title: DMD myoblasts sample 2

city: Normal

first: Andres

last: Vidal-Gadea

state: Illinois

address: 125 S Fell Ave

department: School of Biological Sciences

institute: Illinois State University

description: Library name: DMD2

data_processing:
Adapter and low-quality sequences were removed using Trimmomatic v0.36.
Clean reads were aligned to the GRCh38 (or relevant) reference genome using STAR v2.5.2b
featureCounts (Subread v1.5.2) was used to generate exon-level unique gene counts
Differential expression analysis was performed using DESeq2, with genes identified as significantly different at adjusted p-value < 0.05
Assembly: GRCh38
Supplementary files format and content: fastq files

source_name: skeletal muscle (paravertebral)

growth_protocol: myoblasts were grown in PromoCell Skeletal Muscle Growth Medium, used within the first 6 passages, and kepy under 40% confluency

extract_protocol:
RNA was extracted using the Zymo DirectZol RNA Miniprep kit
A. mRNA enrichment, mRNA fragmentation, and random priming B. first and second strand cDNA synthesis C. end repair, 5' phosphorylation and dA-Tailing D. Adaptor ligation, PCR enrichment, and sequencing

value: skeletal muscle (paravertebral)

value: skeletal myoblasts

value: DMD


title: DMD myoblasts sample 1

status: Public on Sep 01 2025

type: SRA

country: USA

description: Library name: DMD1

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: untreated


title: Cel6-2

city: Macau

first: Dingqi

last: Zhang

address: Taipa

country: Macau

institute: Macau University of Science and Technology

description: Library name: Cel6-2

data_processing:
Sequencing reads were demultiplexed based on sample barcode with idemux (https://github.com/Lexogen-Tools/idemux).
Demultiplexed reads were trimmed with cutadapt to remove polyA, adaptor and low-quality sequences.
Reads were mapped to human GRCh38 reference assembly with STAR aligner.
PCR duplicates were removed based on UMI with UMI-tools. Htseq-count was used to generate read counts.
Normalized counts were generated with DESeq2, accounting for total reads counts.
Assembly: GRCh38
Supplementary files format and content: Normalized counts matrix. The column names are sample names. The row names are gene symbols.

source_name: Immortalized RAFLS

growth_protocol: Immortalized RAFLS was purchased from Meisen CTCC (Cat. #CTCC-001-0385, Pan’an, Zhejiang, China) and cultured in DMEM/F-12 supplemented with 10% FBS, 1% Insulin-Transferrin-Selenium (ITS) and 1% Penicillin-Streptomycin-Glutamate.

extract_protocol:
Total RNA was extracted with routine Trizol method.
Transcriptomic profiling was performed with an in-house, proprietary method that captures the 3’ primed end of mRNA molecules for sequencing.

treatment_protocol: All cells are simulated with 1 ng/mL TNFα for 24h, and exposed to different treatments during the last 4 hours.

value: Immortalized RAFLS

value: Rheumatoid arthritis fibroblast-like synoviocytes


title: Locus Coeruleus tissue, 5xFAD transgenic, 65#

city: Shanghai

first: Ziyue

last: Zhou

address: 100 Haike Road, Zhangjiang Hi-Tech Park, Pudong

country: China

institute: The Interdisciplinary Research Center on Biology and Chemistry

description:
Library name: Sample 5
Column name in WT_vs_FAD_TPM.csv: Tg_65_clean_L005

data_processing:
The Bioinformatics pipeline [ref.1] was used to process sequencing data. STAR [ref.2] was used to align reads to mm39 genome build and RSEM was used to quantify expression at the gene level [ref.3]. Differential expression analysis was conducted using DESeq2 with default parameters [ref.4]. Differential gene expression was identified using a statistical cut-off of padj < 0.05(Additional file: gene table).   [ref.1]: https://github.com/emc2cube/Bioinformatics [ref.2]: STAR: ultrafast universal RNA-seq aligner [ref.3]: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome [ref.4]: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Assembly: mm39
Supplementary files format and content: csv file including TPM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Locus Coeruleus

extract_protocol:
Total RNA was isolated from tissue using the TRIzol® Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Only high-quality RNA samples (OD260 / 280 = 1.8 ~ 2.2, OD260 / 230 ≥ 1.9, RIN ≥ 9.0) were used to construct a sequencing library.
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesize dusing random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on an Illumina Novaseq 6000 by Shanghai Personal Biotechnology Cp. Ltd.

value: Locus Coeruleus


title: Dmso_1

city: changchun

first: 富强

last: 李

state: 吉林省

address: 前进

institute: 吉林大学

data_processing:
clc genomics workbench V11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited  text file include raw counts for each  sample

source_name: gastric

growth_protocol: BGC823 cells were cultured in RPMI-1640 medium (Meilunbio®, Dalian, China) containing 10% fetal bovine serum (KangYuan Biology, Tianjin, China) and 1% penicillin-streptomycin (Thermo-Fisher Scientific) and maintained at 37°C and 5% CO2. Each cell line was authenticated via short tandem repeat (STR) profiling within 3 years. All experiments were performed with mycoplasma-free cells.

extract_protocol:
Enrichment of eukaryotic mRNA with magnetic beads bearing Oligo (dT)
The first cDNA strand was synthesized with six-base random primers (random hexamers) using mRNA as a template, then the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H, and DNA polymerase I. The cDNA was purified by using AMPure XP beads; the purified double-stranded cDNA was then subjected to end repair, addition of the A tails and connected to sequencing junctions, and then fragment size selection was performed with AMPure XP beads; Finally, the cDNA library was enriched by PCR.

treatment_protocol: BGC823 cells (2 × 10^4 cells/well) were seeded and cultured overnight in 6-well plates. The culture medium was changed to contain 200 μg/mL of Rg3 every 24 hours, for a total duration of 48 hours.

value: gastric

value: gastric cancer cell

value: wt

value: dmso


title: DMD myoblasts sample 3

description: Library name: DMD3


title: healthy myoblasts sample 3

description: Library name: WT3

value: wildtype


title: RIOK1-kd gRNA-1 REP2

city: Bronx

first: David

last: Shechter

state: New York

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

description:
salmon.merged.gene_counts_length_scaled.tsv
condition_RIOK1.1_vs_CONTROL_DESEQ2.csv

data_processing:
nf-core/rnaseq v3.9
DESeq2
Assembly: hg38
Supplementary files format and content: .tsv,salmon length normalized gene counts
Supplementary files format and content: .csv,DESeq2 output files for each knockdown

extract_protocol: non-directional, polyA capture

value: Puromycin (1ug/mL), Blasticidin S (5 ug/mL)


title: Locus Coeruleus tissue, 5xFAD transgenic, 64#

description:
Library name: Sample 4
Column name in WT_vs_FAD_TPM.csv: Tg_64_clean_L004


title: healthy myoblasts sample 1

description: Library name: WT1


title: RIOK1-kd gRNA-1 REP3


title: Retinal ganglion cells, wild-type, rep1

city: Berkeley

first: Matthew

middle: A

last: Po

state: California

address: Stanley Hall

department: Chemical and Biomolecular Engineering

institute: UC Berkeley

description:
Library name: Sample 1
10X Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell libraries were aligned to the UCSC mm10 genome assembly using Cellranger v7.1.0 (10X Genomics). This alignment was performed separately on each sample (three P7 WT samples, four P7 β2KO samples), and the resulting cells-by-genes expression matrices were combined to obtain an expression matrix for each condition.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated value files of cell barcodes and features (genes), matrix file of read counts

source_name: Retina

extract_protocol:
P7 C57BL/6J and β2KO mice were anesthetized in an isoflurane induction chamber and euthanized by decapitation. All the solutions were filtered using 0.22 µm syringe filter (Fisher #9720511). Eyes were enucleated and retinas were immediately dissected in oxygenated (95% oxygen/5% carbon dioxide) Ames’ media with L-glutamine and sodium bicarbonate (pH ~7.4) at room temperature under light scope. Retinas (6 to 8 per sample) were digested for 10 min at 37oC in 70 µl papain (Fisher #LS003126) + 50 µl DNase (Sigma #D4527-40KU) + 50 µl L-cysteine (Sigma #C1276-10G) in 5 ml Ames, which was activated at 37oC for 15 min. Samples were gently swirled once during this incubation. Following this, papain was removed and samples was gently triturated with P1000 pipette tips in 1 ml 10x ovomucoid (Fisher #NC9931428) + 50 µl DNase + 9 ml Ames. Manual trituration was performed using 2 ml of ovo solution at a time and the supernatant was filtered using 40 μm cell strainer in a new tube. This cell suspension was spun down at 450 g for 8 min. Supernatant was discarded and the pellet was resuspended in 250 μl of Ames + bovine serum albumin (BSA). This solution was prepared using 27 ml Ames + 3 ml 4% BSA (Sigma #A9418-5G) + 50 µl DNase. Cells were counted using hemocytometer (1:100 dilution factor with trypan blue). 10 million cells were incubated in 10 µl CD90.2 microbeads (Miltenyi Biotec #130-121-278) for 10 min at 4oC. Following incubation, 6 ml Ames + BSA solution was added and cells were spun down at 450 g for 8 min. Supernatant was discarded and cells were resuspended in fresh 500 µl Ames + BSA solution. Cell suspension was subjected to magnetic-activated cell sorting (MACS) using large cell columns (Miltenyi Biotec #130-042-202) to sort RGCs. To obtain a high number of RGCs, the tube containing the cells was washed with 500 µl Ames + BSA solution for 2 times. To obtain better purity, MACS was repeated one more time on eluted CD90.2+ RGCs using fresh columns. This cell suspension was spun down at 450 g for 8 min and the supernatant was removed. Pellet obtained was resuspended in ~1000 μl of Ames + BSA and cell concentration was counted using hemocytometer (dilution factor 2). This spun down strategy was employed to obtain a highly concentrated sample in a small volume of ~100 μl Ames + BSA.
Single-cell libraries on RGCs isolated were prepared using Chromium Next GEM Single Cell 3' Kit v3.1 (10X Genomics, Pleasanton, CA) following manufacturer’s protocol.

value: Retina

value: Retinal ganglion cells

value: Wild-type

tag: Sex

value: pooled male and female


title: GSK591 Chromatin - DmSpikeIn - control REP2

data_processing:
hg38_dm6 combined genome prepared
nf-core/rnaseq v3.14
DESeq2 analysis with sizefactors calculated from all called dm6 spike-in genes (>10 counts)
Assembly: hg38_dm6
Supplementary files format and content: salmon output counts - not spike-in normalized
Supplementary files format and content: DESeq2 .csv

extract_protocol:
RNA from each fraction was extracted with Trizol containing 5% Drosophila S2 cells
Directional polyA captured mRNA


title: healthy myoblasts sample 2

description: Library name: WT2

value: skeletal muscle (paravertebral)


title: RIOK1-kd gRNA-3 REP3

description:
salmon.merged.gene_counts_length_scaled.tsv
condition_RIOK1.3_vs_CONTROL_DESEQ2.csv


title: GSK591 Chromatin - DmSpikeIn - control REP1


title: RIOK1-kd gRNA-1 REP1


title: Locus Coeruleus tissue, wildtype, 62#

description:
Library name: Sample 1
Column name in WT_vs_FAD_TPM.csv: WT_62_clean_L001


title: Locus Coeruleus tissue, wildtype, 63#

description:
Library name: Sample 2
Column name in WT_vs_FAD_TPM.csv: WT_63_clean_L002


title: pICln-kd gRNA-3 REP3

description:
salmon.merged.gene_counts_length_scaled.tsv
condition_pICln.3_vs_CONTROL_DESEQ2.csv


title: GSK591 Nucleoplasm - DmSpikeIn - control REP2


title: pICln-kd gRNA-3 REP2


title: GSK591 Cytoplasm - DmSpikeIn - control REP3


title: GSK591 Nucleoplasm - DmSpikeIn - control REP1


title: TT-seq_SRCAP_degron_1h_rep2

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

data_processing:
Raw reads with spike-in were firstly trimmed by Cutadapt software and then mapped to mm10 and dm6 genome using Bowtie2 software
PCR duplicated, multiple mapped and discordant reads were discarded for further analysis.
Bam files were converted to bw format by deepTools software normalized by the reads mapped to dm6 genome.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: TT-Seq

molecule: nuclear RNA

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in 2i/mLIF medium, which composed of DMEM containing 1 mM L-glutamine, 1× nucleosides (Sigma, ES-008), 1× nonessential amino acids (Milipore, TMS-001-C), 1× sodium pyruvate (Gibco, 11360070), 1× penicillin/ streptomycin (Gibco, 15140-122), 0.1 mM β-mercaptoethanol (Sigma, M3148), 3 μM CHIR99021 (Selleck, S1036) and 1 μM PD0325901 (Selleck, S1263), 1000 U/ml mouse leukemia inhibiting factor (mLIF) (Milipore, ESG1107), and also supplemented with 15% fetal bovine serum (FBS) (VivaCell, 04-001-1A), incubated at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
4SU is a derivative of uracil that can be recognized by the RNA polymerase in cells and incorporated into the RNA chain being synthesized. The biotin is chemically labeled on the RNA molecule containing 4SU. The newly synthesized and biotin-labeled RNA is then separated from the total RNA using magnetic beads coated with streptavidin.Extracted twice using Trizol reagent following the instruction.
The native RNAs were isolated and examined. After checked the quantity and quality and poly(A) RNA depletion, the TT-seq RNA library were generated using the no coding RNA library method with random primers and sequencing analyzed using Nova PE150 platform.

