title: RNA from microtom seeds treated with osmopriming (PEG 8000 -1MPa) for 48h rep2

value: Biol rep 2

value: uTom


title: dmso-24h-n-2

status: Public on Sep 01 2025

type: SRA

city: Utrecht

first: Amir

last: Giladi

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: transcriptomic

data_processing:
Bulk RNA-seq libraries were generated via the SORT-seq method (REF), and sequenced on a NextSeq500 Illumina machine. Resulting bulk RNA-seq data was mapped to the mouse genome (mm38) using STAR (version 2.7.8a). umi_tools (version 1.1.1) was used to collapse PCR-amplified reads into distinct transcripts. Samples with less than 500,000 transcripts were determined as low quality and discarded from further analysis, resulting in median depth of 960,086 transcripts per sample.
Assembly: mm38
Supplementary files format and content: Tab-delimited text file containing number of unique transcripts (UMI) per gene per sample.

molecule: polyA RNA

organism: Mus musculus

source_name: duodenum-derived organoids

growth_protocol: All organoids were obtained from the duodenum of male or virgin female mice older than 8 weeks as described previously52. Organoids were embedded in BME and cultured with ENR media including Advanced DMEM/F-12 (Life Technologies) supplemented with; murine recombinant epidermal growth factor (50 ng/ml; Life Technologies), murine recombinant Noggin (100 ng/ml; PeproTech), human recombinant R-Spondin 1 (500 ng/ml; Peprotech), n-acetylcysteine (1 mM; Sigma-Aldrich), N2 supplement (1×; Life Technologies) and B27 supplement (1×; Life Technologies), GlutaMAX (2 mM; Life Technologies), Hepes (10 mM; Life Technologies), and penicillin-streptomycin (100 U/ml; 100 μg/ml; Life Technologies). For passaging, organoids were removed from BME and mechanically dissociated into single-crypt domains, and then transferred to fresh BME. Passage was performed every 1-2 weeks with a 1:5 split ratio. Conditions were kept stable in the incubator with 5% CO2 and 20% O2 at 37°C.

extract_protocol:
Organoids (20-50 organoids per sample) were harvested from the microfluidic chip. Total RNA was isolated using TRIzol Reagent (Invitrogen, #15596018).
Bulk RNA sequencing was performed according to the Sort-seq method (Muraro, M. J. et al. A Single-Cell Transcriptome Atlas of the Human Pancreas, Cell Syst 3, 385-394 e383, doi:10.1016/j.cels.2016.09.002) 2016

treatment_protocol: Microfluidics experiments were performed as described previously38,53. In short, a mold for microfluidic chips was made using a 3D printer (Atum3D) (chip design available upon request). PDMS (SYLGARD #01673921/ #01673921, 1:8 ratio) was poured in the mold to create the microfluidic chip. The chip and a glass slide (Marienfeld, No 1.5H, high precision, 70x70 mm) were bonded using plasma treatment (Diener electronic, Femto). Chip and Tubing were UV cleaned and the microfluidic chip (in PBS with Pen/strep) was degassed together with the conditioned and DAPT media for 4 hours. The concentration of the DAPT media depended on the pulse timing (90min: 1.38µM, 130min: 2µM, 170min; 2.6µM, 2µM; for 170 min we tested two different concentrations to find one that did not change oscillation amplitude or absolute intensity (Fig. 4 and Extended Data Fig. 12). Organoids were passaged 3-4 days before performing a live-imaged microfluidic experiment for 20-24h. For the RNA bulk sequencing and immunofluorescence microfluidic experiments organoids were passaged 1 day before a 72h experiment, 2 days before 48h experiment and 3 days before a 24h experiment. The day of the experiment, two wells of a 24-well plate were harvested and washed with ice cold Advanced DMEM/F12 supplemented with GlutaMAX (2 mM; Life Technologies), Hepes (10 mM; Life Technologies), and penicillin-streptomycin (100 U/ml; 100 μg/ml; Life Technologies) to remove the BME. Organoids are resuspended in BME to a final concentration of 50% and carefully loaded into the microfluidic chip which was pre-filled with ENR culture media. After loading organoids on the chip, all tubing (4x inlet tubing of 3 meters, and 2x outlet tubing of 1 meter) was connected and during the experiment the organoids were cultured under a flow rate of 200 µl/h, using a microfluidic pump (Harvard apparatus #70-45060). After approximately 30 min culturing in culture medium, pumping program to induce drug pulses was started. For the bulk RNAseq and immunofluorescence microfluidic experiments, organoids were removed by aspirating the organoids out of the chip with a 200ul pipet via the organoid inlets and follow-up methods were performed as described.

tag: tissue

value: duodenum-derived organoids

tag: cell type

value: Non-enriched for cell type

tag: strain

tag: treatment

value: DMSO control

tag: time

value: 24 hours


title: iBAT from C57BL/6N ADCY3∆AT, replicate 2

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Transcriptome assembly was done using StringTie and determined Adcy3-at transcript was added manually to Ensembl reference
Quantification of transcripts done using Salmon on Ensembl GRCm38 reference including Adcy3-at transcript
Normalisation and differential gene expression analysis was done using EdgeR
Assembly: GRCm38
Supplementary files format and content: Raw Salmon gene counts are provided in iBAT_WT_AT.cts.txt. The Gene summarization was done using summarizeToGene() from tximport package for R.

source_name: Interscapular Brown Adipose Tissue (iBAT)

extract_protocol:
Tissues were homogenised and lysed in TRIZol using FastPrep24 homogenizer. Total RNA was isolated using EconoSpin All-In-One Mini Spin Columns (EconoSpin 1920-250).
Paired end libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s protocol.
Paired-end mRNA-seq

tag: genotype


title: C_cut_24h_3

city: Guiyang

first: Zhao

last: Yanchi

state: Guizhou

address: No. 9 Beijing Road

country: China

institute: Guizhou Medical University

data_processing:
Hisat software was used to compare the sequencing data with the zebrafish referenced genome. To evaluate the expression level of all mRNAs, we first realized sample reads through StringTie, and then calculated the FPKM (fragments per kilobase of transcript per million mapped reads) using stringtie and edgeR software. Finally, the differentially expressed genes (DEGs) were screened by the R software package according to the following criteria: log2 (fold-change) > 1 or <−1 and at p < 0.05. These DEGs were used for further analysis of functions and signaling pathways using Gene Ontology (GO; http://geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (KEGG; https://www.genome.jp/kegg/).
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

molecule: total RNA

organism: Danio rerio

source_name: whole organism

extract_protocol:
Total RNA was extracted using Invitrogen TRizol reagent (California, USA), and generation of the Illumina RNA sequence library and paired end sequencing (300±50 bp) were performed on an Illumina NovaSeq 6000 using aliquots (5 mg) of qualified total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: whole organism

value: WT

value: 24 hours after cut the caudal fin with regular culture medium


title: C_cut_48h_1

value: 48 hours after cut the caudal fin with regular culture medium


title: iBAT from C57BL/6N ADCY3∆AT, replicate 3

value: Interscapular Brown Adipose Tissue (iBAT)


title: dmso-48h-n-2

value: 48 hours


title: RNA from microtom seeds treated with osmopriming (PEG 8000 -1MPa) for 48h rep1

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
After adapter trimming and quality control, high quality reads were mapped on the tomato reference transcriptome based on SL4.0 genome version and ITAG4.0 annotation (Hosmani et al., 2019),using quasi-mapping alignment and quantification methods of Salmon algorithm v.1.2 (Patro et al., 2017). For gene expression analysis, raw RNA-Seq counts were first normalized as Transcripts Per Kilobase Million (TPM).
Assembly: tomato reference transcriptome based on SL4.0 genome version and ITAG4.0 annotation (Hosmani et al., 2019)
Supplementary files format and content: tab-delimited text (counts and TPM)

organism: Solanum lycopersicum

source_name: primed seeds

growth_protocol: Seed osmopriming solutions were prepared as following: 28.5 g of polyethylene glycol (PEG) 8000 were added to 100 ml of MilliQ sterile water to generate a solution with osmotic potential of -1 MPa at RT. Elicitor treatment used: 2 mM of MeJA (Sigma-Aldrich, St. Louis, USA) and water for control seeds. Two ml of seed priming solution (1 MPa ± elicitors) were then added into 30 mm Ø sterile glass Petri dishes containing 30 dry mature seeds on sterile Whatman filter paper to imbibe in dark at 20°C for 48h. Three biological replicates of 30 seeds each were used for each treatment. Seeds were then abundantly washed under tap water to remove the priming solution, blot-dried, and placed into a desiccator at 43% RH for 48h to re-dry them.

extract_protocol:
RNA samples were extracted from the same seed lot used to produce exudates following the seed priming treatment with or without elicitors using the NucleoSpin RNA Plant and Fungi kit (Macherey-Nagel, Düren, Germany) with lysis buffer containing 1% of polyvinylpyrrolidone (PVP-40) followed by incubation at room temperature for 10 minutes. RNA quantity and quality was measured using a NanoDrop ND‐1000 (NanoDrop Technologies, Wilmington, DE, USA) and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), respectively.
All samples showing 260/280 and 260/230 absorbance ratio >1.8, RNA Integrity Number, RIN>7 and 28S/18S>1.7 were sent to Beijing Genomics Institute (https:// www.bgi.com) (Hong Kong, China) for library preparation and sequencing on BGISEQ-500 platform, generating a minimum of 20M reads of 100 bp per sample (20M PE100).
PolyA enrichement library done by BGI

treatment_protocol: Elicitor treatment used: 2 mM of MeJA (Sigma-Aldrich, St Louis, USA) and water for control seeds

value: primed seeds

tag: replicates

value: Biol rep 1

value: mature seed (re-dried 48h after seed priming)

tag: elicitation

value: water


title: dapt-90min-72h-n-3

value: DAPT pulses of 90 minutes

value: 72 hours


title: C_cut_24h_2


title: iBAT from C57BL/6N WT, replicate 3

value: wt/wt


title: C_cut_24h_1


title: iBAT from C57BL/6N ADCY3∆AT, replicate 1


title: dapt-90min-72h-n-2

value: duodenum-derived organoids


title: Merged_SB_81_S105373

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Trimmed sequence reads were mapped to GRCm38 using STAR
Read count extraction and normalization were performed using SeqMonk software.
Assembly: GRCm38
Supplementary files format and content: Read counts

