title: M296_melioidosis

first: PATPONG

last: RONGKARD

address: Du Cane Rd

department: National Heart and Lung Institute

institute: Imperial College London

description: Library name: M296

data_processing:
Raw sequencing data (FASTQ files) were pre-processed and quality checked by the service. The FASTQ files were mapped using human reference genome UCSC hg38.p2 version 20201using STAR aligner (version 2.6.1d). Raw counts (uniquely mapped reads) were generated from the mapped read files (.bam) using featureCounts function of Subread package (version 1.6.2) as tab-delimited text files.
Assembly: UCSC hg38.p2 version 20201
Supplementary files format and content: tab-delimited text files inlcudes raw counts for each sample

source_name: Whole blood

extract_protocol:
For the melioidosis cohort, we isolated total RNA from whole blood sample of 81 melioidosis patients and 29 uninfected control participants (DM control, n=15; healthy donor, n=14) collected in Tempus blood RNA tube using the Tempus Spin RNA. A ribozero library preparation and the globin depletion workflow were performed by the Oxford Genomics Centre, Wellcome Centre for Human Genetics, University of Oxford.
Ribozero library preparation with globin depletion workflow (HTG 384 UDI RNA-Seq Ribozero) was performed by  the Oxford Genomics Centre, Wellcome Centre for Human Genetics, University of Oxford. And the samples were sequenced for 75-base pair pair-end, 50 million reads.

value: Whole blood

tag: group

tag: age

tag: Sex

value: Male

tag: 28day mortality

value: survivor


title: BxPC3, no ko, Replicate3, RNA-seq

status: Public on Jun 24 2026

type: SRA

city: NEW YORK

first: Xinhe

last: Xue

state: New York

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center/New York University

description: Library name: BxPC3_NT_Rep3

library_source: transcriptomic

data_processing:
For fastq files, adaptors were trimmed with Cutadapt (Martin et al., 2011) v4.4 with options -q 20 -m 20 --trim -n.
Reads from were aligned to GRCh38 (gencode.v36.annotation) with HISAT2 aligner (version 2.2.1) (Kim et al., 2019).
Assembly: hg38
Supplementary files format and content: feature count

molecule: total RNA

organism: Homo sapiens

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

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Purification Kit (Zymo R2062) with DNaseI treatment (n = 4 biological replicates).
For the library preparation, 500ng total RNA was used for the RNA library preparation with Stranded mRNA Prep kit (Illumina 20040534) and RNA UD Indexes Set A Ligation kit (Illumina 20040553). Samples were sequenced on Illumina NovaSeq X sequencing platform to generate 50 million read pairs or more per sample.

treatment_protocol: In BxPC-3 cells, FOXA3 was perturbed using pCC_01 (Addgene 139086) encoding FOXA3- targeting gRNA or non-targeting gRNA. Cells were selected with 2 ug/mL puromycin for 5 days. Following selection, cells were treated with 100 IU/mL IFNγ for 48 hours.

tag: tissue

tag: cell line

value: PDAC

tag: treatment

value: IFNγ treatment


title: old5

city: Hangzhou

first: Bowen

last: Wu

state: Zhejiang

address: NO.79 Qinchun Road

country: China

institute: The First Affiliated Hospital, Zhejiang University School of  Medicine

description: Library name: Sample11

data_processing:
RNA-seq
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/) to map reads to the reference genome of homo sapiens Ensembl_v107. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: homo_sapiens Ensembl_v107
Supplementary files format and content: FPKM values for each sample

molecule: polyA RNA

source_name: Blood

extract_protocol:
Total RNA from the cells was collected using RNA-Quick Purification Kit (YiShan Biotech, China) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 400±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ X Plus (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Blood

tag: cell type

value: PBMC

value: macrophage

tag: genotype

tag: sample group

value: old

value: induced with MSCF (20 ng/ml) for five days, and LPS (100 ng/ml) for two days


title: M300_melioidosis

city: London

country: United Kingdom

description: Library name: M300

value: Female


title: old4

description: Library name: Sample10


title: W82_PBMC_G2_GEX

city: La Jolla

first: Patrick

last: Madden

state: CA

address: 9420 Athena Circle

department: Center for Vaccine Innovation

institute: La Jolla Institute for Immunology

description:
Library name: W82_PBMC_G2_GEX
GEX 5' mRNA library

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
N332-GT5 epitope-specific B cells were isolated from peripheral blood samples collected from rhesus macaques immunized with N332-GT5 and subsequent heterologous boost immunizations. Probes for each boost immunogen were included in flow cytometry staining for each respective Group, allowing determination of the proportion of N332-GT5 epitope-specific cells cross-binding the boost immunogen (N332-GT5++KO– Boost++). Thawed cells were incubated with both N332-GT5 KO and Boost KO probes for twenty minutes at 4°C. Following that, cells were sequentially incubated with the combined Booster WT probes for fifteen minutes at 4°C and then with the combined N332-GT5 WT probes for thirty minutes at 4°C. A master mix of surface staining antibodies was added next, with 2 μg per 5 million cells of anti-human Total-Seq-C hashtag antibodies (Biolegend) following the surface staining, and incubated for thirty minutes at 4°C. Cells were then washed twice and prepared for sorting on BD FACSymphony S6 (BD Biosciences). Epitope-specific B cells were sorted at all time points.Once sorted, epitope-specific PBMC and LN FNA B cells were washed with PBS and loaded onto a Chromium chip and controller following the manufacturers protocol (10X Genomics).  Indexed V(D)J, Feature Barcode, and Gene Expression libraries were prepared following the 10X Genomics protocol with the Feature Barcoding Kit (10X Genomics) and sequenced on a NovaSeq 6000 (Illumina).
Libraries were constructed according to the manufacturer's protocol using the Chromium Next GEM Single Cell 5’ Reagent Kit v3.

value: B cells

value: Protein immunized


title: BxPC3, no ko, Replicate2, RNA-seq

description: Library name: BxPC3_NT_Rep2


title: M298_melioidosis

description: Library name: M298


title: W82_PBMC_G2_VDJ

description:
Library name: W82_PBMC_G2_VDJ
VDJ 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: BCR-Seq


title: old3

description: Library name: Sample9


title: BxPC3, no ko, Replicate1, RNA-seq

description: Library name: BxPC3_NT_Rep1


title: W82_PBMC_G1_HTO

description:
Library name: W82_PBMC_G1_HTO
HTO 5' mRNA library

library_source: other

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein


title: M297_melioidosis

description: Library name: M297


title: old2

description: Library name: Sample8


title: W82_PBMC_G1_GEX

description:
Library name: W82_PBMC_G1_GEX
GEX 5' mRNA library


title: M295_melioidosis

description: Library name: M295


title: BxPC3,FOXA3 ko, S124L mutant FOXA3 Resue, Replicate2, ATAC-seq

description:
Library name: BxPC3_FOXA3 ko_S124L mutant FOXA3 Resue_Rep2
FOXA3KO_S124L_Rescue_merged.bw
FeatureCountMatrix_ConsensusPeaks.txt

library_source: genomic

data_processing:
For Illumina data, adaptors were trimmed with trimmomatic (version 0.39) with the options ILLUMINACLIP:Trimmomatic-0.39/adapters/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:24 (Bolger, Lohse and Usadel, 2014). For Ultima data, cram files were converted to fastq using samtools (version 1.9), and trimmed using cutadapt (version 4.0) (Danecek et al., 2021; Martin, 2011).
Reads from both sequencing platforms were aligned to GRCh38 with bowtie2 (version 2.4.4) (Langmead and Salzberg, 2012), deduplicated with picard through gatk MarkDuplicates (version 4.2.5.0), and downsampled to the sample with the lowest reads using samtools, then peaks were called with MACS2 callpeak (version 2.2.7.1) with default parameters (Zhang.,2008).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak, feature count matrix

molecule: genomic DNA

extract_protocol:
ATAC-seq was performed using homemade transposomes with minor modifications that are detailed below (Buenrostro et al.,2013; Picelli et al., 2014)). For each replicate, we trypsinized, washed, and resuspended 250,000 cells in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40, 0.1% tween-20, 0.01% digitonin) and lysed for 10 minutes on ice (Corces et al., 2017). After lysis, 50,000 cells were resuspended in transposase reaction mix (1ul Tn5 (0.5 µM), 4ul 5X TD-TAPS (50mM TAPS-NaOH, 25mM MgCl2, 50% DMF), 5ul dilution buffer (10mM Tris-HCl, pH 7.4, 100mM NaCl, 1mM DTT, 50% glycerol), 2ul 10% Tween, and 8ul PBS) and tagmentation was performed at 37°C for 30 minutes. Next, samples were purified using the Zymo Clean and Concentrate kit.
For the library preparation, DNA was amplified with NEBNext High-Fidelity 2× PCR Master Mix as previously described (Buenrostro et al.,2013). The PCR program was as followed: 72 °C for 5 minutes, 98 °C for 30 seconds, (98 °C for 10 seconds, 63 °C for 30 seconds, 72 °C for 60 seconds) x 12 cycles. Samples were sequenced on both Illumina NextSeq 500 and Ultima Genomics platforms.

treatment_protocol: In BxPC-3 cells, FOXA3 was perturbed using pCC_01 (Addgene 139086) encoding FOXA3- targeting gRNAs. Cells were selected with 2 ug/mL puromycin for 5 days. To rescue the FOXA3 function, cells were then transduced with the lentiviral plasmid expressing GFP, wild-type FOXA3 or mutant FOXA3. Cells were selected with 2.5 ug/mL blasticidin for 5 days. Following selection, cells were treated with 100 IU/mL IFNγ for 48 hours.


title: old1

description: Library name: Sample7


title: BxPC3,FOXA3 ko, S124L mutant FOXA3 Resue, Replicate3, ATAC-seq

description:
Library name: BxPC3_FOXA3 ko_S124L mutant FOXA3 Resue_Rep3
FOXA3KO_S124L_Rescue_merged.bw
FeatureCountMatrix_ConsensusPeaks.txt


title: M294_melioidosis

description: Library name: M294


title: W82_PBMC_G1_VDJ

description:
Library name: W82_PBMC_G1_VDJ
VDJ 5' mRNA library


title: young6

description: Library name: Sample6

value: young


title: BxPC3,FOXA3 ko, S124L mutant FOXA3 Resue, Replicate1, ATAC-seq

description:
Library name: BxPC3_FOXA3 ko_S124L mutant FOXA3 Resue_Rep1
FOXA3KO_S124L_Rescue_merged.bw
FeatureCountMatrix_ConsensusPeaks.txt


title: M292_melioidosis

description: Library name: M292


title: W72_PBMC_G4_HTO

description:
Library name: W72_PBMC_G4_HTO
HTO 5' mRNA library


title: young5

description: Library name: Sample5


title: young4

description: Library name: Sample4


title: W72_PBMC_G4_GEX

description:
Library name: W72_PBMC_G4_GEX
GEX 5' mRNA library


title: BxPC3,FOXA3 ko, wild-type FOXA3 Resue, Replicate3, ATAC-seq

description:
Library name: BxPC3_FOXA3 ko_wild-type FOXA3 Resue_Rep3
FOXA3KO_FOXA3_Rescue_merged.bw
FeatureCountMatrix_ConsensusPeaks.txt


title: M291_melioidosis

description: Library name: M291


title: BxPC3,FOXA3 ko, wild-type FOXA3 Resue, Replicate2, ATAC-seq

description:
Library name: BxPC3_FOXA3 ko_wild-type FOXA3 Resue_Rep2
FOXA3KO_FOXA3_Rescue_merged.bw
FeatureCountMatrix_ConsensusPeaks.txt