treatment_protocol: For target protein degradation, the degron cells were firstly induced with 1 μg/ml Dox in the 2i medium to express the OsTir1 for 12 h, then 500 μM auxin were added to induced the degradation for 1h, then cells were harvested for next assays.

value: mouse embryonic stem cells

value: SRCAP degron 1h


title: pICln-kd gRNA-3 REP1


title: GSK591 Cytoplasm - DmSpikeIn - control REP1


title: GSK591 Cytoplasm - DmSpikeIn - control REP2


title: pICln-kd gRNA-2 REP3

description:
salmon.merged.gene_counts_length_scaled.tsv
condition_pICln.2_vs_CONTROL_DESEQ2.csv


title: Locus Coeruleus tissue, wildtype, 66#

description:
Library name: Sample 3
Column name in WT_vs_FAD_TPM.csv: WT_66_clean_L003


title: TT-seq_SRCAP_degron_0h_rep2

value: SRCAP degron 0h


title: DMSO Chromatin - DmSpikeIn - control REP2


title: DMSO Chromatin - DmSpikeIn - control REP3


title: TT-seq_SRCAP_degron_1h_rep1


title: GSK591 Nucleoplasm - DmSpikeIn - control REP3


title: GSK591 Chromatin - DmSpikeIn - control REP3


title: pICln-kd gRNA-2 REP2


title: TT-seq_SRCAP_degron_0h_rep1


title: pICln-kd gRNA-2 REP1


title: DMSO Nucleoplasm - DmSpikeIn - control REP3


title: DMSO Nucleoplasm - DmSpikeIn - control REP2


title: TT-seq_P400_degron_1h_rep2

value: P400 degron 1h


title: DMSO Cytoplasm - DmSpikeIn - control REP2


title: CoPR5-kd gRNA-3 REP2

description:
salmon.merged.gene_counts_length_scaled.tsv
condition_CoPR5.3_vs_CONTROL_DESEQ2.csv


title: DMSO Cytoplasm - DmSpikeIn - control REP1


title: TT-seq_P400_degron_0h_rep2

value: P400 degron 0h


title: DMSO Nucleoplasm - DmSpikeIn - control REP1


title: CoPR5-kd gRNA-3 REP3


title: Human, hydrogel organoid, rep1

city: Boston

first: Charlotte

last: Kuperwasser

state: MA

address: 136 Harrison Ave

institute: Tufts University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexting, barcode processing, and gene counting were done using the Cell Ranger software v8.0.0.
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files

source_name: Breast tissue

extract_protocol:
Cells were isolated out of the hydrogels by digestion buffer (500ug/mL collagenase in PBS) at 37C on a rotator for 30 min. Cells were washed in PBS and incubated in Trypsin at 37C until fully dissociated. Trypsin was quenched with DTI and cells were washed in PBS and passed through 40um cell strainer.
10X Genomics 3' RNA library prep was perfomed by Novogene according to manufacture's protocol

value: Breast tissue

value: breast epithelial cells

value: Hydrogel organoid


title: DMSO Cytoplasm - DmSpikeIn - control REP3


title: TT-seq_P400_degron_0h_rep1


title: RNA-seq of Acinetobacter baumannii C3-1

city: Hangzhou

first: Junjie

last: Huang

state: Zhejiang

address: 150 Dongfang Street Xiasha, Qiantang District

department: Center for AI and Intelligent Medicine

institute: Hangzhou Institute of Medicine, Chinese Academy of Sciences

description: Library name: C3-1

data_processing:
Raw reads QC: adapters removed; low-quality bases trimmed (Q>=30 threshold); reads containing N removed; reads shorter than 60 bp discarded; QC assessed by FastQC.
Alignment: HISAT2 to the reference genome (GCA_009035845.1 ASM903584v1). Quantification: StringTie for expression (FPKM, raw counts). Differential expression: DESeq2.
Assembly: GCA_009035845.1_ ASM903584v1
Supplementary files format and content: tab-delimited text file includes raw counds and FPKM values for each Sample

organism: Acinetobacter baumannii

extract_protocol:
Prokaryotic rRNA depletion to enrich mRNA; fragmentation buffer to shear RNA; first-strand cDNA synthesis with random hexamers; second-strand cDNA synthesis with DNA polymerase I and RNase H; AMPure XP purification; end repair, A-tailing, adapter ligation; size selection with AMPure XP; PCR amplification; library quantification by Qubit and qPCR; insert size checked by Agilent 2100 Bioanalyzer.
Standard Illumina RNA-seq library construction following vendor protocols as described: rRNA removal (prokaryote), fragmentation, cDNA synthesis, end repair, A-tailing, adapter ligation, PCR amplification, and AMPure XP-based size selection.

tag: strain

value: PBS


title: RNA-seq of Acinetobacter baumannii C3-3

description: Library name: C3-3


title: RNA-seq of Acinetobacter baumannii C3-2

description: Library name: C3-2


title: CoPR5-kd gRNA-1 REP3

description:
salmon.merged.gene_counts_length_scaled.tsv
condition_CoPR5.1_vs_CONTROL_DESEQ2.csv


title: TT-seq_INO80_degron_1h_rep2

value: INO80 degron 1h


title: TT-seq_INO80_degron_1h_rep1


title: DMSO Chromatin - DmSpikeIn - control REP1


title: CoPR5-kd gRNA-1 REP2


title: RNA-seq of Acinetobacter baumannii A1-3

description: Library name: A1-3


title: TT-seq_INO80_degron_0h_rep2

value: INO80 degron 0h


title: RNA-seq of Acinetobacter baumannii A1-1

description: Library name: A1-1


title: C_auris_CAS+POSA-3.

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

description: Library name: sample 12

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of C. auris B8441.
The DESeq algorithm (StrandNGS software) was used to obtain normalized gene transcription values.
Gene transcription differences between treated and control groups were compared by a moderated t test; the Benjamini-Hochberg false discovery rate was used for multiple-testing correction, and a corrected P value of <0.05 was considered significant.
Assembly: C. auris genome version gca002759435.2 ; https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002759435.2; accessed on 03/05/2024
Supplementary files format and content: Excel file includes normalized data for each Samples

organism: Candidozyma auris

source_name: fungal cells

growth_protocol: C. auris isolate was cultured in yeast extract–peptone–dextrose (YPD) agar plates [1% yeast extract (Alfa Aesar, USA), 2% mycological peptone (Oxoid, United Kingdom), 2% dextrose, and 2% agar (VWR International LLC, Hungary), pH 5.6] for 48 h at 37 °C. Cell suspension was prepared in RPMI-1640 medium at a concentration of 1 × 10⁶ CFU/mL using a Bürker chamber. Then cells were inoculated into tissue culture dishes (TPP, Trasadingen, Switzerland). After incubation at 37˚C for 24 h, non-adherent cells were removed by washing with sterile physiological saline. Caspofungin (1 mg/L) and posaconazole (0.25 mg/L), either alone or in combination, were added and incubated at 37˚C for 24 h.

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: One-day-old biofilms of isolate 10, treated with caspofungin (1 mg/L) and/or posaconazole (0.25 mg/L), were scraped from tissue culture dishes (TPP, Trasadingen, Switzerland), pooled, and washed three times with physiological saline. Three biological replicates of the biofilm-forming cell suspensions were centrifuged at 3,000 × g for 10 minutes at 4°C. The resulting pellets were used for RNA extraction.

value: fungal cells

value: Isolate 10

value: 1.0 mg/l CAS +0.25 mg/l POSA treated


title: RNA-seq of Acinetobacter baumannii A1-2

description: Library name: A1-2


title: PRMT5-kd gRNA-4 REP3

description:
salmon.merged.gene_counts_length_scaled.tsv
condition_PRMT5.4_vs_CONTROL_DESEQ2.csv

value: Puromycin (1ug/mL), Blasticidin S (5 ug/mL)


title: TT-seq_P400_degron_1h_rep1


title: PRMT5-kd gRNA-4 REP2


title: CoPR5-kd gRNA-1 REP1


title: C_auris_CAS+POSA-2.

description: Library name: sample 11


title: C_auris_POSA-2.

description: Library name: sample 8

value: 0.25 mg/l POSA treated


title: C_auris_CAS+POSA-1.

description: Library name: sample 10


title: C_auris_POSA-1.

description: Library name: sample 7


title: RNA-seq_SRCAP_degron_1h_rep2

data_processing:
Raw reads with spike-in were firstly trimmed by Cutadapt software and then mapped to mm10 and dm6 genome using STAR software.
PCR duplicates, reads that were not primarily mapped were discarded for further analysis.
Bam files were converted to bw format by deepTools software normalized by the reads mapped to dm6 genome.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Extracted total RNA using Trizol reagent following the instruction
Cells were lysed directly in Trizol reagent and extracted RNA according to the manufacturer’s instruction, after examination the concentration and integrity of the total RNA, samples were delivered for poly(A) RNA library generation

treatment_protocol: For target protein degradation, the degron cells were firstly induced with 1 μg/ml Dox in the 2i medium to express the OsTir1 for 12 h, then 500 μM auxin were added to induced the degradation for 24h, then cells were harvested for next assays.


title: C_auris_POSA-3.

description: Library name: sample 9


title: PRMT5-kd gRNA-4 REP1


title: C_auris_CAS-3.

description: Library name: sample 6

value: 1.0 mg/l CAS treated


title: PRMT5-kd gRNA-3 REP3

description:
salmon.merged.gene_counts_length_scaled.tsv
condition_PRMT5.3_vs_CONTROL_DESEQ2.csv


title: TT-seq_INO80_degron_0h_rep1

value: mouse embryonic stem cells


title: RNA-seq_SRCAP_degron_1h_rep1

value: SRCAP degron 1h


title: CoPR5-kd gRNA-3 REP1


title: C_auris_CAS-1.

description: Library name: sample 4


title: RNA-seq_SRCAP_degron_0h_rep2

value: SRCAP degron 0h


title: C_auris_Control-2.

description: Library name: sample 2

value: untreated


title: C_auris_Control-1.

description: Library name: sample 1


title: PRMT5-kd gRNA-3 REP2


title: Scrambled gRNA control REP3

description: salmon.merged.gene_counts_length_scaled.tsv


title: RNA-seq_P400_degron_1h_rep2

value: P400 degron 1h


title: RNA-seq_P400_degron_1h_rep1


title: prostate_PC_13

type: RNA

city: Wrocław

first: Maciej

last: Zacharski

state: dolnoslaskie

address: Norwida, 31

department: Department of Biochemistry and Molecular Biology

country: Poland

institute: Wroclaw University of Environmental and Life Sciences

hyb_protocol: The samples were prepared for nCounter mRNA expression profiling according to the manufacturer’s recommendations (NanoString Technologies, USA).  RNA samples were prepared by hybridization (65°C) to nCounter Reporter and Capture probes according to the manufacturer protocol. Subsequent to the automated sample cleanup, reporter capture, and alignment on the cartridge by the nCounter Prep Station, the RNA samples were deemed ready for analysis. The sample cartridges were then placed in the nCounter Digital Analyzer for data collection.

scan_protocol: Each sample was scanned on the nCounter Digital Analyzer for data collection. The study incorporated 555 field-of-view readings.

data_processing: nSolver Advanced Analysis software (NanoString) was used for data analysis including normalization with the folowing settings: Omit Low Count Data” with default settings of Auto: checked, Threshold Count Value: 20, Observation Frequency: 0.5. Default threshold settings: 20 counts, and an observation frequency of 0.5 (eg 50%). Normalization default with the GeNorm algorithm.