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, #12034977) and Monarch RNA Clean-up kit (NEB, #T2030L).
NGS libraries were prepared using the QuantSeq 3’ mRNA-Seq FWD library preparation protocol

value: HoxB8 myeloid progenitor cell line


title: Merged_SB_80_S105384


title: dmso-48h-n-3

value: Non-enriched for cell type

value: DMSO control


title: C_cut_3h_3

value: whole organism

value: 3 hours after cut the caudal fin with regular culture medium


title: iBAT from C57BL/6N WT, replicate 2


title: dapt-90min-72h-n-1


title: Merged_SB_79_S105383


title: C_cut_3h_2

value: WT


title: iBAT from C57BL/6N WT, replicate 1


title: C_cut_3h_1


title: Merged_SB_78_S105382


title: iBAT from cold exposed C57BL/6N Adcy3 Ad-cKO, replicate 3

data_processing:
Transcriptome assembly was done using StringTie and determined Adcy3-at transcript was added manually to Ensembl reference
Quantification of transcripts done using Salmon on Ensembl GRCm38 reference including Adcy3-at transcript
Normalisation and differential gene expression analysis was done using EdgeR
Assembly: GRCm38
Supplementary files format and content: Raw Salmon gene counts are provided in iBAT_WT_AdKO_cold.cts.txt. The Gene summarization was done using summarizeToGene() from tximport package for R.

treatment_protocol: Mice were fed chow diet (Ssniff V1554) for 20 weeks and exposed to 5degree celcius for 24 hours prior to tissue collection

value: cold


title: Merged_SB_77_S105381


title: dapt-90min-48h-n-3


title: no_cut_222_3

value: Do not cut the caudal fin with 222mM glucose


title: Merged_SB_76_S105380


title: dapt-90min-24h-n-3

value: 24 hours


title: iBAT from cold exposed C57BL/6N Adcy3 Ad-cKO, replicate 1

value: Interscapular Brown Adipose Tissue (iBAT)


title: Merged_SB_72_S105391


title: dapt-90min-24h-n-2


title: Merged_SB_71_S105392


title: dapt-90min-24h-n-1


title: no_cut_222_2


title: iBAT from cold exposed C57BL/6N WT, replicate 2


title: no_cut_130_3

value: Do not cut the caudal fin with 130mM glucose


title: dapt-170min-72h-n-3

value: DAPT pulses of 170 minutes


title: no_cut_130_2


title: Merged_SB_69_S105390


title: dapt-170min-72h-n-2


title: Merged_SB_70_S105389


title: dapt-90min-48h-n-2

value: 48 hours


title: iBAT from C57BL/6N replicate 4, Adcy3 Ad-cKO

data_processing:
Transcriptome assembly was done using StringTie and determined Adcy3-at transcript was added manually to Ensembl reference
Quantification of transcripts done using Salmon on Ensembl GRCm38 reference including Adcy3-at transcript
Normalisation and differential gene expression analysis was done using EdgeR
Assembly: GRCm38
Supplementary files format and content: Raw Salmon gene counts are provided in iBAT_WT_AdKO.cts.txt. The Gene summarization was done using summarizeToGene() from tximport package for R.

extract_protocol:
Tissues were homogenized and lysed in TRIZol using FastPrep24 homogenizer. Total RNA was isolated using EconoSpin All-In-One Mini Spin Columns (EconoSpin 1920-250).
Paired end libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s protocol.


title: iBAT from cold exposed C57BL/6N Adcy3 Ad-cKO, replicate 2


title: Merged_SB_68_S105387


title: dapt-90min-48h-n-1

value: DAPT pulses of 90 minutes


title: no_cut_130_1


title: iBAT from C57BL/6N replicate 3, Adcy3 Ad-cKO


title: C_no_cut_3

value: Do not cut the caudal fin with regular culture medium


title: Merged_SB_67_S105388


title: iBAT from cold exposed C57BL/6N WT, replicate 3


title: dapt-170min-48h-n-3


title: iBAT from cold exposed C57BL/6N WT, replicate 1


title: C_no_cut_2


title: dapt-170min-48h-n-2


title: no_cut_222_1


title: iBAT from C57BL/6N replicate 1, Adcy3 Ad-cKO


title: C_no_cut_1


title: dapt-170min-48h-n-1


title: iBAT from C57BL/6N replicate 4, WT


title: Merged_SB_61_S105398


title: Leaf, FLL

city: Birmingham

first: Robyn

last: Emmerson

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

library_source: genomic

data_processing:
Files were trimmed with Trimmomatic 0.39 (HEADCROP:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) and mapped to the TAIR10 genome using Bismark and Bowtie2 (-N 1 -L20 -p 4 -score_min L,0,-0.6)
Cytosine methylation reads were extracted with bismark_methylation extractor
CX reports were analysed with R package DMR caller. Reports from each regime were pooled together using poolMethylationDatasets
The bins method was used to compute DMRs between regimes for each context (CG, CHG, CHH) using the following parameters: binSize=150, test=score, pValueThreshold=0.01 minCytosineCount and minReadsPerCytosine=4, minProportionDifference=0.2 for CG and CHG, 0.1 for CHH, minGap=200, minSize=50
Assembly: TAIR10
Supplementary files format and content: comma separated files with the location of DMRs, the proportion difference, p-values, and annotation

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Plants were grown under one of four light regimes. They were maintainted at 22°C under well watered conditions

extract_protocol:
CTAB DNA extraction Porebski, Bailey and Baum (1997)
EZ lightening methylation conversion kit

value: Leaf


title: dapt-170min-24h-n-3

value: duodenum-derived organoids


title: iBAT from C57BL/6N replicate 3, WT


title: Merged_SB_60_S105395

value: HoxB8 myeloid progenitor cell line


title: Leaf, FLH


title: Leaf, SQL


title: dapt-170min-72h-n-1

value: Non-enriched for cell type

value: 72 hours


title: Merged_SB_59_S105396


title: dapt-170min-24h-n-2


title: iBAT from C57BL/6N replicate 2, WT


title: dapt-170min-24h-n-1


title: iBAT from C57BL/6N replicate 2, Adcy3 Ad-cKO


title: Merged_SB_58_S105344


title: iBAT from C57BL/6N replicate 1, WT


title: Merged_SB_63_S105400


title: Leaf, SQH


title: dapt-130min-72h-n-3

value: DAPT pulses of 130 minutes


title: Leaf, FLL, rep2

data_processing:
Files were aligned to the TAIR10 genome using HISAT2 and sorted with samtools. These were then sorted and indexed with HISAT2. featureCounts was performed on each pair end file to generate a tab file
The tab file was loaded into R and analyzed using DESeq2. Differentially expressed genes were filtered using a p-adj value of 0.05 and log2-fold change of 0.5
Assembly: TAIR10
Supplementary files format and content: comma separated files with the gene annotation of DEGs, lo2 fold change, p-values, and p-adjusted value

extract_protocol:
the Macherey-Nagel Mini kit for RNA purification
end repair, A-tailing, adapter ligation, size selection, amplification, and purification


title: Merged_SB_53_S105339


title: dapt-130min-72h-n-2


title: Merged_SB_62_S105397


title: XJC_1_20210609NA

city: Shanghai

first: Junchao

last: Xie

address: Middle 301 Yanchang Road

department: Neurology

institute: Shanghai Tenth People's Hospital

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

source_name: cerebral cortex

extract_protocol:
The brains were collected quickly on an ice-platform. Cerebral cortex was separated and collected promptly in conservation buffer (Genenergy, Shanghai, China) for further experiments.
For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer by Adult Brain Dissociation Kit (Miltenyi Biotec. Cat. No. 130-107-677), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

value: cerebral cortex

tag: age

value: 24 week-old

value: The normoxia control


title: dapt-130min-72h-n-1


title: Leaf, FLL, rep1


title: Mav-infected organoids 7

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

description:
Library name: Sample 7
100 nucleotides
Infected_2

data_processing:
RNAseq reads of infected organoids and uninfected control were aligned and mapped to the mouse genome  GRCm39 using CLC genomic workbench 24
Differential gene expression was analyzed by using CLC genomic workbench 24
Assembly: GRCm39
Supplementary files format and content: Expression browser in Excel format with total read counts, RPKM, TPM and CPM of the mapped reads for all samples
Supplementary files format and content: Excel file with study versus control: Fold change, p value, FDR p  value, Bonferroni values

source_name: small intestinal organoids

extract_protocol:
Mouse small intestinal organoids from  all groups  groups (n=10; N=4) were resuspended and crushed in 0.5 ml of TRIzol Reagent
RNAseq was performed as follows: Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA 1. with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: wild type

value: small intestinal organoids

tag: infection

value: Mav-infected

value: 24 hpi


title: Leaf, FLH, rep3


title: Merged_SB_52_S105342


title: dapt-130min-48h-n-3


title: Mav-infected organoids 6

description:
Library name: Sample 6
100 nucleotides
Infected_1


title: dapt-130min-48h-n-2


title: Merged_SB_50_S105352


title: Leaf, FLH, rep1


title: dapt-130min-48h-1


title: Mav-infected organoids 5

description:
Library name: Sample 5
100 nucleotides
Infected_0


title: Leaf, SQL, rep3


title: Merged_SB_54_S105340


title: dapt-130min-24h-3

value: 24 hours


title: uninfected organoids 4

description:
Library name: Sample 4
100 nucleotides
Control_3

value: uninfected


title: Merged_SB_49_S105351


title: Merged_SB_20_S105414

value: bone marrow derived cells


title: uninfected organoids 3

description:
Library name: Sample 3
100 nucleotides
Control_2


title: XJC_2_20210609NA

value: The mice were kept in the chamber and 8percent O2 were supplied for 5 hours.


