title: Rectal tissue RNA-seq sample 111R from ART-treated PWH donor 111

city: shenzhen

first: huang

last: peiming

state: Guangdong

address: xinhu

institute: Sun Yat-sen University

description: Library name: 111R

data_processing:
Raw paired-end FASTQ files were assessed using FastQC v0.12.1.
Raw FASTQ files were processed with fastp v0.23.2 for adapter trimming and quality control using --detect_adapter_for_pe, --trim_poly_g, and --cut_right; filtered reads were written to the cleandata directory.
Clean reads were aligned to the human reference genome GRCh38 primary assembly using HISAT2 v2.2.1.
SAM files were converted to BAM format and sorted using samtools v1.9.
Gene-level read counts were generated using featureCounts v2.0.1 with paired-end exon-level counting summarized by gene_id; count files from all samples were merged into a count matrix for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited gene-level raw count matrix generated by featureCounts. Rows are Ensembl gene IDs and columns are the 14 final analysis samples.

source_name: rectum

growth_protocol: No growth protocol was used. Primary clinical samples were collected from ART-treated people with HIV.

extract_protocol:
PBMCs, rectal tissue, and subcutaneous adipose tissue were collected from ART-treated people with HIV. Total RNA was extracted from isolated cells or tissue samples, and RNA concentration and quality were assessed before library preparation.
Bulk RNA-seq libraries were constructed from total RNA according to the sequencing provider protocol and sequenced as paired-end reads on the DNBSEQ-T7 platform.

treatment_protocol: Participants were receiving suppressive antiretroviral therapy. No ex vivo treatment was applied to samples before RNA extraction.

value: rectum

value: bulk tissue

value: suppressive antiretroviral therapy


title: WT_18C_BioRep1

status: Public on Jun 25 2026

type: SRA

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

country: USA

institute: National Institutes of Health

description:
Library name: RNAseq_6
WT_18C

library_source: transcriptomic

data_processing:
Single ended short reads from RNAseq experiments were quality trimmed using fastp (Chen et al. 2018) and aligned to the reference genome using the STAR aligner (Dobin, A. et al., 2013). Wig files, normalized to counts per million mapped reads, were generated by STAR.
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

molecule: total RNA

organism: Schizosaccharomyces pombe

source_name: Yeast Whole Cells

growth_protocol: For RNA Seq, cells were grown in YEA at 30°C, 18°C or  36°C for 5 hours for temperature-sensitive strains  as mentioned

extract_protocol:
Total RNA isolated using the MasterPure Yeast RNA Purification Kit following the manufacturer's protocol
For RNA Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).
Total RNA isolated was first ribodepleted using the Ribo-Zero gold plus for humans (Illumina) supplemented with probes against S. pombe ribosomal DNA (IDT) for library construction

tag: strain

tag: genotype

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI

tag: cell type

value: Yeast Whole Cells

tag: growth

value: Growth in YEA 18°C


title: L. interrogans serogroup Icterohaemorrhagiae 202102576 in EMJH medium replicate #2

city: Paris

first: Rania

last: Ouazahrou

address: 28 rue docteur Roux

country: France

institute: Institut Pasteur Paris

description:
Library name: IC2_EMJH_2_S8
IC2_raw_counts.txt

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.19.2)
FeatureCounts 2.0.1 was used to produce the count matrix, assigning reads to features using corresponding primary annotation with strand-specificity information.
Differential expression testing was conducted using DESeq2 (PMID: 25516281)
Assembly: L. interrogans serogroup Icterohaemorrhagiae (G4) : isolate 202101402 (IC1) ; 202102576 (IC2) ; 202102995 (IC3) ; 202100001 (IC4) ; 202102907 (IC5). L. interrogans serogroup Pomona (G13) :  201801210 (PO1) ; 201700303 (PO2) ; 201902969 (PO3) ; 202100004 (PO4).
Supplementary files format and content: Tabulated files containing raw counts for each sample

organism: Leptospira interrogans

source_name: serogroup Icterohaemorrhagiae isolate 202102576

growth_protocol: Leptospira strains were cultivated aerobically in Ellighausen-McCullough-Johnson-Harris liquid medium (EMJH) at 30°C with shaking at 100 rpm.

extract_protocol:
Total RNAs were extracted using RNeasy Mini Kit (Qiagen), with a DNAse digestion (Qiagen) incorporated in the protocol.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus prep kit with the addition of custom primer that target L. interrogans rRNA following manufacturer's protocol.

treatment_protocol: Exponential phase cultures of the five G4 strains and the four G13 strains used (each strain, at least, in duplicate) in EMJH and EMEM medium at 3 days post-incubation.

tag: serogroup

value: Icterohaemorrhagiae

value: Bacterial cell

tag: treatment

value: EMJH medium


title: A549, Avobenzone, CA10, 6h, A02

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

institute: Procter & Gamble

description: Library name: CA10_T1_D3_A02

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

organism: Homo sapiens

source_name: lung

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

tag: tissue

value: lung

tag: cell line

value: epithelial cell

value: Adenocarcinoma

value: test

tag: batch


title: PBMC RNA-seq sample 111P from ART-treated PWH donor 111

country: China

description: Library name: 111P

source_name: blood

value: blood

value: peripheral blood mononuclear cell


title: Subcutaneous adipose tissue RNA-seq sample 104S from ART-treated PWH donor 104

description: Library name: 104S

source_name: subcutaneous adipose tissue

value: subcutaneous adipose tissue


title: L. interrogans serogroup Icterohaemorrhagiae 202102576 in EMJH medium replicate #1

description:
Library name: IC2_EMJH_1_S7
IC2_raw_counts.txt


title: cwf10-1_36C

description:
Library name: RNAseq_5
cwf10-1_36C

value: Growth in YEA at 26°C then shifted to  36°C for 5hrs


title: A549, Avobenzone, CA10, 6h, H01

description: Library name: CA10_T1_D2_H01


title: L. interrogans serogroup Icterohaemorrhagiae 202101402 in EMJH medium replicate #3

description:
Library name: IC1_EMJH_3_S6
IC1_raw_counts.txt

source_name: serogroup Icterohaemorrhagiae isolate 202101402


title: A549, Avobenzone, CA10, 6h, F04

description: Library name: CA10_T1_D2_F04


title: WT_36C_a

description:
Library name: RNAseq_4
WT_36C


title: PBMC RNA-seq sample 104P from ART-treated PWH donor 104

description: Library name: 104P


title: L. interrogans serogroup Icterohaemorrhagiae 202101402 in EMJH medium replicate #2

description:
Library name: IC1_EMJH_2_S5
IC1_raw_counts.txt


title: mug174-3HA_KanMX_30C

description:
Library name: RNAseq_3
mug174-3HA_30C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI mug174-1-3HA<<KanMX

value: Growth in YEA 30°C


title: Subcutaneous adipose tissue RNA-seq sample 097S from ART-treated PWH donor 097

description: Library name: 097S

value: bulk tissue

value: suppressive antiretroviral therapy


title: L. interrogans serogroup Icterohaemorrhagiae 202101402 in EMJH medium replicate #1

description:
Library name: IC1_EMJH_1_S4
IC1_raw_counts.txt


title: A549, Avobenzone, CA10, 6h, E07

description: Library name: CA10_T1_D2_E07


title: tgs1∆_30C

description:
Library name: RNAseq_2
tgs1∆_30C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI tgs1D::KanMX

value: Yeast Whole Cells


title: A549, Avobenzone, CA10, 6h, D10

description: Library name: CA10_T1_D2_D10


title: L. interrogans serogroup Icterohaemorrhagiae 202102907 in cell medium replicate #3

description:
Library name: IC5_cell-med_3_S36
IC5_raw_counts.txt

source_name: serogroup Icterohaemorrhagiae isolate 202102907

value: Icterohaemorrhagiae

value: cell medium


title: PBMC RNA-seq sample 097P from ART-treated PWH donor 097

description: Library name: 097P


title: WT_30C_a

description:
Library name: RNAseq_1
WT_30C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI


title: Subcutaneous adipose tissue RNA-seq sample 095S from ART-treated PWH donor 095

description: Library name: 095S


title: A549, Avobenzone, CA10, 6h, G01

description: Library name: CA10_T1_D1_G01

value: lung


title: tgs1∆_ura4cenCIs

description:
Library name: SRNAseq_8
tgs1∆_rrp6∆_ura4cenCIs_30C

data_processing:
Number of reads normalized to counts per 10 million for each sample
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: SGR format of  multi-mapping (all reads) and single-mapping (unique reads, “filtered”) counts per 10 million mapped reads (CP10M).

growth_protocol: Samples were grown at 30°C on rich YEA media

extract_protocol:
Total RNA was first isolated using the MasterPure Yeast RNA Purification Kit following the manufacturer's protocol. Small RNA was separated  from the total RNA by running a 15% urea- PAGE
For small RNA Seq-Sequencing libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina and analyzed using an Agilent 4200 TapeStation system (Agilent).

value: Msmt0 leu1-32 ade6-216 his2 Pura4-ura4:cenCIs<<Kan tgs1D::NatMX


title: A549, Avobenzone, CA10, 6h, E04

description: Library name: CA10_T1_D1_E04

value: epithelial cell

value: Adenocarcinoma


title: L. interrogans serogroup Icterohaemorrhagiae 202102907 in cell medium replicate #1

description:
Library name: IC5_cell-med_1_S12
IC5_raw_counts.txt

value: Bacterial cell


title: PBMC RNA-seq sample 095P from ART-treated PWH donor 095

description: Library name: 095P

value: blood

value: peripheral blood mononuclear cell


title: L. interrogans serogroup Icterohaemorrhagiae 202102907 in cell medium replicate #2

description:
Library name: IC5_cell-med_2_S35
IC5_raw_counts.txt


title: WT_ura4cenCIs

description:
Library name: SRNAseq_7
WT_ura4cenCIs_30C

value: Msmt0  leu1-32 ade6-216 his2 Pura4-ura4:cenCIs<<Kan


title: A549, Avobenzone, CA10, 6h, D07

description: Library name: CA10_T1_D1_D07

value: test


title: eas1∆_BioRep2

description:
Library name: 251012c
eas1∆_18C

data_processing:
Single ended short reads from RNAseq experiments were quality trimmed using fastp (Chen et al. 2018) and aligned to the reference genome using the STAR aligner (Dobin, A. et al., 2013). Wig files, normalized to counts per million mapped reads, were generated by STAR.
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT); HG19 human genome reference; T2T.CHM13v2.0 human telomere-to-telomere human reference.
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

extract_protocol:
Total RNA isolated using the MasterPure Yeast RNA Purification Kit following the manufacturer's protocol
For RNA Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent). Total RNA isolated was first ribodepleted using the Ribo-Zero gold plus for humans (Illumina) supplemented with probes against S. pombe ribosomal DNA (IDT) for library construction.

