A0_6h_3

description: Library name: 8bp-UDP0082


title: Ecoli_T30_S0.5_A0_6h_1

description: Library name: 8bp-UDP0084V3


title: Naive nerve cells (not co-cultured), sample 1

description: Library name: NervesNaive1_LIB042636.genome_accepted_hits.bam


title: day14.rep3

type: RNA

city: Nanning

first: Xiao

last: Ru

state: Guangxi Zhuang Autonomous Region

address: 22 Shuangyong Road, Zhongshan Street, Qingxiu District, Nanning City, Guangxi Pr

institute: Guangxi Medical University

description:
Gene expression after culturing in collagen hydrogel for 14 days
3D culture,14d,replicate 3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryctolagus cuniculus

source_name: 3D culture,14d

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: After mixing rabbit bone marrow mesenchymal stem cells with collagen hydrogel, the mixture was cultured in a humidified incubator at 37°C with 5% CO₂. 3D culture model was maintained for 0 day , 7 days, 14 days and 21 days,respectively.

extract_protocol: Total RNA of cells in 3D culture model for 0, 7, 14, and 21 days was extracted with a HiPure Total RNA Kit (Mgenbio, Shanghai, China) and quantified with the NanoDrop2000. RNA was amplified and retroscribed into cDNA.

value: bone marrow mesenchymal stem cells

tag: sample type

value: 3D culture


title: day21.rep1

description:
Gene expression after culturing in collagen hydrogel for 21 days
3D culture,21d,replicate 1

source_name: 3D culture,21d

treatment_protocol: After mixing rabbit bone marrow mesenchymal stem cells with collagen hydrogel, the mixture was cultured in a humidified incubator at 37°C with 5% CO₂. 3D culture model was maintained for 0 day , 7 days, 14 days and 21 days,respectively.


title: Nerve cells co-cultured with IL-1ϐ stimulated IVD cells, sample 3

description: Library name: NervesIVDStim3_LIB042643.genome_accepted_hits.bam


title: Naive nerve cells (not co-cultured), sample 3

description: Library name: NervesNaive3_LIB042644.genome_accepted_hits.bam


title: Ecoli_T30_S0_A1000_6h_3

description: Library name: 8bp-UDP0089


title: Ecoli_T25_S0_A1000_6h_3

description: Library name: 8bp-UDP0083


title: day14.rep1

description:
Gene expression after culturing in collagen hydrogel for 14 days
3D culture,14d,replicate 1


title: day14.rep2

description:
Gene expression after culturing in collagen hydrogel for 14 days
3D culture,14d,replicate 2


title: Ecoli_T25_S0.5_A1000_6h_2

description: Library name: 8bp-UDP0080


title: Ecoli_T25_S0_A0_6h_2

description: Library name: 8bp-UDP0077


title: Ecoli_T25_S0_A1000_6h_2

description: Library name: 8bp-UDP0079


title: Ecoli_T25_S0.5_A0_6h_1

description: Library name: 8bp-UDP0074V3


title: day7.rep1

description:
Gene expression after culturing in collagen hydrogel for 7 days
3D culture,7d,replicate 1

source_name: 3D culture,7d


title: day7.rep2

description:
Gene expression after culturing in collagen hydrogel for 7 days
3D culture,7d,replicate 2


title: Endothelial cells co-cultured with Vegf siRNA transfected IVD cells, sample 3; technical replicate 2

description: Library name: EndoVegfa3.2_LIB018987.genome_accepted_hits.bam

value: Endothelial


title: OVCA420 PRSS23 shRNA_46 replicate 2

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description:
Library name: OVCA420_PRSS23_shRNA46_rep2
RNA-seq library from OVCA420 cells treated with PRSS23 shRNA_46 (biological replicate 2).

data_processing:
Demultiplexing and base calling were performed by the sequencing core standard pipeline.
Read quality control was performed using FastQC and summarized with MultiQC.
Reads were aligned to the human reference genome (hg38/GRCh38) with STAR to generate BAM alignment files.
Gene-level quantification was performed using Ensembl gene models to generate a complete gene count matrix.
Downstream normalization and differential expression analyses were performed as described in the manuscript.
Assembly: hg38 (GRCh38)
Supplementary files format and content: PRSS23_RNAseq_gene_counts.tsv.gz: tab-delimited matrix of gene-level raw read counts (rows=Ensembl gene IDs; columns=12 libraries).

source_name: ovary

growth_protocol: Cell lines were maintained under standard culture conditions as described in the manuscript (Materials and Methods: Cell Lines and Culture Conditions).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen); RNA quality was assessed and high-quality RNA (RIN ≥ 8) was used for RNA-seq.
Poly(A)+ strand-specific RNA-seq libraries were prepared by the sequencing core using its standard protocol and sequenced as paired-end reads (2×101 bp) on an Illumina platform.

treatment_protocol: Cells were transduced with lentiviral PRSS23-targeting shRNAs (shRNA_30 or shRNA_46) or a non-targeting shRNA control (NT) as described in the manuscript.

value: ovary

value: ovarian cancer cell line

value: PRSS23 shRNA_46


title: OVCA420 PRSS23 shRNA_46 replicate 1

description:
Library name: OVCA420_PRSS23_shRNA46_rep1
RNA-seq library from OVCA420 cells treated with PRSS23 shRNA_46 (biological replicate 1).


title: day0.rep3

description:
Gene expression after culturing in collagen hydrogel for 0 day
3D culture,0d,replicate 3

source_name: 3D culture,0d


title: day21.rep3

description:
Gene expression after culturing in collagen hydrogel for 21 days
3D culture,21d,replicate 3


title: day0.rep1

description:
Gene expression after culturing in collagen hydrogel for 0 day
3D culture,0d,replicate 1


title: Nerve cells co-cultured with IL-1ϐ stimulated IVD cells, sample 2

description: Library name: NervesIVDStim2_LIB042639.genome_accepted_hits.bam


title: Nerve cells co-cultured with IL-1ϐ stimulated IVD cells, sample 1

description: Library name: NervesIVDStim1_LIB042635.genome_accepted_hits.bam


title: OVCA420 non-targeting shRNA control replicate 2

description:
Library name: OVCA420_NT_rep2
RNA-seq library from OVCA420 cells treated with non-targeting shRNA control (biological replicate 2).

value: non-targeting shRNA control


title: Endothelial cells co-cultured with Vegf siRNA transfected IVD cells, sample 2; technical replicate 2

description: Library name: EndoVegfa2.2_LIB018983.genome_accepted_hits.bam


title: Endothelial cells co-cultured with Vegf siRNA transfected IVD cells, sample 3; technical replicate 1

description: Library name: EndoVegfa3.1_LIB018986.genome_accepted_hits.bam


title: Ecoli_T25_S0.5_A1000_6h_1

description: Library name: 8bp-UDP0076V3


title: OVCA420 PRSS23 shRNA_30 replicate 1

description:
Library name: OVCA420_PRSS23_shRNA30_rep1
RNA-seq library from OVCA420 cells treated with PRSS23 shRNA_30 (biological replicate 1).

value: PRSS23 shRNA_30


title: Ecoli_T30_S0_A0_6h_3

description: Library name: 8bp-UDP0072V3


title: Ecoli_T30_S0_A0_6h_2

description: Library name: 8bp-UDP0071V3


title: Endothelial cells co-cultured with Vegf siRNA transfected IVD cells, sample 2; technical replicate 1

description: Library name: EndoVegfa2.1_LIB018982.genome_accepted_hits.bam


title: JHOC-5 PRSS23 shRNA_46 replicate 2

description:
Library name: JHOC5_PRSS23_shRNA46_rep2
RNA-seq library from JHOC-5 cells treated with PRSS23 shRNA_46 (biological replicate 2).


title: OVCA420 non-targeting shRNA control replicate 1

description:
Library name: OVCA420_NT_rep1
RNA-seq library from OVCA420 cells treated with non-targeting shRNA control (biological replicate 1).