title: M290_melioidosis

description: Library name: M290


title: W72_PBMC_G4_VDJ

description:
Library name: W72_PBMC_G4_VDJ
VDJ 5' mRNA library


title: young3

description: Library name: Sample3


title: BxPC3,FOXA3 ko, wild-type FOXA3 Resue, Replicate1, ATAC-seq

description:
Library name: BxPC3_FOXA3 ko_wild-type FOXA3 Resue_Rep1
FOXA3KO_FOXA3_Rescue_merged.bw
FeatureCountMatrix_ConsensusPeaks.txt


title: M289_melioidosis

description: Library name: M289


title: W72_PBMC_G3_HTO

description:
Library name: W72_PBMC_G3_HTO
HTO 5' mRNA library


title: BxPC3,FOXA3 ko, GFP vector Resue, Replicate3, ATAC-seq

description:
Library name: BxPC3_FOXA3 ko_GFP vector Resue_Rep3
FOXA3KO_GFP_noRescue_merged.bw
FeatureCountMatrix_ConsensusPeaks.txt


title: young2

description: Library name: Sample2


title: W72_PBMC_G3_GEX

description:
Library name: W72_PBMC_G3_GEX
GEX 5' mRNA library


title: young1

description: Library name: Sample1


title: BxPC3,FOXA3 ko, GFP vector Resue, Replicate2, ATAC-seq

description:
Library name: BxPC3_FOXA3 ko_GFP vector Resue_Rep2
FOXA3KO_GFP_noRescue_merged.bw
FeatureCountMatrix_ConsensusPeaks.txt


title: M287_melioidosis

description: Library name: M287


title: BxPC3,FOXA3 ko, GFP vector Resue, Replicate1, ATAC-seq

description:
Library name: BxPC3_FOXA3 ko_GFP vector Resue_Rep1
FOXA3KO_GFP_noRescue_merged.bw
FeatureCountMatrix_ConsensusPeaks.txt


title: M286_melioidosis

description: Library name: M286


title: W72_PBMC_G2_HTO

description:
Library name: W72_PBMC_G2_HTO
HTO 5' mRNA library


title: Muscle Gaa-/- 9 mo biological rep4

type: RNA

city: Nantes

first: Candice

last: BABARIT

address: 101 route de Gachet

department: Santé Animale

country: France

institute: INRAE

description: Gene expression data from 9 mo Gaa-/- mouse

hyb_protocol: 2,3 µg of the fragmented cDNA was hybridized to mouse Clariom S array (#902931, Applied Biosystems) for 16 h at 45°C. Microarrays were washed and stained with streptavidin phycoerythrin conjugate in an Affymetrix Fluidics Station 450 (Affymetrix,California, USA).

scan_protocol: Fluorescent images were captured using gene Array Scanner 2500 (Affymetrix)

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the R affy package

label: biotin

organism: Mus musculus

source_name: Tibialis anterior , Gaa-/- mouse,  9-month-old

label_protocol: One hundred ng of RNA was used to generate double strand cDNA, which was fragmented and biotin-labeled using Genechip WT Plus Reagent Kit (#900720, Applied Biosystems, Warrington, UK).

extract_protocol: Total RNA was extracted from about 20 mg of tissues preserved in RNAlater®, using the Nucleozol RNA extraction kit (#740406, Macherey-Nagel, Hœrdt, France) according to the manufacturer’s instructions. Each sample was treated with DNAse I (#AM2235, Life technologies, Saint-Aubin, France). RNA was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Illkirch, France) and its integrity was determined using the Agilent Eukaryote Total RNA Nano kit (#5067, Agilent Technologies, Les Ulis, France) with the 2100 Bioanalyzer (Agilent Technologies).

value: Tibialis anterior

tag: strain

value: GAA-KO 6neo/6neo


title: W72_PBMC_G2_GEX

description:
Library name: W72_PBMC_G2_GEX
GEX 5' mRNA library


title: M285_melioidosis

description: Library name: M285


title: Muscle Gaa-/- 9 mo biological rep3


title: M284_melioidosis

description: Library name: M284


title: Muscle Gaa-/- 9 mo biological rep2


title: HS-SY-II RNA-seq, WA-68 (100 nM), 48h, biol rep 2

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

description: Library name: HSSYII_WA68_48h_rep2

data_processing:
Basecalling and demultiplexing performed with Illumina bcl2fastq.
Raw reads were quality-checked with FastQC and adapters trimmed with Trim Galore (cutadapt backend).
Reads were aligned to GRCh38 with STAR and gene-level counts generated using featureCounts against Ensembl gene annotations.
Per-sample counts were merged into a single gene x sample matrix (merged_counts.tsv).
Assembly: GRCh38 (Ensembl)
Supplementary files format and content: merged_counts.tsv (tab-delimited raw gene-level counts matrix: rows = Ensembl gene IDs, columns = samples)

source_name: HS-SY-II

growth_protocol: HS-SY-II synovial sarcoma cells were maintained in DMEM with 10% FBS and 1x penicillin/streptomycin at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted using standard column-based purification.
Stranded mRNA libraries were prepared using poly(A) selection and sequenced on an Illumina NovaSeq X (paired-end, 150 bp).

treatment_protocol: Cells were treated with 100 nM WA-68 (BRD9 PROTAC degrader) or DMSO vehicle control and harvested at DMSO control, 12 h, 24 h, 48 h, or 96 h post-treatment.

value: HS-SY-II

value: synovial sarcoma cell line


title: W72_PBMC_G1_HTO

description:
Library name: W72_PBMC_G1_HTO
HTO 5' mRNA library


title: M282_melioidosis

description: Library name: M282

value: Whole blood

value: Male


title: HS-SY-II RNA-seq, WA-68 (100 nM), 48h, biol rep 1

description: Library name: HSSYII_WA68_48h_rep1


title: W72_PBMC_G1_GEX

description:
Library name: W72_PBMC_G1_GEX
GEX 5' mRNA library


title: M281_melioidosis

description: Library name: M281

value: survivor


title: Muscle Gaa-/- 9 mo biological rep1


title: Muscle Gaa-/- 6 mo biological rep4

description: Gene expression data from 6 mo Gaa-/- mouse

source_name: Tibialis anterior , Gaa-/- mouse,  6-month-old


title: Muscle Gaa-/- 6 mo biological rep3


title: HS-SY-II RNA-seq, WA-68 (100 nM), 24h, biol rep 2

description: Library name: HSSYII_WA68_24h_rep2


title: W72_PBMC_G1_VDJ

description:
Library name: W72_PBMC_G1_VDJ
VDJ 5' mRNA library


title: HS-SY-II RNA-seq, WA-68 (100 nM), 24h, biol rep 1

description: Library name: HSSYII_WA68_24h_rep1


title: W56_PBMC_1_G4_HTO

description:
Library name: W56_PBMC_1_G4_HTO
HTO 5' mRNA library


title: W56_PBMC_1_G4_GEX

description:
Library name: W56_PBMC_1_G4_GEX
GEX 5' mRNA library


title: Muscle Gaa-/- 6 mo biologica rep1


title: M280_melioidosis

description: Library name: M280


title: HS-SY-II RNA-seq, WA-68 (100 nM), 12h, biol rep 1

description: Library name: HSSYII_WA68_12h_rep1


title: Muscle Gaa-/- 4 mo biological rep4

description: Gene expression data from 4 mo Gaa-/- mouse

source_name: Tibialis anterior , Gaa-/- mouse,  4-month-old


title: M277_melioidosis

description: Library name: M277


title: W56_PBMC_1_G4_VDJ

description:
Library name: W56_PBMC_1_G4_VDJ
VDJ 5' mRNA library


title: HS-SY-II RNA-seq, DMSO, biol rep 2

description: Library name: HSSYII_WA68_DMSO_rep2

value: DMSO


title: M276_melioidosis

description: Library name: M276


title: W56_PBMC_1_G3_HTO

description:
Library name: W56_PBMC_1_G3_HTO
HTO 5' mRNA library


title: Muscle Gaa-/- 4 mo biological rep3


title: M275_melioidosis

description: Library name: M275


title: HS-SY-II RNA-seq, DMSO, biol rep 1

description: Library name: HSSYII_WA68_DMSO_rep1


title: W56_PBMC_1_G3_GEX

description:
Library name: W56_PBMC_1_G3_GEX
GEX 5' mRNA library


title: Muscle Gaa-/- 4 mo biological rep2


title: M288_melioidosis

description: Library name: M288


title: W72_PBMC_G3_VDJ

description:
Library name: W72_PBMC_G3_VDJ
VDJ 5' mRNA library


title: HS-SY-II ChIP-seq input, WA-68 (100 nM), 96h

description: Library name: HSSYII_WA68_96h_input

data_processing:
Basecalling and demultiplexing performed with Illumina bcl2fastq.
Raw paired-end FASTQ reads quality-checked with FastQC and adapters trimmed with Trim Galore (cutadapt backend).
Reads aligned to GRCh38 with BWA-MEM2; sorted/indexed with SAMtools; PCR/optical duplicates removed with Picard MarkDuplicates.
Low mapping quality reads (MAPQ < 30) and secondary alignments filtered out.
Peaks called with MACS2 (narrow peak mode) using matched input as control. Genome-wide normalized bigWig coverage tracks generated with deepTools.
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigWig (normalized genome coverage); narrowPeak (MACS2 peak calls)

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine. After lysis, chromatin was sonicated to ~200-500 bp fragments. Immunoprecipitation was performed with antibodies against GLTSCR1 or anti-HA (recognizing HA-tagged SS18::SSX fusion) overnight at 4°C with Protein A/G beads. Beads were washed, eluted, reverse-crosslinked, and DNA was purified for library construction. Matched input chromatin controls were prepared in parallel.
ChIP and input DNA were used to construct Illumina sequencing libraries for paired-end sequencing.

value: WT

tag: chip antibody


title: M273_melioidosis

description: Library name: M273


title: HS-SY-II RNA-seq, WA-68 (100 nM), 96h, biol rep 2

description: Library name: HSSYII_WA68_96h_rep2


title: Muscle Gaa-/- 4 mo biological rep1


title: W56_PBMC_1_G3_VDJ

description:
Library name: W56_PBMC_1_G3_VDJ
VDJ 5' mRNA library

value: PBMC


title: HS-SY-II RNA-seq, WA-68 (100 nM), 96h, biol rep 1

description: Library name: HSSYII_WA68_96h_rep1


title: W72_PBMC_G2_VDJ

description:
Library name: W72_PBMC_G2_VDJ
VDJ 5' mRNA library


title: W56_PBMC_1_G2_HTO

description:
Library name: W56_PBMC_1_G2_HTO
HTO 5' mRNA library


title: M272_melioidosis

description: Library name: M272


title: Muscle Gaa-/- 1.5 mo biological rep4

description: Gene expression data from 1.5 mo Gaa-/- mouse

source_name: Tibialis anterior , Gaa-/- mouse,  1.5-month-old


title: HS-SY-II ChIP-seq input, WA-68 (100 nM), 48h

description: Library name: HSSYII_WA68_48h_input


title: HS-SY-II ChIP-seq input, WA-68 (100 nM), 24h

description: Library name: HSSYII_WA68_24h_input


title: M270_melioidosis

description: Library name: M270


title: Muscle Gaa-/- 1.5 mo biological rep3


title: W56_PBMC_1_G2_GEX

description:
Library name: W56_PBMC_1_G2_GEX
GEX 5' mRNA library


title: HS-SY-II ChIP-seq input, WA-68 (100 nM), 12h

description: Library name: HSSYII_WA68_12h_input


title: M269_melioidosis

description: Library name: M269


title: Muscle Gaa-/- 1.5 mo biological rep2


title: W56_PBMC_1_G2_VDJ

description:
Library name: W56_PBMC_1_G2_VDJ
VDJ 5' mRNA library


title: HS-SY-II ChIP-seq input, DMSO

description: Library name: HSSYII_WA68_DMSO_input


title: M268_melioidosis

description: Library name: M268


title: W56_PBMC_1_G1_HTO

description:
Library name: W56_PBMC_1_G1_HTO
HTO 5' mRNA library


title: Muscle Gaa-/- 1.5 mo biological rep1


title: M279_melioidosis

description: Library name: M279


title: HS-SY-II ChIP-seq SS18::SSX fusion (HA-tag), WA-68 (100 nM), 48h

description: Library name: HSSYII_WA68_48h_fusion

value: HA-tag (anti-HA, recognizing HA-tagged SS18::SSX fusion)


