title: DrogA rep 3

first: Tung

last: Le

address: Colney Lane

institute: John Innes Centre

description: Library name: EJB6

data_processing:
All data processing was done in the Galaxy platform.
Sequencing reads were checked for quality using FastQC.
Reads were then mapped to the NA1000 reference genome using Hisat2
Mapped reads were assigned to gene IDs using htseq-count
Assembly: Caulobacter crescentus NA1000 reference genome (NC_011916.1)
Supplementary files format and content: Tab-delimited text files containg raw read counts generated by htseq-count. One per sample

source_name: bacterial cell

extract_protocol:
Genomic DNA was isolated from bacteria using a standard protocol (cell lysis, protein precipitation and DNA purification by isopropanol precipitation)
Purified genomic DNA was sheared into 200-500 bp fragments and libraries were constructed for Illumina sequencing by PCR amplification using a universal P5-ME primer annealing to the transposon and a specific index primer annealing to adaptor-ligated sheared DNA fragments.

value: bacterial cell

value: DrogA


title: SON_deltaC-term_siSON_rep1

status: Public on Feb 25 2026

type: SRA

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

description: Library name: FeSHn468_siSON_rep1

library_source: transcriptomic

data_processing:
Base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: RPKM normalized RNA-seq coverage in bigWig format

molecule: polyA RNA

organism: Homo sapiens

source_name: Flp-In T-Rex HEK293

extract_protocol:
Total RNA was extracted from cells with Quick-RNA MicroPrep kit (Zymo) after fractionation. Polyadenylated RNA was then isolated using Dynabeads™ mRNA Purification Kit. Purification was done twice to increase purity.
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit (Roche)

tag: cell line

value: Flp-In T-Rex HEK293

tag: genotype

tag: treatment

value: siRNA against SON


title: DrogA rep 2

city: Norwich

department: Molecular Microbiology

country: United Kingdom

description: Library name: EJB5

library_source: genomic

molecule: genomic DNA

organism: Caulobacter vibrioides

tag: strain

tag: cell type


title: SON_full-length_siSON_rep3

description: Library name: FeSHn467_siSON_rep3


title: DrogA rep 1

description: Library name: EJB4


title: Wildtype rep 3

description: Library name: EJB3

value: Wildtype


title: Wildtype rep 2

description: Library name: EJB2


title: Sample_45_Gran9 ,DI4D_Control IgG

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

description: Library name: Sample_45_Gran9

data_processing:
bcl2fastq software (Illumina inc.)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trimmomatic, then mapped to genome Mmul_10 version using STAR
Assembly: Mmul_10
Supplementary files format and content: tab-delimited text files include counts values for each Sample and Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Macaca mulatta

source_name: granuloma

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (50) (cat# 74134) according to the manufacturers’ recommendation (QIAGEN).
The library preparation was done using the QIAseq RNA Library Kit (QIAGEN). A total of 5ul total RNA was converted into RNA NGS libraries. Adapters containing UMIs were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR, the samples were purified. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent).

tag: tissue

value: granuloma

value: Control IgG

tag: Sex

value: M

tag: infection

value: Mtb infected

tag: batch


title: Wildtype rep 1

description: Library name: EJB1


title: SON_full-length_siSON_rep2

description: Library name: FeSHn467_siSON_rep2


title: Sample_44_Gran8 ,DI4D_Control IgG

description: Library name: Sample_44_Gran8


title: AAV2_Ola_Rep2

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

country: USA

institute: University of Wisconsin

description: Library name: AAV2 Olaparib V3C-seq Replicate 2

data_processing:
Reads were aligned to the human hg38 genome using Minimap2.
Aligned V3C-seq samples were sorted using Samtools, and the resulting aligned and sorted Bam files were converted to Bedgraph files using BEDtools.
Regions that were shared between independent biological replicates of these experiments were determined using BEDtools.
Mapped reads were partitioned into bins corresponding to HindIII restriction fragments across the human genome, such that each read was allocated to the fragment defined by its genomic position. Based on this, the top 150 HindIII fragments that had the highest number of reads were sorted from each experimental condition in the intersected datafile between 2 independent biological replicates.
Assembly: Human hg38
Supplementary files format and content: bedgraph

source_name: Kidney

growth_protocol: Female Human Embryonic Kidney (HEK293T) cells were maintained in Dulbecco’s Modified Eagle’s Medium [DMEM, high glucose (Gibco)] supplemented with 5% Serum Plus (Sigma‑Aldrich) and 50 µg/mL gentamicin (Gibco). The cells were cultured at 37 °C in 5% CO₂ incubators. wtAAV2 infection was carried out at a Multiplicity of infection (MOI) of 5000 and cells were harvested at 24 hours. Samples were processed for Chromosome Conformation Capture (V3C-seq) assays.

extract_protocol:
For Viral Chromosome Conformation Capture assay, wtAAV2-infected cells at 24 hpi were crosslinked with 1% formaldehyde for 10 minutes, quenched with 0.125 M glycine, lysed in NP-40 lysis buffer for 10 minutes on ice, before resuspending the nuclei in restriction enzyme buffer (Buffer 2.1). Samples were permeabilized in 0.3% SDS for 1 hour on a 37 degree C shaker, sequestered in 2% Triton X-100 for 1 hour on a 37 degree C shaker. Pellet was resuspended in restriction enzyme buffer (Buffer 2.1) and digested overnight in 400 U of HindIII enzyme. Digestion was continued for 4 more hours next day with 300 U more HindIII enzyme. The restriction enzyme was inactivated with SDS and heat for 20 mins, and samples were subjected to intramolecular ligation with T4 DNA Ligase at room temperature for 4 hours. Samples were then reverse-crosslinked and purified before digestion with the secondary restriction enzyme NlaIII (NEB). NlaIII was heat-inactivated, samples were purified using phenol: chloroform, and circularized using T4 DNA Ligase. Samples were purified using a PCR Purification Kit (Qiagen), and equivalent amounts of DNA was used to perform inverse PCR with primers complementary to the wtAAV2 genome. Samples were purified using a PCR Purification Kit (Qiagen), and equivalent amounts of DNA was used to perform inverse PCR with primers complementary to the AAV2 genome. Inverse PCR samples were diluted 1:100 in TE, before being used as templates for nested-inverse PCR reactions. 6 independent nested-inverse PCR reactions were pooled and submitted for library preparation and high-throughput sequencing. Libraries were prepared from 1 microgram of DNA using NEBNext Ultra II DNA Library Prep Kit and sequenced using single-end sequencing on an Illumina NextSeq platform spiked with 25% phiX spike-in to increase library complexity.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (cat # E7645L) according to the manufacturer's instructions. Six samples were pooled per run and samples were analyzed by 75 bp paired-end sequencing on the NextSeq 500 (Illumina).

treatment_protocol: HEK293T cells were seeded at 5*10^6 in DMEM, high glucose (Gibco), supplemented with 5% Serum Plus (Sigma‑Aldrich) and 50 µg/mL gentamicin (Gibco) for 24 hours. Cells were infected with wtAAV2, wtAAV∆KLF4 at an MOI of 5000 or treated with pan-PARP1/2 inhibitor Olaparib (AZD2281; Selleck Chemicals S1060), applied at a concentration of 1 µM concurrently with virus inoculum.

value: Kidney

value: HEK 293

value: Human Embryonic Kidney

value: Olaparib


title: AAV2_Ola_Rep1

description: Library name: AAV2 Olaparib V3C-seq Replicate 1


title: AAV2_KLF4_Rep2

description: Library name: AAV2 Delta KLF4 V3C-seq Replicate 2


title: SON_C-term-RSRP-NEG_siSON_rep2

description: Library name: FeSHn459_siSON_rep2


title: AAV2_KLF4_Rep1

description: Library name: AAV2 Delta KLF4 V3C-seq Replicate 1


title: Sample_85_Gran49 ,DI5T_rmIFNγR1-IgG

description: Library name: Sample_85_Gran49


title: SON_full-length_siSON_rep1

description: Library name: FeSHn467_siSON_rep1


title: SON_C-term-RSRP-NEG_siSON_rep1

description: Library name: FeSHn459_siSON_rep1


title: child/038-curette

city: Leiden

first: Simon

last: Jochems

address: P4-32, LUMC, Albinusdreef 2

country: Netherlands

institute: LUMC

description: Library name: 238-54

data_processing:
UMI deduplication as per https://github.com/CGATOxford/UMI-tools
alignment using STAR to ref genome
Assembly: GRCh38.p13
Supplementary files format and content: text file including raw counts after UMI deduplication for each sample

source_name: primary cells

growth_protocol: cells were directly analysed ex vivo

extract_protocol:
Split RNA extraction kit was used as per manufacturer protocols. RNA quantity was checked with Qubit
QuantSeq fwd library prep (Lexogen)

treatment_protocol: cells were frozen in RNAprotect ex vivo and thawed followed by extraction

value: nasal

value: nasal cells

tag: developmental stage

value: child


title: Sample_40_Gran4 ,DI4D_Control IgG

description: Library name: Sample_40_Gran4


title: Sample_41_Gran5 ,DI4D_Control IgG

description: Library name: Sample_41_Gran5


title: Sample_42_Gran6 ,DI4D_Control IgG

description: Library name: Sample_42_Gran6


title: Sample_46_Gran10 ,DI4D_Control IgG

description: Library name: Sample_46_Gran10


title: SON_C-term-RSRP-NEG_siSON_rep3

description: Library name: FeSHn459_siSON_rep3


title: SON_C-term-RSRP_siSON_rep2

description: Library name: FeSHn458_siSON_rep2


title: child/037-NPS

description: Library name: 238-52


title: SON_C-term-RSRP_siSON_rep1

description: Library name: FeSHn458_siSON_rep1


title: TF-AA mutation, STAT3,rep1

city: Guangzhou

first: Chao

last: Wei

address: No.74 Zhongshan Rd.2

country: China

institute: Sun Yat-Sen University

description: Library name: Sample 13

data_processing:
The Fastq data underwent quality checking using trim_galore
subsequent alignment of paired-end reads to the MM9 reference genome was performed using STAR
Gene-specific read counts were generated using Htseq-count
Assembly: mm9
Supplementary files format and content: tab-delimited txt and bigwig files
Supplementary files format and content: tab-delimited txt and bigwig files

organism: Mus musculus

source_name: embryonic stem cell

growth_protocol: ESCs were cultured in ESC medium containing DMEM (Hyclone), 15% (v/v) fetal bovine serum (FBS, Hyclone), 0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), 1% (v/v) nucleoside mix (Sigma), 1000 U/mL recombinant LIF (Millipore) in 37 C, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent
RNA library for RNA-seq was performed according the manufacture's protocol

treatment_protocol: Mouse Rybp-floxed ESCs (Rybp+/+) were cultured in ESC medium, RYBP-depleted ESCs (Rybp-/-) were generated by supplementing the medium with 5 μM 4-hydroxytamoxifen (4-OHT, Sigma) for 4 days.

value: embryonic stem cell

value: TF-AA mutation


title: siSLC16A1-AS1, replicate 2

city: Wenzhou

first: wenjing

last: zhao

address: Central North Road

institute: wenzhou medical university

description:
Library name: siSLC16A1-AS1_2
s_1_1

data_processing:
Raw sequencing data quality control was performed, and adapters were trimmed. Duplicate gene reads with extremely low counts were filtered out.
Assembly: GRCh38/hg38
Supplementary files format and content: TXT files contain normalized expression matrices; XLSX files contain differential expression results, GO analysis, and KEGG pathway analysis results.

