title: 3D fibroblasts_3 of final LSE without trehalose

source_name: 3D fibroblasts of final LSE without trehalose

value: untreated


title: Incipient TB_followup_NPRIF_1790101_SV12

status: Public on Jan 10 2023

type: SRA

city: Bergen

first: Harleen

last: Grewal

address: The Laboratory Building, 5th floor, 5021

department: Department of Clinical Science

country: Norway

institute: University of Bergen

library_source: transcriptomic

data_processing:
Demultiplexing using bcl2fastq v2.20.0.422
Alignment of RNAseq fastq files to GRCh38.p10 using hisat2-2.05
Quantification of RNAseq data against genome using featurecount 1.5.2.
Normalization of quantized reads and differential gene expression calculation using DEseq2 1.34.0
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Expression matrix for 144 samples rounded to two digits with group information derived from expression matrix calculated by DEseq2

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Peripheral whole blood (approx. 2.5 ml) was drawn into PAXgene blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland) and stored at -80°C until RNA extraction (PAXgene Blood RNA kit; PreAnalytiX, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Whole Blood

tag: distinct stages of tb

value: Incipient TB/Non-Progressor_followup

tag: age in years

tag: chest x-ray

value: Normal

tag: mtb culture

value: Negative

tag: tst in mm

tag: qft result


title: Day 14 ALPK3 mutant hPSC-derived cardiomyocytes - replicate 1

city: Melbourne

first: Enzo

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

description:
mRNA extraction from hPSCCM
mut_d14_rep1

data_processing:
Trimming using the Skewer (version 0.2.2).
Aligned to the human genome (GRCh38.105/hg38) using STAR (version 2.5.3a).
Reads aligning to Ensembl-annotated with a strict mapping quality (Q≥30) were counted with featureCounts (subread 2.0.0).
Genes with > 0.5 counts per million in at least 4 samples were retained for statistical analysis.
Assembly: GRCh38.105/hg38
Supplementary files format and content: Raw counts or filtered counts of sequencing reads.

source_name: stem cell derived cardiomycytes

extract_protocol:
Total RNA was extracted from cells using Trizol reagent and cleaned up with Qiagen RNeasy kit.
Samples were processed at VCGS using Illumina TruSeq stranded mRNA Library Prep kit

tag: cell type

value: stem cell derived cardiomycytes

tag: genotype

value: ALPK3 mutant

tag: time point

value: Day 14


title: Day 30 wild-type hPSC-derived cardiomyocytes - replicate 2

description:
mRNA extraction from hPSCCM
wt_d30_rep2

value: wild-type

value: Day 30


title: hypothalamus_ct58_young

city: Gainesville

first: Karyn

middle: A

last: Esser

state: Florida

address: 1345 Center Drive

department: PHYSIOLOGY & FUNCTIONAL GENOMICS

country: USA

institute: University of Florida

data_processing:
Alignment was performed by using HISAT2 software
Duplicated aligned reads were marked and removed using the Picardtools software
The gene expression count data were extracted using the HTseq software
The raw count data were normalized to cpm (counts per million reads)
Assembly: GRCm38 (mm10)
Supplementary files format and content: count_216.csv: gene expression count data
Supplementary files format and content: cpm_216.csv: normalized count data (count per million reads)

organism: Mus musculus

source_name: hypothalamus

extract_protocol:
Samples were homogenized in Trizol, and RNA extracted accordinng to manufacturer protocol
RNAseq libraries were prepared with Illumina RNA-Seq libraries (Poly A) kit following manufacturer's protocols.

value: hypothalamus

tag: strain

tag: Sex

value: Male

tag: age group

value: young

tag: circadian time


title: hypothalamus_ct54_old

value: old


title: Day 30 wild-type hPSC-derived cardiomyocytes - replicate 1

description:
mRNA extraction from hPSCCM
wt_d30_rep1


title: Day 14 ALPK3 mutant hPSC-derived cardiomyocytes - replicate 2

description:
mRNA extraction from hPSCCM
mut_d14_rep2


title: Day 14 wild-type hPSC-derived cardiomyocytes - replicate 4

description:
mRNA extraction from hPSCCM
wt_d14_rep4


title: 3D fibroblasts_2 of final LSE without trehalose

city: Toon

first: Jun

last: Muto

address: Shitsukawa 454

department: Department of Dermatology

country: Japan

institute: Ehime University Graduate School of Medicine

data_processing:
FASTQ files produced by Illimina NEXTSeq were imported to CLC Genomics Workbench software (ver.12.0.3).
Reads with more than 2 ambiguous nucleotides and reads with quality scores less  than 20 as calculated by the Phred program were removed using CLC Genomics Workbench software (ver.12.0.3). Long reads with more than 1000 nucleotides and short reads with fewer than 20 nucleotides were also discarded.
The trimmed reads were mapped to the human reference genome GRCh37 release-75 using CLC Genomics Workbench software (ver.12.0.3) with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.12.0.3).
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each sample.

growth_protocol: Normal human epidermal keratinocytes were isolated from normal human skin and cultured under serum-free   conditions, following a previously described method. The cells were used for LSE cultures in their fourth passage. Fibroblasts were isolated from normal human skin and cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal calf serum, and fifth-passage cells were used to construct the LSEs.  (Shirakata Y, Tokumaru S, Yamasaki K, Sayama K, and Hashimoto K. So-called biological dressing effects of cultured epidermal sheets are mediated by the production of EGF family, TGF-beta and VEGF. J Dermatol Sci. 2003;32(3):209-15.)

extract_protocol:
Total RNA was isolated from the fibroblasts or keratinocyte using the RNeasy Mini Kit (Qiagen). Polyadenylated  mRNA was purified with oligo dT beads (NEBNext Poly (A) mRNA magnet Isolation Module, New England Biolabs, NEB). Complementary DNA (cDNA) libraries for Illumina sequencing were generated with NEBNext Ultra II RNA library Prep kit (NEB) and NEBNextplex Oligos for Illumina.
Extracted mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences were inserted to cDNA fragments with PCR amplification. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Bioanalyzer. The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina Next-seq DNA sequencer with 75 bp pair-end cycle sequencing kit (Illumina).

treatment_protocol: The method used for LSE preparation was described previously. Briefly, a collagen gel was prepared by mixing six volumes of ice-cold porcine collagen type I solution (Nitta Gelatin) with one volume of 8 × DMEM (Gibco), 10 volumes of 1 × DMEM supplemented with 20% FBS, and one volume of 0.1 N NaOH, of which 1 ml was added to each culture insert (Transwell, Costar) in a six-well culture plate (Costar). Following polymerization of the gel in the inserts at 37°C, two volumes of fibroblast suspension solution 5 × 10e5 cells/ml in 1 × DMEM supplemented with 10% FBS were added to eight volumes of the collagen solution (thus, the final collagen concentration was 0.8 mg/ml). Then, 3.5 ml of the fibroblast-containing collagen solution was applied to each insert. When the fibroblast-containing gel polymerized, DMEM supplemented with 10% FBS and ascorbic acid (final concentration 50 ng/ml) was added with or without trehalose (100 mg/ml). The gel was submerged in culture for 5 days. For 4DF-T1-3 samples, the fibroblasts in the gel with trehalose were harvested after 3 days.  After the fibroblasts contracted the gel, 6 × 10e5 keratinocytes in 60 µl MCDB 153 type II were seeded onto the surface of the contracted gel. The resulting LSE was maintained submerged in culture medium for 2 days. When the keratinocytes reached confluence, the LSE was raised to the air-liquid interface. LSEs were harvested 14 days after airlifting. (Yang L, Shirakata Y, Tamai K, Dai X, Hanakawa Y, Tokumaru S, et al. Microbubble-enhanced ultrasound for gene transfer into living skin equivalents. J Dermatol Sci. 2005;40(2):105-14.)

value: primary fibroblast

tag: treatment


title: Incipient TB_followup_NPRIF_1540101_SV12

value: Positive


title: hypothalamus_ct54_aged

value: aged


title: Incipient TB_followup_NPRIF_7600203_SV12


title: hypothalamus_ct50_young


title: 3D fibroblasts_3 of final LSE with trehalose

source_name: 3D fibroblasts of final LSE with trehalose

value: treated with trehalose for 14 days


title: 3D fibroblasts_1 of final LSE without trehalose

value: untreated


title: Incipient TB_baseline_NPRIB_1540101_SV0

value: Whole Blood

value: Incipient TB/Non-Progressor_baseline

tag: gender


title: hypothalamus_ct50_old


title: Day 14 wild-type hPSC-derived cardiomyocytes - replicate 2

description:
mRNA extraction from hPSCCM
wt_d14_rep2


title: hypothalamus_ct50_aged


title: Day 14 wild-type hPSC-derived cardiomyocytes - replicate 1

description:
mRNA extraction from hPSCCM
wt_d14_rep1


title: Incipient TB_baseline_NPRIB_7600203_SV0

value: Normal


title: Day 14 wild-type hPSC-derived cardiomyocytes - replicate 3

description:
mRNA extraction from hPSCCM
wt_d14_rep3

value: stem cell derived cardiomycytes


title: Day 30 wild-type hPSC-derived cardiomyocytes - replicate 3

description:
mRNA extraction from hPSCCM
wt_d30_rep3


title: Incipient TB_followup_NPRIF_6770102_SV12

value: Incipient TB/Non-Progressor_followup

value: Negative


title: hypothalamus_ct46_young


title: 3D fibroblasts_1 of final LSE with trehalose


title: Incipient TB_baseline_NPRIB_6770102_SV0

value: Female


title: RNA_THP1_DB2313_rep2

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: RNA-seq in THP-1 cells treated with DB2313

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using HISAT 2.1.0
Fragments with read qualities greater than 10 were considered for further analysis. Reads mapping to the coding strand of exonic regions were counted using htseq, with gene definitions obtained from the refGene table of RefSeq genes in the UCSC Table Browser.
The table of all counts was processed using DESeq2, using default parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including total numbers of reads overlapping each transcript for each sample.

molecule: polyA RNA

source_name: THP-1 cells

growth_protocol: Cells were cultured in 10% FBS RPMI medium using standard approaches.

extract_protocol:
RNA was extracted from cells using TRIzol reagent. Following purification, mRNA was enriched by poly(dT) capture. RNA was fragmented, converted to DNA, then size-selected for 200-400 bp DNA fragments before PCR amplification.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with either 1 uM BRM014 or an equivalent volume of DMSO for either 24 or 72 h prior to library construction. PMA differentiation of THP-1 cells was performed by addition of 10 nM PMA for 48 h, followed by removal of PMA to allow cells to rest for 24 h. For DB2313, cells were treated with 3 uM DB2313 for 72 h.

tag: cell line

tag: marker

value: WT


title: hypothalamus_ct46_old

tag: tissue

value: hypothalamus


title: RNA_THP1_DB2313_rep1


title: Incipient TB_followup_NPRIF_7600202_SV12

tag: distinct stages of tb

tag: age in years


title: 2D fibroblasts_1 treated without trehalose

source_name: 2D fibroblasts treated without trehalose


title: 2D fibroblasts_2 treated without trehalose


title: Incipient TB_baseline_NPRIB_7600202_SV0

value: Male

tag: chest x-ray

value: Abnormal TB

tag: mtb culture


title: hypothalamus_ct46_aged


title: hypothalamus_ct42_young

value: young


title: Incipient TB_followup_NPRIF_3510302_SV12

tag: tst in mm

tag: qft result


title: LPS 24 h, LPS 4 h, biol rep 2

city: Moscow

first: Mikhail

last: Pashenkov

address: Kashirskoe shosse 24

country: Russia

institute: Institute of Immunology

description: Sample s_18

data_processing:
FASTQ files were generated using bcl2fastq v2.20 Conversion Software (Illumina)
Quality of reads was assessed using FastQC
Alignment of reads against reference human transcriptome (ftp://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/cdna/Homo_sapiens. GRCh38.cdna.abinitio.fa.gz), counting and normalization were done using Salmon software package
Genes were selected for further analysis according to abundance of their transcripts (at least 50 raw counts in at least one library in each of the two experiments) and function (only protein-coding genes), which yielded a set of 11,964 genes
RPM values were calculated using Excel
Assembly: GRCh38
Supplementary files format and content: An Excel file containing two separate tabs for each of the two biological replicates. Each tab contains columns with gene names, gene descriptions and RPM values for each sample

source_name: Macrophages

growth_protocol: Human macrophages were generated by culturing blood monocytes with granulocyte-macrophage colony-stimulating factor (40 ng/ml) for 6 days

extract_protocol:
Total RNA was extracted using a kit from Jena Bioscience (Jena, Germany, cat# PP-210) and treated with DNase (NEB, Ipswich, MA, cat# M0303). mRNA was purified using oligo-dT-coated superparamagnetic beads (NEB, cat# E7490).
Barcoded cDNA libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (NEB, cat# E7765) and NEBNext® Multiplex Oligos for Illumina® (NEB, cat# E7335 and E7500) according to manufacturer’s instructions.

