title: Ileum_intFXRKO_5

city: Lille

first: Simon

last: Peschard

address: 1, rue du professeur Calmette BP245

institute: INSERM UMR 1011

hyb_protocol: Hybridation was performed in an Affymetrix rotisserie hoven for 16 hours at 45°C with 60 rpm, according to standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000-7G.

data_processing: The data were normalized by Robust Multi-Average method before being analyzed for differential expression with LIMMA R package

source_name: Ileum of intFXR KO mouse after 24 weeks of HFSC diet

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol

growth_protocol: Adult 8 weeks-old C57Bl6/J mice either Ctrl-flox or intFXR KO were maintained in accordance to ethical guidelines, with 12:12h light/dark cycle in a 21-24°C environment, with ad libitum access to food (MASH-inducing diet) and water.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissue were snap-frozen at dissection time into liquid nitrogen, then stored at -80°C until RNA extraction.

tag: gender

value: male

value: Ileum

value: intFXRKO


title: Ileum_intFXRKO_4

status: Public on Jun 09 2026

type: RNA

country: France

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: genotype


title: hippocampus, MELANOMA + ICI3

type: SRA

city: IRVINE

first: Devyani

last: swami

state: CA

address: 811 Health Sciences Road

department: Anatomy & Neurobiology

country: USA

institute: UNIVERSITY OF CALIFORNIA IRVINE

description:
Library name: MEL-ICI-72
Raw counts_MEL ICI-72

library_source: transcriptomic

data_processing:
Read counts were normalized to adjust for various factors, such as variations of sequencing yield between samples (software package DESeq2 v.1.16.1
Assembly: The trimmed reads were mapped to Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Supplementary files format and content: TXT files containing Raw count for each sample

source_name: Brain Hippocampus

growth_protocol: For  Bulk RNA seq data, fresh frozen single hippocampi from N=5 brains /groups were excised from the mouse brain and were sent to Azenta Life science

extract_protocol:
Total RNA was extracted from frozen tissue samples using the Qiagen RNeasy Plus Universal Mini kit following the manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: All animals used in this study were housed and cared for in accordance with National Institutes of Health (NIH) guidelines and protocols approved by the Institutional Animal Care and Use Committee (IACUC). Adult male wild-type (WT) mice aged 10–12 weeks were randomly assigned to one of the following experimental groups: (i) WT mice receiving isotype-matched control antibodies (intraperitoneal, i.p.); (ii) WT mice bearing D4M-3A.UV2 tumors and treated with isotype-matched control antibodies (i.p.); (iii) WT mice treated with immune checkpoint inhibitors (ICIs), including anti–CTLA-4 (1 mg per dose, three times weekly, i.p.) and anti–PD-1 (200 µg per dose, twice weekly, i.p.); and (iv) WT mice bearing D4M-3A.UV2 tumors treated with the same combination ICI regimen for three weeks. For tumor induction, mice in the cancer groups received bilateral intradermal injections of 5 × 10⁵ syngeneic D4M-3A.UV2 melanoma cells. Tumors were allowed to engraft for one week prior to initiating ITC or ICI treatments. Following completion of the treatment regimen, mice were euthanized 72 hours after the final injection, and brains were harvested for downstream analyses.

value: Brain Hippocampus

tag: treatment

value: MELANOMA + ICI


title: mRNA_TC2_WT_13h

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: Sample 14

data_processing:
RNA-seq data was mapped to the C. elegans genome (ce11) using the Align (qAlign) function from the QuasR (v1.41.2) package in R with splicedAlignement = TRUE, using the aligner HISAT2 (v1.20.0) including an exon-exon junction database (WS270). Gene expression levels were quantified using the qCount() function, counting the reads on the opposite strand of annotated transcripts. For paired-end samples, the first read was considered for counting. For annotations, coding transcript information from WormBase WS270 was used. We further compensated for differences in library sizes by scaling each library to the average library size. Finally, we log2 transformed the data using a pseudo count of 8 (log2(x+8)).
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw gene expression read counts
Supplementary files format and content: tab-delimited text file with normalized gene expression read counts

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Synchronized L1 animals were grown in liquid culture (S-Basal supplemented with OP50; OD600 = 2.7; 1000 animals/ml) at 25°C shaking at 180 rpm.

extract_protocol:
At the time of sample collection, animals were washed off the plates with M9 buffer, washed twice with M9 buffer, resuspended in TRI Reagent (MRC, TR-118) and snap-frozen in liquid nitrogen. Prior to RNA extraction, animals were lysed by five cycles of thawing (42°C) and snap-freezing in liquid nitrogen. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062; DNase treatment included) according to the manufacturer’s protocol. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
TruSeq Illumina mRNA-seq

value: whole organism

tag: time (h)


title: NCI-H1299 cells, shControl-3

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

country: China

institute: Southeast University

data_processing:
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to hg38 genome by STAR 2.7.10a
BAM files were counted by featureCounts
Deseq2 was used to perform differential analysis
Assembly: hg38
Supplementary files format and content: DEG.xlsx, xlsx format, containing the differential expressed genes

organism: Homo sapiens

source_name: lung adenocarcinoma

growth_protocol: NCI-H1299 cell lines were maintained in RPMI1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5%CO2 at 37℃.

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
RNA libraries for RIP-seq were prepared using Tru-seq Library Prep Kit following manufacturer's protocols

value: lung adenocarcinoma

tag: cell line

tag: cell type

value: Human lung adenocarcinoma cell


title: hippocampus, MELANOMA + ICI2

description:
Library name: MEL-ICI-71
Raw counts_MEL ICI-71


title: mRNA_TC2_WT_12h

description: Library name: Sample 13


title: NCI-H1299 cells, shControl-2


title: hippocampus, MELANOMA + ICI1

description:
Library name: MEL-ICI-64
Raw counts_MEL ICI-64


title: mRNA_TC2_WT_11h

description: Library name: Sample 12


title: Ileum_intFXRKO_2


title: NCI-H1299 cells, shControl-1


title: Ileum_intFXRKO_3


title: hippocampus, MELANOMA5

description:
Library name: MEL-52
Raw counts_MEL-52

value: MELANOMA


title: NCI-H1299,Input rep2

data_processing:
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to hg38 genome by STAR 2.7.10a
BAM files were counted by featureCounts
Deseq2 was used to perform differential analysis
Assembly: hg38
Supplementary files format and content: DRIP.xlsx, xlsx format, containing the enriched genes
Supplementary files format and content: bw format, containing the peak for visualization


title: mRNA_TC2_WT_10h

description: Library name: Sample 11


title: Ileum_CtrlFlox_5

source_name: Ileum of Control floxed mouse after 24 weeks of HFSC diet

value: CtrlFlox


title: Ileum_intFXRKO_1


title: hippocampus, MELANOMA4

description:
Library name: MEL-44
Raw counts_MEL-44


title: mRNA_TC2_WT_9h

description: Library name: Sample 10


title: NCI-H1299,Input rep1


title: Ileum_CtrlFlox_4


title: hippocampus, MELANOMA3

description:
Library name: MEL-33
Raw counts_MEL-33


title: mRNA_TC2_WT_8h

description: Library name: Sample 9


title: NCI-H1299,P5CS rep2


title: Ileum_CtrlFlox_3


title: mRNA_TC2_WT_7h

description: Library name: Sample 8


title: NCI-H1299,P5CS rep1


title: hippocampus, MELANOMA2

description:
Library name: MEL-32
Raw counts_MEL-32


title: Ileum_CtrlFlox_2


title: hippocampus, MELANOMA1

description:
Library name: MEL-12
Raw counts_MEL-12


title: mRNA_TC2_WT_6h

description: Library name: Sample 7


title: Ileum_CtrlFlox_1


title: hippocampus, CONTROL + ICI5

description:
Library name: ICI-64
Raw counts_ICI-64

value: CONTROL + ICI


title: mRNA_TC2_WT_5h

description: Library name: Sample 6


title: NCI-H1299,IgG rep2

data_processing:
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to hg38 genome by STAR 2.7.10a
Peak calling was performed by pureclip
Assembly: hg38
Supplementary files format and content: bw format, containing the peak for visualization
Library strategy: LACE-seq

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
RNA libraries for LACE-seq were prepared using LACE-seq buffers following manufacturer's protocols


title: NCI-H1299,IgG rep1


title: Liver_intFXRKO_5

source_name: Liver of intFXR KO mouse after 24 weeks of HFSC diet

value: Liver


title: mRNA_TC2_WT_4h

description: Library name: Sample 5


title: NCI-H1299,P5CS rep2


title: hippocampus, CONTROL + ICI4

description:
Library name: ICI-63
Raw counts_ICI-63


title: Liver_intFXRKO_4


title: mRNA_TC2_WT_3h

description: Library name: Sample 4


title: hippocampus, CONTROL + ICI3

description:
Library name: ICI-61
Raw counts_ICI-61


title: hippocampus, CONTROL + ICI2

description:
Library name: ICI-54
Raw counts_ICI-54


title: mRNA_TC2_WT_2h

description: Library name: Sample 3


title: NCI-H1299,P5CS rep1


title: CV169_HIV+

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Raw demultiplexed fastq paired end read files were trimmed of adapters and filtered using the program skewer to throw out any with an average phred quality score of less than 30 or a length of less than 10.
Trimmed reads were then aligned using the STAR aligner to the Homo sapiens NCBI reference genome assembly version GRCh38 and sorted using SAMtools
Aligned reads were counted and assigned to gene meta-features using the program featureCounts as part of the Subread package.
Count files were imported into the R programming language and were assessed for quality control, normalized and analyzed utilizing the limma voom method with quantile normalization.
Assembly: GRCh38
Supplementary files format and content: CSV file contains raw counts for each sample.
Supplementary files format and content: CSV file contains quantile normalized counts for each sample.

source_name: PBMC

growth_protocol: in vivo

extract_protocol:
Cell viability was measured prior to RNA extraction for PBMC samplesusing the Countess II FL Automated Cell Counter (ThermoFisher), and RNA extraction was performed using the RNeasymini kit (Qiagen). The quality of all RNA was determined using the RNA integrity number as calculated from the Agilent Fragment Analyzer with the SS RNA assay kit (Agilent) while the concentration was determined by NanoDrop (ThermoFisher).
Total RNA prepared above was normalized to 100 ng input for library preparation with the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina). The resulting libraries were assessed on the Agilent Fragment Analyzer with the HS NGS assay (Agilent) and quantified using theNEBNext® Library Quant Kit for Illumina®(New England Biolabs, Inc.)on anApplied Biosystems QuantStudio 7 Flex Real-Time PCR (ThermoFisher).