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI eas1D::NatMX

value: Growth in YEA 18°C


title: pir2-1_rrp6∆

description:
Library name: SRNAseq_6
pir2-1_rrp6∆_30C

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E rrp6D::KanMX pir2-1-FLAG::KanMX

value: Growth in YEA 30°C


title: L. interrogans serogroup Icterohaemorrhagiae 202100001 in cell medium replicate #1

description:
Library name: IC4_cell-med_3_S34
IC4_raw_counts.txt

source_name: serogroup Icterohaemorrhagiae isolate 202100001


title: Rectal tissue RNA-seq sample 092R from ART-treated PWH donor 092

description: Library name: 092R

value: rectum

value: bulk tissue

value: suppressive antiretroviral therapy


title: A549, Avobenzone, CA10, 6h, B10

description: Library name: CA10_T1_D1_B10


title: PBMC RNA-seq sample 092P from ART-treated PWH donor 092

description: Library name: 092P


title: rrp6∆_BioRep3

description:
Library name: SRNAseq_5
rrp6∆_30C

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E rrp6D::KanMX

value: Yeast Whole Cells


title: L. interrogans serogroup Icterohaemorrhagiae 202102995 in cell medium replicate #2

description:
Library name: IC3_cell-med_3_S33
IC3_raw_counts.txt

source_name: serogroup Icterohaemorrhagiae isolate 202102995

value: Icterohaemorrhagiae

value: cell medium


title: Rectal tissue RNA-seq sample 084R from ART-treated PWH donor 084

description: Library name: 084R


title: L. interrogans serogroup Icterohaemorrhagiae 202102995 in cell medium replicate #1

description:
Library name: IC3_cell-med_1_S8
IC3_raw_counts.txt


title: A549, DMSO, CA10, 6h, F05

description: Library name: CA10_DMSO_F05

value: lung

value: epithelial cell

value: Adenocarcinoma

value: vehicle


title: PBMC RNA-seq sample 084P from ART-treated PWH donor 084

description: Library name: 084P

value: blood

value: peripheral blood mononuclear cell


title: L. interrogans serogroup Icterohaemorrhagiae 202102576 in cell medium replicate #1

description:
Library name: IC2_cell-med_1_S6
IC2_raw_counts.txt

value: Bacterial cell


title: tgs1∆_BioRep2

description:
Library name: 251012b
tgs1∆_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI  tgs1D::KanMX

value: Growth in YEA 18°C


title: A549, DMSO, CA10, 6h, D02

description: Library name: CA10_DMSO_D02


title: rrp6∆_BioRep2

description:
Library name: SRNAseq_3
rrp6∆_30C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1 CI rrp6D::hygR

value: Growth in YEA 30°C


title: Rectal tissue RNA-seq sample 048R from ART-treated PWH donor 048

description: Library name: 048R

value: rectum

value: bulk tissue


title: tgs1∆_rrp6∆_BioRep1

description:
Library name: SRNAseq_2
tgs1∆_rrp6∆_30C

value: Msmt0 leu1-32 ade6-216 his2 ura4::tf2-1CI_tgs1D::KanMX rrp6D::hygR


title: A549, DMSO, CA10, 6h, C10

description: Library name: CA10_DMSO_C10


title: L. interrogans serogroup Icterohaemorrhagiae 202101402 in cell medium replicate #2

description:
Library name: IC1_cell-med_3_S5
IC1_raw_counts.txt


title: L. interrogans serogroup Icterohaemorrhagiae 202101402 in cell medium replicate #1

description:
Library name: IC1_cell-med_1_S31
IC1_raw_counts.txt


title: PBMC RNA-seq sample 048P from ART-treated PWH donor 048

description: Library name: 048P

value: suppressive antiretroviral therapy


title: rrp6∆_BioRep1

description:
Library name: SRNAseq_1
rrp6∆_30C

value: Yeast Whole Cells


title: A549, DMSO, CA10, 6h, B12

description: Library name: CA10_DMSO_B12


title: NCC_rep2

status: Public on Jun 24 2026

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic was employed to trim reads ends where average base calling qualities (in 5 bp windows) were below Q20. Only reads with minimum length of 30 bp were kept for further analyses.
To separate reads that originated from human and chicken cells, we concatenated Ensembl human genome version hg38 (GRCh38) and Ensembl chicken genome version galgal5 (5.0.90), created an index file for this “chimeric reference genome”, and aligned all trimmed and filtered reads into it by using STAR version 2.7.1a.
Uniquely mapped reads were counted using featureCounts in Subread toolkit 1.6.473. By this approach, each read was only aligned and counted for the reference genome that had higher similarity to, and the reads with equal similarity to both genomes were excluded.
Counts normalization and differential expression analysis were performed using the R/Bioconductor package DESeq2. Genes having absolute log2 fold-change higher than 1 and Benjamini-Hochberg adjusted P-value less than 0.05 were considered as significant differentially expressed genes (DEGs).
The shrinkage of log fold changes was performed using “ashr” shrinkage estimator. Visualization of the results was done by ggplot2, pheatmap and EnhancedVolcano packages. Overrepresentation analysis was performed in DAVID Bioinformatics Resources76. Gene set enrichment analysis was performed using Broad Institute GSEA software.
Assembly: hg38 (GRCh38) / galgal5 (5.0.90)
Supplementary files format and content: Txt file of raw counts

organism: Gallus gallus

source_name: Cerebral cortex

extract_protocol:
miRNeasy micro kit (Qiagen)
Libraries for cell and tissue samples were generated by SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takar Bio).

value: Cerebral cortex

value: WT


title: NCC_rep1


title: TeO_rep3

source_name: Optic tectum

value: Optic tectum


title: COLXIV_KO_ZT_4 biol rep 3

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description: Library name: K_4_3

data_processing:
Adapters from reads were removed using TrimGalore with default parameters.
Reads were aligned to the mm10 version of musmusculus using STAR (v.2.7.10a) with default parameters
Count matrix was generated using the featureCounts function from the Rsubread R package using the Entrez gene annotation
Assembly: GRCm38.102
Supplementary files format and content: Count matrix in excel format

molecule: polyA RNA

organism: Mus musculus

source_name: epidermis

extract_protocol:
RNA was extracted from epidermal cell pellets frozen in Trizol using the NZY Total RNA Isolation Kit (NZY Tech)
Libraries were prepared using the TruSeq stranded mRNA Library Prep (20020595, Illumina) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing. Briefly, 500 ng of total RNA were used for polyA‐mRNA selection using Oligo‐dT beads, and two rounds of purification were performed. During the second elution of the mRNA, this was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis, which was performed using reverse transcriptase (SuperScript II; 18064‐014, Invitrogen). Then, second strand cDNA was synthesised, incorporating dUTP in place of dTTP and generating blunt‐ended ds cDNA. A single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments (A‐tailing) and immediately afterwards the Truseq adapter was ligated. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed using Unique Dual Indexes and the master mix provided with the kit. All purification steps were performed using AgenCourt AMPure XP beads (A63882, Beckman Coulter). Final libraries were analysed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (5067‐1504 or DNF‐473, Agilent) to estimate the quantity and validate the size distribution and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (07960204001, Roche).

treatment_protocol: Epidermal cells suspensions were obtained from the skin of 47 weeks old ColXIV KO and WT mice that were sacrificed at different times of the day (ZT0, 4, 8, 12, 16, 20).

value: epidermis

value: ColXIV KO


title: TeO_rep1


title: TeO_rep2


title: iTeO_iPS_rep2

source_name: Ectopic optic tectum

value: Ectopic optic tectum


title: tgs1∆_rrp6∆_BioRep2

description:
Library name: SRNAseq_4
tgs1∆_rrp6∆_30C


title: iTeO_iPS_rep1


title: iTeO_ES_rep1


title: iTeO_ES_rep2


title: Colon crypts from Muc2-/- mouse, replicate 2

city: Novosibirsk

first: Snezhanna

last: Medvedeva

address: Acad. Lavrentiev Ave. 8/2

country: Russia

institute: Institute of Molecular and Cellular Biology SB RAS

description: Library name: mut3_5

data_processing:
Raw data (FASTQ) were processed through in-house Perl scripts. Clean reads were obtained by removing reads containing adapter, reads containing poly-N, and low-quality reads from raw data. Q20, Q30, and GC content of the clean data were calculated.
Paired-end clean reads were aligned to the reference genome using HISAT2 (version 2.0.5) with default parameters
Transcript assembly was performed using StringTie v1.3.3b in a reference-based approach
featureCounts v1.5.0-p3 was used to count the reads mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (version 1.20.0). The resulting p-values were adjusted using the Benjamini and Hochberg approach for controlling the false discovery rate. Genes with an adjusted p-value <= 0.05 were considered differentially expressed.
Assembly: mm10
Supplementary files format and content: gene_count.txt: tab-delimited text file containing raw gene counts for each sample. Columns: GeneID followed by individual sample names
Supplementary files format and content: gene_fpkm.txt: tab-delimited text file containing FPKM values for each sample. Columns: GeneID followed by individual sample names

source_name: colon

growth_protocol: C57BL/6 and Muc2-/- mice of 12 weeks age were maintained under standard laboratory conditions. Colon tissues were dissected, and descending colon segments were collected for RNA extraction.

extract_protocol:
Total RNA was isolated from colon tissue samples using QIAzol lysis reagent (79306, Qiagen, Germany). Genomic DNA was removed by DNaseI (Roche, Germany) according to the manufacturers' recommendations. RNA concentration was analyzed using a NanoDrop 2000 spectrophotometer (ThermoScientific, USA).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. After end repair, A-tailing, adapter ligation, size selection, amplification, and purification, the library was completed. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on an Illumina platform according to effective library concentration and data amount, and paired-end reads were generated.

treatment_protocol: No specific treatment was applied to the animals prior to tissue collection.

value: colon


title: Colon crypts from Muc2-/- mouse, replicate 3

description: Library name: mut16


title: Colon crypts from Muc2-/- mouse, replicate 1

description: Library name: mut1_2


title: Colon crypts from wild-type mouse, replicate 2

description: Library name: wt3_7

value: wild-type


title: Colon crypts from wild-type mouse, replicate 1

description: Library name: wt1_2


title: Colon crypts from wild-type mouse, replicate 3

description: Library name: wt5_9


title: Pparg-flox, Mouse 3

city: Minneapolis

first: Hai-Bin

last: Ruan

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

description: Library name: Ppargwt3

data_processing:
PURR is the RNASeq analysis pipeline that is housed within CHURP, the Collection of Hierarchical UMII/RIS Pipelines. CHURP is developed and maintained by the Research Informatics Solutions (RIS) group at MSI with funding provided by the University of Minnesota Informatics Institute (UMII). https://www.msi.umn.edu/ https://research.umn.edu/units/umii
Read QC A subsample of 10,000 reads or read pairs were sampled from each sample's reads. This subsample of 10,000 reads was searched for contamination from ribosomal RNA using a representative rRNA sequence list from the SILVA database release 132. Raw reads were summarized with FastQC, and optionally trimmed with Trimmomatic. If trimmed, the cleaned reads are re-assessed with FastQC. Length, quality, and duplication metrics were extracted from each FastQC run.
Alignment Trimmed reads (or raw reads, if --no-trim was specified) were aligned to the reference genome with HISAT2. Duplicate reads based on alignment position were marked with SAMTools. If --rmdup was specified, then the positional duplicates were removed instead of marked. Alignments with duplicates marked were summarized with RNASeQC to quantify the proportion of positional duplicates, identify risosomal alignments, and quantify the proportion of "on-target" reads. Processed alignments were filtered of reads that have a mapping quality of less than 60, and sorted by query name rather than position.
Counts Cleaned and name-sorted alignments were processed with the featureCounts tool from the subread package. Fragments were counted in a strand-specific manner, unless the --strand U option was passed for a library that was prepared in a strand-unspecific way. Both mates of a read pair were required to map to a feature to be counted, if the data were paired-end.
Assembly: GRCm38
Supplementary files format and content: Raw counts excel

source_name: BAT

extract_protocol:
Qiagen RNA extraction Kit
Unique dual-indexed (UDI) TruSeq stranded mRNA libraries

value: BAT

value: 24h cold


title: Pparg-flox, Mouse 4

description: Library name: Ppargwt4


title: Pparg-flox, Mouse 2

description: Library name: Ppargwt2


title: Pparg-flox, Mouse 1

description: Library name: Ppargwt1


title: Pparg-flox, Myl1-Cre, Mouse 4

description: Library name: Ppargko4

value: KO


title: Pparg-flox, Myl1-Cre, Mouse 2

description: Library name: Ppargko2


title: Pparg-flox, Myl1-Cre, Mouse 1

description: Library name: Ppargko1


title: VTA_smoke

city: 杭州

first: XING

last: JI

state: State

address: 余杭塘路866号

institute: zhejiang university

description: Library name: Sample 6

library_source: transcriptomic single cell

data_processing:
Alignment, demultiplexing, barcode assignment and UMI quantification
Clustering and gene expression analysis
Assembly: mm10
Supplementary files format and content: Cell Ranger output files as Matrix (.mtx) and .tsv formats, and gene expression analysis from Seurat as Excel Spreadsheet (.xlsx)