source_name: AGS

growth_protocol: AGS gastric cancer cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted from AGS-siNC and AGS-siSLC16A1-AS1 cells using TRIzol reagent following the standard protocol. RNA quality was assessed using Agilent 2100 Bioanalyzer.
RNA-seq libraries were constructed using the NEBNext Ultra RNA Library Prep Kit following manufacturer's instructions. PolyA-selected mRNA was used for library preparation.

treatment_protocol: Cells were transfected with siSLC16A1-AS1 or siNC (negative control) using Lipofectamine 3000 according to manufacturer's instructions. Cells were harvested 48 hours post-transfection for RNA extraction.

value: AGS

value: gastric adenocarcinoma cells

value: SLC16A1-AS2 knockdown cells


title: Sample_37_Gran1 ,DI4D_Control IgG

description: Library name: Sample_37_Gran1


title: siSLC16A1-AS1, replicate 1

description:
Library name: siSLC16A1-AS1_1
s_1

value: SLC16A1-AS1 knockdown cells


title: child/044-curette

description: Library name: 238-56


title: child/044-NPS

description: Library name: 238-50


title: Sample_38_Gran2 ,DI4D_Control IgG

description: Library name: Sample_38_Gran2

value: granuloma


title: child/026-curette

description: Library name: 238-55


title: AAV2_Rep2

description: Library name: AAV2 V3C-seq Replicate 2


title: AAV2_Rep1

description: Library name: AAV2 V3C-seq Replicate 1


title: siSLC16A1-AS1, replicate 3

description:
Library name: siSLC16A1-AS1_3
s_1_2

value: SLC16A1-AS3 knockdown cells


title: SON_C-term-only_siSON_rep2

description: Library name: FeSHn456_siSON_rep2

value: Flp-In T-Rex HEK293

value: siRNA against SON


title: Uncomplicated_MalariaSample_6

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: Labeled cRNA samples were fragmented at 60°C and hybridized onto an Agilent Custom Plasmodium falciparum Gene Expression Microarray 8X60K using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404)

scan_protocol: The hybridized slides were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method .

organism: Plasmodium falciparum

source_name: Total RNA, Control Sample 6

label_protocol: Samples were labeled using an Agilent Quick-Amp labeling Kit (p/n5190-0442). Total RNA was reverse transcribed at 40°C using an oligo dT primer tagged to a T7 polymerase promoter and converted to double-stranded cDNA. Synthesized double-stranded cDNA was used as the template for cRNA generation. cRNA was generated by in vitro transcription, and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C.

growth_protocol: Clinical samples collected from malaria patients

extract_protocol: RNA from enriched blood was isolated using TRIzol as per manufacture's protocols.

treatment_protocol: Total RNA was extracted from venous blood samples collected from malaria patients. The patients exhibited symptoms categorized as un-complicated (n =6), hepatic dysfunction (n=12), cerebral malaria (n=4) and thrombocytopenia (n=6).

value: Enriched blood sample

tag: clinical complication

value: Uncomplicated Malaria


title: SON_C-term-RSRP_siSON_rep3

description: Library name: FeSHn458_siSON_rep3


title: child/028-NPS

description: Library name: 238-53


title: SAM, 26DAS, bulk RNA-seq, Rep2

city: Shenzhen

first: liang

last: dong

address: No. 66, Gongchang Road, Guangming District, Shenzhen

description: Library name: 26DAS rep2

data_processing:
For bulk RNA-seq, raw sequencing data quality was assessed using Trimmomatic (v.0.33) with parameters “LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:20”. Clean reads underwent alignment to the B73 AGPv4 reference genome via HISAT2 under default settings. Uniquely mapped reads were extracted using SAMtools (v.1.9)  with filtering criteria “rmdup and mapq > 10”. For tsCUT&Tag and ATAC-seq, raw sequencing data quality control was performed using Trimmomatic with parameters “LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:20”. Clean tsCUT&Tag and ATAC-seq reads were mapped to the maize genome (B73 AGPv4) via bowtie2. Post-alignment processing involved removing PCR duplicates and low-quality reads (mapping quality < 10) using samtools. For bulk RNA-seq, clean UMI data were aligned to the maize genome using STAR mapping with customized parameters to derive UMI counts per sample. All scRNA-seq preprocessing was executed in Seurat (v.4.3.0). Cellular metrics including detected total genes (nFeature_RNA), molecules (nCount_RNA), and mitochondrial/chloroplast genome mapping percentages (percent.mt/percent.pt) were quantified per sample. Quality control applied sequential filters: cells retaining 1,800-10,000 expressed genes and 2,800-50,000 UMIs; genes detected in at least 3 cells; exclusion of cells with percent. mt or percent.pt ≥ 10%; and doublet removal via DoubletFinder (v.2.0.3).
Assembly: B73 RefGen_v4
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: matrix files

organism: Zea mays

source_name: 26DAS SAM

extract_protocol:
For bulk RNA-seq, SAM samples at 14, 16, 18, 22, 26, and 28 DAS were flash-frozen with liquid nitrogen immediately after collection. Total RNA was extracted using the Direct-zol RNA Microprep Kit (Zymo Research). For ATAC-seq, approximately 25 freshly dissected SAMs were digested in 15 μl protoplast lysis buffer at the bottom of 1.5 ml tube for 2 h at room temperature in the dark with gentle shaking. For scRNA-seq, approximately ~300 SAMs with two youngest leaf primordia were dissected and enzymatically digested in 50 μl protoplast lysis buffer at the bottom of 2 ml tube for 2 h at room temperature in the dark with gentle shaking to release protoplasts. After digestion, the reaction was stopped by dilution using 1.5 ml protoplast washing buffer (lysis buffer without enzyme) and filtered through 30-μm strainers to remove debris and large aggregates. The filtrate was then centrifuged at 300 g for 3 min at room temperature to collect protoplasts. Pellets were gently resuspended and washed twice with protoplast washing buffer under the same centrifugation conditions. After washing, a final filtration step was performed to remove cell aggregates and obtained a suspension of single, dissociated cells. Cell concentration and viability were assessed by fluorescein diacetate (FDA) staining using a hemocytometer. Only samples with ≥ 75% viable cells were used.
For bulk RNA-seq, sequencing libraries were constructed with the MGIEasy RNA Library Prep Kit according to the manufacturer’s instructions. Nuclei were released by adding 1 ml release buffer (1 × PBS, 1 × protease inhibitor, 0.3% Triton X-100) and gentle pipetting. For ATAC-seq, nuclei were then collected by centrifugation and resuspended in 20 μl 1 × TTBL buffer (Vazyme, TD501). Nuclei integrity and concentration were assessed by DAPI staining. Approximately 5,000 nuclei were subjected to Tn5 transposition (Vazyme, TD501) in the presence of 0.3% Triton X-100 at 37 °C for 30 min. Transposed DNA was immediately purified using Qiagen MinElute kits and amplified for 10-13 PCR cycles according to the manufacturer’s instructions (VAHTS, TD501). Amplified DNA was size-selected using KAPA DNA Clean Beads (150-650 bp) to generate the final library, which was sequenced on an Illumina HiSeq X Ten platform (paired-end, 2 × 150 bp). For  tsCUT&Tag, full-length coding sequences of ZmMADS69 and ZmRap2.7 were cloned into the PM999-GFP vector, and plasmids were purified to transfection grade. Protoplasts were prepared from etiolated B73 seedlings grown in the dark and transfected with the GFP-tagged constructs using PEG-mediated transformation. After overnight incubation, protoplasts were processed using the Hyperactive In-Situ ChIP Library Prep Kit (Vazyme, Nanjing, China) according to the manufacturer’s instructions. Chromatin was immunoprecipitated with anti-GFP antibody (1:100 dilution), and tagmented DNA fragments were PCR-amplified and size-selected to generate sequencing libraries. Libraries were subjected to paired-end sequencing (2 × 150 bp) on an Illumina NovaSeq 6000 platform. For scRNA-seq, approximately 15,000 protoplasts were loaded into the BD Rhapsody™ Single-Cell Capture system (BD Biosciences) for scRNA-seq library construction according to the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads.

value: 26DAS SAM


title: child/028-curette

description: Library name: 238-48


title: WT_siSON_rep3

description: Library name: WT_siSON_rep3

value: wt


title: SAM, 26DAS, bulk RNA-seq, Rep1

description: Library name: 26DAS rep1


title: child/045-NPS

description: Library name: 238-51

value: nasal


title: child/037-curette

description: Library name: 238-47

value: nasal cells


title: Adjacent normal tissue, patient 255, RNA-Seq

description: Library name: 255N.mock

data_processing:
Raw reads were quality controlled with Q30 threshold and adapters were trimmed using cutadapt (v1.9.3).
MeRIP-Seq reads were aligned using STAR (v2.5.1b), m5C peaks called using MACS2 (v2.2.7.1).
Differential expression analysis performed using edgeR (v3.16.5), GO and KEGG enrichment analysis conducted for differentially expressed genes.
Assembly: GRCh37/hg19
Supplementary files format and content: BED files contain m5C peak locations; TXT files contain raw gene counts; XLSX files contain differential expression results and clinical metadata.

source_name: RNA-Seq of adjacent normal tissue

extract_protocol:
Total RNA was extracted from gastric cancer tissues and adjacent normal tissues using TRIzol reagent (Invitrogen) following the manufacturer's protocol. RNA quality was assessed by Agilent 2100 Bioanalyzer with RIN >7.0 for all samples.
RNA was fragmented and immunoprecipitated with anti-m5C antibody, then library construction was performed using KAPA HyperPrep Kit.

value: stomach


title: SON_C-term-only_siSON_rep3

description: Library name: FeSHn456_siSON_rep3


title: siNC control, replicate 3

description:
Library name: siNC_3
s_NC_2

value: Control cells with non-targeting siRNA


title: SAM, 22DAS, bulk RNA-seq, Rep2

description: Library name: 22DAS rep2

source_name: 22DAS SAM

value: 22DAS SAM


title: SAM, 28DAS, bulk RNA-seq, Rep2

description: Library name: 28DAS rep2

source_name: 28DAS SAM

value: 28DAS SAM


title: SAM, 28DAS, bulk RNA-seq, Rep1

description: Library name: 28DAS rep1


title: siNC control, replicate 2

description:
Library name: siNC_2
s_NC_1

value: AGS

value: gastric adenocarcinoma cells


title: SON_C-term-only_siSON_rep1

description: Library name: FeSHn456_siSON_rep1


title: siNC control, replicate 1

description:
Library name: siNC_1
s_NC


title: WT_siMOCK_rep3

description: Library name: WT_siMOCK_rep3

value: control


title: child/024-NPS

description: Library name: 238-60

value: child


title: Adjacent normal tissue, patient 260, RNA-Seq

description: Library name: 260N.mock


title: SAM, 18DAS, bulk RNA-seq, Rep2

description: Library name: 18DAS rep2

source_name: 18DAS SAM

value: 18DAS SAM


title: WT_siSON_rep2

description: Library name: WT_siSON_rep2

value: Flp-In T-Rex HEK293


title: child/025-curette

description: Library name: 238-46


title: Gastric cancer tissue, patient 255, RNA-Seq

description: Library name: 255C.mock

source_name: RNA-Seq of cancer tissue


title: SAM, 16DAS, bulk RNA-seq, Rep2

description: Library name: 16DAS rep2

source_name: 16DAS SAM

value: 16DAS SAM


title: child/027-curette

description: Library name: 238-12


title: SAM, 22DAS, bulk RNA-seq, Rep1

description: Library name: 22DAS rep1


title: Gastric cancer tissue, patient 260, RNA-Seq

description: Library name: 260C.mock


title: Adjacent normal tissue, patient 260, MeRIP-Seq

description: Library name: 260N.m5c

data_processing:
Raw reads were quality controlled with Q30 threshold and adapters were trimmed using cutadapt (v1.9.3).
MeRIP-Seq reads were aligned using STAR (v2.5.1b), m5C peaks called using MACS2 (v2.2.7.1).
Differential expression analysis performed using edgeR (v3.16.5), GO and KEGG enrichment analysis conducted for differentially expressed genes.
Assembly: GRCh37/hg19
Supplementary files format and content: BED files contain m5C peak locations; TXT files contain raw gene counts; XLSX files contain differential expression results and clinical metadata.
Library strategy: MeRIP-Seq