tag: donor id

value: PBMC

tag: Sex

value: F

tag: hiv status

value: HIV+


title: Liver_intFXRKO_2


title: Liver_intFXRKO_3


title: mRNA_TC2_WT_1h

description: Library name: Sample 2


title: hippocampus, CONTROL + ICI1

description:
Library name: ICI-53
Raw counts_ICI-53


title: CV077_HIV-

value: HIV-


title: Liver_CtrlFlox_5

source_name: Liver of Control floxed mouse after 24 weeks of HFSC diet


title: mRNA_TC2_WT_0h

description: Library name: Sample 1


title: hippocampus, CONTROL5

description:
Library name: Ctrl-113
Raw counts_Ctrl-113

value: CONTROL


title: CV051_HIV+


title: Liver_CtrlFlox_4

value: male


title: hippocampus, CONTROL4

description:
Library name: Ctrl-112
Raw counts_Ctrl-112


title: iHFSC2-circSmad5-Sh

city: Chongqing

first: Yuhong

last: Li

address: Gaotanyan Street No.30 Shapingba

department: Cell Biology

institute: Army Medical University

description: Library name: Sample 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM values for each sample

growth_protocol: iHFSC2 cells were cultured as previously described. Cells were maintained in culture medium at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: iHFSC2 cells were infected with lentivirus packaged with pwslv-shcircSmad5 (target sequence: TCCAGCAGAGGACTTGCACTA) or empty vector. At 4 days after infection, puromycin was added to the culture medium to exclude the uninfected cells. At 15 days after infection, stable cell lines were established and used for subsequent experiments.

value: hair follicle stem cell

value: shcircSmad5 lentivirus infection


title: CVD147_HIV-


title: Liver_CtrlFlox_3


title: hippocampus, CONTROL3

description:
Library name: Ctrl-104
Raw counts_Ctrl-104

value: Brain Hippocampus


title: iHFSC2

description: Library name: Sample 1

value: empty vector control


title: CVD122_HIV-


title: Liver_CtrlFlox_2


title: hippocampus, CONTROL2

description:
Library name: Ctrl-103
Raw counts_Ctrl-103


title: 4T1, WT, rep5

city: Phoenix

first: Bogang

last: Wu

state: AZ

address: 5777 E. Mayo Blvd.

department: Immunology

institute: Mayo Clinic Arizona

description: Library name: control170

data_processing:
Analysis was done on HiSeq Control Software. Raw fastq file for each tumor sample was generated by demultiplexing with Illumina bcl2fastq V.2.17 software.
Assembly: GRCm38
Supplementary files format and content: normalized gene counts for all samples

source_name: tumor tissue

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, 74134). RNA integrity was checked with Agilent 4200 TapeStation System.
Following DNA contaminant removal and rRNA depletion, RNA-seq libraries were constructed using NEBNext Ultra II RNA Library Preparation Kit for Illumina. In brief, RNAs were fragmented at 94°C for 15 min. First and second strand cDNA synthesis was done using primers for random priming sites and unique molecular identifiers, which were incorporated into final cDNA. After adapter ligation, cDNAs were purified and enriched by PCR to generate sequencing libraries.

value: tumor tissue

value: WT

value: in vivo growth

tag: batch


title: CVD115_HIV-

value: M


title: Liver_CtrlFlox_1

value: CtrlFlox


title: hippocampus, CONTROL1

description:
Library name: Ctrl-102
Raw counts_Ctrl-102


title: 4T1, WT, rep4

description: Library name: RESUB-168R


title: Liver_intFXRKO_1

value: intFXRKO


title: CVD099_HIV-


title: b8Cell_embryo, RNA-Seq Control samples _Replicate2

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

description: Library name: E8C_CTRL_D

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by Trim Galore (version 0.6.7) (-q 25 –length 20 –max_n 3 –stringency 3).
Preprocessed RNA-seq reads were aligned to the bovine genome (ARS-UCD1.3) using HISAT2 (version 2.2.1) with default parameters.  The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14).
Assembly: bovine genome (ARS-UCD1.3)
Supplementary files format and content: Read counts of all samples were quantified using featureCounts (version 2.0.1) with the bovine genome as a reference and were adjusted to provide counts per million (CPM) mapped reads.
Supplementary files format and content: txt; raw read counts

organism: Bos taurus

source_name: Embryo

growth_protocol: Oocytes were collected from slaughterhouse-derived bovine ovaries. Cumulus-oocyte complexes (COCs) from 3–5 mm follicles were selected based on morphology and matured in BO-IVM medium at 38.5°C with 6% CO₂ for 22–23 hours. After confirming polar body extrusion, matured oocytes were fertilized in vitro using cryopreserved Holstein semen (2 × 10⁶ sperm/ml) for 18 hours. Presumptive zygotes were cultured in SOF-BE2 medium (30 embryos/50 µl drop) under mineral oil at 38.5°C in 5% CO₂, 5% O₂, and 90% N₂ until day 7.5.

extract_protocol:
samples were lysed in TRIsolution (Sigma), followed by phase separation with chloroform. The aqueous phase was collected, and RNA was precipitated with isopropanol, washed with ethanol, and resuspended in nuclease-free water.
Five embryos per stage per group were lysed, and mRNA was captured and amplified using the Smart-seq2 v4 kit (Clontech). Amplified cDNA was purified with AMPure XP beads and used for library preparation with the Nextera XT DNA Library Prep Kit (Illumina), followed by multiplexing with Nextera XT Indexes.

treatment_protocol: Bovine embryos were produced by IVF and collected at the zygote stage for prime editing. PEmax with gRNA was delivered via cytoplasmic microinjection in SOF-BE2 medium using a micromanipulator-equipped inverted microscope. After injection, embryos were cultured in IVF-BIO IVC medium at 38.5°C under 5% CO₂, 5% O₂, and 90% N₂ until the 4-cell and 8-cell stages. Control and base-edited embryos were collected at each stage for analysis.

value: Embryo


title: 4T1, WT, rep3

description: Library name: RESUB-169R


title: PTEN Inh 4

city: Miami

first: Anthony

last: Griswold

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description: Library name: Sample 8

data_processing:
FASTQ files were processeed using Partek software
Reads were aligned to the mouse genome reference (mm39) using STAR v2.7.8a
Gene counts were quantified and normalized in Partek
Assembly: GRCm39
Supplementary files format and content: processed data is a tab delimited normalized gene count matrix
Supplementary files format and content: Gene counts were normalized using the median ratio method (DESeq2) implemented in Partek software

source_name: Skin

extract_protocol:
Total RNA was extracted using Rneasy Midi Kit (Qiagen)
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: Skin

value: C57 wt

value: pten inh


title: CVD083_HIV-

value: PBMC

value: HIV-


title: b8Cell_embryo, RNA-Seq Control samples _Replicate1

description: Library name: E8C_CTRL_B


title: PTEN Inh 3

description: Library name: Sample 7


title: 4T1, WT, rep2

description: Library name: RESUB-170R


title: CVD081_HIV-


title: b8Cell_embryo, RNA-Seq Base Edited samples _Replicate2

description: Library name: E8C_BE_D


title: CTRL 4

description: Library name: Sample 6

value: vehicle


title: 4T1, WT, rep1

description: Library name: RESUB-171R


title: CVD050_HIV+

value: HIV+


title: b8Cell_embryo, RNA-Seq Base Edited samples _Replicate1

description: Library name: E8C_BE_C


title: 4T1, KO, rep5

description: Library name: RESUB-KO163R

value: Trop2 KO


title: PTEN Inh 2

description: Library name: Sample 5


title: CVD032_HIV+

value: F


title: b4Cell_embryo, RNA-Seq Control samples _Replicate2

description: Library name: E4C_CTRL_D

source_name: Oocytes

value: Oocytes


title: CTRL 3

description: Library name: Sample 4


title: 4T1, KO, rep4

description: Library name: KO172

value: tumor tissue


title: CVD028_HIV+


title: b4Cell_embryo, RNA-Seq Control samples _Replicate1

description: Library name: E4C_CTRL_A


title: 4T1, KO, rep3

description: Library name: KO165


title: PTEN Inh 1

description: Library name: Sample 3


title: CVD004_HIV+


title: b4Cell_embryo, RNA-Seq Base Edited samples _Replicate2

description: Library name: E4C_BE_D


title: CTRL 2

description: Library name: Sample 2


title: 4T1, KO, rep2

description: Library name: KO164


title: CVD001_HIV+


title: CTRL 1

description: Library name: Sample 1


title: 4T1, KO, rep1

description: Library name: KO162


title: b4Cell_embryo, RNA-Seq Base Edited samples _Replicate1

description: Library name: E4C_BE_C


title: RNA-Seq, 3LW, larvae, H33WT, rep2

status: Public on Jun 08 2026

city: Chapel Hill

first: Jeanne-Marie

middle: E.

last: McPherson

state: North Carolina

address: 3344 Genome Sciences Building, 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

description:
Library name: H33WT, 3LW, rep2
PE100
wt_3LW_rep2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk (parameters: ktrim=r, k=23, rcomp=t, tbo=t, tpe=t, hdist=1, mink=11). BBMap v38.67.
Dm6 genome files for use with the STAR aligner were generated using parameters: sjdbOverhang 99. Paired-end sequencing reads were aligned using STAR v2.7.7a with default parameters.
Bam files were indexed and sorted using samtools v1.9.
Bam files were converted to bed files using bbtools bamtobed with default parameters (bedtools v2.26).
Bam files were converted to bigwig files using deeptools v3.2.0. Samples were RPGC normalization, and a bin size of 10 was used. A genome size of 137547960 was used.
featureCounts (subread v2.0.1) was used for read summarization with parameters: -t exon, -s 1, --countReadPairs
DESeq2 (v1.34.0) was used to identify differentially expressed genes.
Assembly: dm6
Supplementary files format and content: DESeq2 output xlsx file including log2FoldChange, lfcSE, stat, pvalue, padj, baseMean.log, and Log10padj data for all genes.
Supplementary files format and content: featureCounts read counts text file including fbgn gene ID and read counts for each sample

organism: Drosophila melanogaster

source_name: third instar larvae

extract_protocol:
8 brains were dissected 1dAE and 10dAE heads and homogenized in Trizol solution. RNA was isolated from the Trizol aqueous phase using the Zymo Direct-zol RNA Miniprep Kit (Zymo Research ZR2070) including treatment with DNAse I, as per the manufacturer’s instructions.
Libraries were prepared from total RNA using the Tecan Universal Plus Total RNA-seq with NuQuant kit, with custom Drosophila melanogaster rRNA depletion (Tecan #30185152)

value: third instar larvae

value: female

tag: age (days_after_eclosion)