title: M267_melioidosis

description: Library name: M267


title: Muscle WT 9 mo biological rep4

description: Gene expression data from 9 mo WT mouse

source_name: Tibialis anterior , WT mouse, 9-month-old

value: Wild type


title: Muscle Gaa-/- 6 mo biological rep2


title: W56_PBMC_1_G1_GEX

description:
Library name: W56_PBMC_1_G1_GEX
GEX 5' mRNA library


title: HS-SY-II RNA-seq, WA-68 (100 nM), 12h, biol rep 2

description: Library name: HSSYII_WA68_12h_rep2


title: M278_melioidosis

description: Library name: M278


title: HS-SY-II ChIP-seq SS18::SSX fusion (HA-tag), WA-68 (100 nM), 24h

description: Library name: HSSYII_WA68_24h_fusion


title: M266_melioidosis

description: Library name: M266


title: Muscle WT 9 mo biological rep3

description: Gene expression data from 9 mo WT mouse


title: W56_PBMC_1_G1_VDJ

description:
Library name: W56_PBMC_1_G1_VDJ
VDJ 5' mRNA library


title: HS-SY-II ChIP-seq SS18::SSX fusion (HA-tag), WA-68 (100 nM), 12h

description: Library name: HSSYII_WA68_12h_fusion


title: Muscle WT 9 mo biological rep2

description: Gene expression data from 9 mo WT mouse


title: M265_melioidosis

description: Library name: M265


title: W56_PBMC_G4_HTO

description:
Library name: W56_PBMC_G4_HTO
HTO 5' mRNA library


title: HS-SY-II ChIP-seq SS18::SSX fusion (HA-tag), DMSO

description: Library name: HSSYII_WA68_DMSO_fusion


title: M264_melioidosis

description: Library name: M264


title: W56_PBMC_G4_GEX

description:
Library name: W56_PBMC_G4_GEX
GEX 5' mRNA library


title: Muscle WT 9 mo biological rep1

description: Gene expression data from 9 mo WT mouse


title: HS-SY-II ChIP-seq GLTSCR1, WA-68 (100 nM), 96h

description: Library name: HSSYII_WA68_96h_GLTSCR1

value: GLTSCR1 antibody


title: M262_melioidosis

description: Library name: M262


title: W56_PBMC_G4_VDJ

description:
Library name: W56_PBMC_G4_VDJ
VDJ 5' mRNA library


title: HS-SY-II ChIP-seq GLTSCR1, WA-68 (100 nM), 48h

description: Library name: HSSYII_WA68_48h_GLTSCR1


title: Muscle WT 6 mo biological rep4

description: Gene expression data from 6 mo WT mouse

source_name: Tibialis anterior , WT mouse, 6-month-old


title: W56_PBMC_G3_HTO

description:
Library name: W56_PBMC_G3_HTO
HTO 5' mRNA library


title: M261_melioidosis

description: Library name: M261


title: Muscle WT 6 mo biological rep3

description: Gene expression data from 6 mo WT mouse


title: HS-SY-II ChIP-seq GLTSCR1, WA-68 (100 nM), 24h

description: Library name: HSSYII_WA68_24h_GLTSCR1


title: W56_PBMC_G3_GEX

description:
Library name: W56_PBMC_G3_GEX
GEX 5' mRNA library


title: M259_melioidosis

description: Library name: M259

value: Female


title: Muscle WT 6 mo biological rep2

description: Gene expression data from 6 mo WT mouse


title: HS-SY-II ChIP-seq GLTSCR1, WA-68 (100 nM), 12h

description: Library name: HSSYII_WA68_12h_GLTSCR1


title: M258_melioidosis

description: Library name: M258


title: W56_PBMC_G3_VDJ

description:
Library name: W56_PBMC_G3_VDJ
VDJ 5' mRNA library

value: B cells


title: HS-SY-II ChIP-seq GLTSCR1, DMSO

description: Library name: HSSYII_WA68_DMSO_GLTSCR1


title: M257_melioidosis

description: Library name: M257


title: W56_PBMC_G2_HTO

description:
Library name: W56_PBMC_G2_HTO
HTO 5' mRNA library

value: Protein immunized


title: Muscle WT 6 mo biological rep1

description: Gene expression data from 6 mo WT mouse


title: W56_PBMC_G2_GEX

description:
Library name: W56_PBMC_G2_GEX
GEX 5' mRNA library


title: M256_melioidosis

description: Library name: M256


title: Muscle WT 4 mo biological rep4

description: Gene expression data from 4 mo WT mouse

source_name: Tibialis anterior , WT mouse, 4-month-old


title: HS-SY-II ATAC-seq, WA-68 (100 nM), 96 h, biol rep 2

description: Library name: HSSYII_WA68_96_rep2

data_processing:
Basecalling and demultiplexing performed with Illumina bcl2fastq.
Raw paired-end FASTQ reads (150 bp) quality-checked with FastQC v0.11.9 and adapters trimmed with Trim Galore v0.6.7.
Reads aligned to GRCh38 with BWA-MEM2 v2.2.1; sorted/indexed with SAMtools v1.15.1; duplicates removed with Picard MarkDuplicates v2.27.4.
Mitochondrial reads, MAPQ<30, and secondary alignments filtered. Tn5 bias corrected (+4/-5 bp shift). Peaks called with MACS2 v2.2.7.1 (BAMPE mode). RPKM-normalized bigWig tracks generated with deepTools v3.5.1.
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigWig (RPKM-normalized genome coverage); broadPeak / narrowPeak (MACS2 peak calls)

growth_protocol: SYO-1 and HS-SY-II synovial sarcoma cell lines were maintained in DMEM with 10% FBS and 1x penicillin/streptomycin at 37C, 5% CO2.

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol. 50,000 cells were pelleted and resuspended in 50 ul cold ATAC-RSB (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2) with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin, incubated on ice for 3 min. After washing, pellets were resuspended in 50 ul transposition mixture (25 ul 2x TD buffer, 2.5 ul transposase [Illumina #20034198], 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) and incubated at 37C for 30 min at 1000 rpm. Tagmented DNA was purified using a DNA Clean and Concentrator kit.
Tagmented DNA was PCR-amplified with indexed Nextera primers and purified for Illumina sequencing.

treatment_protocol: Cells were treated with 100 nM WA-68 (BRD9 PROTAC degrader) or DMSO vehicle control. HS-SY-II time-course samples were harvested at 12, 24, 48, or 96 h post-treatment.


title: Muscle WT 4 mo biological rep3

description: Gene expression data from 4 mo WT mouse


title: HS-SY-II ATAC-seq, WA-68 (100 nM), 96 h, biol rep 1

description: Library name: HSSYII_WA68_96_rep1


title: M255_melioidosis

description: Library name: M255


title: W56_PBMC_G2_VDJ

description:
Library name: W56_PBMC_G2_VDJ
VDJ 5' mRNA library


title: Muscle WT 4 mo biological rep2

description: Gene expression data from 4 mo WT mouse


title: HS-SY-II ATAC-seq, WA-68 (100 nM), 48 h, biol rep 2

description: Library name: HSSYII_WA68_48_rep2


title: M254_melioidosis

description: Library name: M254


title: W56_PBMC_G1_HTO

description:
Library name: W56_PBMC_G1_HTO
HTO 5' mRNA library


title: Muscle WT 4 mo biological rep1

description: Gene expression data from 4 mo WT mouse


title: HS-SY-II ATAC-seq, WA-68 (100 nM), 48 h, biol rep 1

description: Library name: HSSYII_WA68_48_rep1


title: M253_melioidosis

description: Library name: M253


title: W56_PBMC_G1_GEX

description:
Library name: W56_PBMC_G1_GEX
GEX 5' mRNA library


title: HS-SY-II ATAC-seq, WA-68 (100 nM), 24 h, biol rep 2

description: Library name: HSSYII_WA68_24_rep2


title: M252_melioidosis

description: Library name: M252


title: Muscle WT 1.5 mo biological rep4

description: Gene expression data from 1.5 mo WT mouse

source_name: Tibialis anterior , WT mouse, 1.5-month-old


title: W56_PBMC_G1_VDJ

description:
Library name: W56_PBMC_G1_VDJ
VDJ 5' mRNA library


title: Muscle WT 1.5 mo biological rep3


title: M251_melioidosis

description: Library name: M251


title: W46_PBMC_G4_HTO

description:
Library name: W46_PBMC_G4_HTO
HTO 5' mRNA library


title: Muscle WT 1.5 mo biological rep2


title: M250_melioidosis

description: Library name: M250


title: HS-SY-II ATAC-seq, WA-68 (100 nM), 12 h, biol rep 2

description: Library name: HSSYII_WA68_12_rep2


title: chondrocyte, co-culture, IL-1β, rep3

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: DCI3

data_processing:
The constructed libraries underwent quality control (QC), and after passing, they were subjected to sequencing. Sequencing was performed on the DNBSEQ platform with a read length of SE50. The data obtained from sequencing, referred to as raw reads or raw data, underwent QC to determine whether the sequencing data were suitable for subsequent analysis. After QC, clean reads were obtained and aligned to the reference sequence. After alignment, the alignment results were subjected to a second QC, where alignment rate, distribution of reads on the reference sequence, and other metrics were assessed. If the results passed the second QC, gene quantification analysis and various analyses based on gene expression levels (such as principal component analysis (PCA), correlation analysis, differential gene selection, etc.) were conducted.
Assembly: GRCm38
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Primary chondrocyte

extract_protocol:
The skin tissue/cartilage tissue was cut into 1 mm diameter pieces with sterilised ophthalmic scissors. Then skin tissue was digested in 0.5 mg/ml collagenase I (Biosharp, China) and DNase I (Roche, Switzerland) for 3 hours, while cartilage tissue was digested in 0.5 mg/ml collagenase II (Biosharp, China) and DNase I (Roche, Switzerland) for 2 hours. The isolated cell suspension was passed through a 100 μm sieve and then centrifuged to remove the supernatant. DFbs were cultured in alpha-MEM with 1% penicillin-streptomycin and 10% fetal bovine serum. Chondrocytes were cultured in DMEM/F12 containing 1% ITS (OriCell, China), 1% penicillin-streptomycin and 10% fetal bovine serum.
For library construction, total RNA was processed using mRNA enrichment. The mRNA was enriched using magnetic beads with Oligo(dT) to capture mRNA with a polyA tail. The obtained RNA was fragmented using a breaking buffer, and random N6 primers were used for reverse transcription. Subsequently, double-stranded cDNA was synthesized. The ends of the synthesized double-stranded DNA were blunted and 5' end-phosphorylated. A single-base overhang "A" was added to the 3' end, and a bubble-shaped adapter with a protruding "T" at the 3' end was ligated. The ligated products were PCR-amplified using specific primers. The PCR products were denatured to form single-stranded DNA, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries underwent quality control, and after passing, they were subjected to sequencing