title: dapt-130min-24h-2


title: Leaf, SQL, rep2

value: Leaf


title: Leaf, FLH, rep2


title: Merged_SB_19_S105413


title: dapt-130min-24h-n-1

value: duodenum-derived organoids


title: Mav-infected organoids 8

description:
Library name: Sample 8
100 nucleotides
Infected_3


title: uninfected organoids 2

description:
Library name: Sample 2
100 nucleotides
Control_1


title: Leaf, SQL, rep1


title: Merged_SB_18_S105420


title: Leaf, SQH, rep3


title: Merged_SB_51_S105341

value: HoxB8 myeloid progenitor cell line


title: uninfected organoids 1

description:
Library name: Sample 1
100 nucleotides
Control_0


title: Merged_SB_17_S105419


title: RNA-seq of mouse femoral artery (VS2, Rep3)

first: Jingmeng

last: Liu

address: No. 197, Ruijin 2nd Road, Huangpu District, Shanghai

department: Department of Cardiovascular Medicine

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description:
Library name: VS2_Rep3
VV3

data_processing:
Base-calling and quality control: Raw sequencing data were generated by the BGISEQ platform using BGISEQ-500 base-calling software. Adapter trimming and quality filtering were performed using SOAPnuke (v1.5.6) with default parameters. Read alignment: Clean reads were aligned to the mouse reference genome (GRCm38.p6; NCBI GCF_000001635.26) using HISAT2 (v2.1.0) with default settings. The genome and annotation files were obtained from NCBI. Expression quantification: Only uniquely mapped reads were used. Gene-level counts were normalized and differential expression was analyzed using DESeq2 (v1.26.0) in R. Additional notes: All samples were processed using the same pipeline. No batch correction was applied.
Assembly: GRCm38
Supplementary files format and content: Text file containing FPKM, TPM, and raw count values for all samples

source_name: Femoral artery

extract_protocol:
Total RNA was isolated from injured mouse femoral arteries using TRIzol reagent (Invitrogen) according to the manufacturer's protocol.
Total RNA was extracted, and mRNA was enriched using oligo(dT) magnetic beads. The mRNA was fragmented and reverse-transcribed to cDNA. After end repair, A-tailing, adaptor ligation, and PCR amplification, libraries were constructed and sequenced on the BGISEQ platform by BGI.

value: Femoral artery

value: Vascular smooth muscle cells (VSMCs)

tag: batch

value: Batch 1


title: OCI-AML3, gTSR3, Replicate 3

city: Cambridge

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: University of Cambridge

data_processing:
RNA-seq reads were mapped to the human genome assembly GRCh38 using STAR version 6.43, tolerating mismatch rate of 0.01 and allowing maximal intron lengths of 50kb. Read counts were calculated by STAR using Ensembl annotation of GRCh38 version 91 and normalized as fragments per kilobase of gene length per million uniquely mapped reads (FPKM). Differential expression analysis was done by DESeq2 using paired sample design and significant genes were identified using adjusted p-values of 0.05 as cut-off.
Assembly: GRCh38
Supplementary files format and content: Read count

organism: Homo sapiens

source_name: blood

growth_protocol: OCI-AML3 and OCI-AML2 cells were cultured in alpha-MEM (Lonza) supplemented with 20% FBS (Life Technologies) and 1% penicillin/streptomycin/glutamine. MOLM-13 and THP-1 cells were cultured in RPMI-1640 (Invitrogen) supplemented with 10% FBS (Life Technologies) and 1% penicillin/streptomycin/glutamine.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Cat# 74104, QIAGEN) with DNase I treatment (Cat# 79254, QIAGEN). RNA quality was assessed with TapeStation RNA ScreenTape & Reagents (Agilent).
Library preparation was performed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (Cat # E7760, New England Biolabs) and the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (Cat# E6440, E6442 New England Biolabs) in conjunction with NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490, New England Biolabs), with a starting input of 500 ng RNA.

treatment_protocol: For lentiviral production, 293T cells were seeded 24 hours before transfection. On day 1, cells were transfected with the gRNA plasmid and the packaging plasmids pMD2-G (Addgene #12259) and psPAX2 (Addgene #12260) using Lipofectamine™ LTX (Cat# A12621, ThermoFisher Scientific), following the manufacturer’s guidelines. On day 2, the cell medium was removed and refreshed. On day 3, the viral supernatant was collected, centrifuged at 300 rcf for 5 minutes to remove cell debris and stored immediately at −80 oC or it was concentrated using Lenti-X (Cat# 631232, Takara), as per the manufacturers’ instructions. For gRNA transductions (gControl or gTSR3), 0.3x106 cells were mixed with 3-12 μL of concentrated or 300-600μL of non-concentrated viral supernatant, in the presence of 8 μg ml−1 polybrene (Millipore). Cells were spinoculated at 870 rcf, 32 °C for 1 hour and were then diluted with fresh medium. The following day the medium was removed and refreshed.

value: blood

tag: cell line

value: AML

tag: transduction


title: OCI-AML3, gTSR3, Replicate 2


title: RNA-seq of mouse femoral artery (VS2, Rep2)

description:
Library name: VS2_Rep2
VV2


title: Merged_SB_16_S105418


title: Leaf, FLL, rep3


title: Merged_SB_15_S105417


title: OCI-AML3, gTSR3, Replicate 1


title: Leaf, SQH, rep2


title: RNA-seq of mouse femoral artery (VS2, Rep1)

description:
Library name: VS2_Rep1
VV1


title: Leaf, SQH, rep1


title: OCI-AML3, gControl, Replicate 3

value: gControl


title: Merged_SB_13_S105423


title: Merged_SB_14_S105424


title: hda6_37_RNA-seq_rep3

city: Shenzhen

first: Xishi

last: Zhou

address: No 7, Pengfei Road

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
Illumina CASAVA software was used for basecalling
Sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v.0.6.6 program
Clean reads were mapped to the TAIR10 Arabidopsis genome using Hisat2 v. 2.2.1 program
Raw read counts of genes were measured by featureCounts v.2.0.1 program
The differentially expressed genes  were identified using R package DESeq2 v.1.30.1
Assembly: tair10
Supplementary files format and content: .csv files include the log2(fold_change) of normalized read counts and P value to figure out the differentially expressed genes

source_name: seedlings

growth_protocol: Arabidopsis seeds were sown on 1/2 MS medium plates plates under a long-day photoperiod with 16 h of light and 8 h of darkness at 22 °C, and 7-day-old seedlings were harvested for RNA-seq.

extract_protocol:
Seedling samples were harvested and frozen immediately in liquid nitrogen and total RNA was extracted with TRIzol reagent (Invitrogen).
Libraries were prepared following the manufacturer’s instructions with the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: Arabidopsis 7-day-old seedlings were grown under normal condition (22 ℃) or exposed to 37 ℃ for 1 h before harvesting and total RNA extraction.

value: seedlings

value: hda6 EMS line

value: 37 ℃ treatment for 1 h


title: OCI-AML3, gControl, Replicate 2


title: hda6_37_RNA-seq_rep2


title: hda6_37_RNA-seq_rep1


title: RNA-seq of mouse femoral artery (Saline, Rep1)

description:
Library name: Saline_Rep1
VP1

value: Saline


title: OCI-AML3, gControl, Replicate 1


title: hda6_22_RNA-seq_rep3

value: untreated


title: Merged_SB_8_S105425

source_name: MR


title: liver single cell

first: Kunshan

last: Zhang

address: 389 Xincun Rd.

department: Tongji Hospital

institute: Tongji University

description:
10x Genomics
liver_sc

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (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: Liver

extract_protocol:
Livers from adult mice were perfused with 0.5 mg/ml collagenase D through the portal vein. After pelleting down the hepatocytes, the cells remaining in the supernatant were equilibrated with OptiPrep to 17% final concentration. After centrifuging at 400g for 15 min, cells band at the interface were collected and red blood lysis buffer were used after wash. Cell viability was at least 95% (Trypan blue exclusion). Cells were filtered through a 40 um sieve, stored in PBS with 2% FCS. FACS antibodies were incubated for 30 min at 4 ℃. Cells were analyzed or sorted with BD flow cytometer using a 100 μm nozzle.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells 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.

treatment_protocol: Diet containing 0.1% DDC (wt/wt) were put on mice.