treatment_protocol: To induce tolerance, macrophages were treated for 24 h with a NOD1 agonist (M-triDAP), a TLR4 agonist (LPS) or medium as a control. After 24 h, cells were washed and recultured with medium, M-triDAP or LPS for 1 h or 4 h, at which points total RNA samples were collected

tag: cell type

value: Macrophages

value: LPS 24 h, LPS 4 h


title: 2D fibroblasts_2 treated with trehalose for 24 hr

source_name: 2D fibroblasts treated with trehalose for 24 hr

value: primary fibroblast

value: treated with trehalose for 24 hr


title: hypothalamus_ct42_old

value: old


title: Incipient TB_baseline_NPRIB_3510302_SV0

value: Whole Blood

value: Positive


title: Medium 24 h, LPS 4 h, biol rep 2

description: Sample s_16

value: Medium 24 h, LPS 4 h


title: 2D fibroblasts_1 treated with trehalose for 24 hr


title: 2D fibroblasts_3 treated without trehalose

value: untreated


title: LPS 24 h, M-triDAP 4 h, biol rep 2

description: Sample s_15

value: LPS 24 h, M-triDAP 4 h


title: Subclinical TB_baseline_PRSB_5580201_SV0

value: Sub-clinical TB/Progressor_baseline

value: Abnormal not TB

value: Negative


title: Subclinical TB_followup_PRSF_5580201_SV12

value: Sub-clinical TB/Progressor_followup

value: Normal


title: M-triDAP 24 h, M-triDAP 4 h, biol rep 2

description: Sample s_14

value: M-triDAP 24 h, M-triDAP 4 h


title: Subclinical TB_followup_PRSF_5480202_SV12

value: Abnormal possible TB


title: Medium 24 h, M-triDAP 4 h, biol rep 2

description: Sample s_13

value: Macrophages

value: Medium 24 h, M-triDAP 4 h


title: hypothalamus_ct42_aged

value: hypothalamus

value: Male

value: aged


title: hypothalamus_ct38_aged


title: Subclinical TB_baseline_PRSB_5480202_SV0

value: Whole Blood

value: Female


title: hypothalamus_ct38_old

value: old


title: 2D fibroblasts_3 treated with trehalose for 24 hr

value: primary fibroblast

value: treated with trehalose for 24 hr


title: Subclinical TB_followup_PRSF_5090202_SV6

value: Positive


title: hypothalamus_ct34_young

value: young


title: 3D fibroblasts_2 of final LSE with trehalose

value: treated with trehalose for 14 days


title: LPS 24 h, medium 4 h, biol rep 2

description: Sample s_12

value: LPS 24 h, medium 4 h


title: Medium 24 h, medium 4 h, biol rep 2

description: Sample s_10

value: Medium 24 h, medium 4 h


title: Subclinical TB_baseline_PRSB_5090202_SV0

value: Sub-clinical TB/Progressor_baseline

value: Normal

value: Negative


title: RpoD mutatnt Culture  23oC [rpoD_2_C_23_S16]

city: Bethesda

first: Melissa

last: Arroyo-Mendoza

state: MD

address: 8 CENTER DR RM 2A11

department: LBG

institute: NIDDK

data_processing:
Quality trimming (max ambiguity =2) and trimming of 15 nucleotides from the 5’ terminal of all sequences was performed with CLC Genomics Workbench.
Trimmed data was aligned to the E. coli reference genome (NC_000913.3) and an unmapped reads file was generated.
Differential expression experiments consisted of 3 replicates of MG1655 WT and RpoD D445V mutant E. coli grown in LB at either 37o or 23oC.
Count data was normalized to total reads in CLC Genomics Workbench
Statistical analysis was performed in CLC Genomics Workbench using the EDGE test tagwise dispresions with False Discovery Rate (FDR) corrected p values.
Assembly: NC_000913.3
Supplementary files format and content: Comma seperated value text files include: 1) counts for each gene in all replicates prior to normailzation; 2) normalized values for each gene in all replicates; 3) the fold change of each gene in the two samples as determined  in CLC Genomics Workbench using the Baggerley’s Test; 3) False Discovery Rate (FDR) corrected p values.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacteria

growth_protocol: MG1655 WT or RpoD D445V mutant E. coli were grown at 37C or 23C to mid log phase (OD600 ~ 0.5-0.6)

extract_protocol:
RNA was isolated  using method II of (Hinton 1989)
rRNA subtraction was performed with the bacterial RiboMinus Kit (Ambion) according to manufacturer instructions.  cDNA was prepared using the NEBNext strand specific kit (New England BioLabs) according to manufacturer instruction for libraries with 300-450 bp insert size with the following modifications.  Illumina adaptors sequences based on TruSeq HT Sample Prep Kits were purchase from Integrated DNA Technologies and used in the ligation step.  TruSeq-1 and TruSeq-2 primer were used for PCR enrichment of adaptor ligated DNA.  Library size was verified with a Bioanalyzer using an Agilent High Sensitivity DNA kit.  The concentration of each library was determined using the KAPA Library Quantification Kit for Illumina platforms.  Sequencing was performed by the NIDDK Genomics Core facility using a MiSeq system with the MiSeq 2 x 250 bp Sequencing Kit (Illumina).

treatment_protocol: E. coli was grown in LB broth at 37C or 23C

tag: genotype

value: RpoD D445V mutant

value: Grown at 23oC


title: RpoD mutatnt Culture  23oC [rpoD_1_C_23_S24]


title: Subclinical TB_followup_PRSF_4070101_SV12

value: Sub-clinical TB/Progressor_followup


title: RpoD mutatnt Culture  23oC [rpoD_3_C_23_S20]


title: WT Culture  23oC [Wt_1_C_23_S23]

value: WT


title: WT Culture  23oC [Wt_2_C_23_S15]


title: WT Culture  23oC [Wt_3_C_23_S19]


title: hypothalamus_ct38_young

value: hypothalamus

tag: strain

value: Male


title: RpoD mutatnt Culture  37oC [rpoD_3_C_37_S18]

value: Grown at 37oC


title: LPS 24 h, LPS 1 h, biol rep 2

description: Sample s_9

value: Macrophages

value: LPS 24 h, LPS 1 h


title: hypothalamus_ct30_young

tag: Sex


title: M-triDAP 24 h, LPS 4 h, biol rep 2

description: Sample s_17

value: M-triDAP 24 h, LPS 4 h


title: Subclinical TB_baseline_PRSB_4070101_SV0

value: Whole Blood

value: Female

value: Indeterminate


title: M-triDAP 24 h, LPS 1 h, biol rep 2

description: Sample s_8

value: M-triDAP 24 h, LPS 1 h


title: RpoD mutatnt Culture  37oC [rpoD_2_C_37_S14]


title: hypothalamus_ct30_old

tag: age group

value: old


title: M-triDAP 24 h, medium 4 h, biol rep 2

description: Sample s_11

value: M-triDAP 24 h, medium 4 h


title: RpoD mutatnt Culture  37oC [rpoD_1_C_37_S22]


title: Medium 24 h, LPS 1 h, biol rep 2

description: Sample s_7

value: Medium 24 h, LPS 1 h


title: Subclinical TB_baseline_PRSB_3550104_SV0

value: Sub-clinical TB/Progressor_baseline

value: Normal

value: Negative

value: Positive


title: hypothalamus_ct34_old

value: hypothalamus

tag: circadian time


title: Subclinical TB_followup_PRSF_3550104_SV12

value: Sub-clinical TB/Progressor_followup


title: WT Culture  37oC [Wt_3_C_37_S17]

value: WT

tag: treatment

value: Grown at 37oC


title: hypothalamus_ct30_aged

value: Male

value: aged


title: hypothalamus_ct26_young

value: young


title: hypothalamus_ct34_aged


title: LPS 24 h, M-triDAP 1 h, biol rep 2

description: Sample s_6

value: Macrophages

value: LPS 24 h, M-triDAP 1 h


title: Subclinical TB_followup_PRSF_4460107_SV6

value: Whole Blood


title: M-triDAP 24 h, M-triDAP 1 h, biol rep 2

description: Sample s_5

value: M-triDAP 24 h, M-triDAP 1 h


title: Subclinical TB_baseline_PRSB_4460107_SV0

tag: gender

value: Female


title: Medium 24 h, M-triDAP 1 h, biol rep 2

description: Sample s_4

value: Medium 24 h, M-triDAP 1 h


title: hypothalamus_ct26_old

value: old


title: WT Culture  37oC [Wt_1_C_37_S21]


title: Seq_mB7E11R2_merged

city: Buffalo

first: Satrajit

last: Sinha

state: NY

address: 955 Main Street

institute: University at Buffalo

description:
Seq_mB7E11R2
Mouse_DysplasiafeatureCountsOutput.txt

data_processing:
RNA-seq - Reads were mapped to the Mus musculus genome (mm10 build) with HISAT2 (v2.1.0), reads aligned to the UCSC mm10 build were quanitifed with featureCounts (v1.5.0), which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location, DESeq1 (v.1.10.1) was used to normalize the read counts and derive TPM values
Assembly: mm10
Supplementary files format and content: featureCounts output containing gene-level read count summaries for each RNA-seq sample

source_name: cell line

extract_protocol:
RNA-seq - RNA was extracted from mouse cancer cell lines (B4B8, B7E3, B7E11) using the Direct-zol Mini-Prep kit
RNA-seq - Illumina TruSeq RNA sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries

value: cell line

tag: cell line

value: Mouse Oral Squamous Cell Carcinoma


title: Subclinical TB_followup_PRSF_3550102_SV12

value: Normal

value: Positive


title: Seq_mB7E11R1_merged

description:
Seq_mB7E11R1
Mouse_DysplasiafeatureCountsOutput.txt


title: M-triDAP 24 h, medium 1 h, biol rep 2

description: Sample s_2

value: M-triDAP 24 h, medium 1 h


title: hypothalamus_ct22_old

value: hypothalamus


title: hypothalamus_ct22_young


title: Medium 24 h, medium 1 h, biol rep 2

description: Sample s_1

value: Medium 24 h, medium 1 h


title: WT Culture  37oC [Wt_2_C_37_S13]