value: Primary chondrocyte

value: co-culture, IL-1β


title: HS-SY-II ATAC-seq, WA-68 (100 nM), 12 h, biol rep 1

description: Library name: HSSYII_WA68_12_rep1


title: W46_PBMC_G4_GEX

description:
Library name: W46_PBMC_G4_GEX
GEX 5' mRNA library


title: Muscle WT 1.5 mo biological rep1

value: Tibialis anterior


title: W46_PBMC_G4_VDJ

description:
Library name: W46_PBMC_G4_VDJ
VDJ 5' mRNA library


title: M249_melioidosis

description: Library name: M249


title: chondrocyte, co-culture, IL-1β, rep2

description: Library name: DCI2


title: HS-SY-II ATAC-seq, WA-68 (100 nM), biol rep 2

description: Library name: HSSYII_WA68_endpt_rep2

value: HS-SY-II


title: M248_melioidosis

description: Library name: M248


title: W46_PBMC_G3_HTO

description:
Library name: W46_PBMC_G3_HTO
HTO 5' mRNA library


title: chondrocyte, co-culture, IL-1β, rep1

description: Library name: DCI1


title: M246_melioidosis

description: Library name: M246


title: W46_PBMC_G3_GEX

description:
Library name: W46_PBMC_G3_GEX
GEX 5' mRNA library


title: chondrocyte, normal culture, IL-1β, rep3

description: Library name: CI3

value: normal culture, IL-1β


title: HS-SY-II ATAC-seq, WA-68 (100 nM), biol rep 1

description: Library name: HSSYII_WA68_endpt_rep1

value: synovial sarcoma cell line


title: M245_melioidosis

description: Library name: M245

value: Whole blood

value: Male


title: W46_PBMC_G3_VDJ

description:
Library name: W46_PBMC_G3_VDJ
VDJ 5' mRNA library


title: HS-SY-II ATAC-seq, DMSO, biol rep 3

description: Library name: HSSYII_WA68_DMSO_rep3

value: DMSO


title: chondrocyte, normal culture, IL-1β, rep2

description: Library name: CI2

value: WT


title: M244_melioidosis

description: Library name: M244

value: survivor


title: HS-SY-II ATAC-seq, DMSO, biol rep 2

description: Library name: HSSYII_WA68_DMSO_rep2


title: HS-SY-II ATAC-seq, DMSO, biol rep 1

description: Library name: HSSYII_WA68_DMSO_rep1


title: chondrocyte, normal culture, IL-1β, rep1

description: Library name: CI1


title: W46_PBMC_G2_HTO

description:
Library name: W46_PBMC_G2_HTO
HTO 5' mRNA library

value: PBMC


title: M243_melioidosis

description: Library name: M243


title: W46_PBMC_G2_GEX

description:
Library name: W46_PBMC_G2_GEX
GEX 5' mRNA library


title: chondrocyte, normal culture, no IL-1β, rep3

description: Library name: C3

value: normal culture, no IL-1β


title: M242_melioidosis

description: Library name: M242


title: SYO-1 ATAC-seq, WA-68 (100 nM), biol rep 2

description: Library name: SYO1_WA68_rep2


title: W46_PBMC_G2_VDJ

description:
Library name: W46_PBMC_G2_VDJ
VDJ 5' mRNA library


title: chondrocyte, normal culture, no IL-1β, rep2

description: Library name: C2


title: M241_melioidosis

description: Library name: M241


title: W46_PBMC_G1_HTO

description:
Library name: W46_PBMC_G1_HTO
HTO 5' mRNA library


title: SYO-1 ATAC-seq, WA-68 (100 nM), biol rep 1

description: Library name: SYO1_WA68_rep1


title: synovial fibroblast, co-culture, IL-1β, rep3

description: Library name: DFI3

data_processing:
The constructed libraries underwent quality control (QC), and after passing, they were subjected to sequencing. Sequencing was performed on the DNBSEQ platform with a read length of SE50. The data obtained from sequencing, referred to as raw reads or raw data, underwent QC to determine whether the sequencing data were suitable for subsequent analysis. After QC, clean reads were obtained and aligned to the reference sequence. After alignment, the alignment results were subjected to a second QC, where alignment rate, distribution of reads on the reference sequence, and other metrics were assessed. If the results passed the second QC, gene quantification analysis and various analyses based on gene expression levels (such as principal component analysis (PCA), correlation analysis, differential gene selection, etc.) were conducted.
Assembly: GRCm38
Supplementary files format and content: csv file includes FPKM values for each Sample

source_name: synovial fibroblast

extract_protocol:
The skin tissue/synovium tissue was cut into 1 mm diameter pieces with sterilised ophthalmic scissors. Then skin tissue/synovium tissue was digested in 0.5 mg/ml collagenase I (Biosharp, China) and DNase I (Roche, Switzerland) for 3 hours.The isolated cell suspension was passed through a 100 μm sieve and then centrifuged to remove the supernatant.
For library construction, total RNA was processed using mRNA enrichment. The mRNA was enriched using magnetic beads with Oligo(dT) to capture mRNA with a polyA tail. The obtained RNA was fragmented using a breaking buffer, and random N6 primers were used for reverse transcription. Subsequently, double-stranded cDNA was synthesized. The ends of the synthesized double-stranded DNA were blunted and 5' end-phosphorylated. A single-base overhang "A" was added to the 3' end, and a bubble-shaped adapter with a protruding "T" at the 3' end was ligated. The ligated products were PCR-amplified using specific primers. The PCR products were denatured to form single-stranded DNA, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries underwent quality control, and after passing, they were subjected to sequencing

value: synovial fibroblast


title: chondrocyte, normal culture, no IL-1β, rep1

description: Library name: C1


title: M240_melioidosis

description: Library name: M240


title: SYO-1 ATAC-seq, DMSO, biol rep 2

description: Library name: SYO1_DMSO_rep2


title: Cnt0hR3

city: Berkeley

first: Sharon

last: Greenblum

address: 1 Cyclotron Road

institute: DOE Joint Genome Institute

description: Library name: NSWHX

data_processing:
raw data are paired-end interleaved fastq files
BBTools v38.96 bbduk.sh was used to filter raw reads for 1) removal of artifact sequence, RNA spike-in reads, PhiX reads, and reads containing any N, 2) quality trimming with method set at Q6, and 3) removal of reads with <50 bases
Filtered reads from each library were aligned to the A. thaliana TAIR10 reference genome using HISAT2 v2.2.1127
featureCounts was used to generate raw gene counts using Araport 11 gene annotations. Only primary hits assigned to the reverse strand were included (-s 2 -p --primary options)
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: counts.txt: tab-separated matrix containing read counts for each gene (rows) in each library (columns)

organism: Arabidopsis thaliana

source_name: root

growth_protocol: seeds were sterilized, then planted on nylon mesh in agar plates containing 3mM Ca(NO3)2, 1.5mM MgSO4, 1.25mM NH4H2PO4, 1mM KCl, and 1x micronutrients (Murashige and Skoog Micronutrient Salts 100x, MSP18-10LT), in 0.8% agar with pH 5.7. Seeds were sown on plates at a density of 3 rows per plate with ~30 plants per row and plates were placed vertically in a growth chamber under conditions of 16 h light at 22°C, 8 h dark at 19°C

extract_protocol:
mRNA was isolated from an input of 1000 ng of total RNA with oligo dT magnetic beads and fragmented to 300 bp - 400 bp with divalent cations at a high temperature.
Using TruSeq stranded mRNA kit (Illumina), the fragmented mRNA was reverse transcribed to create the first strand of cDNA with random hexamers and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) followed by second strand synthesis. The double stranded cDNA fragments were treated with A-tailing, ligation with NEXTFLEX UDI Barcodes (PerkinElmer) and enriched using 8.0 cycles of PCR. Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell, using 2x150 bp paired-end sequencing.

treatment_protocol: On the 5th day, the nylon mesh and plants were transferred using forceps to agar plates containing either 2 μM ABA, 150 μM SA, or the standard growth medium without added hormones as a negative control. Samples were collected at time points of 0, 1, 2, 4, 7, 24, and 48 hours, separating root and shoot tissues with a single razor blade cut at the time of collection.

value: root

value: control

tag: timepoint

tag: replicate


title: SYO-1 ATAC-seq, DMSO, biol rep 1

description: Library name: SYO1_DMSO_rep1


title: POND-IGF2BP1_50ng_rep2

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

institute: Peking University

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7) (https://github.com/FelixKrueger/TrimGalore) to eliminate low-quality reads and trim adapter sequences.
Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) combined with ERCC spike-in sequences (https://assets.thermofisher.cn/TFS-Assets/LSG/manuals/ERCC92.zip) by STAR (v2.7.10a) using the GENCODE (Human v40 or Mouse vM25) transcript annotation as transcriptome guide, with parameters: --outFilterMismatchNoverLmax 0.04.
The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
For RBP POND-seq data, raw counts were normalized to counts per million (CPM) using ERCC spike-ins, and RBP targets were defined as transcripts with CPM >= 50, log2foldchange > 2, and adjusted P-value < 0.05 in RBP-POND versus control (EPN24 or EPN24-GFP) samples by DESeq2 (v1.36.0).
The POND-seq data for mutated RBPs were also quantified using absolute quantification based on ERCC spike-in controls. The total CPM of wild-type RBP-POND were set to 1,000,000, and the CPM of mutated RBPs-POND were calculated relative to that of wild-type RBP. For transcriptome analysis with PABPC1-POND-seq and RNA-seq, raw counts were normalized to transcripts per million (TPM) as gene expression level.
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawCounts, csv files include DESeq2 results

molecule: cytoplasmic RNA

source_name: HEK293T cell line

growth_protocol: HEK293T, Huh-7, and A549 cells were cultured at 37°C under 5% CO2 in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% FBS (PANSera), penicillin (100 U/ml) and streptomycin (100 µg/ml). V6.5 mouse ESCs were grown on gelatin-coated dish at 37°C under 5% CO2, in KnockOutTM DMEM (Gibco) supplemented with 15% FBS (Hyclone), nonessential amino acids, 2-mercaptoethanol, and 1,000 units/ml lymphocyte inhibitory factor. H1 Human ESCs were grown in mTeSRTM (STEMCELL Technologies) on Matrigel-coated dish at 37°C under 5% CO2.

extract_protocol:
Cell supernatant was clariﬁed by centrifugation at 3,000 g for 5 minutes, then filtrated through a cellulose acetate ﬁlter with 0.45 μm pore size (Corning). 200 μl of supernatant was mixed with 800 μl TRIzol reagent (Magen) and 1 μl diluted External RNA Controls Consortium (ERCC) synthetic spike-in RNAs (ThermoFisher). RNA was extracted and dissolved in 15-20 μl nuclease-free water.
For POND-seq, 5 μl RNA was used for library construction with modified VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). Typically, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) for fragmentation at 85℃ for 6 min. For ribosomal depletion, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) and 0.7 μl FastSelect reagent (Vazyme) for fragmentation at 85℃ for 6 min. Then 8 μl fragmentated RNA was used for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (16-18 cycles) according to the manufacture’s instruction manual. The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene, China) or DNBSEQ-T7 platform (GenePlus, China). For FMR1 mutation screening, library construction was completed with VNL-96P (Vazyme) automated library preparation workstation. Briefly, 4 μl RNA was mixed with 4 μl 2×Prime buffer V2 (Vazyme) and 1 μl FastSelect reagent (Vazyme) for fragmentation at 85°C for 6 min. Then 8 μl fragmentated RNA was adopted for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (17 cycles) according to VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). The NGS sequencing was performed on DNBSEQ-T7 platform (GenePlus). For cellular RNA-seq, the total RNA of HEK293T, Huh-7 and A549 were extracted with TRIzol reagent (Magen) and dissolved in nuclease-free water. 500 ng total RNA was used for library construction with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene) or DNBSEQ-T7 platform (GenePlus).