label: oligonucleotide probe

organism: Canis lupus familiaris

source_name: prostate cancer tissue, primary tumor

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (nanostring technologies inc.) were conducted according to the manufacturer's protocol.

growth_protocol: not applicable

extract_protocol: RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer’s instructions with on column Dnase digestion

treatment_protocol: RNA later, freezing -80 deg C

value: male

tag: breed

value: Labrador Retriever

tag: age in years

tag: hp diagnosis

value: adenocarcinoma

tag: neutering status

value: No

tag: grouping

value: PC


title: prostate_PC_14

value: Maltese Dog

value: Yes


title: prostate_BPH_07

source_name: benign prostatic hyperplasia tissue

value: Entlebucher Mount. Dog

value: BPH


title: PRMT5-kd gRNA-3 REP1

value: Puromycin (1ug/mL), Blasticidin S (5 ug/mL)


title: RNA-seq_P400_degron_0h_rep2

value: P400 degron 0h


title: Scrambled gRNA control REP2


title: C_auris_CAS-2.

description: Library name: sample 5

value: fungal cells

value: Isolate 10

value: 1.0 mg/l CAS treated


title: prostate_PC_15

value: Mixed


title: prostate_PC_12

value: French Bulldog


title: Scrambled gRNA control REP1


title: RNA-seq_P400_degron_0h_rep1

value: mouse embryonic stem cells


title: RNA-seq_INO80_degron_1h_rep2

value: INO80 degron 1h


title: prostate_PC_20

value: male

value: carcinoma


title: RNA-seq_SRCAP_degron_0h_rep1

value: SRCAP degron 0h


title: prostate_BPH_06

value: No


title: prostate_PC_22

value: adenocarcinoma

value: PC


title: Contractile IPSC-CM 2

city: Liverpool

first: Richard

last: Barrett-Jolley

address: 6 West Derby Street

country: United Kingdom

institute: University of Liverpool

data_processing:
These are raw data with adapters removed.
raw FASTQ
Transcript quantification with Salmon
Assembly: GRCh38
Supplementary files format and content: comma-deliminated text file includes TPM values for each biological replicate

source_name: heart left ventricle

extract_protocol:
RNA extraction was performed using the RNeasy kit (Qiagen, UK) as per manufacturer’s instructions. Total RNA integrity was confirmed using the Bioanalyzer (Agilent Technologies, USA). Ribosomal RNA (rRNA) was depleted from RNA samples by using the Ribo-Zero™ rRNA Removal Kit (Epicentre, USA) in accordance with the instructions of the manufacturer.
NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina, so they are paired-end reads but the orientation of the RNA strand is preserved in the first strand
Illumina Hiseq 4000 and NovaSeq series sequencer  2x150

treatment_protocol: Stage of differentiation

value: heart left ventricle

tag: developmental stage

value: Contractile IPSC-CM


title: prostate_PC_19

value: Boxer


title: Contractile IPSC-CM 1


title: RNA-seq_INO80_degron_1h_rep1


title: prostate_PC_10

value: Yes


title: prostate_PC_17


title: prostate_PC_18

value: Staffordshire Bull Terrier


title: Pre-Contractile IPSC-CM 3

value: Pre-Contractile IPSC-CM


title: RNA-seq_INO80_degron_0h_rep2

value: INO80 degron 0h


title: prostate_PC_16


title: RNA-seq_INO80_degron_0h_rep1


title: prostate_PC_21

value: Poodle


title: Contractile IPSC-CM 3


title: prostate_PC_09

value: Mixed


title: Pre-Contractile IPSC-CM 2


title: Cut&Tag_SRCAP_P400_degron_1h_rep1

library_source: genomic

data_processing:
Raw reads were firstly trimmed by Cutadapt software and then mapped to mm10 and genome by Bowtie2 software. Reads with spike-in were mapped to both mm10 and hg19 genome.
PCR duplicated, multiple mapped and discordant reads were discarded for further analysis.
Bam files were converted to bw format by deepTools software using RPGC as the normalization method. Bam files with spike-in were normalized by the reads mapped to hg19 genome.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: cut&tag

molecule: genomic DNA

extract_protocol:
DNA was purified through the Tris saturated equilibrium phenol (phenol: chloroform: isoamyl alcohol (25: 24: 1) (pH8.0) for ChIP-Seq, and gel extraction using DNA extract kit for Cut&Tag
ChIP-seq, briefly, the pretreated cells were harvested by trypsinization following 1% formaldehyde (final concentration, wt/vol) crosslinked and stored at -80 °C for downstream experiments. For chromatin immunoprecipitation, 20 million crosslinked cells (5% HEK293T cell were added as spikein) were lysed gently for chromatin isolation with ice-cold NP-40 lysis buffer and glycerol / urea buffer, finally centrifugated at 12,000 rpm for 1 min at 4 °C, the pellet of chromatin were resuspended in 1 ml sonication buffer, 1000 U MNase (NEB, M0247) and 5 mM CaCl2 were added and incubated for 15 min at 37 °C with 750 rpm shaking. After quenched by 20 μl 0.5 M EDTA and 40 μl 0.5 M EGTA in ice bath, the chromatin was sonicated using Qsonica Q800R3 DNA Shearing Sonicator for 15 min with 60% AMPL. Soluble chromatin was isolated by centrifugation at 1,2000 rpm for 10 min at 4 °C, 20 μl supernatant were sampled as input, the rest supernatant was transferred into 2 new DNase free tube for immunoprecipitation. 1 μl GFP abs (ABcam, ab290), 1 μg RPB1 NTD abs (CST, 14958S), and equal isotype IgG control for each ChIP reaction, respectively. After incubation overnight at 4 °C with low-speed rotation, 30 μl Protein G magnetic beads were added into the mixture to capture for 4 h, then washed beads once with sonication buffer, twice with high-salt wash buffer, twice with LiCl wash buffer and finally three times with TE buffer. For ChIP-seq, beads were eluted and then decrosslinked with 4 μl proteinase K (Sigma, 20 mg/ml) at 65 °C overnight, DNA was purified through the Tris saturated equilibrium phenol (phenol: chloroform: isoamyl alcohol (25: 24: 1) (pH8.0), and the ChIP library was prepared following the instruction of VAHTS Universal Pro DNA Library Prep Kit for Illumina (Vazyme, ND608-01); Cut&Tag was performed according to the manufacture of Hyperactive Universal Cut&Tag Assay Kit for Illumina (Vazyme, TD903-01), with 5% spikein 293T cells

value: mouse embryonic stem cells

value: P400 degron 1h


title: Pre-Contractile IPSC-CM 1


title: IPSC 3

value: IPSC


title: prostate_BPH_04

value: male

value: BPH


title: prostate_BPH_03


title: Cut&Tag_SRCAP_P400_degron_1h_rep2


title: prostate_PC_08


title: PacBio snRNA-Seq of lung cancer cell line mixture

city: Parkville

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Genetics and Gene Regulation

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: Library name: Single_nuclei_PacBio

data_processing:
Assembly: GRCh38
ONT datasets were basecalled with Dorado using the dna_r10.4.1_e8.2_400bps_sup@v5.0.0 model. Reads with mean quality scores <10 were discarded.
Reads were mapped to the reference genome GRCh38 and GENCODE v44 transcriptome using minimap2 (v2.28)
Single-nucleus RNA-seq (Illumina) data were processed using Cell Ranger (v8.0.1) with GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome.
Long-read single-nucleus reads were first demultiplexed using BLAZE (v2.5). The resulting FASTQ files were processed using the FLAMES (v2.0.1) single-cell pipeline, configured to use GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome. Further configurations included skipping novel transcript identification, and the use of Oarfish (v0.6.2) for transcript-level quantification.
Supplementary files format and content:
Count matrix prefix:  ill_sn – single-nucleus. Each matrix is stored in the standard three-file format: <prefix>_barcodes.tsv.gz | <prefix>_features.tsv.gz | <prefix>_matrix.mtx.gz
Count matrices from long-read protocols (ont, pb) are structured as follows:
Gene-level counts: genes_count_matrix.tsv.gz
•       Transcript-level counts: stored across three files which is similar to cellranger output:
•       _barcodes.tsv.gz
•       _features.tsv.gz
•       _matrix.mtx.gz

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with GlutaMAX™ (Thermo Fisher Scientific), 10% heat-inactivated fetal bovine serum (FBS; Gibco), and 1% penicillin-streptomycin (Thermo Fisher Scientific). Cultures were incubated at 37°C in a humidified atmosphere containing 5% CO2. Cells were routinely passaged at 70–80% confluency using standard culture procedures.

extract_protocol:
Suspension cell lines (H211, H526, H146, H69, SHP-77) were prepared for fluorescence-activated cell sorting (FACS). Each cell line was collected from culture, washed twice with PBS, and re-suspended in 500 μL FACS buffer (PBS with 2% FBS). Cells were then passed through a 35 μm strainer cap into FACS tubes and were subsequently stained with 7-amino-actinomycin D for live/dead sorting. Cells were sorted on the BD Aria III to collect 250,000 cells per sample. The remaining 3 adherent lines (H1975, H2228, HCC827) were detached using TrypLE Express (Gibco), washed twice with PBS, and resuspended in FACS buffer. Cell counts were performed in triplicate per cell line on the Countess 3 (Thermo Fisher Scientific) to ensure accuracy, and then 270,000 cells per line were combined into a single mixture. Nuclei isolation was performed using a custom protocol based on the Nuclei EZ Prep kit (Sigma-Aldrich). 1.7M Cells were pelleted at 300 x g for 5 minutes at 4°C, then gently resuspended in 300 μL of cold cell lysis buffer (EZ lysis buffer supplemented with 0.2 U/μL RNaseOUT™). Lysis was carried out on ice for 2.5 minutes to release nuclei, followed by centrifugation at 300 x g for 5 minutes at 4°C. The nuclei pellet was resuspended in 500 μL of cold wash buffer(1X PBS, 1% BSA, 0.2 U/μL RNaseOUT™), incubated on ice for 1 minute, then supplimented with a second 500 μL of wash buffer. Nuclei were gently resuspended by pipetting and pelleted at 200 x g for 5 minutes at 4°C. The pellet was resuspended in 200 μL of wash buffer, topped up to 1 mL, and centrifuged at 130 x g for 5 minutes. Nuclei were finally resuspended in 500 μL of wash buffer for quality assessment via DAPI staining and microscopy using Countess 3 system. The suspension was filtered twice using FlowMi 40 μM filter tips (Sigma-Aldrich) to remove any present clumps and re-counted prior to 10X capture. The nuclei mixture was loaded onto the 10X Genomics Chromium following the same protocol as described for single-cell capture, with a target capture of 5,000 nuclei.
From the cDNA generated by the 10X Genomics single-cell 3’ kit (v3.1, 11 cycles of PCR), libraries were prepared for Illumina, nanopore and Pacbio sequencing. Illumina snRNA-seq libraries were prepared with the 10X Library Construction Kit (PN1000190). The nanopore single-nucleus library was prepared from 10 ng of input cDNA, following the ONT single-cell protocol including the artifact removal step (v9198_v114_revE_06Dec2023). 125 ng of the post-pulldown PCR product were taken to adapter ligation with the ONT SQK-LSK114 kit. The final wash was performed with a 0.5X bead ratio (adjusted from 0.4X) and the short fragment buffer. The Pacbio single-nucleus Kinnex library was prepared with the Kinnex single-cell 12-plex concatenation kit according to the manufacturer’s instructions, which also includes an artifact removal step.

