title: WT_12weeks_batch7_P484_GFP_sorted_Protocol1

status: Public on Jun 30 2026

type: SRA

city: Solna

first: Lara

last: Garcia Merino

state: Stockholm

address: Armégatan 32C

country: Sweden

institute: Karolinska Institutet

description: Library name: P484

library_source: transcriptomic single cell

data_processing:
Trim Galore v.0.4.4, which wraps Cutadapt v.1.11 was used in single-end mode for sequencing read trimming, with the Nextera trasposase adapter sequence (CTGTCTCTTATA). A minimum overlap of 3 bp and  a maximum error rate of 10% were set for adapter matches. The reads were further quality-trimmed at a Phred score cutoff of 20 (ASCII+33 encoding), and reads shorter than 20 bp after trimming were excluded.  The mouse reference genome GRCm38/mm10 was used as reference for alignment, which was done with Hisat2. Subsequently, we applied RSEM for quantifying gene expression and to generate a gene expression count matrix.
Assembly: GRCm38/mm10
Supplementary files format and content: Count matrix for gene expression
Supplementary files format and content: Supplementary file: Plain text file containing progerin and Lamin A transcript counts and metadata

molecule: polyA RNA

organism: Mus musculus

source_name: aorta

extract_protocol:
Dissected aortic arches were processed to generate single-cell suspensions using enzymatic digestion. Two digestion protocols were applied. For both protocols, the aortic arches were first opened longitudinally and cut into approximately 1 mm fragments before enzymatic treatment.  In protocol 1, individual aortic arches were digested in HBSS (Gibco, 14025-092) supplemented with 2% bovine serum albumin (Merck, A9647), collagenase I (250 µg/ml; Merck, C5894), collagenase II (250 µg/ml; Merck, C6885), collagenase IV (250 µg/ml; Merck, C1889), porcine elastase (5.98 U/ml; Worthington Biochemical, LS002279), 2.5 mM CaCl₂, and DNase (125.75 U/µl; Invitrogen, 18047-019). Samples underwent three sequential digestion steps of 10 minutes each at 37°C with shaking at 450 rpm, with 20 resuspensions performed between each incubation. Following digestion, cell suspensions were passed sequentially through 70 µm and 40 µm strainers to remove remaining tissue fragments.  In protocol 2, aortic arches were digested in 24-well culture plates using sterile DMEM supplemented with collagenase IV (2.5 mg/ml; Gibco, 17104-019) and porcine elastase (2.5 U/ml). Digestions were carried out for 2 hours in a humidified incubator at 37°C and 5% CO₂, with gentle resuspension every 30 minutes. Digestion was terminated by transferring the cell suspension to a 50 ml Falcon tube containing 1% BSA in PBS. The resulting suspension was then filtered through 70 µm and 40 µm cell strainers.  After digestion, the arterial cells were pelleted by centrifugation for 5 minutes at 300 × g and 8°C, then resuspended in 1% BSA in PBS. Cell viability was evaluated by staining with 5 µM DRAQ5 (Thermo Scientific, #62251) and 9 µg/ml Calcein Green (Invitrogen, C34852). Following a 15-minute incubation on ice, individual arterial cells were sorted using a BD FACS Aria Fusion based on size and double-positivity for Calcein Green and DRAQ5 into 384-well plates containing Smart-seq2 lysis buffer. In selected experiments, GFP-based sorting was performed to enrich for VSMCs (Table 1). Immediately after sorting, plates were sealed, frozen on dry ice, and stored at −80°C until further processing.
Sequencing was performed at the Single Cell Core Facility of Flemingsberg (SICOF) using  Smart-seq2. Briefly, SuperScript II reverse transcriptase and oligo(dT) primers (ThermoFisher Scientific) were used for cDNA synthesis, with template-switching oligonucleotide for second-strand cDNA synthesis. 23–26 PCR cycles were done for cDNA amplification. TapeStation 4200 or a 2100 Bioanalyzer with a DNA High Sensitivity chip (Agilent Biotechnologies) were used for  quality control (QC) measurements. Samples that passed QC were subsequently fragmented and tagmented) using the Tn5 transposase, and each well was uniquely indexed using the Illumina Nextera XT index kits (Sets A–D). Finally, all uniquely indexed cDNA libraries from a 384-well plate were pooled into a single sample and sequenced on one lane of an Illumina HiSeq 3000 instrument using dual indexing and single-end 50 base-pair reads

tag: tissue

value: aorta

tag: age (weeks)

tag: genotype

value: WT

tag: digestion protocol

value: Protocol 1


title: WT_12weeks_batch7_P483_GFP_sorted_Protocol1

description: Library name: P483


title: Progeria_12weeks_batch3_P482_GFP_sorted_Protocol1

description: Library name: P482

value: Progeria


title: WT_12weeks_batch6_P450_GFP_sorted_Protocol1

description: Library name: P450


title: Progeria_10weeks_batch3_P327_not_GFP_sorted_Protocol1

description: Library name: P327


title: Progeria_10weeks_batch3_P326_not_GFP_sorted_Protocol1

description: Library name: P326


title: Progeria_10weeks_batch2_P324_not_GFP_sorted_Protocol1

description: Library name: P324


title: Progeria_12weeks_batch _P108_not_GFP_sorted_Protocol2

description: Library name: P108

value: Protocol 2


title: Progeria_10weeks_batch2_P325_not_GFP_sorted_Protocol1

description: Library name: P325


title: WT_12weeks_batch4_P089_not_GFP_sorted_Protocol1

description: Library name: P089


title: WT_12weeks_batch5_P105_not_GFP_sorted_Protocol2

description: Library name: P105


title: WT_12weeks_batch4_P088_not_GFP_sorted_Protocol1

description: Library name: P088


title: Progeria_6weeks_batch3_P084_GFP_sorted_Protocol1

description: Library name: P084


title: Progeria_6weeks_batch3_P083_GFP_sorted_Protocol1

description: Library name: P083


title: WT_6weeks_batch3_P082_GFP_sorted_Protocol1

description: Library name: P082


title: Progeria_6weeks_batch2_P080_not_GFP_sorted_Protocol2

description: Library name: P080


title: Progeria_6weeks_batch2_P081_not_GFP_sorted_Protocol2

description: Library name: P081


title: WT_6weeks_batch2_P078_not_GFP_sorted_Protocol2

description: Library name: P078


title: WT_6weeks_batch2_P079_not_GFP_sorted_Protocol2

description: Library name: P079


title: WT_6weeks_batch2_P077_not_GFP_sorted_Protocol2

description: Library name: P077


title: WT_6weeks_batch1_P075_GFP_sorted_Protocol2

description: Library name: P075


title: WT_6weeks_batch1_P074_GFP_sorted_Protocol2

description: Library name: P074


title: Progeria_6weeks_batch1_P073_GFP_sorted_Protocol2

description: Library name: P073


title: Progeria_10weeks_batch3_P016_not_GFP_sorted_Protocol2

description: Library name: P016


title: Progeria_6weeks_batch1_P072_GFP_sorted_Protocol2

description: Library name: P072


title: Progeria_10weeks_batch3_P015_not_GFP_sorted_Protocol2

description: Library name: P015


title: Progeria_10weeks_batch3_P014_not_GFP_sorted_Protocol2

description: Library name: P014


title: NE3

city: Shanghai

first: Hongrui

last: Chen

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

country: China

institute: Shanghai ninth people's hospital

description: Library name: 6

library_source: transcriptomic

data_processing:
fastp  removed adapters and low-quality bases
Assembly: EC;SA
Supplementary files format and content: tab-delimited text file includes counts
Supplementary files format and content: tab-delimited text file includes tpm

molecule: total RNA

organism: Escherichia coli

source_name: Group 1: E. coli treated with AuPt@ZIF-8 + H₂O₂ + NIR

extract_protocol:
Total RNA was extracted. RNA was purified per manufacturer’s instructions and treated with RNase-free DNase I. RNA integrity was assessed on Agilent 2100 Bioanalyzer (RIN ≥ 8.5); concentrations were measured with Qubit RNA HS Assay
Ribosomal RNA was depleted. Strand-specific libraries were prepared: fragmentation at 94 °C for 8 min, adaptor ligation, and 12 PCR cycles. Libraries (~280 bp mean insert) were quantified by qPCR and profiled on Bioanalyzer. Sequencing was performed  with paired-end 150 bp reads.

value: cell

tag: treatment


title: NE1

description: Library name: 4

value: E. coli treated with AuPt@ZIF-8 + H₂O₂ + NIR


title: CE3

description: Library name: 3

source_name: Group 2: untreated E. coli

value: untreated E. coli


title: CE2

description: Library name: 2


title: CE1

description: Library name: 1


title: AML12 EV-3

city: Columbus

first: Xinlei

last: Li

state: OH

address: 700 Children's Dr

department: CCTR

country: USA

institute: Nationwide Children's Hospital

description: Library name: Sample-3

data_processing:
Quality of libraries was determined via Agilent 4200 Tapestation using a High Sensitivity D1000 ScreenTape Assay kit.
The library was then run on Illumina MiniSeq platform.
The Quality Control of the sequencing data was done by miRTrace software.
2x75 paired-end service was applied, but only R1 was used. Read-length distribution was between 1.74M and 2.52M.
The miRNA counts were normalized and subjected to target searching and functional prediction by miRWalk
Assembly: GRCh38
Supplementary files format and content: Excel spreadsheet containing normalized counts of AML12 miRNAs

source_name: Liver

growth_protocol: AML12 cells were cultured with DMEM/F12+10%Fetal bovine serum+1% Antibiotic-Antimycotic+1%ITS+10^(-7)M Dexamethosone in T175 flasks and, when 90% confluent, were washed with DPBS twice and switched to serum-free medium.

extract_protocol:
Three batches of AML12 EVs were used to isolate total RNA with QIAGEN miRNeasy kit. DNA was removed by Dnase I digestion. Approximately 200 ng of RNA was subjected to small RNA-seq.
Multiplex Small RNA Library was prepared using NEBNext® Small RNA Library Prep Set according to the manufacturer’s instructions

treatment_protocol: Supernatants from 48hr culture were subjected to differential centrifugation. EV pellets were recovered after ultracentrifugation at 100,000xg for 70min. The EV pellets were washed and spun down again for resuspension.

value: Liver

tag: cell line

tag: cell type

value: hepatocytes

value: wildtype

value: serum-free medium culture

tag: batch


title: AML12 EV-2

description: Library name: Sample-2


title: H3

city: chengdu

first: ZHENGLU

last: WANG

state: sichuan

address: south of renmin road

institute: Sichuan University

description:
Library name: sample9
mRNA seq

data_processing:
Data quality control
Match the genome
Modifying site recognition (RNA quantification)
Identification of differentially expressed sites (identification of differentially expressed RNAs)
Functional gene enrichment analysis
Assembly: GRCm38
Supplementary files format and content: This table contains the information on RNA modification sites identified for each sample, along with RNA counts and normalized values

source_name: brain

growth_protocol: SPF

extract_protocol:
Total RNA extraction kit
Preprocessing - Database Construction

treatment_protocol: Drinking water

value: brain


title: H2

description:
Library name: sample8
mRNA seq


title: L2

description:
Library name: sample5
mRNA seq


title: L3

description:
Library name: sample6
mRNA seq


title: L1

description:
Library name: sample4
mRNA seq


title: C3

description:
Library name: sample3
mRNA seq


title: C1

description:
Library name: sample1
mRNA seq


title: C2

description:
Library name: sample2
mRNA seq


title: CML-BLBC8

city: Dalian

first: Xuehong

last: Zhang

state: Liaoning

address: No. 9 West Section Lvshun South Road, Dalian 116044, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description: Library name: Sample24

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 27, GRCh38).
The Gene abundances are given as Reads Per Kilobase per Million mapped reads (RPKM) with “cuffnorm” command using the Cufflinks package.
Assembly: human GRCh38
Supplementary files format and content: Excel file includes FPKM values for all Samples