title: RNA-Seq, 3LW, larvae, H33WT, rep1

description:
Library name: H33WT, 3LW, rep1
PE100
wt_3LW_rep1


title: RNA-Seq, 10dAE, brain, H33S31A, F, rep2

description:
Library name: H33S31A, 10dAE, rep2
PE100
H33S31A-10dAE-rep2

source_name: adult brain

value: adult brain


title: RNA-Seq, 10dAE, brain, H33S31A, F, rep3

description:
Library name: H33S31A, 10dAE, rep3
PE100
H33S31A-10dAE-rep3


title: RNA-Seq, 1dAE, brain, H33S31A, F, rep3

description:
Library name: H33S31A, 1dAE, rep3
PE100
H33S31A-1dAE-rep3


title: BRAC1_PARPi_M33_ROI-015_TMA3B

city: Lausanne

first: Aspram

last: Minasyan

address: Bugnon 25A

institute: Ludwig Institute for Cancer Research / CHUV

description: Library name: TMA3B__015

data_processing:
Raw sequencing data were processed with the bcl2fastq program from Illumina to generate FASTQ files.
FASTQ files were converted into Digital Count Conversion (DCC) format through Nanotring's GeoMx DnD pipeline v2.0.0.16.
QC was performed using the R package GeoMxTools v3.4.0.
Batch effect correction was done by substracting  background and then minimum value was added per batch.
Q3 normalization were performed on the merged corrected experiment.
Assembly: probe-based quantification, Mm_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: DCC files are count files converted from FASTQ files
Supplementary files format and content: data_matrix.csv contains corrected and Q3-normalized read counts from all QC-passed AOIs and filtered genes.
Library strategy: Spatial Transcriptomics

source_name: tumor

extract_protocol:
Tissue microarrays were prepared by extracting 2 mm punches from FFPE blocks to prepare nine slides, each containing up to 30 tumor sections. 5µm FFPE tissue microarrays were baked at 60°C for 1hour, then deparaffinized and underwent antigen retrieval at 100°C for 15 minutes, followed by 1µg/mL proteinase K at 37°C for 15 min. The slides were incubated overnight with the RNA probe mix (Whole Transcriptome Atlas).Tissues were stained with visualization markers panCK-AF647, CD68-AF594 and CD3-AF488 along with the nuclear marker Syto83. Tissue slides were then loaded into the GeoMx DSP instrument for scanning. Probe barcodes from each ROI were UV-photocleaved, collected into a 96-well plate, followed by library preparation and sequencing.
GeoMx DSP Whole Transcriptomic Atlas (WTA) library construction involving probe hybridization, ligation and PCR amplification were done according to Nanostring's protocol (GeoMx DSP NGS readout User Manual Library Preparation & GeoMx NGS Pipeline, MAN-10153-01).

treatment_protocol: Treatment of mice carrying ID8 tumors started 10 days after tumor graft and continued for 3 weeks. Mice were vaccinated intradermally with 1 x 106 OCDC every week. Anti-VEGF (40 µg, together with OCDC, Absolute Antibody) and anti-PD1 (200 µg, every 3 days, BioXcell) were given intraperitoneally (i.p.). Olaparib (PARPi) was administered orally at 40 mg/kg/day. As treatment controls, tumor-bearing mice were treated with PBS or isotype controls.

value: tumor

tag: mouse id

tag: slide id

tag: region of_interest

tag: model

value: PARPi

tag: ck

value: low

value: B


title: RNA-Seq, 1dAE, brain, H33S31A, F, rep1

description:
Library name: H33S31A, 1dAE, rep1
PE100
H33S31A-1dAE-rep1


title: RNA-Seq, 10dAE, brain, H33H32, F, rep3

description:
Library name: H33H32, 10dAE, rep3
PE100
H33H32-10dAE-rep3


title: RNA-Seq, 1dAE, brain, H33S31A, F, rep2

description:
Library name: H33S31A, 1dAE, rep2
PE100
H33S31A-1dAE-rep2


title: RNA-Seq, 10dAE, brain, H33H32, F, rep2

description:
Library name: H33H32, 10dAE, rep2
PE100
H33H32-10dAE-rep2


title: RNA-Seq, 10dAE, brain, H33H32, F, rep1

description:
Library name: H33H32, 10dAE, rep1
PE100
H33H32-10dAE-rep1


title: RNA-Seq, 1dAE, brain, H33H32, F, rep2

description:
Library name: H33H32, 1dAE, rep2
PE100
H33H32-1dAE-rep2


title: RNA-Seq, 1dAE, brain, H33H32, F, rep1

description:
Library name: H33H32, 1dAE, rep1
PE100
H33H32-1dAE-rep1


title: RNA-Seq, 1dAE, brain, H33H32, F, rep3

description:
Library name: H33H32, 1dAE, rep3
PE100
H33H32-1dAE-rep3


title: RNA-Seq, 10dAE, brain, H33null, F, rep3

description:
Library name: H33null, 10dAE, rep3
PE100
H33null-10dAE-rep3


title: RNA-Seq, 10dAE, brain, H33null, F, rep2

description:
Library name: H33null, 10dAE, rep2
PE100
H33null-10dAE-rep2


title: RNA-Seq, 10dAE, brain, H33null, F, rep1

description:
Library name: H33null, 10dAE, rep1
PE100
H33null-10dAE-rep1


title: RNA-Seq, 1dAE, brain, H33null, F, rep1

description:
Library name: H33null, 1dAE, rep1
PE100
H33null-1dAE-rep1


title: RNA-Seq, 10dAE, brain, H33WT, F, rep3

description:
Library name: H33WT, 10dAE, rep3
PE100
OreR-10dAE-rep3

value: OreR


title: RNA-Seq, 1dAE, brain, H33null, F, rep2

description:
Library name: H33null, 1dAE, rep2
PE100
H33null-1dAE-rep2


title: RNA-Seq, 1dAE, brain,H33null, F, rep3

description:
Library name: H33null, 1dAE, rep3
PE100
H33null-1dAE-rep3


title: RNA-Seq, 10dAE, brain, H33WT, F, rep2

description:
Library name: H33WT, 10dAE, rep2
PE100
OreR-10dAE-rep2


title: RNA-Seq, 10dAE, brain, H33WT, F, rep1

description:
Library name: H33WT, 10dAE, rep1
PE100
OreR-10dAE-rep1


title: RNA-Seq, 1dAE, brain, H33WT, F, rep3

description:
Library name: H33WT, 1dAE, rep3
PE100
OreR-1dAE-rep3


title: RNA-Seq, 1dAE, brain, H33WT, F, rep2

description:
Library name: H33WT, 1dAE, rep2
PE100
OreR-1dAE-rep2


title: 10dAE, brain, H33S31A, F, rep3

description:
Library name: H33S31A, 10dAE, rep3
PE50

library_source: genomic

molecule: genomic DNA


title: 10dAE, brain, H33S31A, F, rep2

description:
Library name: H33S31A, 10dAE, rep2
PE50


title: 10dAE, brain, H33S31A, F, rep1

description:
Library name: H33S31A, 10dAE, rep1
PE50


title: 1dAE, brain, H33S31A, F, rep3

description:
Library name: H33S31A, 1dAE, rep3
PE50


title: 1dAE, brain, H33S31A, F, rep2

description:
Library name: H33S31A, 1dAE, rep2
PE50


title: 1dAE, brain, H33S31A, F, rep1

description:
Library name: H33S31A, 1dAE, rep1
PE50


title: 10dAE, brain, H33H32, F, rep2

description:
Library name: H33H32, 10dAE, rep2
PE50


title: 10dAE, brain, H33H32, F, rep3

description:
Library name: H33H32, 10dAE, rep3
PE50


title: 10dAE, brain, H33H32, F, rep1

description:
Library name: H33H32, 10dAE, rep1
PE50


title: 1dAE, brain, H33H32, F, rep3

description:
Library name: H33H32, 1dAE, rep3
PE50


title: 1dAE, brain, H33H32, F, rep2

description:
Library name: H33H32, 1dAE, rep2
PE50


title: 1dAE, brain, H33H32, F, rep1

description:
Library name: H33H32, 1dAE, rep1
PE50


title: 10dAE, brain, H33null, F, rep3

description:
Library name: H33null, 10dAE, rep3
PE50


title: 10dAE, brain, H33null, F, rep2

description:
Library name: H33null, 10dAE, rep2
PE50


title: 1dAE, brain,H33null, F, rep3

description:
Library name: H33null, 1dAE, rep3
PE50


title: 10dAE, brain, H33null, F, rep1

description:
Library name: H33null, 10dAE, rep1
PE50


title: 1dAE, brain, H33null, F, rep2

description:
Library name: H33null, 1dAE, rep2
PE50


title: 1dAE, brain, H33null, F, rep1

description:
Library name: H33null, 1dAE, rep1
PE50


title: 10dAE, brain, H33WT, F, rep3

description:
Library name: H33WT, 10dAE, rep3
PE50


title: 10dAE, brain, H33WT, F, rep2

description:
Library name: H33WT, 10dAE, rep2
PE50


title: 10dAE, brain, H33WT, F, rep1

description:
Library name: H33WT, 10dAE, rep1
PE50


title: 1dAE, brain, H33WT, F, rep3

description:
Library name: H33WT, 1dAE, rep3
PE50


title: 1dAE, brain, H33WT, F, rep2

description:
Library name: H33WT, 1dAE, rep2
PE50


title: 1dAE, brain, H33WT, F, rep1

description:
Library name: H33WT, 1dAE, rep1
PE50


title: 50 generations, replicate 2

city: paris

first: Zeynep

last: Baharoglu

address: 25 rue du dr roux

institute: Institut Pasteur

description: Library name: IonXpress_015.8637d5a.fastq

data_processing:
Ion Torrent Ion PGM sequencing technology was used producing 150bp long reads. Reads were then filtered through transposon mapping to ensure the presence of an informative transposon/genome junction using a previously described mapping algorithm (Pierlé et al., 2014, Negro et al., 2019). Detection of at least 10 nucleotides of the transposon sequence were considered sufficient o to retain a read.  Informative reads were extracted, mapped and counted. Fitness scores were then calculated according to van Opijnen (van Opijnen et al., 2009).
Assembly: N16961
Supplementary files format and content: excel file

organism: Vibrio cholerae

source_name: bacteria

growth_protocol: mueller hinton 37°C with agitation

extract_protocol:
DNA extraction kit
A saturated mariner mutant library was generated by conjugation of plasmid pSC1819 from E. coli to V. cholerae. Conjugation was performed for 2 h on 0.45 µM filters. Sequencing libraries were prepared using Agilent’s sureselect XT2 Kit with custom RNA baits designed to hybridize the edges of the Mariner transposon. A total of 12 cycles were used for library amplification. Agilent’s 2100 bioanalzyer was used to verify the size of the pooled libraries and their concentration.