value: WT

value: Grown at 37oC


title: Seq_mB7E3R2_merged

description:
Seq_mB7E3R2
Mouse_DysplasiafeatureCountsOutput.txt


title: Subclinical TB_baseline_PRSB_3550102_SV0

value: Sub-clinical TB/Progressor_baseline

value: Negative


title: hypothalamus_ct22_aged

value: Male

value: aged


title: Subclinical TB_baseline_PRSB_20301_SV0

value: Whole Blood

value: Abnormal not TB


title: Seq_mB7E3R1_merged

description:
Seq_mB7E3R1
Mouse_DysplasiafeatureCountsOutput.txt


title: hypothalamus_ct18_young

value: young


title: LPS 24 h, medium 1 h, biol rep 2

description: Sample s_3

value: Macrophages

value: LPS 24 h, medium 1 h


title: M-triDAP 24 h, LPS 4 h, biol rep 1

description: Sample X17

value: M-triDAP 24 h, LPS 4 h


title: LPS 24 h, LPS 4 h, biol rep 1

description: Sample X18

value: LPS 24 h, LPS 4 h


title: hypothalamus_ct26_aged


title: Subclinical TB_followup_PRSF_7150101_SV2

value: Sub-clinical TB/Progressor_followup

value: Abnormal possible TB

value: Positive


title: Seq_mB4B8R2_merged

description:
Seq_mB4B8R2
Mouse_DysplasiafeatureCountsOutput.txt

value: cell line

value: Mouse Oral Squamous Cell Carcinoma


title: hypothalamus_ct18_old

value: hypothalamus

value: old


title: Subclinical TB_followup_PRSF_20301_SV12

value: Normal


title: Seq_mB4B8R1_merged

description:
Seq_mB4B8R1
Mouse_DysplasiafeatureCountsOutput.txt

value: WT


title: LPS 24 h, M-triDAP 4 h, biol rep 1

description: Sample X15

value: LPS 24 h, M-triDAP 4 h


title: Subclinical TB_followup_PRSF_4440201_SV12

value: Whole Blood


title: heart_ct62_young

source_name: heart

value: heart

value: Male


title: B7E11_Input

description: Input of ChIP-seq

library_source: genomic

data_processing:
ChIP-seq - Reads were mapped to the Mus musculus genome (mm10 build) with bowtie2 (v2.4.4), MACS2 was then used for peak calling to identify enriched areas in the genome
Assembly: mm10
Supplementary files format and content: peak summit files for ChIP-seq

molecule: genomic DNA

extract_protocol:
ChIP-seq - cells were fixed with formaldehyde for 10 mins and then chromatin was extracted
ChIP-seq - libraries were prepared using ThruPLEX DNA-seq kits from Reubicon Genomics

tag: chip antibody


title: Subclinical TB_baseline_PRSB_4440201_SV0

tag: tissue

value: Sub-clinical TB/Progressor_baseline

value: Negative


title: Subclinical TB_baseline_PRSB_7150101_SV0

tag: distinct stages of tb

value: Abnormal TB


title: hypothalamus_ct18_aged

value: aged


title: M-triDAP 24 h, M-triDAP 4 h, biol rep 1

description: Sample X14

value: Macrophages

value: M-triDAP 24 h, M-triDAP 4 h


title: heart_ct62_old


title: B7E11_4A4

description: ChIP-seq of p63


title: LPS 24 h, medium 4 h, biol rep 1

description: Sample X12

value: LPS 24 h, medium 4 h


title: Subclinical TB_baseline_PRSB_2240102_SV0

tag: age in years

value: Female

value: Abnormal not TB

value: Positive


title: MAIT_SkinWoundD4, scRNAseq

city: Paris

first: Martin

last: MESTDAGH

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
10x Genomics
SKIN MAIT Skin Wound

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Skin

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: MAIT

value: Skin

tag: condition

value: Wound D4


title: heart_ct58_young

value: young


title: Subclinical TB_followup_PRSF_20404_SV2

value: Whole Blood

value: Sub-clinical TB/Progressor_followup

tag: chest x-ray

tag: mtb culture


title: Medium 24 h, LPS 4 h, biol rep 1

description: Sample X16

value: Medium 24 h, LPS 4 h


title: M-triDAP 24 h, medium 4 h, biol rep 1

description: Sample X11

value: M-triDAP 24 h, medium 4 h


title: B7E11_E6Q

description: ChIP-seq of p63

value: cell line

value: Mouse Oral Squamous Cell Carcinoma

value: WT

value: p63 E6Q3O CST


title: heart_ct58_old

value: heart

value: Male

value: old


title: MAIT_SkinSTeadyState, scRNAseq

description:
10x Genomics
Skin MAIT Steady State

value: Steady State


title: Subclinical TB_followup_PRSF_2240102_SV12

value: Normal

value: Positive

tag: tst in mm

tag: qft result


title: Subclinical TB_baseline_PRSB_20404_SV0

value: Sub-clinical TB/Progressor_baseline

value: Abnormal TB

value: Negative


title: LPS 24 h, LPS 1 h, biol rep 1

description: Sample X9

tag: cell type

value: Macrophages

value: LPS 24 h, LPS 1 h


title: heart_ct58_aged

tag: strain

value: aged


title: Medium 24 h, medium 4 h, biol rep 1

description: Sample X10

value: Medium 24 h, medium 4 h


title: Active TB_baseline_ATBX_6540100_SV0

value: Whole Blood

value: Active TB_baseline


title: Tfl_day7_mouse3_plate3 [L18-Tfl-M3P3i18]

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

country: Germany

institute: Technical University of Munich

description: scRNA-Seq (SCRB-seq, paired-end, 16 bp read 1, 49 bp read 2)

data_processing:
Pipeline: DropSeqPipe v0.4 was used for raw data processing (available at https://hoohm.github.io/dropSeqPipe). Parameters are provided in the configuration file (see "config.yaml").
Trimming: Cutadapt v1.16 was used for trimming on both fastq files separately.
Filtering: Reads with a missing pair were discarded using bbmap v38.22.
Mappping: STAR v2.5.3a was used for mapping to annotation release #91 and genome build #38 from Mus musculus (Ensembl). Multimapped reads were discarded.
Post-processing: Dropseq_tools v1.13 was used for demultiplexing and file manipulation. A whitelist of cells barcodes with minimum distance of 3 bases was used. Cell barcodes and unique molecular identifiers (UMI) with a hamming distance of 1 and 2 respectively were corrected.
Processed data filtering: Features with a total UMI counts <1 were eliminated. Quality control matrix was computed using calculateQCMetrics provided by scater (v 1.12.2). Cells with total features by counts (number of genes) <500 or total counts (number of UMI read counts) <5000 were excluded, yielding a matrix of 1518 cells with 36310 genes.
Normalization: Gene expression measurements for each cell were column-normalized, multiplied by the scaling factor 10,000 and transformed to log scale using using Seurat v2.3.4.
Dimensional reduction: Highly variable genes (8751 genes) were detected by estimating the average expression and dispersion of each gene across all cells. Principle component analysis (PCA) was applied for linear dimensional reduction. Top 10 principle components and K=200 were chosen for building K-nearest neighbors graph followed by shared nearest neighbor (SNN) construction. T-distributed stochastic neighbor embedding (t-SNE) technique was applied.
Clustering: Modularity optimization-based algorithm was applied for cluster identification on top 10 principal components and resolution 0.8.
Assembly: GRCm38 (release 91)
Supplementary files format and content: Run30_counts.csv is a comma-delimited file containing the read counts for each gene (rows) in each cell (column).
Supplementary files format and content: Run30_metadata_norm_exp.xlsx is a Microsoft Excel file containing the metadata for each cell, with rows being cells and columns being annotated features.

source_name: spleen

extract_protocol:
At day 4 post Lm-N4 infection, splenocytes were enriched for CD45.1+ OT-1 T-cells using anti-CD45.1 biotin/ anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech, Bergisch-Gladbach, Germany). Single-cells were sorted on BD FACS Fusion (100 micron nozzle, standard operation settings, single-cell purity, index sorting). Individual cells meeting the gating strategy were sorted directly in lysis buffer into individual wells of a low-binding PCR plate. Immediately after sorting, each plate was spun down, snap-frozen on dry ice and stored at -80oC until use.
The single-cell libraries were generated using the previously described SCRB-seq protocol, with some modifications. After RNA purification and reverse transcription, the generated single-cell cDNA was amplified for 20 cycles. The barcoded single-cell amplicons were double-purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA was used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024, Illumina). After PCR amplification of the fragmented libraries, the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 µl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626, Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010, Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600, Kapa Biosystems).

treatment_protocol: Tables containing 14 mg Teriflunomide (Aubagio®) were grinded in a mortar and resolved in 0,5% Carboxymethylcellulose (CMC). Drugs and CMC control solutions were applied by oral gavage starting 3 days before infection every other day. Three control and three treated mice were infected intravenously with 1000 to 2000 colony-forming units (CFU) of log-phase Listeria monocytogenes stably expressing Ovalbumin containing the native OT-1 ligand SIINFEKL (Lm-N4).

value: spleen

tag: surface marker

value: OT-1 T-cells

value: 7 days post Teriflunomide treatment and 4 days post Lm-N4 infection

value: Tfl

tag: Sex

value: female

tag: mouse

tag: plate

tag: lane


title: Active TB_baseline_ATBX_5580200_SV0

tag: gender

value: Female


title: M-triDAP 24 h, LPS 1 h, biol rep 1

description: Sample X8

tag: treatment

value: M-triDAP 24 h, LPS 1 h


title: heart_ct62_aged

tag: tissue

value: heart

value: Male

tag: age group

tag: circadian time


title: heart_ct54_young

value: young


title: Active TB_baseline_ATBX_5580100_SV0

tag: distinct stages of tb

tag: age in years

value: Abnormal TB

value: Positive

value: Negative


title: Tfl_day7_mouse3_plate1 [L16-Tfl-M3P1i16]

tag: condition


title: Tfl_day7_mouse3_plate2 [L17-Tfl-M3P2i17]


title: Active TB_baseline_ATBX_4710100_SV0

tag: chest x-ray

tag: mtb culture

tag: tst in mm


title: LPS 24 h, M-triDAP 1 h, biol rep 1

description: Sample X6

tag: cell type

value: Macrophages

value: LPS 24 h, M-triDAP 1 h


title: Medium 24 h, M-triDAP 4 h, biol rep 1

description: Sample X13

value: Medium 24 h, M-triDAP 4 h


title: Medium 24 h, LPS 1 h, biol rep 1

description: Sample X7

value: Medium 24 h, LPS 1 h


title: heart_ct54_old

tag: strain

value: old


title: heart_ct54_aged

tag: Sex

value: aged


title: CMC_day7_mouse3_plate2 [L14-CMC-M3P2i14]

value: spleen

tag: surface marker

value: OT-1 T-cells

value: 7 days post Carboxymethylcellulose treatment and 4 days post Lm-N4 infection

value: CMC

tag: mouse


title: heart_ct50_young


title: Active TB_baseline_ATBX_4070100_SV0

value: Whole Blood

value: Active TB_baseline

tag: qft result


title: heart_ct50_old

value: heart

value: Male


title: CMC_day7_mouse3_plate3 [L15-CMC-M3P3i15]

value: female

tag: plate

tag: lane


title: Active TB_baseline_ATBX_3720100_SV0

tag: tissue

tag: gender

value: Abnormal TB

value: Positive


title: CMC_day7_mouse3_plate1 [L13-CMC-M3P1i13]

tag: treatment


title: M-triDAP 24 h, M-triDAP 1 h, biol rep 1

description: Sample X5

value: Macrophages

value: M-triDAP 24 h, M-triDAP 1 h


title: heart_ct50_aged

tag: age group

tag: circadian time


title: Medium 24 h, M-triDAP 1 h, biol rep 1

description: Sample X4

value: Medium 24 h, M-triDAP 1 h


title: Active TB_baseline_ATBX_3700200_SV0

tag: distinct stages of tb

tag: age in years


title: Tfl_day7_mouse2_plate2 [L11-Tfl-M2P2i11]

value: 7 days post Teriflunomide treatment and 4 days post Lm-N4 infection

tag: condition

value: Tfl


title: Tfl_day7_mouse2_plate3 [L12-Tfl-M2P3i12]


title: M-triDAP 24 h, medium 1 h, biol rep 1

description: Sample X2

value: M-triDAP 24 h, medium 1 h


title: Tfl_day7_mouse2_plate1 [L10-Tfl-M2P1i10]

value: spleen


title: heart_ct46_old

value: old


title: LPS 24 h, medium 1 h, biol rep 1

description: Sample X3

value: LPS 24 h, medium 1 h


title: heart_ct46_young

value: young


title: Medium 24 h, medium 1 h, biol rep 1

description: Sample X1

value: Medium 24 h, medium 1 h


title: CMC_day7_mouse2_plate3 [L9-CMC-M2P3i9]

value: OT-1 T-cells

value: 7 days post Carboxymethylcellulose treatment and 4 days post Lm-N4 infection

value: CMC


title: Active TB_baseline_ATBX_2240100_SV0

value: Whole Blood

value: Active TB_baseline

value: Male

tag: chest x-ray

tag: mtb culture

tag: tst in mm


title: Active TB_baseline_ATBX_3310100_SV0

value: Abnormal TB

value: Positive


title: Active TB_baseline_ATBX_20400_SV0

value: Negative


title: CMC_day7_mouse2_plate2 [L8-CMC-M2P2i8]

tag: cell type

tag: Sex

value: female


title: heart_ct42_young

value: heart

tag: strain


title: mixed [CGINS_TimeCourse_CMP_Sample1-4]

city: New

first: Sean

last: Houghton

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Cellranger 6.0 was run using default parameters to align and generate gene counts.
For the time series data, the cellranger multi routine was run with default parameters to muliplex the samples
Assembly: GRCh38-2020-A
Supplementary files format and content: Filtered feature counts output from cellranger in h5 format

source_name: mixed

growth_protocol: hGSCs were cultured as 2D flat stem cell colonies.