source_name: MeRIP-Seq of adjacent normal tissue


title: SAM, 16DAS, bulk RNA-seq, Rep1

description: Library name: 16DAS rep1


title: WT_siSON_rep1

description: Library name: WT_siSON_rep1

value: siRNA against SON


title: child/018-NPC

description: Library name: 238-59


title: Sample_43_Gran7 ,DI4D_Control IgG

description: Library name: Sample_43_Gran7

value: granuloma

value: Control IgG

value: M

value: Mtb infected


title: Gastric cancer tissue, patient 248, RNA-Seq

description: Library name: 248C.mock


title: HCT116 cells, SON+SRRM2,4sU RNA rep1

description: Library name: HCT116_4sU_SON+SRRM2-depletion_rep1

library_source: other

data_processing:
base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: RPKM normalized RNA-seq coverage in bigWig format

molecule: other

extract_protocol:
After labeling, the RNA was extracted following NucleoSpin RNA kit (Macherey-Nagel). The biotinylated RNA was then purified by μMACS streptavidin MicroBeads (Miltenyi Biotec).
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit with RiboErase HMR protocol (Roche)

value: SON-HaloTag SRRM2-dTAG


title: WT_siMOCK_rep2

description: Library name: WT_siMOCK_rep2

value: wt


title: child/050-curette

description: Library name: 238-58

value: nasal

value: nasal cells


title: Adjacent normal tissue, patient 248, RNA-Seq

description: Library name: 248N.mock

value: stomach


title: child/045-curette

description: Library name: 238-57


title: HCT116 cells,SON,4sU RNA rep2

description: Library name: HCT116_4sU_SON-depletion_rep2


title: WT_siMOCK_rep1

description: Library name: WT_siMOCK_rep1


title: SAM, 18DAS, bulk RNA-seq, Rep1

description: Library name: 18DAS rep1


title: HCT116 cells, SON+SRRM2,4sU RNA rep2

description: Library name: HCT116_4sU_SON+SRRM2-depletion_rep2


title: HCT116 cells,SON,4sU RNA rep1

description: Library name: HCT116_4sU_SON-depletion_rep1


title: SAM, 14DAS, bulk RNA-seq, Rep2

description: Library name: 14DAS rep2

source_name: 14DAS SAM

value: 14DAS SAM


title: HCT116 cells,SRRM2,4sU RNA rep2

description: Library name: HCT116_4sU_SRRM2-depletion_rep2


title: Patient C08

city: Kyoto

first: Kohei

last: Hamada

address: 54 Shogoin Kawahara, Sakyo, Kyoto

department: Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

description: Library name: C08

data_processing:
Raw fastq files were trimmed using Trim-Galore, then mapped to the human reference genome (GRCh38) with the gene annotation of Ensemble GRCh38.v99 using STAR (v2.7.8a). Subsequently, gene expression levels were normalised as TPM or FPKM values using RSEM (v1.3.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes gene TPM values for each sample

source_name: Tumor

extract_protocol:
Tumor specimens were snap-frozen (frozen tumor samples) and total RNA was extracted
Libraries were prepared using the Illumina TruSeq RNA Access Library Kit (current name TruSeq RNA Exome) following the manufacturer’s instructions.

value: Tumor

tag: tissue type

value: clear cell carcinoma (CCC)

tag: age

tag: ps

tag: residual tumor

tag: figo stage

tag: site

value: Primary


title: child/047-curette

description: Library name: 238-42

value: child


title: QM-3

city: Beijing

first: ling

middle: ling

last: xu

address: Beimachang No 97

department: Department of Pharmacology

institute: Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute

description:
Library name: Sample 7
QM3_FPKM

data_processing:
Raw sequencing reads were filtered using Seqtk to remove adapter and low-quality sequences. Clean reads were aligned to the Mycobacterium tuberculosis reference genome using HISAT2 (version 2.0.4). The aligned fragments were assembled and quantified using StringTie (version 1.3.3b). Gene expression levels were normalized by the trimmed mean of M values (TMM) method. Differentially expressed genes (DEGs) were identified with edgeR software, using thresholds of |fold change| > 2 and false discovery rate (FDR) < 0.05.
Raw data generation and quality filtering
Read alignment (Genome mapping)
Gene-level quantification
Normalization and expression estimation
Assembly: Mycobacterium_tuberculosis_H37Rv (GCF_000195955.2)
Supplementary files format and content: the normalized gene expression matrice generated from RNA-seq analysis of Mycobacterium tuberculosis samples

organism: Mycobacterium tuberculosis H37Rv

source_name: mycobacterial culture

growth_protocol: M. tuberculosis H37Rv was cultured in 7H9 medium supplemented with OADC, glycerol, and Tween-80 at 37°C to mid-log phase.

extract_protocol:
Total RNA was extracted from Mycobacterium tuberculosis using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. RNA concentration and integrity were assessed using the Agilent 4200 Bioanalyzer before library construction.
RNA libraries were prepared following Illumina’s standard protocol using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme, China). The Agilent 4200 Bioanalyzer was used to evaluate the concentration and fragment size distribution of cDNA libraries. Qualified libraries were sequenced on an Illumina NovaSeq 6000 platform according to the manufacturer’s high-throughput sequencing procedure.

treatment_protocol: Cultures were treated with Questiomycin A (4MIC) for 6 h; controls DMSO. Cells were harvested and preserved for RNA extraction

value: mycobacterial culture

value: mycobacterial cell

value: wild type

value: QM(4 x MIC, 6 h)

value: batch 1


title: child/051-curette

description: Library name: 238-44


title: SAM, 14DAS, bulk RNA-seq, Rep1

description: Library name: 14DAS rep1


title: Patient C07

description: Library name: C07


title: child/018-curette

description: Library name: 238-45


title: Patient C04

description: Library name: C04


title: Patient C05

description: Library name: C05


title: child/051-NPS

description: Library name: 238-43


title: HCT116 cells,SRRM2,4sU RNA rep1

description: Library name: HCT116_4sU_SRRM2-depletion_rep1

tag: cell line


title: Patient C06

description: Library name: C06


title: QM-2

description:
Library name: Sample 6
QM2_FPKM

tag: genotype


title: child/047-NPS

description: Library name: 238-41


title: Patient C03

description: Library name: C03

value: Metastatic


title: Sample_39_Gran3 ,DI4D_Control IgG

description: Library name: Sample_39_Gran3

source_name: granuloma

value: granuloma

tag: treatment

value: Control IgG

value: M

value: Mtb infected


title: child/021-curette

description: Library name: 238-40

value: nasal

value: nasal cells


title: Patient C02

description: Library name: C02


title: child/049-NPS

description: Library name: 238-39


title: HCT116 cells, control,4sU RNA rep1

description: Library name: HCT116_4sU_control_rep1

value: SON-HaloTag SRRM2-dTAG

value: control


title: QM-1

description:
Library name: Sample 5
QM1_FPKM


title: DMSO-4

description:
Library name: Sample 4
DMSO4_FPKM

value: DMSO control


title: spike_in ChIP, clr4d, H3K9me2, heat-treatment 5 min, rep2

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

department: Department of Biological Sciences

institute: Graduate School of Science, The University of Tokyo

description: Library name: ChIP198

data_processing:
ChIP-seq reads were trimmed using Trimmomatic ver 0.33 with SE, LEADING:30, TRAILING:30, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome and A.thaliana TAIR10 genome (for spike_in ChIP-seq) using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created using deeptools software.
Assembly: ASM294v2, TAIR10
Supplementary files format and content: bigwig file for ChIP-seq

organism: Schizosaccharomyces pombe

source_name: S.pombe cells

growth_protocol: Cells were grown in YES medium until mid-log phase at 30 ºC.

extract_protocol:
Chromatin for ChIP-seq, extracted from cell lysate of 1% formaldehyde fixed-cells, was sonicated using a Picoruptor (Diagenode).
ChIP-seq libraries were constructed using the ThruPLEX DNA-seq Kit (Clontech).

treatment_protocol: The non-treated samples (0 min) were harvested immediately, and the heet-treated samples were moved from a 30 ºC water bath to 37.5 ºC and incuvated during the designated term (2.5, 5 and 25 min) with shaking. In some ChIP-seq experiments, the recovery samples (designated as 5plus2.5min, 5plus5min, 5plus10min) were harvested when they were returned to a 30 ºC water bath 5 minutes after heat treatment at 37.5 ºC and incubated for the specified time (2.5, 5 and 10 minutes) with shaking.

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4d::NatMX6

value: 5 min after heat-treatment


title: DMSO-3

description:
Library name: Sample 3
DMSO3_FPKM

value: mycobacterial culture

value: mycobacterial cell


title: spike_in ChIP, clr4d, H3K9me2, heat-treatment 2.5 min, rep2

description: Library name: ChIP197

value: 2.5 min after heat-treatment


title: child/031-curette

description: Library name: 238-38

source_name: primary cells

value: child


title: HCT116 cells, control,4sU RNA rep2

description: Library name: HCT116_4sU_control_rep2


title: Patient DSP-052

description: Library name: DSP-052

value: Tumor

value: clear cell carcinoma (CCC)

value: Primary


title: child/031-NPS

description: Library name: 238-37


title: DMSO-1

description:
Library name: Sample 1
DMSO1_FPKM

value: wild type

value: batch 1


title: spike_in ChIP, clr4d, H3K9me2, heat-treatment 0 min, rep2

description: Library name: ChIP196

value: 0 min (non treated)


title: Patient DSP-043

description: Library name: DSP-043


title: UOK120 cells, shTFE3-3

city: Nanjing

first: Fan

last: Feng

state: Jiangsu

department: Urology

institute: Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
We aligned reads of all samples to the research species referencegenome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie with default parameters.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes counts values for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values counts for each Sample

source_name: kidney

extract_protocol:
RNA was harvested using RNA easy mini plus kit (Qiagen). 1.3 ug RNA was used for the construction of the squencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mrna-seq library Prep kit following manufacturer's protocols

value: kidney

value: TFE3 rearranged renal cell carcinoma  cell lines


title: spike_in ChIP, clr4d, H3K9me2, heat-treatment 5 min, rep1

description: Library name: ChIP195


title: child/049-curette

description: Library name: 238-36

value: nasal

value: nasal cells


title: Patient DSP-042

description: Library name: DSP-042


title: DMSO-2

description:
Library name: Sample 2
DMSO2_FPKM

value: DMSO control


title: Patient DSP-040

description: Library name: DSP-040


title: child/021-NPS

description: Library name: 238-35


title: child/042-NPS

description: Library name: 238-33


title: UOK120 cells, shTFE3-2

address: Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medic


title: Patient DSP-039

description: Library name: DSP-039


title: spike_in ChIP, clr4d, H3K9me2, heat-treatment 0 min, rep1

description: Library name: ChIP193

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4d::NatMX6


title: spike_in ChIP, clr4d, H3K9me2, heat-treatment 2.5 min, rep1

description: Library name: ChIP194


title: child/042-curette

description: Library name: 238-34


title: spike_in ChIP, WT, H3K9me2, heat-treatment 5 min, rep2

description: Library name: ChIP192

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 5 min after heat-treatment


title: UOK120 cells, shTFE3-1


title: Patient C01

description: Library name: C01


title: UOK120 cells, shNC-3

value: shNC

value: shRNA(nc)


title: child/041-NPS

description: Library name: 238-31

value: child


title: Patient DSP-038

description: Library name: DSP-038

value: Tumor

value: clear cell carcinoma (CCC)


title: 22Rv1-dTAG-FOXA1, DMSO, FOXA1 (ChIP)

city: La Jolla

first: Lauren

last: Hargis

state: CA

address: 10650 N Torrey Pines Road, BCC526

institute: Scripps Research Institute

description: Library name: 22Rv1-dTAG-FOXA1_DMSO, FOXA1 ChIP

data_processing:
Sequencing reads were aligned to human genome build hg19 and RefSeq genes by Bowtie2 with the following parameters: -N 1 -p 10 -x.
Using the unenriched input sample as background, the signal-enriched regions were identified by Model-based Analysis of ChIP-seq (MACS) peak-finding algorithm (v1.4.1) with the P value threshold of 1e-9.
Assembly: hg19
Supplementary files format and content: Genome-wide signal tracks in WIG format (.wig.gz) generated from hg19-aligned ChIP-seq BAM files using MACS. WIG files represent normalized read density (signal pileup) across the genome and are compressed using gzip. These files can be visualized in genome browsers (e.g., IGV or UCSC Genome Browser) to inspect ChIP-seq signal enrichment.