title: day0.rep2

description:
Gene expression after culturing in collagen hydrogel for 0 day
3D culture,0d,replicate 2


title: MAPK14 knockout C2C12 cells, GM. biol rep 3

city: Shanghai

first: Rong

last: Huang

address: Shanghai Jiao Tong University, Minhang Campus, 800 Dongchuan Road, Minhang District, Shanghai 200240, China

institute: Shanghai Jiao Tong university

description: Library name: p38GM3

data_processing:
FASTQ files were aligned to the Mus musculus reference genome (GRCm39) using STAR (version 2.7.1a) with a two-pass alignment strategy.
Gene and transcript quantification was performed using RSEM (version 1.3.3).
Differential expression analysis was conducted in R (version 4.3.1) using the DESeq2 package (version 1.40.2).
Differentially expressed genes were defined with an adjusted P value (false discovery rate, FDR) < 0.05.
Assembly: Mus musculus reference genome GRCm39
Supplementary files format and content: No processed data files are submitted. Raw sequencing data are available in SRA. Data processing and analysis details are described in the Methods section.

organism: Mus musculus

growth_protocol: C2C12 mouse myoblast cells (ATCC, CRL-1772) were cultured in growth medium (GM) consisting of high-glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37 °C in a humidified incubator with 5% CO₂. The medium was replaced every 2 days, and cells were passaged at 70–90% confluence.

extract_protocol:
Total RNA was extracted and purified from all samples using the M5 HiPer Universal Plus RNA Mini Kit (MF167, Mei5 Biotech, Beijing, China) according to the manufacturer’s instructions. RNA quality and integrity were assessed prior to library preparation.
All RNA samples were sent to Novogene Co., Ltd (Beijing, China) for quality control (Sample QC). After RNA library preparation, cDNA libraries are sequenced on Illumina NovaSeq platforms using a paired-end 150 bp sequencing strategy. Approximately 6 Gb of clean data per sample was obtained, with a uniquely mapped read rate exceeding 75%. Three biological replicates were included.

treatment_protocol: For myogenic differentiation, C2C12 cells were seeded in 6-well plates and grown in GM until reaching 50–60% confluence. The culture medium was then replaced with differentiation medium (DM) consisting of DMEM supplemented with 2% horse serum (Gibco). DM was replaced every 24 h to induce myotube formation. For RNA-seq experiments, wild-type and Mapk14 knockout (Mapk14−/−) C2C12 cells were cultured in GM until approximately 60% confluence and then either maintained in GM or switched to DM for 5 days, with medium replacement every 2 days, prior to RNA extraction.

value: Mouse skeletal muscle myoblasts

value: GM (Growth Medium)


title: Ecoli_T25_S0_A1000_6h_1

description: Library name: 8bp-UDP0075V3


title: Endothelial cells co-cultured with Vegf siRNA transfected IVD cells, sample 1; technical replicate 2

description: Library name: EndoVegfa1.2_LIB011929.genome_accepted_hits.bam


title: day7.rep3

description:
Gene expression after culturing in collagen hydrogel for 7 days
3D culture,7d,replicate 3


title: Ecoli_T25_S0_A0_6h_1

description: Library name: 8bp-UDP0073V3


title: OVCA420 PRSS23 shRNA_30 replicate 2

description:
Library name: OVCA420_PRSS23_shRNA30_rep2
RNA-seq library from OVCA420 cells treated with PRSS23 shRNA_30 (biological replicate 2).


title: Ecoli_T25_S0.5_A0_6h_2

description: Library name: 8bp-UDP0078


title: Endothelial cells co-cultured with Vegf siRNA transfected IVD cells, sample 1; technical replicate 1

description: Library name: EndoVegfa1.1_LIB011928.genome_accepted_hits.bam


title: JHOC-5 PRSS23 shRNA_30 replicate 2

description:
Library name: JHOC5_PRSS23_shRNA30_rep2
RNA-seq library from JHOC-5 cells treated with PRSS23 shRNA_30 (biological replicate 2).


title: day21.rep2

description:
Gene expression after culturing in collagen hydrogel for 21 days
3D culture,21d,replicate 2


title: GB2, siHDAC7_2

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

state: NY

address: 1301 Morris Park Avenu

department: Computational and Systems Biology

institute: Albert Einstein College of Medicine

description: Library name: Sample 8

data_processing:
Sequence reads were mapped to the hg38 assembly of the human genome using the hisat2 program.  Reads with a mapping quality of at least 30 were retained.
Read summarization was performed with featureCounts using Refseq annotations as found in http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
Assembly: hg38
Supplementary files format and content: tab-delimited raw_counts.txt file is a table with raw counts for each gene in each sample

growth_protocol: glioma stem cells were maintained in Neural basal A medium supplimented with EGF/FGF, glutamax, heparin, vitamin B27 and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using the Trizol reagent based protocol.
Completed with Genewiz (RNA with PolyA)

treatment_protocol:
HDAC7 was knockdown at a confluency of 60-70%  using siRNA encapsulated in lipid X2
Transfection was performed for 48 hours and RNA was extracted thereafter

value: glioma stem cells

value: HDAC7 knockdown

value: siRNA against HDAC7

value: 48 hours


title: JHOC-5 PRSS23 shRNA_46 replicate 1

description:
Library name: JHOC5_PRSS23_shRNA46_rep1
RNA-seq library from JHOC-5 cells treated with PRSS23 shRNA_46 (biological replicate 1).


title: GB2, siControl_2

description: Library name: Sample 6

value: WT

value: siRNA control


title: JHOC-5 PRSS23 shRNA_30 replicate 1

description:
Library name: JHOC5_PRSS23_shRNA30_rep1
RNA-seq library from JHOC-5 cells treated with PRSS23 shRNA_30 (biological replicate 1).


title: GB2, siControl_1

description: Library name: Sample 5


title: MAPK14 knockout C2C12 cells, GM. biol rep 1

description: Library name: p38GM1


title: Endothelial cells co-cultured with Scrambled siRNA transfected IVD cells, sample 3; technical replicate 2

description: Library name: EndoScram3.2_LIB018985.genome_accepted_hits.bam


title: MAPK14 knockout C2C12 cells, DM. biol rep 3

description: Library name: p38DM3

value: DM (Differentiation Medium)


title: GB2, siHDAC7_1

description: Library name: Sample 7


title: Endothelial cells co-cultured with Scrambled siRNA transfected IVD cells, sample 3; technical replicate 1

description: Library name: EndoScram3.1_LIB018984.genome_accepted_hits.bam


title: MAPK14 knockout C2C12 cells, GM. biol rep 2

description: Library name: p38GM2


title: GB11, siControl_1

description: Library name: Sample 1


title: MAPK14 knockout C2C12 cells, DM. biol rep 2

description: Library name: p38DM2


title: JHOC-5 non-targeting shRNA control replicate 1

description:
Library name: JHOC5_NT_rep1
RNA-seq library from JHOC-5 cells treated with non-targeting shRNA control (biological replicate 1).


title: WT C2C12 cells, GM. biol rep 3

description: Library name: wtGM3


title: SKOV3 cells, GATA4_3

city: Chongqing

first: Xin

last: Yin

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing medical university

data_processing:
We use Bowtie2 to align the clean reads to the genome sequence, and then use RSEM to calculate the gene expression level of each sample. RSEM is a software package for RNA-seq reads to calculate the expression of genes and transcripts.
Abundance estimates were reported in raw read counts (fragments per thousand nucleotides per million mapped reads).
Assembly: hg19_ucsc
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: SKOV8 cells

growth_protocol: SKOV3 epithelial cells were maintained in Mc5a supplemented with 10% fetal bovine serum (FBS) and antibody in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvest using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacture's protocols.

treatment_protocol: SKOV3 epithelial cells were tansfection with vector and GATA4 using PEI for 48 hours, respectively

value: SKOV8 cells

value: epithelial cells

value: GATA4 overexpression


title: Endothelial cells co-cultured with Scrambled siRNA transfected IVD cells, sample 1; technical replicate 2

description: Library name: EndoScram1.2_LIB011927.genome_accepted_hits.bam

value: Endothelial


title: Endothelial cells co-cultured with Scrambled siRNA transfected IVD cells, sample 2; technical replicate 2

description: Library name: EndoScram2.2_LIB018981.genome_accepted_hits.bam


title: Endothelial cells co-cultured with Scrambled siRNA transfected IVD cells, sample 1; technical replicate 1

description: Library name: EndoScram1.1_LIB011926.genome_accepted_hits.bam


title: GB11, siHDAC7_1

description: Library name: Sample 3


title: GB11, siHDAC7_2

description: Library name: Sample 4


title: JHOC-5 non-targeting shRNA control replicate 2

description:
Library name: JHOC5_NT_rep2
RNA-seq library from JHOC-5 cells treated with non-targeting shRNA control (biological replicate 2).