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
Total RNA of cryopreserved mononucleated cells (MNCs) of bone marrow aspirate samples were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

value: Bone Marrow

tag: disease stage

value: CML-BLBC


title: CML-BLBC7

description: Library name: Sample23


title: CML-BLBC6

description: Library name: Sample22


title: CML-BLBC5

description: Library name: Sample21


title: CML-BLBC4

description: Library name: Sample20


title: CML-BLBC2

description: Library name: Sample18


title: CML-BLBC3

description: Library name: Sample19


title: CML-BLBC1

description: Library name: Sample17


title: CML-CP16

description: Library name: Sample16

value: CML-CP


title: CML-CP15

description: Library name: Sample15


title: CML-CP14

description: Library name: Sample14


title: CML-CP12

description: Library name: Sample12


title: Progeria_12weeks_batch2_P452_GFP_sorted_Protocol1

description: Library name: P452


title: CML-CP10

description: Library name: Sample10


title: CML-CP9

description: Library name: Sample9


title: CML-CP6

description: Library name: Sample6


title: CML-CP5

description: Library name: Sample5


title: CML-CP4

description: Library name: Sample4


title: CML-CP3

description: Library name: Sample3


title: CML-CP1

description: Library name: Sample1


title: HEK293T, ERM-LOV*, 1s irradiation, Enrich, rep2

city: Beijing

first: Yuxin

last: Fang

state: Beijing

address: Yiheyuan Road No.5

institute: Peking University

description:
Library name: LITag-ERM_EN_rep2
Column name in ERM-LITag_all_counts.xlsx: EN_rep2

data_processing:
Sequencing reads were firstly processed with Cutadapt (v.1.18) to remove adaptors (For subcellular transcriptome data, adaptor1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adaptor2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; for cancer cell migration study, adaptor1=CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, adaptor2=CTGTCTCTTATACACATCTGACGCTGCCGACGA; other parameters: -q 20 -O 3 -m 20). For GLORI2 data analysis, raw R2 reads were treated by Trim Galore and Seqkit for adaptor trimming and quality control. The m6A sites were called by GLORI-tools. For each mRNA, an m6A strength score was calculated as the sum of m6A ratios across all identified m6A sites.
Trimmed reads were mapped against the corresponding genome assemblies using hisat2 (v.2.1.0).
Number of reads mapped to each gene was counted with HTSeq (v0.7.2) (-s no)
Differential expression analysis was carried out by DESeq2 (v.1.16.1)
Assembly: GRCh38 (hg38), Rnor_6.0, GRCm39
Supplementary files format and content: Excel tables include raw counts for each sample.

growth_protocol: HEK293T and MC38 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and maintained at 37°C with 5% CO2. Cortical neurons were dissected from neonatal Sprague Dawley rats (within 24 hours post-birth), plated onto 10-cm dishes, and cultured with GPM for 3-6 h before switching to neural cell culture medium (Neurobasal medium with 2% (v/v) B-27 supplement, 1% (v/v) GlutaMAX supplement, penicillin and streptomycin). Petri dishes were pre-incubated overnight with 50-100 μg/mL PDL at 37°C. The day of rat dissection was designated as DIV 0 (0 days in vitro), and thereafter, half of the spent culture medium was replaced with fresh neural cell culture medium every 3 days.

extract_protocol:
For the profiling of subcellular transcriptomes, cells were lyzed with TRIzol. Total RNAs were extracted, clicked with biotin handles, enriched with streptavidin-coated beads, and purified again with TRIzol. For the study of cancer cell migration, cells with strong biotin signals were sorted by flow cytometry and lyzed with 0.5% (v/v) Triton X-100 and 0.1 U DNase I.
For the profiling of subcellular transcriptomes, 100 ng Input RNA samples or 5 μL Enrich RNA samples were utilized for NGS library construction. For identifying G3BP1-proximal and OMM-proximal RNAs in the HEK293T cells, rRNAs were removed with Ribo-off rRNA Depletion Kit (Vazyme) following the manufacturer’s protocol. The purified RNAs were dissolved in 5 μL nuclease-free water. NEBNext Ultra II RNA Library Prep Kit for Illumina was used for NGS library construction. RNAs were fragmentated to ~300 nt before first strand synthesis. For the study of cancer cell migration, the sorted cells were used for pseudo-bulk RNA-sequencing library construction following the previously published Sherry2 protocol. Libraries constructed from polyA RNAs (OMM-proximal and G3BP1-proximal RNAs of HEK293T cells, and mRNAs of MC38 cells) were sequenced to a depth of 3 G raw base. And libraries constructed from total RNAs (ERM-proximal RNAs of HEK293T cells and G3BP1-proximal RNAs of rat cortical neurons) were sequenced to a depth of 15 G raw base. For GLORI2.0 library construction, mRNA was isolated from total RNA by the Dynabeads® mRNA Purification Kit (Invitrogen) according to the manufacturer’s instructions. These purified mRNA were fragmented in a 20 μL mixture containing 2 μL 10x RNA fragment buffer (NEB, E6150S), incubated for 5 min at 85oC and immediately placed on ice for 2 min. Subsequently, 2 μL 10x stop buffer (NEB, E6150S) was added. The final solution was purified by Zymo RNA Clean & Concentrator column (Zymo, R1016) according to the manufacturer’s instructions. The purified fragment mRNA were added into 50 μL of reaction buffer containing 13 μL glyoxal solution (Sigma, 50649), 10 μL DMSO, 10 μL 5 M NaNO2 (Sigma, S2252), 5 μL saturated H3BO3 solution (Sigma, B0394), 4 μL 500 mM MES (pH 6.0, Sigma, 76039) and nuclease-free water, incubated for 10 min at 50 °C and immediately placed on ice for 2 min for stopping the reaction. The mixture was purified by ethanol precipitation. The pellets were dissolved by 50 μL deprotection buffer containing 0.5 M TEAA (pH 8.6) and 47.5% Formamide. The mixture was incubated at 95°C for 10 min without shaking and immediately placed on ice for 2 min. The mixture was purified by ethanol precipitation. The pellets were dissolved by 8.5 μL nuclease-free water. The RNA library was constructed by SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa, 634413) according to the manufacturer’s instructions, except for replacing the RT primer with a ternary primer.

treatment_protocol: For general CAP-seq labeling experiments, HEK293T cells were cultured until the confluence reached 90%, incubated with 10 mM propargylamine (PA) in HBSS for 5 min, and irradiated with blue light for 1-120 seconds. For the induction of stress granules, HEK293T cells were incubated with 0.5 mM sodium arsenite for 5-60 minutes. Primary cultures of rat cortical neurons were transduced with a lentivirus expressing G3BP1-Lantern or Lantern-NES at 3 days in vitro (DIV3). At DIV8, neurons were stimulated with 0.25 mM sodium arsenite for 3 hours, and conducted with the CAP-seq labeling procedure. For the cancer cell migration assay, MC38 cells were seeded on coverslips with a culture-insert to create a 500-μm cell-free gap. 24 hours after removing the culture-insert, migrating cells near the gap and remaining cells far from the gap were selectively labeled with DMD-controlled 450-nm laser and 2 mM Bio-NH2 probe.

value: embryonic kidney cells


title: HEK293T, ERM-LOV*, 1s irradiation, Enrich, rep1

description:
Library name: LITag-ERM_EN_rep1
Column name in ERM-LITag_all_counts.xlsx: EN_rep1


title: HEK293T, ERM-LOV*, 1s irradiation, Input, rep2

description:
Library name: LITag-ERM_IN_rep2
Column name in ERM-LITag_all_counts.xlsx: IN_rep2


title: HEK293T, ERM-LOV*, 1s irradiation, Input, rep1

description:
Library name: LITag-ERM_IN_rep1
Column name in ERM-LITag_all_counts.xlsx: IN_rep1


title: HEK293T, mixed culture, Enrich, rep3

description: Library name: mS-G39C-mixded_EN_rep3

library_source: other

molecule: other


title: HEK293T, mixed culture, Enrich, rep1

description: Library name: mS-G39C-mixded_EN_rep1


title: HEK293T, mixed culture, Input, rep2

description: Library name: mS-G39C-mixded_IN_rep2


title: HEK293T, mixed culture, Input, rep1

description: Library name: mS-G39C-mixded_IN_rep1


title: HEK293T, SSM library, Round2, 1min, Enrich, rep2

description: Library name: R2-1min-rep2_EN


title: HEK293T, SSM library, Round2, 1min, Input, rep2

description: Library name: R2-1min-rep2_IN


title: HEK293T, SSM library, Round2, 1min, Enrich, rep1

description: Library name: R2-1min-rep1_EN


title: HEK293T, SSM library, Round2, 1min, Input, rep1

description: Library name: R2-1min-rep1_IN


title: HEK293T, SSM library, Round1, 15min, Enrich

description: Library name: R1-15min-EN


title: HEK293T, SSM library, Round1, 15min, Input

description: Library name: R1-15min-IN


title: HEK293T, SSM library, Round1, 5min, Enrich

description: Library name: R1-5min-EN


title: HEK293T, mixed culture, Enrich, rep2

description: Library name: mS-G39C-mixded_EN_rep2


title: HEK293T, SSM library, Round1, 5min, Input

description: Library name: R1-5min-IN


title: HEK293T, SSM library, Round1, 1min, Enrich

description: Library name: R1-1min-EN


title: HEK293T, mixed culture, Input, rep3

description: Library name: mS-G39C-mixded_IN_rep3


title: HEK293T, SSM library, Round1, 1min, Input

description: Library name: R1-1min-IN


title: T2, OSCC

city: Pune

first: Subhayan

last: Sur

state: Maharashtra

address: Survey No 87/88, Mumbai Bangalore Express Highway, Tathawade

department: Biotechnology

country: India

institute: Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune

description: Library name: Sample 5

data_processing:
Raw FASTQ files were quality checked and preprocessed using fastp v0.20.1
Cleaned reads were aligned to the reference genome using HISAT2 v2.1.0
Gene-level read counts were generated from the alignment files using featureCounts v2.0.1
Supplementary files format and content: Processed data files are provided in .csv formats
Supplementary files format and content: Files include normalized expression matrices (TPM), and differential expression analysis results generated using DESeq2

source_name: Primary tissue

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen)
Total RNA was extracted and assessed for quality and integrity. Poly(A)+ RNA was isolated from total RNA and used for library preparation with the Illumina TruSeq Stranded mRNA Library Preparation Kit according to the manufacturer's protocol. Libraries were generated through RNA fragmentation, first- and second-strand cDNA synthesis, adapter ligation, and PCR enrichment.

value: Primary tissue

tag: tissue type

value: OSCC

value: Unknown


title: T3, OSCC

description: Library name: Sample 6


title: T1, OSCC

description: Library name: Sample 4


title: N3, Non-tumor

description: Library name: Sample 3

value: non-tumor


title: N2, Non-tumor

description: Library name: Sample 2


title: N1, Non-tumor

description: Library name: Sample 1


title: 16HBE14o- cruise terminal UF-PM 32 ug/cm-2 (100 ug mL-1) 24 h, biological replicate 3

city: Southampton

first: Matthew

last: Loxham

address: Tremona Road

department: Faculty of Medicine, Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton

description:
Library name: CrHi_05
Column name in NormalisedCounts_cpm.csv: CrS_3

data_processing:
Raw paired-end FASTQ files were generated from Illumina NovaSeq 6000 sequencing.
Reads were pseudoaligned/quantified against the Homo sapiens GRCh38 RefSeq transcriptome using kallisto.
Transcript-level abundance estimates were imported and summarised using tximport.
Assembly: hg38
Supplementary files format and content: csv file containing counts per million (cpm) values for all samples

source_name: bronchial epithelium

extract_protocol:
Following PM exposure, cells were washed with 1 ml sterile phosphate-buffered saline (PBS) and lysed with 300 µl RNA lysis buffer (Monarch® Total RNA Miniprep Kit, New England BioLabs, Massachusetts, USA) for 10 min to completely lyse cells. Lysates were stored at − 80 °C until further use.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

value: bronchial epithelium

value: bronchial epithelial cell

value: Wild type (SV40-immortalised)

value: Cruise terminal summer season ultrafine PM; 32 ug cm-2 (100 ug mL-1); 24 h


title: 16HBE14o- cruise terminal UF-PM 32 ug/cm-2 (100 ug mL-1) 24 h, biological replicate 2

description:
Library name: CrHi_04
Column name in NormalisedCounts_cpm.csv: CrS_2


title: 16HBE14o- cruise terminal UF-PM 32 ug/cm-2 (100 ug mL-1) 24 h, biological replicate 1

description:
Library name: CrHi_01
Column name in NormalisedCounts_cpm.csv: CrS_1


title: 16HBE14o- medium control 24 h, biological replicate 3

description:
Library name: Med_05
Column name in NormalisedCounts_cpm.csv: Ctrl_3

value: medium control; 24 h


title: WT_6weeks_batch1_P076_GFP_sorted_Protocol2

description: Library name: P076

value: aorta

value: WT

value: Protocol 2


title: 16HBE14o- medium control 24 h, biological replicate 2

description:
Library name: Med_04
Column name in NormalisedCounts_cpm.csv: Ctrl_2


title: 16HBE14o- medium control 24 h, biological replicate 1

description:
Library name: Med_01
Column name in NormalisedCounts_cpm.csv: Ctrl_1


title: Mock CAR-T cells after BT245-Luc2-GFP co-culture

city: Denver

first: Sujatha

last: Venkataraman

state: CO

address: 12800 E. Montview Blvd.

