title: oeSir3_mRNA_Fig6_starvation_replicate

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
72h incubation, starvation after growth in galactose,


title: Sir3_wt2_mRNA_Fig6_30min_after_release_replicate

status: Public on Oct 20 2025

type: SRA

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
30min after release from starvation,

library_source: transcriptomic

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
reads were mapped to the yeast S288C and the S.pombe genomes using BLAT
The read density distribution was determined for each species in each dataset separately. The average S.pombe genomic read density per bp (F and R reads were processed together) was determined for each dataset. For spike-in normalization, S.cerevisiae read densities per bp were then divided with the corresponding S.pombe average genomic read density.
Normalized read densities for each gene were aligned by the transcription start site and divided into sense and antisense transcripts. The median read density for each gene (from the tss to the end of the coding sequence) was then determined for each transcript. Intron regions were excluded from the calculation. Median read densities for each gene in each replicate of each time point were finally divided by the genome average mRNA S.cerevisiae/S.pombe count ratio for the whole time course of the corresponding replicate, to allow for direct comparisons between replicates and strains.
Assembly: Saccer1 and Schizosaccharomyces pombe (assembly ASM294v2)
Supplementary files format and content: tab-delimited text files of  normalized median read densities for each gene in indicated strains and time points.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD or YPGal (for Sir3 over expression  (oeSir3) cells) for 72hrs at 30°C till saturation and growth arrest.  Cells were then released into fresh media and aliquots were flash frozen in liquid N2 in a timecourse for several cell generations. S.pombe  cells  (strain FY2319, courtesy of S. Forsburg) were grown in YES.

extract_protocol:
Cells were resuspended in Trizol, cell walls were broken with bead beating and total RNA was extracted and DNAseI treated. Extracted total RNA amounts were measured with  the Qubit fluorimeter and the Nanodrop spectrophotometer and the quality was checked by a Bioanalyzer scan (Agilent). Each S.cerevisiae total RNA extract was mixed with the S.pombe total RNA extract at a mass ratio of 10:1.
total RNA was used to make stranded Illumina RNA_seq libraries with the Illumina  TruSeq Stranded mRNA kit or the Illumina Stranded mRNA Prep Ligation kit .

treatment_protocol: Cells were flash frozen in liquid N2

tag: cell cycle

value: exit from growth arrest after nutrient depletion

tag: cell type

value: yeast


title: oeSir3_mRNA_Fig6_midlog_replicate

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
log phase before arrest in starvation,

value: exit from starvation after galactose depletion and release into galactose


title: HAN-SCM-M5-EM-B06

city: Sdyney

first: Yanran

last: Zhao

address: Sydney NSW 2033

country: Australia

institute: UNSW

library_source: transcriptomic single cell

data_processing:
Illumina NextSeq500 was used
Sequenced paired-end reads were trimmed using Trimmomatic (v0.39) (using parameters:  LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 4:10, MINLEN = 50), then aligned to the human reference genome (GRCh38) using STAR (v2.7.3a). Gene expression was then quantified at the counts and TPM level with RSEM (v1.3.1)
Assembly: GRCh38
Supplementary files format and content: .mtx.gz files contain matrices including raw counts, TPM and scaled TPM values for each sample and each gene.
Supplementary files format and content: .txt and and .tsv files contain tab delimited information on sample names and gene names (as per ordering in matrices), and gene annotation information.

molecule: total RNA

organism: Homo sapiens

source_name: CD8 T

extract_protocol:
Single CMV-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject

value: HAN

tag: gen1 phenotype

value: SCM

tag: gen2 phenotype

value: EM

tag: clone

tag: epitope

value: NLV

value: CD8 T


title: HAN-SCM-M5-EFF-F10

value: EFF


title: HAN-SCM-M5-EM-B07


title: HAN-SCM-M5-EFF-D11


title: HAN-SCM-M5-EFF-H10


title: Sir3_wt2_mRNA_Fig6_5min_after_release_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
5min after release from starvation,


title: Sir3_wt2_mRNA_Fig6_starvation_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
72h incubation, starvation after growth in glucose,


title: HAN-SCM-M5-EFF-E10


title: Sir3_wt1_mRNA_Fig6_90min_after_release_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
1h30min after release from starvation,


title: Sir3_wt2_mRNA_Fig6_midlog_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
log phase before arrest in starvation,


title: HAN-SCM-M5-EFF-B10


title: HAN-SCM-M5-CCR7-E11


title: Sir3_wt1_mRNA_Fig6_midlog_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
log phase before arrest in starvation,


title: Sir4D_mRNA_Fig6_2_doublings_after_release

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
second doubling after release from starvation,


title: Sir3_wt1_mRNA_Fig6_1_doubling_after_release_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
first doubling after release from starvation,


title: HAN-SCM-M5-EFF-D10


title: HAN-SCM-M5-CCR7-B03

value: CM


title: Sir4D_mRNA_Fig6_90min_after_release

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
1h30min after release from starvation,


title: HAN-SCM-M5-EFF-C11


title: HAN-SCM-M5-EFF-C10


title: Sir4D_mRNA_Fig6_30min_after_release

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
30min after release from starvation,


title: Sir3_wt1_mRNA_Fig6_30min_after_release_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
30min after release from starvation,


title: Sir4D_mRNA_Fig6_5min_after_release

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
5min after release from starvation,


title: HAN-SCM-M5-CCR7-A05


title: Sir4D_mRNA_Fig6_starvation

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
72h incubation, starvation after growth in glucose,


title: HAN-SCM-M5-EFF-B11


title: Sir3_wt1_mRNA_Fig6_5min_after_release_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
5min after release from starvation,


title: oeSir3_mRNA_Fig6_2_doublings_after_release

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
second doubling after release from starvation,


title: HAN-SCM-M5-CCR7-B05


title: HAN-SCM-M5-EFF-G10


title: oeSir3_mRNA_Fig6_90min_after_release

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
1h30min after release from starvation,


title: oeSir3_mRNA_Fig6_5min_after_release

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
5min after release from starvation,


title: HAN-SCM-M5-CCR7-B04


title: oeSir3_mRNA_Fig6_30min_after_release

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
30min after release from starvation,


title: Sir4D_mRNA_Fig6_1_doubling_after_release

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
first doubling after release from starvation,


title: HAN-SCM-L5-SCM-E02


title: HAN-SCM-L5-SCM-C05


title: oeSir3_mRNA_Fig6_midlog

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
log phase before arrest in starvation,


title: oeSir3_mRNA_Fig6_starvation

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
72h incubation, starvation after growth in galactose,


title: Sir4D_mRNA_Fig6_midlog

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
log phase before arrest in starvation,


title: S_1

city: Yangling

first: ya

middle: long

last: an

address: Xinong No.22

country: China

institute: Northwest Agriculture & Forestry University

description: Small interference of NUDT3

data_processing:
Sequence reads were trim-glore for adaptor / low-quality sequence
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited txt files includes raw counts values for each Sample
Supplementary files format and content: tab-delimited txt files includes TPM counts values for each Sample

organism: Sus scrofa

source_name: Porcine subcutaneous adipocytes

extract_protocol:
RNA was harvested using
Library type: DNBSEQ Eukaryotic Strand-specific mRNA library; Sequencing Platform: DNBseq; Sequencing read Length: PE150; Clean fastq phred quality score encoding:Phred+33.

value: Porcine subcutaneous adipocytes

tag: treatment

value: Small interference


title: HAN-SCM-M5-CCR7-B02


title: oeSir3_mRNA_Fig6_1_doubling_after_release

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
first doubling after release from starvation,


title: HAN-SCM-L5-SCM-C03


title: HAN-SCM-L5-SCM-C02


title: HAN-SCM-M5-CCR7-A03


title: HAN-SCM-M5-CCR7-A04


title: Sir3_wt1_mRNA_Fig6_starvation_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
72h incubation, starvation after growth in glucose,


title: HAN-SCM-L5-SCM-G05


title: HAN-SCM-M5-CCR7-A02


title: HAN-SCM-L5-SCM-B04


title: Sir3_wt1_mRNA_Fig6_2_doublings_after_release_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
second doubling after release from starvation,


title: HAN-SCM-L5-SCM-B03


title: HAN-SCM-L5-SCM-E03


title: HAN-SCM-L5-SCM-D12


title: HAN-SCM-L5-EM-H07


title: N_3

description: Ctrol of small interference

value: Ctrol


title: S_3

description: Small interference of NUDT3


title: HAN-SCM-L5-SCM-G04


title: HAN-SCM-L5-SCM-C01


title: PN_3_2

description: Ctrol of Overexpression


title: HAN-SCM-L5-EM-H06


title: PC_3

description: Overexpression of NUDT3

value: Overexpression


title: PN_3_1

description: Ctrol of Overexpression


title: PC_2

description: Overexpression of NUDT3


title: HAN-SCM-L5-EM-H10


title: HAN-SCM-L5-EM-F07


title: BAHD1_WT_H3K4me3

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

country: USA

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

library_source: genomic

data_processing:
All reads were mapped to mouse genome (mm10) using the Bowtie2 alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with default parameters (macs2 callpeak -f BAMPE --keep-dup 1)
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

growth_protocol: The E14 mouse embryonic stem (mES) cells were grown in the DMEM base medium supplemented with 15% of FBS, 1% of antibiotics, 0.1mM of β-mercaptoethanol, 0.1mM of non-essential amino acids, and 1,000 units/ml of leukemia inhibitory factor (LIF).

extract_protocol:
Cells were trypsinized with 0.05% trypsin and pellets were collected for Cut&Run
The Cut&Run DNA library was prepared following the instructions of NEB’s ChIP-seq prep product manual (E7645). ChIP-seq libraries were sequenced on Illuminia Genome Analyzer for sequencing.
Cut&Run

treatment_protocol: Cells were grown in regular medium and collected.

tag: antibody used

value: rabbit anti-H3K4me3 (active motif #39159)


title: BAHD1_WT_GFP-BADH1

value: rabbit anti-GFP (abcam ab290)


title: HAN-SCM-L5-EM-E10


title: N_1

description: Ctrol of small interference


title: HAN-SCM-L5-EM-G07


title: TF-1a cells, Carfilzomib + Lys05, rep 3

city: La Jolla

first: Robert

last: Signer

state: CA

address: 2880 Torrey Pines Scenic Drive

institute: University of California, San Diego

data_processing:
Quality control was performed using FastQC and sequence reads were trimmed using TrimGalore on Galaxy.
Trimmed sequences were mapped to GRCh38 using HiSAT2 on Galaxy.
Gene counts wee obtained using featureCoutns. Normalization and differentially expressed genes were obtained using DESeq2 (v1.40.2).
Assembly: GRCh38.106.gtf
Supplementary files format and content: Excel file includes normalized counts obtained from DESeq2 for each sample.