value: ovary

value: ovarian cancer cell line


title: SKOV3 cells, control2

source_name: SKOV4 cells

value: SKOV4 cells


title: Endothelial cells co-cultured with Scrambled siRNA transfected IVD cells, sample 2; technical replicate 1

description: Library name: EndoScram2.1_LIB018980.genome_accepted_hits.bam


title: WT C2C12 cells, DM. biol rep 3

description: Library name: wtDM3


title: WT C2C12 cells, GM. biol rep 2

description: Library name: wtGM2


title: Naïve endothelial cells (not co-cultured), sample 2; technical replicate 1

description: Library name: EndoNaive2.1_LIB018978.genome_accepted_hits.bam


title: SKOV3 cells, control1

source_name: SKOV3 cells

value: SKOV3 cells


title: SKOV3 cells, GATA4_2

source_name: SKOV7 cells

value: SKOV7 cells


title: Naive endothelial cells (not co-cultured), sample 1; technical replicate 2

description: Library name: EndoNaive1.2_LIB011925.genome_accepted_hits.bam


title: MAPK14 knockout C2C12 cells, DM. biol rep 1

description: Library name: p38DM1

value: Mouse skeletal muscle myoblasts


title: GB11, siControl_2

description: Library name: Sample 2

value: glioma stem cells


title: SKOV3 cells, GATA4_1

source_name: SKOV6 cells

value: SKOV6 cells


title: WT C2C12 cells, DM. biol rep 2

description: Library name: wtDM2


title: WT C2C12 cells, GM. biol rep 1

description: Library name: wtGM1

value: GM (Growth Medium)


title: SKOV3 cells, control3

source_name: SKOV5 cells

value: SKOV5 cells


title: MKP-CTC41-EVs

city: Montpellier

first: Said

last: Assou

state: Languedoc-Roussillon

address: 80 av Augustin fliche, IRMB

country: France

institute: IRMB, Hôpital Saint Eloi

description: Gene expression data from megakaryocyte progenitors

hyb_protocol: Following fragmentation and terminal labeling, 5.5 μg of ds cDNA were hybridized for 16 hrs at 45°C and 60 rpm on Clariom D mouse chips, as per the manufacturer’s protocol (Affymetrix, Santa Clara, CA, USA # 902922). The arrays were stained by using GeneChip Fluidics Station 450.

scan_protocol: Chips were scanned with Affymetrix GeneChip™ scanner 3000

data_processing: Data were generated with Affymetrix Expression Console v 1.4.1.46

label: biotin

source_name: Mice none marrow

label_protocol: Biotinylated ds cDNA was prepared according to the WT PICO kit from 3 ng of total RNA

growth_protocol: Blood was collected from mice via cardiac puncture using sodium citrate as an anticoagulant, and platelets were isolated through centrifugation, with leukocyte contamination assessed microscopically. Platelets from mice of the same group were pooled to ensure sufficient RNA yield, while bone marrow cells were processed by centrifugation, lysis, and fixation. RNA from platelets and megakaryocytes was extracted using the mirVana miRNA Isolation Kit, and RNA quality was assessed with an Agilent BioAnalyzer 2100. Biotinylated cDNA was synthesized from 5 ng of total RNA, fragmented, labeled, and hybridized onto Clariom D Mouse microarrays. The arrays were washed, stained, and scanned, with data generated and analyzed using Affymetrix software for downstream transcriptomic profiling.

extract_protocol: RNeasy Mini Kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: After cell pelleting, pooled of platelets and megakaryocyte progenitors were either directly used for RNA isolation and transcriptome analysis by microarray, or treated with magnetic microbeads to eliminate contaminating leukocytes and erythrocytes before transcriptome analysis.

value: megakaryocyte progenitors


title: WT C2C12 cells, DM. biol rep 1

description: Library name: wtDM1

value: WT


title: tRNA-only oxidative-stressed E. coli replicate 2

city: Martinsried

first: Kirsten

last: Jung

address: Großhaderner Str. 2-4

country: Germany

institute: LMU

description: Library name: oxidative_stress_nanotRNAseq_2

library_source: other

data_processing:
Basecalling with Dorado v5.0.0 using default parameters.
mRNAe samples: alignment to deduplicated E. coli transcriptome (supplementary file "deduplicated_Ecoli_transcriptome.fasta") with Minimap2 v2.26 using parameters ‘-x map-ont -k14’. Nano-tRNAseq samples: alignment to unique E. coli tRNA sequences (supplementary file "Ecoli_tRNAs.fasta") with Minimap2 v2.26 using parameters ‘-y -t8 -ax splice -k7 -w3 -n1 -m13 -s30 -A2 -B1 -O1,32 -E1,0’.
Nano-tRNAseq samples only: demultiplexing by Immagina Biotechnology (Trento, Italy) with proprietary software.
Nano-tRNAseq samples only: remapping to unique E. coli tRNA sequences (supplementary file "Ecoli_tRNAs.fasta") with Minimap2 v2.26 using parameters '-x map-ont -k9'.
Read filtering with SAMtools v1.22 to remove secondary, chimeric, and unmapped reads.
Read filtering with BamQVFilter v0.1.0 at a threshold of Q > 9 (mRNAe samples) or Q > 5 (Nano-tRNAseq samples).
Processing with the script "get_bcerror_freqs.py" (https://github.com/rnabioco/tRNA004/tree/main/src/modifications) to calculate basecalling error at each nucleotide position.
Assembly: mRNAe samples: transcriptome file based on the GCA_000005845 ASM584v2 genome assembly using transcriptional unit coordinates published on RegulonDB (Salgado et al., 2024) with duplicate tRNA/rRNA gene sequences removed (supplementary file "deduplicated_Ecoli_transcriptome.fasta"). Nano-tRNAseq samples: unique E.coli tRNA sequences (supplementary file "Ecoli_tRNAs.fasta").
Supplementary files format and content: Tab-delimited txt files produced with the script "get_bcerror_freqs.py" (https://github.com/rnabioco/tRNA004/tree/main/src/modifications) with genomic position, canonical nucleotide, and RNA biotype added for each site.

molecule: other

organism: Escherichia coli str. K-12 substr. MG1655

source_name: whole cells

extract_protocol:
RNA was isolated using the PCI protocol (Sambrook & Russell, 2006) with some modifications (Petrov et al., 2022).
mRNAe samples were depleted of tRNA/rRNA, then prepared with an Oxford Nanopore Technologies SQK-RNA004 library preparation kit. Nano-tRNAseq samples were prepared with a commercial Nano-tRNAseq library preparation kit (Immagina Biotechnology, Trento, Italy).

value: whole cells

value: H2O2-treated cells


title: tRNA-only oxidative-stressed E. coli replicate 1

description: Library name: oxidative_stress_nanotRNAseq_1


title: S919

city: Charlestown

first: Keisuke

last: Otani

state: MA

address: 149 13th Street, Rm 4406

department: Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
sequencing reads were aligned to GRCh37 (hg19) using Star Aligner ver. 2.4.0 and the resulting .bam files analyzed using Regtools ver. 0.5.2. to detect splicing events.
Using Bowtie2 ver.2.2.1, sequencing reads were aligned to a fasta file containing the union of the aforementioned splice junction sequences.
Assembly: hg19
Supplementary files format and content: processed data are .xlsx format, and they contain the expression level for each splice junctions

source_name: bone

extract_protocol:
RNA was harvested using FormaPure Total kit (Beckman Coulter). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for targeted RNA-seqwere prepared using SureSelectXT RNA Direct (Agilent) following manufacture's protocol.