value: Liver

value: Liver epithelial cells

value: 6-8 weeks


title: Merged_SB_7_S105426

value: bone marrow derived cells


title: OCI-AML2, gTsr3, Replicate 3


title: hda6_22_RNA-seq_rep2


title: LN48A

city: São Paulo

first: Luciana

middle: Cezar de Cerqueira

last: Leite

state: SP

address: Avenida Vital Brasil, 1500

department: Desenvolvimento de Vacinas

country: Brazil

institute: Instituto Butantan

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.90dpi.8

data_processing:
Raw paired-end RNA-Seq data were subjected to quality control using FastQC.
Trimmomatic v.0.36 was used to remove the adaptors and filter low quality bases at termini (quality below 25) (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36).
The filtered reads were aligned to the Mus musculus genome assembly Version GRCm39 using Bowtie2 v.2.3.5.1, with "--very-sensitive" preset, keeping other parameters at default.
The mapped and aligned reads were quantified to obtain the gene-level counts using featureCounts from the package Subread v.2.12 with “is PairedEnd” and “allow MultiOverlap” parameters set to true and the remaining at default settings.
Raw counts were processed using the Bioconductors package DESeq2 v.1.36.0 in R v.4.2.3 and normalized using the DESeq method to remove the library-specific artifacts.
Assembly: Mus musculus genome assembly Version GRCm39 using Bowtie2 v.2.3.5.1
Supplementary files format and content: tab-delimited csv file includes raw counts for each Sample

source_name: Lymph Node

growth_protocol: Total lung and lymph node tissue were maintained in RNAlater (ThermoFisher) at -80ºC until extraction.

extract_protocol:
Total RNA was extracted and purified individually from left lung and accessory lobe samples or from lymph node samples stored in RNAlater (samples from 8 mice per group per time point) using the “RNA Extraction Protocol for Animal Tissue” Document number SOP-SMM-J003, Version A0 (BGI Genomics, Shenzhen, China) according to the manufacturer’s instructions.
Purified RNA integrity was estimated by capillary electrophoresis (Fragment Analyzer; Agilent Technologies, Santa Clara, CA, USA), and samples showed RIN scores 7.0. Non-stranded libraries were constructed using the BGI in-house Library Prep Kit

value: Lymph Node

value: WT

tag: vaccination status

value: Immunized

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

tag: vaccine route

value: subcutaneous

tag: days post_immunization

value: day 90

tag: challenge

value: No

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage

value: No disease


title: Merged_SB_6_S105431

tag: cell type

tag: treatment


title: OCI-AML2, gTsr3, Replicate 2

tag: tissue

value: blood

value: AML


title: LN47A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.90dpi.7

tag: genotype


title: hda6_22_RNA-seq_rep1

value: seedlings

value: hda6 EMS line


title: Merged_SB_5_S105432


title: RNA-seq of mouse femoral artery (Saline, Rep3)

description:
Library name: Saline_Rep3
VP3

value: Femoral artery

value: Vascular smooth muscle cells (VSMCs)

value: Saline

tag: batch

value: Batch 1


title: OCI-AML2, gTsr3, Replicate 1

tag: cell line

tag: transduction


title: LN45A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.90dpi.5

tag: vaccination status

tag: vaccine


title: RNA-seq of mouse femoral artery (Saline, Rep2)

description:
Library name: Saline_Rep2
VP2


title: Merged_SB_4_S105429

source_name: MCSF

value: bone marrow derived cells

value: MCSF


title: OCI-AML2, gControl, Replicate 2

value: gControl


title: LN46A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.90dpi.6

value: Lymph Node

value: WT

value: Immunized

tag: vaccine dose

tag: vaccine route


title: sant-null_37_RNA-seq_rep3

value: sant-null quadruple mutants

value: 37 ℃ treatment for 1 h


title: OCI-AML2, gControl, Replicate 3


title: sant-null_37_RNA-seq_rep2


title: Merged_SB_3_S105430


title: sant-null_37_RNA-seq_rep1


title: sant-null_22_RNA-seq_rep3

value: untreated


title: Merged_SB_1_S105434


title: LN43A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.90dpi.3

value: 10e6 cfu

value: subcutaneous

tag: days post_immunization

value: day 90

tag: challenge

value: No

value: No disease


title: LN42A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.90dpi.2

tag: challenge strain

tag: challenge dose


title: OCI-AML2, gControl, Replicate 1

value: blood

value: AML


title: sant-null_22_RNA-seq_rep2

value: seedlings


title: LN41A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.90dpi.1

tag: challenge route

tag: disease


title: sant-null_22_RNA-seq_rep1


title: Merged_M_R_Tyr_24h_3_S57100

description: All_data_counts_RNA_seq_I_AA_def_GEO.txt

tag: cell type

value: bone marrow derived cells


title: h202_2_77: Line 3 mutation

city: Palo Alto

first: Yu

state: CA

address: 1215 Welch Road

department: CVI

country: USA

institute: Stanford University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg19 whole genome using STAR
TPM value was calculated by RSEM
Assembly: hg19
Supplementary files format and content: TPM value in TXT format

source_name: Cell derivatives from human iPSCs

growth_protocol: Human induced pluripotent stem cells (hiPSCs) were maintained through daily feeding with Essential 8 (E8) medium (A1517001, Thermo Fisher Scientific). The medium was changed daily, and cells were passaged every 3-4 days with 0.5 mM EDTA (15575-020, Thermo Fisher Scientific) between a 1:6 and 1:12 split ratio. hiPSCs were passaged on to tissue culture plates coated with Corning Matrigel membrane matrix (354234, Thermo Fisher Scientific) at a dilution of 1:100 for either maintenance or differentiation. To aid in passaging, we cultured cells for 24 hours with 10 uM of the ROCK inhibitor Y-27632 (HY-10583, MedChem Express).

extract_protocol:
Samples were prepared with the Direct-zol RNA Microprep w/ Zymo-Spin IC Columns (R2060, Zymo Research) and sequenced.
250~300 bp insert cDNA library

treatment_protocol: hiPSCs were differentiated to cardiomyocytes to day 30. At Day 0, hiPSCs were treated with RPMI/B27-insulin free medium containing 6uM of CHIR for 2 days. Cells were then recovered in RPMI/B27-insulin free medium for 1 day. A subsequent 5uM IWR treatment (with the same media) was used for 2 days. Cells were then left to RPMI/B27-insulin free medium for 2 days, before switching to RPMI/B27 medium for 3 days.Two episodes of 3 days glucose-starvation  (RPMI/B27 without glucose) treatments were used. Cells were left on RPMI/B27 medium until day 30. No additional treatments were made.

value: Cell derivatives from human iPSCs

value: Cardiomyocytes

value: PSEN2 mutation

tag: treatment

value: Day 30 post differentiation


title: Col-0_37_RNA-seq_rep3

tag: tissue

value: wild type


title: LN40A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.90dpi.8

value: Lymph Node

tag: genotype

value: WT

value: Immunized

value: BCG

tag: disease stage


title: LN44A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.90dpi.4

value: 10e6 cfu

value: subcutaneous


title: Merged_M_R_Tyr_24h_1_S57102


title: h202_2_54: Line 3 control

tag: cell line

value: control


title: LN39A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.90dpi.7

value: day 90

value: No

value: No disease


title: h114: Line 2 control


title: Merged_SB_2_S105433

value: MCSF


title: LN38A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.90dpi.6


title: Merged_M_R_Pro_24h_2_S57089

value: bone marrow derived cells


title: LN37A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.90dpi.5


title: Col-0_37_RNA-seq_rep2

value: seedlings

value: 37 ℃ treatment for 1 h


title: Col-0_37_RNA-seq_rep1


title: Merged_M_R_Pro_24h_3_S57088


title: h113_1_48: Line 1 control

value: Cell derivatives from human iPSCs

value: Cardiomyocytes


title: Merged_M_R_Gln_24h_3_S57093


title: h114_32: Line 2 mutation

value: PSEN2 mutation

value: Day 30 post differentiation


title: h113_2_5: Line 1 mutation


title: Merged_M_R_Tyr_24h_2_S57101


title: LN36A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.90dpi.4

value: Lymph Node

value: WT


title: LN35A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.90dpi.3

value: Immunized

value: BCG


title: Merged_M_R_Gln_24h_2_S57094


title: h377_1: Line 4 mutation


title: Merged_M_R_Pro_24h_1_S57090


title: Tmprss2CreERT2, lsl-EYFP, castrate, replicate 2, ATACseq

city: New York City

first: Dan

last: Li

state: NY

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

description:
Library name: TYC2
bigWig, narrowPeak files

data_processing:
Reads quality were analyzed by FastQC (version 0.11.9). The sequence data were processed for adapter trimming and aligned to mouse genome (mm10) with bowtie 2 {Langmead, 2012}. Peaks were called using MACS2 {Zhang, 2008}. The BAM file quality were analyzed with qualimap bamqc.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: prostate

extract_protocol:
Transposase-accessible chromatin sequencing (ATAC-seq) was performed using standard protocol {Buenrostro, 2013}. For each sample, 5,000 viable cells were processed for nuclei isolation and transposase treatment. The digestions were carried out for 30 min at 37℃.
The library preparation and next generation sequencing were performed by MSKCC genomics core facility. For each sample, 40-50 million paired-end reads were sequenced on Illunima NovaSeq platform.

value: primary cells

value: prostate

value: 2 weeks after EYFP overexpression, 5 days after castration

value: Tmprss2CreERT2, lsl-EYFP


title: Col-0_22_RNA-seq_rep2

value: wild type

value: untreated


title: hda9_Khib_rep2

description:
hda9_Khib_RPKM_gene.txt
Khib_peaks_hda9_vs_Col-0.txt

data_processing:
Illumina CASAVA software was used for basecalling
Sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v.0.6.6 program
Clean reads were mapped to the TAIR10 Arabidopsis genome using Bowtie2 v.2.2.5 with default parameters
PCR duplicates were removed by Sambamba v.0.6.6 program
Peaks were called and differentially enriched peaks were determined using program SICER2 v.1.0.3 with following parameters: “redundancy threshold=1; window size = 200; effective genome fraction = 0.85; gap size = 200; and FDR = 0.05”.
The read count falling in each gene region which used for generating RPKM (reads per kilobase per million) value for each gene was calculated by “intersect” command from the BEDTools suite.
Assembly: tair10
Supplementary files format and content: Tab-delimited text files include RPKM value of each gene for wild-type (Col-0), san-null, hda6 and hda9.
Supplementary files format and content: Tab-delimited text files include  the normalized read counts falling in each peak and FDR value for wild-type (Col-0), san-null, hda6 and hda9 to figure out the  differentially enriched peaks

growth_protocol: Arabidopsis seeds were sown on 1/2 MS medium plates plates under a long-day photoperiod with 16 h of light and 8 h of darkness at 22 °C, and 12-day-old seedlings were harvested for ChIP-seq.