department: Department of Pediatrics/Neuro-Onc

institute: University of Colorado Anschutz Medical Campus

description:
Library name: sample_5
CD45-positive Mock CAR-T cells isolated following co-culture with BT245-Luc2-GFP tumor cells

data_processing:
Sequence quality was assessed using FastQC. Adapter sequences and low-quality bases were removed using Trim Galore. Cleaned reads were aligned to the human reference genome (GRCh38) using STAR. Gene-level read counts were generated using featureCounts based on GENCODE gene annotations. Count matrices were analyzed in R using DESeq2 and/or edgeR. Batch effects were corrected using SVA when necessary. Data quality was evaluated by principal component analysis and hierarchical clustering. Pathway enrichment analysis was performed using clusterProfiler and fgsea with gene sets obtained from MSigDB.
Assembly: GRCh38
Supplementary files format and content: Raw sequencing data are provided as gzipped FASTQ files generated from paired-end 150 bp RNA sequencing.
Supplementary files format and content: Processed data consist of tab-delimited gene-level count matrices generated by featureCounts and associated sample metadata used for downstream differential expression analyses.

source_name: Peripheral blood

growth_protocol: Human donor T cells were transduced with either mock vector, 10D1-BBz CAR, B7H3 CAR, or LG4 CAR constructs. For co-culture experiments, CAR-T cells were incubated with BT245-Luc2-GFP tumor cells for 24 hours.

extract_protocol:
Cells were washed with 1× PBS, and total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Cat. No. 217084) with QIAzol Lysis Reagent according to the manufacturer's instructions.
RNA library preparation and sequencing were performed by Novogene Corporation Inc. (Sacramento, CA, USA). Transcriptome sequencing was conducted on an Illumina NovaSeq 6000 platform using a paired-end 150 bp sequencing strategy.

treatment_protocol: CAR-T cells were cultured alone or co-cultured with BT245-Luc2-GFP tumor cells for 24 hours. Following co-culture, CD45-positive CAR-T cells were isolated using anti-CD45 microbeads (Miltenyi Biotec, Cat. No. 130-045-801). The CD45-negative fraction was collected separately.

value: Peripheral blood

value: CAR-T cells

value: Mock CAR

value: BT245-Luc2-GFP co-culture


title: 10D1 CAR-T cells after BT245-Luc2-GFP co-culture

description:
Library name: sample_6
CD45-positive 10D1 CAR-T cells isolated following co-culture with BT245-Luc2-GFP tumor cells

value: 10D1 CAR


title: Progeria_6weeks_batch1_P071_GFP_sorted_Protocol2

description: Library name: P071

value: Progeria


title: NE2

description: Library name: 5

value: cell

value: E. coli treated with AuPt@ZIF-8 + H₂O₂ + NIR


title: Donor 36, CD99 CRISPR knockout, CD99-intermediate 10D1 CAR-T cells

description:
Library name: SV7
10x Genomics

data_processing:
Raw base call files were converted to FASTQ files using Illumina software. FASTQ files were processed using Cell Ranger (10x Genomics) for read alignment, barcode assignment, and UMI counting. Reads were aligned to the human reference genome GRCh38. Gene-cell count matrices were generated using Cell Ranger. Downstream analyses including quality control, normalization, clustering, differential expression analysis, and visualization were performed using Seurat v5.0.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited gene expression matrices generated by Cell Ranger containing gene-by-cell UMI counts.

extract_protocol:
This single cell assay doesn't involve RNA extraction in the formal sense, but the closest thing would be the "10X Genomics Next GEM Single Cell 3' Kit v3.1".
10X Genomics Next GEM Single Cell 3' protocol v3.1

value: CAR-T cell

value: CD99 knockout


title: Donor 36, CD99 CRISPR knockout, CD99-negative 10D1 CAR-T cells

description:
Library name: SV6
10x Genomics


title: PMA, rep3

first: Kexin

last: Hu

address: Middle Zhijiang Road 274

institute: Shanghai Municipal Hospital of Traditional Chinese Medicine

description:
Library name: Sample9
PMA03

data_processing:
Samples were sequenced on the Illumina platform to generate image files, which were converted into raw sequencing data in FASTQ format by the platform’s built-in software. Low-quality reads and adapter sequences in the raw data were filtered using fastp (version 0.22.0) to obtain clean data for downstream analysis. Clean reads were aligned to the zebrafish reference genome (GRCz11), and differential gene expression analysis was performed using the DESeq2 R package.
Assembly: GRCz11 (danRer11)
Supplementary files format and content: txt file including raw read counts of each gene for all samples
Supplementary files format and content: txt file including differentially expressed genes with log2 fold change, p-value and adjusted p-value

source_name: bone marrow

extract_protocol:
Total RNA extraction was performed with FastPure Complex Tissue/Cell Total RNA Isolation Kit (Vazyme).
RNA-seq library was constructed by polyA-tailed mRNA selection using NEBNext Ultra II RNA Library Prep Kit for Illumina

value: bone marrow

value: megakaryoblast

value: PMA


title: PMA, rep2

description:
Library name: Sample8
PMA02


title: As2S2, rep2

description:
Library name: Sample5
As02


title: As2S2, rep3

description:
Library name: Sample6
As03


title: As2S2, rep1

description:
Library name: Sample4
As01


title: AML12 EV-1

description: Library name: Sample-1

value: Liver

value: hepatocytes

value: wildtype

value: serum-free medium culture


title: control, rep3

description:
Library name: Sample3
BLANK03

value: control


title: Donor 36, 10D1 CAR-T cells

description:
Library name: SV2
10x Genomics

value: Peripheral blood

value: WT


title: PMA, rep1

description:
Library name: Sample7
PMA01


title: control, rep2

description:
Library name: Sample2
BLANK02


title: H1

description:
Library name: sample7
mRNA seq

value: brain


title: control, rep1

description:
Library name: Sample1
BLANK01

organism: root


title: Cur_2

city: Hangzhou

first: Yunkai

last: Yang

address: Zhejiang provincial people’s hospital

institute: Zhejiang provincial people’s hospital

description:
Library name: Cur_2
Curcumol intervention

data_processing:
Raw sequencing reads were trimmed to eliminate adapters and low-quality bases to generate clean reads. Clean reads were mapped to human reference genome for gene expression calculation. Differential expression analysis was implemented between Curcumol-treated and control groups, and functional enrichment analyses were performed on DEGs to identify curcumol-affected pathways especially glycolysis signaling.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Kidney

extract_protocol:
Clear cell renal cell carcinoma ACHN cells were divided into control group (Ctrl) and Curcumol treatment group. The treatment group was incubated with effective concentration of Curcumol, while the control group received vehicle treatment only. Multiple independent biological replicates were set for both groups under identical culture conditions. Total RNA was extracted from cell pellets for Illumina paired-end RNA-seq. After data quality control and transcript quantification, differentially expressed genes between two groups were screened, and GO, KEGG, GSEA enrichment analyses were conducted to uncover transcriptomic alterations triggered by Curcumol, further exploring the molecular mechanism of Curcumol modulating glycolysis and malignant phenotypes of ccRCC cells.
PolyA mRNA was enriched from qualified total RNA and randomly fragmented. First-strand and second-strand cDNA were synthesized, followed by end repair, sequencing adapter ligation and PCR amplification to construct paired-end RNA-seq libraries. Eligible libraries were sequenced on Illumina high-throughput sequencing platform.

value: Kidney

value: ACHN

value: Clear cell renal cell carcinoma cell

value: Wild-type

value: Curcumol intervention


title: Cur_3

description:
Library name: Cur_3
Curcumol intervention


title: Cur_1

description:
Library name: Cur_1
Curcumol intervention


title: Ctrl_2

description:
Library name: Ctrl_2
vehicle control

value: vehicle control


title: Ctrl_3

description:
Library name: Ctrl_3
vehicle control


title: Ctrl_1

description:
Library name: Ctrl_1
vehicle control


title: HUVEC, LPS, OE-vec-3

city: Chongqing

first: Jin

address: Southeast University

institute: Southeast University

description: Library name: vector_LPS_3

data_processing:
Raw fastq sequencing reads were subjected to quality control using FastQC. Low-quality reads, adapter-contaminated reads and reads containing ambiguous N bases were filtered by Trimmomatic software to generate clean reads. Clean reads were aligned to human reference genome using HISAT2. FeatureCounts was applied to quantify gene-level raw read counts. Differential expression analysis was performed via DESeq2 R package; genes with |log2(fold change)| >= 1 and adjusted P-value < 0.05 were defined as significantly differentially expressed genes.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: umbilical vein

extract_protocol:
Total RNA was extracted from cultured HUVEC cells using TRIzol reagent (Invitrogen). RNA purity was detected by NanoPhotometer spectrophotometer, RNA concentration was quantified by Qubit 2.0 Fluorometer, and RNA integrity was assessed by Agilent 2100 Bioanalyzer. Samples with RIN value higher than 7.0 were used for subsequent library construction. Genomic DNA contamination was removed via DNase I digestion.
mRNA was enriched from total RNA by oligo(dT) magnetic beads, then fragmented at 94 degrees C. First-strand cDNA was synthesized with random hexamer primers, followed by second-strand cDNA synthesis. End repair, 3 prime A-tailing and adapter ligation were performed sequentially. Purified cDNA fragments were amplified by PCR to construct strand-specific RNA-seq libraries. Library quality was verified with Agilent DNA 1000 Assay Kit, and qualified libraries were sequenced on Illumina platform with paired-end 150 bp mode.

value: umbilical vein

value: HUVEC

value: endothelial cell

value: empty vector control

value: LPS, 1μg/ml, 24h


title: Ph+ B-ALL1

description: Library name: Sample25

value: Bone Marrow

value: Ph+ B-ALL


title: HUVEC, LPS, OE-vec-2

description: Library name: vector_LPS_2


title: HUVEC, LPS, OE-vec-1

description: Library name: vector_LPS_1


title: Ph+ B-ALL2

description: Library name: Sample26


title: HUVEC, LPS, OE-USP2-3

description: Library name: OE_LPS_3

value: USP2 overexpression


title: HUVEC, LPS, OE-USP2-2

description: Library name: OE_LPS_2


title: HUVEC, LPS, OE-USP2-1

description: Library name: OE_LPS_1


title: ChIRP LINC01018_control_probe

city: St. Petersburg

first: Xiangbo

last: Ruan

state: Florida

address: 600 Fifth Street S

institute: Johns Hopkins University School of Medicine

description: Library name: XRua-XR15_S15

data_processing:
Sequencing read quality was assessed using FastQC, and adapter sequences and low-quality reads were removed with fastp. Filtered reads were aligned to the GRCh38 Ensembl human genome using STAR. Reads with mapping quality scores below 30 were excluded using SAMtools. PCR duplicates were removed with Picard. ChIRP-enriched RNA peaks were identified using MACS2 in single-end mode with matched input controls.
Assembly: GRCh38 Ensembl human genome
Supplementary files format and content: narrowPeak (except for input samples)
Library strategy: ChIRP-seq

extract_protocol:
RNA was then extracted using Trizol–chloroform, and the aqueous phase was purified using RNeasy Mini columns following the manufacturer’s clean-up and on-column DNase digestion protocols. Purified RNA was eluted in nuclease-free water and used for cDNA synthesis
RNA molecules associated with hLMR1 were isolated by Chromatin Isolation by RNA Purification (ChIRP) using biotinylated antisense oligonucleotide probes. Purified RNA was used for library preparation with the SMARTer Stranded Total RNA-Seq Kit v3 (Takara Bio) according to the manufacturer’s instructions. Libraries were sequenced on the Illumina NovaSeq 6000 platform.