value: Epithelial

value: pooled male and female

tag: disease stage

value: Lung Cancer


title: Cut&Tag_SRCAP_P400_degron_0h_rep1

value: P400 degron 0h


title: prostate_BPH_01


title: PacBio Kinnex Bulk RNA-Seq of lung cancer cell line H211 (SCLC-P)

description: Library name: H211_Bulk_PacBio

data_processing:
Assembly: GRCh38
ONT datasets were basecalled with Dorado using rna004_130bps_sup@v5.1.0 for direct RNA and dna_r10.4.1_e8.2_400bps_sup@v5.0.0 for the cDNA datasets. Reads with mean quality scores <10 were discarded.
Reads were mapped to the reference genome GRCh38 and GENCODE v44 transcriptome using minimap2 (v2.28)
Transcript-level quantification was performed using Salmon (v1.10.2) for short-read datasets and Oarfish (v0.6.2) for long-read datasets, based on the GENCODE v44 transcriptome combined with spike-in sequences from SIRV Set 4 and Sequins.
•       Salmon uses an internal quasi-mapping approach.
•       Long-read datasets were first aligned to the transcriptome using minimap2 (v2.28), followed by quantification with Oarfish.
Supplementary files format and content:
Bulk RNA-seq count matrices follow the naming convention: <protocol>_bulk_<cell line>_matrix.tsv
Where <protocol> is one of:
•       dRNA – ONT direct RNA sequencing
•       ont – ONT PCR cDNA sequencing
•       pb – PacBio Kinnex
•       ill – Illumina

extract_protocol:
Total RNA was isolated from 1.5–2 M cells using TRIzol Reagent (Invitrogen) following the manufacturers guidelines.
llumina bulk RNA-Seq libraries we constructed using the Illumina Truseq v2 Stranded kit with polyA selection. Superscript III was used instead of SuperScript II, and the reverse transcription incubation step was accordingly adjusted to 50°C. Nanopore direct-RNA sequencing libraries were constructed using the ONT SQK-RNA004 kit, with the following modifications: input was increased to 2μg total RNA. RNA CS (calibrating strand) was omitted. NEB Induro Reverse Transcriptase was used in place of SuperScript III.
Nanopore direct-RNA sequencing libraries were constructed using the ONT SQK-RNA004 kit, with the following modifications: input was increased to 2μg total RNA. RNA CS (calibrating strand) was omitted. NEB Induro Reverse Transcriptase was used in place of SuperScript III.
Nanopore PCR-cDNA libraries were constructed using the ONT SQK-PCB114.24 kit, with the following modifications: reverse transcription was perormed for 90 minutes at 42°C, followed by 14 cycles of PCR with an extension time of 4 minutes.
Pacbio Bulk Kinnex libraries were prepared with the Iso-Seq express 2.0 kit and Kinnex PCR 8-fold kit

value: Female


title: IPSC 1

value: heart left ventricle


title: PacBio Kinnex Bulk RNA-Seq of lung cancer cell line H526 (SCLC-P)

description: Library name: H526_Bulk_PacBio

value: Male


title: PacBio scRNA-Seq of lung cancer cell line mixture

description: Library name: Single_cell_PacBio

data_processing:
Assembly: GRCh38
ONT datasets were basecalled with Dorado using the dna_r10.4.1_e8.2_400bps_sup@v5.0.0 model. Reads with mean quality scores <10 were discarded.
Reads were mapped to the reference genome GRCh38 and GENCODE v44 transcriptome using minimap2 (v2.28)
Single-cell RNA-seq (Illumina) data were processed using Cell Ranger (v8.0.1) with GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome.
Long-read single-cell reads were first demultiplexed using BLAZE (v2.5). The resulting FASTQ files were processed using the FLAMES (v2.0.1) single-cell pipeline, configured to use GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome. Further configurations included skipping novel transcript identification, and the use of Oarfish (v0.6.2) for transcript-level quantification.
Supplementary files format and content:
Count matrix prefix:  ill_sn – single-nucleus. Each matrix is stored in the standard three-file format: <prefix>_barcodes.tsv.gz | <prefix>_features.tsv.gz | <prefix>_matrix.mtx.gz
Count matrices from long-read protocols (ont, pb) are structured as follows:
Gene-level counts: genes_count_matrix.tsv.gz
•       Transcript-level counts: stored across three files which is similar to cellranger output:
•       _barcodes.tsv.gz
•       _features.tsv.gz
•       _matrix.mtx.gz

extract_protocol:
Suspension cell lines (H211, H526, H146, H69, SHP-77) were prepared for fluorescence-activated cell sorting (FACS). Each cell line was collected from culture, washed twice with PBS, and re-suspended in 500 μL FACS buffer (PBS with 2% FBS). Cells were then passed through a 35 μm strainer cap into FACS tubes and were subsequently stained with 7-amino-actinomycin D for live/dead sorting. Cells were sorted on the BD Aria III to collect 250,000 cells per sample. The remaining 3 adherent lines (H1975, H2228, HCC827) were detached using TrypLE Express (Gibco), washed twice with PBS, and resuspended in FACS buffer. Cell counts were performed in triplicate per cell line on the Countess 3 (Thermo Fisher Scientific) to ensure accuracy, and then 270,000 cells per line were combined into a single mixture. The cell mixture was loaded onto the 10X Genomics Chromium according to the manufacturer’s protocol using the 10X Chromium NEXT GEM single-cell 3’ kit (v3.1) with a target capture of 5,000 cells.
From the cDNA generated by the 10X Genomics single-cell 3’ kit (v3.1, 11 cycles of PCR), libraries were prepared for Illumina, nanopore and Pacbio sequencing. Illumina scRNA-seq libraries were prepared with the 10X Library Construction Kit (PN- 1000190). The nanopore single-cell library was prepared from 10 ng of input cDNA, following the ONT single-cell protocol including the artifact removal step (v9198_v114_revE_06Dec2023). 125 ng of the post-pulldown PCR product were taken to adapter ligation with the ONT SQK-LSK114 kit. The final wash was performed with a 0.5X bead ratio (adjusted from 0.4X) and the short fragment buffer. The Pacbio single-cell Kinnex library was prepared with the Kinnex single-cell 12-plex concatenation kit according to the manufacturer’s instructions, which also includes an artifact removal step.


title: prostate_BPH_02


title: Cut&Tag_SRCAP_INO80_degron_1h_rep2

value: INO80 degron 1h


title: PacBio Kinnex Bulk RNA-Seq of lung cancer cell line SHP77 (SCLC-A)

description: Library name: SHP77_Bulk_PacBio


title: PacBio Kinnex Bulk RNA-Seq of lung cancer cell line H69 (SCLC-A)

description: Library name: H69_Bulk_PacBio


title: HCT116 cells  ASO3

city: Shenyang

first: Xiaotong

last: Jiang

address: Nanjing North Street, Heping District

institute: The First Affiliated Hospital of China Medical University

data_processing:
mRNA data quality control: FastQC software and R were used to evaluate the quality of raw sequencing data
mRNA reference genome alignment, using STAR software to align the filtered reads with the reference database
mRNA analysis, using Stringtie's analysis workflow to quantify the expression of known genes and transcripts, using Deseq2 software to analyze differential genes, and significantly differentially differentiated gene GO and KEGG enrichment analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: HCT116 cells were cultured in DMEM medium with 10% foetal bovine serum at 37°C in a 5% CO2 incubator.

extract_protocol:
RNA was extracted using TRIZOL with a total amount > 2 μg and OD values between 1.8 and 2.2
The constructed sequencing libraries were quality checked and quantified. Qubit was used to accurately quantify the library concentration and Agilent 2100 Bioanalyzer was used to determine the library fragment size. Distribution

treatment_protocol: Transfection of ASO-SNORA67 to construct SNORA67 knockdown model

value: colon cancer cell

value: SNORA67 knockdown


title: PacBio Kinnex Bulk RNA-Seq of lung cancer cell line H146 (SCLC-A)

description: Library name: H146_Bulk_PacBio


title: HCT116 cells  ASO1


title: PacBio Kinnex Bulk RNA-Seq of lung cancer cell line H2228 (LUAD)

description: Library name: H2228_Bulk_PacBio


title: Cut&Tag_SRCAP_INO80_degron_0h_rep2

value: INO80 degron 0h


title: prostate_BPH_19

value: Mixed

value: No


title: HCT116 cells  ASO2


title: PacBio Kinnex Bulk RNA-Seq of lung cancer cell line H1975 (LUAD)

description: Library name: H1975_Bulk_PacBio


title: Cut&Tag_SRCAP_INO80_degron_0h_rep1

value: mouse embryonic stem cells


title: IPSC 2

value: IPSC


title: Cut&Tag_SRCAP_P400_degron_0h_rep2


title: chk1-24h-3_1

city: kunming

first: Luo

last: huan

address: wujiaying street

institute: yunnan university

description: Library name: Sample 12

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (https://www.omicsmart.com/).
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary files format and content: Expression analysis table include TPM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Orbilia oligospora

source_name: Fungal hyphae

growth_protocol: The WT and ΔAochk1 strains were cultured in a PDA medium for 7 days. Afterward, 200 C. elegans  were added to each plate for 24 hours.

extract_protocol:
After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China)
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mycelium was collected and washed three times with 0.1 mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: Fungal hyphae

value: Fungal hyphae cells

value: Aochk1 knockdown


title: Cut&Tag_P400_SRCAP_degron_1h_rep2

value: SRCAP degron 1h


title: chk1-24h-2_1

description: Library name: Sample 11


title: chk1-24h-1_1

description: Library name: Sample 10


title: Cut&Tag_P400_SRCAP_degron_1h_rep1


title: chk1-0h-3_1

description: Library name: Sample 9


title: HCT116 cells  NC1

value: control


title: HCT116 cells  NC2


title: chk1-0h-2_1

description: Library name: Sample 8


title: chk1-0h-1_1

description: Library name: Sample 7


title: Cut&Tag_SRCAP_INO80_degron_1h_rep1


title: WT-24h-3_1

description: Library name: Sample 6

value: WT


title: Cut&Tag_P400_SRCAP_degron_0h_rep2

value: SRCAP degron 0h


title: IPF distal bronchiole 8

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

description:
Fresh paraffin embedded sptial transcriptome sequencing
P2_IPF_13

data_processing:
Sequencing was performed on the Illumina NovaSeq6000 platform.
Data quality check was performed on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
Q3 normalization was used to normalize read counts across samples.
Assembly: hg38 genome reference
Supplementary files format and content: tab-delimited txt file
Library strategy: Spatial transcriptomics

source_name: Lung distal bronchiole

extract_protocol:
PFA (4%) fixed, paraffin embedded healthy lung and IPF lung blocks were freshly cut using microtomy.
Libraries were prepared using  Nanostring GeoMx® v.1.0 Human NGS Whole Transcriptome Atlas RNA Panel as per manufacturer instructions.

value: Lung distal bronchiole

value: Epithelial cells

value: Idiopathic pulmonary fibrosis lung


title: WT-24h-2_1

description: Library name: Sample 5


title: Cut&Tag_P400_SRCAP_degron_0h_rep1


title: WT-24h-1_1

description: Library name: Sample 4


title: PacBio Kinnex Bulk RNA-Seq of lung cancer cell line HCC827 (LUAD)

description: Library name: HCC827_Bulk_PacBio

value: Epithelial

value: Female

value: Lung Cancer


title: IPF distal bronchiole 7

description:
Fresh paraffin embedded sptial transcriptome sequencing
P2_IPF_12


title: WT-0h-3_1

description: Library name: Sample 3


title: IPF distal bronchiole 6

description:
Fresh paraffin embedded sptial transcriptome sequencing
P2_IPF_11


title: Cut&Tag_P400_INO80_degron_1h_rep2

value: INO80 degron 1h


title: WT-0h-2_1

description: Library name: Sample 2


title: HCT116 cells  NC3

value: colon cancer cell


title: IPF distal bronchiole 5

description:
Fresh paraffin embedded sptial transcriptome sequencing
P2_IPF_10


title: Developing B cells (B220+IgD-IgM-CD24+) isolated from WT mice (DNA Input), Biological replicate 2

city: Clayton

first: Kim

middle: L

last: Good-Jacobson

state: Vitoria

address: 19 Innovation Walk

department: Biochemistry & Molecular Biology

institute: Monash University

description: Library name: Input_H3K79me2_Pro___Pre_Replicate2

data_processing:
FASTQ files were
Pair-end files were coupled, aligned to the mm10 genome using the Bowtie package and then filtered for quality (>20).
PCR duplicates were the removed using the Samstools package.
Peaks were called using the resulting files from the Input and ChIP processed samples via the MACS2 package in order to generate Bigwig files for visualisation using the IGV genome browser and BED files for further downstream analysis.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (BED)

source_name: Bone Marrow

extract_protocol:
Cells were fixed in 0.6% formaldehyde for 8 minutes, while rotating, before quenching with 1.25M glycine and washed thrice with Dulbecco's phosphate buffered saline. Cell were lysed via a BioRuptor sonicator. Histone modification-specific antibodies were used to pull down DNA fragments via chromatin immunoprecipitation and input sampels representing the fragmented DNA prior to pulldown were generated for each sample.
ChIP-processed and input control samples were processed using the MGI Easy DNA FS Library preparation kit V1 (MGI Tech) and sequenced using a MGISEQ-2000RS High-Throughput Sequencing Set (PE100).

treatment_protocol: Mature naïve B cell and early developing B cells were derived from the spleens and bone marrow of naïve wildtype mice. Germinal center B cells were isolated from the spleens of wildtype mice immunized 7-days prior with NP-KLH precipitated in 10% alum. Cells were extracted via fluorescence-assisted cell sorting and resuspended in 10mL RPMI containing 10% foetal calf serum and 2mM glutamine.