extract_protocol:
RNA was hervested using RNAeasy Plus Mini (Qiagen)
RNA libraries were prepared using the SMARTseq2 protocol and sequenced in two lanes

tag: cell line

tag: genotype

value: WT

value: Carflzomib + Lys05


title: TF-1a cells, Control, rep 3

value: Control


title: TF-1a cells, Carfilzomib, rep 3

value: Carfilzomib


title: TF-1a cells, Lys05, rep 3


title: BAHD1_WT_H3K27me3

value: rabbit anti-H3K27me3 (CST #9733)


title: HAN-SCM-L5-EM-G06

value: HAN

value: SCM


title: HAN-SCM-L5-EM-A10

value: EM

value: NLV


title: BAHD1_WT_IgG

value: normal rabbit IgG (CST #2729)


title: HAN-SCM-L5-EM-F10

value: CD8 T


title: HAN-SCM-L5-EM-B10


title: HAN-SCM-L5-EM-E07


title: HAN-SCM-L5-SCM-A03


title: HAN-SCM-L5-EM-A06


title: TF-1a cells, Lys05, rep 2


title: HAN-SCM-L5-EFF-F12

value: EFF


title: HAN-SCM-L5-EFF-G12


title: TF-1a cells, Carfilzomib + Lys05, rep 1


title: HAN-SCM-L5-EFF-H12


title: TF-1a cells, Control, rep 2


title: TF-1a cells, Carfilzomib, rep 2


title: HAN-SCM-L5-EFF-E12


title: TF-1a cells, Control, rep 1


title: HAN-SCM-L5-EFF-D11


title: TF-1a cells, Carfilzomib, rep 1


title: HSF1-/- TF-1a cells, Carfilzomib rep 3

value: HSF1 knockout


title: HAN-SCM-L5-EFF-E06


title: HAN-SCM-L5-EFF-F11


title: HAN-SCM-L5-EFF-C08


title: HAN-SCM-L5-EFF-B12


title: HSF1-/- TF-1a cells, Carfilzomib rep 2


title: TF-1a cells, Carfilzomib + Lys05, rep 2


title: HSF1-/- TF-1a cells, Control rep 3


title: HSF1-/- TF-1a cells, Control rep 2


title: HAN-SCM-L5-EFF-B06


title: HAN-SCM-L5-EFF-C06


title: HSF1-/- TF-1a cells, Carfilzomib rep 1


title: HAN-SCM-L5-EFF-A09


title: HAN-SCM-L5-CM-G02

value: CM


title: HSF1+/+ TF-1a cells, Carfilzomib rep 3


title: HSF1+/+ TF-1a cells, Carfilzomib rep 2


title: HSF1-/- TF-1a cells, Control rep 1


title: HAN-SCM-L5-CM-F04


title: HSF1+/+ TF-1a cells, Carfilzomib rep 1


title: TF-1a cells, Lys05, rep 1


title: HAN-SCM-L5-CM-F02


title: HAN-SCM-L5-CM-D04


title: HAN-SCM-L5-CM-F01


title: OCI-AML3 cells, Lys05, rep 3


title: OCI-AML3 cells, Carfilzomib, rep 3


title: HAN-SCM-L5-CM-B05


title: HAN-SCM-L5-CM-D03


title: OCI-AML3 cells, Control, rep 3


title: HSF1+/+ TF-1a cells, Control rep 3


title: HAN-SCM-L5-CM-A04


title: HAN-SCM-L5-CM-A05


title: HAN-SCM-L5-CM-E01


title: HAN-SCM-L5-CM-A02


title: HSF1+/+ TF-1a cells, Control rep 2


title: OCI-AML3 cells, Carfilzomib, rep 2


title: HSF1+/+ TF-1a cells, Control rep 1


title: HAN-SCM-L5-CM-D02


title: OCI-AML3 cells, Carfilzomib + Lys05, rep 2


title: HAN-SCM-H5-SCM-E05


title: HAN-SCM-H5-SCM-G04


title: OCI-AML3 cells, Control, rep 2


title: HAN-SCM-H5-SCM-F03


title: OCI-AML3 cells, Carfilzomib + Lys05, rep 1


title: OCI-AML3 cells, Carfilzomib + Lys05, rep 3


title: HAN-SCM-L5-CM-E05


title: HAN-SCM-H5-SCM-C03


title: OCI-AML3 cells, Control, rep 1


title: HAN-SCM-H5-SCM-A06


title: OCI-AML3 cells, Carfilzomib, rep 1


title: HAN-SCM-H5-SCM-B06


title: ex vivoT helper 1  donor 3

city: Braunschweig

first: Jochen

last: Huhn

address: Inhoffenstraße 7

country: Germany

institute: HZI - Helmholtz-Zentrum für Infektionsforschung GmbH

data_processing:
library quality assessment using FastQC
Adaptor trimming using cutAdapt, alignment vs. reference genome using STAR with --seedSearchStartLmax 30 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 30
read count quantification using salmon for transcript level and  tximport for gene level.
Detection of differentially expressed genes using DESeq2 using raw count data and default parameters. Cook's distance cutoff filter disabled
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: Matrix table of regularized log normalized counts generated using DESeq2

source_name: peripheral blood from healthy donor

extract_protocol:
Total RNA was isolated from FACS sorted cells using the RNeasy Allprep DNA/RNA Micro Kit (Qiagen)
cDNA was synthesized and amplified using the template switching technology of the SMART‑Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories), followed by purification using the Agencourt AMPure XP Kit (Beckman Coulter). Library preparation was performed with Nextera XT DNA Library Prep Kit (Illumina).

treatment_protocol: Human primary naïve T cells and T helper cells (Th1 and Th17) were ex vivoisolated from LRS filter chambers within 4h after the donation by healthy individuals. Total CD4+T cells were purified with the RosetteSepTM human CD4+T cell enrichment kit (Stemcell Technologies). CD4+ CD45RA+ and CD4+ CD45RA- cells were further separated by using anti-CD45RA MicroBeads and the autoMACS magnetic separation system (Miltenyi Biotec). Both populations were stimulated with PMA (10ng/mL) and ionomycin (0.5μg/mL) for 2h, followed by the combined cytokine secretion assay (Miltenyi Biotec) according to manufacturer’s protocol. After the cytokine secretion assay, both populations were labeled with fluorescence-conjugated antibodies against CD3, CD4, CD45RA, CD127 and CD25 and were sorted by using a FACS Aria-II SORP or FACS Aria-IIu (BD Biosciences). Viable naïve T cells (CD4+CD45RA+CD3+CD127highCD25-IFNγ-IL17α-) were sorted from the CD4+CD45RA+population, viable Th1 cells (CD4+CD45RA-CD3+CD127highCD25-IFNγ+IL17α-) and viable Th17 cells (CD4+CD45RA-CD3+CD127highCD25-IFNγ-IL17α+) were sorted from the CD4+CD45RA-population. Regulatory T cells (CD4+CD3+CD127lowCD25+) were excluded from sorted populations.

tag: tissue

value: peripheral blood

tag: individual

value: healthy donor

tag: developmental stage

value: adult


title: ex vivoT helper 17 donor 3


title: ex vivoT naive donor 2

value: Tn


title: HAN-SCM-H5-EM-C09


title: HAN-SCM-H5-EM-C08


title: HAN-SCM-H5-SCM-A04


title: ex vivoT naive donor 3


title: OCI-AML3 cells, Lys05, rep 1

value: WT


title: OCI-AML3 cells, Lys05, rep 2


title: ex vivoT helper 1  donor 1


title: HAN-SCM-H5-EM-D09


title: HAN-SCM-H5-EM-C07


title: HAN-SCM-H5-EM-D08


title: HAN-SCM-H5-EM-B08


title: HAN-SCM-H5-EM-A09


title: HAN-SCM-H5-EM-D07


title: VMB215.counts

city: Oslo

first: Yohan

last: Lefol

state: Oslo

address: Sognsvannsveien 20 Rikshospitalet

department: Institute of Clinical Medicine

country: Norway

institute: University of Oslo

data_processing:
Alignment was done using HISAT245 with the GRCm38 as the reference genome and Ensembl release 8146 for the gene annotation. Resulting SAM files were sorted and converted to BAM files using SAMtools. StringTie48 was used to assemble transcripts and quantify them into counts.
Assembly: GRCm38 – mm10
Supplementary files format and content: Raw counts (tab seperated)

source_name: Ventral Midbrain

extract_protocol:
Total RNA was isolated from different brain regions using the ALLPrep isolation kit (Qiagen). Before extraction, frozen tissues were transferred to a 2 ml lysing tube containing 1.4 mm zirconium oxide beads (Precellys) and 600 μl of RLT buffer (provided by the Kit). Samples were homogenized using FastPrep (20 seconds, 5000 rpm) and centrifuged at full speed for 5 minutes. The supernatant was transferred to an ALLPrep spin column and isolation proceeded according to the manufacturer's protocol. To improve the quality of the RNA, b-mercapto-ethanol was added to the RLT buffer at the recommended concentration and samples were further treated with DNaseI to digest contaminating DNA. RNA quality and concentration were measured using Agilent Bioanalyser (Agilent Technologies) or Nanodrop.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.  The quality control of library consists of three steps: (1) Qubit 2.0: tests the library concentration preliminarily. (2) Agilent 2100: tests the insert size. (3) Q-PCR: quantifies the library effective concentration precisely.

value: Ventral Midbrain


title: ex vivoT helper 17 donor 2


title: ex vivoT helper 1  donor 2


title: VMB219.counts


title: ex vivoT naive donor 1

description: A _Tn


title: HAN-SCM-H5-EM-A07


title: VMB195.counts


title: HAN-SCM-H5-EM-B07


title: HAN-SCM-H5-EM-A08


title: VMB196.counts


title: HAN-SCM-H5-EFF-G12


title: HAN-SCM-H5-EFF-E10


title: STRI215.counts

source_name: Striatum

value: Striatum


title: VMB194.counts


title: STRI196.counts


title: ex vivoT helper 17 donor 1


title: HAN-SCM-H5-EFF-D12


title: HAN-SCM-H5-EFF-F11


title: VMB193.counts


title: HAN-SCM-H5-EFF-C10


title: HAN-SCM-H5-EFF-B11


title: HAN-SCM-H5-EFF-A11


title: HAN-SCM-H5-EFF-A10


title: STRI219.counts


title: R18.counts

source_name: Olfactory Bulb

value: Olfactory Bulb


title: HAN-SCM-H5-EFF-E12

value: HAN


title: HAN-SCM-H5-EFF-E11

value: SCM


title: HAN-SCM-H5-EFF-A02


title: STRI195.counts


title: R17.counts


title: STRI194.counts


title: HAN-SCM-H5-EFF-A03


title: R16.counts


title: HAN-SCM-H5-CM-G03


title: HPC219.counts

source_name: Hippocampus

value: Hippocampus


title: R15.counts


title: HAN-SCM-H5-CM-E06

value: NLV


title: HAN-SCM-H5-CM-H02


title: HAN-SCM-H5-CM-E04


title: R14.counts


title: STRI193.counts


title: HAN-SCM-H5-CM-G05


title: HPC215.counts


title: HAN-SCM-D4-EM-D07

value: EM


title: HPC195.counts


title: HAN-SCM-D4-EM-D06

value: CD8 T


title: HAN-SCM-H5-CM-C02


title: HPC193.counts


title: HAN-SCM-C4-SCM-B10


title: FC196.counts

source_name: Prefrontal Cortex

value: Prefrontal Cortex


title: HAN-SCM-C4-SCM-B03


title: HPC196.counts


title: HAN-SCM-C4-SCM-B04


title: HAN-SCM-C4-SCM-A12


title: FC219.counts


title: FC194.counts


title: R13.counts


title: HAN-SCM-C4-SCM-A10


title: HAN-SCM-C4-SCM-A02


title: FC215.counts


title: HAN-SCM-C4-EM-B09


title: HAN-SCM-C4-EM-A11


title: KMS-12-PE_CTRL_rep2

city: Cambridge

first: Walter

last: Lenoir

state: MA

address: 301 Binney St

institute: Kronos Bio

data_processing:
First, reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming.
Next, preprocessed reads are aligned by STAR aligner. Aligned reads are summarized to gene-level counts by the featureCounts tool.
FastQC reports, alignment statistics, QoRTs QC, RNA-SeQC and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool.
Assembly: hg19
Supplementary files format and content: IRF4KD_TPM.csv is output genes in TPM format

growth_protocol: Cells were grown in RPMI 1640 media with 10% fetal bovine serum (FBS).

extract_protocol:
RNA purification kit from Zymo following their recommended protocol (R2051)
NEBNext Ultra II RNA Library Prep kit was used for library prep.

treatment_protocol: siRNA (Horizon Discovery L-019668-00-0005) mediated knock down of IRF4 followed by RNA-seq analysis was performed using ON-TARGET pooled siRNA reagents (Dharmacon Horizon Discovery). One million cells were transfected using an electroporation protocol (Neon NxT) with parameters: 1600 V, 10 ms, 3 pulses.