value: Liver

tag: probe set

tag: chirp target


title: ChIRP hLMR1_probe_set_2

description: Library name: XRua-XR14_S14


title: ChIRP hLMR1_probe_set_1

description: Library name: XRua-XR13_S13


title: ChIRP Input

description: Library name: XRua-XR12_S12

value: Input


title: sh_hLMR1 replicate5

description: Library name: XRua-XR24_S9

data_processing:
The quality of raw sequencing reads (FASTQ files) was assessed using FastQC. Adapter sequences and low-quality reads were trimmed or removed using Trimmomatic. Prior to alignment, the GRCh38 Ensembl human genome and the GRCm39 Ensembl mouse genome were merged to enable host–graft read discrimination. Filtered reads were aligned to the merged genome using STAR. Uniquely mapped human reads were extracted from the resulting BAM files using SAMtools. Gene-level read counts for mature mRNA were generated with featureCounts from the Subread package. Genes expressed at raw counts greater than one in two or fewer samples were excluded prior to normalization. For data quality assessment, the count matrix was analyzed in R (version 4.1.0) using DESeq2. The count matrix was normalized and analyzed for differential expression in R using DESeq2.
Assembly: GRCh38 Ensembl human genome
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

extract_protocol:
Total RNA was isolated from liver tissues using TRIzol reagent (Invitrogen). After TURBO DNase treatment (Ambion), RNA samples were used for subsequent analyses.
Strand-specific RNA-seq libraries were prepared using the Illumina Stranded Total RNA Prep Ligation kit and sequenced on the Illumina NovaSeq 6000 platform (paired-end sequencing).


title: sh_hLMR1 replicate4

description: Library name: XRua-XR23_S8


title: sh_hLMR1 replicate3

description: Library name: XRua-XR22_S7


title: sh_hLMR1 replicate2

description: Library name: XRua-XR21_S6


title: sh_LacZ replicate4

description: Library name: XRua-XR19_S4


title: sh_LacZ replicate3

description: Library name: XRua-XR18_S3


title: sh_hLMR1 replicate1

description: Library name: XRua-XR20_S5


title: sh_LacZ replicate2

description: Library name: XRua-XR17_S2


title: sh_LacZ replicate1

description: Library name: XRua-XR16_S1


title: H5_3

city: HENAN

first: ZHENG

last: YUAN

address: Jinming Campus, Henan University, Minglun Street, Longting District, Kaifeng, Henan, China

institute: HENAN University

description: Library name: H5_3

data_processing:
Raw FASTQ reads were processed using in-house Perl scripts to remove adaptor sequences, reads containing N bases, and low-quality reads. Clean reads were mapped to the reference genome using HISAT2 v2.0.5. Gene-level read counts were generated using featureCounts v1.5.0-p3, and FPKM values were calculated based on gene length and mapped read counts. Differential expression analysis was performed using DESeq2, with adjusted P value ≤ 0.05 and |log2 fold change| ≥ 1 used as the threshold for significantly differentially expressed genes.
Assembly: Homo sapiens GRCh38/hg38
Supplementary files format and content: The processed data file is provided as a Microsoft Excel file containing gene-level expression values. The file includes gene names and corresponding FPKM values for each sample,

extract_protocol:
Total RNA was extracted from harvested GBM4 cells transduced with either control shRNA lentivirus or shHEXB lentivirus. The quantity and integrity of total RNA were assessed using the RNA Nano 6000 Assay Kit on the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA samples that met the quality requirements were used for subsequent mRNA library construction and transcriptome sequencing.
mRNA was enriched from total RNA using poly-T oligo-attached magnetic beads and fragmented under elevated temperature. First- and second-strand cDNA were synthesized, followed by end repair, 3′ adenylation, adaptor ligation, size selection using AMPure XP beads, and PCR amplification. The final libraries were purified, quantified, and assessed for insert size using Qubit 2.0 Fluorometer and Agilent 2100 Bioanalyzer. Libraries with an effective concentration greater than 2 nM were used for sequencing.


title: H4_2

description: Library name: H4_2


title: H5_1

description: Library name: H5_1


title: H5_2

description: Library name: H5_2


title: Control_3

description: Library name: HP_3


title: Control_1

description: Library name: HP_1


title: Fresh seminal plasma - replicate 3

first: Longlong

last: Fu

state: --choose--

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: D5
seminal plasma from pooled group3 (n=10 donors), fresh
miRNA_TPM_matrix_seminalplasma_6samples.csv

data_processing:
Raw FASTQ data were processed using cutadapt (v1.14) for adapter trimming, fastx_toolkit (v0.0.13) for quality filtering (Q20 ≥ 80%), and NGSQCToolkit (v2.3.3) to remove reads containing ambiguous bases (N). Sequences with length <15 nt or >41 nt were discarded. The remaining high-quality sequences were designated as CleanReads.
Clean reads were aligned to the human reference genome GRCh38.p13 (GCF_000001405.39) using bowtie (v1.1.1) with parameters -f -p 20 -v 2 (allowing up to 2 mismatches).
Reads were sequentially filtered against the Rfam database (version 10.0) using bowtie to remove non-coding RNAs, including rRNA, tRNA, snRNA, snoRNA, and cis-regulatory elements.
Reads were then aligned to human transcript sequences; reads aligning to transcripts with length >26 nt were considered mRNA degradation fragments and were removed. Reads with lengths between 15-26 nt that did not align to transcripts were retained.
Remaining reads were aligned to the Repbase database using RepeatMasker to identify and remove repetitive elements, including LINEs, SINEs, LTR elements, and DNA transposons.
Assembly: GRCh38.p13 (GCF_000001405.39)
Supplementary files format and content: CSV file containing TPM-normalized miRNA expression matrix for 10 sperm samples (A1-A5: post-thaw; B1-B5: fresh). Rows: miRNA identifiers (miRBase IDs); Columns: samples; Values: TPM (Transcripts Per Million). TPM was calculated as: TPM = (number of reads mapped to miRNA / total number of mapped reads) × 10⁶.
Supplementary files format and content: CSV file containing TPM-normalized miRNA expression matrix for 6 seminal plasma samples (C3, C4, C5: post-thaw; D3, D4, D5: fresh). Rows: miRNA identifiers (miRBase IDs); Columns: samples; Values: TPM (Transcripts Per Million). TPM was calculated as: TPM = (number of reads mapped to miRNA / total number of mapped reads) × 10⁶.

source_name: seminal plasma

extract_protocol:
Total RNA was extracted from 200 μL seminal plasma or from sperm pellets using TRIzol LS Reagent (Invitrogen, USA) or TRIzol Reagent (Invitrogen, USA), respectively, following the manufacturer's protocols. Briefly, samples were mixed with TRIzol reagent and incubated at room temperature for 5 min. Chloroform was added, and the mixture was centrifuged at 12,000 × g for 15 min at 4°C. The aqueous phase was collected, and RNA was precipitated with isopropanol. The RNA pellet was washed with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and purity were assessed using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, USA). RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Pico Kit.
Small RNA libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs, USA) following the manufacturer's protocol. Briefly, 3' and 5' adapters were sequentially ligated to the small RNA fraction. Reverse transcription was performed to generate first-strand cDNA, followed by PCR amplification (15 cycles). The PCR products were purified by PAGE gel electrophoresis to select fragments corresponding to small RNA insert sizes (140-160 bp). Library quality and concentration were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the High Sensitivity DNA Kit.

treatment_protocol: Semen samples were collected from 30 healthy normozoospermic donors aged 25-35 years. For cryopreservation groups (sperm: A1-A5; seminal plasma: C3-C5), samples were mixed with an equal volume of SpermFreeze Solution (Vitrolife, Sweden), loaded into 0.5 mL sterile straws, and cooled using a programmable freezer as follows: cooled from room temperature to 4°C at 1°C/min, then from 4°C to -80°C at 10°C/min, and finally plunged into liquid nitrogen (-196°C) for storage. Samples were stored for a minimum of 2 weeks before thawing. For thawing, straws were incubated in a water bath at 37°C for 5 min. Fresh controls (sperm: B1-B5; seminal plasma: D3-D5) were processed immediately without cryopreservation.

value: seminal plasma

value: fresh


title: Fresh seminal plasma - replicate 2

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: D4
seminal plasma from pooled group2 (n=10 donors), fresh
miRNA_TPM_matrix_seminalplasma_6samples.csv


title: Fresh seminal plasma - replicate 1

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: D3
seminal plasma from pooled group1 (n=10 donors), fresh
miRNA_TPM_matrix_seminalplasma_6samples.csv


title: Post-thaw seminal plasma - replicate 3

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: C5
seminal plasma from pooled group3 (n=10 donors), post-thaw
miRNA_TPM_matrix_seminalplasma_6samples.csv

value: cryopreservation-thawing


title: Post-thaw seminal plasma - replicate 2

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: C4
seminal plasma from pooled group2 (n=10 donors), post-thaw
miRNA_TPM_matrix_seminalplasma_6samples.csv


title: Fresh sperm - replicate 4

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: B4
sperm from donor4, fresh
miRNA_TPM_matrix_sperm_10samples.csv

source_name: sperm

value: sperm


title: Fresh sperm - replicate 5

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: B5
sperm from donor5, fresh
miRNA_TPM_matrix_sperm_10samples.csv


title: Fresh sperm - replicate 3

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: B3
sperm from donor3, fresh
miRNA_TPM_matrix_sperm_10samples.csv


title: Fresh sperm - replicate 2

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: B2
sperm from donor2, fresh
miRNA_TPM_matrix_sperm_10samples.csv


title: Cryopreserved sperm - replicate 2

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: A2
sperm from donor2, post-thaw
miRNA_TPM_matrix_sperm_10samples.csv


title: Cryopreserved sperm - replicate 3

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: A3
sperm from donor3, post-thaw
miRNA_TPM_matrix_sperm_10samples.csv


title: Cryopreserved sperm - replicate 4

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: A4
sperm from donor4, post-thaw
miRNA_TPM_matrix_sperm_10samples.csv


title: Cryopreserved sperm - replicate 1

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: A1
sperm from donor1, post-thaw
miRNA_TPM_matrix_sperm_10samples.csv


title: 231_shAK1_#4

city: seoul

first: Dakyung

last: Lee

address: 101 Daehakro

country: South Korea

institute: University

description:
Library name: WTS0061
Column name in raw_counts_All_Sample.txt: WTS0061

data_processing:
RNA sequencing data were processed using RSEM, which employs the STAR aligner to map reads to the GRCh38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
Total RNA was isolated using TRIzol reagent (Favorgen, Pingtung, Taiwan)
TruSeq RNA


title: 231_shCTL_#1

description:
Library name: WTS0054
Column name in raw_counts_All_Sample.txt: WTS0054


title: FUS_GFP_P525L_ACMS_Rep4

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

country: Germany

institute: University Medical Center Rostock

description:
Library name: L155980
N/A

data_processing:
Libraries from above were sequenced on an Illumina® NovaSeq 6000 in 100 bp paired-end mode to a depth 40 million fragments (short reads) per library. Short reads were aligned to the human reference genome hg38 with support of the Ensembl 104 splice sites using the aligner STAR (v2.7.10b) (associated manuscript: Dobin et al., 2013), and the custom settings “--outSAMmultNmax 1 --sjdbOverhang 100”. Counts per gene and sample were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation using featureCounts (v2.0.1) (associated manuscript: Liao et al., 2014), and the settings “-s 2 -t ‘exon’ -p -Q 1”. Normalization of raw fragments based on library size and testing for differential expression between the different conditions was done with the DESeq2 R package (v1.38.3, R v4.2.2) (associated manuscript: Love et al., 2014). Principal Component Analysis (PCA) based on the 500 most variable genes was performed to explore the relationship between biological replicates and different libraries. DEGs were determined using the Wald test of DESeq2. Resulting p-values of DEGs were calculated from the variance across the four biological replicas of each condition (see above) and corrected for multiple testing with the Independent Hypothesis Weighting package (IHW 1.26.0) (associated manuscript: Ignatiadis et al., 2016). Genes with a maximum of 5% false discovery rate (adjusted p-value ≤ 0.05) and |log2FoldChange| ≥ ± 1.5 were considered significantly differentially expressed. DEGs were calculated for each cell line for ACMS versus UT, respectively, as well as for FUS-GFP P525L UT versus isogenic FUS-GFP WT UT.
Assembly: hg38
Supplementary files format and content: tab-separated excel file includes the output of gene counts. Each columns is either describing characteristics of a gene (gene name, ensembl_id, strand, position, chromosom) or a sample. Each row list genes with the details of the gene and the TPM counts per gene per sample.