value: HEK293T cell line


title: W46_PBMC_G1_VDJ

description:
Library name: W46_PBMC_G1_VDJ
VDJ 5' mRNA library

value: B cells

value: Protein immunized


title: M239_melioidosis

description: Library name: M239

value: Female


title: synovial fibroblast, co-culture, IL-1β, rep2

description: Library name: DFI2

value: co-culture, IL-1β


title: Salmonella Enteritidis challenged replicate 2

city: Wooster

first: Shuja

last: Majeed

state: OH

address: 1119 Townsview Place

department: Animal Sciences

institute: The Ohio State University

description:
Library name: SE2
10x Genomics

data_processing:
FASTQ files processed using Cell Ranger v9.0.1 (10x Genomics). Reads aligned to Gallus gallus reference genome (NCBI RefSeq GCF_016699485.2; GRCg7b). Gene expression count matrices generated.
Count matrices loaded into R v4.4.2 as Seurat v5.0 objects. Ambient RNA removed with SoupX v1.6.2. Cells filtered: mitochondrial% >20%, features <300, or features in <3 cells removed. Doublets removed with DoubletFinder v2.0.4.
Each Seurat object normalized with SCTransform(). Four objects integrated using PrepSCTIntegration(), SelectIntegrationFeatures() (3000 variable features), FindIntegrationAnchors(), and IntegrateData() with SCT normalization.
Assembly: GCF_016699485.2 (Gallus gallus GRCg7b, NCBI RefSeq)
Supplementary files format and content: Processed data are provided as HDF5 files (filtered_feature_bc_matrix.h5) generated by Cell Ranger v9.0.1.

organism: Gallus gallus

source_name: proximal ileum

extract_protocol:
Approximately 10 cm of ileum was excised, flushed with PBS, and opened longitudinally. The mucosa was scraped, resuspended in PBS with 5% chicken serum, 2 mM EDTA, and 2 mM DTT, and shaken at 37C/150 rpm for 45 min. Supernatant was passed through gauze, resuspended in 40% Percoll, and overlaid on 70% Percoll for density gradient centrifugation. IEL fractions from 8 birds were pooled into 4 samples per group (2 birds/pool). Samples were filtered through 40 um strainers and enriched for CD45+ cells by MACS (CD45-biotin antibody, Southern Biotech). For scRNA-seq, 4 pooled samples per group were further combined in pairs to yield 2 scRNA-seq samples per group.
Enriched CD45+ IELs were washed and resuspended in PBS + 5% FBS. Approximately 5000-13000 cells per sample were loaded onto the 10x Genomics Chromium X using the GEM-X Universal 3' Gene Expression v4 kit. Libraries were constructed using 10x Genomics Library Construction Kit C and sequenced on an Illumina NovaSeq X Plus at Admera Health (South Plainfield, NJ) with 2x150 bp paired-end reads at ~70,000 reads/cell.

value: proximal ileum

value: intraepithelial lymphocytes

value: SPF White Leghorn layer chicken

value: Salmonella Enteritidis challenged


title: M238_melioidosis

description: Library name: M238

source_name: Whole blood

value: Whole blood


title: W18_PBMC_G4_HTO

description:
Library name: W18_PBMC_G4_HTO
HTO 5' mRNA library


title: Salmonella Enteritidis challenged replicate 1

description:
Library name: SE1
10x Genomics


title: M237_melioidosis

description: Library name: M237

value: Male


title: synovial fibroblast, co-culture, IL-1β, rep1

description: Library name: DFI1

value: WT


title: Control replicate 2

description:
Library name: CN2
10x Genomics

value: Control (PBS)


title: synovial fibroblast, normal culture, IL-1β, rep3

description: Library name: FI3

value: normal culture, IL-1β


title: W18_PBMC_G4_GEX

description:
Library name: W18_PBMC_G4_GEX
GEX 5' mRNA library

value: PBMC


title: M235_melioidosis

description: Library name: M235

value: survivor


title: W18_PBMC_G4_VDJ

description:
Library name: W18_PBMC_G4_VDJ
VDJ 5' mRNA library


title: Control replicate 1

description:
Library name: CN1
10x Genomics


title: W18_PBMC_G3_HTO

description:
Library name: W18_PBMC_G3_HTO
HTO 5' mRNA library


title: M234_melioidosis

description: Library name: M234


title: synovial fibroblast, normal culture, IL-1β, rep1

description: Library name: FI1

value: synovial fibroblast


title: M233_melioidosis

description: Library name: M233


title: synovial fibroblast, normal culture, no IL-1β, rep3

description: Library name: F3

value: normal culture, no IL-1β


title: W18_PBMC_G3_GEX

description:
Library name: W18_PBMC_G3_GEX
GEX 5' mRNA library

value: B cells


title: M232_melioidosis

description: Library name: M232


title: W46_PBMC_G1_GEX

description:
Library name: W46_PBMC_G1_GEX
GEX 5' mRNA library

value: Protein immunized


title: W18_PBMC_G2_HTO

description:
Library name: W18_PBMC_G2_HTO
HTO 5' mRNA library


title: synovial fibroblast, normal culture, no IL-1β, rep2

description: Library name: F2


title: W18_PBMC_G3_VDJ

description:
Library name: W18_PBMC_G3_VDJ
VDJ 5' mRNA library


title: synovial fibroblast, normal culture, IL-1β, rep2

description: Library name: FI2


title: M231_melioidosis

description: Library name: M231

value: Female


title: Jejunum, WT saline day 7, mouse 206

city: Odense

first: Mark

last: Burton

address: J.B. Winsløvsvej 4

department: Clinical Genetics

country: Denmark

institute: Odense University Hospital

description: Jejunum; one array per animal.

hyb_protocol: Hybridisation, washing and staining were performed automatically on the Affymetrix GeneTitan instrument according to the manufacturer's protocol for the Mouse Transcriptome Array 1.0 (fluidics/staining protocol FS450_0001).

scan_protocol: Arrays were scanned automatically in the Affymetrix GeneTitan instrument.

data_processing: CEL files were summarised at gene (transcript-cluster) level using Signal Space Transformation RMA (SST-RMA) in the Affymetrix Expression Console / Transcriptome Analysis Console (TAC) v3.0; the accompanying matrix contains log2 SST-RMA signal. Differential expression was assessed by ANOVA in TAC v3.0 (FDR < 0.05).

source_name: jejunum

label_protocol: Biotinylated sense-strand cDNA targets were prepared from total RNA using the Affymetrix GeneChip WT PLUS reagent kit according to the manufacturer's protocol.

growth_protocol: Adult 10-12-week-old female Sftpd-/- (KO) mice, backcrossed >10 generations onto the C57BL/6N background, and Sftpd+/+ (WT) littermates were bred in-house. Genotypes were confirmed by DNA PCR.

extract_protocol: Total RNA was isolated from jejunum using TRIzol (Invitrogen) per the manufacturer's instructions; quantity/purity assessed by NanoDrop (all A260/280 >= 1.8) and integrity verified on an Agilent 2100 Bioanalyzer (RNA 6000 Nano kit).

treatment_protocol: At day 0 mice received a single intraperitoneal injection of doxorubicin 20 mg/kg (Doxorubicin Accord) or an equal volume of isotonic saline, and were sacrificed on day 3 or day 7. The small intestine was removed and the jejunum (middle segment) was sampled.

value: Sftpd+/+ (wild-type)

tag: agent

value: isotonic saline (vehicle)

tag: time

value: day 7


title: HS-SY-II ATAC-seq, WA-68 (100 nM), 24 h, biol rep 1

description: Library name: HSSYII_WA68_24_rep1

value: HS-SY-II

value: synovial sarcoma cell line


title: Jejunum, WT saline day 7, mouse 296

description: Jejunum; one array per animal.


title: synovial fibroblast, normal culture, no IL-1β, rep1

description: Library name: F1


title: W18_PBMC_G2_GEX

description:
Library name: W18_PBMC_G2_GEX
GEX 5' mRNA library

source_name: PBMC


title: M229_melioidosis

description: Library name: M229

data_processing:
Raw sequencing data (FASTQ files) were pre-processed and quality checked by the service. The FASTQ files were mapped using human reference genome UCSC hg38.p2 version 20201using STAR aligner (version 2.6.1d). Raw counts (uniquely mapped reads) were generated from the mapped read files (.bam) using featureCounts function of Subread package (version 1.6.2) as tab-delimited text files.
Assembly: UCSC hg38.p2 version 20201
Supplementary files format and content: tab-delimited text files inlcudes raw counts for each sample

value: Whole blood


title: ABA7hS3

description: Library name: NTGPT

source_name: shoot

value: shoot

value: ABA


title: Jejunum, WT saline day 7, mouse 112

description: Jejunum; one array per animal.


title: Cnt0hR1

description: Library name: NSWHU

value: root

value: control


title: Cnt0hR2

description: Library name: NSWHW


title: 8505c_shTAZ_dabrafenib_4

city: Bethesda

first: Myriem

last: Boufraqech

state: Maryland

address: NIH campus, building 10 room 7S261

department: CCR

institute: NCI

description: Library name: MB_16_S16_001

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt v1.18 (parameters: --pair-filter=any nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35)
Trimmed reads were mapped to hg38 reference genome using STAR 2.7.0f aligner
Read count extraction was performed using RSEM v1.3.0
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes RSEM counts for each sample

source_name: thyroid

extract_protocol:
RNA were extracted using RNAeasy kit (Qiagen)
We used 230 ng of total RNA samples to generate the library (Poly A selected) with 12 PCR cycles. The kits used for the library prep were NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB, E6440) as described in the manufacturer’s manual. Sequencing was carried out in the Illumina NextSeq2000 instrument with NextSeq™ 2000 P4 XLEAP-SBS™ Reagent Kit (200 Cycles) 101x101 pair end configuration. The demultiplexing was carried out with the illumina DRAGEN BCL convert software version 4.2.7.

value: thyroid

value: ATC cell line

value: shTAZ+dabra


title: ICH19

city: shanghai

first: Zuopeng

last: Su

address: 170 Xinsong Road, Xinzhuang Town, Minhang District,

department: Department of Neurosurgery,

institute: Minhang Hospital, Fudan University

description:
Library name: sample 19
Hypertension with cerebral hemorrhage group (ICH group),rep19

data_processing:
The raw reads were preprocessed and filtered using Trimmomatic  with the following steps:Removal of P7 and P5 adapter sequences (sequences provided above),trimming of bases with quality scores <20,discarding reads shorter than 50 bp and singleton reads.
Clean reads after quality control were aligned to the reference genome GRCh38.p13 using HISAT2 to acquire mapping positions.
Alignment outputs from HISAT2 were analyzed using htseq-count (v0.6.0)  to quantify read counts per transcript.
Alternative splice events that occurred in the samples were identified by Multivariate Analysis of Transcript Splicing (MATS, http://rnaseq-mats.sourceforge.net/).
Assembly: GRCh38
Supplementary files format and content: expression.xlsx

source_name: Peripheral Blood

extract_protocol:
RNA was harvested using TIANSeq mRNA Capture Kit (TIANGEN Biotech).
Libraries were constructed using the TIANSeq Fast RNA Library Prep Kit for Illumina (TIANGEN Biotech).