value: bone


title: HLPS-D3

first: Jingya

last: Li

address: 189 Guo Shou Jing Road

institute: Shanghai Institute of Materia Medica

description: Library name: SAMPLE12

data_processing:
The library was sequenced using the Illumina NovaSeq 6000 sequencing platform (Paired end150) to generate raw reads.
Assembly: Raw paired-end fastq reads were filtered by TrimGaloreto discard the adapters and low quality bases via calling the Cutadapt tool. The clean reads obtained were then aligned to the mm10/hg19 mouse/human genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie.
Supplementary files format and content: xlsx flie includs FPKM values for each sample

source_name: Liver

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample.
Illumina library construction was performed according to the manufacturer's instructions (Illumina,USA). Oligo-dT primers are used to transverse mRNA to obtain cDNA(APExBIO, Cat. No. K1159). Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA)

value: Liver


title: S918

source_name: prostate

value: prostate


title: Naive endothelial cells (not co-cultured), sample 1; technical replicate 1

description: Library name: EndoNaive1.1_LIB011924.genome_accepted_hits.bam

value: Endothelial


title: S916

source_name: liver

value: liver


title: S917


title: HLPS-D1

description: Library name: SAMPLE10


title: MKP-CTC41.5G-EVs


title: MKP-control (PBS)


title: tRNA-only acid-stressed E. coli replicate 1

description: Library name: acid_stress_nanotRNAseq_1

value: HCl-treated cells


title: PLT-control (PBS)

description: Gene expression data from platelet

source_name: Mice blood

value: platelet


title: S914

source_name: bladder

value: bladder


title: S915


title: LPS-D4

description: Library name: SAMPLE9


title: PLT-CTC41-EVs

description: Gene expression data from platelet


title: S911


title: tRNA-only acid-stressed E. coli replicate 2

description: Library name: acid_stress_nanotRNAseq_2


title: HLPS-D2

description: Library name: SAMPLE11


title: S912


title: S910


title: S913


title: Naive endothelial cells (not co-cultured), sample 2; technical replicate 2

description: Library name: EndoNaive2.2_LIB018979.genome_accepted_hits.bam


title: tRNA-only unstressed E. coli replicate 1

description: Library name: no_stress_nanotRNAseq_1

value: Untreated cells


title: HONC4

description: Library name: SAMPLE6


title: tRNA-only unstressed E. coli replicate 2

description: Library name: no_stress_nanotRNAseq_2


title: PLT-CTC41.5G-EVs

description: Gene expression data from platelet


title: S905


title: LPS-D3

description: Library name: SAMPLE8


title: LPS-D1

description: Library name: SAMPLE7


title: In vitro transcribed E. coli RNA replicate 2

description: Library name: IVT_mRNAe_2

source_name: in vitro transcribed RNA

value: in vitro transcribed RNA


title: S907


title: S909


title: HONC3

description: Library name: SAMPLE5


title: In vitro transcribed E. coli RNA replicate 1

description: Library name: IVT_mRNAe_1


title: S146


title: S147


title: S145


title: S144


title: DFNC4

description: Library name: SAMPLE3


title: DFNC3

description: Library name: SAMPLE2


title: mRNA-enriched oxidative-stressed E. coli replicate 1

description: Library name: oxidative_stress_mRNAe_1


title: S141


title: HONC2

description: Library name: SAMPLE4


title: S139


title: S140


title: DFNC2

description: Library name: SAMPLE1


title: mRNA-enriched acid-stressed E. coli replicate 2

description: Library name: acid_stress_mRNAe_2


title: mRNA-enriched acid-stressed E. coli replicate 1

description: Library name: acid_stress_mRNAe_1


title: 2-week SN Grin2a WT Sample 6

city: Cambridge

first: Ally

last: Nicolella

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

description: Library name: grin2a_P14-SN-WT6

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25/
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: Substantia Nigra

growth_protocol: Brain dissection was performed in the cryostat using frozen brain tissues collected from Grin2b mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.

extract_protocol:
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.
RNA-seq

value: Substantia Nigra

value: Grin2a WT


title: S138


title: mRNA-enriched oxidative-stressed E. coli replicate 2

description: Library name: oxidative_stress_mRNAe_2


title: mRNA-enriched unstressed E. coli replicate 2

description: Library name: no_stress_mRNAe_2


title: S136


title: S135


title: 2-week SN Grin2a WT Sample 5

description: Library name: grin2a_P14-SN-WT5


title: mRNA-enriched unstressed E. coli replicate 1

description: Library name: no_stress_mRNAe_1


title: S142


title: 2-week SN Grin2a WT Sample 4

description: Library name: grin2a_P14-SN-WT4


title: S133


title: S143


title: 2-week SN Grin2a WT Sample 3

description: Library name: grin2a_P14-SN-WT3


title: 2-week SN Grin2a WT Sample 2

description: Library name: grin2a_P14-SN-WT2


title: CRISPRi pool 5 gRNA

city: Santa Monica

first: Lucy

last: Bicks

state: CA

address: 1033 3rd street, apartment 106, apartment 106

department: Neurology

institute: UCLA School of Medicine

description:
Library name: I5_gRNA
10x Genomics - gRNA barcodes

data_processing:
ScRNA and gRNA libraries were aligned to the human genome (GRCh38) with CellRanger (7.0.1). Cells were filtered to include cells with >200 features and percent mitochondria less than 10%. Doublets were then removed using using DoubletFinder (8406 doublets, 13.2%). After QC and doublet filtering prior to selecting uniquely gRNA positive cells, the median nCounts per cell was 17071 and the median nGenes was 4675, from 55216 singlets (Extended Data Figure 13c). Single cell data was then processed using standard best practices for Seurat v5. Briefly, we log-normalized counts and performed integration using SCTransform followed by clustering.
Assembly: GRCh38-2020-A
Supplementary files format and content: Seurat v5 processed single cell object
Supplementary files format and content: Seurat (unprocssed) single cell object with gRNA barcodes assigned to cells
Supplementary files format and content: whitelist showing gene and gRNA (barcode) used
Library strategy: CRISPR Screen

source_name: Neural Progenitor Cells

growth_protocol: A 6 well plate was coated with Matrigel (1:50 in Knockout DMEM) for 2 h at 37˚C. A dox-inducible NGN2 iPSC line, WTC11 (from Li Gan (Weill Cornell), available at Coriell), was seeded at 75,000 cells/cm2 in MTeSR+ supplemented with 10 µM of Y-27632. 24 h afterwards, cells were subjected to Induction Medium (1:100 Glutamax, 1:66.7 20% Glucose in DMEM:F12, N2 supplement 1:100, Doxycycline 2 µg/ml , LDN-193189 200 nM, SB431542 10 µM, XAV939 2µM). Day 2 Involves the induction and selection using the following media: 1:100 Glutamax, 1:66.7 20% Glucose in DMEM:F12, N2 supplement 1:100, Doxycycline 2 µg/ml , LDN-193189 100 nM, SB431542 5 µM, XAV939 1 µM, and Puromycin 5 µg/ml. 24 h post selection, the media is changed fully with NES Complete & selection media (DMEM:F12, Glutamax 1:50, Pen.Strep 1:100, MEM NEAA 1:100, B27 w/o Vitamin A 1:50, N2 Supplement 1:100, EGF 10 ng.ml, bFGF 10 ng/mL, puromycin 5 µg/ml, and Y-27632 1:1,000. One day later and for the duration of the culture, cells are put on NES complete medium which is the same as listed above apart from the use of Y-27632 and puromycin. Once hNPCs have been generated, 500k hNPCs are seeded in every well of a 6 well plate with NPC maintenance media (n= 6 replicates).

extract_protocol:
Sorted cells then underwent single cell RNA extraction using the 10x genomics Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1(PN-1000121).  The 10x protocol for library prep was adapted from Gasperini et al., 2019. gRNA libraries were sequenced separately from scRNA (GEX) libraries.
The 10x protocol for library prep was adapted from Gasperini et al., 2019150. gRNA libraries were sequenced separately from scRNA (GEX) libraries.

treatment_protocol: To each well, GFP-KRAB-dCas9 (40 µL/well of a 6 well) plasmid and CROP-dsRed-gRNA (33 µL/well of a 6 well) were added. Media was replaced daily for 7 days before cells were collected for FACs. FACS was done with BD FACSAria, Software FACS Diva 8.0.2. For FACS, hNPCs were washed with PBS, dissociated into single cell suspension using Accutase, and resuspended in 500 µl FACS buffer per replicate (7.5% BSA, 0.5 M EDTA, RNase inhibitor 1:200, DAPI 0.5mg/ml). A population of NPCs that were not transfected with plasmid were used as a negative control to establish FACs gating. Double positive GFP/TdTomato (dCAS9/sgRNA double expressing) cells were sorted for downstream single cell analyses (~10,000 cells per replicate, ~20 % of live cell fraction).