source_name: VTA

extract_protocol:
brain tissues were finely minced into ~0.1 cm fragments and transferred into a mixture of 1 ml lysis buffer and 1 ml PBS. Samples were washed twice in PBS by centrifugation to remove the supernatant. Tissues were then incubated with 2 ml of pre-chilled lysis buffer on ice for 2 minutes for pre-lysis. Homogenization was carried out using a Dounce homogenizer (Sigma), followed by gentle pipetting (5–6 times) to ensure complete dissociation. The homogenate was kept on ice for 6 minutes, after which 2 ml of pre-chilled 4% BSA was added to dilute the mixture and terminate lysis. This was followed by pipetting (6–8 times) with a Pasteur pipette. Samples were centrifuged at 300 × g for 5 minutes at 4°C, and the supernatant was discarded. The resulting pellet was resuspended in 2 ml of lysis buffer containing 4% BSA and incubated on ice for an additional 3 minutes. Cellular debris was removed using the Miltenyi Biotec Debris Removal Solution (Order no. 130-109-398). After a second centrifugation under the same conditions, the nuclei were resuspended in a nuclear resuspension buffer (1× PBS, 2% BSA, 0.1% RNase inhibitor, Roche). Nuclei were then filtered through a 20-μm cell strainer and counted.
Final libraries were sequenced using an Illumina NovaSeq 6000 platform with paired-end 150 bp reads by LC-Bio Technology Co. (Hangzhou, China).

value: VTA

value: brain cells

value: smoke


title: Pparg-flox, Myl1-Cre, Mouse 3

description: Library name: Ppargko3


title: VTA_Ctrl

description: Library name: Sample 4

value: Ctrl


title: smoke

description: Library name: Sample 3

source_name: brain

value: brain


title: VTA_nicotine

description: Library name: Sample 5

value: nicotine


title: nicotine

description: Library name: Sample 2


title: Ctrl

description: Library name: Sample 1


title: GFP-RIP_Tgs1-GFP_pir1∆_BioRep2

description:
Library name: RIPseq_25
Tgs1-GFP_pir1∆

data_processing:
Normalization done to reads per million for each sample. Normalized samples were subtracted from untagged controls
Samples 1, 7, 12 , 23, 24 uses sample 2 as untagged; Samples 3, 25 and 26 uses sample 5 as untagged; Sample 4 uses sample 6 as untagged; Sample 8 uses sample 9 as untagged; Sample 10 uses sample 11 as untagged; Sample 13 uses sample 14 as untagged; Sample 15, 17 and 20 uses sample 16 as untagged; Sample 18 uses sample 19 as untagged; Sample 21 uses sample 22 as untagged; Sample 27 uses sample 29 as untagged; Sample 28 uses sample 30 as untagged; Sample 31 uses sample 33 as untagged; Sample 32 uses sample 34 as untagged
Sample 18 uses sample 19 as untagged; Sample 21 uses sample 22 as untagged; Sample 29 uses sample 31 as untagged; Sample 30 uses sample 32 as untagged
Sample 33 uses sample 35 as untagged; Sample 34 uses sample 36 as untagged

Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM) (untagged controls) or RPM-normalized counts for the IP minus RPM counts of an untagged control (IPs).
Supplementary files format and content: Figure 3a,3b: Samples 3,4 for Tf2-3, Samples 7,8,9 for other genes
Supplementary files format and content: Figure 4j: Samples 23,24
Supplementary files format and content: Figure 5e: Samples 17,18
Supplementary files format and content: Figure 7a: Samples 27,28

source_name: Yeast Whole Cells

growth_protocol: Cells were grown on YEA rich media at 30°C  for all cases except for experiments performed to check meiotic targets. For meiotic targets, cells grown to 0.1 OD600 at 30°C in YEA was shifted to 18°C for 24 hrs

extract_protocol:
Immunoprecipitation of epitope tagged protein, Proteinase treatment to remove protein; DNAse treatment to remove DNA and acid phenol-chloroform extraction to isolate associated RNA followed by ethanol precipitation
For RIP Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).
RNA coimmunoprecipitated with epitope tagged proteins were used for library preparation.

value: Msmt0 leu1-32 ade6-210 his2 ura4 DS/E Tgs1-GFP::KanMX6 pir1D otr1R(Sph1)::ura4 +

value: Yeast Whole Cells

tag: rip antibody

value: Anti-GFP Ab290

value: Growth in YEA 30°C, shifted to 18°C for 24 hrs


title: MLL-AF9_FLT3-ITD_DMSO_2

city: Edinburgh

first: Yuka

last: Kabayama

address: Max Born Crescent

country: United Kingdom

institute: University of Edinburgh

description:
Library name: MLL-AF9_FLT3-ITD_DMSO_2
raw_counts_All_Samples.txt
MLL-AF9_FLT3-ITD_DMSO_2
MLL_DMSO_C

data_processing:
For 2266- or vehicle-treated Npm1/Flt3-ITD and Mll-AF9/Flt3-ITD cells, and 2266-treated Meis1/Hoxa9 cells, paired-end RNA-seq reads were trimmed with Trim Galore v0.6.5 to remove adapter sequences and low-quality reads. Trimmed reads from these samples were aligned to the Mus musculus mm39/GRCm39 genome assembly using STAR aligner v2.7.9a. Reads mapped to exons were assigned to genes using featureCounts v2.0.dddc6 with Ensembl release 110 gene annotations. Differential gene expression analysis was performed using DESeq2 v1.42.1. For Tut4/7CTL and Tut4/7cKO Meis1/Hoxa9 samples, adapter sequences were removed using cutadapt v1.17, and reads were mapped to the GRCm38 genome_tran reference, release 84, using HISAT2 v2.1.0.Mapped reads from Tut4/7CTL and Tut4/7cKO samples were counted per gene using htseq-count from HTSeq v0.11.1 with the corresponding GTF annotation file. Differential gene expression analysis was performed using DESeq2.
Assembly: Mus musculus mm39/GRCm39 for 2266- or vehicle-treated Npm1/Flt3-ITD and Mll-AF9/Flt3-ITD cells and 2266-treated Meis1/Hoxa9 cells; Mus musculus GRCm38/mm10 genome_tran, release 84, for Tut4/7CTL and Tut4/7cKO Meis1/Hoxa9 cells.
Supplementary files format and content: Tab-delimited text files containing gene-level read counts for each RNA-seq sample. Rows represent genes annotated using the relevant mouse gene annotation, and columns represent individual samples names.

source_name: Cultured leukaemic cells

growth_protocol: Murine leukemic MLL-AF9/Flt3-ITD and NPM1/Flt3-ITD were cultured in X-Vivo 20 Lonza (BE04 448Q with gentamycin), 5% FBS, 1% Pen/Strep/Glutamax, 10ng/ml mIL6, 10ng/ml mIL3, 50ng/ml mSCF. Meis1/HoxA9 cells were cultured in IMDM media supplemented with 10% FCS, 1% Pen/Strep/Glutamax, 40 ng/mL SCF, 20 ng/mL IL3 and 20ng/mL IL6.

extract_protocol:
Direct Zol RNA miniprep (R2050) according to manufacturer's instructions
Libraries from MLL-AF9; Flt3-ITD and NPM1c; Flt3-ITD cells were constructed using Lexogen RiboCop (HMR) and Corall Total RNA-seq V2 library prep kit according to manufacturer’s instructions. Sequencing performed by Novogene. Librarys from Meis1/Hoxa9 cells were produced and sequenced by Novogene following their lncRNA-seq protocol

treatment_protocol: Cells were cultured with 4 µM 2266 or matched controls treated with DMSO vehicle control. 3M cells were harvested after 48 hrs treatment.

value: Cultured leukaemic cells

value: AML

value: Wild type

value: DMSO vehicle


title: MLL-AF9_FLT3-ITD_DMSO_1

description:
Library name: MLL-AF9_FLT3-ITD_DMSO_1
raw_counts_All_Samples.txt
MLL-AF9_FLT3-ITD_DMSO_1
MLL_DMSO_B


title: MLL-AF9_FLT3-ITD_2266_3

description:
Library name: MLL-AF9_FLT3-ITD_2266_3
raw_counts_All_Samples.txt
MLL-AF9_FLT3-ITD_2266_3
MLL_66_C


title: NPM1_FLT3-ITD_DMSO_2

description:
Library name: NPM1_FLT3-ITD_DMSO_2
raw_counts_All_Samples.txt
NPM1_FLT3-ITD_DMSO_2
NPM1_DMSO_C


title: MLL-AF9_FLT3-ITD_2266_1

description:
Library name: MLL-AF9_FLT3-ITD_2266_1
raw_counts_All_Samples.txt
MLL-AF9_FLT3-ITD_2266_1
MLL_66_A


title: NPM1_FLT3-ITD_2266_3

description:
Library name: NPM1_FLT3-ITD_2266_3
raw_counts_All_Samples.txt
NPM1_FLT3-ITD_2266_3
NPM1_66_C


title: NPM1_FLT3-ITD_2266_1

description:
Library name: NPM1_FLT3-ITD_2266_1
raw_counts_All_Samples.txt
NPM1_FLT3-ITD_2266_1
NPM1_66_A


title: MLL-AF9_FLT3-ITD_2266_2

description:
Library name: MLL-AF9_FLT3-ITD_2266_2
raw_counts_All_Samples.txt
MLL-AF9_FLT3-ITD_2266_2
MLL_66_B


title: NPM1_FLT3-ITD_DMSO_1

description:
Library name: NPM1_FLT3-ITD_DMSO_1
raw_counts_All_Samples.txt
NPM1_FLT3-ITD_DMSO_1
NPM1_DMSO_B


title: Meis1Hoxa9_DMSO_4

description:
Library name: Meis1Hoxa9_DMSO_4
raw_counts_All_Samples.txt
Meis1Hoxa9_DMSO_4
Meis1Hoxa9_DMSO_4


title: Meis1Hoxa9_DMSO_5

description:
Library name: Meis1Hoxa9_DMSO_5
raw_counts_All_Samples.txt
Meis1Hoxa9_DMSO_5
Meis1Hoxa9_DMSO_5


title: NPM1_FLT3-ITD_2266_2

description:
Library name: NPM1_FLT3-ITD_2266_2
raw_counts_All_Samples.txt
NPM1_FLT3-ITD_2266_2
NPM1_66_B


title: Meis1Hoxa9_DMSO_3

description:
Library name: Meis1Hoxa9_DMSO_3
raw_counts_All_Samples.txt
Meis1Hoxa9_DMSO_3
Meis1Hoxa9_DMSO_3


title: Meis1Hoxa9_DMSO_2

description:
Library name: Meis1Hoxa9_DMSO_2
raw_counts_All_Samples.txt
Meis1Hoxa9_DMSO_2
Meis1Hoxa9_DMSO_2


title: Meis1Hoxa9_2266_5

description:
Library name: Meis1Hoxa9_2266_5
raw_counts_All_Samples.txt
Meis1Hoxa9_2266_5
Meis1Hoxa9_2266_5


title: Meis1Hoxa9_2266_4

description:
Library name: Meis1Hoxa9_2266_4
raw_counts_All_Samples.txt
Meis1Hoxa9_2266_4
Meis1Hoxa9_2266_4