value: cancer cell line

value: CTRL

value: DMSO 0 Hour


title: KMS-12-PE_CTRL_rep1


title: HAN-SCM-C4-EM-C04


title: sc-RNAseq-MHC2-poumon-porc

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

description:
Library name: Sample 1
10X genomics

data_processing:
Cell cDNA was sequenced using the Truseq Illumina Stranded protocol and the Illumina NextSeq 500 sequencing machine (> 3x108 reads/sample). The reads were aligned with Cell Ranger v3.0.1 on the pig genome assembly version 11.1 using the Ensembl release 99 of gene annotations. The sequencing results were pre-processed and normalized using Seurat v4.3.0. Cells expressing less than 500 genes were removed. A total of 11029 cells were used to generate an UMAP with clustering (dimensions of reduction used = 11, k.param nearest neighbors = 20, resolution = 0.4).
Assembly: pig genome assembly version 11.1 using the Ensembl release 99 of gene annotations
Supplementary files format and content: filtered_barcodes.tsv.gz, filtered_features.tsv.gz, filtered_matrix.mtx.gz correspond to the output og CellRanger analysis
Supplementary files format and content: Pig_expression_data.txt.gz is the cell x genes expression level matrix after being processed by Seurat pipeline

source_name: Lung

extract_protocol:
The pig was anesthetised with ketamine/xylazine and exsanguinated. The lung was perfused with perfadex and a lung biopsy (about 2 g) was isolated. The lung tissue was finely chopped and incubated at 37°C for 45 minutes under rotation in RPMI 1640 supplemented with 100 IU/ml penicillin,100 g/ml streptomycin, and 10% inactivated fetal calf serum (FCS) (Invitrogen, Paisley, UK), containing 3 mg/ml collagenase D, 0.25 mg/ml Dnase I (Sigma-Aldrich) and 0.7 mg/ml dispase II (Gibco®, ThermoFisher Scientific, St Aubin, France). The cell preparation was subsequently filtered on a nylon mesh (1 mm diameter) followed by successive passages through cell strainers (500 µm, 100 µm, 40 µm). Erythrocytes were eliminated with erythrocytes lysis buffer (10 mM NaHCO3, 155 mM NH4Cl, and 10 mM EDTA). The pig lung cells (2 x 107 cells) were incubated with anti-MHC class II (MSA clone, 2 µg/ml) for 30 min, washed, and reacted for 15 min with 20 µl goat anti-mouse IgG-conjugated immunobeads (Myltenyi, Bergisch-Gladbach, Germany). After filtration on a 40 µm cell strainer, MHC class IIpos cells were enriched with a MS Myltenyi separation column (ref 130-042-201), following the manufacturer recommendations. Cells were counted using a counting chamber and checked for viability using trypan blue, and showed over 90% viability. A cell sample (2 x 104) was loaded onto the 10x Chromium to produce a sequencing library, which was processed according to methods provided by 10x Genomics (v3 Chemistry, 3' end).
The library was generated following the 10x Genomics kit (Chromium Next GEM Single Cell 3' GEM,v3 Chemistry)

treatment_protocol: No treatment was applied to the pig donor.

value: Lung

tag: Sex

value: Male

tag: age

value: 3 months

tag: strain

value: Large White


title: FC193.counts

value: WT


title: KMS-12-PE_CTRL_rep3


title: HPC194.counts


title: HAN-SCM-C4-CM-B07

value: CM


title: FC195.counts


title: HAN-SCM-C4-CM-B05


title: KMS-12-PE_siIRF4_rep3

value: siIRF4 48 hour


title: KMS-12-PE_siIRF4_rep1


title: HAN-EM-O17-EM-B05

value: HAN


title: HAN-EM-O17-EM-B02


title: MM1S_CTRL_rep1


title: HAN-EM-O17-EM-A07


title: HAN-SCM-C4-CM-A06

value: SCM


title: KMS-12-PE_siIRF4_rep2


title: MM1S_siIRF4_rep3


title: HAN-SCM-C4-CM-A04


title: MM1S_CTRL_rep3


title: HAN-SCM-C4-CM-A07


title: MM1S_CTRL_rep2


title: HAN-EM-O17-EM-B03


title: HAN-EM-O17-EM-A08


title: MM1S_siIRF4_rep1


title: HAN-EM-O17-CM-E09


title: HAN-EM-O17-CM-E03


title: HAN-EM-O17-EM-A04


title: HAN-EM-G16-EM-H12


title: KMS-12-BM_CTRL_rep3


title: MM1S_siIRF4_rep2


title: HAN-EM-G16-EM-G08


title: HAN-EM-O17-EFF-B06

value: EFF


title: KMS-12-BM_siIRF4_rep2


title: MM1R_CTRL_rep2


title: MM1R_CTRL_rep3


title: HAN-EM-G16-EM-G05

value: NLV


title: HAN-EM-G16-EM-G10

value: EM


title: KMS-12-BM_siIRF4_rep3


title: HAN-EM-O17-EM-A03

value: CD8 T


title: MM1R_siIRF4_rep1


title: HAN-EM-G16-EM-G07


title: MM1R_siIRF4_rep3


title: KMS-12-BM_CTRL_rep1


title: MM1R_CTRL_rep1


title: MM1R_siIRF4_rep2


title: HAN-EFF-O22-SCM-G08


title: HAN-EM-G16-EM-G03


title: HAN-EFF-O22-SCM-G07


title: HAN-EFF-O22-SCM-G06


title: HAN-EM-G16-EM-G11


title: HAN-EFF-O22-SCM-G05


title: KMS-12-BM_siIRF4_rep1


title: KMS-12-BM_CTRL_rep2


title: HAN-EM-G16-EM-G04


title: HAN-EFF-O22-SCM-F09


title: HAN-EFF-O22-SCM-G04


title: HAN-EFF-O22-SCM-D05


title: HAN-EFF-O22-EM-G05


title: HAN-EFF-O22-SCM-A08


title: HAN-EFF-O22-EM-G04


title: HAN-EFF-O22-EM-G03


title: P, Sigmoid, 257236334425_2_4

type: RNA

hyb_protocol: Amplification and labelling efficiency were controlled on the NanoDrop. The cRNA quality was assessed by measuring the RNA absorbance ratio 260nm/280nm. The specific activity of labeled cRNA (pmol Cy3 per ug cRNA) was defined to be 6 or above according to the Agilent recommendations.

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Microarray data was processed/normalized using limma  version 3.48.1. Controls, outliers, and below background genes were removed, duplicate probes were then merged using the avereps function.

source_name: Sigmoid

label_protocol: mRNA amplification, labelling, and hybridization were done following the manufacturer’s instructions (Agilent One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling). In short, 50 ng RNA was amplified and labelled with Cy3 using the Low Input Quick Amp Labeling Kit, one-color (product number 5190-2331), and the labelled cRNA was purified using the Qiagen RNeasy Mini Kit.

extract_protocol: Total RNA was isolated using AllPrep kit(Qiagen, Hilden, Germany). The tissue biopsies were homogenized in Buffer RLT using a 5 mm steal bead in the FastPrep-24™ Classic Instrument (MP Biomedicals, Irvine, CA, USA) at 6 m/s for 40 sec. The samples were centrifuged and the lysate transferred to new tubes. Further processing was per the manufacture’s protocol. RNA concentration was measured using the QiaCubeNanoDrop ND-1000 spectrophotometer (Qiagen). The RNA quality, indicated by the RNA integrity number (RIN), was assessed with an Agilent 2100 Bioanalyzer, Agilent 2100 Expert software and Agilent RNA 6000 Nano Kit (Agilent Technologies Inc., Santa Clara, CA, USA). RNA samples with RIN number below 7.0 was excluded.