source_name: Prostate

extract_protocol:
Cells were washed with PBS, trypsinized, and crosslinked with 1.1 % formaldehyde (final) in 50 mM HEPES pH 7.5, 100 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA for 10 minutes at room temperature. Crosslinking was quenched with 125 mM glycine for 5 minutes. Cells were washed three times with ice-cold PBS and snap-frozen at –80 °C until processing. For chromatin preparation, pellets were resuspended in Lysis Buffer 1 (LB1; 50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % NP-40, 0.25 % Triton X-100, 1× Halt™ Protease Inhibitor Cocktail (Thermo Fisher)) and rotated for 10 minutes at 4 °C, followed by centrifugation at 1,400 × g for 5 minutes at 4 °C. Pellets were then washed with Lysis Buffer 2 (LB2; 10 mM Tris pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× protease inhibitor) and resuspended in Sonication Buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1 % Triton X-100, 0.1 % sodium deoxycholate, 0.5 % SDS, 1× protease inhibitor). Chromatin was sheared using a Diagenode Bioruptor (25 cycles, 30 sec on/off, 10 °C). 50µL of whole cell extract (input) for the DMSO sample was moved to a new tube and stored at -20 °C until the reverse crosslinking step. Sheared chromatin was diluted to 0.1 % SDS and incubated overnight at 4 °C with antibodies conjugated to Dynabeads™ Protein G (Thermo Fisher): 10 µg FOXA1 (Novus Biologicals) or 5 µg H3K27ac (Diagenode). Beads were washed twice with Sonication Buffer (without SDS), once with High-Salt Sonication Buffer (500 mM NaCl, without SDS), once with LiCl Wash Buffer (20 mM Tris pH 7.5, 1 mM EDTA, 250 mM LiCl, 0.5 % NP-40, 0.5 % sodium deoxycholate), and once with TE + 50 mM NaCl. Bound chromatin was eluted in 200µL Elution Buffer (50 mM Tris pH 7.5, 10 mM EDTA, 1 % SDS) at 65 °C for 15 minutes. The input sample was thawed and 150µL of elution buffer was added before crosslinking with the other samples at 65 °C overnight (13 h). Samples were treated sequentially with 8µL 10mg/mL RNase A (37 °C, 2 h), 7µL of 300mM CaCl2 in 10mM Tris at pH 8, and 4µL 20mg/mL Proteinase K (55 °C, 30 min), followed by extraction with phenol:chloroform:isoamyl alcohol (25:24:1). The aqueous phase was isolated and DNA precipitated at -80 °C for 2-3 h.
DNA fragments (300-500 bp) were purified and processed for library preparation using the ThruPLEX® DNA-seq Kit (Takara Bio), indexed with DNA Unique Dual Index Kit -24U Set A (Takara), cleaned with AMPure XP beads (Beckman Coulter), and sequenced on an Illumina NextSeq 2000 (single-end, 75 bp).

value: Prostate

value: prostate carcinoma epithelial cell

value: DMSO

tag: chip-seq antibody

value: FOXA1 (Novus Biologicals, Cat#:NBP2-45354)


title: child/041-curette

description: Library name: 238-32

tag: cell type


title: spike_in ChIP, WT, H3K9me2, heat-treatment 2.5 min, rep3

description: Library name: ChIP191

value: 2.5 min after heat-treatment


title: UOK120 cells, shNC-2

tag: tissue

value: kidney

value: TFE3 rearranged renal cell carcinoma  cell lines


title: Patient DSP-036

description: Library name: DSP-036

value: Primary


title: spike_in ChIP, WT, H3K9me2, heat-treatment 0 min, rep2

description: Library name: ChIP190

value: S.pombe cells

value: 0 min (non treated)


title: child/040-curette

description: Library name: 238-30

value: nasal

value: nasal cells


title: UOK109 cells, shTFE3-3


title: Patient DSP-035

description: Library name: DSP-035


title: child/040-NPS

description: Library name: 238-29


title: UOK109 cells, shTFE3-2


title: Patient DSP-034

description: Library name: DSP-034


title: spike_in ChIP, WT, H3K9me2, heat-treatment 5 min, rep1

description: Library name: ChIP189

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 5 min after heat-treatment


title: child/039-curette

description: Library name: 238-28

value: child


title: Patient DSP-033

description: Library name: DSP-033

value: Tumor


title: spike_in ChIP, WT, H3K9me2, heat-treatment 0 min, rep1

description: Library name: ChIP187


title: UOK120 cells, shNC-1

value: shNC

value: shRNA(nc)


title: UOK109 cells, shNC-3


title: UOK109 cells, shTFE3-1


title: spike_in ChIP, WT, H3K9me2, heat-treatment 2.5 min, rep2

description: Library name: ChIP188


title: child/034-curette

description: Library name: 238-26


title: Patient DSP-031

description: Library name: DSP-031

value: clear cell carcinoma (CCC)


title: child/039-NPS

description: Library name: 238-27


title: UOK109 cells, shNC-2


title: Patient DSP-030

description: Library name: DSP-030


title: child/034-NPS

description: Library name: 238-25


title: spike_in ChIP, clr4d, H3, heat-treatment 2.5 min, rep2

description: Library name: ChIP185

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4d::NatMX6


title: spike_in ChIP, clr4d, H3, heat-treatment 5 min, rep2

description: Library name: ChIP186


title: Patient DSP-028

description: Library name: DSP-028


title: spike_in ChIP, clr4d, H3, heat-treatment 0 min, rep2

description: Library name: ChIP184


title: spike_in ChIP, clr4d, H3, heat-treatment 5 min, rep1

description: Library name: ChIP183


title: child/032-curette

description: Library name: 238-24


title: UOK109 cells, shNC-1


title: AtrophicLiver, OCA, 6

city: Maastricht

first: Frank

middle: G.

last: Schaap

address: Universiteitssingel 50

department: Department of Surgery

institute: Maastricht University

description: Library name: PVE036

data_processing:
Raw FASTQ reads were generated by Eurofins Genomics and processed downstream by the authors. Reads were aligned to the rabbit reference genome OryCun2 (Ensembl; chromosomes only) using STAR, and gene-level raw counts were generated using RSEM. For downstream analysis, count normalisation was performed using DESeq2 separately for ileum and liver samples due to tissue-specific expression distributions. Tissue-specific normalised count tables are provided as processed data.
Assembly: OryCun2 (Oryctolagus cuniculus reference genome, Ensembl; chromosomes only)
Supplementary files format and content: Tab-delimited text file containing DESeq2-normalised gene counts specific for hepatic and ileal samples. Rows correspond to Ensembl rabbit gene IDs and columns to sample/library IDs (PVE001–PVE036) as listed in the metadata file; each cell contains the normalised read count for that gene in that sample.

organism: Oryctolagus cuniculus

source_name: Cranial liver lobe (embolized)

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Strand-specific RNA-seq libraries were prepared by Eurofins Genomics using their standard Illumina-compatible workflow. Libraries were PCR-amplified, size-selected, quality-controlled and sequenced as 150 bp paired-end reads on an Illumina NovaSeq 6000 (S2 flow cell).

value: Cranial liver lobe (embolized)

value: WT

value: OCA


title: child/050-NPS

description: Library name: 238-49


title: Patient DSP-026

description: Library name: DSP-026


title: spike_in ChIP, clr4d, H3, heat-treatment 2.5 min, rep1

description: Library name: ChIP182

value: 2.5 min after heat-treatment


title: child/036-curette

description: Library name: 238-22


title: child/032-NPS

description: Library name: 238-23


title: spike_in ChIP, clr4d, H3, heat-treatment 0 min, rep1

description: Library name: ChIP181


title: Patient DSP-022

description: Library name: DSP-022

value: Primary


title: AtrophicLiver, OCA, 4

description: Library name: PVE034


title: child/036-NPS

description: Library name: 238-21


title: Patient DSP-021

description: Library name: DSP-021


title: child/035-curette

description: Library name: 238-20


title: child/035-NPS

description: Library name: 238-19


title: Patient DSP-020

description: Library name: DSP-020


title: AtrophicLiver, control, 6

description: Library name: PVE033

value: Vehicle


title: Patient DSP-027

description: Library name: DSP-027


title: AtrophicLiver, control, 5

description: Library name: PVE032


title: spike_in ChIP, WT, H3, heat-treatment 0 min, rep2

description: Library name: ChIP178

value: S.pombe cells

value: 0 min (non treated)


title: spike_in ChIP, WT, H3, heat-treatment 2.5 min, rep3

description: Library name: ChIP179


title: AtrophicLiver, OCA, 5

description: Library name: PVE035


title: Patient DSP-017

description: Library name: DSP-017


title: spike_in ChIP, WT, H3, heat-treatment 5 min, rep1

description: Library name: ChIP177


title: AtrophicLiver, control, 4

description: Library name: PVE031


title: spike_in ChIP, WT, H3, heat-treatment 5 min, rep2

description: Library name: ChIP180


title: Patient DSP-015

description: Library name: DSP-015


title: AtrophicLiver, OCA, 1

description: Library name: PVE028


title: child/029-curette

description: Library name: 238-16

value: nasal

value: nasal cells


title: child/029-NPS

description: Library name: 238-15


title: child/030-curette

description: Library name: 238-18


title: Patient DSP-018

description: Library name: DSP-018


title: Patient DSP-013

description: Library name: DSP-013


title: AtrophicLiver, OCA, 3

description: Library name: PVE030


title: spike_in ChIP, WT, H3, heat-treatment 0 min, rep1

description: Library name: ChIP175

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+


title: AtrophicLiver, control, 3

description: Library name: PVE027


title: AtrophicLiver, control, 2

description: Library name: PVE026


title: Patient DSP-012

description: Library name: DSP-012


title: Patient DSP-009

description: Library name: DSP-009


title: AtrophicLiver, OCA, 2

description: Library name: PVE029


title: QM-4

description:
Library name: Sample 8
QM4_FPKM

value: mycobacterial culture

value: mycobacterial cell

value: wild type

value: QM(4 x MIC, 6 h)

value: batch 1


title: AtrophicLiver, control, 1

description: Library name: PVE025


title: PRO, clr4Δ, 2.5 min recovery after heat-treatment for 5 min, rep2

description: Library name: PRO22

data_processing:
PRO-seq reads were mapped on S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: ASM294v2
Supplementary files format and content: bigwig file for PRO-seq
Library strategy: PRO-seq

extract_protocol:
Cell permeabilization and extraction of biotinylated RNA for PRO-seq was performed as previously described (Mahat et al., 2016).
cDNA libraries for PRO-seq were converted from the RNA, to which 3' and 5' adaptors were ligated, by revearse transcription.

treatment_protocol: The recovery samples (designated as 5plus2.5min, 5plus5min, 5plus10min) were harvested, when they were returned to a 30 ºC water bath 5 minutes after heat treatment at 37.5 ºC and incubated for the specified time (2.5, 5 and 10 minutes) with shaking.