value: Neural Progenitor Cells

value: gRNA library treated


title: S129


title: S130


title: S131


title: S137


title: CRISPRi pool 4 gRNA

description:
Library name: I4_gRNA
10x Genomics - gRNA barcodes

value: WT


title: CRISPRi pool 6 gRNA

description:
Library name: I6_gRNA
10x Genomics - gRNA barcodes


title: 2-week SN Grin2a -/-  Sample 5

description: Library name: grin2a_P14-SN-KO5

value: Grin2a -/-


title: S128


title: S127


title: S125


title: S124


title: S132


title: 2-week SN Grin2a -/-  Sample 4

description: Library name: grin2a_P14-SN-KO4


title: S134


title: CRISPRi pool 3 gRNA

description:
Library name: I3_gRNA
10x Genomics - gRNA barcodes


title: S126


title: CRISPRi pool 6 GEX

description:
Library name: I6_GEX
10x Genomics


title: S121


title: S122


title: 2-week SN Grin2a -/-  Sample 3

description: Library name: grin2a_P14-SN-KO3


title: S123


title: CRISPRi pool 1 gRNA

description:
Library name: I1_gRNA
10x Genomics - gRNA barcodes


title: 2-week SN Grin2a -/-  Sample 2

description: Library name: grin2a_P14-SN-KO2


title: S120


title: 2-week SN Grin2a -/-  Sample 1

description: Library name: grin2a_P14-SN-KO1


title: CRISPRi pool 5 GEX

description:
Library name: I5_GEX
10x Genomics


title: S119


title: S118


title: S116


title: 2-week SN Grin2a +/-  Sample 6

description: Library name: grin2a_P14-SN-HT6

value: Grin2a +/-


title: CRISPRi pool 4 GEX

description:
Library name: I4_GEX
10x Genomics


title: CRISPRi pool 2 gRNA

description:
Library name: I2_gRNA
10x Genomics - gRNA barcodes


title: S115


title: 2-week SN Grin2a +/-  Sample 5

description: Library name: grin2a_P14-SN-HT5


title: CRISPRi pool 3 GEX

description:
Library name: I3_GEX
10x Genomics


title: S114


title: S112


title: S113


title: S106


title: S109


title: CRISPRi pool 2 GEX

description:
Library name: I2_GEX
10x Genomics


title: 2-week SN Grin2a +/-  Sample 3

description: Library name: grin2a_P14-SN-HT3


title: S111


title: CRISPRi pool 1 GEX

description:
Library name: I1_GEX
10x Genomics


title: 4-week SN Grin2a WT Sample 5

description: Library name: grin2a_P28-SN-WT5


title: S107


title: HK_I537T_p63alphaKO3

city: Napoli

first: Dario

last: Antonini

address: Strada Vicinale Cupa Cintia, 21

country: Italy

institute: University of Naples "Federico II"

description: Library name: HK_I537T_p63alphaKO3

data_processing:
Alignment of the reads performed with RNA STAR
Measure of gene expression performed with featureCounts
Differential expression analysis performed with DESeq2
Assembly: hg38
Supplementary files format and content: Tabular files of normalized counts contain GeneID, Gene Symbol and normalized counts of each sample

source_name: skin

growth_protocol: cells were growth in FAD Medium supplied with ROCKi and EGF

extract_protocol:
Direct-Zol micro prep kit (Zymo Research, R2061)
Nextflex Rapid Directional RNA-Seq kit 2.0 with Poly(A) 2.0 (PerkinElmer)

treatment_protocol: cells were nucleofected with Cas9 with or without sgRNA1 and sgRNA2 for the generation of p63alpha KO

value: skin

value: primary cells

value: epidermal keratinocytes

value: p63 I537T mutant

value: nucleofection with Cas9 + sgRNA1 and sgRNA2 for the generation of p63alpha KO


title: S105

value: prostate


title: 2-week SN Grin2a +/-  Sample 2

description: Library name: grin2a_P14-SN-HT2


title: HK_I537T_p63alphaKO2

description: Library name: HK_I537T_p63alphaKO2


title: 4-week SN Grin2a WT Sample 4

description: Library name: grin2a_P28-SN-WT4


title: 2-week SN Grin2a +/-  Sample 4

description: Library name: grin2a_P14-SN-HT4


title: HK_I537T_p63alphaKO1

description: Library name: HK_I537T_p63alphaKO1


title: Pre-BIIS from EPO-exposed mice, biological rep2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: Gene expression data from Pre-BIIS precursors isolated from the bone marrow of EPO-exposed mice

hyb_protocol: WT plus hybridation protocol

scan_protocol: GeneChip Hybridization, Wash and Stain kit

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

source_name: Pre-BIIS precursors isolated from mouse bone marrow

label_protocol: WT pico amplification protocol

growth_protocol: C57BL/7 mice were housed in standard conditions and exposed to either PBS (control) or EPO (treatement)

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy Micro Kit

treatment_protocol: Mice were subcutaneously injected every two days for two weeks with either 40 IU/mouse of recombinant human EPO (rhEPO) or control (PBS)

value: bone marrow


title: Pre-BIIS from EPO-exposed mice, biological rep1


title: Pre-BIIS from control mice, biological rep2

description: Gene expression data from Pre-BIIS precursors isolated from the bone marrow of control mice


title: HK_I537T_CTR3

description: Library name: HK_I537T_CTR3

value: nucleofection with Cas9


title: S103


title: S102


title: S101


title: HK_I537T_CTR2

description: Library name: HK_I537T_CTR2


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) , rep4

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

description: Library name: trained4

data_processing:
Quality control was performed using FastQC (v0.11.8).
Adapter trimming and low-quality filtering were performed using Trim Galore! (v0.6.6) with a Phred quality threshold of 20.
Reads were aligned to the Mus musculus reference genome (GRCm38.p6) using STAR aligner (v2.7.5b) with default parameters.
Gene-level read counts were obtained using Salmon (v1.2.1) with GENCODE release M25 as the transcriptome reference.
Genes with fewer than 5 total reads across all samples were removed, and normalization was performed using the median-ratio method from DESeq2 (v1.30.1)
Assembly: GRCm38.p6 (mouse)
Supplementary files format and content: Comma-delimited (CSV) file containing raw counts for each gene in each sample
Supplementary files format and content: Comma-delimited (CSV) file containing normalized counts for each sample

source_name: bone marrow

growth_protocol: Isolated monocytes were seeded at a concentration of 5 x 105 monocytes/mL (1 x 105 monocytes in 200mL of media) in 96-well plates (Corning Inc., Corning, NY). Cell culture media for all conditions was Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 1% Penicillin/Streptomycin (P/S), 1% HEPES, 1% sodium pyruvate, 1% MEM non-essential amino acids (Thermo Fisher Scientific, Waltham, MA), 0.001% 2-mercaptoethanol (Sigma-Aldrich, St. Louis, MO), and 30 ng/mL recombinant murine M-CSF (PeproTech, Cranbury, NJ). For cryopreservation experiments, bone marrow cells were preserved in FBS containing 10% dimethyl sulfoxide (Sigma-Aldrich) and stored in liquid nitrogen for 24h

extract_protocol:
Naive, activated, and trained BMDM were collected and processed for RNA isolation using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Barcoded RNA-seq libraries were generated using the NEBNext® Single Cell/Low Input RNA Library Prep Kit (New England Biolabs, Ipswich, MA). Size and concentration of the libraries were checked using the 2100 Bioanalyzer DNA HS chip (Agilent Technologies). Libraries with different barcodes were equimolarly pooled and concentration of each pool assessed by a Qubit® fluorometer (Thermo Fisher Scientific).
NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs)

treatment_protocol: For naive BMDM, monocytes were culture with media for 6 days, changing the media on day 3. For activated BMDM, monocytes were cultured with media for 6 days, changing the media on day 3, and BMDM were stimulated with 10 ng/mL of LPS from Salmonella enterica serotype abortus equi (Sigma-Aldrich) for 6h. For trained BMDM, monocytes were cultured on day 0 with 10 µg/mL of β-glucan from Saccharomyces cerevisiae (InvivoGen, San Diego, CA) or Candida albicans as previously described. On day 3 the media was changed and, after 3 days of resting, trained BMDM were re-stimulated with LPS for 6h. Supernatants were collected on day 0 (unstimulated), day 3 before washing (stimulus 1), day 6 before washing (resting) and 6h after LPS stimulation (stimulus 2) and stored at -80ºC, while BMDM were recovered using a cell scraper (Corning Inc., Corning, NY) and processed for downstream applications.