treatment_protocol: non treated or tobramycin 0,02 µg/ml

value: bacteria

tag: time point

value: 50 generations


title: 50 generations, replicate 3

description: Library name: IonXpress_016.8637d5b.fastq


title: 50 generations, replicate 1

description: Library name: IonXpress_012.716d5.fastq


title: Time zero, replicate 3

description: Library name: IonXpress_014.8637d0b.fastq

value: Time zero


title: Time zero, replicate 1

description: Library name: IonXpress_011.716d0.fastq


title: Time zero, replicate 2

description: Library name: IonXpress_013.8637d0a.fastq


title: RNA-Seq, 1dAE, brain, H33WT, F, rep1

description:
Library name: H33WT, 1dAE, rep1
PE100
OreR-1dAE-rep1

tag: tissue


title: R5909

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

hyb_protocol: The samples have been processed according to Nanostring CosMxTM SMI profiling standard protocol published by He et al., Nature Biotechnology 2022 PMID: 36203011.

data_processing:
Images were segmented and transcript readouts were assigned to cells according to Nanostring's standard data processing procedures.
The Seurat objects (seurat_object.Rds) contains raw read counts of the merged dataset. Metadata is provided in processed_metadata.csv.

source_name: Cholangiocarcinoma

extract_protocol: FFPE tissue sections were prepared for CosMxTM SMI profiling. Five-micron tissue sections mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C. Serial slides were prepared to stain tissues with H&E. Slides were shiped to NanoString Customer Experience (CX) Lab at NanoString’s headquarters in Seattle for processing.

treatment_protocol: Surgical samples were fixed in formalin and paraffin embedded (FFPE) for NanoString CosMx Spatial Molecular Imager (SMI) and tissue stainings.

tag: specimen


title: 4T1 cells-B-1

city: Changzhou

first: Tianhan

last: Xu

address: 68 Middle Gehu Road

institute: The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University

description:
Library name: Sample1
FPKM_B1

data_processing:
The libraries were sequenced on an Illumina Novaseq X Plus platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCm39.110
Supplementary files format and content: processed data.txt

source_name: mammary gland

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions.

value: mammary gland

tag: treatment


title: R5889

scan_protocol: The samples have been processed according to Nanostring CosMxTM SMI profiling standard protocol published by He et al., Nature Biotechnology 2022 PMID: 36203011.


title: LS_3

city: Pittsburgh

first: Tianhao

last: Liu

address: F28W+RH Pittsburgh, Pennsylvania

institute: University of Pittsburgh

description: Library name: D1

data_processing:
Raw spatial transcriptomics data processing Raw spatial transcriptomics sequencing data were processed using 10x Genomics Space Ranger v2.1.3. High-resolution H&E images were manually aligned to the corresponding CytAssist images to accurately map tissue morphology to spatially resolved gene expression. Space Ranger was then used to generate spot-level gene expression matrices and spatial coordinate information for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: skin_ST_combine_harmony.rds: The processed file with raw counts for gene expression of 55µm spots.
Library strategy: Spatial Transcriptomics

extract_protocol:
Biopsy specimens were processed for 10x Chromium 3′ single-cell RNA sequencing either immediately after tissue dissociation or following cryopreservation in CryoStor® CS10. Adjacent biopsy specimens were formalin-fixed and paraffin-embedded (FFPE) for spatial transcriptomics and hematoxylin and eosin (H&E) staining. A subset of the FFPE-preserved tissues was additionally analyzed using 10x Genomics Flex single-cell RNA sequencing.
Spatial transcriptomics was performed using the Visium v2 Whole Transcriptome (WT) Panel Spatial Gene Expression workflow (55-µm spot diameter). RNA quality was assessed from scrolls generated from each FFPE block. Blocks with a percentage of RNA fragments >200 nucleotides (DV200) of at least 30% were selected for spatial transcriptomics. Tissue sections were mounted on Visium slides and processed in Visium v2 cassettes for library preparation. Spatially barcoded libraries were generated and sequenced according to the manufacturer's protocols.

value: Skin

tag: disease

value: localized scleroderma (LS)


title: LS_2

description: Library name: C1


title: LS_1

description: Library name: B1


title: SSc_1

description: Library name: A1

value: systemic sclerosis (SSc)


title: Healthy control skin, H1 - batch1

city: Boston

first: Ksenia

middle: S

last: Anufrieva

state: MA

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

description: Library name: Flex_H1

library_source: transcriptomic single cell

data_processing:
Cell Ranger multi was used to align reads to GRCh38 (refdata-gex-GRCh38-2020-A) using the Chromium Human Transcriptome Probe Set v1.0.1, demultiplex pooled samples by Probe Barcode, and generate per-sample feature-barcode matrices. Per-sample BAM files were converted to per-sample FASTQ files using cellranger bamtofastq.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger filtered feature-barcode matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz).

source_name: skin

extract_protocol:
Skin biopsies were collected by 4-mm punch biopsy after local anesthesia with 1% lidocaine with epinephrine, placed in formalin, and embedded in paraffin. For each sample, four FFPE curls (25 μm each) were dissociated following the FLEX protocol (CG000632 RevA, 10X Genomics) using the Miltenyi Biotec FFPE Tissue Dissociation Kit.
Cells from each sample were hybridized with a unique Probe Barcode according to the "Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples" user guide (CG000527, 10X Genomics). Post-hybridization, cells from 16 samples were washed, counted, and pooled in equal proportions. Approximately 200,000 cells from the pooled suspension were loaded onto a Chromium Q chip (PN-1000422, 10X Genomics). Sequencing libraries were prepared and sequenced on an Illumina NovaSeq platform using paired-end dual-indexing (28 cycles for Read 1, 10 cycles for i7, 10 cycles for i5, and 90 cycles for Read 2).

value: skin

tag: disease state

value: Healthy


title: Healthy control skin, H5 - batch5

description: Library name: Flex_H8


title: Healthy control skin, H1 - batch5

description: Library name: Flex_H9


title: Cutaneous lupus erythematosus non-lesional skin, NL_CLE5

description: Library name: Flex_NL_CLE5


title: Cutaneous lupus erythematosus non-lesional skin, NL_CLE6

description: Library name: Flex_NL_CLE6


title: Cutaneous lupus erythematosus lesional skin, CLE6

description: Library name: Flex_CLE6

value: CLE


title: Cutaneous lupus erythematosus lesional skin, CLE5

description: Library name: Flex_CLE5


title: Dermatomyositis non-lesional skin, NL_DM2

description: Library name: Flex_NL_DM2


title: Dermatomyositis non-lesional skin, NL_DM1

description: Library name: Flex_NL_DM1


title: Dermatomyositis lesional skin, DM22

description: Library name: Flex_DM22

value: DM


title: smallRNA_TC2_WT_39h

description: Library name: Sample 16

data_processing:
The small RNA-seq fastq files were adapter trimmed (TGGAATTCTCGGGTGCCAAGG) at the 3' end using the function preprocessReads() from the R packege QuasR (version 1.26)  and mapped to the C.elegans genome (ce10) with the R package QuasR (version 1.26) using the alignment algorithm Bowtie. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",maxHits=100)". For miRNA quantification, gene annotation from miRBase v22 was used and lifted over to ce10. We extended the genomic coordinates of the 5' end of each miRNA by 3bp on both sides and counted all the reads that started within those regions using the following command: "qCount(proj,matureMirsExt,orientation="same"). To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Finally the count table was log2 transformed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers.
Assembly: ce10
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with normalized counts for each sample

source_name: whole organism

extract_protocol:
At the time of sample collection, animals were washed off the plates with M9 buffer, washed twice with M9 buffer, resuspended in TRI Reagent (MRC, TR-118) and snap-frozen in liquid nitrogen. Prior to RNA extraction, animals were lysed by five cycles of thawing (42°C) and snap-freezing in liquid nitrogen. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062; DNase treatment included) according to the manufacturer’s protocol. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
Illumina TruSeq Small RNA Library Prep Kit

tag: strain

value: whole organism

tag: genotype

tag: time (h)


title: Cd11b_KO_rep1

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

description: Library name: Cd11b_KO_rep1

data_processing:
Quality control of raw reads was performed with FastQC (v0.11.9), and sequences were aligned to the Mus musculus reference genome (mm10) using STAR (v2.7.10a). Read quantification was carried out using the featureCounts function of the Rsubread package (v2.12.3) at gene-level using GENCODE annotation retaining only uniquely mapping reads.
Assembly: mm10
Supplementary files format and content: comma separated text file (.csv) of raw counts with all samples.

source_name: lung

extract_protocol:
Total RNA was isolated from FACS-sorted spleen and lung cells of WT and Dpp3−/− mice using QIAzol Lysis Reagent (QIAGEN) according to the manufacturer’s instructions. RNA concentration and purity were assessed prior to downstream applications.
total RNA was subjected to poly(A) mRNA sequencing using SMARTer-Stranded Total RNA Kit (Clontech), according to the manufacturer’s instructions.