title: Meis1Hoxa9_DMSO_1

description:
Library name: Meis1Hoxa9_DMSO_1
raw_counts_All_Samples.txt
Meis1Hoxa9_DMSO_1
Meis1Hoxa9_DMSO_1


title: Meis1Hoxa9_2266_3

description:
Library name: Meis1Hoxa9_2266_3
raw_counts_All_Samples.txt
Meis1Hoxa9_2266_3
Meis1Hoxa9_2266_3


title: Meis1Hoxa9_2266_2

description:
Library name: Meis1Hoxa9_2266_2
raw_counts_All_Samples.txt
Meis1Hoxa9_2266_2
Meis1Hoxa9_2266_2


title: Atria, males, NaV1.5 4w HFD&NR - 5

city: New York

first: Paul

last: Zumbo

address: 1300 York Ave

department: Applied Bioinformatics Core

institute: Weill Cornell Medicine

description: Library name: 12430

data_processing:
Raw reads were quality checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm38) using STAR v2.7.6a with default parameters. Gene abundances were calculated with featureCounts v2.0.1  using composite gene models from Gencode release vM25
Assembly: mm10
Supplementary files format and content: Tab-delimited text file of raw gene-level read counts (featureCounts output)

source_name: Atria

extract_protocol:
total RNA was extracted using miRNeasy micro kit, at least 500ng was used for library construction
Truseq Stranded mRNA Sample Prep (Poly A selection)

treatment_protocol: Mice were treated with regular diet (RD), 4 weeks high-fat diet (HFD), 4 weeks high-fat diet vehicle (HFD vehicle) or 4 weeks high-fat diet with nicotinamide riboside (HFD&NR) starting at 5 weeks of age

value: Atria

value: 4w HFD&NR


title: Meis1Hoxa9_2266_1

description:
Library name: Meis1Hoxa9_2266_1
raw_counts_All_Samples.txt
Meis1Hoxa9_2266_1
Meis1Hoxa9_2266_1


title: Atria, males, NaV1.5 4w HFD&NR - 2

description: Library name: 12423


title: Atria, males, NaV1.5 4w HFD&NR - 1

description: Library name: 12421


title: Atria, males Ctrls 4w HFD - 3

description: Library name: 5296

value: 4w HFD


title: Atria, males, NaV1.5 4w HFD&NR - 4

description: Library name: 12425


title: A549, DMSO, CA10, 6h, G08

description: Library name: CA10_DMSO_G08

source_name: lung

value: lung

value: epithelial cell

value: Adenocarcinoma

value: vehicle


title: Atria, males, NaV1.5 4w HFD - 3

description: Library name: 4523


title: Atria, males Ctrls 4w HFD - 4

description: Library name: 5298

value: Ctrl


title: Atria, males, NaV1.5 4w HFD - 4

description: Library name: 5227


title: Atria, males, NaV1.5 4w HFD&NR - 3

description: Library name: 12424


title: Atria, males Ctrls 4w HFD - 1

description: Library name: 3900


title: Atria, males, Ctrls RD - 4

description: Library name: 3899

value: RD


title: Atria, males, NaV1.5 4w HFD - 5

description: Library name: 5230


title: Atria, males, NaV1.5 4w HFD - 2

description: Library name: 3897


title: Atria, males Ctrls 4w HFD - 2

description: Library name: 5223


title: Atria, males, NaV1.5 RD

description: Library name: 5229


title: Atria, males, Ctrls RD - 3

description: Library name: 3894


title: Atria, males, NaV1.5 RD - 3

description: Library name: 3891


title: Atria, males, NaV1.5 RD - 2

description: Library name: 3620


title: Atria, males, Ctrls RD - 2

description: Library name: 2947


title: Atria, males, Ctrls RD -

description: Library name: 2870


title: Atria, males, NaV1.5 RD - 1

description: Library name: 2617


title: WT_Ossicle_wk25_Rep15

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description: Library name: WT_Ossicle_wk25_Rep15

data_processing:
Full RNA-seq data processing pipeline can be found at https://gitlab.com/hssgenomics/pipelines/. The main steps include:
1. fastp -q 15 -n 10 -l 20 –detect_adapter_for_pe  -i target_R1.fastq -I target_R2.fastq (fastp v0.19.10)
2. STAR --readFilesIn target_R1.fastq target_R2.fastq --outSAMtype BAM Unsorted --outFilterMultimapNmax 4 --outFilterType BySJout --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --outSAMstrandField intronMotif --sjdbGTFfile gencode_v33.gtf --outReadsUnmapped Fastx (STAR v2.7.3a)
3. samtools sort -n target_STAR.Aligned.out.bam | samtools fixmate -rm - - | samtools sort - | samtools markdup -l 800 -rs – target_STAR.Aligned.sortedByCoord.out.bam (samtools v1.9)
4. featureCounts -p -a gencode_v33.gtf -s 2 -o reverse_stranded.txt target_STAR.Aligned.sortedByCoord.out.bam (featureCounts v2.0.1)
5. Full details of the differential gene expression workflow are available at: https://gitlab.com/hssgenomics/workflow-rnaseq. Briefly, differential gene expression analysis was performed in R (version 4.5.2) using edgeR (version 4.8).
Assembly: mm10
Supplementary files format and content: edgeR_DEGs_2024-07-25_noSex.xlsx multi-worksheet excel file containing all counts per sample, filtered counts per sample, normalized log transformed counts (log2 cpm) and the results of edgeR differential expression analysis
Supplementary files format and content: edgeR_DEGs_2024-07-15_SexEffect.xlsx multi-worksheet excel file containing all counts per sample, filtered counts per sample, normalized log transformed counts (log2 cpm) and the results of edgeR differential expression analysis

source_name: Ossicle

growth_protocol: Mice were generated by crossing oim/+ (HET) mice to each other. Breeder mice (#001815) were purchased from Jackson Laboratories.

extract_protocol:
Male and female mice with oim/oim (HOM), oim/+ (HET) and +/+ (WT) genotypes were euthanized at 12 or 25 weeks of age. Total RNA was extracted from the otic capsule or marrow-flushed femur using the RNeasy kit (Qiagen). RNA-seq libraries were prepared using the non-stranded TruSeq RNA Sample Preparation Kits and sequenced on the Illumina Novaseq 6000 platform to generate 50bp paired-end reads.
Sequencing libraries were prepared with Illumina TrueSeq kit and sequenced by the Genomics Resource Core Facility at Weill Cornell Medicine.

value: Ossicle

tag: age

value: total cells from auditory bulla

value: WT

tag: mouse id

tag: replica

tag: Sex

value: Male


title: Atria, males, NaV1.5 4w HFD - 1

description: Library name: 2854


title: WT_Ossicle_wk25_Rep16

description: Library name: WT_Ossicle_wk25_Rep16


title: WT_Ossicle_wk25_Rep13

description: Library name: WT_Ossicle_wk25_Rep13

value: Female


title: WT_Ossicle_wk25_Rep14

description: Library name: WT_Ossicle_wk25_Rep14


title: WT_Ossicle_wk25_Rep7

description: Library name: WT_Ossicle_wk25_Rep7


title: WT_Ossicle_wk25_Rep10

description: Library name: WT_Ossicle_wk25_Rep10


title: WT_Ossicle_wk25_Rep8

description: Library name: WT_Ossicle_wk25_Rep8


title: WT_Ossicle_wk25_Rep9

description: Library name: WT_Ossicle_wk25_Rep9


title: WT_Ossicle_wk25_Rep11

description: Library name: WT_Ossicle_wk25_Rep11


title: WT_Ossicle_wk25_Rep12

description: Library name: WT_Ossicle_wk25_Rep12


title: WT_Ossicle_wk25_Rep5

description: Library name: WT_Ossicle_wk25_Rep5


title: WT_Ossicle_wk25_Rep4

description: Library name: WT_Ossicle_wk25_Rep4


title: WT_Ossicle_wk25_Rep3

description: Library name: WT_Ossicle_wk25_Rep3


title: WT_Ossicle_wk25_Rep1

description: Library name: WT_Ossicle_wk25_Rep1


title: WT_Ossicle_wk12_Rep9

description: Library name: WT_Ossicle_wk12_Rep9


title: WT_Ossicle_wk12_Rep7

description: Library name: WT_Ossicle_wk12_Rep7


title: WT_Ossicle_wk12_Rep8

description: Library name: WT_Ossicle_wk12_Rep8


title: WT_Ossicle_wk12_Rep6

description: Library name: WT_Ossicle_wk12_Rep6


title: WT_Ossicle_wk12_Rep5

description: Library name: WT_Ossicle_wk12_Rep5


title: WT_Ossicle_wk12_Rep2

description: Library name: WT_Ossicle_wk12_Rep2


title: WT_Ossicle_wk12_Rep3

description: Library name: WT_Ossicle_wk12_Rep3


title: WT_Femur_wk25_Rep15

description: Library name: WT_Femur_wk25_Rep15

source_name: Femur

value: Femur

value: total non-bone-marrow cells from femur


title: WT_Ossicle_wk12_Rep1

description: Library name: WT_Ossicle_wk12_Rep1


title: WT_Ossicle_wk12_Rep4

description: Library name: WT_Ossicle_wk12_Rep4


title: WT_Femur_wk25_Rep12

description: Library name: WT_Femur_wk25_Rep12


title: WT_Femur_wk25_Rep11

description: Library name: WT_Femur_wk25_Rep11


title: WT_Femur_wk25_Rep13

description: Library name: WT_Femur_wk25_Rep13


title: WT_Femur_wk25_Rep14

description: Library name: WT_Femur_wk25_Rep14


title: WT_Femur_wk25_Rep10

description: Library name: WT_Femur_wk25_Rep10


title: WT_Femur_wk25_Rep9

description: Library name: WT_Femur_wk25_Rep9


title: WT_Femur_wk25_Rep8

description: Library name: WT_Femur_wk25_Rep8


title: WT_Femur_wk25_Rep6

description: Library name: WT_Femur_wk25_Rep6


title: WT_Femur_wk25_Rep2

description: Library name: WT_Femur_wk25_Rep2


title: WT_Femur_wk25_Rep3

description: Library name: WT_Femur_wk25_Rep3


title: WT_Femur_wk12_Rep7

description: Library name: WT_Femur_wk12_Rep7


title: WT_Femur_wk12_Rep10

description: Library name: WT_Femur_wk12_Rep10


title: WT_Femur_wk25_Rep1

description: Library name: WT_Femur_wk25_Rep1


title: WT_Femur_wk12_Rep8

description: Library name: WT_Femur_wk12_Rep8


title: WT_Femur_wk12_Rep9

description: Library name: WT_Femur_wk12_Rep9


title: WT_Femur_wk12_Rep6

description: Library name: WT_Femur_wk12_Rep6


title: OIM_Ossicle_wk25_Rep11

description: Library name: OIM_Ossicle_wk25_Rep11

value: OIM - oim/oim


title: OIM_Ossicle_wk25_Rep9

description: Library name: OIM_Ossicle_wk25_Rep9


title: OIM_Ossicle_wk25_Rep10

description: Library name: OIM_Ossicle_wk25_Rep10


title: OIM_Ossicle_wk25_Rep8

description: Library name: OIM_Ossicle_wk25_Rep8


title: OIM_Ossicle_wk25_Rep7

description: Library name: OIM_Ossicle_wk25_Rep7


title: OIM_Ossicle_wk25_Rep5

description: Library name: OIM_Ossicle_wk25_Rep5


title: OIM_Ossicle_wk25_Rep4

description: Library name: OIM_Ossicle_wk25_Rep4


title: OIM_Ossicle_wk25_Rep2

description: Library name: OIM_Ossicle_wk25_Rep2


title: OIM_Ossicle_wk25_Rep1

description: Library name: OIM_Ossicle_wk25_Rep1


title: OIM_Ossicle_wk12_Rep12

description: Library name: OIM_Ossicle_wk12_Rep12


title: OIM_Ossicle_wk25_Rep3

description: Library name: OIM_Ossicle_wk25_Rep3


title: OIM_Ossicle_wk12_Rep8

description: Library name: OIM_Ossicle_wk12_Rep8


title: OIM_Ossicle_wk12_Rep6

description: Library name: OIM_Ossicle_wk12_Rep6


title: OIM_Ossicle_wk12_Rep10

description: Library name: OIM_Ossicle_wk12_Rep10


title: OIM_Ossicle_wk12_Rep3

description: Library name: OIM_Ossicle_wk12_Rep3


title: OIM_Ossicle_wk12_Rep5

description: Library name: OIM_Ossicle_wk12_Rep5


title: OIM_Ossicle_wk12_Rep4

description: Library name: OIM_Ossicle_wk12_Rep4


title: DMSO, TPO/FL/SCF, 7d, donor3

city: Edogawa-ku

first: Kyungtaek

last: Lim

state: Tokyo

address: 1-16-13, Kitakasai

country: Japan

institute: Daiichi Sankyo Co., Ltd.