value: Peripheral Blood

value: Peripheral Blood Mononuclear Cells


title: PABPC1-POND-Huh7_NoDNASE_rep-1

source_name: Huh-7 cell line

value: Huh-7 cell line


title: ICH11

description:
Library name: sample 11
Hypertension with cerebral hemorrhage group (ICH group),rep11


title: M228_melioidosis

description: Library name: M228

extract_protocol:
For the melioidosis cohort, we isolated total RNA from whole blood sample of 81 melioidosis patients and 29 uninfected control participants (DM control, n=15; healthy donor, n=14) collected in Tempus blood RNA tube using the Tempus Spin RNA. A ribozero library preparation and the globin depletion workflow were performed by the Oxford Genomics Centre, Wellcome Centre for Human Genetics, University of Oxford.
Ribozero library preparation with globin depletion workflow (HTG 384 UDI RNA-Seq Ribozero) was performed by  the Oxford Genomics Centre, Wellcome Centre for Human Genetics, University of Oxford. And the samples were sequenced for 75-base pair pair-end, 50 million reads.

value: Female

value: survivor


title: W18_PBMC_G2_VDJ

description:
Library name: W18_PBMC_G2_VDJ
VDJ 5' mRNA library

value: PBMC

value: B cells

value: Protein immunized


title: Jejunum, WT saline day 7, mouse 104

description: Jejunum; one array per animal.

value: Sftpd+/+ (wild-type)

value: isotonic saline (vehicle)

value: day 7


title: 8505c_shTAZ_dabrafenib_2

description: Library name: MB_14_S14_001


title: W18_PBMC_G1_HTO

description:
Library name: W18_PBMC_G1_HTO
HTO 5' mRNA library


title: M225_melioidosis

description: Library name: M225

value: Whole blood

value: Male


title: W18_PBMC_G1_GEX

description:
Library name: W18_PBMC_G1_GEX
GEX 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files


title: 8505c_shTAZ_dabrafenib_1

description: Library name: MB_13_S13_001


title: Jejunum, WT saline day 3, mouse 190

description: Jejunum; one array per animal.

value: day 3


title: Jejunum, WT saline day 3, mouse 170

description: Jejunum; one array per animal.


title: M224_melioidosis

description: Library name: M224


title: 8505c_shTAZ_vehicle_4

description: Library name: MB_12_S12_001

value: thyroid

value: shTAZ


title: M223_melioidosis

description: Library name: M223


title: W12_PBMC_G4_HTO

description:
Library name: W12_PBMC_G4_HTO
HTO 5' mRNA library


title: 8505c_shTAZ_vehicle_3

description: Library name: MB_11_S11_001

value: ATC cell line


title: M221_melioidosis

description: Library name: M221


title: Jejunum, WT saline day 3, mouse 44

description: Jejunum; one array per animal.


title: W12_PBMC_G4_VDJ

description:
Library name: W12_PBMC_G4_VDJ
VDJ 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: BCR-Seq


title: 8505c_shTAZ_vehicle_1

description: Library name: MB_09_S9_001


title: Jejunum, WT saline day 3, mouse 14

description: Jejunum; one array per animal.


title: M220_melioidosis

description: Library name: M220


title: W12_PBMC_G3_HTO

description:
Library name: W12_PBMC_G3_HTO
HTO 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: CITE-seq


title: 8505c_shCtrl+dabrafenib_4

description: Library name: MB_08_S8_001

value: shC+dabra


title: M219_melioidosis

description: Library name: M219


title: 8505c_shCtrl+dabrafenib_3

description: Library name: MB_07_S7_001


title: W12_PBMC_G3_GEX

description:
Library name: W12_PBMC_G3_GEX
GEX 5' mRNA library


title: W12_PBMC_G3_VDJ

description:
Library name: W12_PBMC_G3_VDJ
VDJ 5' mRNA library


title: 8505c_shCtrl+dabrafenib_2

description: Library name: MB_06_S6_001


title: M217_melioidosis

description: Library name: M217


title: Jejunum, WT doxorubicin day 7, mouse 198

description: Jejunum; one array per animal.

value: doxorubicin (20 mg/kg, single i.p.)


title: Jejunum, WT doxorubicin day 7, mouse 102

description: Jejunum; one array per animal.


title: 8505c_shCtrl+dabrafenib_1

description: Library name: MB_05_S5_001


title: W12_PBMC_1_G2_HTO

description:
Library name: W12_PBMC_1_G2_HTO
HTO 5' mRNA library


title: 8505c_shTAZ_vehicle_2

description: Library name: MB_10_S10_001


title: M216_melioidosis

description: Library name: M216


title: Jejunum, WT doxorubicin day 7, mouse 96

description: Jejunum; one array per animal.


title: W12_PBMC_1_G2_GEX

description:
Library name: W12_PBMC_1_G2_GEX
GEX 5' mRNA library


title: Jejunum, WT doxorubicin day 3, mouse 244

description: Jejunum; one array per animal.


title: 8505c_shCtrl_Vehicle_3

description: Library name: MB_03_S3_001

value: shC


title: Jejunum, WT doxorubicin day 3, mouse 232

description: Jejunum; one array per animal.


title: M214_melioidosis

description: Library name: M214


title: 8505c_shCtrl_Vehicle_2

description: Library name: MB_02_S2_001


title: Jejunum, WT doxorubicin day 3, mouse 192

description: Jejunum; one array per animal.


title: W12_PBMC_G2_GEX

description:
Library name: W12_PBMC_G2_GEX
GEX 5' mRNA library


title: M213_melioidosis

description: Library name: M213

value: Female


title: W12_PBMC_G2_VDJ

description:
Library name: W12_PBMC_G2_VDJ
VDJ 5' mRNA library


title: Jejunum, WT doxorubicin day 3, mouse 146

description: Jejunum; one array per animal.


title: A549 STARR-seq, output, rep5

city: Edinburgh

first: Giovanna

last: Weykopf

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

description: Library name: Output5

data_processing:
Sequencing reads were aligned to a custom reference genome containing the STARR-seq library oligonucleotide sequences using bowtie1 v.1.3.0 (Langmead & Salzberg, 2012) with the parameters -X 300 -p 4 -v 3 --norc -m 1 --best --strata to allow for 3 mismatches and unique alignment only. Aligned sam files were converted to bam file format using samtools v.1.6 (Danecek et al., 2021) and paired end reads aligning to the same sequence featuring identical UMIs collapsed using the umi_tools dedup function from UMI-tools v.1.1.4 (Smith et al., 2017) with the --paired option, thereby removing PCR duplicates. Counts for each library sequence were generated from aligned, UMI-collapsed reads using the htseq-count function with the parameters -s no -m intersection-strict -a 30 -f bam from the HTSeq package v.2.0.2 (Anders et al.,2015). We required sequences to have at least 10 UMI-collapsed read counts for each of the two input replicates and at least 5 UMI-collapsed read counts for each of the five output replicates. The STARR-seq activity for each remaining library sequence (13,461/13,802 oligonucleotide sequences) as log2FC of output/input libraries as well as normalised read counts were computed using DESeq2 v.1.44.0 (Love et al., 2014) in R v.4.4.0 using default parameters with the design formular ~type and fitType=”local”. Library sequences with a log2FC greater than 1 at an adjusted p-value of <0.01 were considered active.
Allele-specific activity was assessed using the mpralm R package (Myint et al., 2019), a linear model developed for MPRA data based on the voom framework (Law et al., 2014), with the parameters normalize=TRUE, aggregate=“none”, block=block_vector, model_type=“corr_groups”, plot=TRUE to estimate log2FC between alleles and test for differential activity using moderated t-statistics. Variants were considered to be amVars if the mpralm adjusted p-value was < 0.01 and at least one of reference and risk allele were determined to be active by DESeq2 analysis. For combinatorial variant pair oligos we performed pairwise contrast testing between the four alleles and computed significance using the mpralm “eBayes” function.
Assembly: GRCh38
Supplementary files format and content: "Results_activity_normalized_counts.xlsx" countains analysed results for each STARR-seq library sequence, including STARR-seq activity (log2FC, padj) and normalized read counts averaged across input or output replicates.

growth_protocol: A549 lung adenocarcinoma cells (ATCC #CLL-185) were maintained in DMEM (Life Technologies #41965039) supplemented with 10% foetal calf serum (FCS) and 1% penicillin/streptomycin at 37°C with 5% CO2 and passaged every 2-3 days.

extract_protocol:
Electroporated cells were lysed and total RNA harvested after 6h, and output libraries processed according to the published UMI-STARR-seq protocol (DOI: https://doi.org/10.1002/cpmb.105)
STARR-seq libraries were tagged with UMIs and libraries prepared according to the published UMI-STARR-seq protocol (DOI:https://doi.org/10.1002/cpmb.105)

treatment_protocol: For each of five biological replicates, performed on different days, 4x10^7 cells were resuspended in 375 μl electroporation buffer (MaxCyte #EPB1) and electroporated with 80 μg STARR-seq plasmid library  making up 25 μl (400 μl total) in an OC-400 electroporation cuvette (MaxCyte #GOC4) using the manufacturer-pre-set ‘A549’ protocol on a MaxCyte GTx system. Following electroporation, cells were let to recover for 25 min at 37°C before gentle transfer to a culture flask with pre-warmed DMEM supplemented with 10% FCS but without antibiotics.

value: lung adenocarcinoma

value: WT

value: screen


title: M206_melioidosis

description: Library name: M206

value: survivor


title: W12_PBMC_G1_HTO

description:
Library name: W12_PBMC_G1_HTO
HTO 5' mRNA library

value: PBMC

value: B cells

value: Protein immunized


title: A549 STARR-seq, output, rep4

description: Library name: Output4


title: M204_melioidosis

description: Library name: M204

value: Whole blood


title: W12_PBMC_G1_GEX

description:
Library name: W12_PBMC_G1_GEX
GEX 5' mRNA library


title: A549 STARR-seq, output, rep3

description: Library name: Output3


title: M203_melioidosis

description: Library name: M203


title: Jejunum, KO saline day 7, mouse 272

description: Jejunum; one array per animal.

value: Sftpd-/- (knockout)

value: isotonic saline (vehicle)

value: day 7


title: Jejunum, KO saline day 7, mouse 224

description: Jejunum; one array per animal.


title: A549 STARR-seq, output, rep2

description: Library name: Output2


title: D100_diabetes control

description: Library name: D100

value: Male


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

city: New York

first: Paul

last: Zumbo

address: 1300 York Ave

department: Applied Bioinformatics Core

institute: Weill Cornell Medicine

description: Library name: 12573-S19

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 vehicle

tag: batch


title: A549 STARR-seq, output, rep1

description: Library name: Output1


title: Jejunum, KO saline day 7, mouse 200

description: Jejunum; one array per animal.