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4d::NatMX6

value: 2.5 min recovery after heat-treatment


title: PRO, clr4Δ, 5 min recovery after heat-treatment for 5 min, rep2

description: Library name: PRO23

value: 5 min recovery after heat-treatment


title: child/030-NPS

description: Library name: 238-17

value: child


title: Patient DSP-008

description: Library name: DSP-008

value: Tumor

value: clear cell carcinoma (CCC)


title: PRO, clr4Δ, 10 min recovery after heat-treatment for 5 min, rep2

description: Library name: PRO24

value: 10 min recovery after heat-treatment


title: child/027-NPS

description: Library name: 238-11


title: spike_in ChIP, WT, H3, heat-treatment 2.5 min, rep2

description: Library name: ChIP176

value: S.pombe cells

value: 2.5 min after heat-treatment


title: child/023-curette

description: Library name: 238-14

value: nasal


title: Patient DSP-005

description: Library name: DSP-005

value: Primary


title: child/022-curette

description: Library name: 238-10

value: nasal cells


title: Patient DSP-004

description: Library name: DSP-004


title: Patient DSP-003

description: Library name: DSP-003


title: HypertrophicLiver, OCA, 4

description: Library name: PVE022

source_name: Caudal liver lobe (non-embolized)

value: Caudal liver lobe (non-embolized)

value: WT

value: OCA


title: child/025-NPS

description: Library name: 238-08


title: PRO, WT, 10 min recovery after heat-treatment for 5 min, rep2

description: Library name: PRO18

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+


title: PRO, clr4Δ, 2.5 min recovery after heat-treatment for 5 min, rep1

description: Library name: PRO19


title: child/022-NPS

description: Library name: 238-09


title: HypertrophicLiver, OCA, 5

description: Library name: PVE023


title: PRO, clr4Δ, 5 min recovery after heat-treatment for 5 min, rep1

description: Library name: PRO20


title: child/016-curette

description: Library name: 238-06


title: RP5_WT_H3K36me3_input_1

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

data_processing:
Raw sequence reads were processed through lcdb-wf v1.6rc (https://github.com/lcdb/lcdb-wf). Briefly, raw sequence reads were trimmed with cutadapt v3.4 to remove adapters and do quality trimming with parameters “-u 3 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 20 –minimum-length=25” for paired-end reads or “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 – minimum-length=25” for single read. fastqc v0.11.9 with default parameters and multiqc v1.10.1 were used to estimate the sequencing library quality. The presence of common sequencing contaminants was evaluated with fastq_screen v0.14.0 with parameters “–subset 100000 –aligner bowtie2.” Trimmed reads were mapped to the human reference genome Gencode v19 GRCh37.p13) using bowtie2 v2.4.2 with parameter “--no-unal”, followed by samtools v1.12 functions view with parameter “-Sb” and function sort to sort the BAM files. Multimapping reads were filtered using samtools view with parameter “-b -q 20”. PCR duplicates were removed with picard v2.25.2 MarkDuplicates with parameters “REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT”. Bigwig files were generated with deeptools v3.5.1 bamCoverage with “--binSize 1 --minMappingQuality 20 --ignoreDuplicates --normalizeUsing CPM --extendReads 300” to visualize the signal in genome browsers. Significant ChIPseq signal peaks were computed with MACS2 v2.2.7.1 callpeak with parameters “-f BAMPE -B” or “-f BAM -B” for paired-end or single read respectively.
Assembly: hg19
Supplementary files format and content: bigwig files contain the mapped reads distribution. Technical replicates were concatenated.
Supplementary files format and content: narrowPeak files are the results of MACS2 peak calling on the IP / input.

source_name: Human cell line (HEK293T)

growth_protocol: HEK293T cells were propagated in Dulbecco’s modified Eagle’s media supplemented to contain fetal bovine serum (10%) and penicillin-streptomycin (1%; 100 U/ml) (DMEM). Cells were grown at 37 °C in humified tissue culture cell incubators.

extract_protocol:
Antibodies for ChIPSeq: FLAG (Sigma; Cat# F1804), RNA Pol II (8WG16 BioLegend; Cat# 664912), H3K4me3 (C42D8 Rabbit mAb #9751 cell signaling), H3K36me3 (Invitrogen; MA5-24687), and MLL1 (Rabbit anti-MLL1 antibody Bethyl; Cat#A300-374A).
ChIP-Seq libraries were constructed from 40 ng of ChIP DNA using Ovation Ultralow System V2 1-96 (Tecan) with 15 cycles of PCR amplification. The final libraries were twice purified using Ampure XP PCR Purification Beads (Agencourt). The pooled libraries were sequenced on a NovaSeq 6000 (Illumina) using version 1.5 chemistry to achieve approximately 80 million 151-base read pairs. The data was processed using RTA version 3.4.4.

treatment_protocol: HEK293T cells were modified with CRIPSR to prevent expression of both the p52 and p75 isoforms of LEDGF. Cas9 with two sgRNAs targeting exon 2 of PSIP1 generated a clone with one allele encoding a frameshift after amino acid 30 adding seven additional amino acids and a second allele with a stop codon at amino acid 24. RNA-seq data from this LEDGF KO cell line revealed nonsense mediated decay allowed only trace levels of expression at any position in the PSIP1 gene. A clone of HEK293T with homozygous alleles of PSIP1 encoding C-terminal 3XFLAG tags were produced with CRISPR and a donor sequence carrying only a silent mutation that removed the PAM sequence.  We expressed N-terminal tagged LEDGF from Sleeping Beauty vectors introduced into the HEK293T cells with the LEDGF KO. A Sleeping Beauty vector, a gift from Todd McFarlan, containing 5’ and 3’ terminal inverted repeats, puro and a PGK promoter to express coding sequence with an N-terminal 3XFLAG tag. At 5’ NcoI and 3’ NheI sites we introduced synthesized coding sequences for wild type LEDGF, LEDGF lacking amino acids 1-93 (deletes PWWP) and LEDGF-1-325 (deletes IBD). We co-transfected these vectors with pCMV-SB100X that expresses the Sleeping Beauty transposase that stably integrated the LEDGF sequences.

value: Human cell line (HEK293T)

tag: chip antibody

value: input

tag: experiment run_number

tag: fraction


title: PRO, WT, 5 min recovery after heat-treatment for 5 min, rep2

description: Library name: PRO17


title: HypertrophicLiver, control, 6

description: Library name: PVE021

value: Vehicle


title: child/026-NPS

description: Library name: 238-07

tag: developmental stage


title: Patient DSP-002

description: Library name: DSP-002


title: HypertrophicLiver, control, 4

description: Library name: PVE019


title: PRO, WT, 10 min recovery after heat-treatment for 5 min, rep1

description: Library name: PRO15


title: child/016-NPS

description: Library name: 238-05


title: H3K4me3-WT_input_1

value: LEDGF-WT


title: PRO, WT, 2.5 min recovery after heat-treatment for 5 min, rep2

description: Library name: PRO16

value: 2.5 min recovery after heat-treatment


title: HypertrophicLiver, control, 5

description: Library name: PVE020


title: child/019-NPS

description: Library name: 238-04

value: child


title: RP29_WT_H3K36me3_IP_1

value: IP


title: Patient DSP-041

description: Library name: DSP-041

value: Tumor

value: clear cell carcinoma (CCC)


title: HypertrophicLiver, OCA, 3

description: Library name: PVE018


title: H3K4me3-WT_IP_2


title: HypertrophicLiver, OCA, 2

description: Library name: PVE017


title: PRO, WT, 5 min recovery after heat-treatment for 5 min, rep1

description: Library name: PRO14

value: S.pombe cells

value: 5 min recovery after heat-treatment


title: child/019-curette

description: Library name: 238-03

value: nasal


title: HypertrophicLiver, OCA, 1

description: Library name: PVE016


title: PRO, WT, 2.5 min recovery after heat-treatment for 5 min, rep1

description: Library name: PRO13


title: H3K4me3-LEDGF-KO_input_1

value: LEDGF-KO


title: child/017-NPS

description: Library name: 238-02

value: nasal cells


title: HypertrophicLiver, control, 3

description: Library name: PVE015

value: Caudal liver lobe (non-embolized)

value: WT


title: child/017-curette

description: Library name: 238-01


title: H3K4me3-LEDGF-KO_IP_2


title: Serum, Case 23

city: Madrid

first: Olga

last: Sanchez Pernaute

address: Avda reyes Catolicos 2

department: Rheumatology

country: Spain

institute: Jimenez Diaz Foundation and Health Research Institute (IIS-FJD)

description: Library name: 30853-028

data_processing:
Raw data de-multiplexed and generation of FASTQ files with bcl2fastq2 software
Reads processed by trimming of the common sequence, UMI and adapters
Filtering reads with length < 15 nt or > 55 nt
Deduplication using their UMI
Assembly: CLC Genomic server 21.0.4 used to map the reads to airbase version 22.
Supplementary files format and content: CPM mapping to miRNA molecules of all samples (csv file)

source_name: Serum

extract_protocol:
RNA isolation with miRNeasy Serum/Plasma Kit (QIAGEN)
QIAseq miRNA Library Kit. Conversion into miRNA NGS libraries. Adapter ligation, followed by introduction of UMIs in the rt step. cDNA amplification using PCR (22 cycles). QC with capillary electrophoresis (Agilent DNA 1000 Chip). Library equimolar pools, quantified with qPCR and sequenced on a NextSeq (Illumina Inc.) instrument.

value: Serum

tag: Sex

value: female

tag: disease state

value: Case, female, younger, fibrotic, early, NSIP, RA, high FVC, stable


title: H3K4me3-LEDGF-KO_IP_1

value: Human cell line (HEK293T)


title: spike-in ChIP, clr4Δ, H3K9me2, heat-treatment 5 min, rep1

description: Library name: ChIP172

data_processing:
ChIP-seq reads were trimmed using Trimmomatic ver 0.33 with SE, LEADING:30, TRAILING:30, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome and A.thaliana TAIR10 genome (for spike-in ChIP-seq) using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created using deeptools software.
Assembly: ASM294v2, TAIR10
Supplementary files format and content: bigwig file for ChIP-seq