value: lung

tag: cell type

value: KO


title: Dermatomyositis lesional skin, DM21

description: Library name: Flex_DM21

tag: batch


title: Healthy control skin, H4 - batch 4

description: Library name: Flex_H6


title: Cutaneous lupus erythematosus lesional skin, CLE9

description: Library name: Flex_CLE9


title: Cutaneous lupus erythematosus lesional skin, CLE7

description: Library name: Flex_CLE7


title: Healthy control skin, H3 - batch3

description: Library name: Flex_H4


title: Healthy control skin, H1 - batch4

description: Library name: Flex_H7


title: Cutaneous lupus erythematosus lesional skin, CLE8

description: Library name: Flex_CLE8


title: Healthy control skin, H2 - batch3

description: Library name: Flex_H3


title: Cutaneous lupus erythematosus non-lesional skin, NL_CLE4

description: Library name: Flex_NL_CLE4


title: Cutaneous lupus erythematosus lesional skin, CLE4

description: Library name: Flex_CLE4


title: Cutaneous lupus erythematosus non-lesional skin, NL_CLE3

description: Library name: Flex_NL_CLE3


title: Healthy control skin, H1 - batch3

description: Library name: Flex_H5


title: Cutaneous lupus erythematosus lesional skin, CLE3

description: Library name: Flex_CLE3


title: Cutaneous lupus erythematosus non-lesional skin, NL_CLE2

description: Library name: Flex_NL_CLE2


title: Cutaneous lupus erythematosus lesional skin, CLE2

description: Library name: Flex_CLE2


title: Cutaneous lupus erythematosus non-lesional skin, NL_CLE1

description: Library name: Flex_NL_CLE1


title: Cutaneous lupus erythematosus lesional skin, CLE1

description: Library name: Flex_CLE1


title: Dermatomyositis lesional skin, DM20

description: Library name: Flex_DM20


title: Dermatomyositis lesional skin, DM18

description: Library name: Flex_DM18


title: Dermatomyositis lesional skin, DM19

description: Library name: Flex_DM19


title: Dermatomyositis lesional skin, DM17

description: Library name: Flex_DM17


title: Healthy control skin, H2 - batch2

description: Library name: Flex_H2


title: Dermatomyositis lesional skin, DM16

description: Library name: Flex_DM16


title: Dermatomyositis lesional skin, DM14

description: Library name: Flex_DM14


title: Dermatomyositis lesional skin, DM15

description: Library name: Flex_DM15


title: Dermatomyositis lesional skin, DM13

description: Library name: Flex_DM13


title: Dermatomyositis lesional skin, DM12

description: Library name: Flex_DM12


title: Dermatomyositis lesional skin, DM11

description: Library name: Flex_DM11


title: Dermatomyositis lesional skin, DM9

description: Library name: Flex_DM9


title: Dermatomyositis lesional skin, DM10

description: Library name: Flex_DM10


title: Dermatomyositis lesional skin, DM8

description: Library name: Flex_DM8


title: Dermatomyositis lesional skin, DM7

description: Library name: Flex_DM7


title: Dermatomyositis lesional skin, DM6

description: Library name: Flex_DM6


title: Cd11b_rep1

description: Library name: Cd11b_rep1

value: WT


title: Dermatomyositis lesional skin, DM5

description: Library name: Flex_DM5


title: Dermatomyositis lesional skin, DM4

description: Library name: Flex_DM4


title: Dermatomyositis lesional skin, DM3

description: Library name: Flex_DM3


title: Dermatomyositis lesional skin, DM2

description: Library name: Flex_DM2


title: Dermatomyositis lesional skin, DM1

description: Library name: Flex_DM1


title: siEIF1_2

city: Yinchuan

first: LI

address: The General Hospital of Ningxia Medical University

institute: Ningxia Medical University General Hospital

description: Library name: Sample5

data_processing:
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (***-AS) and regulated alternative splicing events (***-RAS) between ***-OE and control samples were defined and quantified using the SUVA pipeline described previously . The frequency and proportion of reads of SUVA AS events (pSAR) were calculated.
GRCh38
Assembly: tab-delimited text file includes FPKM value for each Sample.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

extract_protocol:
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).

treatment_protocol: Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.

tag: cell line

value: EIF1 knockdown


title: siEIF1_3

description: Library name: Sample6


title: NC_3

description: Library name: Sample3

value: Negative control


title: siEIF1_1

description: Library name: Sample4


title: NC_2

description: Library name: Sample2


title: NC_1

description: Library name: Sample1


title: F98NNAR

city: Montreal

first: Sahel

last: Jahangiri Esfahani

address: 3775 University Street

country: Canada

institute: McGill

description: Library name: NS.1890.001.NEBNext_dual_i7_149---NEBNext_dual_i5_149.F98NNAR

data_processing:
Neutrophil RNA-seq reads were aligned to the human genome GRCh37/hg19 using STAR. Differential gene expression and interaction-term analyses were performed in R using DESeq2, with age, sex, and BMI included as covariates.
Assembly: GRCh37/hg19
Supplementary files format and content: TPM

source_name: Neutrophil from peripheral blood

extract_protocol:
Peripheral blood was collected from participants and neutrophils were isolated directly from whole blood using the MACSxpress Whole Blood Neutrophil Isolation Kit (Miltenyi Biotec) according to the manufacturer's instructions. Isolated neutrophils were counted using a Cellometer Auto T4 (Nexcelom) and resuspended at a concentration of 1 × 10⁶ cells/mL in RPMI-1640 complete medium supplemented with 2 mM L-glutamine, 10% fetal bovine serum (FBS), and 1% penicillin/streptomycin. Cells were plated in 24-well plates (1 mL per well). For inflammatory stimulation, 100 μL of LPS solution (110 ng/mL) was added to designated wells to achieve a final concentration of 10 ng/mL LPS, while control wells received an equal volume of culture medium. Cells were incubated for 1 hour at 37°C and 5% CO₂. Following incubation, neutrophils were collected, centrifuged at 300 × g for 5 minutes at room temperature, and lysed in 650 μL RLT buffer (QIAGEN) supplemented with β-mercaptoethanol (10 μL of 14.5 M β-ME per mL RLT buffer). Lysates were stored at −80°C until RNA extraction.
Total RNA was extracted using the QIAGEN AllPrep DNA/RNA Mini Kit, and libraries were sequenced at the McGill Genome Quebec Centre on an Illumina NovaSeq 6000 platform with a target depth of approximately 30 million reads per sample.

value: Neutrophil from peripheral blood

value: Neutrophil


title: F98NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_234---NEBNext_dual_i5_282.F98NAR


title: F97NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_148---NEBNext_dual_i5_148.F97NNAR


title: F96NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_147---NEBNext_dual_i5_147.F96NNAR


title: F96NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_211---NEBNext_dual_i5_259.F96NAR


title: F95NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_146---NEBNext_dual_i5_146.F95NNAR


title: F91NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_221---NEBNext_dual_i5_269.F91NNAR


title: F90NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_145---NEBNext_dual_i5_145.F90NNAR


title: F89NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_144---NEBNext_dual_i5_144.F89NNAR


title: F90NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_178---NEBNext_dual_i5_178.F90NAR


title: F88NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_177---NEBNext_dual_i5_177.F88NAR


title: F86NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_125---NEBNext_dual_i5_125.F86NNAR


title: F88NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_126---NEBNext_dual_i5_126.F88NNAR


title: F86NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_176---NEBNext_dual_i5_176.F86NAR


title: F83NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_124---NEBNext_dual_i5_124.F83NNAR


title: F82NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_143---NEBNext_dual_i5_143.F82NNAR


title: F81NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_123---NEBNext_dual_i5_123.F81NNAR


title: F81NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_233---NEBNext_dual_i5_281.F81NAR


title: F80NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_184---NEBNext_dual_i5_184.F80NNAR


title: F78NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_175---NEBNext_dual_i5_175.F78NAR


title: F78NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_220---NEBNext_dual_i5_268.F78NNAR


title: F77NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_121---NEBNext_dual_i5_121.F77NNAR


title: F77NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_232---NEBNext_dual_i5_280.F77NAR


title: F79NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_122---NEBNext_dual_i5_122.F79NNAR


title: F74NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_174---NEBNext_dual_i5_174.F74NAR


title: F74NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_120---NEBNext_dual_i5_120.F74NNAR


title: F72NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_119---NEBNext_dual_i5_119.F72NNAR


title: F68NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_117---NEBNext_dual_i5_117.F68NNAR


title: F70NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_118---NEBNext_dual_i5_118.F70NNAR


title: F67NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_142---NEBNext_dual_i5_142.F67NNAR


title: F68NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_173---NEBNext_dual_i5_173.F68NAR


title: F66NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_116---NEBNext_dual_i5_116.F66NNAR


title: F66NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_172---NEBNext_dual_i5_172.F66NAR


title: F65NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_115---NEBNext_dual_i5_115.F65NNAR


title: F64NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_114---NEBNext_dual_i5_114.F64NNAR


title: F63NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_113---NEBNext_dual_i5_113.F63NNAR


title: F61NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_112---NEBNext_dual_i5_112.F61NNAR


title: F59NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_111---NEBNext_dual_i5_111.F59NNAR


title: F59NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_231---NEBNext_dual_i5_279.F59NAR


title: F58NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_171---NEBNext_dual_i5_171.F58NAR


title: F57NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_109---NEBNext_dual_i5_109.F57NNAR


title: F58NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_110---NEBNext_dual_i5_110.F58NNAR


title: F56NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_108---NEBNext_dual_i5_108.F56NNAR


title: F57NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_230---NEBNext_dual_i5_278.F57NAR


title: F55NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_107---NEBNext_dual_i5_107.F55NNAR


title: F55NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_203---NEBNext_dual_i5_251.F55NAR


title: F54NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_106---NEBNext_dual_i5_106.F54NNAR


title: F54NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_170---NEBNext_dual_i5_170.F54NAR


title: F53NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_105---NEBNext_dual_i5_105.F53NNAR


title: F52NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_104---NEBNext_dual_i5_104.F52NNAR


title: F51NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_103---NEBNext_dual_i5_103.F51NNAR


title: F52NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_168---NEBNext_dual_i5_168.F52NAR


title: F50NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_102---NEBNext_dual_i5_102.F50NNAR


title: F50NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_F7---NEBNext_dual_i5_F7.F50NAR


title: F48NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_101---NEBNext_dual_i5_101.F48NNAR


title: F47NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_100---NEBNext_dual_i5_100.F47NNAR


title: F44NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_98---NEBNext_dual_i5_98.F44NNAR


title: F45NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_99---NEBNext_dual_i5_99.F45NNAR


title: F45NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_229---NEBNext_dual_i5_277.F45NAR


title: F47NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_167---NEBNext_dual_i5_167.F47NAR


title: F44NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_166---NEBNext_dual_i5_166.F44NAR


title: F43NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_217---NEBNext_dual_i5_265.F43NNAR


title: F43NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_228---NEBNext_dual_i5_276.F43NAR


title: F42NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_97---NEBNext_dual_i5_97.F42NNAR


title: F42NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_165---NEBNext_dual_i5_165.F42NAR


title: F40NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_227---NEBNext_dual_i5_275.F40NAR


title: F38NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_141---NEBNext_dual_i5_141.F38NNAR


title: F40NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_F11---NEBNext_dual_i5_F11.F40NNAR


title: F37NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_216---NEBNext_dual_i5_264.F37NNAR


title: F38NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_E7---NEBNext_dual_i5_E7.F38NAR


title: F35NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_D11---NEBNext_dual_i5_D11.F35NNAR


title: F37NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_210---NEBNext_dual_i5_258.F37NAR


title: F35NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_164---NEBNext_dual_i5_164.F35NAR


title: F36NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_E11---NEBNext_dual_i5_E11.F36NNAR


title: F34NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_C11---NEBNext_dual_i5_C11.F34NNAR


title: F36NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_226---NEBNext_dual_i5_274.F36NAR


title: F34NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_200---NEBNext_dual_i5_248.F34NAR


title: F31NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_B11---NEBNext_dual_i5_B11.F31NNAR


title: F31NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_163---NEBNext_dual_i5_163.F31NAR


title: F29NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_A11---NEBNext_dual_i5_A11.F29NNAR


title: F27NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_H10---NEBNext_dual_i5_H10.F27NNAR


title: F29NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_225---NEBNext_dual_i5_273.F29NAR


title: F23NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_257---NEBNext_dual_i5_209.F23NAR