description: 10X Genomics

data_processing:
STAR (v2.5.3a) and RSEM (v1.0.3) were used for read mapping and transcriptome quantification with GENCODE release 32, respectively.
Assembly: GRCh38
Supplementary files format and content: TSV, gene read counts
Supplementary files format and content: TSV, isoform read counts

source_name: bone marrow

growth_protocol: Primary human bone marrow CD34+ cells were cultured in StemSpan serum-free expansion medium (STEMCELL Technologies) in the presence of thrombopoietin (50 ng/mL)/FLT3 ligand (FL, 100 ng/mL)/SCF (100 ng/mL) at 37 ℃ in a 5% CO2 incubator.

extract_protocol:
Cells were stained with anti-human CD41 and CD61 antibodies (BioLegend), and double positive fraction was collected by BD FACS Aria (BD Biosciences). RNA extraction was performed with Maxwell (Promega).
RNA-seq libraries were constructed with the ribosomal RNA depletion method with QIAseq FastSelect (Qiagen), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs). Biomek i7 instruments (Beckman Coulter, Inc) programmed according to the manufacture’s protocols were used for library construction with the following parameters: 5 minutes of fragmentation, RNA quantity ≦ 20 ng, and 14 cycles of polymerase chain reaction amplification.

treatment_protocol: Valemetostat or dimethyl sulfoxide was treated during the cell culture.

value: bone marrow

value: bone marrow CD34+ cells

value: dimethyl sulfoxide 0.01%

tag: stimulation

value: TPO/FL/SCF

tag: time

tag: donor id

tag: experimental batch


title: WT_Femur_wk12_Rep5

description: Library name: WT_Femur_wk12_Rep5

tag: genotype


title: WT_Femur_wk12_Rep4

description: Library name: WT_Femur_wk12_Rep4

tag: cell type


title: OIM_Femur_wk25_Rep12

description: Library name: OIM_Femur_wk25_Rep12


title: OIM_Ossicle_wk12_Rep1

description: Library name: OIM_Ossicle_wk12_Rep1


title: OIM_Ossicle_wk12_Rep2

description: Library name: OIM_Ossicle_wk12_Rep2


title: OIM_Femur_wk25_Rep11

description: Library name: OIM_Femur_wk25_Rep11


title: OIM_Ossicle_wk25_Rep12

description: Library name: OIM_Ossicle_wk25_Rep12


title: OIM_Femur_wk25_Rep10

description: Library name: OIM_Femur_wk25_Rep10


title: OIM_Femur_wk25_Rep9

description: Library name: OIM_Femur_wk25_Rep9


title: OIM_Femur_wk25_Rep6

description: Library name: OIM_Femur_wk25_Rep6


title: OIM_Femur_wk25_Rep8

description: Library name: OIM_Femur_wk25_Rep8


title: OIM_Femur_wk25_Rep7

description: Library name: OIM_Femur_wk25_Rep7


title: OIM_Femur_wk25_Rep5

description: Library name: OIM_Femur_wk25_Rep5


title: OIM_Femur_wk25_Rep4

description: Library name: OIM_Femur_wk25_Rep4


title: OIM_Femur_wk25_Rep2

description: Library name: OIM_Femur_wk25_Rep2


title: OIM_Femur_wk12_Rep12

description: Library name: OIM_Femur_wk12_Rep12


title: OIM_Femur_wk25_Rep1

description: Library name: OIM_Femur_wk25_Rep1


title: OIM_Femur_wk12_Rep11

description: Library name: OIM_Femur_wk12_Rep11


title: OIM_Femur_wk12_Rep10

description: Library name: OIM_Femur_wk12_Rep10


title: OIM_Femur_wk12_Rep9

description: Library name: OIM_Femur_wk12_Rep9


title: OIM_Femur_wk12_Rep8

description: Library name: OIM_Femur_wk12_Rep8


title: OIM_Femur_wk12_Rep5

description: Library name: OIM_Femur_wk12_Rep5


title: OIM_Femur_wk12_Rep4

description: Library name: OIM_Femur_wk12_Rep4


title: OIM_Femur_wk12_Rep3

description: Library name: OIM_Femur_wk12_Rep3


title: OIM_Femur_wk12_Rep2

description: Library name: OIM_Femur_wk12_Rep2


title: OIM_Femur_wk12_Rep1

description: Library name: OIM_Femur_wk12_Rep1


title: HET_Ossicle_wk25_Rep9

description: Library name: HET_Ossicle_wk25_Rep9

value: HET - B6C3Fe a/a-Col1a2oim/J, #001815 Jackson Lab


title: HET_Ossicle_wk25_Rep8

description: Library name: HET_Ossicle_wk25_Rep8


title: HET_Ossicle_wk25_Rep7

description: Library name: HET_Ossicle_wk25_Rep7


title: HET_Ossicle_wk25_Rep6

description: Library name: HET_Ossicle_wk25_Rep6


title: HET_Ossicle_wk25_Rep5

description: Library name: HET_Ossicle_wk25_Rep5


title: HET_Ossicle_wk25_Rep4

description: Library name: HET_Ossicle_wk25_Rep4


title: HET_Ossicle_wk25_Rep3

description: Library name: HET_Ossicle_wk25_Rep3


title: HET_Ossicle_wk25_Rep2

description: Library name: HET_Ossicle_wk25_Rep2


title: HET_Ossicle_wk25_Rep1

description: Library name: HET_Ossicle_wk25_Rep1


title: HET_Ossicle_wk12_Rep11

description: Library name: HET_Ossicle_wk12_Rep11


title: OIM_Femur_wk25_Rep3

description: Library name: OIM_Femur_wk25_Rep3


title: HET_Ossicle_wk12_Rep10

description: Library name: HET_Ossicle_wk12_Rep10


title: WT_Ossicle_wk25_Rep6

description: Library name: WT_Ossicle_wk25_Rep6


title: HET_Ossicle_wk12_Rep9

description: Library name: HET_Ossicle_wk12_Rep9


title: HET_Ossicle_wk12_Rep8

description: Library name: HET_Ossicle_wk12_Rep8


title: WT_Ossicle_wk25_Rep2

description: Library name: WT_Ossicle_wk25_Rep2


title: HET_Ossicle_wk12_Rep7

description: Library name: HET_Ossicle_wk12_Rep7


title: HET_Ossicle_wk12_Rep6

description: Library name: HET_Ossicle_wk12_Rep6


title: HET_Ossicle_wk12_Rep5

description: Library name: HET_Ossicle_wk12_Rep5


title: WT_Ossicle_wk12_Rep10

description: Library name: WT_Ossicle_wk12_Rep10


title: OIM_Femur_wk12_Rep6

description: Library name: OIM_Femur_wk12_Rep6


title: HET_Ossicle_wk12_Rep4

description: Library name: HET_Ossicle_wk12_Rep4


title: OIM_Femur_wk12_Rep7

description: Library name: OIM_Femur_wk12_Rep7


title: HET_Ossicle_wk12_Rep3

description: Library name: HET_Ossicle_wk12_Rep3


title: HET_Ossicle_wk12_Rep2

description: Library name: HET_Ossicle_wk12_Rep2


title: HET_Ossicle_wk12_Rep1

description: Library name: HET_Ossicle_wk12_Rep1


title: HET_Femur_wk25_Rep10

description: Library name: HET_Femur_wk25_Rep10


title: HET_Femur_wk25_Rep9

description: Library name: HET_Femur_wk25_Rep9


title: HET_Femur_wk25_Rep8

description: Library name: HET_Femur_wk25_Rep8


title: HET_Femur_wk25_Rep7

description: Library name: HET_Femur_wk25_Rep7


title: WT_Femur_wk25_Rep4

description: Library name: WT_Femur_wk25_Rep4


title: WT_Femur_wk25_Rep7

description: Library name: WT_Femur_wk25_Rep7


title: DK21052-HC-1-E250Q-iPSC-MOsMPs

city: Yushima, Bunkyo-ku

first: FUMIKO

last: OZAKI

institute: Tokyo medical and dental university

description: all.rpm_DK21052-HC-iPSCs_Neutro_MOsMPs.xlsx

data_processing:
The mRNA profiles were compiled using Cufflinks (ver 2.2.1) software program and expressed as Reads per million mapped reads (PKM).
Assembly: hg38
Supplementary files format and content: xlsx files include RPM value for each sample

source_name: iPSCs derived cells

extract_protocol:
RNA was harvested using RNAeasy mini plus kit (Qiagen). In DK21052, 1 ng of total RNA was used to construct the sequencing library. For DK2220 and DK22223, 25 ng of total RNA was used, and for DK23067, 0.75 ng of total RNA was used.
Using the QuantSeq 3'mRNA-Seq Library Prep Kit, libraries for the NextSeq next-generation sequencer were prepared following the manual's protocol.

value: iPSCs derived cells

value: monocytes/macrophages

value: untreated


title: HET_Femur_wk25_Rep5

description: Library name: HET_Femur_wk25_Rep5


title: HET_Femur_wk25_Rep3

description: Library name: HET_Femur_wk25_Rep3


title: WT_Femur_wk25_Rep5

description: Library name: WT_Femur_wk25_Rep5


title: HET_Femur_wk25_Rep4

description: Library name: HET_Femur_wk25_Rep4


title: HET_Femur_wk25_Rep2

description: Library name: HET_Femur_wk25_Rep2


title: HET_Femur_wk25_Rep6

description: Library name: HET_Femur_wk25_Rep6


title: preLSC, KO, rep4

description: Library name: KO_4

library_source: other

data_processing:
Adapter sequences were removed using cutadapt 5.0.
Trimmed reads were mapped to modified mature miRNA reference sequences retrieved from miRBase using bowtie 1.3.1 without allowing any mismatches (-v 0).
Raw read count was normalised and compared using DESeq2 1.42.1.
Any query miRNAs that have additional T(s) at 3' end were flagged and counted as uridylated by in-house pipeline and these count was used for further analyses.
Assembly: miRBase release 22.1
Supplementary files format and content: preLSC_count_miRNA_mature_for_DESeq2.txt is a tab-delimited file and it contains name of miRNA and raw count for each miRNA from all samples.
Supplementary files format and content: uridyl_unfiltered_samplename.txt is a tab-delimited file. It contains seq=full sequence of query, length=length of query, count=count of query, strand=mapped direction, miRNA=name of mapped miRNA, start=5' end position of query against reference, ref_end=3' end position of query against reference, ref_length=length of reference miRNA with 3 additional Ts, mature_end=length of original reference miRNA, is_uridylated=TRUE if query is uridylated, sample=sample name.