tag: disease state

value: UC

value: P

tag: gender

value: M

tag: salazopyrine

tag: infliximab

tag: adalimumab

tag: vedolizumab

value: Sigmoid


title: P, Rectum, 257236334425_2_1

source_name: Rectum

value: Chronic

value: F

value: Rectum


title: P, Descending, 257236334424_2_2

source_name: Descending

value: Descending


title: HAN-EFF-O22-EM-G02

tag: subject

tag: gen1 phenotype

tag: gen2 phenotype

tag: clone

tag: epitope

tag: cell type


title: P, Ascending, 257236334424_2_4

source_name: Ascending

tag: tissue

value: Ascending


title: P, Ascending, 257236334425_2_2


title: P, Transverse, 257236334425_2_3

source_name: Transverse

value: Transverse


title: P, Sigmoid, 257236334424_2_3


title: P, Descending, 257236334425_1_3


title: P, Rectum, 257236334424_1_4


title: P, Transverse, 257236334425_1_2


title: P, Descending, 257236334424_1_3


title: P, Ascending, 257236334424_2_1


title: P, Sigmoid, 257236334425_1_4


title: P, Ascending, 257236334425_1_1


title: HAN-EFF-O22-SCM-E07


title: HAN-EFF-O22-EM-F05


title: HAN-EFF-O22-SCM-E03


title: P, Transverse, 257236334424_1_2


title: HAN-EFF-O22-EM-F04


title: HAN-EFF-O22-EM-F03


title: HAN-EFF-O22-EM-C03


title: HAN-EFF-O22-EM-F02


title: HAN-EFF-O22-EFF-H12


title: HAN-EFF-O22-EM-A04


title: HAN-EFF-O22-EFF-G12


title: HAN-EFF-O22-EFF-G11


title: P, Rectum, 257236334423_2_4


title: HAN-EFF-O22-EFF-H10


title: HAN-EFF-O22-EFF-F12


title: P, Sigmoid, 257236334423_2_3


title: P, Descending, 257236334423_2_2


title: P, Ascending, 257236334423_2_1


title: HAN-EFF-O22-EFF-E12


title: P, Descending, 257236334423_1_4


title: P, Ascending, 257236334423_1_3


title: HAN-EFF-O22-EFF-D12


title: P, Ascending, 257236327385_2_4


title: HAN-EFF-O22-EFF-H11


title: NP, Rectum, 257236327385_2_3

value: NP


title: HAN-EFF-O22-EFF-D11

value: HAN


title: P, Descending, 257236334423_1_2


title: HAN-EFF-O22-EFF-B12


title: NP, Ascending, 257236327385_2_1


title: NP, Descending, 257236327385_2_2


title: HAN-EFF-O22-EFF-D10


title: HAN-EFF-O22-EFF-B11


title: NP, Rectum, 257236327385_1_4


title: HAN-EFF-O22-EFF-C11


title: NP, Descending, 257236327385_1_3


title: NP, Ascending, 257236327385_1_2


title: P, Transverse, 257236334423_1_1


title: NP, Rectum, 257236327385_1_1


title: HAN-EFF-O22-EFF-A11


title: HAN-EFF-O22-EFF-A10


title: HAN-EFF-O22-CM-F02

value: CM


title: P, Ascending, 257236334424_1_1


title: HAN-EFF-O22-CM-D06

value: EFF


title: HAN-EFF-O22-CM-H05

value: NLV


title: P, Transverse, 257236327384_1_3


title: NP, Ascending, 257236327383_2_1


title: NP, Ascending, 257236327383_1_1


title: HAN-EFF-O22-CM-H03


title: P, Sigmoid, 257236327384_2_2


title: NP, Descending, 257236327383_2_2


title: HAN-EFF-O22-CM-A06


title: HAN-EFF-F22-SCM-H10

value: SCM


title: NP, Descending, 257236327383_1_2


title: NP, Rectum, 257236327383_1_4


title: NP, Rectum, 257236327383_2_3


title: NP, Descending, 257236327379_1_4


title: HAN-EFF-F22-SCM-H03

value: CD8 T


title: HAN-EFF-O22-EFF-A12


title: HAN-EFF-F22-SCM-G11


title: NP, Sigmoid, 257236327378_2_4

value: UC


title: NP, Ascending, 257236327379_1_3


title: HAN-EFF-O22-CM-D03


title: HAN-EFF-F22-SCM-G06


title: NP, Sigmoid, 257236327383_1_3


title: NP, Sigmoid, 257236327379_2_1


title: HAN-EFF-O22-CM-A07


title: NP, Ascending, 257236327379_2_2


title: HAN-EFF-O22-CM-F05


title: HAN-EFF-F22-SCM-F06


title: HAN-EFF-O22-CM-F04


title: HAN-EFF-O22-CM-F03


title: P, Transverse, 257236327378_1_4

value: P


title: NP, Sigmoid, 257236327379_1_1

value: M


title: HAN-EFF-F22-SCM-G08


title: HAN-EFF-F22-SCM-H05


title: HAN-EFF-F22-SCM-H02


title: HAN-EFF-F22-SCM-F04


title: NP, Rectum, 257236327379_1_2


title: NP, Descending, 257236327379_2_3


title: P, Descending, 257236327378_2_3


title: NP, Ascending, 257236327377_2_4


title: HAN-EFF-F22-EM-D06

value: EM


title: HAN-EFF-F22-EM-B10


title: P, Ascending, 257236327378_2_2

value: Chronic


title: HAN-EFF-F22-SCM-G05


title: HAN-EFF-F22-SCM-F05


title: HAN-EFF-F22-EM-B06


title: HAN-EFF-F22-EM-E09


title: HAN-EFF-F22-EM-E05


title: NP, Ascending, 257236327377_2_3


title: NP, Transverse, 257236327373_1_2


title: NP, Descending, 257236327373_2_1


title: NP, Ascending, 257236327373_1_4


title: HAN-EFF-F22-EM-A05


title: HAN-EFF-F22-EM-C06


title: P, Descending, 257236327378_2_1


title: HAN-EFF-F22-EM-B09


title: NP, Rectum, 257236327377_1_1


title: P, Ascending, 257236327378_1_3


title: HAN-EFF-F22-EM-B08


title: HAN-EFF-F22-EFF-D08


title: P, Transverse, 257236327377_1_3


title: P, Descending, 257236327377_2_1


title: HAN-EFF-F22-EFF-D07


title: HAN-EFF-F22-EFF-E02


title: HAN-EFF-F22-EM-A10


title: HAN-EFF-F22-EM-A02


title: P, Rectum, 257236327372_2_4

value: F


title: NP, Descending, 257236327373_2_4


title: NP, Ascending, 257236327373_2_3


title: NP, Rectum, 257236327373_1_3

value: Rectum


title: P, Sigmoid, 257236327372_2_3

value: Sigmoid


title: HAN-EFF-F22-EFF-D04


title: HAN-EFF-F22-EFF-D09


title: HAN-EFF-F22-EFF-C09


title: NP, Ascending, 257236327373_1_1

value: Ascending


title: NP, Rectum, 257236327372_1_2


title: HAN-EFF-F22-EFF-B04


title: NP, Ascending, 257236327371_2_3


title: NP, Descending, 257236327371_2_4

value: Descending


title: HAN-EFF-F22-EFF-C02


title: HAN-EFF-F22-EFF-B02


title: HAN-EFF-F22-EFF-B05


title: P, Ascending, 257236327372_1_3


title: NP, Rectum, 257236327371_2_2

value: NP


title: NP, Ascending, 257236327371_1_4


title: HAN-EFF-F22-EFF-A04

value: HAN


title: HAN-EFF-F22-EFF-C08


title: P, Transverse, 257236327372_2_1

value: Transverse


title: P, Descending, 257236327372_2_2


title: HAN-EFF-F22-CM-H07

value: EFF

value: CM


title: HAN-EFF-F22-CM-H06

value: NLV


title: HAN-EFF-F22-CM-H04

value: CD8 T


title: HAN-EFF-F22-CM-G10


title: NP, Descending, 257236327371_2_1

value: UC


title: NP, Sigmoid, 257236327372_1_1


title: HAN-EFF-F22-CM-G07


title: HAN-EFF-F22-CM-G03


title: HAN-EFF-F22-CM-H12


title: P, Transverse, 257236324324_1_4

value: P


title: HAN-EFF-F22-CM-F11


title: NP, Ascending, 257236327371_1_1

value: M


title: P, Sigmoid, 257236324324_2_2


title: P, Rectum, 257236324324_2_4


title: NP, Sigmoid, 257236324324_1_1


title: NP, Descending, 257236327371_1_2


title: NP, Rectum, 257236327371_1_3


title: HAN-EFF-F22-CM-F08


title: HAN-EFF-F22-CM-F02


title: HAN-CM-E11-EM-F07

value: EM


title: NP, Rectum, 257236324324_1_2


title: NP, Ascending, 257236324323_2_3


title: P, Rectum, 257236324323_2_2


title: NP, Descending, 257236324323_2_4


title: P, Descending, 257236324323_1_4


title: HAN-CM-E11-EM-D08


title: P, Transverse, 257236324323_1_3


title: HAN-CM-E11-EM-D01


title: HAN-CM-E11-EM-G05


title: P, Rectum, 257236324323_1_1


title: HAN-CM-E11-EM-C07


title: HAN-CM-E11-EM-E12


title: P, Rectum, 257236324323_1_2


title: NP, Rectum, 257236324322_2_2


title: HAN-CM-E11-EM-C01


title: HAN-CM-E11-EM-E08


title: NP, Descending, 257236324322_2_4


title: P, Sigmoid, 257236324323_2_1


title: NP, Descending, 257236324322_2_1


title: HAN-CM-E11-CM-B01


title: HAN-CM-E11-CM-D11


title: HAN-CM-E11-CM-H11


title: HAN-EFF-F22-CM-G02


title: HAN-CM-D8-CM-A08


title: HAN-CM-D8-CM-A04


title: HAN-CM-D8-CM-A09


title: HAN-CM-D8-CM-A10


title: HAN-CM-D8-CM-A02


title: NP, Rectum, 257236324322_1_3


title: HAN-CM-C11-CM-E09


title: NP, Sigmoid, 257236324321_1_4


title: NP, Rectum, 257236324321_2_4


title: NP, Ascending, 257236324321_2_2


title: NP, Ascending, 257236324322_1_1


title: NP, Ascending, 257236324322_2_3


title: NP, Ascending, 257236324322_1_4


title: NP, Descending, 257236324321_2_3


title: NP, Ascending, 257236324321_1_3


title: 959-SCM-E13-SCM-F10

value: SCM

value: TPR


title: 959-SCM-E13-SCM-E10


title: NP, Descending, 257236324322_1_2


title: 959-SCM-E13-SCM-E07


title: NP, Rectum, 257236324321_1_2

value: F

value: Rectum


title: 959-SCM-E13-SCM-E02


title: NP, Ascending, 257236324320_2_4

value: Chronic

value: Ascending


title: 959-SCM-E13-SCM-G12


title: HAN-CM-C11-CM-E05


title: NP, Rectum, 257236324321_2_1

value: NP


title: 959-SCM-E13-SCM-B11


title: 959-SCM-E13-SCM-F05


title: 959-SCM-E13-SCM-A06


title: NP, Rectum, 257236324320_1_1


title: NP, Ascending, 257236324320_2_1


title: NP, Descending, 257236324320_2_2

value: Descending


title: 959-SCM-E13-SCM-E03


title: 959-SCM-E13-SCM-C07


title: 959-SCM-E13-SCM-C10


title: NP, Descending, 257236324320_1_3


title: NP, Descending, 257236324321_1_1


title: 959-SCM-E13-SCM-A07


title: 959-SCM-E13-CM-H10


title: NP, Rectum, 257236324320_2_3


title: NP, Ascending, 257236324305_2_3


title: 959-SCM-E13-CM-H05


title: 959-SCM-E13-CM-E09


title: 959-SCM-E13-CM-F11


title: NP, Rectum, 257236324320_1_4


title: NP, Rectum, 257236324305_2_2


title: NP, Ascending, 257236324320_1_2


title: NP, Descending, 257236324305_2_1


title: NP, Descending, 257236324305_2_4


title: NP, Rectum, 257236324305_1_3


title: 959-SCM-E13-CM-F06


title: 959-SCM-E13-CM-D06


title: NP, Descending, 257236324305_1_2


title: 959-SCM-E13-CM-A09


title: NP, Ascending, 257236324305_1_4


title: 959-SCM-E13-CM-D10


title: 959-SCM-D4-SCM-G01


title: rat OFC, 8--17, HEROIN, RFP

city: New York

first: Yasmin

last: Hurd

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
human: TopHat 2.0.8b and Cufflinks 2.1.1; rat: STAR
Assembly: human: GRCh37; rat: mRatBN7.2
Supplementary files format and content: human FPKM (csv); rat raw counts (CSV)

organism: Rattus norvegicus

source_name: orbitofrontal cortex

extract_protocol:
human: Total RNA was extracted using Invitrogen ToTally RNA Kit (Life Technologies); rat: RNA extraction from the isolated tissue was conducted by TRIzol and isopropanol precipitation
human: RNA-seq libraries were prepared from 1 ug of total RNA using Illumina’s TruSeq RNA library preparation kit V2; rat: Using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech), reverse transcription was performed on polyadenylated transcripts, along with second-strand synthesis of full-length cDNA and amplification of the product (Azenta Life Sciences, Chelmsford, MA).

value: orbitofrontal cortex

tag: treatment

value: HEROIN

value: RFP


title: 959-SCM-D4-SCM-G03


title: 959-SCM-E13-CM-C09

value: CM


title: rat OFC, 7--15, SALINE, SHISA7

value: SALINE


title: 959-SCM-E13-CM-C08

value: CD8 T


title: 959-SCM-E13-CM-C11


title: 959-SCM-D4-SCM-F12


title: rat OFC, 6---2, HEROIN, SHISA7


title: rat OFC, 6--14, SALINE, SHISA7


title: 959-SCM-E13-CM-B10


title: 959-SCM-D4-SCM-F09


title: rat OFC, 5--29, SALINE, SHISA7


title: rat OFC, 4--17-2, HEROIN, SHISA7


title: NP, Rectum, 257236323160_2_2

value: UC


title: rat OFC, 3--2, HEROIN, RFP


title: NP, Rectum, 257236323160_1_1

value: M


title: NP, Ascending, 257236324305_1_1


title: NP, Rectum, 257236323161_1_1


title: rat OFC, 9--5, HEROIN, SHISA7


title: NP, Descending, 257236323160_2_4


title: NP, Descending, 257236323161_2_4


title: NP, Ascending, 257236323161_2_3


title: rat OFC, 30--1, HEROIN, RFP


title: 959-SCM-D4-SCM-E08


title: NP, Rectum, 257236323159_2_4


title: NP, Descending, 257236323160_2_1


title: rat OFC, 29--23, HEROIN, RFP


title: rat OFC, 4-2, HEROIN, SHISA7


title: NP, Descending, 257236323159_2_3


title: NP, Ascending, 257236323160_2_3


title: NP, Ascending, 257236323160_1_4


title: 959-SCM-D4-SCM-D11


title: rat OFC, 28--8, HEROIN, RFP


title: P, Transverse, 257236323161_1_3

value: P

value: Transverse


title: rat OFC, 27--13-2, HEROIN, RFP


title: 959-SCM-D4-SCM-F06

value: SCM

value: TPR


title: 959-SCM-D4-SCM-D07


title: rat OFC, 26, HEROIN, RFP


title: rat OFC, 25--19-2, SALINE, RFP


title: rat OFC, 24--12-2, HEROIN, SHISA7


title: mock dark to light for 24h_3

city: Nanjing

first: xingliang

last: Duan

address: weigang 1

institute: Nanjing Agricultural University

data_processing:
Raw data were also cleaned using Fastp v.0.20. Cleaned reads were aligned to the rice reference genome using STAR v.2.7.8a with a splicing-aware method and two-pass mode.
The aligned reads were assembled separately into transcripts for each sample with the reference annotation-based transcript assembly algorithm and generated an updated transcript annotation with a gene transfer format (GTF)-formatted file using StringTie v.2.1.3.
Finally, the expression level of genes was quantified and normalized with the above-updated GTF file using HTSeq, respectively.
Only the genes with a fragments per kilobase of transcript per million fragments mapped >1 in at least six samples were used for downstream gene expression analysis.
Assembly: Col-PEK
Supplementary files format and content: "FPKM.xls" contains the FPKM of each gene
Supplementary files format and content: "Readcount.xls" contains the readcount of each gene

organism: Arabidopsis thaliana

source_name: hypocotyl

extract_protocol:
Total RNA was extracted using TRIzol reagent and digested with RNase-free DNase (Qiagen) according to the manufacturer’s instructions.
Purification of poly-A messenger RNA and construction of complementary DNA were accomplished with a TruSeq RNA Library Preparation Kit (Illumina).