title: F23BNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_186---NEBNext_dual_i5_186.F23BNAR


title: F22NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_215---NEBNext_dual_i5_263.F22NNAR


title: F23ANAR

description: Library name: NS.1911.002.NEBNext_dual_i7_185---NEBNext_dual_i5_185.F23ANAR


title: F25NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_262---NEBNext_dual_i5_214.F25NAR


title: F19NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_224---NEBNext_dual_i5_272.F19NAR


title: F23NNAR

description: Library name: NS.1911.003.NEBNext_dual_i7_235---NEBNext_dual_i5_283.F23NNAR


title: F19NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_189---NEBNext_dual_i5_189.F19NNAR


title: F22NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_237---NEBNext_dual_i5_285.F22NAR


title: F16NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_214---NEBNext_dual_i5_262.F16NNAR


title: F21NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_161---NEBNext_dual_i5_161.F21NAR


title: F15NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_251---NEBNext_dual_i5_203.F15NAR


title: F14NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_188---NEBNext_dual_i5_188.F14NNAR


title: F14NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_H7---NEBNext_dual_i5_H7.F14NAR


title: F12NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_182---NEBNext_dual_i5_182.F12NNAR


title: F12NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_250---NEBNext_dual_i5_202.F12NAR


title: F10NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_181---NEBNext_dual_i5_181.F10NNAR


title: F110NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_209---NEBNext_dual_i5_257.F110NAR


title: F11NNAR

description: Library name: NS.1911.003.NEBNext_dual_i7_268---NEBNext_dual_i5_220.F11NNAR


title: F11NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_249---NEBNext_dual_i5_201.F11NAR


title: F10NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_256---NEBNext_dual_i5_208.F10NAR


title: F108NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_139---NEBNext_dual_i5_139.F108NNAR


title: F107NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_138---NEBNext_dual_i5_138.F107NNAR


title: F108NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_202---NEBNext_dual_i5_250.F108NAR


title: F105NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_137---NEBNext_dual_i5_137.F105NNAR


title: F102NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_G10---NEBNext_dual_i5_G10.F102NNAR


title: F105NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_208---NEBNext_dual_i5_256.F105NAR


title: F102NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_160---NEBNext_dual_i5_160.F102NAR


title: F101NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_219---NEBNext_dual_i5_267.F101NNAR


title: F101NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_D7---NEBNext_dual_i5_D7.F101NAR


title: F09NNAR

description: Library name: NS.1911.003.NEBNext_dual_i7_236---NEBNext_dual_i5_284.F09NNAR


title: F100NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_C7---NEBNext_dual_i5_C7.F100NAR


title: F07NNAR

description: Library name: NS.1911.003.NEBNext_dual_i7_291---NEBNext_dual_i5_243.F07NNAR


title: F09NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_G7---NEBNext_dual_i5_G7.F09NAR


title: F100NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_183---NEBNext_dual_i5_183.F100NNAR


title: F02NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_255---NEBNext_dual_i5_207.F02NAR


title: E66NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_218---NEBNext_dual_i5_266.E66NNAR


title: F01NNAR

description: Library name: NS.1911.003.NEBNext_dual_i7_259---NEBNext_dual_i5_211.F01NNAR


title: E65NNAR

description: Library name: NS.1890.001.NEBNext_dual_i7_136---NEBNext_dual_i5_136.E65NNAR


title: E65NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_B7---NEBNext_dual_i5_B7.E65NAR


title: E64NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_A7---NEBNext_dual_i5_A7.E64NAR


title: E64NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_135---NEBNext_dual_i5_135.E64NNAR


title: E61NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_206---NEBNext_dual_i5_254.E61NAR


title: E60NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_133---NEBNext_dual_i5_133.E60NNAR


title: E62NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_197---NEBNext_dual_i5_245.E62NNAR


title: E58NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_190---NEBNext_dual_i5_190.E58NNAR


title: E61NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_134---NEBNext_dual_i5_134.E61NNAR


title: E57NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_131---NEBNext_dual_i5_131.E57NNAR


title: E56NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_205---NEBNext_dual_i5_253.E56NAR


title: E55NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_130---NEBNext_dual_i5_130.E55NNAR


title: E54NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_159---NEBNext_dual_i5_159.E54NAR


title: E53NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_G6---NEBNext_dual_i5_G6.E53NAR


title: E54NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_F10---NEBNext_dual_i5_F10.E54NNAR


title: E53NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_129---NEBNext_dual_i5_129.E53NNAR


title: E52NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_128---NEBNext_dual_i5_128.E52NNAR


title: E50NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_E10---NEBNext_dual_i5_E10.E50NNAR


title: E50NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_158---NEBNext_dual_i5_158.E50NAR


title: E47NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_D10---NEBNext_dual_i5_D10.E47NNAR


title: E47NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_157---NEBNext_dual_i5_157.E47NAR


title: E46NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_C10---NEBNext_dual_i5_C10.E46NNAR


title: E45NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_199---NEBNext_dual_i5_247.E45NAR


title: E45NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_B10---NEBNext_dual_i5_B10.E45NNAR


title: E44NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_A10---NEBNext_dual_i5_A10.E44NNAR


title: E42NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_156---NEBNext_dual_i5_156.E42NAR


title: E42NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_127---NEBNext_dual_i5_127.E42NNAR


title: E40NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_155---NEBNext_dual_i5_155.E40NAR


title: E40NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_H9---NEBNext_dual_i5_H9.E40NNAR


title: E38NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_F9---NEBNext_dual_i5_F9.E38NNAR


title: E38NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_198---NEBNext_dual_i5_246.E38NAR


title: E37NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_E9---NEBNext_dual_i5_E9.E37NNAR


title: E37NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_201---NEBNext_dual_i5_249.E37NAR


title: E36NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_F6---NEBNext_dual_i5_F6.E36NAR


title: E33NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_B9---NEBNext_dual_i5_B9.E33NNAR


title: E34NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_C9---NEBNext_dual_i5_C9.E34NNAR


title: mRNA_TC2_lin-28(xe192)_31h

city: Basel

first: Dimos

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: Sample 77

data_processing:
RNA-seq data was mapped to the C. elegans genome (ce11) using the Align (qAlign) function from the QuasR (v1.41.2) package in R with splicedAlignement = TRUE, using the aligner HISAT2 (v1.20.0) including an exon-exon junction database (WS270). Gene expression levels were quantified using the qCount() function, counting the reads on the opposite strand of annotated transcripts. For paired-end samples, the first read was considered for counting. For annotations, coding transcript information from WormBase WS270 was used. We further compensated for differences in library sizes by scaling each library to the average library size. Finally, we log2 transformed the data using a pseudo count of 8 (log2(x+8)).
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw gene expression read counts
Supplementary files format and content: tab-delimited text file with normalized gene expression read counts

extract_protocol:
At the time of sample collection, animals were washed off the plates with M9 buffer, washed twice with M9 buffer, resuspended in TRI Reagent (MRC, TR-118) and snap-frozen in liquid nitrogen. Prior to RNA extraction, animals were lysed by five cycles of thawing (42°C) and snap-freezing in liquid nitrogen. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062; DNase treatment included) according to the manufacturer’s protocol. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
TruSeq Illumina mRNA-seq


title: mRNA_TC2_lin-28(xe192)_36h

description: Library name: Sample 82


title: S100A8_A9 experiment 2, 24 hrs of S100A8_A9 treatment

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

country: Germany

institute: University of Ulm

description: Library name: S100A8_A9_24h_2

data_processing:
Raw reads (fastq) were pseudoaligned and quantified with Kallisto quant with bootostrap set to 100. Transcript abundance counts from kallisto quant for all the samples were merged to a single transcript expression count matrix. This transcript expression count matrix was applied for differential transcript expression analyses using DESeq2. Visualization and representation of the transcriptome data were performed by custom R scripts in R-Studio environment.
Assembly: GRCh38
Supplementary files format and content: tab delimited txt file for count data

source_name: adipose tissue derived mesenchymal stromal cell

growth_protocol: cells were cultured in Mesenchymal Stem Cell Growth Medium 2 at 37C and 5% CO2

extract_protocol:
RNA was isolated from the cells using Rneasy plus kit (Qiagen). 1 µg of total RNA was used for the rRNA depletion and library preparation.
Library was prepared using NEBNext Ultra II Directional RNA Library Preparation kit (NEB)

treatment_protocol: Cells were treated either with vehicle or S100A8_A9 (0.5 µg/ml) for 6, 12 or 24 hrs


title: mRNA_TC2_lin-28(xe192)_37h

last: Gaidatzis

description: Library name: Sample 83


title: Populus yunnanensis, 0h, replicate 3

city: Kunming

first: Xiaolin

last: Zhang

address: qingyun street

institute: southwest forestry university

description: Library name: DCK-3

data_processing:
Waiting for submitter
Assembly: Populus trichocarpa GCA_000002775.4
Supplementary files format and content: All_gene_fpkm.list

organism: Populus yunnanensis

source_name: stem

extract_protocol:
Cultivation of two poplars under different growth stage
The mRNA was collected from the stem of cuttings under different growth stage, respectively.
Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, cDNA libraries were sequenced on Illumina high-throughput platform.