extract_protocol: Single-cell RNA-seq

treatment_protocol: hGSC differentiation was initiated by 4OH-Tamoxifen treatment of cultured Ngn3ER-hGSCs for two days, followed by lentiviral integration of a Pdx1-Mafa co-expression cassette. Four days later, the nascent GINS cells were aggregated into spherical organoids. GINS organoids could be transplanted.

tag: tissue/cell type

value: Human gastric stem cells; Endocrine progenitors; GINS precursors/organoids

tag: time points

value: 0, 2, 6 and 20 days post differentiation

tag: stomach region

value: Corpus


title: CMC_day7_mouse2_plate1 [L7-CMC-M2P1i7]

tag: tissue

value: spleen

tag: surface marker

tag: mouse

tag: plate

tag: lane


title: Active TB_baseline_ATBX_1380100_SV0

tag: distinct stages of tb

tag: gender

tag: qft result


title: heart_ct42_old

tag: age group

value: old

tag: circadian time


title: Tfl_day7_mouse1_plate3 [L6-Tfl-M1P3i6]

tag: treatment

value: 7 days post Teriflunomide treatment and 4 days post Lm-N4 infection

tag: condition

value: Tfl


title: Antral GINS organoids [AGINS-4]

source_name: GINS organoids derived from human antral stomach

value: Antral GINS organoids

value: 21 days post differentiation

value: Antrum


title: heart_ct42_aged

tag: Sex

value: aged


title: heart_ct38_young

tag: strain

value: Male

value: young


title: heart_ct38_old


title: heart_ct38_aged


title: Tfl_day7_mouse1_plate2 [L5-Tfl-M1P2i5]

tag: cell type

value: OT-1 T-cells


title: heart_ct34_young


title: T8_TCR

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Mapping was performed with CellRanger (v5.0.1, with default parameters) on the mouse reference refdata-gex-mm10-2020-A to which the SV40 tumor cell transgene was added.
A total of 17’105 barcodes and 32’286 features for the tumor samples, and 33’776 barcodes and 32’286 features for the spleen samples were then processed using Seurat (v4.0.4).
Features found in a minimum of 5 cells were kept, cells with at least 200 unique features detected were kept. Cells with less than 7500 unique features detected in tumor samples, or less than 4000 unique features in spleen samples, and less than 10% features mapping to the mitochondrial genome were kept for a final set of 13’797 cells and 19’605 genes for the tumor samples, and 29’012 cells and 17’481 genes for the spleen samples.
Samples were independently log normalized and integrated using 2000 most variable features. Unsupervised clustering was performed applying the graph-based clustering approach and Louvain algorithm and Uniform Manifold Approximation and Projection (UMAP) dimensional reduction was performed based on the previously computed neighbor graph using the top 30 PCs.
Single-cell TCR-sequencing reads were aligned using 10x Genomics Cell Ranger VDJ 5.0.1 (Zheng et al., 2017), mapping reads to the Mouse reference dataset (GRCm38/Ensembl/10x).
VDJTools (Shugay et al., 2015) version 1.2.1, immunarch (Nazarov et al., 2020) library (version 0.6.4) and R (version 4.0) were used to analyse the scTCRseq data.
Assembly: mm10; GRCm38
Supplementary files format and content: scRNA-seq: matrix.mtx, features.tsv, barcodes.tsv. TCR-seq: clonotype.csv, filtered_contig_annotations.csv

source_name: Tumor

extract_protocol:
Tumors were dissected, cleaned, digested with MA dissociation buffer for 30 min, passed through a 70 um cell strainer and centrifuge 5 min at 1500rpm. ACK lysis was performed for 3 min and centrifuge 5 min at 1500rpm and filter with 70um cell strainer. Cells were resupend in PBS 0.04% BSA and counted.
Spleens were cleaned, smashed on 40um cell strainer and centrifuge 5 min at 1500rpm. ACK lysis was performed for 3 min, centrifuge 5 min at 1500rpm and filter with 40um cell strainer. Cells were resupend in PBS 0.04% BSA and counted.
Cells were prepared for scRNAseq at 10 000 cells/ul (10.106 cells/mL) in PBS 0.04% BSA and 1.106 cells/50uL in PBS 2% BSA. The 10X sample processing was performed according to established protocols, aiming at 4000 cells/sample. Single-cell experiments were performed using the 10X Chromium platform using the 5’ v2 kit (dual index, PN-1000263). TCR V(D)J amplification was performed using 10x Chromium Single Cell mouse TCR amplification kit (PN-1000254).
The libraries were sequenced on an Illumina HiSeq4000 platform, with run conditions as per 10X recommendations, aiming at 50’000 reads/cell.

tag: model

value: Rip-Tag5 PanNET mouse model

tag: mouse model

value: Rip-Tag5 PanNET

value: Tumor

tag: treatment group

value: CTRL

tag: duration of the treatment

value: 10 days

tag: mice id

tag: replicate

tag: batch


title: heart_ct46_aged

tag: tissue

value: heart


title: T7_TCR


title: mixed [CGINS_TimeCourse_GEX_Sample1-4]

tag: tissue/cell type

value: Human gastric stem cells; Endocrine progenitors; GINS precursors/organoids

tag: time points

value: 0, 2, 6 and 20 days post differentiation

tag: stomach region

value: Corpus


title: Tfl_day7_mouse1_plate1 [L4-Tfl-M1P1i4]

value: spleen

tag: surface marker

value: 7 days post Teriflunomide treatment and 4 days post Lm-N4 infection

value: Tfl

value: female

tag: mouse

tag: plate

tag: lane


title: CMC_day7_mouse1_plate2 [L2-CMC-M1P2i2]

tag: treatment

value: 7 days post Carboxymethylcellulose treatment and 4 days post Lm-N4 infection

tag: condition

value: CMC

tag: Sex


title: CMC_day7_mouse1_plate3 [L3-CMC-M1P3i3]

tag: cell type


title: RNA_THP1_PMA_rep1

description: RNA-seq in THP-1 cells treated with PMA

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using HISAT 2.1.0
Fragments with read qualities greater than 10 were considered for further analysis. Reads mapping to the coding strand of exonic regions were counted using htseq, with gene definitions obtained from the refGene table of RefSeq genes in the UCSC Table Browser.
The table of all counts was processed using DESeq2, using default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file including total numbers of reads overlapping each transcript for each sample.

treatment_protocol: Cells were treated with either 1 uM BRM014 or an equivalent volume of DMSO for either 24 or 72 h prior to library construction. PMA differentiation of THP-1 cells was performed by addition of 10 nM PMA for 48 h, followed by removal of PMA to allow cells to rest for 24 h.

tag: cell line

value: THP-1 cells

tag: marker

value: WT

value: PMA


title: T5_TCR

tag: model

value: Rip-Tag5 PanNET mouse model

tag: mouse model

value: Rip-Tag5 PanNET

tag: treatment group

tag: duration of the treatment

tag: mice id


title: T6_TCR

tag: tissue

value: Tumor

tag: replicate

tag: batch


title: T4_TCR

value: PD1-IL2v + aPD-L1

value: 10 days


title: CMC_day7_mouse1_plate1 [L1-CMC-M1P1i1]

tag: surface marker

value: OT-1 T-cells

tag: mouse


title: Corpus GINS cells after transplantation [CGINS-VIVO]

source_name: GINS grafts under mouse renal capsule

tag: tissue/cell type

value: Corpus GINS cells after transplantation

tag: time points

value: 110 days post transplantation

tag: stomach region


title: heart_ct34_old

value: heart

tag: strain

tag: Sex

value: Male

tag: age group

value: old

tag: circadian time


title: heart_ct34_aged

value: aged


title: Hela_NC

type: RNA

city: jinan

first: shi

middle: qi

last: wang

state: shandong

address: Baotu Spring street

country: China

institute: shandong Univercity

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cervical tissue

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: Cells were seeded in 6-well culture plates, starved in serum-free medium for 24 h and then transfected with siRNA using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA).

tag: cell line

value: Hela

tag: gender

value: female

tag: treatment

value: negative control


title: D7_CMC_Mouse3_Run3 [S14-Day7-sort3-CMC-Mouse3]

description:
Combined_Run2+3+17+19Raw.txt
Norm_Run2_Run3_D7.csv
Run2_Run3_DEG_D7_TFL_VS_CMC.xlsx

data_processing:
Pipeline: Reads were processed using snakemake pipelines as indicated under (https://gitlab.lrz.de/ImmunoPhysio/bulkSeqPipe). Parameters are provided in the configuration (see "config.yaml").
Filtering: Reads were filtered using Trimmomatic v0.36.
Mapping: STAR v2.5.3a was used for mapping to annotation release #91 and genome build #38 from Mus musculus (Ensembl). Multimapped reads were discarded.
Processed data filtering: Genes with a total count <10 were discarded.
Dimensional reduction: Batch effects were eliminated using the removeBatchEffect function provided by limma (v 3.40.6) for PCA analysis.
Differential expression: DESeq2 v1.24.0 was used for differential expression analysis. Differences with a Basemean > 50, an absolute log2 fold change >1 and an adjusted p value <0.05 were considered significant.
Assembly: GRCm38 (release 91)
Supplementary files format and content: Combined_Run2+3+17+19Raw.txt contains the read counts for each gene (rows) in each sample (columns).

extract_protocol:
OT-1 enriched T-cell populations were obtained through anti-CD45.1 biotin anti-biotin microbead staining and magnetic cell separation (Miltenyi Biotech). Highly purified populations (>95%) of the indicated phenotypes were obtained through flow cytometry-based cell sorting (FACSAria Fusion cell sorter). RNA was extracted using the Agencourt RNAdvance Cell v2 kit (A47942, Beckman Coulter) and RNA integrity number (RIN) and yield were assessed using RNA 6000 Pico Kit (5067-1513, Agilent). Only samples with RIN>8 were used for downstream cDNA synthesis and library preparation.
cDNA synthesis and PCR amplification using 1 ng of total RNA from each sample (see "Design_Combined_Run2+3+17+19.txt") was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634891, Takara/Clontech). After cDNA synthesis, each sample was subjected to 12 cycles of PCR amplification. The concentration of generated amplicons was determined using the Agilent High Sensitivity DNA Kit (5067-4626, Agilent). 150 pg of the resulting amplified cDNA was used for library preparation with the Illumina Nextera XT DNA Library reagents (FCSHAPING 131-1024, Illumina). After PCR amplification of the fragmented libraries, the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 μl of molecular grade water. The quality of the resulting library was assessed using the High Sensitivity DNA Kit (5067-4626, Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010, Illumina), with the use of KAPA SYBR FAST qPCR Master Mix (KK4600, Kapa Biosystems).

treatment_protocol: Tables containing 100 mg Leflunomide (Arava®) were grinded in a mortar and resolved in 0,5% Carboxymethylcellulose (CMC). Drugs and CMC control solutions were applied by oral gavage starting 3 days before infection and until 7 days post infection every other day and thereafter every third day. Control and treated mice were infected intravenously with 1000 to 2000 colony-forming units (CFU) of log-phase Listeria monocytogenes stably expressing Ovalbumin containing the native OT-1 ligand SIINFEKL (Lm-N4).