value: Bone marrow-derived macrophages (BMDM)

value: Trained


title: 4-week SN Grin2a WT Sample 1

description: Library name: grin2a_P28-SN-WT1

value: Substantia Nigra


title: 4-week SN Grin2a WT Sample 2

description: Library name: grin2a_P28-SN-WT2

value: Grin2a WT


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) , rep3

description: Library name: trained3


title: NHEK_p63alphaKO3

description: Library name: NHEK_p63alphaKO3

value: wild type


title: Pre-BIIL from EPO-exposed mice, biological rep1

description: Gene expression data from Pre-BIIL precursors isolated from the bone marrow of EPO-exposed mice

source_name: Pre-BIIL precursors isolated from mouse bone marrow


title: Pre-BIIL from EPO-exposed mice, biological rep2


title: HK_I537T_CTR1

description: Library name: HK_I537T_CTR1


title: NHEK_p63alphaKO2

description: Library name: NHEK_p63alphaKO2


title: Pre-BIIS from control mice, biological rep1


title: 4-week SN Grin2a WT Sample 3

description: Library name: grin2a_P28-SN-WT3


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) , rep1

description: Library name: trained1


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) , rep2

description: Library name: trained2


title: 4-week SN Grin2a -/-  Sample 2

description: Library name: grin2a_P28-SN-KO2


title: NHEK_CTR3

description: Library name: NHEK_CTR3


title: 4-week SN Grin2a -/-  Sample 3

description: Library name: grin2a_P28-SN-KO3


title: 4-week SN Grin2a -/-  Sample 4

description: Library name: grin2a_P28-SN-KO4


title: Pre-BI from EPO-exposed mice, biological rep1

description: Gene expression data from Pre-BI precursors isolated from the bone marrow of EPO-exposed mice

source_name: Pre-BI precursors isolated from mouse bone marrow


title: 4-week SN Grin2a -/-  Sample 1

description: Library name: grin2a_P28-SN-KO1


title: Pre-BI from EPO-exposed mice, biological rep2


title: Pre-BIIL from control mice, biological rep2

description: Gene expression data from Pre-BIIL precursors isolated from the bone marrow of control mice


title: NHEK_p63alphaKO1

description: Library name: NHEK_p63alphaKO1


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 ng/mL LPS (day 6) , rep4

description: Library name: LPS_activated4

value: LPS activated


title: Pre-BIIL from control mice, biological rep1


title: 4-week SN Grin2a +/-  Sample 5

description: Library name: grin2a_P28-SN-HT5


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 ng/mL LPS (day 6) , rep3

description: Library name: LPS_activated3


title: NHEK_CTR2

description: Library name: NHEK_CTR2


title: 4-week SN Grin2a -/-  Sample 5

description: Library name: grin2a_P28-SN-KO5


title: NHEK_CTR1

description: Library name: NHEK_CTR1


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 ng/mL LPS (day 6) , rep1

description: Library name: LPS_activated1


title: BMDMs from C57BL/6 mice cultured with M-CSF, naive , rep4

description: Library name: naive4

value: Naive


title: 4-week SN Grin2a +/-  Sample 4

description: Library name: grin2a_P28-SN-HT4


title: Pro-B from EPO-exposed mice, biological rep2

description: Gene expression data from Pro-B precursors isolated from the bone marrow of EPO-exposed mice

source_name: Pro-B precursors isolated from mouse bone marrow


title: siGPNMB imHMVECs 3

city: Nashville

first: Ryan

last: Stark

state: Tennessee

address: 2200 Children's Way, 5121 Doctors' Office Tower

institute: Vanderbilt University Medical Center

description:
Library name: 9533-SP-0006
Column name

data_processing:
Raw sequencing reads (FASTQ files) were uploaded to the Partek Flow server (Partek Inc., USA) for quality control and data analysis. Reads were aligned to the human genome (GRCh38/hg38 assembly) using STAR aligner (version 2.7.8a). Gene-level quantification was performed against Ensembl transcript annotations (version 93) using Partek’s expectation-maximization (EM) algorithm. Read counts were normalized to fragments per kilobase of exon per million mapped fragments (FPKM) and log2-transformed with an offset of 0.0001. Hierarchical clustering and principal component analysis (PCA) were performed on normalized data using Partek Genomics Suite. Differential gene expression analysis was visualized using volcano plots generated via VolcaNoseR (https://huygens.science.uva.nl/VolcaNoseR). The top 20 upregulated and downregulated genes were displayed in a heatmap created with Morpheus software (https://software.broadinstitute.org/morpheus/). Gene Ontology (GO) biological process enrichment analysis was conducted using the Enrichr platform (https://maayanlab.cloud/Enrichr/).
Assembly: hg38 assembly
Supplementary files format and content: FPKM values for each sample

growth_protocol: Human dermal microvascular endothelial cells (HMVEC, hTERT-immortalized) were obtained from the American Type Culture Collection (ATCC, #CRL-4060; Manassas, VA, USA). The cells were cultured in Vascular Cell Basal Medium (ATCC; PCS-100-030), supplemented with Microvascular Endothelial Cell Growth Kit-VEGF (ATCC; PCS-110-041), penicillin (100 U/mL), and streptomycin (100 U/mL), at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. On-column DNase I treatment was performed to eliminate potential genomic DNA contamination.
RNA quality and integrity were assessed at the Vanderbilt Technologies for Advanced Genomics (VANTAGE) Core using a NanoDrop spectrophotometer and an Agilent Bioanalyzer (Agilent Technologies, USA). Samples with sufficient RNA concentration, an A260/280 ratio of ~2.0, and high RNA Integrity Number (RIN) were selected for sequencing. Poly(A)-enriched RNA-seq libraries were prepared and sequenced on the Illumina NovaSeq 6000 platform (Illumina, USA) using 150 bp paired-end reads, yielding approximately 60 million passing filter (PF) reads per sample.

treatment_protocol: HMVECs were treated with siRNA (scrambled siControl, siGPNMB). siRNA was procured from Dharmacon (Revvity Inc., Waltham, MA, USA). siRNA (25 nmol/L) was incubated with Dharmafect (Dharmacon) in a serum-free medium for 20 min. The resultant complex of siRNA-Dharmafect was added to the cells in 5% FBS media without antibiotics for 6 h. Afterward, the transfection media was replaced with complete media, including antibiotics, for 72 h siRNA, according to the manufacturer’s guidelines.

value: CRL-4060 hTERT-immortalized

value: human microvascular endothelial cell

value: GPNMB knockdown

value: siRNA GPNMB


title: siGPNMB imHMVECs 2

description:
Library name: 9533-SP-0005
Column name

value: skin


title: Pre-BI from control mice, biological rep2

description: Gene expression data from Pre-BI precursors isolated from the bone marrow of control mice


title: 4-week SN Grin2a +/-  Sample 3

description: Library name: grin2a_P28-SN-HT3

value: Grin2a +/-


title: Pre-BI from control mice, biological rep1


title: 4-week SN Grin2a +/-  Sample 1

description: Library name: grin2a_P28-SN-HT1


title: Pro-B from EPO-exposed mice, biological rep1


title: BMDMs from C57BL/6 mice cultured with M-CSF, naive , rep2

description: Library name: naive2


title: Pro-B from control mice, biological rep2

description: Gene expression data from Pro-B precursors isolated from the bone marrow of control mice


title: siGPNMB imHMVECs 1

description:
Library name: 9533-SP-0004
Column name


title: 4-week SN Grin2a +/-  Sample 2

description: Library name: grin2a_P28-SN-HT2


title: BMDMs from C57BL/6 mice cultured with M-CSF, naive , rep1

description: Library name: naive1


title: siControl imHMVECs 2

description:
Library name: 9533-SP-0002
Column name

value: Wildtype

value: siRNA scrambled control


title: BMDMs from C57BL/6 mice cultured with M-CSF, naive , rep3

description: Library name: naive3

value: bone marrow


title: Patient B1, improving health status after sepsis originating from respiratory infection, miRNA

city: Budapest

first: Zsolt

last: Ronai

address: Ulloi u. 26.