value: stem

tag: Stage

value: growth stage

value: cutting

tag: time


title: S100A8_A9 experiment 1, 12 hrs of S100A8_A9 treatment

description: Library name: S100A8_A9_12h_1

value: adipose tissue derived mesenchymal stromal cell


title: E32NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_213---NEBNext_dual_i5_261.E32NNAR


title: E32NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_223---NEBNext_dual_i5_271.E32NAR


title: E31NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_A9---NEBNext_dual_i5_A9.E31NNAR


title: E31NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_152---NEBNext_dual_i5_152.E31NAR


title: E30NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_H8---NEBNext_dual_i5_H8.E30NNAR


title: E30NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_151---NEBNext_dual_i5_151.E30NAR


title: F02NNAR

description: Library name: NS.1911.003.NEBNext_dual_i7_239---NEBNext_dual_i5_287.F02NNAR


title: F01NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_265---NEBNext_dual_i5_217.F01NAR


title: E66NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_207---NEBNext_dual_i5_255.E66NAR


title: E28NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_E6---NEBNext_dual_i5_E6.E28NAR


title: E28NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_F8---NEBNext_dual_i5_F8.E28NNAR


title: E26NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.E26NNAR


title: E25NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_C8---NEBNext_dual_i5_C8.E25NNAR


title: E27NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_E8---NEBNext_dual_i5_E8.E27NNAR


title: E29NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_G8---NEBNext_dual_i5_G8.E29NNAR


title: E24NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_B8---NEBNext_dual_i5_B8.E24NNAR


title: E23NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_A8---NEBNext_dual_i5_A8.E23NNAR


title: E24NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_222---NEBNext_dual_i5_270.E24NAR


title: E22NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_264---NEBNext_dual_i5_216.E22NAR


title: E57NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_H6---NEBNext_dual_i5_H6.E57NAR


title: E59NNAR

description: Library name: NS.1888.002.NEBNext_dual_i7_132---NEBNext_dual_i5_132.E59NNAR


title: E18NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_D6---NEBNext_dual_i5_D6.E18NAR


title: E17NAR

description: Library name: NS.1911.002.NEBNext_dual_i7_204---NEBNext_dual_i5_252.E17NAR


title: E17NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_H7---NEBNext_dual_i5_H7.E17NNAR


title: E20NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_187---NEBNext_dual_i5_187.E20NNAR


title: E16NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_212---NEBNext_dual_i5_260.E16NNAR


title: E14NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_263---NEBNext_dual_i5_215.E14NAR


title: E11NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_246---NEBNext_dual_i5_198.E11NAR


title: E12NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_247---NEBNext_dual_i5_199.E12NAR


title: E11NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_G7---NEBNext_dual_i5_G7.E11NNAR


title: E16NAR

description: Library name: NS.1888.001.NEBNext_dual_i7_C6---NEBNext_dual_i5_C6.E16NAR


title: E14NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_180---NEBNext_dual_i5_180.E14NNAR


title: Populus yunnanensis, 0h, replicate 1

description: Library name: DCK-1


title: E08NNAR

description: Library name: NS.1911.003.NEBNext_dual_i7_252---NEBNext_dual_i5_204.E08NNAR


title: E08NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_244---NEBNext_dual_i5_292.E08NAR


title: E07NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_243---NEBNext_dual_i5_291.E07NAR


title: E05NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_242---NEBNext_dual_i5_290.E05NAR


title: E06NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_258---NEBNext_dual_i5_210.E06NAR


title: E03NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_241---NEBNext_dual_i5_289.E03NAR


title: E02NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_240---NEBNext_dual_i5_288.E02NAR


title: E02NNAR

description: Library name: NS.1911.003.NEBNext_dual_i7_266---NEBNext_dual_i5_218.E02NNAR


title: 013_Week_4

city: Rochester

first: Emma

last: Durrenberger

state: Minnesota

address: 200 First St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: sample_53
ST-01902613_Week_4

data_processing:
Libraries were multiplexed and sequenced in a single lane using the standard protocol for the Illumina NovaSeq 6000 and the NovaSeq XP 4-Lane kit for individual lane loading. The flow cell was sequenced as 100 X 2 paired-end reads using the NovaSeq S4 sequencing kit and NovaSeq Control Software v1.8.0. Base-calling was performed with Illumina’s RTA version 3.4.4.
The raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.5. MAP-RSeq uses STAR to align reads to the reference human genome build hg38. Gene and exon expression quantification were performed using the Subread package to obtain both raw and normalized (FPKM – Fragments Per Kilobase per Million mapped reads) reads. Finally, comprehensive analyses were run on the aligned reads to assess the quality of the sequenced libraries.
Assembly: hg38
Supplementary files format and content: merged_gene_count.tsv tsv file containing merged raw gene counts for all samples
Supplementary files format and content: merged_gene_count_fpkm_by_read.tsv tsv file containing gene count fpkm by read for all samples

source_name: blood

extract_protocol:
Total RNA concentration and quality were determined using Qubit fluorometry (ThermoFisher Scientific, Waltham, MA) and the Agilent Fragment Analyzer (Santa Clara, CA). The total RNA underwent globin depletion using GLOBINclear (ThermoFisher Scientific, Waltham, MA) and a clean-up with DNase I (Zymo Research, Irvine, CA) treatment.
cDNA libraries were prepared using 100 ng of total RNA according to the manufacturer’s instructions for the Illumina Stranded mRNA Prep, Ligation (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries were determined with the Agilent TapeStation and Qubit fluorometry.

value: blood

value: PBMCs


title: 023_Week_12

description:
Library name: sample_49
023_Week_12


title: 023_Baseline

description:
Library name: sample_48
023_Baseline

value: Baseline


title: 022_Baseline

description:
Library name: sample_45
022_Baseline


title: 022_Week_8

description:
Library name: sample_47
022_Week_8


title: 022_Week_4

description:
Library name: sample_46
022_Week_4


title: 021_Week_8

description:
Library name: sample_44
021_Week_8


title: 021_Week_4

description:
Library name: sample_43
021_Week_4


title: 021_Week_12

description:
Library name: sample_42
021_Week_12


title: 021_Baseline

description:
Library name: sample_41
021_Baseline


title: 019_Week_8

description:
Library name: sample_40
019_Week_8


title: 019_Week_4.

description:
Library name: sample_39
019_Week_4


title: 019_Baseline

description:
Library name: sample_37
019_Baseline


title: 015_Week_4

description:
Library name: sample_33
015_Week_4


title: F53NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_169---NEBNext_dual_i5_169.F53NAR


title: 015_Week_12

description:
Library name: sample_32
015_Week_12


title: 015_Baseline

description:
Library name: sample_31
015_Baseline


title: 014_Week_4

description:
Library name: sample_29
014_Week_4


title: 014_Week_12

description:
Library name: sample_28
014_Week_12


title: 013_Baseline

description:
Library name: sample_25
013_Baseline


title: 012_Week_8

description:
Library name: sample_24
012_Week_8


title: 012_Week_4

description:
Library name: sample_23
012_Week_4


title: 012_Week_12

description:
Library name: sample_22
012_Week_12


title: 012_Baseline

description:
Library name: sample_21
012_Baseline


title: 015_Week_8

description:
Library name: sample_52
15_Week_8


title: 023_Week_8

description:
Library name: sample_51
023_Week_8


title: E04NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_253---NEBNext_dual_i5_205.E04NAR


title: 011_Week_12

description:
Library name: sample_18
011_Week_12


title: 011_Baseline

description:
Library name: sample_17
011_Baseline


title: 009_Week_8

description:
Library name: sample_15
009_Week_8


title: 009_Week_4

description:
Library name: sample_14
009_Week_4


title: 017_Baseline

description:
Library name: sample_34
017_Baseline


title: 017_Week_8

description:
Library name: sample_36
017_Week_8


title: 009_Week_12

description:
Library name: sample_13
009_Week_12


title: 008_Week_12

description:
Library name: sample_9
008_Week_12


title: 008_Week_4

description:
Library name: sample_10
008_Week_4


title: 008_Baseline

description:
Library name: sample_8
008_Baseline


title: 007_Week_8

description:
Library name: sample_7
007_Week_8


title: 007_Week_4

description:
Library name: sample_6
007_Week_4


title: 007_Week_12

description:
Library name: sample_5
007_Week_12


title: 010_Week_12

description:
Library name: sample_3
0010_Week_12


title: 010_Week_4

description:
Library name: sample_2
0000010_Week_4


title: 007_Baseline

description:
Library name: sample_4
007_Baseline


title: 011_Week_8

description:
Library name: sample_20
011_Week_8


title: E39NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_G9---NEBNext_dual_i5_G9.E39NNAR


title: 011_Week_4

description:
Library name: sample_19
011_Week_4


title: 010_Week_8

description:
Library name: sample_16
010_Week_8


title: 010_Baseline

description:
Library name: sample_1
0000010_Baseline


title: Capsid Anchor pGFP Transfected cells (2)

city: hyderabad

first: Musturi

last: Venkataramana

state: telagana

address: Prof.C.R. Rao Road

department: department of biotechnology

country: India

institute: University of hyderabad

description:
Library name: Sample 4
HEK293 cells transfected with capsid-anchor-pEGFP, replicate 2

data_processing:
Quality Control & Trimming:
Tool: Trimmomatic
Parameters considered for filtration are as follows:  SLIDINGWINDOW: Sliding window trimming of 10 bp, cutting once the average quality within the window falls below a threshold of 25. LEADING: Cut bases off the start of a read, if below a threshold quality of 25. TRAILING: Cut bases off the end of a read, if below a threshold quality of 25.
Assembly: Homo sapiens GRCh (hg 19)
Supplementary files format and content: Processed data includes normalized gene expression counts, differential expression matrices (fold-change and p-values). Output formats: Excel spreadsheets (.xlsx) containing quantified expression data and statistical comparisons.

source_name: HEK Cells

growth_protocol: HEK293 were cultured in Dulbecco’s Modified Eagle Medium (DMEM). were incubated at 37°C in a humidified atmosphere containing 5% CO₂. Antibiotic-Antimycotics (Anti-Anti) from Gibco(cat# 15240062) were used at 1% concentration.

extract_protocol:
Total RNA was extracted from the received human cells samples using TRIzol method followed by column purification using Quick RNA Mini Plus kit (Zymo Research) as per manufacturer’s instruction. Quality and quantity of the extracted RNA samples were checked on NanoDrop followed by Agilent Tape station using High Sensitivity RNA ScreenTape.
The sequenced raw data of 4 samples were processed to obtain high quality clean reads using Trimmomatic v0.39 to remove adapter sequences, ambiguous reads (reads with unknown nucleotides “N” larger than 5%), and low-quality sequences (reads with more than 10% quality threshold (QV) < 25 phred score). A minimum length of 100 nt (nucleotide) after trimming was applied. After removing the adapter and low-quality sequences from the raw data, high quality reads were obtained. These high quality (QV>25), paired-end reads were used for reference based read mapping.

treatment_protocol: HEK293 cells were transfected with pEGFP-N1 vector and plasmids encoding capsid-anchor (c-anc)  using Lipofectamine 3000 (Invitrogen). Briefly, recombinant plasmid DNA and transfection reagent were mixed in a 1:2 ratio in serum-free DMEM, incubated for 15 minutes at room temperature (RT) and then added dropwise onto the cells. After 5 hours, the transfection medium was replaced with complete DMEM. Analyses were carried out 48 hours post-transfections.