extract_protocol:
Seedling samples were harvested and fixed in 1% formaldehyde for 15 min and then ground into powder in liquid nitrogen. Histone-DNA complexes were isolated with anti-Khib antibody .
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

value: hda9 T-DNA insertion line

tag: chip antibody

value: Khib antibody (PTM-802, PTM Bio-labs, Hangzhou, China)


title: Merged_M_R_Gln_24h_1_S57087

value: bone marrow derived cells


title: LN34A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.90dpi.2

tag: vaccination status

value: 10e6 cfu

value: subcutaneous

value: day 90

value: No

value: No disease


title: Tmprss2CreERT2, lsl-EYFP, castrate, replicate 1, ATACseq

description:
Library name: TYC1
bigWig, narrowPeak files


title: hda9_Khib_rep1

value: seedlings


title: Merged_M_R_full_24h_3_S57084


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, replicate 2, ATACseq

description:
Library name: TYA2
bigWig, narrowPeak files

value: 2 weeks after EYFP overexpression, Ar deletion

value: Tmprss2CreERT2, lsl-EYFP, Arf/Y


title: Merged_M_R_full_24h_2_S57083


title: hda9_input_rep2


title: LN31A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.90dpi.7

value: Lymph Node

value: WT

value: Not immunized

tag: vaccine

value: Saline


title: LN32A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.90dpi.8

tag: vaccine dose


title: Merged_M_R_full_24h_1_S57086


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, replicate 1, ATACseq

description:
Library name: TYA1
bigWig, narrowPeak files

value: primary cells

value: prostate


title: hda9_input_rep1

value: hda9 T-DNA insertion line

value: untreated


title: Tmprss2CreERT2, lsl-EYFP, replicate 2, ATACseq

description:
Library name: TY2
bigWig, narrowPeak files

value: 2 weeks after EYFP overexpression

value: Tmprss2CreERT2, lsl-EYFP


title: LN30A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.90dpi.6

tag: vaccine route

value: subcutaneous


title: Tmprss2CreERT2, lsl-EYFP, replicate 1, ATACseq

description:
Library name: TY1
bigWig, narrowPeak files


title: Col-0_22_RNA-seq_rep1

value: wild type


title: hda6_Khib_rep1

description:
hda6_Khib_RPKM_gene.txt
Khib_peaks_hda6_vs_Col-0.txt

value: hda6 EMS line

value: Khib antibody (PTM-802, PTM Bio-labs, Hangzhou, China)


title: Tmprss2CreERT2, lsl-EYFP, castrate, replicate 3, RNAseq

description: Library name: TYC3

data_processing:
Reads quality were analyzed by FastQC (version 0.11.9) and mapped to Human genome (mm10) using STAR_2.5.3a. The BAM file quality were analyzed with qualimap bamqc and RNA-seq quality was analyzed with qualimap rnaseq (QualiMap v.2.2.2-dev). The counts per gene were quantified with STAR --quantMode GeneCounts
Assembly: mm10
Supplementary files format and content: comma-separated read counts

extract_protocol:
Total RNA was extracted from FACS sorted Epcam positive, CD24a positive and EYFP positive prostate cells with TRIzol reagent following the manufacture’s instruction (#15596026, Invitrogen).
RNAseq libraries were prepared using standard Illumina PolyA library preparation protocol. Next generation sequencing was performed by Illumina NovaSeq platform with paired-end of 100bp for 30-40 million reads. The sequence data were mapped to the mouse genome (mm10) using STAR

value: 2 weeks after EYFP overexpression, 5 days after castration


title: Merged_M_R_Cys_24h_2_S57096

description: All_data_counts_RNA_seq_I_AA_def_GEO.txt

value: bone marrow derived cells


title: hda6_Khib_rep2

value: seedlings


title: Merged_M_R_Cys_24h_3_S57095


title: LN28A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.90dpi.4

value: Lymph Node

tag: days post_immunization

value: day 90

value: No

value: No disease


title: hda6_input_rep2


title: Merged_M_R_Cys_24h_1_S57097


title: LN29A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.90dpi.5

value: WT

value: Not immunized

value: Saline

tag: challenge


title: LN33A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.90dpi.1

value: Immunized

value: BCG

value: 10e6 cfu

tag: challenge strain


title: hda6_input_rep1

value: untreated


title: Tmprss2CreERT2, lsl-EYFP, castrate, replicate 2, RNAseq

description: Library name: TYC2

value: primary cells

value: prostate

value: Tmprss2CreERT2, lsl-EYFP


title: Merged_M_R_Arg_24h_3_S57098


title: Tmprss2CreERT2, lsl-EYFP, castrate, replicate 1, RNAseq

description: Library name: TYC1

value: 2 weeks after EYFP overexpression, 5 days after castration


title: LN26A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.90dpi.2

value: subcutaneous

tag: challenge dose


title: sant-null_Khib_rep2

description:
sant-null_Khib_RPKM_gene.txt
Khib_peaks_sant-null_vs_Col-0.txt

value: seedlings

value: sant-null quadruple mutants

value: Khib antibody (PTM-802, PTM Bio-labs, Hangzhou, China)


title: sant-null_Khib_rep1


title: Merged_M_R_Arg_24h_2_S57091

value: bone marrow derived cells


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, replicate 2, RNAseq

description: Library name: TYA2

value: 2 weeks after EYFP overexpression, Ar deletion

value: Tmprss2CreERT2, lsl-EYFP, Arf/Y


title: Merged_M_R_Arg_24h_1_S57092


title: h377_p3: Line 4 control

value: Cell derivatives from human iPSCs

value: Cardiomyocytes

value: control

value: Day 30 post differentiation


title: LN25A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.90dpi.1

value: Lymph Node

value: WT

value: Not immunized

value: Saline

value: day 90

value: No

tag: challenge route

value: No disease


title: sant-null_input_rep2

value: seedlings

value: untreated


title: LN24A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.7dpi.8

value: Immunized

value: 10e6 cfu

value: subcutaneous

value: day 7

tag: disease


title: Sample_Leo

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.0.1) pipeline to generate FASTQ files
Sequences were aligned to Mnem_1.0 genome to gene expression count using Cell Ranger's default settings
Gene expression level of genes were quantified using Cell Ranger's default settings
Assembly: Macaca_nemestrina Mnem_1.0
Supplementary files format and content: barcodes.tsv.gz: tab-separated file with 10x barcodes
Supplementary files format and content: features.tsv.gz: tab-separated file with features (genes)
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format

organism: Macaca nemestrina

extract_protocol:
Non-human primates (NHP) biliary epithelial cells (BEC) enriched in cholangiocytes obtained from the enzymatic digestion of liver pieces of 2 NHP (one untreated and one LV-treated at 3e9 TU/kg)
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1, 10x Genomics, ref. CG000204).

value: Liver

tag: cell type

value: Biliary epithelial cells (BEC)


title: Col-0_22_RNA-seq_rep3

value: wild type

tag: treatment


title: LN23A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.7dpi.7

tag: tissue


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, replicate 1, RNAseq

description: Library name: TYA1

value: primary cells

value: prostate

value: 2 weeks after EYFP overexpression, Ar deletion

tag: genotype

value: Tmprss2CreERT2, lsl-EYFP, Arf/Y


title: Col-0_Khib_rep2

value: Khib antibody (PTM-802, PTM Bio-labs, Hangzhou, China)


title: CBO-KOLF2.2J_Day32-WT3, WT

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

institute: EMBL-EBI

description:
Library name: KOLF2_CBO_Day32_R3_GT24-12071_CGGCGTGA-ACAGGCGC_S61_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: study11_featureCounts.csv study11_genesCounts.csv study11_genesRawCounts.csv study11_genesTPM.csv study11_stats.csv study11_txCounts.csv study11_txRawCounts.csv study11_txTPM.csv

extract_protocol:
RNeasy Mini Kit QIAGEN NucleoSpin RNA Plus MACHEREY-NAGEL
KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina NovaSeq X

value: iPSC

tag: time

value: day 32

tag: model system

value: Cortical brain (dorsal forebrain patterning)

tag: parental cell_line


title: Sample_Acqua


title: LN22A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.7dpi.6

value: Lymph Node

value: WT

tag: vaccination status

value: No

tag: disease stage

value: No disease


title: Col-0_Khib_rep1

value: seedlings

value: untreated

tag: chip antibody


title: Tmprss2CreERT2, lsl-EYFP, replicate 3, RNAseq

description: Library name: TY3

value: 2 weeks after EYFP overexpression

value: Tmprss2CreERT2, lsl-EYFP


title: CBO-KOLF2.2J_Day32-WT2, WT

description:
Library name: KOLF2_CBO_Day32_R2_GT24-12070_TAATACAG-GTGAATAT_S44_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: cell line