value: Bone Marrow

value: Pro and pre B cells

value: Wildtype

tag: chip antibody


title: WT-0h-1_1

description: Library name: Sample 1

value: Fungal hyphae

value: Fungal hyphae cells


title: Cut&Tag_P400_INO80_degron_1h_rep1

value: mouse embryonic stem cells


title: Developing B cells (B220+IgD-IgM-CD24+) isolated from WT mice (DNA Input), Biological replicate 1

description: Library name: Input_H3K79me2_Pro___Pre_Replicate1


title: Developing B cells (B220+IgD-IgM-CD24+) isolated from WT mice (H3K79me2 ChIP), Biological replicate 2

description: Library name: ChIP_H3K79me2_Pro___Pre_Replicate2


title: Cut&Tag_P400_INO80_degron_0h_rep2

value: INO80 degron 0h


title: Developing B cells (B220+IgD-IgM-CD24+) isolated from WT mice (H3K79me2 ChIP), Biological replicate 1

description: Library name: ChIP_H3K79me2_Pro___Pre_Replicate1


title: C_auris_Control-3.

description: Library name: sample 3

value: fungal cells

value: Isolate 10

value: untreated


title: IPF distal bronchiole 4

description:
Fresh paraffin embedded sptial transcriptome sequencing
P1_IPF_09

value: Lung distal bronchiole

value: Epithelial cells


title: Cut&Tag_P400_INO80_degron_0h_rep1


title: MYC_P53KO_GNS5_R2

city: Worcester

first: Emma

middle: V.

last: Watson

address: AS7-1045 Albert Sherman Center, 368 Plantation St

department: Systems Biology

institute: UMass Chan Medical School

description: Library name: Sample15

data_processing:
Reads were aligned using BWA (v 0.7.17) to the T2T-CHM13 human reference genome for samples from human cell lines and GRCm39 mouse reference genome for samples from mouse cell line.
The aligned reads were sorted using SAMtools (v1.16.1), and gene-level read counts were obtained using featureCounts (subread, v1.6.2).
Assembly: T2T-CHM13 for human, GRCm39 for mouse
Supplementary files format and content: csv file with TPM values for each gene in each sample

source_name: MYC-cap, p53KO

extract_protocol:
1 ug of RNA was utilized for mRNA isolation per sample, which was completed using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA Library Prep Kits for Illumina kit.

value: MYC-cap, p53KO

value: Prostate cancer cell line


title: IPF distal bronchiole 1

description:
Fresh paraffin embedded sptial transcriptome sequencing
P1_IPF_06

value: Idiopathic pulmonary fibrosis lung


title: IPF distal bronchiole 2

description:
Fresh paraffin embedded sptial transcriptome sequencing
P1_IPF_07


title: MYC_P53KO_GNS5_R3

description: Library name: Sample16


title: IPF distal bronchiole 3

description:
Fresh paraffin embedded sptial transcriptome sequencing
P1_IPF_08


title: MYC_P53KO_DMSO_R1

description: Library name: Sample11

value: DMSO


title: LSK_PBS_R1

city: Nouzilly

first: Pascal

last: Froment

address: INRAE Nouzilly

department: UMR 7247 INRAE/CNRS/Université de Tours/IFCE

country: France

institute: INRAE

description: Library name: LSK_P1

data_processing:
Quality control and preprocessing of data were performed by SciLicium (Rennes, France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the mus musculus reference transcriptome from the UCSC website (release mm10) using BWA version 0.7.4.4 with the parameter “-l 24”
Assembly: mm10
Supplementary files format and content: Expression file in dat (tab separated plain text) format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 17,484 genes detected.

source_name: bone marrow

extract_protocol:
For each cell population, batches of 100 cells (4–5 replicates) were sorted by FACS in 96-well V-bottom plate wells containing 2 mL of lysis buffer (Ultra-pure Water, 10% Triton X-100, RNasinPlus 40U/l; Promega). After evaporation of the lysis buffer at 95C for 3 min, first strand cDNA synthesis was performed using the Maxima H Minus Reverse Transcriptase (Thermo Fisher), E3V6NEXT primers (specific primer for each well) and Template Switching Primer: E5V6NEXT. Resulting cDNAs were pooled and purified by the DNA Clean and Concentrator TM-5 kit (Zymo research) and treated with Exonuclease I (New England Biolabs) before amplification using the Advantage 2 PCR kit (Clontech) and the SINGV6 primer (95°C for 1 min, 15 cycles at 95°C for 15 s, 65°C for 30 s, 68°C for 6 min and 72°C for 10 min). PCR products were purified by Agencourt AMPure XP (Beckman Coulter).
Libraries were prepared using the Illumina DNA Prep kit (Illumina) according to the manufacturer’s guidelines.

value: bone marrow

value: hematopoietic progenitor

value: PBS


title: Cut&Tag_INO80_SRCAP_degron_1h_rep1

value: SRCAP degron 1h


title: Healthy lung distal bronchiole 3

description:
Fresh paraffin embedded sptial transcriptome sequencing
P0_HL_05

value: Healthy Lung


title: Cut&Tag_INO80_SRCAP_degron_0h_rep2

value: SRCAP degron 0h


title: Cut&Tag_INO80_SRCAP_degron_0h_rep1

value: mouse embryonic stem cells


title: LSK_PBS_R2

description: Library name: LSK_P2


title: LSK_PBS_R3

description: Library name: LSK_P3


title: Healthy lung distal bronchiole 2

description:
Fresh paraffin embedded sptial transcriptome sequencing
P0_HL_04


title: LSK_PBS_R4

description: Library name: LSK_P4


title: Cut&Tag_INO80_P400_degron_1h_rep2

value: P400 degron 1h


title: LMPP_PBS_R1

description: Library name: LMPP_P1


title: Healthy lung distal bronchiole 1

description:
Fresh paraffin embedded sptial transcriptome sequencing
P0_HL_03


title: LMPP_PBS_R3

description: Library name: LMPP_P3


title: MYC_P53KO_GNS5_R1

description: Library name: Sample14


title: Cut&Tag_INO80_SRCAP_degron_1h_rep2


title: MYC_P53KO_DMSO_R3

description: Library name: Sample13


title: PLEC knockdown4

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
aligment was done with STAR - 2.7.8a
Quantify to annotation model (Partek E/M) Ensembl_release109
Normailzation method DESEq2
Assembly: hg38 genome reference
Supplementary files format and content: tab-delimited txt

growth_protocol: Small Airway Epithelial Cells were purchased from Lonza (CC-2547). To expand, the cells were cultured on culture dishes coated with 0.05mg/ml human placenta derived COLIV (Sigma) in Bronchial epithelial cell growth medium with added supplements according to manufacturer’s recommendation (BEBM-Lonza).

extract_protocol:
SAECs after knockdown were washed with PBS and total RNA from the samples wereextracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The RNA concentrations and purity were measured on a NanoDrop ND-1000 spectrophotometer, followed by tapestation
RNA quality was determined initially using nanodrop, followed by Agilent 2200 and TapeStation Analysis Software 3.2. All samples had excellent quality with RNA integrity number (RIN) 10. Libraries for RNA-Seq were prepared with KAPA mRNA-Seq Hyper Prep Kit according to manufacturer's instructions.  cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.
Libraries for RNA-Seq were prepared with KAPA mRNA-Seq Hyper Prep Kit. The workflow consists of (1) mRNA enrichment and fragmentation, (2) first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and (3) incorporating dUTP into the second cDNA strand. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification.

treatment_protocol: SAECs from early passages (P3-P4) were  treated with P3 primary cell 4D-nucleofector reagents (Lonza) according to manufacturer’s directions and treated with 50nM JUP siRNA, PLEC siRNA or Scrambled siRNA (Origene).  Cells were then subjected to electroporation using the preset ‘Normal human bronchial epithelial cell’ Nucleofector program, plated on culture plates and after 72 hr, cells were washed in 1X PBS, and then subjected to total RNA  isolation

value: Small airway epithelial cells

value: PLEC knockdown

value: PLEC gene knockdown


title: MYC_P53KO_DMSO_R2

description: Library name: Sample12


title: Cut&Tag_INO80_P400_degron_0h_rep2

value: P400 degron 0h


title: LMPP_PBS_R4

description: Library name: LMPP_P4


title: LMPP_PBS_R5

description: Library name: LMPP_P5


title: CLP_PBS_R1

description: Library name: CLP_P1

value: lymphoid progenitor


title: CLP_PBS_R2

description: Library name: CLP_P2


title: Cut&Tag_INO80_P400_degron_0h_rep1


title: CLP_PBS_R3

description: Library name: CLP_P3


title: Cut&Tag_H33_SRCAP_degron_1h_rep2


title: LMPP_EXPO_R1

description: Library name: LMPP_E1

value: EPO


title: PLEC knockdown1

value: Lung distal bronchiole

value: Epithelial cells


title: Cut&Tag_H33_SRCAP_degron_1h_rep1


title: LMPP_EXPO_R2

description: Library name: LMPP_E2


title: LSK_EXPO_R1

description: Library name: LSK_E1


title: JUP knockdown4

value: JUP Knockdown

value: JUP gene Knockdown


title: LSK_EXPO_R2

description: Library name: LSK_E2

value: bone marrow

value: hematopoietic progenitor


title: LMPP_PBS_R2

description: Library name: LMPP_P2

value: PBS


title: Cut&Tag_INO80_P400_degron_1h_rep1


title: Cut&Tag_H33_SRCAP_degron_0h_rep2


title: LSK_EXPO_R3

description: Library name: LSK_E3


title: JUP knockdown3


title: LSK_EXPO_R4

description: Library name: LSK_E4


title: GMP_PBS_R1

description: Library name: GMP_P1

value: myeloid progenitor


title: GMP_PBS_R2

description: Library name: GMP_P2


title: JUP knockdown1


title: PLEC knockdown3


title: Cut&Tag_H33_P400_degron_1h_rep2


title: PLEC knockdown2


title: GMP_PBS_R4

description: Library name: GMP_P4


title: JUP knockdown2


title: Scrambled4

value: Scrambled

value: Control siRNA treated


title: CLP_PBS_R5

description: Library name: CLP_P5


title: Cut&Tag_H33_P400_degron_0h_rep2

value: mouse embryonic stem cells


title: GMP_PBS_R3

description: Library name: GMP_P3


title: CLP_PBS_R4

description: Library name: CLP_P4


title: LMPP_EXPO_R3

description: Library name: LMPP_E3


title: Cut&Tag_H33_P400_degron_1h_rep1

value: P400 degron 1h


title: LMPP_EXPO_R4

description: Library name: LMPP_E4


title: Cut&Tag_H33_P400_degron_0h_rep1


title: Scrambled3

value: Small airway epithelial cells


title: CLP_EXPO_R1

description: Library name: CLP_E1


title: Cut&Tag_H33_INO80_degron_1h_rep2

value: INO80 degron 1h


title: Scrambled2


title: LMPP_EXPO_R5

description: Library name: LMPP_E5


title: Scrambled1


title: CLP_EXPO_R3

description: Library name: CLP_E3


title: Cut&Tag_H33_SRCAP_degron_0h_rep1

value: SRCAP degron 0h


title: Cut&Tag_H33_INO80_degron_1h_rep1


title: CLP_EXPO_R2

description: Library name: CLP_E2

value: lymphoid progenitor


title: CLP_EXPO_R4

description: Library name: CLP_E4

value: EPO


title: 96-hour, direct, IgG, rep5

city: Cleveland

first: Oliver

last: Wessely

state: OH

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore!(v0.6.10) using the default parameters
Sequence reads were aligned to human genome (GrCH38/hg38) using STAR (v2.7.11A ) using the default parameters
Read count extraction using FeatureCounts in Galaxy (Galaxy Version 2.0.3+galaxy2) using the default parameters
Read count were normalized using DESeq2 in Galaxy (Galaxy Version 2.11.40.8+galaxy1)
Assembly: GrCH38/hg38
Supplementary files format and content: tab-delimited text file including the normalized counts for each sample in a matrix table

source_name: kidney

extract_protocol:
miRNeasy Micro kit (Qiagen, 217084)
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio Inc.)