value: HEK Cells

value: c-anc transfected

value: pEGFP-C-Anchor transfected


title: pEGFPNI Vector transfected HEK Cells (2)

description:
Library name: Sample 3
HEK293 cells transfected with pEGFPNI vector, replicate 2

value: pEGFPN1 vector transfected


title: Capsid Anchor pGFP Transfected cells (1)

description:
Library name: Sample 2
HEK293 cells transfected with capsid-anchor-pEGFP, replicate 1

value: vector control


title: E36NNAR

description: Library name: NS.1888.001.NEBNext_dual_i7_D9---NEBNext_dual_i5_D9.E36NNAR


title: ChIP-seq: anti-GFP in GFP tagged YY1 stable transfection Rep 2

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: Library name: ChIP_CL0004_YY1_Rep2_E005846

data_processing:
ChIP-seq alignment, quality control, and peak calling was performed using a version of the ChIP-Seq Transcription Factor Pipeline v2.2.0 from the ENCODE Project slightly modified to run within a Nextflow environment.
ChIP-seq reads were aligned to the human genome (hg38) using Bowtie2. Aligned reads were then sorted using samtools and duplicate reads were removed using Picard.
Peaks were called using the default parameters of MACS2.
Conservative overlap peaks, generated from the ENCODE pipeline, were obtained for each transfection plasmid and used for downstream analyses.
Assembly: hg38
Supplementary files format and content: Conservative overlap peaks in narrowPeak format.
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10

growth_protocol: To generate Flp-In-293 cells expressing GFP-tagged YY1, 100,000 cells were plated per well in a 48 well plate DMEM supplemented with 10% FBS and 0.1% Anti-anti.  24 hours later, media was removed and replaced with 200mL pre-warmed Opti-MEM per well.  For each well, a total of 500ng DNA plasmids (450 ng pOG44and 50 ng pcDNA5_FRT_TO_GFP_YY1) were incubated with 2 mL TransIT-2020 in 100 mL Opti-MEM for 10 minutes before being added drop-wise.  Plates were centrifuged at 500 g for 15 minutes and incubated at 37C/5% CO2 for 4 hours.  Transfection reagent was replaced with pre-warmed complete media and cells were incubated for another 18 hours.  Complete media was again replaced.  Two days post-transfection the media was changed to media containing hygromycin at 50 mg/mL and the hygromycin was gradually increased over time to 200 mg/mL to produce a pool of cells stably expressing GFP-tagged YY1.

extract_protocol:
Cells were crosslinked and nuclei were sonicated as described previously (Lu et al. 2015).
Libraries were prepared via ChIPmentation (Schmidl et al. 2015).

tag: antibody

value: Abcam ab290

tag: antibody lot_number


title: pEGFPNI Vector transfected HEK Cells (1)

description:
Library name: Sample1
HEK293 cells transfected with pEGFPNI vector, replicate 1


title: E34NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_154---NEBNext_dual_i5_154.E34NAR


title: E33NAR

description: Library name: NS.1890.001.NEBNext_dual_i7_153---NEBNext_dual_i5_153.E33NAR


title: ChIP-seq: anti-EBNA2 in Ramos B cells Rep 2

description: Library name: ChIP_EBNA2_Ramos_Rep2_E002334

source_name: Ramos B cells

growth_protocol: Cells were cultured in 10% FBS supplemented RPMI medium 1640 for 2 weeks.

treatment_protocol: Ramos cells were infected with EBV with EBNA+ strain (B95.8).

value: Ramos B cells

tag: chip target

value: Abcam ab90543


title: ChIP-seq: anti-GFP in GFP tagged YY1 stable transfection Rep 1

description: Library name: ChIP_CL0004_YY1_Rep1_E005783


title: ChIP-seq: anti-EBNA2 in Ramos B cells Rep 1

description: Library name: ChIP_EBNA2_Ramos_Rep1_E002333


title: MKN-45, NNMT knockdown 3

city: Nanning

first: Lingzhang

last: Meng

state: Guangxi

address: Qingxiu District

institute: Guangxi Academy of Medical Sciences

description:
Library name: Sample MKN-45_6
MKN-45 gastric cancer cells were transfected with control or NNMT-targeting shRNA. Total RNA was extracted using TRIzol reagent, RNA integrity was confirmed (RIN > 8.0), libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit, and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor sequences, low-quality bases, and reads with excessive ambiguous nucleotides. Clean reads were aligned to the human reference genome using a splice-aware aligner. Gene-level read counts were generated based on annotated gene models. Expression levels were normalized and used for downstream differential expression analysis.
Assembly: Human reference genome GRCh38 (hg38), with corresponding gene annotation from GENCODE.
Supplementary files format and content: Raw data: FASTQ files containing paired-end sequencing reads  Processed data:  Gene-level read count matrix (tab-delimited text file), with rows representing genes and columns representing samples  Normalized expression values (e.g., TPM or FPKM) for each gene  Metadata: Sample annotation table describing experimental conditions, biological replicates, and sequencing information
Supplementary files format and content: File name: gene_counts.txt.Format: Tab-delimited text file. Content: The file contains an expression matrix of raw read counts. The first column contains [Gene Symbols / Ensembl IDs]. Subsequent columns represent the 6 samples: 3 Control replicates and 3 NNMT Knockout replicates.

growth_protocol: MKN-45 human gastric adenocarcinoma cells (Delf-10168, Hefei Wanwu Biotechnology Co., LTD, China) were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37 °C in a humidified incubator containing 5% CO₂. Cells were routinely passaged every 2–3 days and maintained in logarithmic growth phase. For RNA sequencing experiments, cells were seeded at appropriate density and cultured for 24 h prior to experimental treatments.

extract_protocol:
Total RNA was extracted using TRIzol reagent (15596018CN, Invitrogen, USA) following the manufacturer’s protocol. Briefly, cells were lysed directly in culture dishes, chloroform was added for phase separation, and RNA was precipitated with isopropanol. The RNA pellet was washed with 75% ethanol and resuspended in RNase-free water. RNA concentration and purity were assessed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was evaluated by agarose gel electrophoresis or Agilent Bioanalyzer.
RNA-seq libraries were prepared using a standard Illumina stranded mRNA library preparation protocol. Briefly, poly(A)+ RNA was enriched from total RNA using oligo(dT) magnetic beads, followed by fragmentation, first-strand and second-strand cDNA synthesis. After end repair, A-tailing, and adapter ligation, libraries were amplified by PCR and purified. Library quality and size distribution were assessed using an Agilent Bioanalyzer, and libraries were quantified prior to sequencing.

treatment_protocol: Cells were transfected with NNMT-targeting small interfering RNA (siNNMT) or non-targeting negative control siRNA using Lipofectamine RNAiMAX according to the manufacturer’s instructions. Briefly, siRNAs were diluted in Opti-MEM medium and incubated with transfection reagent before being added to cells. Cells were harvested 48 h after transfection for RNA extraction. Three independent biological replicates were prepared for each condition.

value: gastric adenocarcinoma cell

value: NNMT knockdown

value: shRNA-mediated NNMT knockdown


title: MKN-45, NNMT knockdown 2

description:
Library name: Sample MKN-45_5
MKN-45 gastric cancer cells were transfected with control or NNMT-targeting shRNA. Total RNA was extracted using TRIzol reagent, RNA integrity was confirmed (RIN > 8.0), libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit, and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.


title: 009_Baseline

description:
Library name: sample_12
009_Baseline

tag: time point


title: MKN-45, Control, 3

description:
Library name: Sample MKN-45_3
MKN-45 gastric cancer cells were transfected with control or NNMT-targeting shRNA. Total RNA was extracted using TRIzol reagent, RNA integrity was confirmed (RIN > 8.0), libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit, and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

value: shRNA negative control

value: control shRNA transfection


title: MKN-45, NNMT knockdown 1

description:
Library name: Sample MKN-45_4
MKN-45 gastric cancer cells were transfected with control or NNMT-targeting shRNA. Total RNA was extracted using TRIzol reagent, RNA integrity was confirmed (RIN > 8.0), libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit, and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.


title: MKN-45, Control, 2

description:
Library name: Sample MKN-45_2
MKN-45 gastric cancer cells were transfected with control or NNMT-targeting shRNA. Total RNA was extracted using TRIzol reagent, RNA integrity was confirmed (RIN > 8.0), libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit, and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.


title: 008_Week_8

description:
Library name: sample_11
008_Week_8

tag: tissue


title: MKN-45, Control, 1

description:
Library name: Sample MKN-45_1
MKN-45 gastric cancer cells were transfected with control or NNMT-targeting shRNA. Total RNA was extracted using TRIzol reagent, RNA integrity was confirmed (RIN > 8.0), libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit, and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.


title: CCA PDM217, shCLDN1, rep2

description: Library name: PDM217_sh2

data_processing:
Base calling was performed by CASAVA and raw data was stored in FASTQ format.
Raw reads were filtered to remove reads with (I) adapter contamination, (II) more than 10 % uncertain nucleotides (Ns), and (III) with more than 50 % of low quality nucleotides (base quality less than 5).
Reads were mapped using HISAT2 v2.2.1 to the human genome GRCh38.
FeatureCounts v2.0.6 was used to generate gene counts.
Assembly: GRCh38
Supplementary files format and content: Tabulator separated matrix table with raw gene counts for every gene and every sample

source_name: Patient-derived organoids from cholangiocarcinoma tumors

growth_protocol: Organoids were re-suspended in 50 µl Cultrex Basement Membrane Extract (BME) Type 2 (#3532-005-02, R&D), seeded as domes onto 24 well plates and covered with organoid medium.

extract_protocol:
Organoids were harvested for RNA extraction using PicoPure™ RNA Isolation Kit (#KIT0204, Applied Biosystems™) according to the manufacturer’s instructions
RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis

treatment_protocol: CCA organoids HCM-CSHL-0433-C24 (ATCC, PDM-217) were transduced using shRNA lentivirus targeting CLDN1 or its corresponding control as follows. Organoids were disrupted as single cells and resuspended in 1 ml of lentivirus with 8 µg/ml polybrene (Santa Cruz #sc-134220) and 10 µM of Y-27632 (Tocris Bioscience #1254) for 4 h at 37 °C with resuspension every hour. Organoids were then plated in 48 well plate well as previously described with 10 µM of Y-27632 in the medium. GFP expression was used to follow the transduction efficacy, and organoids were selected using 1.5 µg/mL puromycin (InvivoGen #ant-pr-1).

value: CLDN1 knockdown


title: CCA PDM217, shCLDN1, rep1

description: Library name: PDM217_sh1

value: Patient-derived organoids from cholangiocarcinoma tumors


title: CCA PDM217, shCLDN1, rep3

description: Library name: PDM217_sh3


title: CCA PDM217, control, rep3

description: Library name: PDM217_CTL3

value: Control


title: CCA PDM217, control, rep2

description: Library name: PDM217_CTL2


title: CCA PDM217, control, rep1

description: Library name: PDM217_CTL1


title: CDX, HuCC-A1 CLDN1 KO, rep5

description: Library name: CDX_A1_KO215

source_name: Cell line-Derived Xenograft

extract_protocol:
RNA was extracted using Triazol
RNA-Seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA)

treatment_protocol: Mice were engrafted with HuCC-A1 CLDN1 KO cells or CTRL cells

value: Cell line-Derived Xenograft

value: HuCC-A1 CLDN1 KO


title: CDX, HuCC-A1 CLDN1 KO, rep6

description: Library name: CDX_A1_KO220