source_name: Skin

growth_protocol: Spinal MNs were differentiated from cryoconserved neuronal progenitor cells (NPCs) derived from iPSCs as illustrated in Fig. 1H of the associated manuscript. The coating and assembly of MFCs (Xona Microfluidics RD900) to prepare for the seeding of MNs was performed as described (refer to associated manuscript: Naumann et al., 2018; Pal et al., 2018, 2021). MNs were seeded for maturation into one site of a MFC to obtain a fully compartmentalized culture with proximal somata and their dendrites being physically separated from their distal axons as only the latter type of neurite was capable to grow from the proximal seeding site through a microgroove barrier of 900 µm-long microchannels to the distal site where they sprouted out from the distal channel exits to the open space. ACMS sessions were performed at 30, 35, 40 and 45 DIV of axon growth and MN maturation as shown in Fig. 1H, J of the associated manuscript. All subsequent total RNA extractions for RNA-seq were performed at 48 DIV.

extract_protocol:
Total RNA from entire MFC MN cultures was extracted and purified at 48 DIV as illustrated in associated manuscript: Fig. 1J either after ACMS (at 25 Hz, perpendicular field orientation and 10 mT) or from untreated controls (UT). The preparation was performed with the Qiagen RNeasy® Plus kit (Cat no. 74134) according to the manufacture’s manual and typically resulting in 5-10 µg of total RNA dissolved in a total volume of 80 µl of DNAse/RNAse-free water. Concentration and integrity of each RNA sample was analyzed on an Agilent® 2100 Bioanalyzer (assay class: eukaryote total RNA nano, version 2.6), all resultant RNA integrity numbers (RIN) were in the range of 8.7 - 9.7, indicating high purity and integrity of all samples.
Messenger RNA was isolated from 500 ng of each total RNA sample (see above) by poly-dT enrichment using the New England Biolabs® (NEB) Next Poly-A mRNA Magnetic Isolation Module according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation, Next Adapters for Illumina of the NEB Next Multiplex Oligos for Illumina kit were used. After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 0.9:1 to the samples. Unique dual indexing was performed during the following PCR enrichment (12 cycles) using amplification primers carrying the same sequence for i7 and i5 index (i5: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, i7: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (0.9:1), libraries were quantified using the Fragment Analyzer (Agilent®).

treatment_protocol: We designed and fabricated electromagnetic coils (solenoids) with cylindrical geometry for operation inside standard cell culture incubators. To compensate for heating beyond 37 °C due to ohmic losses, we equipped the coils with a water-cooling system. The solenoids with an open central bore of 50 mm diameter and a height of 100 mm could harbor up to six cell culture dishes (35 mm diameter and 12 mm height) within their central bore in custom-tailored sample holders to expose them to a homogeneous magnetic field. For field generation, we applied alternating currents (AC) by using a function generator connected to an amplifier. The entire ACMS protocol comprised four consecutive treatment sessions as illustrated in Fig. 1J of the associated manuscript and was performed with a biphasic sine waveform at a field strength of 10 mT (time-averaged mean) at 25 Hz. The first ACMS session was performed at 30, the second at 35, the third at 40 and the fourth at 45 DIV with field-less resting intervals for the cells of four days each between. After the fourth and final ACMS treatment session, the cells were maintained in culture for two more resting days before the sustained impact of the ACMS was assessed at 48 DIV by RNA-seq.

value: Skin

value: Fibroblast (iPSC source)

value: iPSC-derived spinal motor neurons

value: isogenic mutant

tag: mutation/tag

value: FUS P525L with carboxyterminal eGFP

tag: biological replica_(rep)_#

value: ACMS


title: FUS_GFP_P525L_ACMS_Rep1

description:
Library name: L155977
N/A


title: FUS_R495X_ACMS_Rep4

description:
Library name: L155976
N/A

value: non-isogenic mutant


title: FUS_R495X_ACMS_Rep3

description:
Library name: L155975
N/A


title: FUS_R521L_ACMS_Rep4

description:
Library name: L155972
N/A

value: FUS R521Lhet


title: FUS_R521L_ACMS_Rep3

description:
Library name: L155971
N/A


title: FUS_R521L_ACMS_Rep2

description:
Library name: L155970
N/A


title: FUS_R521L_ACMS_Rep1

description:
Library name: L155969
N/A


title: FUS_R521C_ACMS_Rep2

description:
Library name: L155966
N/A

value: FUS R521Chet


title: FUS_R521C_ACMS_Rep1

description:
Library name: L155965
N/A


title: FUS_GFP_WT_ACMS_Rep4

description:
Library name: L155964
N/A

value: isogenic control

value: FUS WT with carboxyterminal eGFP


title: FUS_GFP_WT_ACMS_Rep2

description:
Library name: L155962
N/A


title: Ctrl3_ACMS_Rep4

description:
Library name: L155960
N/A

value: non-isogenic control

value: wild type (WT)


title: Ctrl3_ACMS_Rep3

description:
Library name: L155959
N/A


title: Ctrl3_ACMS_Rep2

description:
Library name: L155958
N/A


title: Ctrl3_ACMS_Rep1

description:
Library name: L155957
N/A


title: Ctrl_AKC5_ACMS_Rep3

description:
Library name: L155955
N/A


title: Ctrl_AKC5_ACMS_Rep2

description:
Library name: L155954
N/A


title: Ctrl_AKC5_ACMS_Rep1

description:
Library name: L155953
N/A


title: Ctrl1_ACMS_Rep4

description:
Library name: L155952
N/A


title: Ctrl1_ACMS_Rep3

description:
Library name: L155951
N/A


title: Ctrl_AKC5_ACMS_Rep4

description:
Library name: L155956
N/A


title: Ctrl1_ACMS_Rep2

description:
Library name: L155950
N/A


title: Ctrl1_ACMS_Rep1

description:
Library name: L155949
N/A


title: FUS_GFP_P525L_untreated_Rep4

description:
Library name: L155948
N/A

value: Untreated


title: FUS_GFP_P525L_untreated_Rep3

description:
Library name: L155947
N/A


title: FUS_GFP_P525L_untreated_Rep2

description:
Library name: L155946
N/A


title: FUS_GFP_P525L_untreated_Rep1

description:
Library name: L155945
N/A


title: H4_1

description: Library name: H4_1


title: H4_3

description: Library name: H4_3


title: FUS_R495X_untreated_Rep4

description:
Library name: L155944
N/A


title: Control_2

description: Library name: HP_2


title: FUS_R495X_untreated_Rep3

description:
Library name: L155943
N/A


title: Post-thaw seminal plasma - replicate 1

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: C3
seminal plasma from pooled group1 (n=10 donors), post-thaw
miRNA_TPM_matrix_seminalplasma_6samples.csv

value: seminal plasma


title: Fresh sperm - replicate 1

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: B1
sperm from donor1, fresh
miRNA_TPM_matrix_sperm_10samples.csv

value: fresh


title: Cryopreserved sperm - replicate 5

address: 大慧寺12号，科研楼2楼，精子库

institute: 国家卫生健康委科学技术研究所

description:
Library name: A5
sperm from donor5, post-thaw
miRNA_TPM_matrix_sperm_10samples.csv

value: sperm

value: cryopreservation-thawing


title: FUS_R495X_untreated_Rep2

description:
Library name: L155942
N/A

value: Skin

value: Fibroblast (iPSC source)


title: FUS_R495X_untreated_Rep1

description:
Library name: L155941
N/A

value: iPSC-derived spinal motor neurons


title: 231_shAK1_#2

description:
Library name: WTS0059
Column name in raw_counts_All_Sample.txt: WTS0059


title: 231_shAK1_#1

description:
Library name: WTS0058
Column name in raw_counts_All_Sample.txt: WTS0058


title: FUS_R521L_untreated_Rep4

description:
Library name: L155940
N/A


title: 231_shCTL_#4

description:
Library name: WTS0057
Column name in raw_counts_All_Sample.txt: WTS0057


title: 231_shCTL_#2

description:
Library name: WTS0055
Column name in raw_counts_All_Sample.txt: WTS0055


title: FUS_R521L_untreated_Rep3

description:
Library name: L155939
N/A


title: FUS_GFP_P525L_ACMS_Rep3

description:
Library name: L155979
N/A

value: isogenic mutant

value: FUS P525L with carboxyterminal eGFP


title: FUS_GFP_P525L_ACMS_Rep2

description:
Library name: L155978
N/A

value: ACMS


title: FUS_R521L_untreated_Rep2

description:
Library name: L155938
N/A

value: non-isogenic mutant

value: FUS R521Lhet


title: FUS_R521L_untreated_Rep1

description:
Library name: L155937
N/A


title: FUS_R495X_ACMS_Rep1

description:
Library name: L155973
N/A


title: FUS_R521C_untreated_Rep4

description:
Library name: L155936
N/A

value: FUS R521Chet


title: FUS_R495X_ACMS_Rep2

description:
Library name: L155974
N/A


title: FUS_R521C_untreated_Rep3

description:
Library name: L155935
N/A


title: FUS-GFP_WT_untreated_Rep2

description:
Library name: L155930
N/A

value: isogenic control

value: FUS WT with carboxyterminal eGFP


title: FUS_R521C_untreated_Rep2

description:
Library name: L155934
N/A


title: FUS-GFP_WT_untreated_Rep3

description:
Library name: L155931
N/A


title: FUS-GFP_WT_untreated_Rep4

description:
Library name: L155932
N/A


title: FUS_R521C_untreated_Rep1

description:
Library name: L155933
N/A


title: Ctrl3_untreated_Rep4

description:
Library name: L155928
N/A

value: non-isogenic control

value: wild type (WT)


title: Ctrl3_untreated_Rep3

description:
Library name: L155927
N/A

value: Untreated


title: FUS-GFP_WT_untreated_Rep1

description:
Library name: L155929
N/A


title: Ctrl3_untreated_Rep1

description:
Library name: L155925
N/A


title: Ctrl3_untreated_Rep2

description:
Library name: L155926
N/A


title: Ctrl2_untreated_Rep3

description:
Library name: L155923
N/A


title: Ctrl2_untreated_Rep4

description:
Library name: L155924
N/A


title: FUS_R521C_ACMS_Rep3

description:
Library name: L155967
N/A


title: FUS_R521C_ACMS_Rep4

description:
Library name: L155968
N/A


title: Ctrl2_untreated_Rep1

description:
Library name: L155921
N/A


title: Ctrl1_untreated_Rep4

description:
Library name: L155920
N/A


title: Ctrl2_untreated_Rep2

description:
Library name: L155922
N/A


title: Ctrl1_untreated_Rep3

description:
Library name: L155919
N/A


title: Ctrl1_untreated_Rep1

description: Library name: L155917


title: SNHG29 shRNA control replicate 3

city: Frankfurt

first: Robert

last: Winkler

state: Hesse

address: Theodor-Stern-Kai 7

department: Department of Pediatrics

institute: Goethe University Frankfurt

description:
Library name: RW16_ctrl
Column name in deseq2_normalized_counts.tsv: RW16_ctrl

data_processing:
Raw sequencing data were processed using the nf-core/rnaseq pipeline v3.18 with default settings.
Reads were aligned to the hg38 reference genome using STAR 2.7.11b and quantified using Salmon 1.10.3 against the Ensembl transcriptome version 108.
Differential expression analysis was performed in R 4.4.2 using DESeq2 1.46.0 with design formula ~ method + logqpcr, where method accounts for baseline differences between CRISPRi and shRNA, and logqpcr models the knockdown efficacy. Log fold changes were shrunk using apeGLM 1.28.0.
DESeq2 size-factor normalized counts were extracted from the fitted combined model (all 15 samples analyzed jointly).
Assembly: GRCh38 (Ensembl release 108)
Supplementary files format and content: deseq2_normalized_counts.tsv: Tab-delimited text file containing DESeq2 size-factor normalized gene counts for all 15 samples. Columns: gene_id (Ensembl gene ID) and one column per sample with normalized count values.