value: spleen

tag: cell type

value: 10 days post Carboxymethylcellulose treatment and 7 days post Lm-N4 infection

tag: condition

value: CMC

tag: run


title: HeLa_si-KNTC1

value: transfected with siKNTC1


title: RNA_THP1_DMSO_rep1

description: RNA-seq in THP-1 cells treated with DMSO

value: THP-1 cells

tag: marker

value: WT

value: DMSO


title: RNA_THP1_PMA_rep2

description: RNA-seq in THP-1 cells treated with PMA

value: PMA


title: T3_TCR

tag: model

value: Rip-Tag5 PanNET mouse model

tag: mouse model

value: Rip-Tag5 PanNET

tag: tissue

value: Tumor

tag: treatment group

value: PD1-IL2v + aPD-L1

tag: duration of the treatment

value: 10 days

tag: mice id

tag: replicate

tag: batch


title: heart_ct30_young

value: heart

tag: strain

tag: Sex

value: Male

tag: age group

value: young


title: RNA_THP1_BRM014-72h_rep2

description: RNA-seq in THP-1 cells treated with BRM014 for 72 h

tag: cell line

value: BRM014 for 72 h


title: RNA_THP1_DMSO_rep2

tag: treatment


title: T2_TCR


title: D7_CMC_Mouse1_Run3 [S12-Day7-sort3-CMC-Mouse1]

value: spleen

tag: surface marker

tag: cell type

value: OT-1 T-cells

tag: mouse


title: D7_CMC_Mouse2_Run3 [S13-Day7-sort3-CMC-Mouse2]

value: 10 days post Carboxymethylcellulose treatment and 7 days post Lm-N4 infection

tag: condition

value: CMC

tag: run


title: RNA_THP1_BRM014-72h_rep1

value: THP-1 cells

tag: marker


title: heart_ct30_aged

tag: tissue

value: aged

tag: circadian time


title: D7_CMC_Mouse2_Run2 [S4-D7-CMC-Mouse2]


title: heart_ct30_old

value: old


title: RNA_THP1_BRM014-24h_rep2

description: RNA-seq in THP-1 cells treated with BRM014 for 24 h

value: WT

value: BRM014 for 24 h


title: Corpus GINS organoids [CGINS-3]

source_name: GINS organoids derived from human corpus stomach

tag: tissue/cell type

value: Corpus GINS organoids

tag: time points

value: 21 days post differentiation

tag: stomach region

value: Corpus


title: RNA_THP1_BRM014-24h_rep1


title: heart_ct26_young


title: RNA_MV411_DMSO_rep2

description: RNA-seq in MV-4-11 cells treated with DMSO

source_name: MV-4-11 cells

value: MV-4-11 cells

value: DMSO


title: SP7

source_name: Spleen

tag: model

value: Rip-Tag5 PanNET mouse model

tag: mouse model

value: Rip-Tag5 PanNET

value: Spleen

tag: treatment group

value: CTRL

tag: duration of the treatment

value: 10 days

tag: mice id

tag: replicate

tag: batch


title: SP6


title: T1_TCR

value: Tumor


title: D7_TFL_Mouse3_Run3 [S11-Day7-sort3-Tfl-Mouse4]

value: spleen

tag: surface marker

tag: cell type

value: OT-1 T-cells

tag: treatment

value: 10 days post Teriflunomide treatment and 7 days post Lm-N4 infection

value: Tfl


title: heart_ct26_old

value: heart

tag: strain

tag: Sex

value: Male

tag: age group

value: old


title: heart_ct26_aged

tag: tissue

value: aged

tag: circadian time


title: RNA_MV411_BRM014-72h_rep2

description: RNA-seq in MV-4-11 cells treated with BRM014 for 72 h

tag: cell line

tag: marker

value: WT

value: BRM014 for 72 h


title: SP5

tag: model


title: D7_TFL_Mouse2_Run3 [S10-Day7-sort3-Tfl-Mouse2]

tag: condition

tag: mouse

tag: run


title: D7_TFL_Mouse1_Run3 [S9-Day7-sort3-Tfl-Mouse1]


title: RNA_MV411_DMSO_rep1

value: MV-4-11 cells

value: DMSO


title: heart_ct22_young

value: young


title: SP4

value: Rip-Tag5 PanNET mouse model

tag: mouse model

value: Rip-Tag5 PanNET

value: Spleen

tag: treatment group

value: PD1-IL2v + aPD-L1

tag: duration of the treatment

tag: mice id


title: RNA_MV411_BRM014-72h_rep1


title: heart_ct22_old


title: D7_TFL_Mouse2_Run2 [S2-D7-Tfl-Mouse2]

value: spleen

tag: surface marker

tag: cell type


title: D7_CMC_Mouse1_Run2 [S3-D7-CMC-Mouse1]

value: OT-1 T-cells

tag: treatment

value: 10 days post Carboxymethylcellulose treatment and 7 days post Lm-N4 infection

value: CMC


title: SP3

value: 10 days

tag: replicate

tag: batch


title: RNA_MV411_BRM014-24h_rep2

description: RNA-seq in MV-4-11 cells treated with BRM014 for 24 h

value: BRM014 for 24 h


title: heart_ct22_aged

tag: tissue

value: heart

tag: strain

tag: Sex

value: Male

tag: age group


title: SP2

tag: model


title: RNA_MV411_BRM014-24h_rep1

tag: cell line

tag: marker

value: WT


title: SP8

value: CTRL


title: D7_TFL_Mouse1_Run2 [S1-D7-Tfl-Mouse1]

value: 10 days post Teriflunomide treatment and 7 days post Lm-N4 infection

tag: condition

value: Tfl

tag: mouse

tag: run


title: D28_CMC_Mouse5_Run3 [S8-D27-CMC-Mouse5]

description:
Combined_Run2+3+17+19Raw.txt
Norm_Run2_Run3_D28.csv
Run2_Run3_DEG_D28_TFL_VS_CMC.xlsx

value: 31 days post Carboxymethylcellulose treatment and 28 days post Lm-N4 infection


title: heart_ct18_young

value: young

tag: circadian time


title: SP1

value: Rip-Tag5 PanNET mouse model

tag: mouse model

value: Rip-Tag5 PanNET

tag: treatment group

tag: duration of the treatment

tag: mice id


title: RNA_MOLM_DMSO_rep2

description: RNA-seq in MOLM-13 cells treated with DMSO

source_name: MOLM-13 cells

value: MOLM-13 cells

tag: treatment

value: DMSO


title: T8

value: Tumor

tag: replicate

tag: batch


title: RNA_MOLM_DMSO_rep1


title: D28_CMC_Mouse4_Run3 [S19-Day33-sort1-CMC-Mouse4]

tag: tissue

value: spleen

tag: surface marker

tag: cell type

value: OT-1 T-cells


title: heart_ct18_aged

tag: strain

tag: Sex

tag: age group

value: aged


title: RNA_MOLM_BRM014-72h_rep2

description: RNA-seq in MOLM-13 cells treated with BRM014 for 72 h

tag: cell line

tag: marker

value: BRM014 for 72 h


title: heart_ct18_old

value: heart

value: old


title: T7

tag: model

value: 10 days


title: adrenal_ct62_young

source_name: adrenal

value: adrenal

value: Male

tag: circadian time


title: D28_CMC_Mouse5_Run2 [S20-Day33-sort1-CMC-Mouse5]

tag: condition

value: CMC

tag: mouse

tag: run


title: D28_CMC_Mouse4_Run2 [S7-D27-CMC-Mouse4]

value: 31 days post Carboxymethylcellulose treatment and 28 days post Lm-N4 infection


title: adrenal_ct62_old


title: D28_TFL_Mouse3_Run3 [S18-Day33-sort1-Tfl-Mouse3]

value: 31 days post Teriflunomide treatment and 28 days post Lm-N4 infection

value: Tfl


title: RNA_MOLM_BRM014-24h_rep2

description: RNA-seq in MOLM-13 cells treated with BRM014 for 24 h

value: WT

value: BRM014 for 24 h


title: adrenal_ct62_aged


title: RNA_MOLM_BRM014-72h_rep1

value: MOLM-13 cells


title: T5

value: Rip-Tag5 PanNET mouse model

tag: mouse model

value: Rip-Tag5 PanNET

value: Tumor

tag: treatment group

tag: duration of the treatment

tag: mice id


title: T4

tag: tissue

value: PD1-IL2v + aPD-L1

tag: replicate

tag: batch


title: adrenal_ct58_young

tag: strain

value: young


title: D28_CMC_Mouse1_Run3 [S16-Day27-sort3-CMC-Mouse1]

value: spleen

tag: surface marker

tag: cell type

value: OT-1 T-cells

tag: treatment


title: D28_TFL_Mouse4_Run3 [S15-Day27-sort3-Tfl-Mouse4]


title: D28_TFL_Mouse2_Run3 [S17-Day33-sort1-Tfl-Mouse2]


title: T3

value: 10 days


title: T2


title: RNA_MOLM_BRM014-24h_rep1

tag: cell line

tag: marker


title: adrenal_ct58_aged

value: adrenal

tag: Sex

tag: age group

value: aged

tag: circadian time


title: P953

city: La Jolla

first: Mariko

last: Horii

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Quality control was performed using FastQC (v. 0.11.3). Reads were mapped to GRCh38.89 (Ensembl) using STAR (v. 2.5.3a) (Dobin et al., 2013). The STAR parameters used were: --runThreadN 24 --sjdbOverhang 99 --genomeDir ref_ensembl_GRCh38_89/star_index --sjdbGTFtagExonParentGene gene_id --sjdbGTFfile ref_ensembl_GRCh38_89/Homo_sapiens.GRCh38.89.gtf --outSAMtype BAM Unsorted SortedByCoordinate --outReadsUnmapped Fastx --quantMode GeneCounts. Ensembl genes with at least 10 counts in 25% of samples were filtered for the analysis. Normalization and differential expression analysis were performed using R (v. 4.0.3) package DESeq2 (v. 1.30.1) (Love 2014). BiomaRt (v. 2.42.1) was used to convert Ensembl gene ID to HUGO gene names (Durinck 2009), and gene set enrichment analysis was done using R (v. 4.0.3) package FGSEA (v. 1.16.0).
Genome_build: GRCh38.89(Ensembl)
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample post filtering

source_name: Placental tissue

extract_protocol:
Total RNA was isolated using mirVana RNA Isolation Kit (ThermoFisher). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by Aligent 2100 bioanalyzer. All samples had a RIN above 7.0.
RNAseq libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit with Ribo-Zero Gold (Illumina).

tag: disease

value: Non-hypertensive Control

tag: gender

value: Male

tag: sga

value: yes


title: adrenal_ct58_old

value: old


title: adrenal_ct54_old


title: T1

tag: model

tag: mouse model

tag: treatment group

tag: duration of the treatment


title: P869

value: Severe preeclampsia


title: D28_TFL_Mouse3_Run2 [S5-D27-Tfl-Mouse3]

tag: tissue

value: 31 days post Teriflunomide treatment and 28 days post Lm-N4 infection

tag: condition

value: Tfl

tag: mouse

tag: run


title: CD127_D7_CMC_Mouse4_Run19 [L4-19-D7-CD127-CMC4]

description:
Combined_Run2+3+17+19Raw.txt
Norm_Run17_Run19_D7.csv
Run17_Run19_DEG_D7_TFL_VS_CMC.xlsx

tag: surface marker

tag: cell type

tag: treatment

value: 10 days post Carboxymethylcellulose treatment and 7 days post Lm-N4 infection

value: CMC


title: D28_TFL_Mouse2_Run2 [S6-D27-Tfl-Mouse2]


title: T6

value: Rip-Tag5 PanNET mouse model

value: Rip-Tag5 PanNET

value: Tumor

tag: mice id

tag: replicate

tag: batch


title: P760

tag: disease


title: adrenal_ct50_young

tag: strain

tag: Sex

tag: age group

value: young

tag: circadian time


title: CD127_D7_CMC_Mouse3_Run19 [L3-19-D7-CD127-CMC3]

value: spleen

value: OT-1 T-cells


title: adrenal_ct54_young

value: adrenal


title: adrenal_ct50_aged

value: aged


title: adrenal_ct50_old


title: adrenal_ct54_aged


title: CD127_D7_CMC_Mouse1_Run19 [L1-19-D7-CD127-CMC1]


title: CD127_D7_CMC_Mouse5_Run17 [S5-Seq17-CMC-S1M5A2]


title: P716

value: Non-hypertensive Control

tag: gender

tag: sga


title: adrenal_ct46_young

tag: tissue

value: Male


title: CD127_D7_CMC_Mouse4_Run17 [S4-Seq17-CMC-S1M4A2]

tag: condition


title: DCs_rep2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: dendritic cells