title: sant-null_input_rep1

value: sant-null quadruple mutants


title: LN21A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.7dpi.5

value: Immunized

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

tag: vaccine route

value: subcutaneous

tag: days post_immunization

value: day 7


title: Tmprss2CreERT2, lsl-EYFP, replicate 1, RNAseq

description: Library name: TY1

value: primary cells

value: prostate


title: Tmprss2CreERT2, lsl-EYFP, replicate 2, RNAseq

description: Library name: TY2


title: LN27A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.90dpi.3

value: Not immunized

value: Saline

value: day 90

tag: challenge

tag: challenge strain

tag: challenge dose

tag: challenge route


title: LN20A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.7dpi.4

tag: tissue

value: Lymph Node

value: WT

tag: disease


title: Col-0_input_rep2

tag: genotype

value: wild type

tag: treatment


title: CBO-KOLF2.2J_Day32-WT1, WT

description:
Library name: KOLF2_CBO_Day32_R1_GT24-12069_TGACGAAT-GCCTACTG_S50_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: cell type

value: iPSC

tag: time

value: day 32

tag: model system

value: Cortical brain (dorsal forebrain patterning)

tag: parental cell_line


title: Tmprss2CreERT2, lsl-EYFP, Arf/Y, replicate 3, RNAseq

description: Library name: TYA3

value: 2 weeks after EYFP overexpression, Ar deletion

value: Tmprss2CreERT2, lsl-EYFP, Arf/Y


title: Kmt2a KO-6271

city: Xiamen

first: Aobo

last: Lian

state: No

address: Xiang'an South Road, Xiang'an District, Xiamen

institute: xiamen university

description: Library name: Sample 14

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: GRCm38 (mm10)
Supplementary files format and content: The excel files include count and FPKM values for each sample
Supplementary files format and content: raw_counts

source_name: Lung

extract_protocol:
Peritoneal cavity macrophage was isolated and sent to Novogene Co., Ltd. Beijing, China.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Lung

value: Kmt2a KO


title: LN19A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.7dpi.3

tag: vaccination status

value: Immunized

value: 10e6 cfu

value: subcutaneous

value: No

tag: disease stage

value: No disease


title: LN18A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.7dpi.2

tag: vaccine

tag: vaccine dose

value: day 7


title: CBO-KOLF2.2J_Day25-WT4, WT

description:
Library name: KOLF2_CBO_Day25_R4_GT24-12068_CAGTAGGC-ATTCGTCA_S43_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: cell line

value: day 25


title: Col-0_input_rep1

value: seedlings

value: untreated


title: DAP9

city: Beijing

first: Chunxia

middle: ZL

state: Beijing

address: nstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiao Street, Dongzhimennei, Dongcheng District, Beijing, China

department: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description:
Library name: sample9
DAP9_FPKM

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome mm10 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Rattus norvegicus

source_name: Cartilage and subchondral bone

growth_protocol: Sprague-Dawley rats were housed under 12h light/dark cycle with ad libitum access to food and water

extract_protocol:
Total RNA was isolated from cartilage and subchondral bone tissue using the RNeasy mini kit, and mRNA containing poly-A tails was enriched with poly-T oligonucleotide magnetic beads.
The RNA library construction steps include: enriching poly-A mRNA via polyA enrichment, fragmenting, synthesizing first-strand cDNA with magnetic bead purification, second-strand cDNA synthesis, followed by end repair, 3' adenylation, adapter ligation, purification, and library amplification to complete the sequencing library.

treatment_protocol: Rats received local drug treatment daily for 5 consecutive weeks, with 2 hours of treatment per day.

value: Cartilage and subchondral bone

value: DAP


title: Kmt2a KO-6242

description: Library name: Sample 12


title: LN17A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.rBCG.7dpi.1

value: Lymph Node

value: WT

tag: vaccine route

tag: days post_immunization

tag: challenge


title: CBO-KOLF2.2J_Day25-WT2, WT

description:
Library name: KOLF2_CBO_Day25_R2_GT24-12067_TTGGACTC-CTGCTTCC_S52_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

value: iPSC

value: Cortical brain (dorsal forebrain patterning)


title: DAP6

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description:
Library name: sample8
DAP6_FPKM


title: CBO-KOLF2.2J_Day25-WT1, WT

description:
Library name: KOLF2_CBO_Day25_R1_GT24-12066_CCAAGTCT-TCATCCTT_S49_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm


title: Kmt2a-6273

description: Library name: Sample 11

value: Lung


title: DAP5

description:
Library name: sample7
DAP5_FPKM


title: LN16A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.7dpi.8

value: BCG

tag: challenge strain

tag: challenge dose

tag: challenge route


title: CBO-KOLF2.2J_Day20-WT3, WT

description:
Library name: KOLF2_CBO_Day20_R3_GT24-12064_TCTCTACT-GAACCGCG_S42_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

value: day 20


title: LN14A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.7dpi.6

tag: tissue

tag: genotype

value: Immunized

value: 10e6 cfu

tag: disease


title: Kmt2a-6247

description: Library name: Sample 9


title: Mode12

description:
Library name: sample6
Model12_FPKM

tag: treatment

value: No


title: Kmt2a-6248

description: Library name: Sample 10


title: Men1 KO-6084

description: Library name: Sample 8

value: Men1 KO


title: LN13A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.7dpi.5

value: subcutaneous

value: day 7

value: No disease


title: Model2

description:
Library name: sample4
Model2_FPKM


title: CBO-KOLF2.2J_Day5-WT4, WT

description:
Library name: KOLF2_CBO_Day5_R4_GT24-12062_AGTTCAGG-TCTGTTGG_S35_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: cell type

tag: time

value: day 5

tag: model system


title: Model11

description:
Library name: sample5
Model11_FPKM

value: Cartilage and subchondral bone


title: Men1 KO-6076

description: Library name: Sample 7


title: LN12A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.7dpi.4

tag: vaccination status

tag: disease stage


title: Control3

description:
Library name: sample3
Control3_FPKM


title: Kmt2a KO-6270

description: Library name: Sample 13

value: Kmt2a KO


title: CBO-KOLF2.2J_Day5-WT2, WT

description:
Library name: KOLF2_CBO_Day5_R2_GT24-12061_TGGATCGA-TATCGCAC_S54_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: parental cell_line


title: Men1 KO-6075

description: Library name: Sample 6


title: LN11A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.7dpi.3

value: Lymph Node

tag: vaccine

tag: vaccine dose


title: Control2

description:
Library name: sample2
Control2_FPKM


title: CBO-KOLF2.2J_Day20-WT4, WT

description:
Library name: KOLF2_CBO_Day20_R4_GT24-12065_CTCTCGTC-AGGTTATA_S59_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: cell line


title: LN10A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.7dpi.2

value: WT

tag: vaccine route

tag: days post_immunization

tag: challenge


title: LN15A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.7dpi.7

tag: challenge strain

tag: challenge dose

tag: challenge route


title: Men1 KO-6086

description: Library name: Sample 5

tag: tissue

tag: genotype


title: CBO-KOLF2.2J_Day4-WT4, WT

description:
Library name: KOLF2_CBO_Day4_R4_GT24-12059_GCTTGTCA-GTATGTTC_S57_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: cell type

value: iPSC

value: day 4


title: Men1-6074

description: Library name: Sample 4

value: Lung


title: LN9A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.BCG.7dpi.1

value: BCG

tag: disease


title: CBO-KOLF2.2J_Day4-WT3, WT

description:
Library name: KOLF2_CBO_Day4_R3_GT24-12058_ATCCACTG-ACGCACCT_S36_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: time

tag: model system

value: Cortical brain (dorsal forebrain patterning)


title: CBO-KOLF2.2J_Day20-WT1, WT

description:
Library name: KOLF2_CBO_Day20_R1_GT24-12063_GACCTGAA-CTCACCAA_S37_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

value: day 20


title: CBO-KOLF2.2J_Day5-WT1, WT

description:
Library name: KOLF2_CBO_Day5_R1_GT24-12060_CAAGCTAG-CGCTATGT_S34_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm


title: High anxiety Wistar rats treated with urolithin A for 2 months, nucleus accumbens

city: Lausanne

first: Dogukan

middle: Hazar

last: Ulgen

address: EPFL SV BMI Station 19

department: Brain Mind Institute

country: Switzerland

institute: EPFL

description:
Library name: HAUA_DM
10x Genomics

data_processing:
Illumina’s ‘BCL Convert’ software was used to demultiplex reads, after which 10X Genomics Cell Ranger Single Cell Software Suite (v7.1) was used to perform barcode processing and 3’ gene counting using 10X Genomics custom annotation of rat genome assembly mRatBN7.2 (Ensembl 110).
Assembly: MRatBN7.2 (Ensembl 110)
Supplementary files format and content: CellRanger output. Tab-separated values, matrix and barcode files.

source_name: Brain

extract_protocol:
Punches from the NAc from 5 hemispheres (16 weeks of age) were pooled for each nuclei isolation. The lysate was homogenized in solution D (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tris-HCl pH 7.5), centrifuged at 300 g for 5 min, and the pellet was resuspended in solution D supplemented with Optiprep Density Gradient Medium (Sigma #D1556). After centrifugation (1500 g, 5 min), supernatant was discarded, and the pellet was washed once again with solution D + Optiprep. After another centrifugation, the pellet was resuspended in 1X PBS (Corning #21-040-CV) + 0.05% BSA (Sigma #A9418) The isolated nuclei were passed through a 40-µm Flowmi cell strainer (Merck #BAH136800040) to remove debris. The remaining, intact nuclei were counted with a hemocytometer and the concentration was adjusted to ~1000 nuclei/µl.
Library preparation was started immediately by washing the nuclei with PBS + 0.05% BSA. After filtration through a 40 µm Flowmi strainer (Bel-Art, Wayne, NJ), nuclei were checked for absence of significant doublets or aggregates and loaded into a Chromium X (10x Genomics) chip together with beads, reverse transcription master mix reagents and oil to generate single-cell-containing droplets. Single-cell gene expression libraries were then prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 following the manufacturer’s instruction (protocol CG000315). Quality control was performed with a TapeStation 4200 (Agilent) and QuBit dsDNA High Sensitivity assay (Thermo Scientific) following manufacturer instructions. The sequencing libraries were loaded onto an Illumina NovaSeq 6000 Flow Cell and sequenced using read lengths of 28 nt for read1 and 90 nt for read2, at a depth of 50-90k reads/cell.