growth_protocol: Human myeloid leukemia cell line M-07e was procured from DSMZ (Braunschweig, Germany). Cells were maintained as per the supplier's recommendations and were subjected to routine testing for Mycoplasma contamination.

extract_protocol:
Total RNA was extracted on days 3 (shRNA) or 7 (CRISPRi) post-transduction using the RNeasy Plus Mini Kit (Qiagen).
rRNA-depleted libraries were prepared and sequenced by Novogene on an Illumina NovaSeq 6000 (150 bp paired-end).

treatment_protocol: Stable cell lines expressing the CRISPRi effector were generated with pLKO5d.SFFV.dCas9-KRAB.MeCP2.P2A.BSD. Individual sgRNAs, designed with the CCTop2 platform, were delivered via the SGL40C.EFS.E2Crimson vector (Addgene #100894). shRNA sequences were designed using the miR-N tool and cloned into the SIN40C.SFFV.eGFP.miR30n (Addgene #169278) or SIN40C.SFFV.dTomato.miR30n (Addgene #169277) backbone via BsmBI digestion. Constructs targeting firefly luciferase were used as non-targeting negative controls. Lentiviral particles were generated via PEI-mediated co-transfection of HEK293T cells with the respective expression vector alongside packaging plasmids pMD2.G (Addgene #12259) and psPAX2 (Addgene #12260). Virus-containing supernatant was harvested and concentrated by ultracentrifugation. Target cells were transduced by incubation with the concentrated virus in media supplemented with 5 ug/ml Polybrene (Sigma-Aldrich).

value: acute myeloid leukemia

tag: knockdown method

value: shRNA

tag: guide or_shrna

value: shRNA control

tag: biological replicate


title: SNHG29 shRNA knockdown (shRNA 1) replicate 3

description:
Library name: RW17_sh3
Column name in deseq2_normalized_counts.tsv: RW17_sh3

value: shRNA 1


title: SNHG29 shRNA knockdown (shRNA 2) replicate 3

description:
Library name: RW18_sh5
Column name in deseq2_normalized_counts.tsv: RW18_sh5

value: shRNA 2


title: SNHG29 shRNA knockdown (shRNA 1) replicate 2

description:
Library name: RW14_sh3
Column name in deseq2_normalized_counts.tsv: RW14_sh3


title: Ctrl1_untreated_Rep2

description:
Library name: L155918
N/A

tag: tissue

value: Skin

value: Fibroblast (iPSC source)

value: iPSC-derived spinal motor neurons


title: SNHG29 shRNA knockdown (shRNA 2) replicate 2

description:
Library name: RW15_sh5
Column name in deseq2_normalized_counts.tsv: RW15_sh5


title: SNHG29 shRNA knockdown (shRNA 2) replicate 1

description:
Library name: RW12_sh5
Column name in deseq2_normalized_counts.tsv: RW12_sh5


title: SNHG29 shRNA knockdown (shRNA 1) replicate 1

description:
Library name: RW11_sh3
Column name in deseq2_normalized_counts.tsv: RW11_sh3


title: SNHG29 CRISPRi control (Luciferase sgRNA) replicate 3

description:
Library name: RW7_LUC
Column name in deseq2_normalized_counts.tsv: RW7_LUC

value: CRISPRi

value: Luciferase sgRNA


title: SNHG29 CRISPRi knockdown (sgRNA 2) replicate 3

description:
Library name: RW9_sg3
Column name in deseq2_normalized_counts.tsv: RW9_sg3

value: sgRNA 2


title: SNHG29 CRISPRi knockdown (sgRNA 2) replicate 2

description:
Library name: RW6_sg3
Column name in deseq2_normalized_counts.tsv: RW6_sg3


title: SNHG29 CRISPRi knockdown (sgRNA 1) replicate 3

description:
Library name: RW8_sg2
Column name in deseq2_normalized_counts.tsv: RW8_sg2

value: sgRNA 1


title: SNHG29 CRISPRi control (Luciferase sgRNA) replicate 2

description:
Library name: RW4_LUC
Column name in deseq2_normalized_counts.tsv: RW4_LUC


title: Human ovarian cancer tissue 3

city: Nanjing

first: Xiyi

address: No.123 Mochou Road

institute: Women’s Hospital of Nanjing Medical University

description: Library name: T-20201596

data_processing:
For circRNA expression analysis, the reads were to mapped genome using the STAR and DCC was used to identify the cirRNA and to estimate the circRNA expression. TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program.
Assembly: GRCh38
Supplementary files format and content: circRNA_reads_count.xlsx lists the normalized read counts assessed by RNC-seq of all samples listed.

source_name: Human ovarian cancer

extract_protocol:
After grinding the tissue in liquid nitrogen, a specific lysis buffer was added. Following centrifugation, 200 μL of the lysate was collected, and total RNA was extracted using the Takara RNAiso Plus method. The extracted total RNA was then subjected to quality control. Subsequently, the tissue lysate was applied to MicroSpin S-400 HR Columns to separate ribosomal complexes. RNA was then extracted from the isolated ribosomal complexes using the Takara RNAiso Plus method.
After the samples passed quality control, libraries were constructed using the Total RNA-seq (H/M/R) Library Prep Kit for Illumina®. First, designed DNA probes were hybridized with the RNA samples to remove rRNA from total RNA. Subsequently, the RNA was fragmented, and first-strand cDNA was synthesized. Using a strand-specific approach, dUTP was incorporated during second-strand cDNA synthesis to label the second strand, while end repair was completed in the same step. This was followed by A-tailing, adapter ligation, purification of the ligation products, size selection, and library amplification. Prior to PCR amplification, the dUTP-containing second-strand cDNA template was digested using UDG enzyme. After amplification, the libraries were purified and recovered using magnetic beads, yielding the final RNA-seq libraries.

value: Human ovarian cancer


title: Human ovarian cancer tissue 1

description: Library name: T-19201922


title: Human ovary tissue 3

description: Library name: N-20215301

source_name: Human ovary

value: Human ovary


title: SNHG29 CRISPRi knockdown (sgRNA 1) replicate 2

description:
Library name: RW5_sg2
Column name in deseq2_normalized_counts.tsv: RW5_sg2


title: Human ovary tissue 1

description: Library name: N-20215257


title: Human glomerular endothelial cell, Donor 3, 24hr hypoxia, RNA

city: Singapore

first: Chong Yun

last: Pang

address: 60 Nanyang Dr, School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
Library name: Sample12
Column in rawcount file: L_rawcount

data_processing:
mRNA sequencing was processed using Galaxy. Trimming was done with Trimmomatic for adapter removal, alignment was done with STAR and counts obtained using HTseq. Filtering was applied to protein-coding genes only.
Assembly: Gencode GRCh38 v40 for mRNA
Supplementary files format and content: csv files include rawcounts for mRNA.

source_name: Primary glomerular endothelial cells

growth_protocol: Primary glomerular endothelial cells were cultured with complete endothelial media (Cell Biologics) in a humidified incubator at 37C.

extract_protocol:
RNA were extracted using miRNeasy mini kit (Qiagen). 1ug of Total RNA was sent to  Newcastle University Genomics Core for mRNA library preparation.
mRNA library was prepared using TruSeq stranded mRNA library kit (Illumina).

treatment_protocol: Cells were cultured under 1% oxygen condition in a hypoxic incubator to mimic ischemia for the stipulated duration.

value: Primary glomerular endothelial cells

value: Hypoxia


title: Human glomerular endothelial cell, Donor 3, 4hr hypoxia,RNA

description:
Library name: Sample10
Column in rawcount file: J_rawcount


title: Human glomerular endothelial cell, Donor 3, Untreated,RNA

description:
Library name: Sample9
Column in rawcount file: I_rawcount

value: Untreated


title: Human glomerular endothelial cell, Donor 3, 12hr hypoxia,RNA

description:
Library name: Sample11
Column in rawcount file: K_rawcount


title: Human glomerular endothelial cell, Donor 2, 24hr hypoxia,RNA

description:
Library name: Sample8
Column in rawcount file: H_rawcount


title: Human glomerular endothelial cell, Donor 2, 12hr hypoxia,RNA

description:
Library name: Sample7
Column in rawcount file: G_rawcount


title: Human glomerular endothelial cell, Donor 2, Untreated,RNA

description:
Library name: Sample5
Column in rawcount file: E_rawcount


title: Human glomerular endothelial cell, Donor 1, 12hr hypoxia,RNA

description:
Library name: Sample3
Column in rawcount file: C_rawcount


title: Human glomerular endothelial cell, Donor 1, 24hr hypoxia,RNA

description:
Library name: Sample4
Column in rawcount file: D_rawcount


title: Human glomerular endothelial cell, Donor 1, Untreated,RNA

description:
Library name: Sample1
Column in rawcount file: A_rawcount


title: Human glomerular endothelial cell, Donor 1, 4hr hypoxia,RNA

description:
Library name: Sample2
Column in rawcount file: B_rawcount


title: HCC liver L_035 Normal rep1

city: Kunming

first: Fen

last: Huang

address: 727 Jingming Rd

institute: Ku

description:
Library name: L_035
3' scRNAseq

data_processing:
Raw base call files were analyzed using Cell Ranger v.9.0.0 using the Duke Cluster Computing platform. The bcl2fastq2 command was used to generate FASTQ files from bcl Illumina sequencer output files.
CellRanger v.9.0.0 ‘counts’ command was used to generate raw gene-barcode matrices aligned to the GRCh38-2024-A
Assembly: GRCh38-2024-A
Supplementary files format and content: filtered feature bc matrices  contain matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz

source_name: liver

extract_protocol:
Tumor resection samples and adjacent liver tissue were digested in RPMI containing Collagenase I & II (0.1 mg/ml, Thermo Fisher Scientific) and DNAse I, minced, and digested for one hour using the GentleMACS system (Miltenyi Biotec).
Single-cell suspensions were loaded onto 10X Chromium chip in order to capture 5000-10,000 single cells, following the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3). The captured single cells underwent cDNA amplification and library construction using the standard protocol of the 3’ kit (V3). The single-cell libraries were sequenced on Illumina NovaSeq 6000 sequencing system

value: liver

tag: sample group

value: HCC liver_normal


title: HCC liver L_036 Normal rep2

description:
Library name: L_036
3' scRNAseq


title: HCC liver L_038 Normal rep3

description:
Library name: L_038
3' scRNAseq


title: HCC liver L_033 Acute rep2

description:
Library name: L_033
3' scRNAseq

value: HCC liver_Acute


title: HCC liver L_034 Acute  rep3

description:
Library name: L_034
3' scRNAseq


title: HCC liver L_031 Acute rep1

description:
Library name: L_031
3' scRNAseq


title: MDA, experimental standards

city: Taichung City

first: Ling

last: Chen

address: Rm. 7, 4F., No. 99, Jingke S. Rd., Nantun Dist.