treatment_protocol: Human primary podocytes in the outer chambers were injured with (i) a cytopathic anti-podocyte antibody (IgG; 10 mg/ml), (ii) Adriamycin/doxorubicin (ADR; 2 ug/ml; Sigma-Aldrich D1515), or (iii) puromycin aminonucleoside (PAN; 50 ug/ml; Sigma-Aldrich SBR00017)

value: kidney

tag: time point

value: podocyte

value: IgG


title: Cut&Tag_H33_INO80_degron_0h_rep2

value: INO80 degron 0h


title: GMP_EXPO_R1

description: Library name: GMP_E1

value: bone marrow


title: 96-hour, direct, IgG, rep4


title: GMP_EXPO_R2

description: Library name: GMP_E2


title: Cut&Tag_H33_INO80_degron_0h_rep1


title: GMP_EXPO_R3

description: Library name: GMP_E3


title: CLP_EXPO_R5

description: Library name: CLP_E5


title: GMP_EXPO_R4

description: Library name: GMP_E4


title: Cut&Tag_H2AZac_SRCAP_degron_1h_rep2

value: SRCAP degron 1h


title: PreProB_PBS_R1

description: Library name: PreProB_P1

value: B lymphoid precursor

value: PBS


title: 96-hour, direct, IgG, rep2


title: PreProB_PBS_R2

description: Library name: PreProB_P2


title: Cut&Tag_H2AZac_SRCAP_degron_1h_rep1


title: PreProB_PBS_R3

description: Library name: PreProB_P3


title: 96-hour, direct, IgG, rep1


title: PreProB_PBS_R4

description: Library name: PreProB_P4


title: Cut&Tag_H2AZac_SRCAP_degron_0h_rep2


title: 96-hour, direct, ADR, rep5

value: ADR


title: ProB_PBS_R1

description: Library name: ProB_P1


title: ProB_PBS_R2

description: Library name: ProB_P2


title: Cut&Tag_H2AZac_SRCAP_degron_0h_rep1


title: ProB_PBS_R3

description: Library name: ProB_P3


title: 96-hour, direct, ADR, rep4


title: ProB_PBS_R4

description: Library name: ProB_P4


title: 96-hour, direct, ADR, rep3


title: Cut&Tag_H2AZac_P400_degron_1h_rep2


title: PreBI_PBS_R1

description: Library name: PreBI_P1


title: Cut&Tag_H2AZac_P400_degron_1h_rep1


title: ProB_PBS_R5

description: Library name: ProB_P5


title: 96-hour, direct, IgG, rep3


title: PreBI_PBS_R2

description: Library name: PreBI_P2


title: 96-hour, direct, ADR, rep2


title: Cut&Tag_H2AZac_P400_degron_0h_rep2

value: P400 degron 0h


title: PreBIIS_PBS_R1

description: Library name: PreBIIS_P1


title: 96-hour, direct, ADR, rep1


title: PreBIIS_PBS_R2

description: Library name: PreBIIS_P2


title: Cut&Tag_H2AZac_P400_degron_0h_rep1

value: mouse embryonic stem cells


title: 96-hour, direct, PAN, rep5

value: PAN


title: PreBIIS_PBS_R4

description: Library name: PreBIIS_P4


title: PreProB_PBS_R5

description: Library name: PreProB_P5


title: PreBIIS_PBS_R3

description: Library name: PreBIIS_P3


title: PreBIIL_PBS_R1

description: Library name: PreBIIL_P1


title: PreBIIL_PBS_R3

description: Library name: PreBIIL_P3


title: Cut&Tag_H2AZac_INO80_degron_1h_rep1


title: PreBIIL_PBS_R2

description: Library name: PreBIIL_P2


title: 96-hour, direct, PAN, rep3


title: PreBI_PBS_R3

description: Library name: PreBI_P3


title: PreBIIL_PBS_R4

description: Library name: PreBIIL_P4


title: PreBIIL_PBS_R5

description: Library name: PreBIIL_P5


title: Cut&Tag_H2AZac_INO80_degron_0h_rep1


title: Cut&Tag_H2AZac_INO80_degron_0h_rep2


title: 96-hour, direct, PAN, rep2


title: PreBI_PBS_R4

description: Library name: PreBI_P4


title: 96-hour, direct, PAN, rep1


title: PreBI_PBS_R5

description: Library name: PreBI_P5


title: ChIP-seq_BRD2_SRCAP_degron_1h_rep2

data_processing:
Raw reads were firstly trimmed by Cutadapt software and then mapped to mm10 and genome by Bowtie2 software. Reads with spike-in were mapped to both mm10 and hg19 genome.
PCR duplicated, multiple mapped and discordant reads were discarded for further analysis.
Bam files were converted to bw format by deepTools software using RPGC as the normalization method. Bam files with spike-in were normalized by the reads mapped to hg19 genome.
Assembly: mm10
Supplementary files format and content: bigwig


title: 96-hour, direct, untreated, rep5

value: untreated


title: PreBIIS_PBS_R5

description: Library name: PreBIIS_P5


title: Immature_PBS_R1

description: Library name: Immatures_P1

value: B lymphocyte


title: ChIP-seq_BRD2_SRCAP_degron_1h_rep1


title: Cut&Tag_H2AZac_INO80_degron_1h_rep2

value: INO80 degron 1h


title: 96-hour, direct, untreated, rep4


title: Immature_PBS_R2

description: Library name: Immatures_P2


title: Immature_PBS_R3

description: Library name: Immatures_P3


title: ChIP-seq_BRD2_SRCAP_degron_0h_rep2

value: SRCAP degron 0h


title: Immature_PBS_R4

description: Library name: Immatures_P4


title: 96-hour, direct, untreated, rep3


title: 96-hour, direct, PAN, rep4


title: Immature_EXPO_R1

description: Library name: Immatures_E1

value: EPO


title: ChIP-seq_BRD2_SRCAP_degron_0h_rep1


title: Immature_PBS_R5

description: Library name: Immatures_P5


title: 96-hour, direct, untreated, rep2

value: kidney


title: ChIP-seq_BRD2_P400_degron_1h_rep2

value: P400 degron 1h


title: 96-hour, direct, untreated, rep1

value: podocyte


title: Immature_EXPO_R4

description: Library name: Immatures_E4


title: PreBIIS_EXPO_R1

description: Library name: PreBIIS_E1


title: ChIP-seq_BRD2_P400_degron_1h_rep1


title: 96-hour, indirect, PAN, rep5


title: PreBI_EXPO_R1

description: Library name: PreBI_E1


title: ChIP-seq_BRD2_P400_degron_0h_rep2


title: 96-hour, indirect, PAN, rep4


title: PreBI_EXPO_R2

description: Library name: PreBI_E2


title: ChIP-seq_BRD2_P400_degron_0h_rep1


title: PreBI_EXPO_R3

description: Library name: PreBI_E3


title: 96-hour, indirect, PAN, rep3


title: ChIP-seq_BRD2_INO80_degron_1h_rep2


title: PreBIIL_EXPO_R1

description: Library name: PreBIIL_E1


title: PreBIIL_EXPO_R2

description: Library name: PreBIIL_E2


title: PreBIIL_EXPO_R3

description: Library name: PreBIIL_E3


title: ChIP-seq_BRD2_INO80_degron_0h_rep2

value: INO80 degron 0h


title: 96-hour, indirect, PAN, rep1


title: ChIP-seq_BRD2_INO80_degron_1h_rep1


title: PreBIIS_EXPO_R2

description: Library name: PreBIIS_E2

value: bone marrow


title: 96-hour, indirect, IgG, rep5

value: IgG


title: PreBIIL_EXPO_R5

description: Library name: PreBIIL_E5

value: B lymphoid precursor


title: PreBIIL_EXPO_R4

description: Library name: PreBIIL_E4


title: 96-hour, indirect, PAN, rep2


title: PreBIIS_EXPO_R4

description: Library name: PreBIIS_E4


title: Immature_EXPO_R3

description: Library name: Immatures_E3


title: Immature_EXPO_R5

description: Library name: Immatures_E5


title: Immature_EXPO_R2

description: Library name: Immatures_E2


title: 96-hour, indirect, IgG, rep4


title: eosinophils, IL33+SID26681509-3, 8h

first: Yinling

last: Han

address: Jiefang Road

institute: Key Laboratory of Respiratory Disease of Zhejiang Province

data_processing:
omicsmart system of Gene Denovo Corporation (https://www.omicsmart.com)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Eosinophils

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina

value: Eosinophils

value: WT


title: PreBIIS_EXPO_R5

description: Library name: PreBIIS_E5


title: PreBI_EXPO_R5

description: Library name: PreBI__E5


title: eosinophils, IL33+SID26681509-2, 8h


title: 96-hour, indirect, IgG, rep3


title: ProB_EXPO_R1

description: Library name: ProB_E1


title: 96-hour, indirect, IgG, rep2


title: ProB_EXPO_R2

description: Library name: ProB_E2


title: eosinophils, IL33+SID26681509-1, 8h


title: ProB_EXPO_R3

description: Library name: ProB_E3


title: ProB_EXPO_R4

description: Library name: ProB_E4


title: 96-hour, indirect, IgG, rep1


title: eosinophils, SID26681509-3, 8h


title: ProB_EXPO_R5

description: Library name: ProB_E5


title: PreBIIS_EXPO_R3

description: Library name: PreBIIS_E3


title: 96-hour, indirect, ADR, rep3

value: ADR


title: PreProB_EXPO_R1

description: Library name: PreProB_E1


title: eosinophils, SID26681509-2, 8h


title: ChIP-seq_BRD2_INO80_degron_0h_rep1

value: mouse embryonic stem cells


title: 96-hour, indirect, ADR, rep2


title: PreProB_EXPO_R2

description: Library name: PreProB_E2


title: PreProB_EXPO_R3

description: Library name: PreProB_E3


title: eosinophils, SID26681509-1, 8h


title: 96-hour, indirect, ADR, rep1


title: PreProB_EXPO_R4

description: Library name: PreProB_E4


title: eosinophils, IL33-3, 8h


title: PreBI_EXPO_R4

description: Library name: PreBI__E4


title: FoP_WT_2

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

description: WT duplicate 2/2

data_processing:
Mapped with STAR
read count assigned with FeatureCounts
Assembly: hg38
Supplementary files format and content: readcounts, tsv-file

source_name: Tongue

extract_protocol:
Qiagen RNA-easy kit
Truseq stranded mRNA

value: Tongue

value: FoP organoid

value: Various


title: PreProB_EXPO_R5

description: Library name: PreProB_E5


title: 96-hour, indirect, untreated, rep5

value: untreated


title: f2.5_1

description: Clone 2.5 duplicate 1/2

value: Foxe1 knock-out

value: Genetic modification


title: eosinophils, IL33-2, 8h


title: eosinophils, IL33-1, 8h


title: 96-hour, indirect, untreated, rep4

value: kidney


title: f2.5_2

description: Clone 2.5 duplicate 2/2


title: f2.4_2

description: Clone 2.4 duplicate 2/2


title: 96-hour, indirect, untreated, rep3


title: f2.4_1

description: Clone 2.4 duplicate 1/2


title: eosinophils, dmso-3, 8h

value: DMSO


title: eosinophils, dmso-2, 8h


title: 96-hour, indirect, untreated, rep2

value: podocyte


title: 96-hour, indirect, untreated, rep1


title: CVP_WT_1

description: WT duplicate 1/2

value: CVP organoid


title: c2.10_2

description: Clone 2.10 duplicate 2/2


title: CVP_WT_2

description: WT duplicate 2/2


title: eosinophils, dmso-1, 8h


title: c2.9_2

description: Clone 2.9 duplicate 2/2


title: c2.10_1

description: Clone 2.10 duplicate 1/2


title: TAR4/4;RAD23AKD bio rep 10

city: London

first: Ravindra

middle: Singh

last: Prajapati

state: UK

address: 2nd floor, Maurice Wohl Clinical Neuroscience Inst, 5 Cutcombe Road

department: BCN, Maurice Wohl Clinical Neuroscience Ins

institute: King's College London

data_processing:
Low-quality reads (Phred<20), and adapters were removed using Trim-galore (V0.6.7)
Reads were aligned to the GRCm38/mm10 build using RNA STAR Gapped-read mapper (V-2.7.11a+galaxy1 or V-2.7.8a+galaxy1)
To quantify expressed genes, mapped reads were we counted on exons (GRCm38.99.gtf) using featureCounts(V 2.0.1+galaxy2)
Assembly: GRCm38/mm10
Supplementary files format and content: tabular
Supplementary files format and content: read counts

source_name: motor cortex

extract_protocol:
Total RNA was extracted (Qiagen cat. No. 1023539)
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit, following the manufacturer’s instructions (NEB, Ipswich, MA, USA)

treatment_protocol: The motor cortices of WT, Tar4/Tar4 and Rad23 ASOs treated mice were dissected from left hemispheres of mice

value: motor cortex

value: Rad23a KD ASOs


title: FoP_WT_1

description: WT duplicate 1/2


title: TAR4/4;RAD23AKD bio rep 9


title: 24-hour, direct, IgG-treated, rep5

value: IgG


title: 24-hour, direct, IgG-treated, rep4


title: replicate 1, day 3

city: Bad Nauheim

first: Noah

last: Knoppik

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max-Planck-Institute for Heart and Lung Research

description: 10x Genomics

data_processing:
Prior to analysis, reads were aligned against the mouse genome (GRCm38.p6) and quantified using StarSolo.
Analysis was conducted with the Scanpy software.
After quality filtering, raw cell counts were normalized to the median count over all cells and transformed into log space for variance stabilization.
Principal component analysis (PCA) identified 14 and 11 components on days 3 and 7 pi, respectively.
Uniform Manifold Approximation and Projection (UMAP) embedding was created to identify cell type clusters through Leiden clustering.
Doublet analysis was conducted on day 7 using Scrublet, leading to the removal of a doublet cluster (118 cells).
Final data visualization was done by scanpy and cellxgene packages.
Assembly: GRCm38.p6
Supplementary files format and content: starsolo outputs

source_name: lung

growth_protocol: Wild-type C57Bl6/N mice were acquired from Charles River Laboratories and bred under SPF conditions in our mice facility (Biomedizinisches Forschungszentrum Seltersberg).