molecule: other

source_name: preleukemic cells

growth_protocol: Meis1/Hoxa9 preleukemic cells were cultured at 200,000 cells/mL in IMDM supplemented with 10% FBS, Stem Cell Factor (40 ng/mL), IL-6 (20 ng/mL), IL-3 (20 ng/mL), Penicillin and Streptomycin, 5% CO2 at 37C.

extract_protocol:
Total RNA was purified using QIAzol and small RNA fraction (15-40 nt) was retrieved from 1 ug of total RNA after running acrylamide gel electrophoresis.
All retrieved small RNA fraction was used for generating libraries using NEBNext small RNA library prep kit. 16 PCR was performed to amplify libraries and amplicons were size selected on acrylamide gel. Detailed size distribution was confirmed by Tapestation D1000 and concentration of each library was measured using Qubit.

value: preleukemic cells

value: Tut4/7 Vav-iCre KO


title: HET_Femur_wk25_Rep1

description: Library name: HET_Femur_wk25_Rep1


title: WT_Femur_wk12_Rep3

description: Library name: WT_Femur_wk12_Rep3


title: HET_Femur_wk12_Rep11

description: Library name: HET_Femur_wk12_Rep11


title: HET_Femur_wk12_Rep10

description: Library name: HET_Femur_wk12_Rep10


title: WT_Femur_wk12_Rep2

description: Library name: WT_Femur_wk12_Rep2


title: preLSC, KO, rep3

description: Library name: KO_3


title: HET_Femur_wk12_Rep8

description: Library name: HET_Femur_wk12_Rep8


title: HET_Femur_wk12_Rep9

description: Library name: HET_Femur_wk12_Rep9


title: preLSC, KO, rep2

description: Library name: KO_2


title: WT_Femur_wk12_Rep1

description: Library name: WT_Femur_wk12_Rep1


title: preLSC, KO, rep1

description: Library name: KO_1


title: HET_Femur_wk12_Rep7

description: Library name: HET_Femur_wk12_Rep7


title: preLSC, WT, rep5

description: Library name: Control_5


title: HET_Femur_wk12_Rep6

description: Library name: HET_Femur_wk12_Rep6


title: HET_Femur_wk12_Rep5

description: Library name: HET_Femur_wk12_Rep5


title: preLSC, WT, rep4

description: Library name: Control_4


title: preLSC, WT, rep3

description: Library name: Control_3


title: OIM_Ossicle_wk25_Rep6

description: Library name: OIM_Ossicle_wk25_Rep6

value: Ossicle

value: total cells from auditory bulla


title: preLSC, WT, rep2

description: Library name: Control_2

value: WT


title: HET_Femur_wk12_Rep4

description: Library name: HET_Femur_wk12_Rep4

value: Male


title: HET_Femur_wk12_Rep3

description: Library name: HET_Femur_wk12_Rep3

value: Femur


title: preLSC, WT, rep1

description: Library name: Control_1


title: H1299, dCas9-KRAB TERT-targeting sgRNA, biological replicate 2

city: Seoul

first: Juyoung

last: Hong

address: 222 Wangsimni-ro, Seongdong-gu

country: South Korea

institute: Hanyang University

description:
Library name: H1299_TERT_rep2
TERT-targeting, biological replicate 2

data_processing:
Sequencing reads were aligned to the human reference genome (GRCh38).
Duplicate reads were removed.
Gene-level read counts were generated using htseq-count against Ensembl gene annotation.
Differential expression analysis was performed in R 4.5.1 with DESeq2 v1.48.2; genes were prefiltered to at least 10 counts in at least two samples; shrunken log2 fold changes were estimated with lfcShrink (apeglm v1.30.0); significance was defined as FDR < 0.05 and absolute log2 fold change >= 1.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files of raw gene-level read counts generated by htseq-count. Rows are Ensembl gene IDs; per-sample files contain one count column, and the combined matrix contains one column per sample.

growth_protocol: NCI-H1299 cells (Korean Cell Line Bank, KCLB No. 25803) were cultured in RPMI-1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37 C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using TRIzol reagent. Messenger RNA was isolated from 1 ug of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1).

treatment_protocol: Cells were transduced with concentrated lentiviral particles (dCas9-KRAB with no guide RNA, or with a TERT-targeting single-guide RNA) at a multiplicity of infection of 0.8, selected with puromycin (2 ug/mL for 6 days), allowed to recover for 3 days, and harvested at day 33 after transduction. Bulk populations were used for all analyses.

value: dCas9-KRAB + TERT-targeting single-guide RNA

value: lentiviral transduction; puromycin selection; harvested day 33


title: H1299, dCas9-KRAB TERT-targeting sgRNA, biological replicate 1

description:
Library name: H1299_TERT_rep1
TERT-targeting, biological replicate 1


title: HET_Femur_wk12_Rep2

description: Library name: HET_Femur_wk12_Rep2

value: total non-bone-marrow cells from femur


title: HET_Femur_wk12_Rep1

description: Library name: HET_Femur_wk12_Rep1


title: WT4-lung-day-4

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description: Library name: WT4-lung-day-4

data_processing:
Raw fastq was trimmed using TrimGalore! And cutadapt to remove standard Illumina adapters. The trimmed reads were aligned to mouse reference genome GRCm38 with hisat2 v2.1.0 [1].  Gene wise counts were generated with featureCounts from the subread package v1.5.1 [2] for genes annotated by ensembl Mus_musculus.GRCm38.102.
Assembly: GRCm38
Supplementary files format and content: raw counts from featureCounts

source_name: Lung

growth_protocol: Bone marrow chimeric mice were generated by lethal irradiation of C57BL/6 wild-type (WT) recipient mice with two doses of 6.5 Gy, followed by reconstitution via tail vein injection of 2×10⁶ to 4×10⁶ donor bone marrow cells from either WT or Casp11⁻/⁻ donors, generating WT→WT (WT chimeras) and Casp11⁻/⁻→WT (Casp11⁻/⁻ chimeras) groups. Recipients were allowed to reconstitute their circulating leukocyte pools for a minimum of 6 weeks prior to infection. Mice were approximately 6 months of age at the time of infection. Food and water were provided ad libitum under standard specific-pathogen-free conditions at The Ohio State University.

extract_protocol:
Total RNA was extracted from the left lung lobe using TRIzol reagent (Thermo Fisher Scientific, Cat. 15596026) according to the manufacturer's instructions. RNA cleaning and concentration were performed using the Zymo Research RNA Clean & Concentrator-5 kit (Cat. R1015). RNA quantity was assessed using a Qubit 4.0 Fluorometer (Thermo Fisher Scientific) and RNA integrity was assessed using TapeStation (Agilent Technologies).
Library preparation was performed at GENEWIZ from Azenta Life Sciences (South Plainfield, NJ, USA) using the NEBNext Ultra II RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) according to the manufacturer's recommendations. Briefly, mRNAs were enriched using Oligo-d(T) beads, fragmented for 15 minutes at 94°C, and used as template for first- and second-strand cDNA synthesis. cDNA fragments were end-repaired and adenylated at 3' ends, followed by ligation of universal adapters, index addition, and library enrichment by limited-cycle PCR. Library quality and quantity were assessed using the Agilent TapeStation (Agilent Technologies), Qubit 4.0 Fluorometer (Thermo Fisher Scientific), and quantitative PCR (KAPA Biosystems). Sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument and sequenced using a 2×150 bp paired-end (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from the Illumina NovaSeq instrument were converted into FASTQ files and demultiplexed using Illumina bcl2fastq 2.20 software, allowing one mismatch for index sequence identification.

treatment_protocol: Mice were anesthetized by isoflurane induction at 2–3% concentration in an induction chamber for approximately 5 minutes. Mice were infected intranasally with 1×10⁵ TCID50 of mouse-adapted SARS-CoV-2 strain MA10 in 50 μL sterile PBS (25 μL per nare). Lungs were harvested at day 4 post-infection. The left lung lobe was snap frozen in liquid nitrogen and stored at −80°C prior to RNA extraction.

value: Lung

value: WT chimera

value: Intranasal infection with 1×10⁵ TCID50 mouse-adapted SARS-CoV-2 (MA10 strain); lung harvest at day 4 post-infection


title: H1299, dCas9-KRAB non-targeting control, biological replicate 2

description:
Library name: H1299_NT_rep2
non-targeting control, biological replicate 2

value: dCas9-KRAB, no guide RNA (non-targeting control)


title: WT1-lung-day-4

description: Library name: WT1-lung-day-4


title: WT2-lung-day-4

description: Library name: WT2-lung-day-4


title: H1299, dCas9-KRAB non-targeting control, biological replicate 1

description:
Library name: H1299_NT_rep1
non-targeting control, biological replicate 1


title: SH2

city: Nanchang

first: Fangmin

last: Zhong

address: the NO.1 Minde Road, Donghu District, Nanchang, Jiangxi, China

institute: The Second Affiliated Hospital of Nanchang University

description:
Library name: Sample5
SRSF10SH2_2

data_processing:
Raw RNA-seq data were subjected to quality control using FastQC and trimmed using Trim_galore.
Assembly: GRCh38
Supplementary files format and content: text file with RPKM abundance measurements

source_name: blood

extract_protocol:
RNA was extracted from stable cells and harvested using Trizol reagent. The suitable fragments are selected for the PCR amplification. During the QC steps, Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. Then the library is sequenced using Illumina NovaSeq 6000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

value: acute myeloid leukemia cells

value: SRSF10 knockdown


title: WT3-lung-day-4

description: Library name: WT3-lung-day-4


title: SH3

description:
Library name: Sample6
SRSF10SH2_3


title: OIM_Ossicle_wk12_Rep11

description: Library name: OIM_Ossicle_wk12_Rep11

value: OIM - oim/oim

value: Female


title: CASP11-4-lung-day-4

description: Library name: CASP11-4-lung-day-4

value: Casp11 KO chimera


title: CASP11-2-lung-day-4

description: Library name: CASP11-2-lung-day-4


title: NC3

description:
Library name: Sample3
SRSF10SH3


title: SH1

description:
Library name: Sample4
SRSF10SH2_1


title: CASP11-3-lung-day-4

description: Library name: CASP11-3-lung-day-4


title: NC2

description:
Library name: Sample2
SRSF10SH2


title: CreControls-7

description: Library name: FLOX-7

growth_protocol: Cx3cr1-CreERT2; Casp11^WT/WT (Cx3cr1-Cre control) and Cx3cr1-CreERT2; Casp11^flox/flox (Cx3cr1-MPS-Casp11⁻/⁻) mice were housed under standard specific-pathogen-free conditions at The Ohio State University. Both groups are homozygous for the Cx3cr1-CreERT2 knock-in allele. To induce Cre-mediated recombination, mice were administered tamoxifen at 75 mg/kg dissolved in corn oil via intraperitoneal injection for 7 consecutive days, followed by a 3-day washout period. Mice were 3–4 months of age at the time of infection. Food and water were provided ad libitum.

extract_protocol:
Total RNA was extracted from the left lung lobe using TRIzol reagent (Thermo Fisher Scientific, Cat. 15596026) according to the manufacturer's instructions. RNA cleaning and concentration were performed using the Zymo Research RNA Clean & Concentrator-5 kit (Cat. R1015). RNA integrity and quantity were assessed using an RNA Biochip and Qubit RNA Fluorescence Dye (Invitrogen).
The RNA sample received was quantified using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), including clustering and sequencing reagents, was utilized according to the manufacturer's recommendations. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3' ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

treatment_protocol: Mice were anesthetized by isoflurane induction at 2–3% concentration in an induction chamber for approximately 5 minutes. Mice were infected intranasally with 5×10⁵ TCID50 of mouse-adapted SARS-CoV-2 strain MA10 in 50 μL sterile PBS (25 μL per nare). Lungs were harvested at day 4 post-infection. The left lung lobe was snap frozen in liquid nitrogen and stored at −80°C prior to RNA extraction.