value: Brain

tag: strain

value: Outbred Wistar rats

tag: treatment

value: Urolithin A for 2 months


title: Men1-6100

description: Library name: Sample 3


title: High anxiety Wistar rats, nucleus accumbens

description:
Library name: HA_DM
10x Genomics

value: No treatment


title: LN4A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.7dpi.4

tag: vaccination status

value: Not immunized

tag: vaccine

value: Saline

value: subcutaneous

value: day 7

value: No

tag: disease stage


title: Men1-6097

description: Library name: Sample 2


title: CBO-KOLF2.2J_Day3-WT4, WT

description:
Library name: KOLF2_CBO_Day3_R4_GT24-12056_GGACTTGG-CGTCTGCG_S38_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: cell line

value: day 3

tag: parental cell_line


title: Control1

description:
Library name: sample1
Control1_FPKM

value: Cartilage and subchondral bone


title: LN2A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.7dpi.2

value: Lymph Node

value: WT

tag: vaccine dose

tag: vaccine route

tag: days post_immunization

tag: challenge

value: No disease


title: Low anxiety Wistar rats, nucleus accumbens

description:
Library name: LA_DM
10x Genomics

tag: tissue


title: CBO-KOLF2.2J_Day4-WT2, WT

description:
Library name: KOLF2_CBO_Day4_R2_GT24-12057_AAGTCCAA-TACTCATA_S53_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

value: iPSC

value: day 4


title: 250nM estradiol, rep3 [RNA]

first: Li

last: Jin

state: -- None selected --

address: Department of Obstetrics and Gynecology

institute: peking union medical college hospital

data_processing:
The quality of the samples, experiment, and the analysis data were completed by the Genesky Biotechnologies Inc.
The known mature miRNA expression profile was generated by using the quantifier module of the miRDeep2 package, which gives read counts for the known miRNAs.
The raw reads’ expression profiles generated for all the replicates of the samples were subjected to trimmed mean of M-values’ (TMM) normalization using the Bioconductor package edgeR.
Assembly: oryCun2
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: endometrium

growth_protocol: ECC cells were cultured in MEM containing NEAA ( 11140050, Gibco), and 10% FBS (10099141, Gibco), at 37℃ in a 5% CO2 incubator. Cells were seeded at a density of 2 × 105 viable cells /mL, and passaged every 3–4 days.

extract_protocol:
For RNA isolation, total RNA was isolated using TRIzol reagent.
A total of 2 μg of RNA/sample was used as input material for the miRNA library. The miRNA sequencing libraries were generated using a TruSeq Small RNA Sample Preparation Kit, and index codes were added to attribute sequences to each sample.

treatment_protocol: β-estradiol power (E2257,Sigma) was dissolved in DMSO with 3.7% filtered sodium hydrogen carbonate. After incubation of the final concentration of β-estradiol with 250nmol/L, cells were incubated at 37°C and 5% CO2 for 48 h before harvested.

value: endometrium

value: endometrioid endometrial carcinoma

value: estradiol


title: S18_DKO_BM_gls1

city: Paris

first: Sebastien

last: Dussaud

address: 91 bd de l'hopital

institute: UPMC

description: Library name: Sample 29

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained using in-house scripts based on MACS and HTSeq (https://github.com/ctlab/quant3p).
Assembly: mm10
Supplementary files format and content: raw_counts.txt

growth_protocol: BMDMs were obtained from Gls1-/- and control mice. PCMs were obtained from atherosclerosis-prone Ldlr-/- mice backcrossed with or without Gls2-/- and transplanted with Gls1-/- or control bone marrow.

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and amount was assessed by Nanodrop (Ozyme)
Library construction were conducted by BGI Hong Kong Company Limited using a DNBseqTM platform

treatment_protocol: Bone marrow-derived macrophages were generated from Gls1-/- and control mice and cultured for the last 24h in presence or absence of interleukin-4 and glutamine synthase inhibitor (MSO). Atherosclerosis-prone Ldlr-/-  mice were backrossed with or without Gls2-/- mice and served as recipients for transplantation of Gls1-/- or control bone marrow. Then, hyperlipidemia was induced in these mice by feeding them with an atherogenic diet (Western diet, TD88137, Ssniff) for 11 weeks. Peritoneal macrophages were obtained from all four genotypes at the end of the study.


title: Men1-6094

description: Library name: Sample 1

value: Lung

tag: genotype


title: CBO-KOLF2.2J_Day3-WT2, WT

description:
Library name: KOLF2_CBO_Day3_R2_GT24-12055_TTATAACC-TCGATATC_S45_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: cell type

value: Cortical brain (dorsal forebrain patterning)


title: 250nM estradiol, rep2 [RNA]


title: LN1A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.7dpi.1

value: Not immunized

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease


title: CBO-KOLF2.2J_Day3-WT1, WT

description:
Library name: KOLF2_CBO_Day3_R1_GT24-12054_CCGCGGTT-CTAGCGCT_S40_L007
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: time

tag: model system


title: L96A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.30dpc.8

tag: vaccination status

value: Immunized

tag: vaccine

value: 10e6 cfu

value: day 120

value: Yes

value: Mtb H37Rv

value: 500 cfu

value: Intranasal

value: Tuberculosis

value: Active tuberculosis


title: S17_DKO_BM_gls1

description: Library name: Sample 28

tag: cell line


title: 250nM estradiol, rep1 [RNA]

tag: treatment


title: S12_DKO_BM_ctl

description: Library name: Sample 27


title: L95A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.30dpc.7

value: WT

tag: vaccine dose

value: subcutaneous

tag: disease stage


title: ENDO-MOK20030_31-WT2, WT

description:
Library name: WT_ENDO_REP2_GT25-00008_TGGATCGA-TATCGCAC_S699_L004
KOLF2.2J differentiated to endoderm

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: study10_featureCounts.csv study10_genesCounts.csv study10_genesRawCounts.csv study10_genesTPM.csv study10_stats.csv study10_txCounts.csv study10_txRawCounts.csv study10_txTPM.csv

value: iPSC

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

value: day 5

value: endoderm

tag: parental cell_line


title: Control, rep2 [RNA]

tag: tissue

value: endometrium

tag: cell type

value: endometrioid endometrial carcinoma


title: ENDO-MOK20030_31-WT1, WT

description:
Library name: WT_ENDO_REP1_GT25-00007_CAAGCTAG-CGCTATGT_S718_L004
KOLF2.2J differentiated to endoderm


title: L94A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.30dpc.6

value: Lung

tag: genotype

value: Immunized

tag: vaccine route

tag: days post_immunization

tag: challenge

tag: challenge strain

tag: challenge dose


title: LN3A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
LN.Sal.7dpi.3

value: Lymph Node

tag: vaccination status

value: Not immunized

tag: vaccine

value: Saline

value: day 7

value: No

tag: challenge route

tag: disease

value: No disease


title: S10_DKO_BM_ctl

description: Library name: Sample 25

tag: cell line


title: Control, rep1 [RNA]

tag: treatment


title: L93A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.30dpc.5

tag: vaccine dose

value: 10e6 cfu

value: day 120

value: Yes

value: Mtb H37Rv

value: 500 cfu

value: Intranasal

value: Tuberculosis

tag: disease stage

value: Active tuberculosis


title: S39_CTL_BM_gls1

description: Library name: Sample 24

value: Ldlr-/-


title: ENDO-MOK20031W-A10, KO

description:
Library name: EOMES_KO_A10_GT25-00006_GCTTGTCA-GTATGTTC_S709_L004
KOLF2.2J derived knockout cell line, EOMES KO, differentiated to endoderm

value: iPSC

tag: editing strategy

value: Full coding length

tag: altered gene_symbol

value: EOMES

tag: altered locus

tag: time

value: day 5

tag: model system

value: endoderm

tag: parental cell_line


title: ENDO-MOK20031W-A04, KO

description:
Library name: EOMES_KO_A4_GT25-00005_ATCCACTG-ACGCACCT_S716_L004
KOLF2.2J derived knockout cell line, EOMES KO, differentiated to endoderm

tag: cell type


title: S37_CTL_BM_gls1

description: Library name: Sample 23


title: Control RO1, D320

city: HOUSTON

first: Rui

last: Chen

state: Texas

address: One Baylor Plaza, Taub Building, 8th floor, room T836

department: Department of Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
The FASTQ raw feature count matrices generated from scRNA sequencing were first analyzed by the 10x Genomics Cell Ranger software (version 5.0.1)27 to filter out empty droplets using the method EmptyDrops developed by Lun et al28.
Assembly: hg19
Supplementary files format and content: A .h5ad file of count matrix.