value: hypocotyl

tag: cell line

value: hypocotyl cells


title: 959-SCM-D4-SCM-C08


title: 959-SCM-D4-SCM-B11


title: 959-SCM-D4-SCM-A07


title: rat OFC, 26--3-2, HEROIN, SHISA7


title: mock dark to light for 24h_2


title: NP, Ascending, 257236323159_1_3

value: Ascending


title: NP, Ascending, 257236323159_2_2

value: NP


title: NP, Rectum, 257236323159_2_1

value: Rectum


title: rat OFC, 2--28, SALINE, SHISA7

value: orbitofrontal cortex


title: rat OFC, 22, HEROIN, SHISA7

value: HEROIN


title: NP, Rectum, 257236323159_1_2


title: rat OFC, 23--1-2, HEROIN, RFP

value: RFP


title: rat OFC, 22--9-2, SALINE, RFP


title: rat OFC, 21, HEROIN, RFP


title: mock dark to light for 24h_1


title: NP, Descending, 257236323159_1_4

value: Descending


title: 959-SCM-D4-CM-H04

value: CM


title: rat OFC, 20--18-2, SALINE, RFP

value: SALINE


title: mock dark to light for 12h_3


title: 959-SCM-D4-CM-H02

value: CD8 T


title: rat OFC, 20, HEROIN, SHISA7


title: rat OFC, 19--4, SALINE, SHISA7


title: rat OFC, 18--15-2, SALINE, RFP


title: mock dark to light for 12h_2


title: mock dark to light for 12h_1


title: rat OFC, 17--21-2, HEROIN, SHISA7


title: rat OFC, 16, HEROIN, SHISA7


title: 959-SCM-D4-CM-F01


title: rat OFC, 16--11-2, HEROIN, RFP


title: mock treatment at 0h_3


title: 959-SCM-D4-SCM-A06


title: rat OFC, 15--13, SALINE, SHISA7


title: 959-SCM-D4-CM-E09


title: rat OFC, 14--7-2, SALINE, RFP


title: rat OFC, 14---2, HEROIN, SHISA7


title: rat OFC, 13--9, HEROIN, RFP


title: mock treatment at 0h_1


title: rat OFC, 12--24, HEROIN, SHISA7


title: 959-SCM-D4-CM-C10


title: rat OFC, 1--30, SALINE, SHISA7


title: 959-SCM-D4-CM-C01


title: dark to light for 24h_3

value: dark to light for 24h


title: 959-SCM-D4-CM-G10


title: dark to light for 24h_2


title: 959-SCM-D4-CM-B05


title: dark to light for 24h_1


title: Endometrium, cp-transplanted, rep1

city: Sungnam

first: Danbi

last: Lee

address: sampyeongro 335, Seongnam-Si, Kyounggido, Republic of Korea

department: Department of biological sciences

country: South Korea

institute: CHA university

description: Library name: ASCP1

data_processing:
Illumina NextSeq500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: using Exdega program

source_name: Endometrium

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1000 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: AS induction (AS), EEP transplantation following AS induction (EEP), CP transplantation following AS indcution (CP)

value: Endometrium


title: Endometrium, cp-transplanted, rep3

description: Library name: ASCP3


title: rat OFC, 11--8-2, HEROIN, RFP


title: Endometrium, EEP-transplanted, rep3

description: Library name: AS3L3


title: dark to light for 12h_3

value: dark to light for 12h


title: 959-SCM-D4-CM-A08

source_name: CD8 T

value: SCM


title: 959-SCM-B22-SCM-H10

value: TPR


title: mock treatment at 0h_2

value: hypocotyl


title: Endometrium, EEP-transplanted, rep1

description: Library name: AS3L1


title: 959-SCM-D4-CM-D06


title: 959-SCM-B22-SCM-H09


title: dark to light for 12h_2

value: hypocotyl cells


title: Endometrium, as-induced, rep2

description: Library name: AS2


title: Endometrium, as-induced, rep1

description: Library name: AS1


title: rat OFC, 10--11, HEROIN, RFP


title: before treatment_3


title: Endometrium, normal, rep1

description: Library name: N1


title: Endometrium, cp-transplanted, rep2

description: Library name: ASCP2


title: Endometrium, normal, rep3

description: Library name: N3


title: rat OFC, 21--16-2, HEROIN, SHISA7


title: Endometrium, normal, rep2

description: Library name: N2


title: before treatment_2


title: 959-SCM-B22-SCM-H04


title: CRD111, baseline visit

first: Jeffrey

last: Berger

address: 435 E. 30th Street  Science Building, 723L

department: Department of Cardiology

institute: NYU Langone Health

description: Library name: CRD111.1

data_processing:
Samples were analyed using the Seq-N-Slide pipeline
Reads were aligned to the hg38 genome using STAR v2.6.1
Reads were quantified using featureCounts v1.6.3
Read quality was assessed using FASTQC v0.11.7
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-separated file with genes as rows and samples as columns, containing integer raw read counts.
Supplementary files format and content: Tab-separated file with genes as rows and samples as columns, containing floating-point variance-stabilized transformed (VST) expression values from DESeq2.

source_name: platelets

extract_protocol:
Platelets were isolated using CD45 and TER119-targeted microbeads to deplete leukocytes and red blood cells and lysed with Qiazol lysis reagent followed by platelet RNA isolation with Direct-zol RNA microspin columns (Zymo Research). A total of 1000 ng RNA was used for the construction of sequencing libraries.
Sequencing libraries were prepared using the Clontech SMART-Seq HT with Nxt HT kit.

value: platelets

tag: time

value: Day 0

tag: mpa group

value: MPA high


title: 959-SCM-B22-SCM-G06


title: Endometrium, as-induced, rep3

description: Library name: AS3


title: h9A,S6D7,batch2

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

description: Library name: h9_S6D7_A_2

data_processing:
We processed Smart-seq3 scRNA-seq data beginning with the removal of index, primer, and adaptor sequences from the paired-end reads, utilizing Trimmomatic software (version 0.39). Post-trimming, the forward reads (Read 1) were aligned to the Homo sapiens reference genome (hg38) employing HISAT2 (version 2.1.0). The aligned reads were then annotated to gene features using the featureCounts tool (version 2.0.0), taking into account both 5' and internal fragments.  For 10x Genomics scRNA-seq data, initial processing was performed with the Cell Ranger software (version 3.0.1) using default parameters and the GRCh38 reference genome (version 3.0.0).The initial processing of raw snATAC-seq data was conducted using the cellranger-atac software, version 1.2.0, employing the standard parameters and referencing the refdata-cellranger-atac-GRCh38-1.2.0 genome assembly.
Assembly: hg38
Supplementary files format and content: TPM

growth_protocol: hESC and hiPSC lines were maintained cultured on surfaces coated with Matrigel (Corning, Cat#354230) and cultured in mTeSR1 media (Stem Cell Technologies, Cat#85850) at 37°C. The cells were passaged using Versene solution (ThermoFisher Scientific, Cat#15040066), and routine screenings for Mycoplasma contamination were performed employing the MycoBlue Mycoplasma Detector Kit (Vazyme, Cat#D101).     For differentiation experiments, hESCs and hiPSCs were dissociated to single-cell suspensions using TrypLE™ Express Enzyme (ThermoFisher Scientific, Cat#12605) and plated at a density of 0.53 x 106 cells/cm2 on surface coated with Matrigel diluted 1:30 (Corning, Cat#356231) in mTeSR1 media. This medium was supplemented with 10 μM Y-27632 (Selleckchem, Cat#S1049) to enhance cell survival. Differentiation was initiated within 24 hours post-seeding. Prior to introducing differentiation media, cells were washed with 1× DPBS without Mg2+ and Ca2+ (Meilunbio, Cat#MA0015). The cells were cultured at 37 °C with 5% (vol/vol) CO2.     The differentiation of stem cells into pancreatic lineages was conducted following modified versions of the protocols established by Rezania et al. and Hogrebe et al., herein referred to as protocols A and B, respectively. Additionally, a novel differentiation protocol developed within this study is referred to as protocol C.

extract_protocol:
SC-derived cells or islets were dissociated into single cells with 0.25% trypsin at 37 °C for 3-5 min, and the digestion was halted by adding 0.4 volumes of FBS. Partially dissociated SC-islets underwent a secondary trypsinization at 37°C for 3 minutes to ensure complete dissociation. Cells from both dissociation steps were pooled for further analysis. Retrieved grafts from the renal capsule were finely minced and enzymatically dissociated using 0.25% trypsin at 37°C for 5 minutes. The enzymatic reaction was halted by adding 0.4 volumes of FBS.
ScRNA-seq via the Smart-seq3 method was carried out in accordance with established procedures. Briefly, individual cells were sorted into 384-well plates containing lysis buffer (0.3 μL per well). The reverse transcription of mRNA was facilitated using a 0.1 μL aliquot of reverse transcription mix, followed by pre-amplification employing a 0.6 μL aliquot of PCR mix. A diluted sample of the resulting cDNA from each cell was analyzed using quantitative PCR (qPCR) employing ChamQ™ SYBR® qPCR Master Mix (Vazyme, Q321-02) and primers targeting ACTB: forward 5’-ACAGAGCCTCGCCTTTGCC-3’ and reverse 5’-GATATCATCATCCATGGTGAGCTGG-3’. Cells exhibiting cycle threshold (Ct) values under 21 for ACTB were selected for library preparation. To differentiate human cells within grafts, GAPDH expression was quantified using specific primers: forward 5’-CTCTGCTCCTCCTGTTCGAC-3’ and reverse 5’-GCGCCCAATACGACCAAATC-3’, considering cells as human if Ct values were below 25 and melting temperatures surpassed 85°C. Library construction was performed utilizing the TruePrep DNA Library Prep Kit (Vazyme, Cat#TD501), and sequencing was conducted on the MGIseq-2000 platform, generating 100 bp paired-end reads.     For 10x Genomics scRNA-seq, cells purified through FACS were processed on a Chromium controller. This step was followed by cDNA synthesis and library preparation in line with the protocols provided with the Single Cell 3′ Reagent Kit v3.1. The prepared libraries were then sequenced using the Illumina HiSeq 4000 system, yielding 150 bp paired-end reads.Cell suspensions were initially stained with DAPI to facilitate the sorting of live single cells utilizing the FACSAria™ Fusion flow cytometer. Subsequent to sorting, nuclei were isolated in accordance with the protocols detailed in the Chromium NEXT GEM Single Cell ATAC Reagent Kits v2 (10x Genomics). The prepared libraries were then subjected to sequencing on the NovaSeq 6000 platform, achieving 50 bp paired-end reads.     In the context of protocol A, one set of samples consisted of a composite of cells from stages S2D2, S4D3, S5D3, and S6D3, combined in a ratio of 1:2:2:3. An alternative set comprised cells from stages S3D2, S4D3, and S5D3, merged in a ratio of 1:2:3. Within the framework of protocol C, one sample amalgamated cells from stages S2D2, S3D3, S4D3, and S5D3, in a ratio of 1:2:2:3, whereas another ensemble included cells from stages S2D4, S3D3, and S4D3, in a ratio of 1:2:3.

tag: Stage

tag: batch

tag: treat

value: A


title: 959-SCM-B22-SCM-G02


title: CRD104, baseline visit

description: Library name: CRD104.1


title: h9A,S6D7,batch1

description: Library name: h9_S6D7_A_1


title: CRD099, baseline visit

description: Library name: CRD099.1


title: dark to light for 12h_1


title: CRD089, baseline visit

description: Library name: CRD089.1


title: 959-SCM-B22-SCM-H07


title: 959-SCM-B22-SCM-G01


title: healthy individuals

city: Dalian

first: aihui

last: Zhang

state: Liaoning province

address: Longtou Subdistrict

institute: Dalian Medical University

description: The Expression Levels of  lncRNAs and mRNAs

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing:
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 2 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Serum from peripheral blood of healthy women, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Serum was obtained by centrifugation from freshly drawn peripheral blood of healthy volunteers and volunteers with infertility.