extract_protocol:
On day 3 or day 7 after infection, mice were sacrificed by exsanguination under anesthesia. To this purpose, xylazine hydrochloride (application 16mg/kg; diluted in 0.9% sterile NaCl to 3.33mg/ml) and ketamine hydrochloride (application 100mg/kg; diluted in 0.9% sterile NaCl plus 3.33mg/ml xylazine hydrochloride to a concentration of 20mg/ml) were applied intraperitoneally at 0.2ml per 20g body weight. Exsanguination was then performed through puncture of the left ventricle. Following that, the trachea was exposed through an incision in the neck skin and separation of the salivary glands and sternohyoid muscles. A 21G cannula was then inserted in the trachea via a small incision and fixed in place with the help of surgical suture. Mouse chest cavity was then opened, and lungs were perfused with sterile HBSS via the right heart ventricle. Once 1.5ml of sterile dispase had been administered into the lungs, the cannula was removed, and the trachea was tightly sealed with suture. Lungs and trachea were removed, washed in HBSS, and placed in dispase for 40min at RT. Next, heart, trachea, and large airways were removed, and the remaining lung tissue was dissected in DMEM/2,5% HEPES plus 0.01% DNase in C tubes using the gentleMACS dissociator (Miltenyi Biotec). Cells were filtered through 100 and 40μm cell filters, washed, centrifuged at 1.5g/4°C for 5min, resuspended in 1ml DMEM/2.5% HEPES, and counted. After a blocking step of unspecific binding with 0.01ml immune globulin blocking solution [10% Gamunex-C (Grifols, USA)/1% BSA/0.02% NaAz], cells were washed and incubated in 0.1ml MACS buffer (PBS, 7.4% EDTA, 0.5% FCS pH 7.2). containing a rat antu-mouse CD45 APC/Cy7 antibody (clone 30-F11, BioLegend), in a concentration of 1:100 for 20min at 4°C. Cells were washed between staining steps with MACS buffer and resuspended in 0.5ml MACS buffer before sorting. SytoxTM blue (ThermoScientific, USA) was added at a concentration of 1:1000 immediately before sorting. Fluorescence-activated cell sorting of 500,000 live leukocytes/sample was performed on a BD Aria III. Four mice were used per time point of analysis.
Following quality control, single cell suspension with ~10,000 cells were loaded onto a Chromium Chip B (10X Genomics). Gel beads in emulsion (GEM) generation, cDNA synthesis and amplification, and library preparation were preformed using the Chromium Single Cell 3’ Reagent Kit v3.1 (10X Genomics), according to the manufacturer’s protocol. In short, single cell suspensions were mixed with the appropriate amount of nuclease-free water for a targeted cell recovery ofapproximately 10,000 cells, then mixed with a MasterMix containing RT Reagent B, Template Switch Oligo, Reducing Agent B, RT Enzyme C, for a total volume of 75µl per sample. Cells were then loaded on a Chromium Next GEM Chip G. Following gel beads (50µl) and partitioning oil (45µl) addition, the chip was run in a Chromium Controller. After GEM-RT incubation on an AppliedBiosystems Veriti 96-well Thermal Cycler, recovery agent (125µl) and a dynabeads cleanup mix (200µl) was added to each sample (100µl) for a total of 10min incubation, after which post GEM-RT cleanup was performed through the addition of Elution Solution I (Buffer EB, 10% Tween-20, Reducing Agent B) on a 10x Magnetic Separator. Cleanup was performed according to the manufacturer´s instructions. cDNA synthesis and amplification was then performed on a n AppliedBiosystems Veriti 96-well Thermal Cycler, according to the manufacturer´s protocol., followed by cDNA cleanup and SPRIselect. Library preparation was then performed following cDNA fragmentation, end repair, A-tailing, and then post-fragmentation end repair & A-tailing, double sided size selection (SPRIselect). Adaptor ligation was also performed on the AppliedBiosystems Veriti 96-well Thermal Cycler, again followed by post-ligation cleanup (SPRI select). Sample index PCR was then performed to ensure that no sample indices overlapped in the multiplexed sequencing run, with a post-PCR SPRIselect step. Samples were then stored at -20°.  Following a post-library construction quality contol, we proceeded with sequencing of the indexed libraries.

treatment_protocol: For infection experiments, mice between 10-12 weeks of age were orotracheally infected with 500 foci forming units (ffu) A/Puerto Rico/8/1934 (PR8, H1N1) influenza virus diluted in 70µl PBS.

value: lung

value: leukocytes (gated as Sytox- CD45+)

value: IAV-infected

tag: time


title: TAR4/4;RAD23AKD bio rep 8

tag: tissue


title: replicate 2, day 3

description: 10x Genomics


title: 24-hour, direct, IgG-treated, rep3


title: 24-hour, direct, IgG-treated, rep2


title: replicate 4, day 7

description: 10x Genomics


title: replicate 2, day 7

description: 10x Genomics


title: TAR4/4;RAD23AKD bio rep 7


title: TAR4/4;RAD23AKD bio rep 6


title: 24-hour, direct, IgG-treated, rep1


title: FC sorted host monocytes at 2yrs post-BMT3

city: Pittsburgh

first: Xiaohua

last: Chen

state: PA

address: 4401 Penn Ave

institute: UPMC CHP BMTCT

description: Library name: BBMT1_2YhMONO3

data_processing:
CLC Genomic workbench software v25 was used for reading, mapping and gen expression profiling, following the protocol provided by company
Assembly: hg38 human genome, ENSEMBLv91 anotation
Supplementary files format and content: tab deliminated text files with both raw counts and normalized counts

source_name: Peripheral blood

growth_protocol: T cells grew in RPMI1640+10%HS for 7 days at 37C+5%CO2.

extract_protocol:
QIAGENÒ RNeasyÒ plus micro kit protocol
RNA libraries for RNAseq were prepared using Truseq stranded total RNA protocol for T cells and Illumina stranded total RNAseq protocol

treatment_protocol: T cells were either stimulated with or withour host Dendritic cells.

value: Peripheral blood

value: PB monocytes

value: IL-7R deficiency

tag: batch

value: batch 2


title: FC sorted host monocytes at 2yrs post-BMT2

description: Library name: BBMT1_2YhMONO2

tag: cell type


title: 24-hour, direct, ADR-treated, rep5

value: ADR


title: FC sorted host monocytes at 2yrs post-BMT1

description: Library name: BBMT1_2YhMONO1

tag: genotype


title: FC sorted donor monocytes at 2yrs post-BMT2

description: Library name: BBMT1_2YgMONO2

value: WT

tag: treatment


title: TAR4/4;RAD23AKD bio rep 5


title: 24-hour, direct, ADR-treated, rep4


title: c2.9_1

description: Clone 2.9 duplicate 1/2

value: Tongue

tag: cell line

value: Various

value: Foxe1 knock-out

value: Genetic modification


title: replicate 3, day 3

description: 10x Genomics

tag: strain


title: FC sorted donor monocytes at 2yrs post-BMT3

description: Library name: BBMT1_2YgMONO3


title: TAR4/4;RAD23AKD bio rep 4


title: 24-hour, direct, ADR-treated, rep3

value: kidney

value: podocyte


title: host monocytes pre-BMT3

description: Library name: BBMT1_prehMONO3


title: host monocytes pre-BMT2

description: Library name: BBMT1_prehMONO2


title: replicate 3, day 7

description: 10x Genomics


title: TAR4/4;RAD23AKD bio rep 3

value: motor cortex

value: Rad23a KD ASOs


title: host monocytes pre-BMT1

description: Library name: BBMT1_prehMONO1


title: 24-hour, direct, ADR-treated, rep1


title: 24-hour, direct, ADR-treated, rep2


title: graft monocytes2

description: Library name: BBMT1_gMONO2

source_name: Bone marrow

value: Bone marrow

value: BM monocytes


title: TAR4/4;RAD23AKD bio rep 2


title: TAR4/4;RAD23AKD bio rep 1


title: graft monocytes1

description: Library name: BBMT1_gMONO1


title: 24-hour, direct, PAN-treated, rep5

value: PAN


title: replicate 1, day 7

description: 10x Genomics

value: lung

value: leukocytes (gated as Sytox- CD45+)

value: IAV-infected


title: Illumina snRNA-Seq of lung cancer cell line mixture

first: Matthew

description: Library name: Single_nuclei_Illumina

data_processing:
Assembly: GRCh38
ONT datasets were basecalled with Dorado using the dna_r10.4.1_e8.2_400bps_sup@v5.0.0 model. Reads with mean quality scores <10 were discarded.
Reads were mapped to the reference genome GRCh38 and GENCODE v44 transcriptome using minimap2 (v2.28)
Single-nucleus RNA-seq (Illumina) data were processed using Cell Ranger (v8.0.1) with GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome.
Long-read single-nucleus reads were first demultiplexed using BLAZE (v2.5). The resulting FASTQ files were processed using the FLAMES (v2.0.1) single-cell pipeline, configured to use GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome. Further configurations included skipping novel transcript identification, and the use of Oarfish (v0.6.2) for transcript-level quantification.
Supplementary files format and content:
Count matrix prefix:  ill_sn – single-nucleus. Each matrix is stored in the standard three-file format: <prefix>_barcodes.tsv.gz | <prefix>_features.tsv.gz | <prefix>_matrix.mtx.gz
Count matrices from long-read protocols (ont, pb) are structured as follows:
Gene-level counts: genes_count_matrix.tsv.gz
•       Transcript-level counts: stored across three files which is similar to cellranger output:
•       _barcodes.tsv.gz
•       _features.tsv.gz
•       _matrix.mtx.gz

value: Epithelial

tag: Sex

value: pooled male and female

value: Lung Cancer


title: TAR4/4;RAD23ASCR bio rep 10

value: scramble ASOs


title: TAR4/4;RAD23ASCR bio rep 9


title: Illumina Bulk RNA-Seq of lung cancer cell line H211 (SCLC-P)

description: Library name: H211_Bulk_Illumina

data_processing:
Assembly: GRCh38
ONT datasets were basecalled with Dorado using rna004_130bps_sup@v5.1.0 for direct RNA and dna_r10.4.1_e8.2_400bps_sup@v5.0.0 for the cDNA datasets. Reads with mean quality scores <10 were discarded.
Reads were mapped to the reference genome GRCh38 and GENCODE v44 transcriptome using minimap2 (v2.28)
Transcript-level quantification was performed using Salmon (v1.10.2) for short-read datasets and Oarfish (v0.6.2) for long-read datasets, based on the GENCODE v44 transcriptome combined with spike-in sequences from SIRV Set 4 and Sequins.
•       Salmon uses an internal quasi-mapping approach.
•       Long-read datasets were first aligned to the transcriptome using minimap2 (v2.28), followed by quantification with Oarfish.
Supplementary files format and content:
Bulk RNA-seq count matrices follow the naming convention: <protocol>_bulk_<cell line>_matrix.tsv
Where <protocol> is one of:
•       dRNA – ONT direct RNA sequencing
•       ont – ONT PCR cDNA sequencing
•       pb – PacBio Kinnex
•       ill – Illumina