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4d::NatMX6

value: 5 min after heat-treatment


title: Serum, Case 24

description: Library name: 30853-029

value: Case, female, younger, non fibrotic, early, NSIP, ARS, high FVC, stable


title: spike-in ChIP, clr4Δ, H3K9me2, heat-treatment 0 min, rep1

description: Library name: ChIP171

value: 0 min (non treated)


title: AA16-HL13-3XFLAG-LEDGF-dPWWP_Input

value: input


title: ileum, OCA, 6

description: Library name: PVE012

source_name: Terminal ileum

value: Terminal ileum

value: OCA


title: spike-in ChIP, clr4Δ, H3K9me2, heat-treatment 0 min, rep2

description: Library name: ChIP173

value: S.pombe cells


title: H3K4me3-WT_IP_1

value: LEDGF-WT

value: IP


title: Serum, Case 22

description: Library name: 30853-027

value: Case, female, older, non fibrotic, early, NSIP, RA, high FVC, progressive


title: spike-in ChIP, WT, H3K9me2, heat-treatment 5 min, rep2

description: Library name: ChIP170

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+


title: spike-in ChIP, clr4Δ, H3K9me2, heat-treatment 5 min, rep2

description: Library name: ChIP174


title: HypertrophicLiver, control, 1

description: Library name: PVE013

value: Caudal liver lobe (non-embolized)

value: WT

value: Vehicle


title: AA15-HL13-3XFLAG-LEDGF-dPWWP_FLAG-IP_Rep3


title: ileum, OCA, 5

description: Library name: PVE011


title: spike-in ChIP, WT, H3K9me2, heat-treatment 0 min, rep2

description: Library name: ChIP169


title: ileum, OCA, 4

description: Library name: PVE010


title: Serum, Case 21

description: Library name: 30853-026

value: Serum

value: female

value: Case, female, older, fibrotic, UIP, uAIP, high FVC, stable


title: Serum, Case 20

description: Library name: 30853-025

value: Case, female, older, fibrotic, IPAF, low FVC, progressive


title: AA14-HL13-3XFLAG-LEDGF-dPWWP_FLAG-IP_Rep2

value: Human cell line (HEK293T)


title: spike-in ChIP, WT, H3K9me2, heat-treatment 5 min, rep1

description: Library name: ChIP168

value: 5 min after heat-treatment


title: ileum, control, 6

description: Library name: PVE009


title: spike-in ChIP, WT, H3K9me2, heat-treatment 0 min, rep1

description: Library name: ChIP167

value: 0 min (non treated)


title: Serum, Case 19

description: Library name: 30853-024

value: Case, female, older, fibrotic, uAIP, high FVC, stable


title: AA13-HL13-3XFLAG-LEDGF-dPWWP_FLAG-IP_Rep1


title: AA12-HL3-3XFLAG-LEDGF_Input

value: input


title: spike-in ChIP, clr4Δ, H3, heat-treatment 5 min, rep2

description: Library name: ChIP166

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4d::NatMX6


title: Serum, Case 18

description: Library name: 30853-023


title: ileum, control, 4

description: Library name: PVE007

value: Terminal ileum


title: AA11-HL3-WT_3XFLAG-LEDGF_FLAG-IP_Rep3

value: IP


title: spike-in ChIP, clr4Δ, H3, heat-treatment 0 min, rep2

description: Library name: ChIP165


title: AA10-HL3-WT_3XFLAG-LEDGF_FLAG-IP_Rep2


title: ileum, OCA, 3

description: Library name: PVE006

value: OCA


title: Serum, Case 17

description: Library name: 30853-022

value: Case, female, older, fibrotic, early, NSIP, IPAF, high FVC, stable


title: Serum, Case 16

description: Library name: 30853-021

value: Case, female, older, fibrotic, early, UIP, RA, high FVC, stable


title: AA9-HL3-WT_3XFLAG-LEDGF_FLAG-IP_Rep1


title: spike-in ChIP, clr4Δ, H3, heat-treatment 0 min, rep1

description: Library name: ChIP163


title: Serum, Case 15

description: Library name: 30853-020

value: Case, female, older, fibrotic, early, UIP, IPAF, high FVC, stable


title: ileum, OCA, 2

description: Library name: PVE005

value: WT


title: spike-in ChIP, clr4Δ, H3, heat-treatment 5 min, rep1

description: Library name: ChIP164


title: ileum, control, 5

description: Library name: PVE008

value: Vehicle


title: Activated (Vehicle)-Donor #11

city: Washington

first: Adonia

middle: Evangelos

last: Papathanassiu

state: DC

address: 416 Marietta PL, NW

institute: Ergon Pharmaceuticals LLC

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15
Differentially expressed genes were identified using the edgeR program.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: T cell

growth_protocol: CD8+ T cells were grown in RPMI containing 10%FBS and antibiotics.

extract_protocol:
RNA was obtained using RNeasy Plus Mini kit (Qiagen). 250 ng of total RNA was used for library construction.
RNA-Seq library was prepared according to KAPA mRNA HyperPrep kit with 200-300 bp insert size (Roche, Wilmington, MA)

treatment_protocol: CD8+ T cells were activated with Dynabeads (ThermoFisher) in the presence and absence of 200 mM ERG245. Dynabeads were then removed, cells were washed 2X with PBS, and collected for processing.

value: T cell

tag: gender

value: male

value: primary

value: Activated and treated with Vehicle (PBS) for 24h


title: spike-in ChIP, WT, H3, heat-treatment 5 min, rep2

description: Library name: ChIP162

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 5 min after heat-treatment


title: ileum, OCA, 1

description: Library name: PVE004


title: ileum, control, 2

description: Library name: PVE002


title: Serum, Case 14

description: Library name: 30853-019

value: Serum

value: female


title: Activated (ERG245)-Donor #11

value: Activated and treated with 200 mM ERG245 (PBS) for 24h


title: spike-in ChIP, WT, H3, heat-treatment 0 min, rep2

description: Library name: ChIP161

value: S.pombe cells

value: 0 min (non treated)


title: Serum, Case 13

description: Library name: 30853-018

value: Case, female, younger, early, IPAF, low FVC, stable


title: Serum, Case 12

description: Library name: 30853-017

value: Case, female, older, fibrotic, NSIP, SSc, high FVC, stable


title: Serum, Case 11

description: Library name: 30853-016

value: Case, female, younger, non fibrotic, NSIP, IPAF, low FVC, stable


title: Activated (ERG245)-Donor #7


title: ileum, control, 3

description: Library name: PVE003

value: Terminal ileum


title: Activated (ERG245)-Donor #12

value: WT


title: spike-in ChIP, WT, H3, heat-treatment 0 min, rep1

description: Library name: ChIP159


title: rVSV-D14-TCR

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Library name: rVSV-D14-TCR

data_processing:
10x TCR sequencing data was analysed with the cellranger software (version 7.0.0). The cellranger vdj command with option "--chain TR" was run for each of the six samples separately using the vdj-GRCm38-alts-ensembl-7.0.0 references provided by 10x.
Assembly: vdj-GRCm38-alts-ensembl-7.0.0
Supplementary files format and content: comma separated text file with filtered contig annotations (for file format description see: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-5p-outputs-annotations-vdj)
Library strategy: TCR-Seq

source_name: Spleen

extract_protocol:
Murine spleens were isolated and mechanically disrupted using a metal mesh and a syringe plunger, and cells were counted with a Immunospot S6 device (C.T.L.). CD8 T cells were enriched by magnetic-activated cell sorting using the CD8+ T cells Isolation Kit, mouse (STEMCELL), but the antibody mix in the kit was replaced by a mix containing the following biotin-conjugated antibodies from BioLegend: anti-B220 (RA3-6B2), anti-CD19 (6D5), Ly-76 (TER-119), anti-CD4 (H129.19) and anti-CD138 (281-2). Cell suspensions were stained with antibodies against CD45R/B220 (RA3-6B2), CD8 (53-6.7) and DAPI purchased from BioLegend, PE-conjugated H2-Kb tetramers loaded with the SARS-CoV-2 spike epitope VNFNFNGL (produced by the University of Lausanne Tetramer core facility).  Cells were stained with oligo-conjugated antibodies (ADT) for surface markers using TotalSeq-C0250 anti-KLRG1 (138433, BioLegend), TotalSeq-C0563 anti-CX3CR1 (149043, BioLegend), TotalSeq-C0198 anti-CD127 (104455, BioLegend) and TotalSeq-C0112 anti-CD62L (135047, BioLegend) . Each condition included 3 biological replicates which were labelled with hashtag oligos (HTOs): TotalSeq-C0301 (155861, BioLegend), TotalSeq-C0302 (155863, BioLegend) or TotalSeq-C0303 (155865, BioLegend) before being pooled Tetramer-binding CD8 T cells were FACS-sorted (FACS Aria II, BD) and the recovered cells were immediately processed for cell capture and library preparation
Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping (CG000330 Rev D)

value: Spleen

value: CD8 T cells

value: rVSV

tag: timepoint

tag: library type

value: TCR


title: ileum, control, 1

description: Library name: PVE001

value: Vehicle


title: spike-in ChIP, WT, H3, heat-treatment 5 min, rep1

description: Library name: ChIP160

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+


title: Activated (Vehicle)-Donor #7

value: T cell

value: male

value: primary

value: Activated and treated with Vehicle (PBS) for 24h


title: Activated (Vehicle)-Donor #12


title: HypertrophicLiver, control, 2

description: Library name: PVE014

value: Caudal liver lobe (non-embolized)


title: ChIP, WT, H3K9me2, 10 min recovery after heat-treatment for 5 min, rep3

description: Library name: ChIP158

value: S.pombe cells

value: 10 min recovery after heat-treatment


title: Serum, Case 10

description: Library name: 30853-015

value: Serum

value: female

value: Case, female, younger, non fibrotic, IPAF, low FVC, stable


title: rVSVMq-D14-TCR

description: Library name: rVSVMq-D14-TCR

value: rVSVMq


title: Serum, Case 9

description: Library name: 30853-014

value: Case, female, older, fibrotic, early, UIP, uAIP, high FVC, progressive


title: Lung, docosahexaenoic acid diet, ozone, 6

city: Columbus

first: Michael

middle: J

last: Yaeger

state: OH

address: 473 W 12th Ave

institute: The Ohio State University

description: Library name: 5936

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence Partek Flow
Trimmed sequence reads were mapped to mm39 using STAR in Partek Flow
Read count extraction and normalization were performed using HT-seq on Partek Flow
Assembly: mm39
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

source_name: Lung

extract_protocol:
RNA was extrated using the Qiagen RNeasy Mini Kit (Fisher Scientific)
RNA libraries for RNA-seq were prepared by Genewiz.