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

description: Library name: 12572-S18


title: U095_healthy donor

description: Library name: U095

tag: group


title: D095_diabetes control

description: Library name: D095

tag: age


title: Jejunum, KO saline day 3, mouse 292

description: Jejunum; one array per animal.

value: day 3


title: A549 STARR-seq, input, rep1

description: Library name: Input1

value: input


title: Jejunum, KO saline day 3, mouse 254

description: Jejunum; one array per animal.


title: U094_healthy donor

description: Library name: U094

tag: Sex


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

description: Library name: 12566-S20


title: Bioreactor or manual (hand) grown lung organoids

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

country: Germany

institute: University Hospital Essen

description:
Library name: DIA5
BD Rhapsody

data_processing:
scRNA-seq: cwl-runner v.2.0 was used to obtain counts
Samples are tagged with sample tag (see feature Readme)
scRNA-seq: The demultiplexing, barcoded processing, gene counting and aggregation were madeaccording to previously published protocolls (for details se M&M).
Assembly: hg38
Supplementary files format and content: barcodes, features, matrix contain the raw unfiltered data as result from Rhapsodys cwl runner v2.0
Supplementary files format and content: rds file contains the filtered cells already as Seurat object, feature_readme contains the single sample_tag assignment

source_name: lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Library was performed according to the manufacter’s instructions (see also M&M).

treatment_protocol: iPSC-derived lung organoids were generated either manually or via bioreactor culturing (d30-35) and total RNA was isolated prior RNAseq, for scRNAseq lung organoids were enzymatically digested and sc analyses were perfomed (bioractor and manuall condition) and

value: lung

value: HBEC3-KT/ HS-5

value: various lung cell types

value: bioreactor/hand


title: Jejunum, KO saline day 7, mouse 114

description: Jejunum; one array per animal.


title: Jejunum, KO saline day 3, mouse 220

description: Jejunum; one array per animal.


title: D091_diabetes control

description: Library name: D091

tag: 28day mortality

value: survivor


title: A549 STARR-seq, input, rep2

description: Library name: Input2

value: lung adenocarcinoma

value: WT


title: Atria, males, NaV1.5 4w HFD&NR - 7

description: Library name: 12544-S16

tag: tissue

value: 4w HFD&NR


title: PC99_GEX

city: Morgantown

first: Gangqing

last: Hu

state: WV

address: 64 Medical Center Drive

institute: West Virginia University

description: Library name: PC99_GEX

data_processing:
The snMultiome datasets was processed by cellranger-arc version 2.0.2. The reference genome was GRCh38. cellranger-arc count was used to generated the gene and peaks feature for the libraries.
Assembly: GRCh38
Supplementary files format and content: *.filtered_feature_bc_matrix.h5 : Filtered feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells.

molecule: nuclear RNA

source_name: Pancreas

extract_protocol:
Isolation procedure was adapted from nuclei isolation from complex tissues for Single Cell Multiome ATAC + Gene Expression Sequencing (CG000375). Nuclei were isolated from 50 mg of frozen tissue cut into five small sections with a razor blade. The tissue pieces were homogenised for 1.5 min with a tissue homogeniser and pestle in 10 mM Tris–HCl, 10 mM NaCl, 3 mM MgCl2, .1% Nonidet P40 substitute and 1 mM dithiothreitol (DTT) in nuclease-free water. Tissue was dissociated in lysis buffer for 5 min before passing through a 70 μm cell strainer. The solution was then centrifuged (500 × g, 4°C, 5 min). The supernatant was removed and replaced with 1 mL 1% BSA in DPBS and allowed to incubate for 5 min before resuspension. The nuclei were centrifuged again (500 × g, 4°C, 5 min). The pellet was resuspended in 1 mL 1% BSA in DPBS and passed through a 30 μm cell strainer. All steps were performed on ice. Nuclei were stained with 7-aminoactinomycin D (7-AAD) readymade solution 1:100 (Sigma, SML-1633) and sorted with a FACSAria III Cell Sorter. Nuclei were collected into 10% BSA. For snMultiomics, 1 U/mL RNase inhibitor (Sigma–Aldrich, 03335402001) was added to all final solutions.
Prepared per manufacturer's instructions (10X Genomics, 1000283; CG000338 Rev E)

value: Pancreas

value: responder

value: FOLFIRINOX


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

description: Library name: 12567-S21


title: 8505c_shTAZ_dabrafenib_3

description: Library name: MB_15_S15_001

value: thyroid

tag: cell line

value: ATC cell line

value: shTAZ+dabra


title: M226_melioidosis

first: PATPONG

last: RONGKARD

address: Du Cane Rd

institute: Imperial College London

description: Library name: M226

value: Whole blood

value: Female


title: U085_healthy donor

description: Library name: U085

value: Male


title: Jejunum, WT saline day 7, mouse 28

description: Jejunum; one array per animal.

value: Sftpd+/+ (wild-type)

value: isotonic saline (vehicle)

value: day 7


title: Jejunum, KO saline day 3, mouse 182

description: Jejunum; one array per animal.

value: Sftpd-/- (knockout)

value: day 3


title: Jejunum, WT saline day 3, mouse 46

description: Jejunum; one array per animal.


title: W18_PBMC_G1_VDJ

description:
Library name: W18_PBMC_G1_VDJ
VDJ 5' mRNA library

extract_protocol:
N332-GT5 epitope-specific B cells were isolated from peripheral blood samples collected from rhesus macaques immunized with N332-GT5 and subsequent heterologous boost immunizations. Probes for each boost immunogen were included in flow cytometry staining for each respective Group, allowing determination of the proportion of N332-GT5 epitope-specific cells cross-binding the boost immunogen (N332-GT5++KO– Boost++). Thawed cells were incubated with both N332-GT5 KO and Boost KO probes for twenty minutes at 4°C. Following that, cells were sequentially incubated with the combined Booster WT probes for fifteen minutes at 4°C and then with the combined N332-GT5 WT probes for thirty minutes at 4°C. A master mix of surface staining antibodies was added next, with 2 μg per 5 million cells of anti-human Total-Seq-C hashtag antibodies (Biolegend) following the surface staining, and incubated for thirty minutes at 4°C. Cells were then washed twice and prepared for sorting on BD FACSymphony S6 (BD Biosciences). Epitope-specific B cells were sorted at all time points.Once sorted, epitope-specific PBMC and LN FNA B cells were washed with PBS and loaded onto a Chromium chip and controller following the manufacturers protocol (10X Genomics).  Indexed V(D)J, Feature Barcode, and Gene Expression libraries were prepared following the 10X Genomics protocol with the Feature Barcoding Kit (10X Genomics) and sequenced on a NovaSeq 6000 (Illumina).
Libraries were constructed according to the manufacturer's protocol using the Chromium Next GEM Single Cell 5’ Reagent Kit v3.

value: PBMC

value: B cells

tag: treatment

value: Protein immunized


title: M222_melioidosis

description: Library name: M222

value: survivor


title: PC187_GEX

description: Library name: PC187_GEX

value: Pancreas

value: nonresponder

value: Gem/Abraxane


title: D090_diabetes control

description: Library name: D090


title: W12_PBMC_G4_GEX

description:
Library name: W12_PBMC_G4_GEX
GEX 5' mRNA library

tag: cell type


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

description: Library name: 12389-S17

value: Atria

tag: genotype

value: 4w HFD vehicle


title: PC173_GEX

description: Library name: PC173_GEX

value: responder

value: FOLFIRINOX


title: Jejunum, KO saline day 3, mouse 168

description: Jejunum; one array per animal.


title: Jejunum, WT doxorubicin day 7, mouse 42263

description: Jejunum; one array per animal.

value: doxorubicin (20 mg/kg, single i.p.)


title: U082_healthy donor

description: Library name: U082

value: Whole blood

value: Female


title: Jejunum, WT doxorubicin day 7, mouse 216

description: Jejunum; one array per animal.

value: Sftpd+/+ (wild-type)

value: day 7


title: Jejunum, KO doxorubicin day 7, mouse 42300

description: Jejunum; one array per animal.

value: Sftpd-/- (knockout)


title: PC172_GEX

description: Library name: PC172_GEX


title: M218_melioidosis

description: Library name: M218

value: Male


title: PC169_GEX

description: Library name: PC169_GEX


title: D088_diabetes control

description: Library name: D088


title: AAV-Yap5SA Sample 2

city: Houston

first: Justin

last: Dhindsa

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

description:
Library name: yap5sa2
10x Genomics

data_processing:
10x Genomics gene expression libraries were aligned to the GRCm39 reference genome (refdata-gex-GRCm39-2024-A) using Cell Ranger v.8.0.0.
Assembly: Mouse GRCm39
Supplementary files format and content: Tab-separated features and barcode files, matrix gene expression file, and filtered h5 file

source_name: Retina

extract_protocol:
Retinas were dissected in ice-cold PBS and enzymatically dissociated using 10 units of papain and 60 units of DNase (500 μL/30 μL for 3-6 retinas) for 25-30 minutes in a shaking water bath at 37°C. Following digestion, tissues were gently triturated 10 times with a fire-polished pipette, and the reaction was quenched by adding EBSS containing ovomucoid and DNase. The resulting cell suspension was filtered through a 40 μm strainer and centrifuged at 900 RPM for 8- 10 minutes. For fluorescent-activated cell sorting (FACS) prior to single-cell mRNA sequencing, cell pellets were resuspended in a solution of DNase, ovomucoid, and Neurobasal medium (1:1:10) and kept on ice. FACS was performed using a Sony MA900 cell sorter (BD Biosciences) with an 80-micron nozzle to isolate tdTomato-positive and -negative cells. Sorted cells were collected into pre-chilled tubes containing 0.04% ultrapure BSA in 0.1 M PBS and immediately processed for single-cell RNA sequencing;
Library construction was performed according to the manufacturer's protocol (10x Chromium Single Cell 3' v3.1). Single-cell RNA sequencing was performed using the 10X Genomics Chromium platform. Cell concentration and viability were assessed, and approximately 10,000 viable cells per condition were loaded onto the Chromium Controller for single-cell capture and barcoding. Following reverse transcription and barcoded cDNA amplification according to the manufacturer's protocol, sequencing libraries were prepared and submitted to Admera Health (South Plainfield, NJ) for sequencing. Libraries were pooled and sequenced on an Illumina NovaSeq X Plus platform using 10B flow cells with 2×150 bp paired-end sequencing (NovaSeq X Plus 10B 2×150 configuration) to achieve a target depth of approximately 50,000-100,000 reads per cell. Demultiplexing was performed by the sequencing facility, and raw sequencing data were delivered via Illumina BaseSpace with MD5 checksums and quality control summary reports.

treatment_protocol: AAV-mkate or AAV-Yap5sa treatment

value: Retina

value: Muller Glia (FACS purified)

value: 12-20 weeks

value: pooled male and female

value: Glast-CreERT2; Rosa26-Ai65 (C57BL/6J)


title: AAV-Yap5SA Sample 3

description:
Library name: yap5sa3
10x Genomics


title: Jejunum, KO doxorubicin day 7, mouse 42299

description: Jejunum; one array per animal.


title: U079_healthy donor

description: Library name: U079

value: survivor


title: AAV-Yap5SA Sample 1

description:
Library name: yap5sa1
10x Genomics


title: PC167_GEX

description: Library name: PC167_GEX

value: Pancreas


title: Atria, males, NaV1.5 4w HFD&NR - 6

description: Library name: 12539-S15

value: Atria

value: 4w HFD&NR


title: Jejunum, KO doxorubicin day 7, mouse 124

description: Jejunum; one array per animal.


title: Jejunum, KO doxorubicin day 7, mouse 136

description: Jejunum; one array per animal.