value: Whole blood

tag: gender

value: female


title: CRD083, baseline visit

description: Library name: CRD083.1

value: MPA low


title: infertile patients

source_name: Serum from peripheral blood of infertile patients,  replicate 1


title: h9A,S6D3,batch2

description: Library name: h9_S6D3_A_2


title: Endometrium, EEP-transplanted, rep2

description: Library name: AS3L2


title: h9A,S6D3,batch1

description: Library name: h9_S6D3_A_1


title: CRD074, baseline visit

description: Library name: CRD074.1


title: 959-SCM-B22-SCM-G11


title: CRD076, baseline visit

description: Library name: CRD076.1


title: CRD071, baseline visit

description: Library name: CRD071.1


title: 959-SCM-B22-SCM-F06


title: before treatment_1


title: CRD068, baseline visit

description: Library name: CRD068.1


title: CRD070, baseline visit

description: Library name: CRD070.1


title: CRD114, baseline visit

description: Library name: CRD114.1


title: CRD067, baseline visit

description: Library name: CRD067.1


title: 959-SCM-B22-SCM-F01


title: 959-SCM-B22-SCM-F11


title: h9D,S5D7,batch1

description: Library name: h9_S5D7_D_1

value: D


title: CRD065, baseline visit

description: Library name: CRD065.1


title: 959-SCM-B22-SCM-E10


title: CRD064, baseline visit

description: Library name: CRD064.1


title: CRD063, baseline visit

description: Library name: CRD063.1


title: h9D,S5D3,batch2

description: Library name: h9_S5D3_D_2


title: 959-SCM-B22-EM-H05

value: EM


title: CRD062, baseline visit

description: Library name: CRD062.1


title: h9D,S5D3,batch1

description: Library name: h9_S5D3_D_1


title: 959-SCM-B22-EM-H02

value: CD8 T


title: h9A,S5D3,batch2

description: Library name: h9_S5D3_A_2


title: CRD048, baseline visit

description: Library name: CRD048.1


title: CRD060, baseline visit

description: Library name: CRD060.1


title: 959-SCM-B22-EM-G10


title: h9D,S5D7,batch2

description: Library name: h9_S5D7_D_2


title: CRD046, baseline visit

description: Library name: CRD046.1


title: h9A,S5D3,batch1

description: Library name: h9_S5D3_A_1


title: CRD038, baseline visit

description: Library name: CRD038.1


title: 959-SCM-B22-EM-G08


title: CRD037, baseline visit

description: Library name: CRD037.1


title: CRD033, baseline visit

description: Library name: CRD033.1


title: h9A,S5D1,batch1

description: Library name: h9_S5D1_A_1


title: 959-SCM-B22-EM-G05


title: 959-SCM-B22-EM-G04


title: 959-SCM-B22-EM-F10


title: CRD018, baseline visit

description: Library name: CRD018.1


title: h9D,S4D3,batch1

description: Library name: h9_S4D3_D_1


title: CRD021, baseline visit

description: Library name: CRD021.1


title: CRD014, baseline visit

description: Library name: CRD014.1


title: CRD028, baseline visit

description: Library name: CRD028.1


title: h9D,S4D3,batch2

description: Library name: h9_S4D3_D_2


title: CRD013, baseline visit

description: Library name: CRD013.1


title: h9A,S4D3,batch3

description: Library name: h9_S4D3_A_3


title: CRD061, baseline visit

description: Library name: CRD061.1


title: CRD010, baseline visit

description: Library name: CRD010.1


title: h9A,S4D3,batch2

description: Library name: h9_S4D3_A_2


title: 959-SCM-B22-EM-E09


title: 959-SCM-B22-EM-E12


title: h9A,S5D1,batch2

description: Library name: h9_S5D1_A_2


title: 959-SCM-B22-EM-E01


title: CRD006, baseline visit

description: Library name: CRD006.1


title: CRD003, baseline visit

description: Library name: CRD003.1


title: 959-SCM-B22-EM-D01


title: h9A,S4D3,batch1

description: Library name: h9_S4D3_A_1


title: h9D,S4D1,batch2

description: Library name: h9_S4D1_D_2


title: CRD005, baseline visit

description: Library name: CRD005.1


title: CRD032, baseline visit

description: Library name: CRD032.1


title: CRD023, baseline visit

description: Library name: CRD023.1


title: CRD025, baseline visit

description: Library name: CRD025.1


title: CRD001, baseline visit

description: Library name: CRD001.1


title: 959-SCM-B22-EFF-H11

value: EFF


title: CRD002, baseline visit

description: Library name: CRD002.1


title: h9D,S4D1,batch1

description: Library name: h9_S4D1_D_1


title: NR21_M_FULL

city: GLASGOW

first: Cecilia

last: Ansalone

address: Sir Graeme Davies Building - 120 University Place Glasgow

department: School of Infection & Immunity

country: United Kingdom

institute: University of Glasgow

description:
Library name: 3d1697e8-0718-4f30-b890-21b85301a999
M, FULL segment from donor NR21

data_processing:
Sequencing was performed externally, and raw FASTQ files were processed using the NanoString GeoMx NGS Pipeline: – Batch 1: version 2.3.4 – Batch 2: version 2.3.3.10  These pipelines converted FASTQ reads into digital count conversion (DCC) files per segment (ROI), which were imported into GeoMx DSP Analysis Suite (v3.1.0.222). An Initial Dataset was generated with default settings — no background correction, probe QC filtering, or Q3 normalisation was applied.  The Initial Dataset included multiple samples processed in parallel. To isolate only the segments relevant to this study, the exported Excel file was manually filtered to exclude unrelated samples. The resulting curated dataset was saved as a raw  count matrix in CSV format (Raw_Batch1-2_ExpressionMatrix.csv), retaining unnormalised digital counts per gene per segment.  Segment-level annotations were similarly filtered and exported to produce the final SegmentProperties metadata files (Batch1_SegmentProperties.csv, Batch2_SegmentProperties.csv), containing ROI-specific identifiers, region types, tissue compartment annotations, and processing metadata (e.g., nuclei count, detection QC metrics).  Raw digital counts were exported from the DSP Analysis Suite, and technical replicates within the same sample were merged. Quality control (QC) was performed using technical metrics from the GeoMx run. Each ROI was assessed for raw read count, aligned reads, sequencing saturation, nuclei counts, and surface area. ROIs with <50,000 or >1,000,000 raw transcript counts and/or <70% alignment rate were flagged as outliers and excluded from downstream analysis.  Normalised expression matrices were generated in R (v4.2.2) using the DESeq2 package (v1.38.3) to correct for library size and sequencing depth. CD45+ and FULL segments were normalised independently.
Assembly: GeoMx WTA is a probe-based assay targeting 18,000+ genes; no genome alignment is performed.
Supplementary files format and content: Processed data are provided as comma-separated values (.csv) files. – Files processed_CD45_A_em.csv and processed_FULL_areas_em.csv contain DESeq2-normalised expression matrices for CD45+ immune segments and full tissue segments, respectively. – Companion files processed_CD45_A_ss.csv and processed_FULL_areas_ss.csv contain corresponding segment-level statistics (e.g. nuclei counts, detection QC). All expression matrices contain gene symbols as row names and segment identifiers as columns. Segment annotations and sample-level metadata are provided in the accompanying SegmentProperties and clinical data.xlsx files.
Library strategy: Spatial Transcriptomics

source_name: temporal artery

extract_protocol:
Tissue sections were processed using the NanoString GeoMx DSP protocol: 5 µm FFPE sections were mounted on slides, deparaffinised, underwent antigen retrieval and proteinase K digestion, followed by overnight hybridisation with the Human Whole Transcriptome Atlas probes. ROIs were selected unsegmented (Full ROI) and segmented based on immunofluorescence (CD45+) and oligonucleotide tags were released by UV photocleavage.
Photocleaved oligonucleotides from each segment were collected into individual wells and underwent PCR amplification with unique i5/i7 dual indices using the GeoMx NGS Library Prep Kit. Indexed libraries were purified using AMPure beads, quantified, and pooled for paired-end sequencing.

value: temporal artery


title: 959-SCM-B22-EFF-H06


title: 959-SCM-B22-EFF-H03


title: h9D,S3D3,batch3

description: Library name: h9_S3D3_D_3


title: NR21_A_FULL

description:
Library name: 61fc9fd3-8830-449a-8e82-f401ae143a92
A, FULL segment from donor NR21


title: NR30_M_FULL...36

description:
Library name: 10435dd7-fd1a-42bc-a8cb-f084a327233a
M, FULL segment from donor NR30


title: NR30_A_CD45

description:
Library name: 7c62c914-74dd-46b3-9ed6-20b0d52bd8b6
A, CD45 segment from donor NR30


title: CRD007, baseline visit

description: Library name: CRD007.1


title: NR30_A_FULL...33

description:
Library name: 2c2bee0d-644b-43d1-84da-17d5ca91d3bf
A, FULL segment from donor NR30


title: NR30_A_FULL...34

description:
Library name: eeeaf306-f8e6-4fb7-88b9-8ccb8e6d981d
A, FULL segment from donor NR30


title: h9D,S3D3,batch2

description: Library name: h9_S3D3_D_2


title: NR26_A_CD45...32

description:
Library name: 274df848-0fb7-4b59-98e1-d5fb7b56b4e3
A, CD45 segment from donor NR26


title: h9A,S3D2,batch3

description: Library name: h9_S3D2_A_3


title: SR26_M_FULL

description:
Library name: be23a978-57ae-4fc9-8d46-e645d1c9eaf7
M, FULL segment from donor SR26


title: 959-SCM-B22-EFF-F07


title: 959-SCM-B22-EFF-G07


title: SR26_A_CD45...28

description:
Library name: 37672b2d-b0b0-4307-8113-49edc0fce152
A, CD45 segment from donor SR26


title: h9A,S3D2,batch1

description: Library name: h9_S3D2_A_1


title: SR26_A_CD45...27

description:
Library name: 534a2906-d72b-4961-89bb-29db57f59804
A, CD45 segment from donor SR26


title: 959-SCM-B22-EFF-F04


title: SR26_I_FULL

description:
Library name: d3dcd8c0-fbf7-416e-8c64-7a7a344dbcbe
I, FULL segment from donor SR26


title: SR26_A_FULL

description:
Library name: ef8cbe3d-6de0-4961-b9db-4faf65e5d8da
A, FULL segment from donor SR26


title: h9A,S3D2,batch2

description: Library name: h9_S3D2_A_2


title: h9D,S2D4,batch3

description: Library name: h9_S2D4_D_3


title: SR25_M_FULL

description:
Library name: 569da6a8-2b2c-441d-95d8-7cdc963be939
M, FULL segment from donor SR25


title: NR30_M_FULL...37

description:
Library name: 68130b15-7371-4c85-9362-53ed916311c0
M, FULL segment from donor NR30


title: 959-SCM-B22-EFF-F02


title: SR25_I_FULL

description:
Library name: e37c7ca2-e781-412c-aa22-d3991e5166c0
I, FULL segment from donor SR25


title: SR25_A_CD45...22

description:
Library name: 5de33160-b3af-4aa4-8162-b277295b4538
A, CD45 segment from donor SR25


title: SR25_A_CD45...23

description:
Library name: c077ffec-86f8-4316-ab8f-6de0a18abb25
A, CD45 segment from donor SR25


title: 959-SCM-B22-CM-H12

value: CM


title: h9D,S2D4,batch2

description: Library name: h9_S2D4_D_2


title: 959-SCM-B22-CM-H08

value: SCM


title: SR22_M_FULL

description:
Library name: 290805ed-b02d-4242-be73-8d8a4a512a11
M, FULL segment from donor SR22


title: NR26_A_CD45...31

description:
Library name: 2e1d9994-d2ab-4075-b8fa-dc000c30c670
A, CD45 segment from donor NR26


title: h9D,S2D4,batch1

description: Library name: h9_S2D4_D_1


title: h9D,S3D3,batch1

description: Library name: h9_S3D3_D_1


title: 959-SCM-B22-CM-H01

value: TPR


title: h9D,S2D2,batch3

description: Library name: h9_S2D2_D_3


title: SR22_I_FULL

description:
Library name: fdbc4d86-891e-4ad0-b04f-5453975daea9
I, FULL segment from donor SR22


title: 959-SCM-B22-EFF-G09


title: 959-SCM-B22-CM-G03


title: SR25_A_FULL

description:
Library name: 1b00b83a-ec22-4332-a1a9-51157fc450c8
A, FULL segment from donor SR25


title: SR22_A_CD45...18

description:
Library name: fe0f04a1-c16d-45dd-8704-58ea83741197
A, CD45 segment from donor SR22


title: SR22_A_CD45...17

description:
Library name: cc678cee-aea1-4c1e-9314-8a2b14a391a4
A, CD45 segment from donor SR22


title: h9D,S2D2,batch1

description: Library name: h9_S2D2_D_1


title: SR27_M_FULL...15

description:
Library name: c1c8fac8-95c6-490c-99e8-e18f553c2a69
M, FULL segment from donor SR27


title: SR22_A_FULL

description:
Library name: 6385de4e-d664-4f37-8abd-f2cf7d14b51a
A, FULL segment from donor SR22