value: Lung


title: ChIP, WT, H3K9me2, 5 min recovery after heat-treatment for 5 min, rep3

description: Library name: ChIP157

value: 5 min recovery after heat-treatment


title: rLCMV-D14-TCR

description: Library name: rLCMV-D14-TCR

value: Spleen

value: CD8 T cells

value: rLCMV

value: TCR


title: rVSV-D7-TCR

description: Library name: rVSV-D7-TCR

value: rVSV


title: Lung, docosahexaenoic acid diet, ozone, 5

description: Library name: 5935


title: Lung, docosahexaenoic acid diet, ozone, 4

description: Library name: 5934


title: Serum, Case 7

description: Library name: 30853-012

value: Case, female, younger, non fibrotic, NSIP, SSc, high FVC, progressive


title: Serum, Case 8

description: Library name: 30853-013

value: Case, female, younger, non fibrotic, early, IPAF, high FVC, stable


title: HypertrophicLiver, OCA, 6

description: Library name: PVE024

value: Caudal liver lobe (non-embolized)

value: WT

value: OCA


title: ChIP, WT, H3K9me2, heat-treatment 5 min, rep3

description: Library name: ChIP155

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 5 min after heat-treatment


title: ChIP, WT, H3K9me2, 2.5 min recovery after heat-treatment for 5 min, rep3

description: Library name: ChIP156

value: 2.5 min recovery after heat-treatment


title: Serum, Case 6

description: Library name: 30853-011

value: Serum

value: male

value: Case, male, older, fibrotic, uAIP, high FVC, stable


title: Lung, docosahexaenoic acid diet, ozone, 3

description: Library name: 5933

value: Lung


title: rLCMV-D7-TCR

description: Library name: rLCMV-D7-TCR

value: Spleen

value: CD8 T cells


title: Serum, Case 5

description: Library name: 30853-010

value: female

value: Case, female, older, non fibrotic, SSc, low FVC, progressive


title: ChIP, WT, H3K9me2, heat-treatment 2.5 min, rep3

description: Library name: ChIP154

value: 2.5 min after heat-treatment


title: Lung, docosahexaenoic acid diet, ozone, 2

description: Library name: 5932


title: PRO, clr4Δ, 10 min recovery after heat-treatment for 5 min, rep1

description: Library name: PRO21

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4d::NatMX6

value: 10 min recovery after heat-treatment


title: rVSV-D14-CellSurface

description: Library name: rVSV-D14-CellSurface

data_processing:
The mRNA data was mapped to the mm10 genome using the STARsolo framework (STAR version 2.7.10a) (Dobin et al. 2013).
Gene quantification made use of a custom GFT file based on the ensembl gene annotation (version 102). The cell barcode whitelist used for STAR is the file 737K-august-2016.txt provided by 10x. Other non-standard command line options for STAR included "--outFilterType BySJout --outFilterMultimapNmax 10 --outSAMmultNmax 1 --outSAMtype BAMSortedByCoordinate --outSAMunmapped Within --soloType CB_UMI_Simple --soloStrand Reverse --outFilterScoreMin 30 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter None --soloMultiMappers EM --soloBarcodeReadLength 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloFeatures Gene --outSAMattributes NH HI AS nM CR CY UR UY GX GN CB UB".
The cDNA fastq files for cell surface hashtag data (ADT+HTO) were first trimmed with the tool fastp (version 0.20.1) (Chen et al. 2018) and command line options "-b 15 -f 10 -t 0 -A -Q -G -L". After cDNA trimming cell surface hastag data was mapped and quantified with STARsolo, by using the same cell barcode whitelist as for GEX data. The genome index was build from the hashtag sequences as well as the GTF file used for quantification. Additional command line options included "--outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --soloType CB_UMI_Simple --soloStrand Forward --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter None --soloBarcodeReadLength 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloFeatures Gene".
Assembly: Mouse mm10
Supplementary files format and content: Three files per sample which are the raw output of STARsolo: 1. gene counts (<sample_id>_matrix.mtx), 2. tab separated text file with gene/cell surface hashtag IDs (<sample_id>_features.tsv), 3. tab separated text file with cell barcodes (<sample_id>_barcodes.tsv)
Library strategy: CITE-seq

molecule: protein

value: rVSV

value: ADT+HTO


title: ChIP, WT, H3K9me2, heat-treatment 0 min, rep3

description: Library name: ChIP153

value: S.pombe cells

value: 0 min (non treated)


title: rVSVMq-D7-TCR

description: Library name: rVSVMq-D7-TCR

value: rVSVMq

value: TCR


title: Lung, docosahexaenoic acid diet, ozone, 1

description: Library name: 5931


title: Serum, Case 2

description: Library name: 30853-007

value: Serum

value: Case, female, younger, non fibrotic, early disease, IPAF, high FVC, stable


title: Lung, control diet, ozone, 6

description: Library name: 5930


title: ChIP, WT, H3, 2.5 min recovery after heat-treatment for 5 min, rep3

description: Library name: ChIP150

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 2.5 min recovery after heat-treatment


title: ChIP, WT, H3, 5 min recovery after heat-treatment for 5 min, rep3

description: Library name: ChIP151

value: 5 min recovery after heat-treatment


title: rVSVMq-D14-CellSurface

description: Library name: rVSVMq-D14-CellSurface

value: Spleen

value: CD8 T cells


title: Serum, Case 1

description: Library name: 30853-006

value: female

value: Case, female, older, fibrotic IP, UIP, SSc, low FVC, progressive


title: Serum, Case 4

description: Library name: 30853-009

value: Case, female, younger, non fibrotic, early, NSIP, ARS/SSC overlapping, low FVC, stable


title: rVSVMq-D7-CellSurface

description: Library name: rVSVMq-D7-CellSurface


title: Lung, control diet, ozone, 4

description: Library name: 5928

value: Lung


title: Serum, Case 3

description: Library name: 30853-008

value: Case, female, older, fibrotic, UIP, IPAF, high FVC, stable


title: Serum, Healthy Control 5

description: Library name: 30853-005

value: Healthy, younger, female


title: ChIP, WT, H3, heat-treatment 2.5 min, rep3

description: Library name: ChIP148

value: S.pombe cells

value: 2.5 min after heat-treatment


title: rLCMV-D14-CellSurface

description: Library name: rLCMV-D14-CellSurface

value: rLCMV

value: ADT+HTO


title: Lung, control diet, ozone, 5

description: Library name: 5929


title: Lung, control diet, ozone, 2

description: Library name: 5926


title: Serum, Healthy Control 4

description: Library name: 30853-004

value: Serum

value: male

value: Healthy, Younger, male


title: rVSV-D7-CellSurface

description: Library name: rVSV-D7-CellSurface

value: rVSV


title: rVSV-D14-GEX

description: Library name: rVSV-D14-GEX

library_source: transcriptomic single cell

data_processing:
The mRNA data was mapped to the mm10 genome using the STARsolo framework (STAR version 2.7.10a) (Dobin et al. 2013).
Gene quantification made use of a custom GFT file based on the ensembl gene annotation (version 102). The cell barcode whitelist used for STAR is the file 737K-august-2016.txt provided by 10x. Other non-standard command line options for STAR included "--outFilterType BySJout --outFilterMultimapNmax 10 --outSAMmultNmax 1 --outSAMtype BAMSortedByCoordinate --outSAMunmapped Within --soloType CB_UMI_Simple --soloStrand Reverse --outFilterScoreMin 30 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter None --soloMultiMappers EM --soloBarcodeReadLength 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloFeatures Gene --outSAMattributes NH HI AS nM CR CY UR UY GX GN CB UB".
The cDNA fastq files for cell surface hashtag data (ADT+HTO) were first trimmed with the tool fastp (version 0.20.1) (Chen et al. 2018) and command line options "-b 15 -f 10 -t 0 -A -Q -G -L". After cDNA trimming cell surface hastag data was mapped and quantified with STARsolo, by using the same cell barcode whitelist as for GEX data. The genome index was build from the hashtag sequences as well as the GTF file used for quantification. Additional command line options included "--outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --soloType CB_UMI_Simple --soloStrand Forward --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter None --soloBarcodeReadLength 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloFeatures Gene".
Assembly: Mouse mm10
Supplementary files format and content: Three files per sample which are the raw output of STARsolo: 1. gene counts (<sample_id>_matrix.mtx), 2. tab separated text file with gene/cell surface hashtag IDs (<sample_id>_features.tsv), 3. tab separated text file with cell barcodes (<sample_id>_barcodes.tsv)

value: GEX


title: ChIP, WT, H3, heat-treatment 0 min, rep3

description: Library name: ChIP147

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 0 min (non treated)


title: ChIP, WT, H3, heat-treatment 5 min, rep3

description: Library name: ChIP149

value: 5 min after heat-treatment


title: Lung, control diet, ozone, 1

description: Library name: 5925


title: Serum, Healthy Control 3

description: Library name: 30853-003

value: female


title: Lung, control diet, ozone, 3

description: Library name: 5927


title: Serum, Healthy Control 2

description: Library name: 30853-002


title: rLCMV-D14-GEX

description: Library name: rLCMV-D14-GEX

value: Spleen

value: CD8 T cells


title: rVSVMq-D14-GEX

description: Library name: rVSVMq-D14-GEX

value: rVSVMq


title: ChIP, WT, H3K9me2, 2.5 min recovery after heat-treatment for 5 min, rep2

description: Library name: ChIP144

value: 2.5 min recovery after heat-treatment


title: Lung, docosahexaenoic acid diet, filtered air, 6

description: Library name: 5924

value: Lung


title: Serum, Healthy Control 1

description: Library name: 30853-001

value: Healthy, younger, female


title: Lung, docosahexaenoic acid diet, filtered air, 5

description: Library name: 5923


title: rLCMV-D7-CellSurface

description: Library name: rLCMV-D7-CellSurface

value: rLCMV


title: ChIP, WT, H3K9me2, 5 min recovery after heat-treatment for 5 min, rep2

description: Library name: ChIP145

value: S.pombe cells

value: 5 min recovery after heat-treatment


title: ChIP, WT, H3, 10 min recovery after heat-treatment for 5 min, rep2

description: Library name: ChIP143

value: 10 min recovery after heat-treatment


title: rVSVMq-D7-GEX

description: Library name: rVSVMq-D7-GEX


title: ChIP, WT, H3K9me2, 10 min recovery after heat-treatment for 5 min, rep2

description: Library name: ChIP146


title: Lung, docosahexaenoic acid diet, filtered air, 4

description: Library name: 5922


title: Lung, docosahexaenoic acid diet, filtered air, 2

description: Library name: 5920


title: ChIP, WT, H3, 10 min recovery after heat-treatment for 5 min, rep3

description: Library name: ChIP152


title: rLCMV-D7-GEX

description: Library name: rLCMV-D7-GEX


title: ChIP, WT, H3, 5 min recovery after heat-treatment for 5 min, rep2

description: Library name: ChIP142


title: Molm13-XR

city: Taipei

first: Yu-Hsuan

last: Fu

address: No.1, Chang-Te St

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

data_processing:
Sequencing was performed on Illumina NextSeq 500 platform.
Paired-end sequencing alignment toward hg19 and reads mapping to known genes were performed by Bowtie2.
Gene expression level was calculated by RSEM with Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model.
Differentially expressed genes (DEGs) identification between groups were conducted with EBSeq, with a threshold of fold change ≥ 2 or ≤ 0.5 and p-value of ≤ 0.05.
Assembly: hg19 (GRCh37)
Supplementary files format and content: *csv: comma-separated values of row counts for each known gene (HGNC symbol) in columns and sample in rows.

growth_protocol: Indiacted cells were cultured in RPMI1640 medium suppled with 10% FBS and 1% antibiotic in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNAs were isolated with NucleoSpin® RNA kit (Macherey-Nagel); The final library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.
Strand-specific RNA library were built by TruSeq stranded protocols from Illumina

treatment_protocol: The cabozantinib-resistant cells (Molm13-XR and MV4-11-XR) were derived by culturing the parental cells in low-concentration cabozantinib and escalating the dose once the cells were recovered.

value: The cabozantinib-resistant cells (Molm13-XR) were derived by culturing the parental cells in low-concentration cabozantinib and escalating the dose once the cells were recovered.


title: Molm13

value: parental


title: Lung, docosahexaenoic acid diet, filtered air, 3

description: Library name: 5921


title: MV4-11


title: PRO2, clr4Δ, heat-treatment 5min, rep2

data_processing:
library strategy: PRO-seq
ChIP-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created using deeptools software.
RNA-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- quantMode GeneCounts parameters. When we analyzed the expression of DNA sequence inculding repeat regions such as heterochromatin genes, we calculated the readcounts from bedgraph file, which was produced using the coverage function of BEDTools ver 2.17.0. Those readcount files were named as “mRNA_XXX_for_HGs.txt".
PRO-seq reads were mapped on S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: ASM294v2
Supplementary files format and content: bigwig file for ChIP-seq and PRO-seq
Supplementary files format and content: tab-delimited text file for RNA-seq

extract_protocol:
Total RNA for mRNA-seq was extracted by the hot-phenol method, as previously described (Iyer,V. and Struhl,K. 1996). Cell permeabilization and extraction of biotinylated RNA for PRO-seq was performed as previously described (Mahat et al., 2016). Chromatin for ChIP-seq, extracted from cell lysate of 1% formaldehyde fixed-cells, was sonicated using a Picoruptor (Diagenode).
ChIP-seq libraries were constructed using the ThruPLEX DNA-seq Kit (Clontech). mRNA-seq libraries were constructed using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). cDNA libraries for PRO-seq were converted from the RNA, to which 3' and 5' adaptors were ligated, by revearse transcription.

treatment_protocol: The non-treated samples (0 min) were harvested immediately, and the heet-treated samples were moved from a 30 ºC water bath to 37.5 ºC and incuvated during the designated term (2.5, 5 and 25 min) with shaking.