title: 8505c_shCtrl_Vehicle_4

description: Library name: MB_04_S4_001

value: thyroid

value: ATC cell line

value: shC


title: AAV-mKate Control Sample 2

description:
Library name: mKate2
10x Genomics


title: PC159_GEX

description: Library name: PC159_GEX

value: nonresponder

value: FOLFIRINOX


title: U077_healthy donor

description: Library name: U077

value: Whole blood

value: Female


title: PC158_GEX

description: Library name: PC158_GEX

value: FOLFIRINOX, Gem/Abraxane


title: D087_diabetes control

description: Library name: D087


title: W12_PBMC_1_G2_VDJ

description:
Library name: W12_PBMC_1_G2_VDJ
VDJ 5' mRNA library

value: PBMC

value: B cells

value: Protein immunized


title: AAV-mKate Control Sample 1

description:
Library name: mKate1
10x Genomics

value: Retina

value: Muller Glia (FACS purified)

value: 12-20 weeks

value: pooled male and female


title: M215_melioidosis

description: Library name: M215

value: Male


title: IgG control

first: Kan

last: Huang

address: 130, Dongan Road

institute: Fudan University

description: Library name: IgG

data_processing:
Low quality reads and sequencing adaptors of the CUT&Tag reads were trimmed using fastp v0.24.0 with the parameter of "-T 1 -5 -l 50 -q 20 -u 50 -g -c --detect_adapter_for_pe -w 9"
CUT&Tag reads were local-aligned to the mouse mm10 genome and the DNA Spike-in sequence seperately using bowtie2 v2.5.4 with the parameter of "-p 9 -q --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700"
Scaling factors of each sample were calculated as 10,000 / (fragments mapped to Spike-in sequence). Normalized coverage for each sample was calculated as the primary genome coverage multiplied by the scaling factor.
Peaks were called using MACS v3.0.3 with the significance cut-off q-value <= 0.01.
BigWig files were generated using the bamCoverage function of deeptools v3.5.6. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: mm10
Supplementary files format and content: bigWig (except for IgG sample)
Library strategy: CUT&Tag

source_name: lung adenocarcinoma

growth_protocol: KP lung adenocarcinoma cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5% CO2 at 37℃

extract_protocol:
CUT&Tag experiment was conducted using CUT&Tag kit complemented with  Hyperactive TF Enhancer Module  from Vazyme (TD904-C2). Briefly, cells were collected and treated with TF enhancer. Subsequently, cells were bound with Concanavalin A-coated magnetic beads, and the plasma membrane was permeabilized with digitonin. Through the use of a primary antibody targeting HA or non-targeting IgG control, a corresponding secondary antibody, and Protein A/G, the transposase fused to Protein A/G was guided to precisely cleave DNA sequences near the target protein. During cleavage, adaptor sequences were added to both ends of the DNA fragments, which were then amplified by PCR to generate libraries for high-throughput sequencing.
CUT&Tag libraries were prepared using the CUT&Tag kit complemented with  Hyperactive TF Enhancer Module  (TD904-C2) and TruePrep Index Kit V2 for Illumina (TD202) from Vazyme. All of the cleaved DNA extracted using CUT&Tag kit was used as starting material for anti-HA and anti-IgG samples. Before PCR anplification, 0.05 pg DNA Spike-in was added into each sample as a reference standard, primarily for inter-sample normalization of the sequencing data. Libraries were then amplified using 16 cycles on the thermocycler. Libraries ere validated using the Fragment Analyzer 5300 system.

value: lung adenocarcinoma

value: KP

value: lung adenocarcinoma cells


title: D082_diabetes control

description: Library name: D082

value: survivor


title: U075_healthy donor

description: Library name: U075


title: Jejunum, KO doxorubicin day 7, mouse 116

description: Jejunum; one array per animal.

value: Sftpd-/- (knockout)

value: doxorubicin (20 mg/kg, single i.p.)

value: day 7


title: KP cells, Dmap1 KD, replicate 2

description: Library name: HA_KD_rep2

value: Dmap1 knockdown


title: PC131_GEX

description: Library name: PC131_GEX

value: Pancreas

value: responder

value: FOLFIRINOX


title: Jejunum, KO doxorubicin day 3, mouse 236

description: Jejunum; one array per animal.

value: day 3


title: KP cells, Dmap1 KD, replicate 1

description: Library name: HA_KD_rep1


title: PC123_GEX

description: Library name: PC123_GEX

value: nonresponder


title: D079_diabetes control

description: Library name: D079

value: Whole blood

value: Female


title: PC102_GEX

description: Library name: PC102_GEX

value: Gem/Abraxane


title: Jejunum, KO doxorubicin day 3, mouse 196

description: Jejunum; one array per animal.


title: KP cells, WT, replicate 1

description: Library name: HA_ctrl_rep1

value: WT


title: PC99_ATAC

description: Library name: PC99_ATAC

library_source: genomic single cell


title: D074_diabetes control

description: Library name: D074

value: Male


title: Adipose tissue, Aged_burn_3

city: Hamilton

first: Punit

last: Bhattachan

state: Ontario

address: 20 Copeland Avenue

department: Surgery

country: Canada

institute: McMaster University

description:
Library name: Sample12
Columnname in raw_counts_Aged_Samples.txt: Aged_burn_3

data_processing:
Galaxy
The quality of FASTQ files was examined by FastQC and MultiQC. Cutadapt tool was used to trim the reads.
The trimmed reads were maped to the mouse genome mm10/GRC38 using HISAT2 tool.
The featureCounts tool was used to generate count matrix.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for Adult Samples
Supplementary files format and content: tab-delimited text file includes raw counts for Aged Samples

source_name: Adipose tissue

extract_protocol:
Total RNA was extracted from the adipose tissue using Trizol reagent according to manufacture's protocols and mRNA was isolated by NEBNext poly(A) kit.
NEBNext Ultra II directional RNA library kit was used for the library construction.

treatment_protocol: Adult mice with 30% and aged mice with 20% TBSA was subjected to scald burn injury. A water bath was set to 98 oC and mouse was immersed for 10 seconds on the dorsal side to get 20% TBSA and only 2 seconds on ventral side for additional 10% TBSA. Buprenorphine (0.01-0.5 mg/kg) was used for the pain management.

value: Adipose tissue

value: Day 7

value: Scald burn injury


title: Jejunum, KO doxorubicin day 3, mouse 162

description: Jejunum; one array per animal.

value: Sftpd-/- (knockout)


title: Jejunum, KO doxorubicin day 3, mouse 2

description: Jejunum; one array per animal.

value: doxorubicin (20 mg/kg, single i.p.)


title: U068_healthy donor

city: London

description: Library name: U068

value: survivor


title: C57Bl/6 subcutaneous tumor for wildtype KP cells

description:
Library name: L
GEXSCOPE

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17  to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a  to map reads to the reference genome GRCm38. UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1  software, and used to generate expression matrix files for subsequent analysis.
Assembly: mouse mm10
Supplementary files format and content: Tab-seperated value files and matrix files

extract_protocol:
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) . Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: lung adenocarcinoma

value: KP

value: lung adenocarcinoma cells

value: shLacZ


title: PC187_ATAC

description: Library name: PC187_ATAC

value: Pancreas


title: Adipose tissue, Aged_burn_2

description:
Library name: Sample11
Columnname in raw_counts_Aged_Samples.txt: Aged_burn_2


title: C57Bl/6 subcutaneous tumor for Dmap1 knockdown KP cells

description:
Library name: D
GEXSCOPE

value: Dmap1 knockdown


title: Jejunum, KO doxorubicin day 3, mouse 248

description: Jejunum; one array per animal.

value: day 3


title: PC173_ATAC

description: Library name: PC173_ATAC

value: responder

value: FOLFIRINOX


title: D073_diabetes control

description: Library name: D073

value: Whole blood


title: Adipose tissue, Aged_burn_1

description:
Library name: Sample10
Columnname in raw_counts_Aged_Samples.txt: Aged_burn_1

value: WT


title: M-27

city: guangzhou

first: Lu

last: Xiao

state: Please Select

address: No. 601 Huangpu Avenue West

institute: The First Affiliated Hospital of Jinan University

description:
Library name: sample9
M-27

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: processed data files format all.xlsx

source_name: liver

extract_protocol:
RNA was harvested using Trizol. 0.2 ug of total RNA was used for the construction of sequencing libraties
RNA libraries for RNA-seq were prepared using Novogene fast RNA-seq Library Perp Kit V2 following manufacturer's protocols

value: liver

value: hepatocyte


title: PC172_ATAC

description: Library name: PC172_ATAC

value: nonresponder


title: U063_healthy donor

description: Library name: U063

value: Female


title: M-26

description:
Library name: sample8
M-26


title: D051_diabetes control

description: Library name: D051


title: PC169_ATAC

description: Library name: PC169_ATAC


title: U059_healthy donor

description: Library name: U059


title: Adipose tissue, Aged_control_2

description:
Library name: Sample8
Columnname in raw_counts_Aged_Samples.txt: Aged_control_2

value: Adipose tissue

value: Day 7

value: Untreated


title: M-24

description:
Library name: sample7
M-24


title: PC167_ATAC

description: Library name: PC167_ATAC


title: Adipose tissue, Aged_control_1

description:
Library name: Sample7
Columnname in raw_counts_Aged_Samples.txt: Aged_control_1


title: A-C-12

description:
Library name: sample6
A-C-12


title: D072_diabetes control

description: Library name: D072

value: survivor


title: Adipose tissue, Adult_burn_3

description:
Library name: Sample6
Columnname in raw_counts_Adult_Samples.txt: Adult_burn_3

value: Scald burn injury


title: PC159_ATAC

description: Library name: PC159_ATAC


title: U056_healthy donor

description: Library name: U056

value: Male


title: D063_diabetes control

description: Library name: D063


title: PC158_ATAC

description: Library name: PC158_ATAC

value: Pancreas

value: FOLFIRINOX, Gem/Abraxane


title: A-C-6

description:
Library name: sample4
A-C-6


title: U054_healthy donor

description: Library name: U054


title: Adipose tissue, Adult_burn_1

description:
Library name: Sample4
Columnname in raw_counts_Adult_Samples.txt: Adult_burn_1


title: C-4

description:
Library name: sample3
C-4


title: PC131_ATAC

description: Library name: PC131_ATAC


title: Adipose tissue, Adult_control_3

description:
Library name: Sample3
Columnname in raw_counts_Adult_Samples.txt: Adult_control_3


title: C-3

description:
Library name: sample2
C-3


title: D060_diabetes control

description: Library name: D060


title: PC123_ATAC

description: Library name: PC123_ATAC


title: U053_healthy donor

description: Library name: U053


title: Adipose tissue, Adult_control_2

description:
Library name: Sample2
Columnname in raw_counts_Adult_Samples.txt: Adult_control_2


title: C-2

description:
Library name: sample1
C-2


title: PC102_ATAC

description: Library name: PC102_ATAC

value: Gem/Abraxane


title: Adipose tissue, Adult_control_1

description:
Library name: Sample1
Columnname in raw_counts_Adult_Samples.txt: Adult_control_1


title: Mouse cerebella, Yy1 cKO, rep 2

status: Public on Jun 23 2026

city: Hong Kong

first: Kin Ming

last: Kwan

address: Room EG03, Science Center East Block, The Chinese University of Hong Kong

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: Yy1 cKO 2

data_processing:
Raw sequencing files were checked with FastQC version 0.11.8 to confirm the absence of adapters. Quality trimming was performed using Trimmomatic version 0.39. The trimmed reads were aligned to the mouse reference genome GRCm38 using STAR version 2.7.1a. Gene expression quantification was conducted with the featureCounts function in Rsubread version 2.0.0 using GENCODE vM23 annotation. Normalization and differential expression analysis were performed using DESeq2 version 1.26.0.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes DESeq2 normalized counts for each sample

source_name: Cerebella

extract_protocol:
Total cerebellum RNA from control and cKO mutant mice was extracted using TRIzol reagent (Life Technologies), following the previously established protocol (doi:10.1101/pdb.prot5439) followed by ribosomal RNA (rRNA) depletion. The RNA dissovled in RNase-free ddH2O and the concentration was checked by Qubit.
Strand-specific, rRNA depletion

value: Cerebella

value: Pcp2 Cre/+; Yy1 fx/fx


title: Mouse cerebella, Yy1 cKO, rep 1

description: Library name: Yy1 cKO 1


title: Mouse cerebella, control, rep 2

description: Library name: Control 2

value: Pcp2 Cre/+; Yy1 fx/+


title: Mouse cerebella, Yy1 cKO, rep 3

description: Library name: Yy1 cKO 3