department: Molecular Biology

country: Hungary

institute: Semmelweis University

description: Library name: SZ373mic

data_processing:
Trimmed sequence sets (FASTQ-formatted) were aligned to the genome sequences using HISAT2 with default parameters.
The aligned reads were collected in bam files and were aligned according to genomic coordinates using the SAMTOOLS program package before further use.
The function featureCounts (Rsubread R package) were used for counting reads for each gene.
Assembly: GRCH38 genome sequence version 39
Supplementary files format and content: tab delimited text file contains raw counts for each sample in case of both mRNA and miRNA datasets

source_name: 47-year-old male patient, day 3

extract_protocol:
RNAs from blood samples were isolated with TRIzol protocol and Tempus™ Spin RNA Isolation Kit according to the manufacturers’ instructions (TRIzol™ Reagent User Guide1 – ThermoFisher Scientific, Inc., Waltham, MA, USA; Tempus Blood RNA Tube and Tempus Spin RNA Isolation Kit User Guide2 ThermoFisher Scientific, Inc., Waltham, MA, USA). RNA concentration, quality and RNA integrity number (RIN) of each sample were measured using Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA) instruments using Eukaryotic Total RNA Nano Kit (RNA 6000) (Agilent Technologies, Inc., Santa Clara, CA, USA) according to manufacturer’s protocol.
RNA-Seq libraries were prepared from total RNA using Ultra II RNA Sample Prep kit (New England BioLabs, Inc., Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, poly-A RNAs were captured by oligo-dT conjugated magnetic beads then the mRNAs were eluted and fragmented at 94-Celsius degree. First strand cDNA was generated by random priming reverse transcription and after second strand synthesis step double stranded cDNA was generated. After repairing ends, A-tailing and adapter ligation steps adapter ligated fragments were amplified in enrichment PCR and finally sequencing libraries were generated.

value: blood

tag: gender

value: male

tag: condition


title: 12-week SN Grin2a WT Sample 5

description: Library name: grin2a_12w-SN-WT5


title: siControl imHMVECs 1

description:
Library name: 9533-SP-0001
Column name


title: siControl imHMVECs 3

description:
Library name: 9533-SP-0003
Column name


title: 12-week SN Grin2a WT Sample 3

description: Library name: grin2a_12w-SN-WT3


title: 12-week SN Grin2a WT Sample 4

description: Library name: grin2a_12w-SN-WT4


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) rep4

description: Library name: trained4

data_processing:
Reads were first evaluated for their quality using FastQC (v0.11.8)
Reads were trimmed for adapter sequences using Trim Galore! (v0.6.6)
Reads were aligned to the mouse genome reference GRCm38.p6 using Bowtie2 (version 2.2.8) with end-to-end mode, --sensitive and -X 2000 parameters
Reads aligned to mtDNA and noncanonical chromosome were removed.Picard (v2.2.4) was used to remove duplicated reads
Post-filtering bam file for samples from the same experimental condition were merged using the merge function from Samtools (v1.11), followed by peak calling using MACS (v2.1.0) with parameters --nomodel --nolambda –keepdup all –slocal 10000
Peak summits were extended +/- 200bp, and quantification of reads in peaks was performed using BEDTools multicov (v2.29.2)..Coverage tracks were generated from bam files using deepTools (v3.2.1) bamCoverage with parameters –normalizeUsingRPKM –binsize 10
Bigwig files were further normalized using the normalization factor calculated by DESeq2 using total counts in peak regions. Bigwigs from the same condition were merged together and uploaded to UCSC genome browser for visualization.
Assembly: GRCm38.p6 (mouse)
Supplementary files format and content: bigwig files
Supplementary files format and content: narrowPeak files containing peak coordinates

extract_protocol:
5 × 10⁴ viable BMDMs were lysed in buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl₂, 0.1% TritonX-100) at 4°C for 5 min, nuclei were pelleted, resuspended in transposase reaction buffer with Tn5 (1 μL per 5 × 10⁴ cells), incubated at 37°C for 30 min, treated with 0.1% SDS at 40°C for 30 min to stop the reaction, and DNA was isolated using KAPA Pure beads (SPRI beads) with concentrations measured by Qubit® fluorometer (Thermo Fisher Scientific).
For DNA library preparation, qPCR with i5 and i7 primers was performed using NEXTERA barcoding, followed by incubation with 0.5× SPRI beads (discarded), then 1.8× SPRI beads; beads were washed twice with 70% ethanol, eluted with EB buffer, measured using a Qubit® fluorometer, and library size and quality were assessed using an Agilent 2100 Bioanalyzer HS.

value: Bone marrow-derived macrophages (BMDM)

value: Trained


title: Pooled human OA chondrocytes, Cobimetinib, rep 2

city: Rotterdam

first: Gerjo

last: van osch

address: Dr. Molewaterplein 40

department: Orthopaedics and Sports Medicine

country: Netherlands

institute: Erasmus MC

description:
Library name: cobi2
10x Genomics

data_processing:
FASTQ files were constructed using cellranger mkfastq (version 7.1.0) in combination with blc2fastq (version 2.20.0.422). The resulting FASTQ files were processed using cellranger count (version 7.1.0). The genome version used in processing was GRCh38. Cells were assigned to the correct donor sample present in the multiplexed pools using vireo (version 0.2.3) in combination with cellsnp-lite (version 1.2.3).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files, matrix files and tab-seperated text files

source_name: Osteoarthritic knee cartilage

growth_protocol: 3mm biopsy punches from full tickness cartilage were cultured in a 12 well plate and calibrated for 24h in DMEM-LG supplemented with 1% ITS+, 50ug/ml gentamicin and 1.5ug/ml amphotericin B, after which treatment started.

extract_protocol:
Cartilage explants were cut into smaller piecees and subjected to a digestion protocol of 10mg/ml protease from streptomyces griseus for 45 minutes, followed by 4mg/ml collagenase B until everything was digested (~4.5hours). The cell suspension obtained was put on a 70um cell strainer and cell viability and concentration was determined with trypan blue staining. Donors were pooled equally per experimental condition.
Samples were prepared using 10x genomics chemistry version 3' v3 and the resulting libraries were sequenced on a Novaseq6000 platform (Illumina, San Diego, CA, USA).

treatment_protocol: 6 days of treatment with 1000nM Cobimetinib or DMSO 0.01% as a vehicle control. Medium was refreshed after 3 days and 24h prior to extraction.

value: Osteoarthritic knee cartilage

value: Chondrocytes

value: Cobimetinib 1000nM


title: Pro-B from control mice, biological rep1


title: Patient B1, recovered health status after respiratory infection, miRNA

description: Library name: SZ374mic

source_name: 47-year-old male patient, day 6


title: Patient B5, recovered health status after urogenital infection, miRNA

description: Library name: SZ357mic

source_name: 64-year-old female patient, day 1

value: female


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) rep3

description: Library name: trained3


title: 12-week SN Grin2a WT Sample 1

description: Library name: grin2a_12w-SN-WT1

value: Substantia Nigra

value: Grin2a WT


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) rep5

description: Library name: trained5


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) rep6

description: Library name: trained6


title: Pooled human OA chondrocytes, Cobimetinib, rep 1

description:
Library name: cobi1
10x Genomics


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) rep2

description: Library name: trained2


title: Patient B1, severe sepsis originating from respiratory infection, miRNA

description: Library name: SZ372mic

source_name: 47-year-old male patient, day 0


title: Patient B5, severe sepsis originating from urogenital infection, miRNA

description: Library name: SZ356mic

source_name: 64-year-old female patient, day 0


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 µg/mL β-glucan (day 0) and 10 ng/mL LPS (day 6) rep1

description: Library name: trained1


title: 12-week SN Grin2a WT Sample 2

description: Library name: grin2a_12w-SN-WT2


title: Patient B4, recovered health status after urogenital infection, miRNA

description: Library name: SZ352mic

source_name: 72-year-old female patient, day 2


title: 12-week SN Grin2a -/-  Sample 4

description: Library name: grin2a_12w-SN-KO4

value: Grin2a -/-


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 ng/mL LPS (day 6) rep4

description: Library name: LPS_activated4

value: LPS activated


title: Donor_D2_MACS_basophils_Surface_Protein

city: Solna

first: Joakim

middle: S

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

description:
Library name: DonorD2_MACS_basophils_Surface_Protein
10X Genomics

data_processing:
Illumina data was processed using cellranger count (Cellranger Pipeline 5.0.1 with the option include-introns for sample Donor B sorted basophils and Cellranger Pipeline 7.0.1 for the rest of the samples with default parameters)
Long-read data was processed using epi2me-labs/wf-single-cell
Assembly: GRCh38
Supplementary files format and content: count tables 10X Genomics .h5
Supplementary files format and content: count tables ONT .tsv
Library strategy: CITE-seq

molecule: protein

source_name: peripheral blood

extract_protocol:
The isolated cells from each sample were used for GEM generation, barcoding, cleanup, cDNA amplification according to the protocol provided from 10x Genomics Chromium Next GEM Single Cell 3' Reagent kit v3.1 with feature barcode technology.
Illumina library construction was done using the protocol and reagents from the 10x Genomics Chromium Next GEM Single Cell 3' Reagent kit v3.1 with feature barcode technology. Long-read libraries were generated using a modified FLT-seq protocol (Tian et al, 2021, Genome Biology).