value: lung

value: Cx3cr1-CreERT2; Casp11^WT/WT


title: NC1

description:
Library name: Sample1
SRSF10SH1

value: WT


title: BxPC3, IgG, plus IFNγ, Replicate3, CUT&RUN

city: NEW YORK

first: Xinhe

last: Xue

address: 101 Avenue of the Americas

institute: New York Genome Center/New York University

description:
Library name: BxPC3_IgG_plusIFNγ_Rep1_Rep3
BxPC3_CUTRUN_IgG_plusIFNγ_3reps.bw
BxPC3_CUTRUN_IgG_plusIFNγ_3reps_peaks.narrowPeak

library_source: genomic

data_processing:
The fastq files were trimmed and quality-controlled with Trim Galore (version 0.6.10 with the default options in a pair-end mode. The resulting reads were aligned to hg38 using bowtie2 (version 2.4.4) with options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700 (Langmead & Salzberg, 2012). The alignment files were sorted by coordinate, then unpaired reads were removed, and indexed with samtools (version 1.14) (Danecek et al., 2021).
For reads visualization on genome tracks, the processed bam files were merged with samtools and visualized via the Integrative Genomics Viewer (version 2.16.1) (Robinson et al., 2011).
For peak identification, peaks and summits were called with MACS2 (version 2.2.7.1) using all three individual bam files for all replicates targeting the protein of interest (-t) and all three targeting IgG as controls (-c) with options --format BAMPE --gsize 2.7e9 --keep-dup all (Zhang et al., 2008).sortRegions descend (Ramirez et al., 2016).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: BxPC-3 cells were cultured in RPMI-1640 (Thermo Fisher Scientific) supplemented with 10% Serum Plus-II (Thermo Fisher)

extract_protocol:
We performed CUT&RUN in BxPC-3 cells using CUTANA ChIC/CUT&RUN Kit (EpiCypher) following the manufacturer’s protocol (Skene & Henikoff, 2017). In brief, 500,000 cells were trypsinized, washed, and bound to activated Concanavalin A-conjugated paramagnetic beads (EpiCypher). The cell-bead conjugates were then resuspended in recommended buffer with 0.5 μg antibody targeting the protein of interest: Anti-H3K27ac (Active Motif 39135), Anti-H3K4me3 (EpiCypher 13-0041k) as positive control, and Anti-IgG (EpiCypher 13-0042k) as negative control. The suspensions were incubated overnight at 4 °C with gentle shaking. Then, the cell-bead conjugates were washed twice with the kit’s permeabilization buffer, and incubated with pAG-MNase (Epicypher 15-1016) for 10 min at room temperature. Subsequently, the unbound pAG-MNase was washed away, and the MNase was activated by adding CaCl2 to a final concentration of 2 mM. The reaction was stopped after the pAG-MNase was allowed to digest and release the antibody-bound chromatin for 2 hours at 4 °C. Finally, the released DNA was purified with the spin columns provided by the kit (EpiCypher).
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs). The libraries were sequenced on a IlluminaNovaSeq 6000  SP using 2x50 bp reads.

value: PDAC

tag: cut&run antibody

value: IgG (EpiCypher 13-0042k)

value: plus IFNγ


title: CASP11-1-lung-day-4

description: Library name: CASP11-1-lung-day-4


title: CreControls-6

description: Library name: FLOX-6


title: BxPC3, IgG, plus IFNγ, Replicate2, CUT&RUN

description:
Library name: BxPC3_IgG_plusIFNγ_Rep1_Rep2
BxPC3_CUTRUN_IgG_plusIFNγ_3reps.bw
BxPC3_CUTRUN_IgG_plusIFNγ_3reps_peaks.narrowPeak


title: OIM_Ossicle_wk12_Rep7

description: Library name: OIM_Ossicle_wk12_Rep7

value: Ossicle

value: total cells from auditory bulla


title: BxPC3, H3K4me3, plus IFNγ, Replicate3, CUT&RUN

description:
Library name: BxPC3_H3K4me3_plusIFNγ_Rep3
BxPC3_CUTRUN_H3K4me3_plusIFNγ_3reps.bw
BxPC3_CUTRUN_H3K4me3_plusIFNγ_3reps_peaks.narrowPeak

value: H3K4me3 (EpiCypher 13-0041k)


title: OIM_Ossicle_wk12_Rep9

description: Library name: OIM_Ossicle_wk12_Rep9


title: CreControls-5

description: Library name: FLOX-5


title: CreControls-1

description: Library name: FLOX-1


title: BxPC3, H3K4me3, plus IFNγ, Replicate2, CUT&RUN

description:
Library name: BxPC3_H3K4me3_plusIFNγ_Rep2
BxPC3_CUTRUN_H3K4me3_plusIFNγ_3reps.bw
BxPC3_CUTRUN_H3K4me3_plusIFNγ_3reps_peaks.narrowPeak


title: BxPC3, H3K4me3, plus IFNγ, Replicate1, CUT&RUN

description:
Library name: BxPC3_H3K4me3_plusIFNγ_Rep1
BxPC3_CUTRUN_H3K4me3_plusIFNγ_3reps.bw
BxPC3_CUTRUN_H3K4me3_plusIFNγ_3reps_peaks.narrowPeak


title: CreControls-2

description: Library name: FLOX-2


title: BxPC3, H3K27ac, plus IFNγ, Replicate3, CUT&RUN

description:
Library name: BxPC3_H3K27ac_plusIFNγ_Rep3
BxPC3_CUTRUN_H3K27ac_plusIFNγ_3reps.bw
BxPC3_CUTRUN_H3K27ac_plusIFNγ_3reps_peaks.narrowPeak

value: H3K27ac (Active Motif 39135)


title: CREFLOX-12

description: Library name: CREFLOX-12

value: Cx3cr1-CreERT2; Casp11^flox/flox


title: BxPC3, H3K27ac, plus IFNγ, Replicate2, CUT&RUN

description:
Library name: BxPC3_H3K27ac_plusIFNγ_Rep2
BxPC3_CUTRUN_H3K27ac_plusIFNγ_3reps.bw
BxPC3_CUTRUN_H3K27ac_plusIFNγ_3reps_peaks.narrowPeak


title: BxPC3, H3K27ac, plus IFNγ, Replicate1, CUT&RUN

description:
Library name: BxPC3_H3K27ac_plusIFNγ_Rep1
BxPC3_CUTRUN_H3K27ac_plusIFNγ_3reps.bw
BxPC3_CUTRUN_H3K27ac_plusIFNγ_3reps_peaks.narrowPeak


title: 5

description: Library name: 5

data_processing:
Raw paired-end reads were assessed for quality using FastQC and trimmed for adapter sequences and low-quality bases prior to alignment.
Reads were quantified against the Mus musculus GRCm39 reference transcriptome (Ensembl release 109) using Salmon (v1.10.3) with sequence-bias correction enabled.
Transcript-level quantifications were imported into R and summarized to gene-level counts using the tximport package (v1.30.0) with transcript-to-gene mappings derived from the GRCm39.109 GTF annotation via GenomicFeatures.
Assembly: Mus musculus GRCm39 (Ensembl release 109)
Supplementary files format and content: Tab-delimited text file containing gene-level count matrix (raw counts) for all samples, with Ensembl gene IDs and gene symbols.

growth_protocol: C57BL/6 wild-type (WT) and Casp11⁻/⁻ mice were housed under standard specific-pathogen-free conditions at The Ohio State University. Mice were 3–4 months of age at the time of infection. Food and water were provided ad libitum.

value: Lung

value: MA10 SARS-CoV-2 infection


title: 1

description: Library name: 1


title: BxPC3, H3K4me3, no IFNγ, Replicate3, CUT&RUN

description:
Library name: BxPC3_H3K4me3_noIFNγ_Rep3
BxPC3_CUTRUN_H3K4me3_noIFNγ_3reps.bw
BxPC3_CUTRUN_H3K4me3_noIFNγ_3reps_peaks.narrowPeak

value: no IFNγ


title: BxPC3, H3K4me3, no IFNγ, Replicate2, CUT&RUN

description:
Library name: BxPC3_H3K4me3_noIFNγ_Rep2
BxPC3_CUTRUN_H3K4me3_noIFNγ_3reps.bw
BxPC3_CUTRUN_H3K4me3_noIFNγ_3reps_peaks.narrowPeak


title: 13

description: Library name: 13

value: Caspase 11 KO


title: BxPC3, H3K27ac, no IFNγ, Replicate3, CUT&RUN

description:
Library name: BxPC3_H3K27ac_noIFNγ_Rep3
BxPC3_CUTRUN_H3K27ac_noIFNγ_3reps.bw
BxPC3_CUTRUN_H3K27ac_noIFNγ_3reps_peaks.narrowPeak


title: 18

description: Library name: 18


title: 10

description: Library name: 10


title: patient infected with Sparsely granulated somatotroph adenoma, a subtype of growth hormone-producing pituitary adenoma

city: Wuhan

first: Haobin

last: Ren

state: Hubei

address: G9P7+CP8, Wuchang District

institute: Wuhan University

description: Library name: PAs103

data_processing:
FastQC for QC
Trim Galore for trimming
BWA-MEM for alignment
Circle-Map for ecDNA detection
Assembly: hg38
Supplementary files format and content: txt for identified ecDNA

source_name: Pituitary gland

extract_protocol:
ecDNA purification was performed on DNA extracted from meningioma, glioblastoma, pituitary adenoma and vestibular schwannoma. After confirming the successful enrichment of ecDNA from total DNA samples, Phi29-assisted ecDNA rolling circle amplification was performed before DNA library preparation.
Amplicon was sonicated into DNA fragments with average size as 350bp using Bioruptor. Library preparation was performed using Vazyme DNA library preparation kit (Vazyme) following the standard protocol starting with 300 ng of sonicated DNA per sample. Library quality and fragment size distribution were assessed using the Qsep400 system (BiOptic).

value: Pituitary gland

tag: infection


title: patient infected with Pituitary adenoma (Gonadotroph adenoma), a subtype of pituitary neuroendocrine tumor

description: Library name: PAs102


title: scRNA-seq of C1

city: Shanghai

first: Lei

last: Shi

state: 请选择

address: 115 Jinzun Road, Pudong New Area, Shanghai

institute: Shanghai Jiaotong university

description: Library name: C1

data_processing:
The raw reads were mapped to the rat reference genome (refdata-gex-Rnor6-2022/Rnor_6) using DNBC4Tools (v 2.1.2) with default parameters, the digital expression matrix was extracted from the“filtered_feature_bc_matrix” folder outputted by the DNBC4Tools count pipeline.
Assembly: MM39
Supplementary files format and content: matrix

source_name: Knee joint synovial tissue

extract_protocol:
Samples were minced with a sterile scalpel into 1 mm3 fragments, suspended in 5ml of digestion buffer consisting of 2 mg/mL Collagenase type I (Sigma，C0130)，2 mg/mL Collagenase type II (Sigma, C6885) and 200U/ml DNase I (Worthington, LS006344) in RPMI medium (Coring,10-040-CV), and incubated in 37℃ water bath with shaking for 60 min. The suspension was passed through a 100 μm filter (Falcon,3523260) and centrifugated (400g, 10 min, 4℃). Pelleted cells were resuspended in red blood cell lysis buffer (Solarbio,R1010), incubated for 2 min, passed through a 40 μm filter (Falcon,3523240), collected by centrifugation (400g, 10 min, 4℃) and resuspended in PBS (BI, 02-024-1ACS)  containing 0.04% BSA (Sigma,B2064). Cells were manually counted by Trypan blue (Thermo, T10282) and AO-PI (LUNA, D23001) after each centrifugation (400g, 10 min, 4℃) and resuspended.
Single-cell libraries were constructed with the DNBelab C Series Single-Cell Library Prep Kit (MGI, Cat. # 940-001818-00). Briefly, single-cell suspensions were subjected to droplet generation, emulsion breakage, bead collection, reverse transcription, and cDNA amplification to generate barcoded libraries. Library quantification and quality control were performed using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Q33216) and an Agilent 4200 TapeStation (Agilent, G2991AA), respectively. Finally, DNA nanoballs (DNBs) were loaded into patterned nanoarrays and sequenced on a DNBSEQ platform. The sequencing run was configured with the following read lengths: 30 bp for read 1, inclusive of 10 bp cell barcode 1, 10 bp cell barcode 2, and 10 bp unique molecular identifier (UMI), 100 bp of transcript sequence for read 2, and 10 bp for sample index.