country: Taiwan

institute: AllBio Life, Inc.

description: Library name: MDA

data_processing:
Raw sequencing data were processed using Bcl2fastq (v2.20.0.422) for base calling and preliminary quality analysis.
Quality assessment of the sequencing data was performed using FastQC (v0.10.1), which evaluated base quality scores, sequence quality distribution, and nucleotide content across all bases.
Adapter sequences and low-quality reads were removed using Cutadapt (v1.9.1) with the following parameters: removal of 5' or 3' end bases with N' s or quality values below 20, and elimination of reads shorter than 75 bp after trimming.
Assembly: Clean reads were aligned to the human reference genome (hg38) using Hisat2 (v2.2.1) with default parameters.
Supplementary files format and content: a csv file inclide FPKM values for each Sample

extract_protocol:
Total RNA was extracted from CAMA-1 and T47D breast cancer cell lines treated with 50 μM Olaparib or vehicle control for 72 hours using the TransZol Up Plus RNA Kit (Transgene, cat. ER501-01) according to the manufacturer’s instructions
RNA sequencing libraries were validated and subsequently sequenced on an Illumina platform to generate 150 bp paired-end reads with a target depth of approximately 46-48 million reads per sample.

value: breast cancer cell lines


title: SUM159, shCTNNB1, 1% O2 (biol rep 3)

city: Baltimore

first: YAJING

last: LYU

state: MD

address: 733 N Broadway

department: ICE

institute: Johns Hopkins University

description: Library name: CT_1pct-3

data_processing:
RNA-seq data were processed and analyzed using Genialis Expressions software (https://www.genialis.com).
The automated data analysis on the Genialis platform consisted of the following steps: sequence quality checks were performed on raw and trimmed reads (FastQC), trimming and quality filtering of reads (BBDuk), mapping to reference human genome Ensembl v.92 (STAR), expression quantification (featureCounts), and expression normalization (RNA.norm).
Key QC metrics (e.g., mapping statistics) were collected. As an additional quality control step, a sample of one million reads (Seqtk tool) was mapped (STAR) separately to human rRNA and globin sequences to evaluate the proportion of these reads in the sample.
Differential gene expression analyses were performed with DESeq2. Lowly-expressed genes, which have expression count summed overall samples below 10, were filtered out from the differential expression analysis input matrix.
Assembly: GRCh38
Supplementary files format and content: Excel tables containing TPM values for all genes from each replicate across all groups.
Supplementary files format and content: Excel tables containing fold-change and FDR values for the selected genes.

source_name: breast cancer cell

growth_protocol: SUM159 subclones were cultured in DMEM/F12 medium with 10% FBS and maintained at 37 °C in a humidified incubator containing 5% CO₂ and 95% air.

extract_protocol:
RNA was harvested using TRIzol (Invitrogen) and treated with DNase (Qiagen).
Library preparation and sequencing using the NovaSeq 6000 platform (Illumina) were performed by the Johns Hopkins Genetics Resources Core Facility High-Throughput Sequencing Center.

treatment_protocol: NTC, HIF1A-KD, PPME1-KD, and CTNNB1-KD subclones of SUM159 cells were exposed to 20% or 1% O2 for 24 hours

value: breast cancer cell

value: SUM159 cell line

value: breast cancer cell line

tag: genotype


title: T47D cells, wild-type

description: Library name: T47D


title: SUM159, shCTNNB1, 1% O2 (biol rep 2)

description: Library name: CT_1pct-2


title: SUM159, shCTNNB1, 1% O2 (biol rep 1)

description: Library name: CT_1pct-1


title: SUM159, shCTNNB1, 20% O2 (biol rep 3)

description: Library name: CT_20pct-3


title: SUM159, shCTNNB1, 20% O2 (biol rep 2)

description: Library name: CT_20pct-2


title: SUM159, shPPME1, 1% O2 (biol rep 3)

description: Library name: PME_1pct-3


title: SUM159, shCTNNB1, 20% O2 (biol rep 1)

description: Library name: CT_20pct-1


title: SUM159, shPPME1, 1% O2 (biol rep 1)

description: Library name: PME_1pct-1


title: SUM159, shPPME1, 20% O2 (biol rep 3)

description: Library name: PME_20pct-3


title: SUM159, shPPME1, 20% O2 (biol rep 2)

description: Library name: PME_20pct-2


title: SUM159, shPPME1, 20% O2 (biol rep 1)

description: Library name: PME_20pct-1


title: SUM159, shHIF1A, 1% O2 (biol rep 3)

description: Library name: HIF_1pct-3


title: SUM159, shHIF1A, 1% O2 (biol rep 2)

description: Library name: HIF_1pct-2


title: SNHG29 shRNA control replicate 1

description:
Library name: RW10_ctrl
Column name in deseq2_normalized_counts.tsv: RW10_ctrl

value: acute myeloid leukemia

value: shRNA

value: shRNA control


title: SUM159, shHIF1A, 20% O2 (biol rep 3)

description: Library name: HIF_20pct-3


title: SUM159, shHIF1A, 1% O2 (biol rep 1)

description: Library name: HIF_1pct-1


title: SUM159, shHIF1A, 20% O2 (biol rep 2)

description: Library name: HIF_20pct-2


title: SUM159, shNTC, 1% O2 (biol rep 3)

description: Library name: NTC_1pct-3

value: NTC


title: SUM159, shNTC, 1% O2 (biol rep 2)

description: Library name: NTC_1pct-2


title: SUM159, shNTC, 20% O2 (biol rep 3)

description: Library name: NTC_20pct-3


title: SUM159, shNTC, 20% O2 (biol rep 2)

description: Library name: NTC_20pct-2


title: SUM159, shNTC, 20% O2 (biol rep 1)

description: Library name: NTC_20pct-1


title: MUC29526

city: Freiburg

first: Natalie

last: Garzorz-Stark

address: Hauptstraße 7

department: Department of Dermatology and Venereology

institute: University of Freiburg

description: Library name: MUC29526

data_processing:
Sequence alignment was performed using STAR aligner with human genome reference hg38
Assembly: reference hg38
Supplementary files format and content: Processed_data.h5

growth_protocol: no growth

extract_protocol:
miRNeasy Tissue kit, Qiagen
TruSeq Stranded Total RNA Kit (Illumina)

treatment_protocol: no treatment

value: Skin

tag: condition

value: Eczema

tag: individual


title: MUC29524

description: Library name: MUC29524


title: MUC29525

description: Library name: MUC29525


title: MUC29523

description: Library name: MUC29523


title: MUC29522

description: Library name: MUC29522

value: Psoriasis


title: MUC29520

description: Library name: MUC29520


title: MUC29517

description: Library name: MUC29517


title: MUC29518

description: Library name: MUC29518


title: MUC29513

description: Library name: MUC29513


title: MUC29509

description: Library name: MUC29509


title: MUC29508

description: Library name: MUC29508


title: MUC26159

description: Library name: MUC26159


title: MUC26160

description: Library name: MUC26160


title: MUC26158

description: Library name: MUC26158


title: MUC14402

description: Library name: MUC14402


title: SVZ_1643

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

description: Library name: FETHB2_0005_01_LB02-01

library_source: genomic

data_processing:
A standard bioinformatics pipeline was used to process the EMseq data; processing statistics are reported in Supplementary Table 2.  Fastp 0.23.213 was used to ascertain read quality and perform adapter trimming. Reads were aligned to the hg38 genome using bwa-meth 0.2.514. Duplicates were filtered using Picard MarkDuplicates (https://broadinstitute.github.io/picard/). MethylDackel (https://github.com/dpryan79/MethylDackel) was used to compute Mbias plots. MethylDackel extract --maxVariantFrac 0.2 --minOppositeDepth 5 --cytosine_report --OT 0,0,0,147 --OB: 3,0,5,0 was used to compute cytosine-level methylation reports while removing potential C > T variants. Methylation non-conversion rate was measured using the methylation level of the lambda phage genome. Samples had a mean non-conversion rate of 0.34% (range 0.21 - 0.64) and all samples were retained. All samples showed consistent patterns of genome-wide methylation with over 50% of CpGs having 90% methylation and 10% CpGs with <10% methylation. Hierarchical clustering of CpG methylation in the region of SOX2 and EOMES largely separated the rhombic lip ventricular zone and subventricular zone samples, and no samples were excluded from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Cytosine report files generated by MethylDackel
Library strategy: EM-seq

molecule: genomic DNA

source_name: Cerebellar rhombic lip

growth_protocol: These data were generated from primary human tissue; therefore, this column is not applicable.

extract_protocol:
DNA was extracted using a protocol based on Qiagen Puregene.
The NEBNext Enzymatic Methyl-seq Kit was used.

treatment_protocol: This project was approved by the Research Ethic Board at the University of Toronto (RIS Human Protocol #42524). We received frozen mid-gestation human hindbrains from the University of Maryland Brain and Tissue Bank. Tissue cryosectioning and immunohistochemistry was performed by the University Health Network Pathology Research Program Laboratory. Brain tissue was cryosectioned on the mid-sagittal plane and stained for cresyl violet, SOX2 (CST Sox2 (D6D9) XP Rabbit mAb #3579) and KI67 (Dako #M7240 Mouse monoclonal antibody). The rhombic lip was identified at the edge of the fourth ventricle by its size and prominent KI67+ staining.  Selected sections were stained with CD34 (Dako #M7165 Monoclonal Mouse Anti-Human) and GFAP (Dako #Z334) to identify the vascular bed that separates the rhombic lip ventricular zone and subventricular zone (Supplementary Figure 1). Using immunohistochemistry, we identified the rhombic lip ventricular (SOX2+ KI67+) and subventricular (SOX2- KI67+) zone in each sample. We used laser capture microdissection (LCM) to isolate tissue separately from the rhombic lip ventricular zone and subventricular zone. LCM was performed by the Ontario Institute for Cancer Research Tissue Portal using the Leica LMD6 instrument; cresyl violet was used to visualize the tissue.

value: Cerebellar rhombic lip

tag: cell compartment

value: SVZ

tag: gestation weeks

tag: ethnicity

value: Black or African-American

tag: Sex

value: Male

tag: pmi hours


title: VZ_1643

description: Library name: FETHB2_0005_01_LB01-01

value: VZ

tag: batch


title: SVZ_1757

description: Library name: FETHB2_0004_01_LB02-01


title: SVZ_1644

description: Library name: FETHB2_0003_01_LB01-01

value: White


title: SVZ_1320

description: Library name: FETHB2_0002_01_LB02-01


title: VZ_1320

description: Library name: FETHB2_0002_01_LB01-01


title: HCT116-H2b-GFP, Stretched (+Peristalsis), Bottom Channel (Invaded)

city: Los Angeles

first: Shannon

last: Mumenthaler

state: California

address: 12414 Exposition Blvd

department: Translational Research

institute: Ellison Medical Institute

description: Library name: Sample 3

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq will be converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger mkfastq command. Subsequent UMI and cell barcode de-convolution along with mapping to respective genome will be performed using 10X Genomics’ cellranger software package to generate the final digital gene expression matrices and cloupe files.
Assembly: hg38
Supplementary files format and content: Cell ranger count matrix for each sample as (.mtx) file with corresponding barcodes and features files as (.tsv)

extract_protocol:
Cells were removed from the OOC using 0.25% trypsin for 5 min at 37C added to both the top (non-invaded) and bottom (invaded) channels, repeated three times to ensure full collection.  After collection, the GFP labeled tumor cells were seclected using the FACS Melody Cell Sorter (Beckton Dickenson, Brea, CA, USA)
Single cell RNA libraries were be generated using the Chromium Single Cell 3’ kit (10X Genomics, CA, USA). Viability was checked with Thermo Fisher Countess II FL with Nuc blue for all cell nucleus staining and PI for dead cell nucleus staining. The PCR enzyme used was part of the 10x kit and the number of PCR cycles were 12. Loading was performed to target capture of ~10,000 GEMs per sample for downstream analysis, and samples were processed through the Chromium Controller following the standard manufacturer’s specifications.  The sequencing libraries were evaluated for quality on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and pooled libraries were quantified using qPCR (Applied Biosystems, Carlsbad, CA, USA) prior to loading onto an Illumina HiSeq4000 or equivalent. The samples were sequenced at a configuration compatible with the recommended guidelines as outlined by 10X Genomics.