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4{delta}::NatMX6

value: 5 min atter heat-treatment


title: CEBPB ChIPseq

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

description: Library name: CHIP_CEBPB

data_processing:
Fastq files were mapped to hg38/GRCh37 genome with Bowtie2 (1.2.3). ChIP-seq peaks were then called with MACS2 (2.2.7.1) using default parameters. From this output, ‘robust’ peaks were selected by specifying a minimum fold-enrichment of 5.
Assembly: hg38
Supplementary files format and content: bw files are generated as the final processed file for data visualization

source_name: coronary artery

extract_protocol:
1,000,000 HCASMCs were cross linked in 1% formaldehyde for 10 minutes and washed with PBS and replaced with hypotonic buffer (20 mM Hepes (pH 7.9), 10 mM KCl, 1 mM EDTA (pH 8) and 10% glycerol) and incubated on ice for 6 minutes. Cells were then sonicated using a Branson 250 Sonifier (using power setting 5, constant duty for 10 rounds of 30-second pulses) with confirmation of chromatin fragments at 250-400 babse pairs. Lysates were then incubated overnight with 5 µg of anti-CEBPB (Santa Cruz sc-150), TEAD(Cell Signaling 12292S), or H3K27ac(Abcam 4729). Protein-DNA complexes were captured with Protein G agarose beads (Sigma 8104) and eluted in 1% SDS TE buffer at 65 °C. After reverse cross-linking followed by RNase A and proteinase K digestion, chromatin was purified using a QIAquick PCR purification kit (Qiagen 28706).
ChIP DNA sequencing libraries were prepared using the Kappa HyperPrep (Roche 07962347001)

value: coronary artery

value: 2105 hTERT

value: smooth muscle


title: Lung, docosahexaenoic acid diet, filtered air, 1

description: Library name: 5919


title: PLEA3

city: Jinan

first: Donghai

last: Wang

state: Shandong

address: Wenhuaxi Road

institute: Qilu Hospital of Shandong University

description:
Library name: Sample6
PLEA3

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork (parmeter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarty faction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwvork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: Brain

growth_protocol: Male wild-type C57 mice; housed in SPF conditions (12 h light/dark, 22 ± 2 °C, 50 ± 10% humidity); food and water ad libitum.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3ug of total RNA was yused for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER MRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Photochemically induced stroke models were established via intravenous injection at a dose of 100 mg/kg. A 250 mW 532 nm laser with a 1.5 mm diameter was focused on the left cerebral hemisphere and irradiated for 5 minutes. At 2 hours post-photothrombosis, 100 μL of saline or PLEA nanoparticles was administered via tail vein injection.The mice were then perfused with pre-chilled phosphate-buffered saline (PBS). Brains were promptly harvested and snap-frozen in liquid nitrogen for subsequent storage.

value: Brain

value: WT

value: PLEA

tag: batch

value: Day 3


title: ChIP, WT, H3, 2.5 min recovery after heat-treatment for 5 min, rep2

description: Library name: ChIP141

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 2.5 min recovery after heat-treatment


title: Lung, control diet, filtered air, 6

description: Library name: 5918

value: Lung


title: Lung, control diet, filtered air, 5

description: Library name: 5917


title: PLEA1

description:
Library name: Sample4
PLEA1


title: HoLEP30 [HoLEP_30B_S77]

city: San Francisco

first: Jon

last: Akutagawa

address: 513 Parnassus Ave

institute: UCSF

description:
Library name: HoLEP_30B_S77
SeqWell

data_processing:
The sequenced data were preprocessed and aligned using the dropseq_workflow on Terra (app.terra.bio). A digital gene expression matrix was generated for each sample, parsed, and analyzed following a customized pipeline
Sequencing results were received as paired FASTQ files. Each pair of FASTQ files was aligned against GRCh38 reference genome using a WDL-based Dropseq workflow (https://cumulus.readthedocs.io/en/latest/drop_seq.html) on Terra. All default parameters were used in the alignment except the parameter –dropseq_tools_force_cells set as 2,000 to ensure maximum cell capture. The alignment results include aligned and corrected bam files, gene expression matrices in .txt.gz format, and txt files of alignment reports such as the list of barcodes, the number of reads, and alignment summaries.
Assembly: hg38
Supplementary files format and content: differential gene expression matrix files

extract_protocol:
Patients were positioned in the lithotomy position. The 2 lateral lobes and median lobe of the prostate were enucleated using a Holmium laser. Each lobe was dissected away from the surgical capsule in a distal to proximal approach and released from the bladder neck. Prostate tissue was minced and evacuated by a Piranha morcellator (Richard Wolf). Morcellation was performed according to manufacturer’s recommendations up to 1,500 rpm with dual inflow saline irrigation. Morcellated tissue was collected in a canister and placed on ice prior to dissociation and preparation for single cell RNA-sequencing. Morcellated tissue was immediately delivered to the laboratory and further minced to ~1-5mm3 pieces with surgical scissors in a petri dish with 10 mL RP-10 (RPMI + 10% FBS) on ice for up to 5 mins and washed with cold RP-10 (RPMI + 10% FBS). Each sample was centrifuged at 1200 rpm x5 mins at 4°C and resuspended in 10 mL warmed digestive media (HBSS + 1% HEPES) with 1,000 U/mL collagenase type IV (Worthington, Cat: LS004188), and rotated for 30 min at 37 °C. Samples were triturated by pipetting 10 times at the end of the incubation. Each sample was filtered through a 70-µm filter (Falcon, Cat: 352350), washed with RP-10, centrifuged at 1200 rpm x5 mins at 4°C, washed again with RP-10, and resuspended in RP-10.
Sequencing was largely based on the Seq-Well S^3 protocol. One to two arrays were used per sample. Each array was loaded as previously described with approximately 110,000 barcoded mRNA capture beads (ChemGenes, Cat: MACOSKO-2011-10(V+)) and with 15,000–20,000 cells. Arrays were sealed with functionalized polycarbonate membranes (Sterlitech, Cat: PCT00162X22100) and were incubated at 37 °C for 40 min. After sealing, each array was incubated in lysis buffer (5 M guanidine thiocyanate, 1 mM EDTA, 0.5% sarkosyl, 1% BME). After detachment and removal of the top slides, arrays were rotated at 50 rpm for 20 min. Each array was washed with hybridization buffer (2 M NaCl, 4% PEG8000) and was then rocked in a hybridization buffer for 40 min. Beads from different arrays were collected separately. Each array was washed ten times with wash buffer (2 M NaCl, 3 mM MgCl2, 20 mM Tris-HCl pH 8.0, 4% PEG8000) and scraped ten times with a glass slide to collect beads into a conical tube. For each array, beads were washed with Maxima RT buffer (ThermoFisher, Cat: EP0753) and resuspended in reverse transcription mastermix with Maxima RT buffer, PEG8000, Template Switch Oligo, dNTPs (NEB, Cat: N0447L), RNase inhibitor (Life Technologies, Cat: AM2696) and Maxima H Minus Reverse Transcriptase (ThermoFisher, Cat: EP0753) in water. Samples were rotated end-to-end, first at room temperature for 30 min and then at 52 °C overnight. Beads were washed once with TE-TW, once with TE-SDS, twice with TE-TW, and once with 10 mM Tris-HCl pH 8.0.
They were treated with exonuclease I (NEB), rotating for 50 min at 37 °C. Beads were washed once with TE-SDS and twice with TE-TW. They were resuspended in 0.1 M NaOH and rotated for 5 min at room temperature. They were subsequently washed with TE-TW and TE. They were taken through second strand synthesis with Maxima RT buffer, PEG8000, dNTPs, dN-SMRT oligo, and Klenow Exo- (NEB, Cat: M0212L) in water. After rotating at 37 °C for 1 h, beads were washed twice with TE-TW, once with TE and once with water. KAPA HiFi Hotstart Readymix PCR Kit (Kapa Biosystems, Cat: KK2602) and SMART PCR Primer were used in whole transcriptome amplification (WTA). For each array, beads were distributed among 24 PCR reactions. Following WTA, three pools of eight reactions were made and were then purified using SPRI beads (Beckman Coulter), first at 0.6× and then at a 1× volumetric ratio. For each sample, one pool was run on an HSD5000 tape (Agilent, Cat: 5067–5592). The concentration of DNA for each of the three pools was measured via the Qubit dsDNA HS Assay kit (ThermoFisher, Cat: Q33230). Libraries were prepared for each pool, using 1000 pg of DNA and the Nextera XT DNA Library Preparation Kit. They were dual-indexed with N700 and N500 oligonucleotides.

value: Prostate

tag: age

tag: prostate size_(cc)

tag: ethnicity

value: White

tag: 5ari treatment

value: Yes


title: Saline3

description:
Library name: Sample3
Saline3

tag: genotype

tag: treatment

value: Saline


title: child/023-NPS

city: Leiden

first: Simon

last: Jochems

address: P4-32, LUMC, Albinusdreef 2

institute: LUMC

description: Library name: 238-13

data_processing:
UMI deduplication as per https://github.com/CGATOxford/UMI-tools
alignment using STAR to ref genome
Assembly: GRCh38.p13
Supplementary files format and content: text file including raw counts after UMI deduplication for each sample

extract_protocol:
Split RNA extraction kit was used as per manufacturer protocols. RNA quantity was checked with Qubit
QuantSeq fwd library prep (Lexogen)

tag: tissue

value: nasal

tag: cell type

value: nasal cells

value: child


title: PRO2, clr4Δ, heat-treatment 2.5min, rep2

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ clr4{delta}::NatMX6

value: 2.5 min atter heat-treatment


title: PRO2, clr4Δ, heat-treatment 0min, rep2

value: 0 min (non treated)


title: PLEA2

description:
Library name: Sample5
PLEA2

value: Brain

value: WT


title: PRO2, clr4Δ, heat-treatment 5min, rep1

value: 5 min atter heat-treatment


title: Lung, control diet, filtered air, 4

description: Library name: 5916


title: HoLEP30 [HoLEP_30A_S100]

description:
Library name: HoLEP_30A_S100
SeqWell


title: PRO2, clr4Δ, heat-treatment 2.5min, rep1


title: HoLEP29 [HoLEP_29B_S91]

description:
Library name: HoLEP_29B_S91
SeqWell

value: Korean


title: Saline2

description:
Library name: Sample2
Saline2

value: Day 3


title: Lung, control diet, filtered air, 3

description: Library name: 5915

value: Lung