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

source_name: dendritic cells

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 50 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA was extracted from cells with an miRNeasy Mini kit (Qiagen) following the manufacturer’s instruction.

value: dendritic cells


title: adrenal_ct46_old

value: old


title: 6G- BM-MDSC_rep2

description: MDSCs differentiated in the absence of Ly-6G+ BM cells

value: myeloid-derived suppressor cells


title: P855

value: Severe preeclampsia

value: Female

value: yes


title: DCs_rep1

description: dendritic cells


title: 6G- BM-MDSC_rep1

source_name: MDSCs differentiated in the absence of Ly-6G+ BM cells


title: P641


title: adrenal_ct46_aged


title: adrenal_ct42_young


title: MDSC (conv.)_rep1

description: MDSCs with dendritic cells

source_name: MDSCs differentiated from whole BM cells


title: CD127_D7_CMC_Mouse3_Run17 [S3-Seq17-CMC-S1M3A2]

value: 10 days post Carboxymethylcellulose treatment and 7 days post Lm-N4 infection

value: CMC

tag: mouse


title: P611


title: P686


title: MDSC (conv.)_rep2

description: MDSCs with dendritic cells


title: CD127_D7_CMC_Mouse5_Run19 [L5-19-D7-CD127-CMC5]

tag: run


title: HASMC M(Hb) OS 4

city: Gaithersburg

first: Atsushi

last: Sakamoto

address: 19 Firstfield Road

institute: CVPath Institute

hyb_protocol: All reactions and hybridizations were carried out according to the manufacturer's protocol (Affymetrix; Thermo Fisher Scientific). Affymetrix GeneChip Human Clariom S array (Thermo Fisher Scientific) were washed using the GeneChipTM Fluidics Station 450 (Thermo Fischer Scientific).

scan_protocol: Affymetrix GeneChip Human Clariom S arrays were scanned with the GeneChip Scanner 3000 (Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fischer Scientific) using default analysis setting. GO enrichment analysis of unbiased differentially expressed genes (DEGs) were conducted by DAVID v6.8 bioinformatics resources.

label: biotin

source_name: HASMC, M(Hb)+OS, 6h.

label_protocol: GeneChipTM WT Plus Reagent Kit were used for generating biotinylated ss-cDNA for hybridization.

growth_protocol: HASMC (Cell applications) were cultured using the smooth muscle cell growth medium (Cell applications) in humidified air (5% of CO2) at 37 °C.

extract_protocol: Total RNA was extracted using Rneasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Human Peripheral blood mononuclear cells (PBMC) collected from healthy volunteers (Astarte Biologics) were seeded into culture plates (3-4 x 106 cell/well). After 6 hours incubation, non-attached cells were removed, and culture media was replaced. Remaining monocyte/macrophage fraction were differentiated over 6 days into macrophages with RPMI 1640 medium supplemented with 10% human serum and penicillin-streptomycin in humidified air (5% of CO2) at 37 °C. Prior to use, human hemoglobin and haptoglobin were reconstituted in RPMI 1640 medium, which were added to cultured monocytes at 6 hours after plating (hemoglobin:haptoglobin complexes [HH], final concentration of 0.1 mg/ml,). After differentiation of human monocytes over 6-days with or without HH, supernatant from control macrophages [M(con)] and HH-differentiated [M(Hb)] macrophages were used in further experiments. HASMCs were cultivated for 6 hours in M(con) or M(Hb) macrophage supernatant supplemented by CaCl2 (4 mM), β-glycerophosphate (5 mM), l-ascorbic acid (50 µg/mL), insulin (1 µM), and dexamethasone (0.1 µM) (osteogenic media components [OS]).

value: HASMC exposed to M(Hb) supernatant and osteogenic components (6 hours)

value: human aortic smooth muscle cell (HASMC)


title: P691


title: HASMC M(Hb) OS 3


title: adrenal_ct42_aged

data_processing:
Alignment was performed by using HISAT2 software
Duplicated aligned reads were marked and removed using the Picardtools software
The gene expression count data were extracted using the HTseq software
The raw count data were normalized to cpm (counts per million reads)
Assembly: GRCm38 (mm10)
Supplementary files format and content: count_216.csv: gene expression count data
Supplementary files format and content: cpm_216.csv: normalized count data (count per million reads)


title: adrenal_ct42_old


title: HASMC M(Hb) OS 1


title: CD127_D7_TFL_Mouse5_Run19 [L10-19-D7-CD127-Tfl5]

tag: surface marker

value: 10 days post Teriflunomide treatment and 7 days post Lm-N4 infection

value: Tfl


title: CD127_D7_CMC_Mouse1_Run17 [S1-Seq17-CMC-S1M1A2]

value: spleen

tag: cell type

value: OT-1 T-cells


title: CD127_D7_CMC_Mouse2_Run19 [L2-19-D7-CD127-CMC2]

tag: treatment


title: adrenal_ct38_young

value: adrenal

value: young


title: HASMC M(Hb) OS 2


title: HASMC M(con) OS 4

source_name: HASMC, M(con)+OS, 6h.

value: HASMC exposed to M(con) supernatant and osteogenic components (6 hours)


title: P571


title: CD127_D7_CMC_Mouse2_Run17 [S2-Seq17-CMC-S1M2A2]

source_name: spleen


title: P550


title: adrenal_ct38_old

value: Male


title: CD127_D7_TFL_Mouse3_Run19 [L8-19-D7-CD127-Tfl3]


title: HASMC M(con) OS 3


title: CD127_D7_TFL_Mouse4_Run19 [L9-19-D7-CD127-Tfl4]


title: CD127_D7_TFL_Mouse2_Run19 [L7-19-D7-CD127-Tfl2]


title: P538


title: P606

value: Non-hypertensive Control

value: no


title: adrenal_ct38_aged

value: aged


title: P1940


title: HASMC M(con) OS 2


title: adrenal_ct34_young


title: HASMC M(con) OS 1


title: D3_2, standard Malus robusta flowers

city: Baoding

first: Guofang

last: Li

address: No.289 street

institute: Hebei Agricultural University

data_processing:
mapped reads of each sample were assembled by StringTie (v1.3.3b)
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package
ClusterProfiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways
Assembly: apple HFTH1 Whole Genome v1.0
Supplementary files format and content: Tab-separated values files

organism: Malus x robusta

source_name: flower

extract_protocol:
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)
cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA)

value: flower

tag: genotype

value: standard

tag: developmental stage

value: late flowering stage


title: D3_1, standard Malus robusta flowers


title: D2_3, weakly fragrant flower

value: weakly fragrant


title: D3_3, standard Malus robusta flowers


title: P1866

value: Severe preeclampsia

value: Female

value: yes


title: adrenal_ct34_old

extract_protocol:
Samples were homogenized in Trizol, and RNA extracted accordinng to manufacturer protocol
RNAseq libraries were prepared with Illumina RNA-Seq libraries (Poly A) kit following manufacturer's protocols.

value: old


title: CD127_D7_TFL_Mouse3_Run17 [S8-Seq17-Tfl-S1M4A1]

value: spleen

value: 10 days post Teriflunomide treatment and 7 days post Lm-N4 infection

value: Tfl


title: adrenal_ct34_aged

value: adrenal


title: CD127_D7_TFL_Mouse2_Run17 [S7-Seq17-Tfl-S1M3A1]

value: OT-1 T-cells


title: adrenal_ct30_young

value: Male

value: young


title: D2_2, weakly fragrant flower


title: CD127_D7_TFL_Mouse1_Run17 [S6-Seq17-Tfl-S1M2A0]


title: adrenal_ct30_old


title: adrenal_ct30_aged


title: P1802

value: Non-hypertensive Control


title: CD127_D7_TFL_Mouse4_Run17 [S9-Seq17-Tfl-S1M5A1]


title: Dox-WD-plus-10D-minus-49D-Rep2 (RNA-seq)

city: Shenzhen

first: Qing

last: Ma

address: 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, P.R.China

institute: Shenzhen Institutes of Advanced Technology

data_processing:
Raw reads were aligned to the mouse reference sequences NCBI Build 37/mm9 with STAR aligner.
Expression levels of RefSeq annotated genes were calculated using RSEM.
The differential analysis was conducted using R package DESeq2.
The Benjamini hochberg procedure was used to adjust for multiple hypothesis testing.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: breast

growth_protocol: The cells were cultured in DMEM/F-12 media with 5% Tet System Approved FBS, 1% P/S Penicillin-Streptomycin, 5 μg/mL insulin from bovine and 1 μg/mL hydrocortisol.

extract_protocol:
Total RNA of iHOT+ cells with different treatments were extracted by Trizol following RNA clean-5 kit.
Poly-A-selected RNA was isolated and the libraties were prepared with the dUTP protocol

treatment_protocol: Three conditions of iHOT+ cells were used in this study: Dox+, Dox- and Dox withdrawal (DoxWD). In the Dox+ group, iHOT+ cells were treated with 2 μg/mL DOX for 7 days or 18 days; in the Dox- group, iHOT+ cells were treated with solvent control for 18 days or 59 days; and in the DoxWD group, iHOT+ cells were first treated with DOX for 10 days then removed for another 49 days.

value: breast

tag: cell line

value: primary breast tumor

value: epithelioid cell

value: iHOT+ rtTA+ PyMT+

value: DoxWD


title: CD127_D7_TFL_Mouse1_Run19 [L6-19-D7-CD127-Tfl1]


title: D1_2, strongly fragrant flower

value: flower

value: strongly fragrant

value: late flowering stage


title: D2_1, weakly fragrant flower

value: weakly fragrant


title: adrenal_ct26_young


title: Dox-WD-plus-10D-minus-49D-Rep1 (RNA-seq)


title: adrenal_ct26_aged

value: aged


title: C3_3, standard Malus robusta flowers

value: standard

value: early flowering stage


title: Dox-plus-7D-Rep1 (RNA-seq)

value: Dox+


title: adrenal_ct26_old

value: adrenal

value: old


title: P1702

tag: disease

value: Female

value: no


title: Dox-plus-18D-Rep2 (RNA-seq)

value: breast


title: adrenal_ct22_old

tag: strain

value: Male


title: Dox-plus-7D-Rep2 (RNA-seq)

value: primary breast tumor

value: epithelioid cell


title: P1737

value: Non-hypertensive Control


title: adrenal_ct22_young

tag: Sex

value: young


title: P1565

value: Severe preeclampsia

value: yes


title: P1632


title: D1_3, strongly fragrant flower

value: flower

value: strongly fragrant

value: late flowering stage


title: adrenal_ct22_aged

tag: age group

value: aged


title: C3_2, standard Malus robusta flowers

value: standard

value: early flowering stage


title: Dox-plus-18D-Rep1 (RNA-seq)

value: iHOT+ rtTA+ PyMT+

value: Dox+


title: C2_3, weakly fragrant flower

value: weakly fragrant


title: Dox-minus-18D-Rep2 (RNA-seq)

value: breast

value: Dox-


title: Dox-minus-18D-Rep1 (RNA-seq)

value: primary breast tumor


title: C3_1, standard Malus robusta flowers


title: adrenal_ct18_young

value: adrenal

value: Male

tag: circadian time


title: adrenal_ct18_old

value: old


title: Dox-minus-59D-Rep2 (RNA-seq)

value: epithelioid cell


title: D1_1, strongly fragrant flower


title: C2_1, weakly fragrant flower


title: P1449

value: Severe preeclampsia

tag: gender

value: yes


title: Dox-minus-59D-Rep1 (RNA-seq)