title: 959-SCM-B22-CM-F12


title: 959-SCM-B22-CM-F09


title: 959-SCM-B22-CM-F08


title: SR27_M_FULL...14

description:
Library name: 5c2272c0-1e77-4c39-a8e8-8020d0560666
M, FULL segment from donor SR27


title: SR27_I_FULL

description:
Library name: bc47185c-849b-4748-a616-8c732b65de36
I, FULL segment from donor SR27


title: SR35_A_CD45...9

description:
Library name: 1a2b2247-8920-42b1-a6df-25c6353aeaea
A, CD45 segment from donor SR35


title: SR27_A_FULL...11

description:
Library name: 484513a2-32c5-48eb-8db7-8655e3382827
A, FULL segment from donor SR27


title: h9A,S2D2,batch1

description: Library name: h9_S2D2_A_1


title: h9A,S2D2,batch2

description: Library name: h9_S2D2_A_2


title: 959-SCM-B22-CM-F03


title: SR24_M_FULL

description:
Library name: cab7f5e0-ca1a-4bdd-a4e8-658bfc5178ff
M, FULL segment from donor SR24


title: SR35_A_CD45...8

description:
Library name: 6ff17b1a-c7a8-4459-81aa-3f5a5e7219e9
A, CD45 segment from donor SR35


title: SR24_I_FULL

description:
Library name: d566f394-8d30-4727-8289-08d889be3a38
I, FULL segment from donor SR24


title: SR24_A_CD45...5

description:
Library name: b3d74651-0d99-40d3-abc8-9a7b4384f40a
A, CD45 segment from donor SR24


title: h9A,S1D2,batch3

description: Library name: h9_S1D2_A_3


title: h9A,S1D2,batch2

description: Library name: h9_S1D2_A_2


title: SR24_A_CD45...4

description:
Library name: 07399a7c-b492-45f3-ac2a-041f9d7979ae
A, CD45 segment from donor SR24


title: 959-SCM-B22-CM-C01


title: SR24_A_FULL

description:
Library name: c6971bbf-1d50-4c60-b9bf-3e6e1fc22684
A, FULL segment from donor SR24


title: SR2_M_FULL

description:
Library name: 6a37ad48-8475-42a3-9406-1167ac115e67
M, FULL segment from donor SR2


title: h9A,S1D2,batch1

description: Library name: h9_S1D2_A_1


title: SR2_I_FULL

description:
Library name: bec4c511-c2d2-4cb4-8d0b-0c8c8f49066f
I, FULL segment from donor SR2


title: 697-SCM-CL4-SCM-F02

value: NLV


title: SR27_A_FULL...12

description:
Library name: a0106f23-22e3-4df9-a04a-d683e7cee391
A, FULL segment from donor SR27


title: 697-SCM-CL4-SCM-E06


title: ProtocolD+C,S5D7,batch2

description: Library name: DC_S5D7_2

value: D+C


title: SR2_A_CD45

description:
Library name: 6f4451d8-cd28-49a7-a66a-846fef525628
A, CD45 segment from donor SR2


title: SR2_A_FULL

description:
Library name: b8bc35f5-1254-4a78-8bce-660dd05c83fe
A, FULL segment from donor SR2


title: 959-SCM-B22-CM-F05


title: ProtocolD+C,S5D7,batch1

description: Library name: DC_S5D7_1


title: SR35_A_CD45...10

description:
Library name: 7acbfb0c-9198-4f5f-903c-55551906b36f
A, CD45 segment from donor SR35


title: SR1_M_FULL

description:
Library name: 9148e89c-c0f4-47e5-a50b-ea222b4ddeac
M, FULL segment from donor SR1


title: ProtocolD+C,S5D3,batch2

description: Library name: DC_S5D3_2


title: SR1_I_FULL

description:
Library name: 0d218152-c040-4b4d-bd72-ba42de8f2ac6
I, FULL segment from donor SR1


title: 697-SCM-CL4-SCM-D03


title: 959-SCM-B22-CM-E11


title: SR1_A_FULL

description:
Library name: 22aac985-a5cc-4604-8c9a-fe38acebef5e
A, FULL segment from donor SR1


title: SR1_A_CD45...65

description:
Library name: f7ba85bb-9c3a-49a6-82d1-4b954f0804a9
A, CD45 segment from donor SR1


title: SR1_A_CD45...66

description:
Library name: d33f1076-4528-4b11-9cbe-8d47b05e7cde
A, CD45 segment from donor SR1


title: ProtocolD+C,S5D3,batch1

description: Library name: DC_S5D3_1


title: 697-SCM-CL4-SCM-C03


title: NR4_M_FULL

description:
Library name: eb3c414a-7012-4803-81e0-20266820a625
M, FULL segment from donor NR4


title: ProtocolD+C,S4D4,batch3

description: Library name: DC_S4D4_3


title: 697-SCM-CL4-SCM-B05


title: h9A,S2D2,batch3

description: Library name: h9_S2D2_A_3


title: NR4_A_FULL

description:
Library name: 0849a18e-8797-4444-9185-4536fd49d0b9
A, FULL segment from donor NR4


title: NR4_A_CD45...61

description:
Library name: a0c25596-7dc3-43db-889c-7fe943bd7969
A, CD45 segment from donor NR4


title: 697-SCM-CL4-SCM-A07


title: ProtocolD+C,S4D4,batch2

description: Library name: DC_S4D4_2


title: ProtocolD+C,S4D4,batch1

description: Library name: DC_S4D4_1


title: NR4_A_CD45...60

description:
Library name: 6ac2574c-3487-4e63-add7-588c2f921f48
A, CD45 segment from donor NR4


title: 697-SCM-CL4-SCM-E05


title: 697-SCM-CL4-EM-H09


title: NR3_I_FULL

description:
Library name: f3eaa7ef-6a20-40cb-9f28-1893e6d78e08
I, FULL segment from donor NR3


title: ProtocolD+C,S4D2,batch3

description: Library name: DC_S4D2_3


title: NR3_A_CD45...56

description:
Library name: 3b41cad5-33af-47fe-9db9-14d60bbb8ea4
A, CD45 segment from donor NR3


title: NR3_A_FULL

description:
Library name: da08fbc7-1943-412a-ab84-bc12eb748f72
A, FULL segment from donor NR3


title: 697-SCM-CL4-EM-G10


title: NR3_A_CD45...55

description:
Library name: 553a4337-157e-4cee-bd17-4b0ee2f523e9
A, CD45 segment from donor NR3


title: NR2_M_FULL

description:
Library name: 58fb4240-e83d-42da-acf5-11fb878ce539
M, FULL segment from donor NR2


title: ProtocolD+C,S4D2,batch1

description: Library name: DC_S4D2_1


title: ProtocolD+C,S4D2,batch2

description: Library name: DC_S4D2_2


title: NR4_I_FULL

description:
Library name: 6418883b-79cf-4eab-9312-af9ccb7c2d6d
I, FULL segment from donor NR4


title: NR2_A_FULL

description:
Library name: 2fe060da-1ac0-46d9-be8a-1fb53b7ee687
A, FULL segment from donor NR2


title: 697-SCM-CL4-EM-G09


title: ProtocolC,S2treated,S4D4,batch3

description: Library name: ProCcondition_A10C0.3_3


title: NR3_M_FULL

description:
Library name: 28594023-fa89-47b8-9953-231f56d940e8
M, FULL segment from donor NR3


title: 697-SCM-CL4-EM-F09


title: NR2_A_CD45

description:
Library name: b733bd7e-7897-4d3b-8c96-fc22a651a7ce
A, CD45 segment from donor NR2


title: ProtocolC,S2treated,S4D4,batch2

description: Library name: ProCcondition_A10C0.3_2


title: NR1_I_FULL

description:
Library name: 17afb3c0-e7a7-4634-8368-f51cea434564
I, FULL segment from donor NR1


title: NR1_M_FULL

description:
Library name: 6c5b45bc-7cc7-4c47-a561-9f2d800da252
M, FULL segment from donor NR1


title: 697-SCM-CL4-EM-E09


title: NR1_A_FULL

description:
Library name: 57646d5e-acca-4289-afb0-378b3382aa3e
A, FULL segment from donor NR1


title: 697-SCM-CL4-SCM-A03


title: 697-SCM-CL4-EM-D09


title: ProtocolC,S2treated,S4D4,batch1

description: Library name: ProCcondition_A10C0.3_1


title: NR1_A_CD45...47

description:
Library name: 8ef1065b-7f5a-4414-8d82-971294f6bd5f
A, CD45 segment from donor NR1


title: SR6_M_FULL

description:
Library name: e145cee1-0656-4523-9f72-2672f032f2e9
M, FULL segment from donor SR6


title: NR1_A_CD45...46

description:
Library name: bbe9f970-f80b-4213-8505-d6d0c555d506
A, CD45 segment from donor NR1


title: 697-SCM-CL4-EM-D08


title: ProtocolC,control,S4D4,batch3

description: Library name: ProCcondition_0_3

value: C,control


title: 697-SCM-CL4-EM-C10


title: SR6_A_CD45

description:
Library name: 0dfaf481-cb16-4f1c-a922-435b47cab72a
A, CD45 segment from donor SR6


title: ProtocolC,control,S4D4,batch1

description: Library name: ProCcondition_0_1


title: SR5_A_FULL

description:
Library name: 37a7030c-3fc7-42b1-a0e7-9a49897bdc7c
A, FULL segment from donor SR5


title: SR5_M_FULL

description:
Library name: 83e567c5-e46f-4e2e-adfc-a0199c5d356f
M, FULL segment from donor SR5


title: 697-SCM-CL4-EM-A10


title: hIPSC_D_S6D7_2

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx

data_processing:
We processed Smart-seq3 scRNA-seq data beginning with the removal of index, primer, and adaptor sequences from the paired-end reads, utilizing Trimmomatic software (version 0.39). Post-trimming, the forward reads (Read 1) were aligned to the Homo sapiens reference genome (hg38) employing HISAT2 (version 2.1.0). The aligned reads were then annotated to gene features using the featureCounts tool (version 2.0.0), taking into account both 5' and internal fragments.  For 10x Genomics scRNA-seq data, initial processing was performed with the Cell Ranger software (version 3.0.1) using default parameters and the GRCh38 reference genome (version 3.0.0).The initial processing of raw snATAC-seq data was conducted using the cellranger-atac software, version 1.2.0, employing the standard parameters and referencing the refdata-cellranger-atac-GRCh38-1.2.0 genome assembly.
Assembly: hg38
Supplementary files format and content: sparse matrix: read count
Supplementary files format and content: fragments.tsv

source_name: hIPSC

value: hIPSC


title: 697-SCM-CL4-EM-C08

data_processing:
Illumina NextSeq500 was used
Sequenced paired-end reads were trimmed using Trimmomatic (v0.39) (using parameters:  LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 4:10, MINLEN = 50), then aligned to the human reference genome (GRCh38) using STAR (v2.7.3a). Gene expression was then quantified at the counts and TPM level with RSEM (v1.3.1)
Assembly: GRCh38
Supplementary files format and content: .mtx.gz files contain matrices including raw counts, TPM and scaled TPM values for each sample and each gene.
Supplementary files format and content: .txt and and .tsv files contain tab delimited information on sample names and gene names (as per ordering in matrices), and gene annotation information.


title: NR2_I_FULL

description:
Library name: c319865d-77d4-4910-bf56-e2db6c80a121
I, FULL segment from donor NR2


title: C6_I_FULL...38

description:
Library name: efa1e71d-2760-47ff-bf66-ce0cb08dc951
I, FULL segment from donor C6


title: hIPSC_D_S6D7_1


title: SR5_I_FULL

description:
Library name: bde72445-dbfb-4b4a-97f5-6b72ebab682e
I, FULL segment from donor SR5


title: 697-SCM-CL4-EM-A09


title: hIPSC_D_S6D3_2


title: DNA methylation array, Lymph node metastasis

type: genomic

city: Augsburg

first: Pascal

middle: David

last: Johann

address: Stenglinstrasse 2

department: Paediatric Oncology

institute: University Hospital Augsburg

hyb_protocol: DNA isolated from the FFPE material (lymph nodes) was restored using the Illumina FFPE DNA restoration kit prior to bisulfite conversion. The remaining steps of the Infinium Methylation EPIC v2 array were identical for all samples, according to the manufacturer's protocols.