tag: cell line

tag: cell type

value: Colon Epithelial Cells

tag: treatment

value: (+peristalsis)


title: HCT116-H2b-GFP, Not Stretched (-Peristalsis), Top Channel (Non-Invaded)

description: Library name: Sample 2

value: (-peristalsis)


title: HCT116-H2b-GFP, Stretched (+Peristalsis), Top Channel (Non-Invaded)

description: Library name: Sample 1


title: CuB-rep2

city: Luzhou

first: Mengdie

last: Xu

address: Taiping str.25

institute: The Affiliated Hospital of Southwest Medical University

description: Library name: CuB_100nM_6h_2

data_processing:
Illumina Casava2.19 software used for basecalling.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample ...

extract_protocol:
A375 cells were separately treated with DMSO (control) or 0.2 μM CuB for 6 hours. After being washed with pre-cooled PBS, cells were lysed on ice with Trizol reagent. RNA was harvested. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tumor cells

value: CuB


title: CuB-rep1

description: Library name: CuB_100nM_6h_1


title: DMSO-rep3

description: Library name: control_3

value: DMSO


title: SVZ_1007

description: Library name: FETHB2_0001_01_LB01-01


title: SNHG29 shRNA control replicate 2

description:
Library name: RW13_ctrl
Column name in deseq2_normalized_counts.tsv: RW13_ctrl

value: acute myeloid leukemia

tag: knockdown method

value: shRNA

value: shRNA control


title: DMSO-rep2

description: Library name: control_2


title: DMSO-rep1

description: Library name: control_1


title: Human ovary tissue 2

description: Library name: N-20215246

value: Human ovary


title: FIX00179-3491BW Tcell IFNb

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: FIX00179
10x Genomics Flex

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the  Fixed RNA Profiling capability (version 7.0.0, released May 17, 2022), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
scRNA counts matrices were normalized and scaled using Seurat. Cell populations were manually re-labelled via clustering using a combination of selected reference markers for each cell type. Cells mapping to dendritic cell populations were removed. Doublets were identified and removed using Scrublet.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

source_name: Blood

growth_protocol: Frozen Ficoll purified PBMC from healthy subjects were acquired from Bloodworks Northwest (#4570). T cells, B cells, NK cells or CD14 monocytes in each donor from freshly thawed frozen PBMC were enriched by magnetic negative selection kits (STEMCELL technologies) for human T cells (#19051), human pan B  cells (#19554), human NK cells (#19055) or human CD14 monocytes (#19059), respectively. To ensure high purity in enriched B, NK, and CD14 monocytes, contaminated T cells were further depleted by using CD3 kit (STEMCELL technologies #17851). Three to eight hundred thousand of enriched cells from each immune cell subset or total PBMC were seeded in 200 uL of 10 % human AB serum (Millipore Sigma #H3667-20ML) containing RPMI-1640 media (ThermoScientific #11875093) per well.

extract_protocol:
After 21 hour stimulation with various IFNs, cells were washed, counted, and fixed in 4% Paraformaldehyde for 1 hour (25°C). Fixed samples were quenched and subsequently washed with an additional 200 uL of PBS + 0.02% BSA (Costar). Samples were barcoded for multiplexing using 10X Genomics Fixed RNA Feature Barcode Multiplexing Kit (#PN-1000628). Probe hybridization was completed according to the 10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673,  Rev A). Up to 2 million fixed cells were hybridized per sample. After 16-24 hours of probe hybridization incubation (42°C), samples were diluted in Post-Hyb Wash buffer and 11 µL was removed for counting. The counting fraction was stained 1:5 with 44 uL of PI solution and counted on a Nexcelom Cellaca MX cell counter.
Samples were then pooled at equivalent cell concentrations at a minimum of 50,000 cells/sample, incubated for 3 rounds of 10 minutes at 42°C, washed in Post-Hyb wash buffer, and strained using 30 uM strainers (Miltenyi). The single cell suspension pool was loaded onto Chip Q for GEM generation at an overloaded concentration of 400,000 cells. Final scRNAseq libraries were sequenced using a NovaSeq X 25B PE300, Novaseq S2 PE200, or a NovaSeq S4 PE100 flow cell, targeting a minimum read depth of 10,000 reads per cell.

treatment_protocol: Each enriced immune cells were stimulated with IFN-a2A (1000 units/mL, PBL Assay Science #11101-2) or IFN-b (100 units/mL, R&D #8499-IF-010/CF) or IFN-g (25 ng/mL, Biolegend #570206) or IFN-L1 (100 ng/mL, R&D #1598-IL-025/CF) or no stimulation for 21 hours in 37°C.

value: Blood

value: Tcell

value: IFNb

tag: subject id

tag: age at_blood_drawn

value: male

tag: ethnics/race

value: Caucasian/Non-hisp

tag: cmv stats

value: Positive

tag: treatment time

value: 21 hours

tag: batch id

tag: pool id

value: PD

tag: batch pool

tag: probe barcode_id


title: Human ovarian cancer tissue 2

description: Library name: T-18218410

tag: tissue

value: Human ovarian cancer


title: FIX00178-3491BW Tcell IFNa

description:
Library name: FIX00178
10x Genomics Flex

value: IFNa

tag: Sex


title: CuB-rep3

description: Library name: CuB_100nM_6h_3

value: tumor cells


title: Human glomerular endothelial cell, Donor 2, 4hr hypoxia,RNA

description:
Library name: Sample6
Column in rawcount file: F_rawcount

value: Primary glomerular endothelial cells

value: Hypoxia


title: FIX00177-3491BW Tcell none

description:
Library name: FIX00177
10x Genomics Flex


title: FIX00188-3491BW NK IFNg

description:
Library name: FIX00188
10x Genomics Flex

value: NK

value: IFNg


title: FIX00189-3491BW NK IFN-L1

description:
Library name: FIX00189
10x Genomics Flex


title: FIX00187-3491BW NK IFNb

description:
Library name: FIX00187
10x Genomics Flex


title: FIX00186-3491BW NK IFNa

description:
Library name: FIX00186
10x Genomics Flex


title: FIX00185-3491BW NK none

description:
Library name: FIX00185
10x Genomics Flex


title: CAMA-1 cells, heterozygous BRCA1 SNPs (rs799917, rs16941, rs16942, rs1799966)

description: Library name: CAMA

value: breast cancer cell lines


title: FIX00165-3491BW Monocyte IFN-L1

description:
Library name: FIX00165
10x Genomics Flex

value: Monocyte

value: PC


title: FIX00164-3491BW Monocyte IFNg

description:
Library name: FIX00164
10x Genomics Flex

value: Blood


title: FIX00161-3491BW Monocyte none

description:
Library name: FIX00161
10x Genomics Flex


title: FIX00162-3491BW Monocyte IFNa

description:
Library name: FIX00162
10x Genomics Flex


title: FIX00163-3491BW Monocyte IFNb

description:
Library name: FIX00163
10x Genomics Flex

value: IFNb


title: FIX00184-3491BW Bcell IFN-L1

description:
Library name: FIX00184
10x Genomics Flex

value: Bcell

value: male


title: FIX00182-3491BW Bcell IFNb

description:
Library name: FIX00182
10x Genomics Flex

value: Caucasian/Non-hisp

value: Positive


title: FIX00180-3491BW Bcell none

description:
Library name: FIX00180
10x Genomics Flex

value: 21 hours

value: PD


title: FIX00181-3491BW Bcell IFNa

description:
Library name: FIX00181
10x Genomics Flex

value: IFNa


title: FIX04861-025-6811BW Tcell IFNb

description:
Library name: FIX04861-025
10x Genomics Flex

value: Tcell


title: FIX04861-024-6811BW Tcell IFNa

description:
Library name: FIX04861-024
10x Genomics Flex


title: FIX04861-023-6811BW Tcell none

description:
Library name: FIX04861-023
10x Genomics Flex


title: SUM159, shHIF1A, 20% O2 (biol rep 1)

description: Library name: HIF_20pct-1

value: breast cancer cell

value: SUM159 cell line

value: breast cancer cell line

tag: genotype


title: FIX04861-035-6811BW NK IFN-L1

description:
Library name: FIX04861-035
10x Genomics Flex

value: NK


title: FIX04861-033-6811BW NK IFNb

description:
Library name: FIX04861-033
10x Genomics Flex


title: FIX04861-034-6811BW NK IFNg

description:
Library name: FIX04861-034
10x Genomics Flex

value: IFNg


title: SUM159, shPPME1, 1% O2 (biol rep 2)

description: Library name: PME_1pct-2


title: SUM159, shNTC, 1% O2 (biol rep 1)

description: Library name: NTC_1pct-1

value: NTC


title: FIX04861-032-6811BW NK IFNa

description:
Library name: FIX04861-032
10x Genomics Flex


title: FIX04861-031-6811BW NK none

description:
Library name: FIX04861-031
10x Genomics Flex


title: MUC29528

description: Library name: MUC29528

value: Skin

tag: condition

value: Eczema

tag: individual

tag: batch


title: FIX04861-011-6811BW Monocyte IFN-L1

description:
Library name: FIX04861-011
10x Genomics Flex

value: Blood

tag: cell type

value: Monocyte

tag: treatment

value: PC


title: FIX04861-010-6811BW Monocyte IFNg

description:
Library name: FIX04861-010
10x Genomics Flex

tag: subject id

value: male

value: Caucasian/Non-hisp


title: FIX04861-009-6811BW Monocyte IFNb

description:
Library name: FIX04861-009
10x Genomics Flex

value: IFNb

tag: age at_blood_drawn

value: Positive

value: 21 hours


title: MUC29527

description: Library name: MUC29527


title: FIX04861-007-6811BW Monocyte none

description:
Library name: FIX04861-007
10x Genomics Flex

tag: ethnics/race


title: FIX04861-008-6811BW Monocyte IFNa

description:
Library name: FIX04861-008
10x Genomics Flex

value: IFNa

tag: cmv stats


title: FIX04861-030-6811BW Bcell IFN-L1

description:
Library name: FIX04861-030
10x Genomics Flex

value: Bcell

tag: treatment time

value: PD


title: FIX04861-029-6811BW Bcell IFNg

description:
Library name: FIX04861-029
10x Genomics Flex

tag: batch id


title: FIX04861-028-6811BW Bcell IFNb

description:
Library name: FIX04861-028
10x Genomics Flex

tag: pool id


title: FIX04861-027-6811BW Bcell IFNa

description:
Library name: FIX04861-027
10x Genomics Flex

tag: batch pool


title: FIX04861-026-6811BW Bcell none

description:
Library name: FIX04861-026
10x Genomics Flex

tag: probe barcode_id


title: MUC29521

description: Library name: MUC29521

tag: tissue

value: Psoriasis


title: FIX00139-2616BW Tcell IFNb

description:
Library name: FIX00139
10x Genomics Flex

value: Tcell

tag: Sex

value: Negative

value: PB


title: MUC29519

description: Library name: MUC29519

value: Skin


title: FIX00138-2616BW Tcell IFNa

description:
Library name: FIX00138
10x Genomics Flex


title: FIX00137-2616BW Tcell none

description:
Library name: FIX00137
10x Genomics Flex


title: MUC29514

description: Library name: MUC29514


title: FIX00148-2616BW NK IFNg

description:
Library name: FIX00148
10x Genomics Flex

value: NK

value: IFNg


title: FIX00147-2616BW NK IFNb

description:
Library name: FIX00147
10x Genomics Flex

value: Blood


title: FIX00149-2616BW NK IFN-L1

description:
Library name: FIX00149
10x Genomics Flex