title: C2_2, weakly fragrant flower

value: flower


title: C1_3, strongly fragrant flower

value: strongly fragrant


title: C1_2, strongly fragrant flower


title: Lefl-Spleen4

description: scRNA-Seq (10x Genomics)

data_processing:
Pipeline: Read alignment and gene counting with single-cell resolution were performed with 10x Genomics Cell Ranger v6.0.180, using the default parameters and the pre-built mouse reference v2020-A (10x Genomics, Inc) based on mm10 - GENCODE vM23/Ensembl 98.
Filtering: Only cells with more than 2000 genes detected, less than 10% of mitochondrial genes and with UMI counts less than 3 standard deviations above the mean were kept for downstream analysis. Only data for genes detected in at least 3 cells in each sample were kept. Contaminating cells were filtered out based on the cluster expression of the marker genes Cd14, Lyz2, Fcgr3, Ms4a7, Fcer1g, Cst3, H2-Aa, Ly6d, Ms4a1, Cd19 and mitochondrial genes.
Normalization: Filtered read counts from a treatment and control replicates were merged and the merged replicates were normalized separately using the R package sctransform v0.3.281 (with glmGamPoi method).
Integration: Anchors between replicates were identified on top 1000 highly variable genes and integration performed on first 20 dimensions using the R package Seurat v4.0.1. PCA was calculated on the top 1000 highly variable genes.
Dimensional reduction: KNN graph was computed on the first 20 PCA dimensions and 30 nearest neighbors, similarly to UMAP calculation, which was performed using spread 1 and minimal distance 0.1.
Clustering: Shared nearest neighbor (SNN) modularity optimization-based algorithm was applied for cluster identification on top 20 principal components and resolution 0.33 using the Louvain algorithm.
Trajectory: Diffusion maps were calculated using the R package destiny v3.4.083. The top 1000 highly variable genes and first 50 principal components were used and the maps were rotated for better visualization. Transcriptional trajectory was identified using the diffusion pseudotime algorithm.
Assembly: GRCm38.p6 (release 98) - GENCODE Release M23
Supplementary files format and content: Cellranger compressed files contain the filtered UMI counts matrix (Market Exchange Format for sparse matrices) and TSV files with genes and barcode sequences (corresponding to row and column indices respectively) as output by Cell Ranger.
Supplementary files format and content: The file OT1_Lefl_vs_CMC_norm.txt contains the metadata for each cell in the whole experiment, with rows being cells and columns being annotated features. It also contains the normalized expression data for each gene (column) in each cell (row).

extract_protocol:
At day 4 post Lm-OVA infection, splenocytes were enriched for CD45.1+ OT-1 T-cells using anti-CD45.1 biotin/ anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech, Bergisch-Gladbach, Germany). Single-cells were sorted on a BD FACS Fusion (100 micron nozzle, standard operation settings, single-cell purity, index sorting). 5000 individual living CD8+ CD45.1+ cells were recovered and resuspended in complete media.
Gene expression libraries for single cell sequencing were prepared by using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 and the 10x Chromium Controller (10x Genomics) following the manufacturer’s protocol (CG000204 Rev D). Single Index Kit T Set A was used for multiplexing (i7 index read, 8bp). The samples were sequenced in a paired-end run (read 1: 28bp, read 2: 91bp) on a NovaSeq6000 platform using S1 v1.5 (100 cycles) sequencing kits (Illumina).

treatment_protocol: Tables containing 100 mg Leflunomide (Arava®) were grinded in a mortar and resolved in 0,5% Carboxymethylcellulose (CMC). Drugs and CMC control solutions were applied by oral gavage starting 3 days before infection every other day. Four control and Four treated mice were infected intravenously with 1000 to 2000 colony-forming units (CFU) of log-phase Listeria monocytogenes stably expressing Ovalbumin containing the native OT-1 ligand SIINFEKL (Lm-N4).

value: spleen

value: OT-1 T-cells

value: 7 days post Teriflunomide treatment and 4 days post Lm-N4 infection

value: Lefl

value: female


title: P1389

value: Non-hypertensive Control

value: Female

tag: sga

value: no


title: Dox-WD-plus-10D-minus-49D-Rep1 (ATAC-seq)

data_processing:
Adaptor sequence trimming using in-house software and mapping to mm9 using Bowtie2 were performed.
The reads were then filtered for mitochondrial reads, low-quality reads, PCR duplicates, and black list regions. The filtered reads for each group were merged, and peak calling was performed by MACS2.
The reads in peaks for each individual sample were quantified using BEDTools multicov with the merged MACS2 narrow peaks. Peak counts were then combined into an N × M matrix where N represents called peaks, M represents the samples, and each value Di,j represents the peak intensity for respective peak i in sample j.
Each peak was annotated by the nearest gene. This matrix was then normalized using R package DESeq2, and differential analysis was conducted using negative binomial models.
The Benjamini hochberg procedure was used to adjust for multiple hypothesis testing.
Assembly: mm9
Supplementary files format and content: bigWig

extract_protocol:
ATAC–seq of iHOT+ cells with different treatments were performed as previously described (Corces et al., 2017). Briefly, 50000 cells were pelleted, resuspended in 50 μl of lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% NP-40 (Igepal CA-630)), and immediately centrifuged at 500g for 10 min at 4 °C. The nuclei pellets were resuspended in 50 μl of transposition buffer (25 μl of 2× TD buffer, 22.5 μl of distilled water, 2.5 μl of Illumina Tn5 transposase) and incubated at 37 °C for 30 min. Transposed DNA was purified with the MinElute PCR Purification kit (Qiagen), and eluted in 10 μl of EB buffer.
Library fragments were amplified using NEBnext PCR master mix as previously described (Corces et al., 2017)

tag: tissue

value: breast

value: primary breast tumor

value: iHOT+ rtTA+ PyMT+

value: DoxWD


title: C1_1, strongly fragrant flower

value: early flowering stage


title: Dox-WD-plus-10D-minus-49D-Rep2 (ATAC-seq)

value: epithelioid cell


title: Lefl-Spleen2

description: scRNA-Seq (10x Genomics)

tag: condition


title: A3_3, standard Malus robusta flowers

value: standard

value: small balloon stage


title: Lefl-Spleen1

description: scRNA-Seq (10x Genomics)

tag: mouse


title: Dox-plus-7D-Rep1 (ATAC-seq)

value: Dox+


title: A3_2, standard Malus robusta flowers

value: flower


title: CMC-Spleen5

description: scRNA-Seq (10x Genomics)

value: spleen

value: OT-1 T-cells

value: 7 days post Carboxymethylcellulose treatment and 4 days post Lm-N4 infection

value: CMC


title: adrenal_ct18_aged

value: adrenal

value: Male

value: aged


title: A3_1,standard Malus robusta flowers


title: CMC-Spleen3

description: scRNA-Seq (10x Genomics)

value: female


title: A2_3, weakly fragrant flower

value: weakly fragrant


title: A2_2, weakly fragrant flower


title: P1213

value: Severe preeclampsia

value: Female

value: yes


title: P1232


title: CMC-Spleen2

description: scRNA-Seq (10x Genomics)


title: A2_1, weakly fragrant flower


title: CMC-Spleen1

description: scRNA-Seq (10x Genomics)


title: Lefl-Spleen3

description: scRNA-Seq (10x Genomics)

value: 7 days post Teriflunomide treatment and 4 days post Lm-N4 infection

value: Lefl


title: A1_3, strongly fragrant flower

value: strongly fragrant

value: small balloon stage


title: P1080


title: Dox-minus-59D-Rep2 (ATAC-seq)

value: breast

value: primary breast tumor

value: epithelioid cell

value: iHOT+ rtTA+ PyMT+

value: Dox-


title: Dox-minus-18D-Rep2 (ATAC-seq)


title: Dox-minus-59D-Rep1 (ATAC-seq)


title: A1_2, strongly fragrant flower

value: flower


title: Dox-plus-18D-Rep2 (ATAC-seq)

value: Dox+


title: A1_1, strongly fragrant flower


title: Dox-plus-18D-Rep1 (ATAC-seq)


title: Dox-minus-18D-Rep1 (ATAC-seq)


title: P1017

value: Male


title: Dox-plus-7D-Rep2 (ATAC-seq)


title: P1160


title: P1138

value: Non-hypertensive Control


title: KHYG-1_Glycodelin_8h_4

status: Public on Jan 09 2023

city: Heidelberg

first: Sarah

last: Richtmann

address: Roentgenstr. 1

department: Translational Research Unit

institute: Thoraxklinik Heidelberg

hyb_protocol: Fragmented cRNAs (10 µg each) were hybridized to Affymetrix U133 Plus 2.0 arrays at 45 ºC for 16 hours (GeneChip®  Hybridization Oven 640, Affymetrix). Washing and staining involving conjugate R-Phycoerythrin Streptavidin SAPE (Invitrogen, Carlsbad, CA, USA) and Biotinylated anti-streptavidin antibody (Vector Laboratories, Burlingame, CA, USA) was performed using an Affymetrix GeneChip® Fluidics Station 450

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 using Affymetrix ROC protocol.

data_processing: Data were analyzed using Transcriptome Analysis Console and Ingenuity Pathway Analysis Software

source_name: cell line KHYG-1

label_protocol: cRNA was generated, biotin-labeled and fragmented using GeneChip Expression 3´-Amplification Reagents for IVT Labeling Kit and GeneChip Sample Cleanup Module, Affymetrix. RNA integrity was controlled with an Agilent 2100 Bioanalyzer and an Agilent RNA 6000 Nano Kit

growth_protocol: 5x10^5 cells were seeded in serum deprived medium in 12 well plates.

extract_protocol: Cells were washed and frozen prior to RNA extraction with AllPreP DNA/RNA Mini Kit (Qiagen)

treatment_protocol: Control or knockdown 4950T cell culture supernatant was concentrated using an Amicon filter column with a 30 kDa cutoff and glycodelin levels were measured via ELISA. The supernatants were diluted to final glycodelin concentrations of 200 ng/ml (control) and 60 ng/ml (knockdown) in RPMI without FBS (+ 10 ng/ml IL-2 for KHYG-1 treatment). The immune cell lines Jurkat, THP1, and KHYG-1 were washed and 5 x 10^5 cells were treated with 1 ml of condensed supernatant for 3, 8, or 24 h.

value: Natural killer cell leukemia

value: Peripheral blood

tag: agent

value: Glycodelin

tag: time point


title: KHYG-1_Glycodelin_24h_1

tag: cell type


title: KHYG-1_noGlycodelin_24h_1


title: KHYG-1_Glycodelin_24h_5


title: KHYG-1_Glycodelin_8h_2


title: KHYG-1_noGlycodelin_8h_4


title: KHYG-1_noGlycodelin_24h_5


title: KHYG-1_noGlycodelin_3h_3


title: KHYG-1_Glycodelin_8h_3


title: KHYG-1_noGlycodelin_3h_2


title: KHYG-1_Glycodelin_8h_1


title: KHYG-1_noGlycodelin_24h_4


title: KHYG-1_noGlycodelin_8h_1


title: KHYG-1_Glycodelin_3h_1


title: KHYG-1_Glycodelin_24h_4


title: KHYG-1_noGlycodelin_8h_3


title: THP1_noGlycodelin_24h_2

source_name: cell line THP1

value: Acute monocytic leukemia monocyte


title: KHYG-1_Glycodelin_3h_4


title: S1M ST2 expression 15% or more. biological rep1

city: ChunCheon-si

first: Jun Won

last: Park

address: Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Kangwondaehak-gil

country: South Korea

institute: kangwon national univercity

description: Gene expression data from ST2 high S1M cell

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse ST 2.0 Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

organism: Mus

source_name: S1M ST2 expression 15% or more

label_protocol: The sense cDNA was fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: S1M cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37˚C in a 5% CO2 humidified incubator.

extract_protocol: total cellular RNA were extracted with a HiYield Total RNA Mini Kit (YRB100; Real Biotech Corporation, Banqiao, the Republic of China) following the accompanying instructions.