value: Knee joint synovial tissue

tag: group

value: control


title: scRNA-seq of D3

description: Library name: D3

tag: tissue

value: treat with GFP fibroblast


title: scRNA-seq of D2

description: Library name: D2


title: patient infected with Vestibular Schwannoma, a benign nerve sheath tumor

description: Library name: VS102

source_name: Right cerebellopontine angle

value: Right cerebellopontine angle


title: scRNA-seq of D1

description: Library name: D1


title: patient infected with Sample tube, specimen from vestibular schwannoma patient

description: Library name: VS101

source_name: Left cerebellopontine angle

value: Left cerebellopontine angle


title: patient infected with Glioblastoma (WHO grade IV, IDH-wildtype)

description: Library name: GBM103

source_name: Right occipital lobe

value: Right occipital lobe


title: scRNA-seq of P2

description: Library name: P2

value: treat with PBS


title: CHIP029, Input, CRISPRi_Scr, rep1

city: Philadelphia

first: Ricardo

middle: A

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

description:
Library name: CHIP029
LB1_SCR.CPM_1kb.woTNR.e120.S10Kb.bw
LB1_SCR.b5s15_5_wBlklst_domains.final.bed

data_processing:
Basecalls were performed using bcl2fastq v2.20.
ChIP-seq reads were deduplicated and trimmed using fastp v0.23.2. Low complexity reads were discarded.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.1. Only uniquely mapping reads with a MAPQ >20 were retained using sambamba 1.0.0.
To create ChIP-seq coverage plots of LB1 and H3K9me2, the locations of the mapped ChIP-seq reads were extended to 100 bp to represent sequenced fragments, normalized (to counts per million, cpm) and log2 normalized against their corresponding inputs. The resulting bigwig files were generated using deeptools v3.1.3. Bigwigs for RAD21 were generated using macs2 version 2.2.6 representing a fold enrichment over their corresponding inputs. ENCODE blacklisted regions (hg38-blacklist.v2.bed) were excluded from analysis.
RAD21 peaks were called using MACS v2.2.6 with the significance cut-off q-value <=0.01. Broad domains for LB1 or H3K9me2 were identified using HMMDomainCaller doi:10.1038/s41588-021-00821-2.
Assembly: hg38
Supplementary files format and content: bigWig files with input normalized ChIP-seq signal for each condition as described above. Bed and narrowPeak files with domain calls per condition as described above.

source_name: WT fibroblast

growth_protocol: Human skin non-treatment control (NTC) fibroblasts and fibroblasts from a Freidrich's Ataxia patient (FRDA) fibroblast cells were cultured in DMEM (Gibco #11965084) supplemented with 10% fetal bovine serum (Cytiva SH30910.03), 1% penicillin/streptomycin (Invitrogen #15140122), and 1% non-essential amino acids (Invitrogen # 11140050) at 37C with 20% O2 and 5% CO2. RAD21-mAID-HCT116 cells were cultured in McCoys (Invitrogen #16600082) supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin at 37C with 20% O2 and 5% CO2.

extract_protocol:
Samples for ChIP were processed as previously described (3). Human NTC and FRDA fibroblasts and Rad21-mAID-HCT116 cells were cultured in 10cm dishes and crosslinked in culture using methanol-free formaldehyde for 10 min at RT with gentle rotation (final 1% v/v). Crosslinking was quenched by addition of glycine for 5 min at RT with gentle rotation (final 125mM). Cells were washed with 1x PBS once before collection via scraping and PBS removal by centrifugation (250xg for 5 minutes at RT). Resulting pellets were flash frozen on dry ice and stored at -80C. For each ChIP sample, 30µL protein G magnetic beads (Invitrogen #10004D) were washed 3 times in blocking buffer (0.5% BSA in 1x PBS) before beads were resuspended in 250µL blocking buffer and 2µg (anti-LaminB1 [Abcam #ab16048], anti-H3K9me2 [Active Motif #39239]) or 4µg (anti-RAD21 [Abcam, #ab992]) antibody and rotated at 4C overnight. Nuclei were isolated from frozen pellets as follows: pellets were resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 1mMEDTA, 140mM NaCl, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Remaining pellet was resuspended in 10mL cold Lysis buffer (220mM NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Nuclei were resuspended in 1mL cold Lysis Buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitor). Samples were transferred to a pre-chilled 1mL Covaris AFA tube (Covaris #520130) and sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes). TrintonX-100 (final 1%) was added to lysates and centrifuged at top speed for 10 min at 4C. Supernatant was collected and protein concentration measured via Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer and resuspended in 50µL blocking buffer before 500µg protein lysate was added and allowed to rotate overnight at 4C. For inputs, 50µg protein lysate was aliquoted and stored at -20C. The next day, antibody-conjugated beads with lysate were washed 5 times for 2 min each at 4C with rotation in 1mL RIPA buffer (50mM HEPES-KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were washed in 1mL Final Wash buffer (1XTE, 50mM NaCl) for 2 min with rotation at RT. Lastly, beads were resuspended in 210µL Elution Buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65C for 30 min with agitation. 200µL eluate was removed and all samples were incubated at 65C with agitation for a minimum of 12 h, but no more than 18 h. 200µL of 1X TE was added the resulting samples followed by addition of RNase (final 0.2mg/mL, Sigma #10109169001) and incubated at 37C for 2 h. Proteinase K was subsequently added (final 0.2mg/mL, Roche #3115879001) and incubated at 55C for 2 h. DNA was isolated via phenol:chloroform extraction and resuspended in 10mM Tris-HCl pH8.0. DNA was quantified by Qubit.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB #E7770L). Samples were prepared with dual unique indices for multiplex sequencing using NEBNext Multiplex Oligos (NEB #E7630). Library quality was determined by BioAnalyzer or 2% agarose gel electrophoresis and quantified by qPCR using NEBNext Library Quant Kit (NEB #E7630S). Libraries were pooled, re-quantified, and single-end sequenced on the Illumina NextSeq500 or NextSeq1000/2000 platforms

treatment_protocol: Human fibroblasts were grown in complete media (DMEM, 10% FBS, 1% penicillin/streptomycin) and plated at 40% confluency. The next day, dCas9-KRAB-FXN guide or dCas9-KRAB-Scramble guide was introduced into NTC fibroblasts for 2d followed by 2d selection in blasticidin. RAD21-mAID-HCT116 cells were propagated in standard medium (McCoy’s with 10% FBS and 1% penicillin/streptomycin) and plated in 10cm dishes at 40% density and grown overnight. The following morning, a time course was started for three conditions (DMSO control, triptolide-only, and auxin + triptolide). At time 0, DMSO control and triptolide-only cells were incubated in fresh media alone; auxin + triptolide cells were incubated in fresh media + 1μM auxin (5-Ph-IAA, Tocris Bioscience). After 1 hour, 200nM final triptolide (Selleckchem) was added to triptolide-only and auxin + triptolide cells. 12 hours post-triptolide, all cells were harvested for ChIP (see “ChIP and library preparation for sequencing”). DMSO was used as a vehicle control.

tag: cell line

value: WT fibroblast

value: Human fibroblast

tag: chip antibody

value: Input

tag: treatment


title: A549, DMSO, CA11, 6h, D02

city: Mason

first: Yuqing

last: Shan

institute: Procter & Gamble

description: Library name: CA11_DMSO_D02

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: lung

value: epithelial cell

value: Adenocarcinoma

value: vehicle

tag: batch


title: COLXIV_KO_ZT_0 biol rep 3

city: Barcelona

first: Camille

last: Stephan Otto Attolini

institute: IRB Barcelona

description: Library name: K_Z_4

data_processing:
Adapters from reads were removed using TrimGalore with default parameters.
Reads were aligned to the mm10 version of musmusculus using STAR (v.2.7.10a) with default parameters
Count matrix was generated using the featureCounts function from the Rsubread R package using the Entrez gene annotation
Assembly: GRCm38.102
Supplementary files format and content: Count matrix in excel format

source_name: epidermis

extract_protocol:
RNA was extracted from epidermal cell pellets frozen in Trizol using the NZY Total RNA Isolation Kit (NZY Tech)
Libraries were prepared using the TruSeq stranded mRNA Library Prep (20020595, Illumina) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing. Briefly, 500 ng of total RNA were used for polyA‐mRNA selection using Oligo‐dT beads, and two rounds of purification were performed. During the second elution of the mRNA, this was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis, which was performed using reverse transcriptase (SuperScript II; 18064‐014, Invitrogen). Then, second strand cDNA was synthesised, incorporating dUTP in place of dTTP and generating blunt‐ended ds cDNA. A single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments (A‐tailing) and immediately afterwards the Truseq adapter was ligated. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed using Unique Dual Indexes and the master mix provided with the kit. All purification steps were performed using AgenCourt AMPure XP beads (A63882, Beckman Coulter). Final libraries were analysed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (5067‐1504 or DNF‐473, Agilent) to estimate the quantity and validate the size distribution and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (07960204001, Roche).

value: epidermis

value: ColXIV KO


title: gD2-gE1 rep3

city: Tianjin

first: Zhao

last: Wenying

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

description: Library name: SAMPLES 12

data_processing:
lllumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al.,Nucleic Acids Research,2009.In short, exons from all isoforms.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM yalues for each Sample

source_name: draining lymph nodes

extract_protocol:
RNA was harvested using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit(Cat#FC-122-1001) was used with 1ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: draining lymph nodes

tag: strain

value: BABL/c

value: 10μg gD2 + 10μg gC1


title: patient infected with Glioblastoma (IDH1 mutant type; WHO Grade IV).

description: Library name: GBM101

source_name: Left frontal lobe

value: Left frontal lobe


title: patient infected with Meningioma (Meningothelial type, WHO grade I)

description: Library name: MG103

source_name: Left tentorium

value: Left tentorium


title: gD2-gE1 rep2

description: Library name: SAMPLES 11


title: patient infected with Meningioma (Fibrous type, WHO grade I)

description: Library name: MG102

source_name: Peripheral artery

value: Peripheral artery

value: Meningioma (Fibrous type, WHO grade I)


title: gD2-gE1 rep1

description: Library name: SAMPLES 10


title: pir1∆_BioRep4

city: Bethesda

first: Shiv

last: Grewal

address: 9000 Rockville Pike

institute: National Institutes of Health

description:
Library name: 251012g
pir1∆_18C

data_processing:
Single ended short reads from RNAseq experiments were quality trimmed using fastp (Chen et al. 2018) and aligned to the reference genome using the STAR aligner (Dobin, A. et al., 2013). Wig files, normalized to counts per million mapped reads, were generated by STAR.
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT); HG19 human genome reference; T2T.CHM13v2.0 human telomere-to-telomere human reference.
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

extract_protocol:
Total RNA isolated using the MasterPure Yeast RNA Purification Kit following the manufacturer's protocol
For RNA Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent). Total RNA isolated was first ribodepleted using the Ribo-Zero gold plus for humans (Illumina) supplemented with probes against S. pombe ribosomal DNA (IDT) for library construction.

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E pir1D::KanMX otr1R(Sph1)::ura4+

tag: growth

value: Growth in YEA 18°C