value: Female


title: Illumina Bulk RNA-Seq of lung cancer cell line H526 (SCLC-P)

description: Library name: H526_Bulk_Illumina

value: Male


title: Illumina Bulk RNA-Seq of lung cancer cell line SHP77 (SCLC-A)

description: Library name: SHP77_Bulk_Illumina


title: TAR4/4;RAD23ASCR bio rep 8


title: 24-hour, direct, PAN-treated, rep3


title: Illumina Bulk RNA-Seq of lung cancer cell line H69 (SCLC-A)

description: Library name: H69_Bulk_Illumina


title: 24-hour, direct, PAN-treated, rep2


title: Illumina Bulk RNA-Seq of lung cancer cell line H146 (SCLC-A)

description: Library name: H146_Bulk_Illumina


title: Illumina Bulk RNA-Seq of lung cancer cell line H2228 (LUAD)

description: Library name: H2228_Bulk_Illumina


title: graft monocytes3

description: Library name: BBMT1_gMONO3

value: WT

value: batch 2


title: TAR4/4;RAD23ASCR bio rep 7


title: Illumina Bulk RNA-Seq of lung cancer cell line HCC827 (LUAD)

description: Library name: HCC827_Bulk_Illumina


title: Illumina Bulk RNA-Seq of lung cancer cell line H1975 (LUAD)

description: Library name: H1975_Bulk_Illumina


title: TAR4/4;RAD23ASCR bio rep 6


title: J-Lat 8.4 cells, RBP4, rep3

city: Ulm

first: Konstantin

middle: MJ

last: Sparrer

address: Meyerhofstr. 1

department: Institute of Molecular Virology

institute: Ulm University Medical Center

description:
Library name: 8.4 RBP4 N=3
Column name in Non-NormalizedCounts-AllSamples.txt : RBP4_8.4_3

data_processing:
The proviral HIV-1 sequence from J-Lat10.6 (GenBank: MN989412.1) was added as a separate chromosome to hg38. Reads were quality checked with fastqc-0.11.8. (Andrews, 2010) mapped using STAR-2.7.9 aligner to this artificial genome (Dobin et al., 2013) and counted with featureCounts (subread-2.0.2) (Liao et al., 2013). Differential gene expression analysis was performed with DESeq2 (v1.42.1) (Love et al., 2014).
Enrichment analysis searching the MSigDB Hallmark database (Liberzon et al., 2015) was performed using enrichR (v 3.4)(Chen et al., 2013).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes not-normalized counts for each sample

source_name: J-Lat 8.4

growth_protocol: Jlat 10.6 and 8.4 HIV reporter cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using QuickRNA Miniprep kit (Zymo). 1000 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using sparQ RNA-Seq HMR Kit (QuantaBio) with sparQ PureMag Beads (QuantaBio) and sparQ UDI Adapters (QuantaBio) following manufacturer's protocols.

treatment_protocol: Cells were treated with 100 µg/mL of RBP4 or left untreated for 48 hours.

value: J-Lat 8.4

value: T acute lymphoblastic leukemia cells

tag: genetic modification

value: Jurkat latently infected with HIV-1 strain R7/E-/GFP


title: 24-hour, direct, untreated, rep4

value: kidney

value: podocyte

value: untreated


title: TAR4/4;RAD23ASCR bio rep 5

value: motor cortex


title: TAR4/4;RAD23ASCR bio rep 4


title: J-Lat 8.4 cells, RBP4, rep2

description:
Library name: 8.4 RBP4 N=2
Column name in Non-NormalizedCounts-AllSamples.txt : RBP4_8.4_2


title: 24-hour, direct, untreated, rep3


title: J-Lat 8.4 cells, RBP4, rep1

description:
Library name: 8.4 RBP4 N=1
Column name in Non-NormalizedCounts-AllSamples.txt : RBP4_8.4_1


title: Illumina scRNA-Seq of lung cancer cell line mixture

description: Library name: Single_cell_Illumina

data_processing:
Assembly: GRCh38
ONT datasets were basecalled with Dorado using the dna_r10.4.1_e8.2_400bps_sup@v5.0.0 model. Reads with mean quality scores <10 were discarded.
Reads were mapped to the reference genome GRCh38 and GENCODE v44 transcriptome using minimap2 (v2.28)
Single-cell RNA-seq (Illumina) data were processed using Cell Ranger (v8.0.1) with GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome.
Long-read single-cell reads were first demultiplexed using BLAZE (v2.5). The resulting FASTQ files were processed using the FLAMES (v2.0.1) single-cell pipeline, configured to use GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome. Further configurations included skipping novel transcript identification, and the use of Oarfish (v0.6.2) for transcript-level quantification.
Supplementary files format and content:
Count matrix prefix:  ill_sn – single-nucleus. Each matrix is stored in the standard three-file format: <prefix>_barcodes.tsv.gz | <prefix>_features.tsv.gz | <prefix>_matrix.mtx.gz
Count matrices from long-read protocols (ont, pb) are structured as follows:
Gene-level counts: genes_count_matrix.tsv.gz
•       Transcript-level counts: stored across three files which is similar to cellranger output:
•       _barcodes.tsv.gz
•       _features.tsv.gz
•       _matrix.mtx.gz


title: 24-hour, direct, PAN-treated, rep4

value: PAN


title: J-Lat 8.4 cells, control, rep3

description:
Library name: 8.4 UT N=3
Column name in Non-NormalizedCounts-AllSamples.txt : UT_8.4_3

value: control


title: J-Lat 8.4 cells, control, rep2

description:
Library name: 8.4 UT N=2
Column name in Non-NormalizedCounts-AllSamples.txt : UT_8.4_2


title: TAR4/4;RAD23ASCR bio rep 3


title: TAR4/4;RAD23ASCR bio rep 2


title: J-Lat 10.6 cells, RBP4, rep3

description:
Library name: 10.6 RBP4 N=3
Column name in Non-NormalizedCounts-AllSamples.txt : RBP4_10.6_3


title: 24-hour, direct, untreated, rep1


title: J-Lat 10.6 cells, RBP4, rep2

description:
Library name: 10.6 RBP4 N=2
Column name in Non-NormalizedCounts-AllSamples.txt : RBP4_10.6_2


title: J-Lat 8.4 cells, control, rep1

description:
Library name: 8.4 UT N=1
Column name in Non-NormalizedCounts-AllSamples.txt : UT_8.4_1


title: J-Lat 10.6 cells, RBP4, rep1

description:
Library name: 10.6 RBP4 N=1
Column name in Non-NormalizedCounts-AllSamples.txt : RBP4_10.6_1


title: TAR4/4;RAD23ASCR bio rep 1


title: 24-hour, direct, untreated, rep5


title: 24-hour, direct, PAN-treated, rep1


title: WT/WT;RAD23AKD bio rep 10

value: WT/WT

value: Rad23a KD ASOs


title: J-Lat 10.6 cells, control, rep3

description:
Library name: 10.6 UT N=3
Column name in Non-NormalizedCounts-AllSamples.txt : UT_10.6_3


title: J-Lat 10.6 cells, control, rep1

description:
Library name: 10.6 UT N=1
Column name in Non-NormalizedCounts-AllSamples.txt : UT_10.6_1


title: T47D CM S17

city: Turku

first: Sirpa

last: Jalkanen

address: Tykistökatu 6a

department: Medical Microbiology and Immunology

country: Finland

institute: Univeristy of Turku

description:
Read length 2x50bp
200004_16_HLEC_T47D

data_processing:
The raw sequencing data was uploaded to the BaseSpace Sequence Hub (Illumina) as fastq files for further analysis. The quality control was performed using the FastQC application of BaseSpace and subsequently, the sequences were aligned against the human reference genome hg19 (UCSC, RefSeq gene annotation) with the RNA-Seq Alignment application, which uses the STAR aligner for read mapping and salmon for quantification of reference genes and transcripts. The differences in gene expression between the samples were identified with the RNA-Seq Differential Expression application using DESeq2. The genes exhibiting a fold change (FC) >2 (log2ratio ≥1 and ≤-1) and q-values (FDR) < 0.05 were selected as differentially expressed genes (DEG)
Assembly: hg19
Supplementary files format and content: Excel file with normalized abundance measurements

extract_protocol:
RNA was extracted with the NucleoSpin RNA kit (Macherey-Nagel), 300ng were used for library preparation
TruSeq® Stranded mRNA Sample Preparation, Illumina (15031047)

value: Human Lymphatic Endothelial Cells


title: J-Lat 10.6 cells, control, rep2

description:
Library name: 10.6 UT N=2
Column name in Non-NormalizedCounts-AllSamples.txt : UT_10.6_2


title: Senescent cells, GNF7 treated 24 hrs, biol rep 3

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: Fermin Caballero 56, 3D

country: Spain

institute: CNIO

description: Library name: HT-S-C1-24-3

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq (v2.20.0.422) program.
STAR (2.7.9a) was used to index the human genome (Homo sapiens, GRCh38) obtained from Ensembl and then map the fastq files.
featureCounts (v1.5.1) was used to count mapped reads in annotated exons using gene annotations from Ensembl (Homo_sapiens.GRCh38.101.gtf).
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file that contains Ensembl gene IDs and the gene raw counts, one column for each sample.

growth_protocol: HT-1080 cells were grown in DMEM supplemented with 10% tet-free serum and 1% Penicilin-Streptomycin, at 37C with 5% oxygen and 5% carbon dioxide

extract_protocol:
RNA was extracted from a cell pellet using a Purelink RNA Mini Kit (Invitrogen #12183025) following manufacturer’s instructions
Illumina stranded mRNA prep ligation sample preparation protocol was used with a starting concentration of total RNA between 25-1000 ng

treatment_protocol: Human fibrosarcoma cancer cell line HT-1080 was treated for 6 or 24 hours with the compound (GNF7) or a vehicle control (DMSO).

value: human fibrosarcoma cells

value: senescent


title: Senescent cells, GNF7 treated 24 hrs, biol rep 2

description: Library name: HT-S-C1-24-2


title: T47D CM S15

description:
Read length 2x50bp
200004_15_HLEC_T47D


title: T47D CM S12

description:
Read length 2x50bp
200004_14_HLEC_T47D


title: Senescent cells, DMSO treated 24 hrs, biol rep 3

description: Library name: HT-S-NT-24-3


title: Senescent cells, GNF7 treated 24 hrs, biol rep 1

description: Library name: HT-S-C1-24-1


title: FC sorted donor monocytes at 2yrs post-BMT1

description: Library name: BBMT1_2YgMONO1

value: Peripheral blood

value: PB monocytes


title: T47D CM S10

description:
Read length 2x50bp
200004_13_HLEC_T47D


title: WT/WT;RAD23AKD bio rep 9


title: WT/WT;RAD23AKD bio rep 8


title: Senescent cells, DMSO treated 24 hrs, biol rep 2

description: Library name: HT-S-NT-24-2


title: MDA-MB-231 CM S8

description:
Read length 2x50bp
200004_12_HLEC_MDAMB


title: Senescent cells, DMSO treated 24 hrs, biol rep 1

description: Library name: HT-S-NT-24-1


title: 24-hour, direct, untreated, rep2


title: WT/WT;RAD23AKD bio rep 7


title: Senescent cells, GNF7 treated 6 hrs, biol rep 3

description: Library name: HT-S-C1-6-3

value: 6 h


title: Senescent cells, GNF7 treated 6 hrs, biol rep 1

description: Library name: HT-S-C1-6-1


title: WT/WT;RAD23AKD bio rep 5


title: Senescent cells, DMSO treated, biol rep 3

description: Library name: HT-S-NT-6-3


title: MDA-MB-231 CM S4

description:
Read length 2x50bp
200004_10_HLEC_MDAMB


title: WT/WT;RAD23AKD bio rep 6


title: WT/WT;RAD23AKD bio rep 4


title: Senescent cells, DMSO treated, biol rep 2

description: Library name: HT-S-NT-6-2


title: Senescent cells, DMSO treated, biol rep 1

description: Library name: HT-S-NT-6-1


title: Cycling cells, DMSO treated, biol rep 2

description: Library name: HT-P-NT-2

value: cycling


title: MCF-7 CM S16

description:
Read length 2x50bp
200004_8_HLEC_MCF7


title: Cycling cells, DMSO treated, biol rep 1

description: Library name: HT-P-NT-1


title: MCF-7 CM S14

description:
Read length 2x50bp
200004_7_HLEC_MCF7


title: MDA-MB-231 CM S2

description:
Read length 2x50bp
200004_9_HLEC_MDAMB