treatment_protocol: To separate ST2 high low expression, murine GC cells were dissociated into single cells by TrypLE (12605-028; Invitrogen, Carlsbad, CA, USA) and stained with PE-rat monoclonal anti- IL-33R(ST2) antibody (12-9335-80, eBioscience, San Diego, CA, USA)  for 1 hour at 4˚C in the dark.  Then, the top 15% and bottom 15% of st2 expression were separated using Flow Cytometry Sorter. They were rinsed with DPBS and LYSIS was performed. (HiYield Total RNA Mini Kit)

value: gastric cancer

value: ChetPS mouse model, named S1

tag: age

value: passage 31


title: THP1_noGlycodelin_24h_1


title: THP1_noGlycodelin_24h_4


title: KHYG-1_Glycodelin_3h_3


title: KHYG-1_noGlycodelin_3h_4


title: KHYG-1_noGlycodelin_8h_2


title: KHYG-1_noGlycodelin_3h_1


title: S1M ST2 expression 15% or less. biological rep1

description: Gene expression data from ST2 low S1M cell

source_name: S1M ST2 expression 15% or less

tag: genotype


title: THP1_noGlycodelin_24h_3


title: THP1_Glycodelin_24h_4


title: KHYG-1_Glycodelin_3h_2


title: THP1_Glycodelin_24h_3


title: THP1_Glycodelin_24h_2


title: THP1_noGlycodelin_8h_3


title: THP1_noGlycodelin_8h_4


title: THP1_noGlycodelin_8h_1


title: THP1_Glycodelin_8h_4


title: THP1_noGlycodelin_3h_2


title: THP1_Glycodelin_8h_2


title: THP1_Glycodelin_8h_1


title: THP1_Glycodelin_3h_4


title: THP1_Glycodelin_3h_3


title: THP1_Glycodelin_24h_1


title: THP1_Glycodelin_3h_2


title: THP1_noGlycodelin_8h_2


title: THP1_Glycodelin_8h_3


title: Jurkat_Glycodelin_24h_3

source_name: cell line Jurkat

value: T cell leukemia

value: Jurkat


title: THP1_noGlycodelin_3h_3


title: Jurkat_noGlycodelin_24h_3


title: Jurkat_Glycodelin_24h_2


title: Jurkat_noGlycodelin_24h_2


title: Jurkat_Glycodelin_24h_1


title: THP1_noGlycodelin_3h_4


title: Jurkat_noGlycodelin_24h_4


title: Jurkat_noGlycodelin_8h_2


title: Jurkat_noGlycodelin_8h_4


title: THP1_Glycodelin_3h_1


title: Jurkat_Glycodelin_24h_4


title: Jurkat_noGlycodelin_8h_3


title: Jurkat_noGlycodelin_24h_1


title: Jurkat_Glycodelin_8h_4


title: THP1_noGlycodelin_3h_1


title: Jurkat_noGlycodelin_8h_1


title: 4502511-1A

city: Stanford

first: Myung Chang

last: Lee

address: 265 Campus Drive, G2065

department: Pediatrics and Genetics

institute: Stanford University

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software. Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fatq files and de-multiplexed using Illumina bcl2fastq 2.20 software.
Sequenced reads were trimmed for adapter sequences.
Transcript quantification was conducted using Salmon v0.12.0 with GRCm38 mouse genome
Tximeta package (v1.12.4) running on R (v4.1.0) was used for mapping Ensembl transcript IDs to gene symbols and for quantifying scaledTPM values.
Assembly: GRCm38

source_name: Transformed lung epithelial cell

extract_protocol:
Total RNA extraction, polyA selection, and quality control were performed by Azenta Inc.
RNA library was constructed by Azenta Inc. using NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (New Englad Biolabs, Ipswich, MA, USA).

value: Lung

tag: treatment

value: Intratracheal transduction with HIV-PGK-Cre


title: 4482861-1

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-PGK-Cre


title: 4482862-1R

value: Intratracheal transduction with Ad-CMV-Cre


title: Jurkat_Glycodelin_8h_3

tag: cell line


title: NL354

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with Ad-CMV-Cre


title: p27_d2_RNA

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

description: RNA from 2+1 DIV differentiating WT cells. Replicate 2

data_processing:
Read file QC Total reads were analysed with FastQC and visually inspected to make sure each sequenced sample met the adequate quality standards.
Adapter clipping, quality trimming and filtering Adapter clipping and low-quality read filtering with Trimmomatic and Cutadapt.
Genome alignment Raw sequences were aligned to the Ensembl mouse transcriptome using STAR
Read count extraction Read counts per gene were extracted with RSEM
Filtering by expression and normalization DESeq2 outlier removal, low count filtering, and normalization.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file containing the RSEM raw read count matrix

source_name: mouse brain NSC cultures

growth_protocol: Methods for NSC culture derived from SEZ have been previously described in detail (Belenguer et al, 2016 https://doi.org/10.1016/j.diff.2016.01.005).

extract_protocol:
Samples were lysed with the QIAzol Lysis Reagent (Qiagen, 79306) and RNA was extracted with the miRNeasy micro kit (Qiagen, 217084). RNA quality was verified with a 2100 Bioanalyzer (Agilent Technologies)
cDNA was generated using Ovation RNA-seq System V2 (Tecan, 7102-A01) and libraries were constructed using the Ovation Ultralow System V2 (Tecan, 0344NB-A01)

treatment_protocol: For proliferation assays, NSCs were grown in neurosphere control medium containing 20 ng/ml epidermal growth factor (EGF) (Invitrogen, 53003-018) and 10 ng/ml fibroblast growth factor (FGF) (Sigma, F0291). Importantly, for bulk differentiation assays on secondary neurospheres, 40,000 cells/cm2 were seeded for 2 days (2 DIV) in Matrigel®-coated coverslips and in control medium with FGF. After these 48 h, mitogens were removed and cells were grown in control medium supplemented with 2% Fetal Bovine Serum (FBS). Differentiating cultures were analyzed 24 h (2+1 DIV), or 5 days (2+5 DIV) after mitogen withdrawal depending on the experimental procedure.

value: Cdkn1b (p27KO)

value: brain subependymal zone

value: 10 weeks

tag: cells

value: adult NSC cultures


title: p27_d1_RNA

description: RNA from 2+1 DIV differentiating WT cells. Replicate 1


title: p27_p2_RNA

description: RNA from 3 DIV proliferating WT cells. Replicate 2


title: p27_p1_RNA

description: RNA from 3 DIV proliferating WT cells. Replicate 1


title: Jurkat_Glycodelin_8h_2

value: Peripheral blood


title: Jurkat_Glycodelin_8h_1

value: Glycodelin


title: Jurkat_noGlycodelin_3h_2


title: 4482862-2R


title: wt_d2_RNA

value: WT


title: wt_p1_RNA


title: wt_p3_RNA

description: RNA from 3 DIV proliferating WT cells. Replicate 3


title: Jurkat_Glycodelin_3h_4


title: wt_d1_RNA


title: wt_d3_RNA

description: RNA from 2+1 DIV differentiating WT cells. Replicate 3


title: Jurkat_noGlycodelin_3h_3


title: Jurkat_noGlycodelin_3h_4


title: Jurkat_Glycodelin_3h_3


title: Jurkat_noGlycodelin_3h_1


title: p27_p2_ATAC

description: ATAC from 3 DIV proliferating WT cells. Replicate 2

data_processing:
Read file QC Paired-end sequencing files were analyzed with FastQC, summarized with MultiQC and visually inspected for major quality issues.
Adapter clipping, quality trimming and filtering We used Cutadapt to clip the Nextera 3’ R1 and R2 adapters and then Trimmomatic to trim low-quality portions and filter reads shorter than 20 bases.
Genome alignment High quality reads were mapped to the mouse genome with Bowtie2, using the Mus musculus GRCm38 (mm10) genome as reference and allowing mate dovetailing.
Read count extraction Peak calling was performed with MACS2, choosing narrowpeaks, no-model and 0.05 FDR as options.
Filtering by expression and normalization
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: bed files with narrow peaks called by MACS

extract_protocol:
50.000 cells were centrifuged (500 x g, 5 min, 4ºC), washed in ice-cold PBS and lysed in cold lysis buffer. Nuclei were then pelleted and used as input material for tagmentation.
Tagmentation with the Nextera DNA Library Prep Kit (Illumina, FC-121-1030), followed by DNA purification with the MiniElute PCR Purification Kit (Qiagen, 28004). Amplification and barcoding with the NEBNext High Fidelity 2X PCR master Mix (New England Labs, M0541).


title: p27_d2_ATAC

description: ATAC from 2+1 DIV differentiating WT cells. Replicate 2


title: p27_d1_ATAC

description: ATAC from 2+1 DIV differentiating WT cells. Replicate 1


title: p27_p1_ATAC

description: ATAC from 3 DIV proliferating WT cells. Replicate 1


title: Jurkat_Glycodelin_3h_2


title: wt_p2_RNA


title: wt_p3_ATAC

description: ATAC from 3 DIV proliferating WT cells. Replicate 3


title: wt_d2_ATAC


title: wt_d3_ATAC

description: ATAC from 2+1 DIV differentiating WT cells. Replicate 3


title: wt_p1_ATAC


title: wt_p2_ATAC


title: wt_d1_ATAC


title: Jurkat_Glycodelin_3h_1


title: ada2b-cspc_30d_rep3

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates for 12 days, then transplanted into soil and continued to grow up to 30 days under a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Total RNA was extracted from 30-day-old Arabidopsis plants in soil with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing).

value: seedlings


title: spc_30d_rep1

value: spc-/-


title: spc_30d_rep3


title: ada2b-c_30d_rep3


title: ada2b-cada2a_30d_rep1


title: ada2b-c_30d_rep1


title: ada2b-cspc_30d_rep1


title: ada2b-cspc_30d_rep2


title: ada2b-cada2a_30d_rep2


title: ada2a_30d_rep1


title: gcn5_30d_rep3


title: gcn5_30d_rep1


title: ada2a_30d_rep2


title: Col-0_30d_rep2

value: wild type


title: Col-0_30d_rep3


title: Col-0_30d_rep1


title: spcing1_H3K14Ac_rep2

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
SICER2 was used to identify H3K14Ac ChIP-enriched peaks.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with H3K14Ac antibodies.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

tag: ecotype

tag: antibody

tag: chip antibody

value: Millipore, 07-353


title: spcing1_H3K14Ac_rep1


title: ada2a_H3K14Ac_rep2


title: ada2b-cada2a_30d_rep3


title: ada2b_H3K14Ac_rep2


title: spc_30d_rep2


title: ada2b_H3K14Ac_rep1


title: ada2a_H3K14Ac_rep1


title: gcn5_H3K14Ac_rep1


title: ada2b-c_30d_rep2


title: gcn5_H3K14Ac_rep2


title: gcn5_30d_rep2


title: ada2a_30d_rep3


title: spcing1_12d_rep2

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing).

value: spc-/-ing1-/- mutant


title: spcing1_12d_rep3


title: Col-0_H3K14Ac_rep1


title: input_H3K14Ac_rep2


title: Col-0_H3K14Ac_rep2


title: ada2aspc_12d_rep3

value: ada2a-/-spc-/- mutant


title: ada2aspc_12d_rep2


title: sdrl_12d_rep3

value: sdrl-/- mutant


title: sdrl_12d_rep2


title: spc_12d_rep3

value: spc-/- mutant


title: eaf6_12d_rep1

value: eaf6-/- mutant


title: eaf6_12d_rep3


title: sdrl_12d_rep1


title: spc_12d_rep2


title: eaf6_12d_rep2


title: spc_12d_rep1


title: ing1_12d_rep3

value: ing1-/- mutant


title: ing1_12d_rep2


title: gcn5_12d_rep3

value: gcn5-/- mutant


title: gcn5_12d_rep2


title: gcn5_12d_rep1


title: ing1_12d_rep1


title: ada2aspc_12d_rep1


title: ada2b_12d_rep3

value: ada2b-/- mutant


title: ada2b_12d_rep2


title: ada2b_12d_rep1


title: ada2a_12d_rep1

value: ada2a-/- mutant


title: ada2a_12d_rep3


title: ada2a_12d_rep2


title: spcing1_12d_rep1


title: Col-0_12d_rep1