value: peripheral blood

tag: dataset number

value: CCR3 enriched low-density leukocytes

tag: library type

value: ADT

tag: adt

value: TotalSeq B Human Universal Cocktail v1.0 (Biolegend)


title: Patient B4, improving health status after sepsis originating from urogenital infection, miRNA

description: Library name: SZ351mic

source_name: 72-year-old female patient, day 1

tag: tissue


title: Donor D1 MACS basophils_Gene_Expression

description:
Library name: DonorD1_MACS_basophils_Gene_Expression
10X Genomics

tag: cell type

value: mRNA


title: 12-week SN Grin2a -/-  Sample 6

description: Library name: grin2a_12w-SN-KO6

source_name: Substantia Nigra

tag: genotype


title: Pooled human OA chondrocytes, Control

description:
Library name: control
10x Genomics

tag: treatment


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 ng/mL LPS (day 6) rep5

description: Library name: LPS_activated5

value: bone marrow

tag: batch


title: Donor D2 MACS basophils_Gene_Expression

description:
Library name: DonorD2_MACS_basophils_Gene_Expression
10X Genomics


title: Donor C MACS basophils Gene Expression

description:
Library name: DonorC_MACS_basophils_Gene_Expression
10X Genomics


title: 12-week SN Grin2a -/-  Sample 2

description: Library name: grin2a_12w-SN-KO2


title: Patient B3, recovered health status after respiratory infection, miRNA

description: Library name: SZ347mic

source_name: 52-year-old male patient, day 9

value: blood

value: male


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 ng/mL LPS (day 6) rep3

description: Library name: LPS_activated3

value: Bone marrow-derived macrophages (BMDM)


title: 12-week SN Grin2a -/-  Sample 3

description: Library name: grin2a_12w-SN-KO3


title: Patient B2, recovered health status after urogenital infection, miRNA

description: Library name: SZ340mic

source_name: 83-year-old female patient, day 4


title: 12-week SN Grin2a -/-  Sample 1

description: Library name: grin2a_12w-SN-KO1


title: BMDMs from C57BL/6 mice cultured with M-CSF, naive rep6

description: Library name: naive6

value: Naive


title: Patient B3, severe sepsis originating from respiratory infection, miRNA

description: Library name: SZ341mic

source_name: 52-year-old male patient, day 0


title: Donor B sorted basophils Surface Protein

description:
Library name: DonorB_sorted_basophils_Surface_Protein
10X Genomics

value: Sorted basophils

value: TotalSeq-B0090 Mouse IgG1 isotype control, TotalSeq-B0391 anti-human CD45, TotalSeq-B0953 PE-streptavidin, TotalSeq-B0085 anti-human CD25, TotalSeq-B0061 anti-human CD117


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 ng/mL LPS (day 6) rep1

description: Library name: LPS_activated1

source_name: bone marrow


title: 12-week SN Grin2a +/-  Sample 4

description: Library name: grin2a_12w-SN-HT4

value: Grin2a +/-


title: Donor D1 MACS basophils_Surface_Protein

description:
Library name: DonorD1_MACS_basophils_Surface_Protein
10X Genomics


title: BMDMs from C57BL/6 mice cultured with M-CSF, stimulated with 10 ng/mL LPS (day 6) rep2

description: Library name: LPS_activated2


title: Patient B4, severe sepsis originating from urogenital infection, miRNA

description: Library name: SZ350mic

source_name: 72-year-old female patient, day 0

value: female


title: Donor A pbmcs Surface Protein

description:
Library name: DonorA_pbmcs_Surface_Protein
10X Genomics

value: Sorted low-density leukocytes plus basophils

value: TotalSeq-B0090 Mouse IgG1 isotype control, TotalSeq-B0391 anti-human CD45, TotalSeq-B0953 PE-streptavidin


title: 12-week SN Grin2a +/-  Sample 3

description: Library name: grin2a_12w-SN-HT3

value: Substantia Nigra


title: Donor C MACS basophils_Surface_Protein

description:
Library name: DonorC_MACS_basophils_Surface_Protein
10X Genomics

value: peripheral blood


title: 12-week SN Grin2a +/-  Sample 6

description: Library name: grin2a_12w-SN-HT6


title: BMDMs from C57BL/6 mice cultured with M-CSF, naive rep5

description: Library name: naive5


title: Patient B2, improving health status after sepsis originating from urogenital infection, miRNA

description: Library name: SZ336mic

source_name: 83-year-old female patient, day 1


title: BMDMs from C57BL/6 mice cultured with M-CSF, naive rep4

description: Library name: naive4


title: 12-week SN Grin2a +/-  Sample 2

description: Library name: grin2a_12w-SN-HT2


title: Patient B3, improving health status after sepsis originating from respiratory infection, miRNA

description: Library name: SZ345mic

source_name: 52-year-old male patient, day 5


title: Patient B6, recovered health status after respiratory infection, miRNA

description: Library name: SZ334mic

source_name: 46-year-old female patient, day 14


title: 12-week SN Grin2a +/-  Sample 1

description: Library name: grin2a_12w-SN-HT1


title: Patient B2, severe sepsis originating from urogenital infection, miRNA

description: Library name: SZ335mic

source_name: 83-year-old female patient, day 0


title: BMDMs from C57BL/6 mice cultured with M-CSF, naive rep3

description: Library name: naive3


title: A549 cells,RNAseq_ADAR_OE_SFTSV,rep3

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

description:
Library name: sample47
EXE3

data_processing:
The Illumina sequencing reads were initially processed with cutadapt v4.3 to remove adapters and perform quality-based trimming.
After trimming adapters and filtering out low-quality reads, all the cleaned FASTQ files were aligned to either the human reference genome hg38 or miRBase version 22, utilizing STAR version 2.7.5a and Bowtie2.
Gene expression levels were quantified using featureCounts v2.0.6.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: A549 cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions
RNA sample were subjected to library construction using SMARTer Stranded Total RNA-Seq Kit v2—Pico Input Mammalian according to the manufacturer’s protocol. miRNA-seq libraries construction were used VAHTS® Small RNA Library Prep Kit for Illumina (NR801). All of the quality-ensured libraries were sequenced on the Illumina Nova seq 6000 platform in 150 bp paired-end mode (sequenced by Genewiz).

tag: cell line

value: A549 cells


title: 20-week SN Grin2a WT Sample 11

description: Library name: grin2a_20w-SN-WT11

value: Grin2a WT


title: Patient B6, severe sepsis originating from respiratory infection, miRNA

description: Library name: SZ329mic

source_name: 46-year-old female patient, day 0


title: BMDMs from C57BL/6 mice cultured with M-CSF, naive rep2

description: Library name: naive2


title: A549 cells,RNAseq_ADAR_OE_SFTSV,rep2

description:
Library name: sample46
EXE2


title: Donor B sorted basophils Gene Expression

description:
Library name: DonorB_sorted_basophils_Gene_Expression
10X Genomics


title: 20-week SN Grin2a WT Sample 10

description: Library name: grin2a_20w-SN-WT10


title: Donor A pbmcs Gene Expression

description:
Library name: DonorA_pbmcs_Gene_Expression
10X Genomics


title: 20-week SN Grin2a WT Sample 9

description: Library name: grin2a_20w-SN-WT9