scan_protocol: Arrays wree imaged using Illumina NextSeq550 using the standard protocols.

data_processing: Data was processed in R with minfi and conumee 2.0 packages.

label: Cy3 and Cy5

source_name: Lymph node - melanoma

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA from the primary tumour fresh-frozen material was isolated using the Qiagen All Prep Mini kit, and from the FFPE material (healthy lymph node and lymph node metastasis samples) using the Qiagen FFPE All Prep kit, according to manufacturer’s protocol.

value: Lymph node - melanoma

tag: tissue type

value: FFPE


title: C6_M_FULL...37

description:
Library name: 6f761cde-4cac-4881-bdb9-4643571ca6c2
M, FULL segment from donor C6


title: 697-SCM-CL4-EM-A08

extract_protocol:
Single CMV-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols


title: DNA methylation array, Healthy lymph node

source_name: Lymph node - healthy

value: Lymph node - healthy


title: SR5_A_CD45

description:
Library name: e65ea690-4b87-4976-b264-40a785e87e90
A, CD45 segment from donor SR5


title: hIPSC_D_S6D3_1


title: 697-SCM-CL4-CM-H06


title: C6_M_FULL...36

description:
Library name: 074f8881-a2e1-4911-8a3e-de1868237774
M, FULL segment from donor C6


title: C6_I_FULL...35

description:
Library name: 04d2db13-a319-42a6-8a29-a3b9400f5254
I, FULL segment from donor C6


title: DNA methylation array, Primary tumour

source_name: Melanoma

value: Melanoma

value: Fresh frozen


title: SR6_I_FULL

description:
Library name: 9be6195e-e3fd-45b9-aa8e-c5e8cb2a3cd0
I, FULL segment from donor SR6


title: 697-SCM-CL4-CM-H04


title: hIPSC_D_S5D7_2

value: D


title: ProtocolC,control,S4D4,batch2

description: Library name: ProCcondition_0_2


title: hIPSC_D_S5D7_1


title: C6_A_FULL...33

description:
Library name: 9cfcbab2-7bf2-4c39-a26a-b590925637f5
A, FULL segment from donor C6


title: RAW 264.7 cells, 4 hr TBHQ treatment, 12 hr PIC stimulation, rep 3

city: Clemson

first: Alyssa

middle: Marie

last: Whisel

state: SC

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

description: Library name: PIC+TBHQ rep 3

data_processing:
Initial quality control, read alignment to Mus musculus reference genome (GRCm38/mm39), transcript assembly, and normalization using fragments per kilobase of transcript per million mapped reads (FPKM) were performed by Novogene Corporation, Inc. (Sacramento, CA, USA). Briefly, raw data was processed through in-house perl scripts and data was cleaned. Hisat2 v2.0.5 was used to map reads against the reference genome. Mapped reads were assembled with StringTie v1.3.3b. FeatureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene. The FPKM of each gene was calculated.
Assembly: GRCm38/mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM normalized counts for each sample

extract_protocol:
RNA was isolated using the Direct-zol RNA Miniprep Kit (R2051A, Zymo Research, Irvine, CA, USA) according to the manufacturer's protocol.
Initial quality control, read alignment to Mus musculus reference genome (GRCm38/mm39), transcript assembly, and normalization using fragments per kilobase of transcript per million mapped reads (FPKM) were performed by Novogene Corporation, Inc. (Sacramento, CA, USA). Briefly, directional and non-directional libraries were prepared from mRNA purified from total RNA using poly-T oligo-attached magnetic beads. cDNA was synthesized after fragmentation using random heamer primers and dUTP/dTTP for second strand cDNA synthesis. End repair, A-tailing, adapter ligation, size selection USER enzyme digestion (directional library), amplification, and purification were performed thereafter.


title: RAW 264.7 cells, 4 hr TBHQ treatment, 12 hr PIC stimulation, rep 2

description: Library name: PIC+TBHQ rep 2


title: hIPSC_D_S5D3_2


title: 697-SCM-CL4-CM-G02

first: Yanran

last: Zhao

address: Sydney NSW 2033

institute: UNSW


title: RAW 264.7 cells, 4 hr TBHQ treatment, 12 hr PIC stimulation, rep 1

description: Library name: PIC+TBHQ rep 1


title: 697-SCM-CL4-CM-G05


title: hIPSC_D_S5D3_1


title: 697-SCM-CL4-CM-F05


title: h9D,S2D2,batch2

description: Library name: h9_S2D2_D_2


title: C5_M_FULL...32

description:
Library name: 419c7c6f-9f85-4e11-bed9-0638d99e68be
M, FULL segment from donor C5


title: C5_M_FULL...31

description:
Library name: 34798c58-624c-4e23-a9d2-1c7549d219c5
M, FULL segment from donor C5


title: 697-SCM-CL4-CM-F03


title: hIPSC_D_S4D3_2


title: hIPSC_D_S4D3_1


title: RAW 264.7 cells, 4 hr TBHQ treatment, 12 hr LPS stimulation, rep 2

description: Library name: LPS+TBHQ rep 2


title: RAW 264.7 cells, 4 hr TBHQ treatment, 12 hr LPS stimulation, rep 1

description: Library name: LPS+TBHQ rep 1


title: C5_I_FULL...29

description:
Library name: f1194f6d-8fa1-4c85-8c09-93b4bf61029b
I, FULL segment from donor C5


title: hIPSC_D_S4D1_1


title: 697-SCM-CL4-CM-E07


title: C5_A_FULL...28

description:
Library name: a53fadbc-f19f-4fde-a40f-d230fb1a3891
A, FULL segment from donor C5


title: RAW 264.7 cells, 4 hr TBHQ treatment, rep 3

description: Library name: TBHQ rep 3

value: 4 hr TBHQ treatment


title: 697-SCM-CL4-CM-E02

value: CD8 T


title: hIPSC_D_S3D3_2


title: C6_A_FULL...34

description:
Library name: dd60112e-f319-4ecf-89ad-e40de0539269
A, FULL segment from donor C6


title: 697-SCM-CL4-CM-D05


title: C5_A_FULL...27

description:
Library name: 2891d790-e9b2-46b7-b963-8d021a8ed05c
A, FULL segment from donor C5


title: RAW 264.7 cells, 4 hr TBHQ treatment, rep 2

description: Library name: TBHQ rep 2


title: 697-SCM-CL4-CM-C05


title: C5_A_FULL...26

description:
Library name: 8e6391ea-4ced-4282-a538-2861c7c235bf
A, FULL segment from donor C5


title: hIPSC_D_S2D4_2

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx


title: hIPSC_D_S3D3_1


title: RAW 264.7 cells, 4 hr TBHQ treatment, 12 hr LPS stimulation, rep 3

description: Library name: LPS+TBHQ rep 3


title: 697-SCM-CL4-CM-A05


title: RAW 264.7 cells, 12 hr PIC stimulation, rep 2

description: Library name: PIC rep 2

value: 12 hr PIC stimulation


title: NR6_M_FULL

description:
Library name: d22a6f3c-5600-42e2-bfdc-4be1bd31c4a7
M, FULL segment from donor NR6

value: temporal artery


title: hIPSC_D_S2D4_1


title: 697-SCM-CL2-EM-H02

value: EM


title: RAW 264.7 cells, 4 hr TBHQ treatment, rep 1

description: Library name: TBHQ rep 1


title: 697-SCM-CL2-EM-E06

value: SCM


title: RAW 264.7 cells, 12 hr PIC stimulation, rep 1

description: Library name: PIC rep 1


title: NR6_I_FULL

description:
Library name: 7b2ecb60-95ab-470a-b20d-2a9ed53ca0af
I, FULL segment from donor NR6


title: 697-SCM-CL2-EM-E05


title: NR6_A_CD45

description:
Library name: 9efe4135-0e0a-4b8a-851d-a28f6e83e467
A, CD45 segment from donor NR6


title: RAW 264.7 cells, 12 hr LPS stimulation, rep 3

description: Library name: LPS rep 3

value: 12 hr LPS stimulation


title: 697-SCM-CL2-EM-D06

value: NLV


title: hIPSC_A_S7D7_2

value: A


title: NR6_A_FULL

description:
Library name: beb19043-6f0b-45dc-9df8-26eaa41f68bb
A, FULL segment from donor NR6


title: hIPSC_A_S7D7_1


title: C5_I_FULL...30

description:
Library name: 414d14b7-e46e-4bc2-8b11-9d8599540030
I, FULL segment from donor C5


title: hIPSC_D_S2D2_1


title: C5_A_FULL...25

description:
Library name: 59ac63a9-10dc-4270-ac04-10aefbd885e2
A, FULL segment from donor C5


title: RAW 264.7 cells, 12 hr PIC stimulation, rep 3

description: Library name: PIC rep 3


title: RAW 264.7 cells, 12 hr LPS stimulation, rep 2

description: Library name: LPS rep 2


title: RAW 264.7 cells, control, rep 3

description: Library name: Control rep 3

value: control


title: NR5_I_FULL

description:
Library name: 4d7bb0f1-14ff-479f-88a1-c47b3b7db139
I, FULL segment from donor NR5


title: hIPSC_A_S7D3_1

value: hIPSC


title: hIPSC_D_S2D2_2


title: hIPSC_A_S7D3_2


title: RAW 264.7 cells, control, rep 2

description: Library name: Control rep 2


title: hIPSC_A_S6D7_2


title: 697-SCM-CL2-EM-C04


title: 697-SCM-CL2-EM-A12


title: NR5_M_FULL

description:
Library name: 0b545e46-29d7-435c-8950-98bf417e7cd0
M, FULL segment from donor NR5


title: RAW 264.7 cells, control, rep 1

description: Library name: Control rep 1


title: NR5_A_FULL...17

description:
Library name: 0bd7881f-6d6f-4ac5-8b5d-6e9039e7cf23
A, FULL segment from donor NR5


title: 697-SCM-CL2-EM-A03


title: hIPSC_A_S6D3_2


title: C4_I_FULL

description:
Library name: 5baca8d7-f4bc-4da0-9263-18d0ce484311
I, FULL segment from donor C4


title: BRAF-SOX2 Tum, R3

city: Glasgow

first: Patricia

last: Centeno

state: Scotland

address: Switchback Rd, Bearsden, Glasgow

institute: Beatson Institute for Cancer Research

description: Library name: sample_3

data_processing:
Raw sequence quality control was performed using FastQC (v0.11.8) before and after removing adapters and low-quality base calls (Phred score <20) using TrimGalore with default options (v0.6.6).
Trimmed reads were aligned to GRCm38, release 100 (mouse samples) using Hisat2 (v2.1.0).
RNA-Seq
Gene counts were subsequently estimated using featurecounts (subread/1.6.3).
Assembly: mm10/100
Supplementary files format and content: csv  file includes raw counts for each sample

source_name: Skin tumour cSCC

growth_protocol: BRAFV600E and SOX2 were induced in IVL+ skin cell specific populations in mice from 7-10 weeks old following tamoxifen inducible CreRT2 recombination.

extract_protocol:
RNA was extracted from fresh frozen tumour samplesusing AllPrep DNA/RNA kit (74104, Qiagen) according to the manufacturer’s instructions.
rRNA-depleted libraries were prepared using 200 ng of total RNA. Total RNA libraries were sequenced using Illumina NovaSeq 6000 XP SP, 200 cycles, paired-end reads (2 x 150 bp) 30 million reads. RNA preparation and sequencing were performed by GENEWIZ Azenta.

treatment_protocol: BRAFV600E and SOX2 overexpression were induced in IVL+ skin population via topical tamoxifen inductions. Tumours were grown until clinical endpoint and frozen in RNA later until extraction.

value: Skin tumour cSCC

value: Male

value: squamous cell carcinoma

tag: genotype


title: hIPSC_A_S6D3_1


title: 697-SCM-CL2-EM-C11

city: Sdyney

tag: subject


title: BRAF-SOX2 Tum, R2

description: Library name: sample_2

value: Female


title: RAW 264.7 cells, 12 hr LPS stimulation, rep 1

description: Library name: LPS rep 1


title: BRAF-SOX2 Tum, R1

description: Library name: sample_1


title: hIPSC_A_S5D3_2