source_name: retinal organoid

extract_protocol:
Small aggregates of iPSCs were suspended in ice-cold Matrigel (CorningTM, Cat. 354234). After incubating at 37 °C with 5% CO2 for 20 min, the iPSC/Matrigel clump was gently dispersed in N2B27 medium [DMEM/F12 (GibcoTM, Cat. 11330032): neurobasal medium (GibcoTM, 21103049) = 1:1, 0.5× B27 supplement (GibcoTM, Cat. 21103049), 0.5× N2 supplement (GibcoTM, Cat. 21103049), 0.1 mM β-mercaptoethanol (GibcoTM, Cat. 21985023), and 2 mM GlutaMAX (GibcoTM, Cat. 35050061)] for floating culture in 24-well plates. Around day 14, the adherent cultures were partially lifted at their edges via a 25-min dispase treatment (0.5 mg/mL in DMEM/F12), rinsed with DMEM/F12 medium, and then grown in a B27 medium [DMEM/F12 (3:1), 2% B27, and NEAA (GibcoTM, Cat. 11140050)]. In about 1 week, ROs spontaneously formed, displaying a bright ring when viewed under an inverted microscope, and were grown (three to five ROs per well on low-attachment 24-well plates) in a serum medium [DMEM/F12 (3:1), 8% FCS (GibcoTM, Cat. 26140095), 2% B27, NEAA, 100 mM taurine (Sigma, T0625), and 2 mM GlutaMAX].
Single-cell RNA-Seq was performed at the Single Cell Genomics Core at Baylor College of Medicine. The single-cell cDNA library preparation and sequencing followed the manufacturer's protocols (https://www.10xgenomics.com). Single-cell suspension at 1000 cells/µl in PBS was loaded on a Chromium controller to generate single-cell GEMS (Gel Beads-In-Emulsions).
The scRNA-Seq library was prepared with chromium single cell 3’ reagent kit v3.1 from 10x Genomics. The product was amplified by PCR and sequenced on Illumina Novaseq 6000 (https://www.illumina.com).

tag: tissue

value: retinal organoid

tag: disease state

value: healthy control

value: no treatment

tag: genotype

value: wild-type

tag: age

tag: individual

value: Sample 3


title: S11_DKO_BM_ctl

description: Library name: Sample 26


title: L77A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.30dpc.5

value: Lung

value: WT

tag: vaccination status

value: Not immunized

tag: vaccine

value: Saline

tag: vaccine route

value: subcutaneous

tag: days post_immunization

value: day 120

tag: challenge

value: Yes

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease


title: Control RO1, D130

tag: treatment


title: ENDO-MOK20031W-A03, KO

description:
Library name: EOMES_KO_A3_GT25-00004_AAGTCCAA-TACTCATA_S728_L004
KOLF2.2J derived knockout cell line, EOMES KO, differentiated to endoderm

tag: cell line

value: iPSC

tag: editing strategy

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

tag: parental cell_line


title: S36_CTL_BM_ctl

description: Library name: Sample 22

tag: cell type

value: Ldlr-/-


title: L76A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.30dpc.4

tag: tissue

tag: genotype

tag: vaccination status

tag: vaccine

tag: vaccine dose

value: Mtb H37Rv

value: 500 cfu

value: Intranasal

value: Tuberculosis

tag: disease stage

value: Active tuberculosis


title: ENDO-MOK20030W-B07, KO

description:
Library name: NKX-2_KO_B7_GT25-00003_GGACTTGG-CGTCTGCG_S702_L004
KOLF2.2J derived knockout cell line, NKX2-1 KO, differentiated to endoderm

value: Full coding length

value: day 5

value: endoderm


title: Patient RO2, D262

value: retinal organoid

tag: disease state

value: Stardgart's Disease

value: no treatment

tag: age

tag: individual

value: Sample 2


title: S31_CTL_BM_ctl

description: Library name: Sample 21

tag: cell line


title: L75A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.30dpc.3

value: Lung

value: WT

value: Not immunized

value: Saline

tag: vaccine route

value: subcutaneous

tag: days post_immunization

tag: challenge

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease


title: Control, rep3 [RNA]

tag: tissue

value: endometrium

tag: cell type

value: endometrioid endometrial carcinoma

tag: treatment


title: ENDO-MOK20030W-A06, KO

description:
Library name: NKX-2_KO_A6_GT25-00002_TTATAACC-TCGATATC_S722_L004
KOLF2.2J derived knockout cell line, NKX2-1 KO, differentiated to endoderm

value: iPSC

tag: editing strategy

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

tag: parental cell_line


title: ENDO-MOK20030_31-WT4, WT

description:
Library name: WT_ENDO_REP4_GT25-00009_AGTTCAGG-TCTGTTGG_S713_L004
KOLF2.2J differentiated to endoderm

tag: cell line

value: Not applicable


title: L74A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.30dpc.2

tag: genotype

tag: vaccination status

tag: vaccine

tag: vaccine dose

tag: vaccine route

value: day 120

value: Yes

value: Mtb H37Rv

value: 500 cfu

value: Intranasal

value: Tuberculosis

tag: disease stage

value: Active tuberculosis


title: Patient RO2, D135

value: retinal organoid

tag: disease state

value: Stardgart's Disease

value: no treatment

tag: age

tag: individual

value: Sample 2


title: IL4.MSO_GLS1_3

description: Library name: Sample 20

tag: cell type

value: Cell culture + interleukin-4 (IL-4)


title: L73A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.30dpc.1

tag: tissue

value: Lung

value: WT

value: Not immunized

value: Saline

value: subcutaneous

tag: days post_immunization

tag: challenge

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease


title: L78A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.30dpc.6

tag: genotype

value: day 120


title: IL4.MSO_GLS1_2

description: Library name: Sample 19

tag: cell line


title: MESO-MOK20015-WT4, WT

description:
Library name: ISL1_ENDO_WT_4_GT24-12116_ACCTTGGC-ATGAGGCC_S84_L008
KOLF2.2J differentiated to mesoderm

value: iPSC

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 5

tag: model system

value: mesoderm

tag: parental cell_line


title: Patient RO1, D135

tag: disease state

tag: treatment

tag: age

tag: individual

value: Sample 1


title: ENDO-MOK20030W-A03, KO

description:
Library name: NKX-2_KO_A3_GT25-00001_CCGCGGTT-CTAGCGCT_S727_L004
KOLF2.2J derived knockout cell line, NKX2-1 KO, differentiated to endoderm

tag: cell type

value: Full coding length

value: endoderm


title: IL4.MSO_GLS1_1

description: Library name: Sample 18


title: MESO-MOK20015-WT3, WT

description:
Library name: ISL1_ENDO_WT_3_GT24-12115_GTTCCAAT-GCAGAATT_S79_L008
KOLF2.2J differentiated to mesoderm


title: HAEC, RNA, IL1b, 32h, rep3

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

country: Finland

institute: A. I. Virtanen Institute

data_processing:
Reads obtained were trimmed to 3' A-stretches originating from the library preparation and poor-quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Remaining reads were aligned to GRCh37hg19 reference genome using STAR v2.5.4b with ENCODE recommended options for long RNA-seq analysis.
Assembly: hg19
Supplementary files format and content: bedGraphs

source_name: human aortic endothelial cells

growth_protocol: Human aortic endothelial cells (HAEC) (unknown ref number because they were thawed at passage 3 from Maria’s LONZA’s tubes) were maintained in endothelial cell growth medium (EGM; basal medium with SingleQuots supplements CC-4133; Lonza) supplemented with 10% fetal bovine serum (FBS; GIBCO) on T-75 cell culture flasks coated with 10 g/ml fibronectin (Sigma, St Louis, MO, USA) and 0.05% gelatin at 37°C in a humidified atmosphere at 5% CO2 and used at passage 4 to 6.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (74104, QIAGEN) according to manufacturer’s protocol.
RNA > 200 nts, rRNA depleted
Extracted RNA was sent to the Sequencing Service GeneCore Sequencing Facility (EMBL, www.genecore.embl.de) for NGS library sequencing.

treatment_protocol: Prior to IL-1b stimulation, HAEC medium was changed with fresh endothelial cell growth medium (EGM; basal medium; Lonza) supplemented with 1% fetal bovine serum (FBS; GIBCO). HAEC were then stimulated with 10 ng/mL of IL-1β (PHC0814, GIBCO) at 2 h, 8 h, and 23 h time points.

value: human aortic endothelial cells

tag: timepoint

value: 32 hours


title: L72A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpc.8

tag: tissue

tag: vaccination status

value: Immunized

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

tag: vaccine route

tag: days post_immunization

value: day 97

tag: challenge

value: Yes

tag: challenge strain

value: Mtb H37Rv

tag: challenge dose

value: 500 cfu

value: Intranasal

value: Tuberculosis

tag: disease stage

value: Early infection


title: HAEC, RNA, IL1b, 32h, rep2


title: L71A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpc.7

value: Lung

tag: genotype

value: WT

value: subcutaneous

tag: challenge route

tag: disease


title: L70A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpc.6


title: MESO-MOK20015-WT1, WT

description:
Library name: ISL1_ENDO_WT_1_GT24-12114_GCAATGCA-AACGTTCC_S78_L008
KOLF2.2J differentiated to mesoderm

tag: cell line

value: iPSC

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 5

tag: model system

value: mesoderm

tag: parental cell_line


title: Patient RO1, D262

tag: tissue

value: retinal organoid

tag: disease state

value: Stardgart's Disease

tag: treatment

value: no treatment

tag: age

tag: individual

value: Sample 1


title: IL4.MSO_CTL1

description: Library name: Sample 15

tag: cell type

value: Cell culture + interleukin-4 (IL-4)


title: MESO-MOK20015P-D12, KO

description:
Library name: ISL1_ENDO_PTC_D12_GT24-12113_ATGGCATG-GGTACCTT_S74_L008
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

value: Termination codon


title: IL4.MSO_CTL2

description: Library name: Sample 16


title: L69A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpc.5

tag: vaccination status

value: Immunized

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

tag: vaccine route

tag: days post_immunization

value: day 97

tag: challenge

value: Yes

tag: challenge strain

value: Mtb H37Rv

tag: challenge dose

value: 500 cfu

tag: disease stage


title: HAEC, RNA, IL1b, 14h, rep3

value: human aortic endothelial cells

tag: timepoint

value: 14 hours


title: MESO-MOK20015P-D10, KO

description:
Library name: ISL1_ENDO_PTC_D10_GT24-12112_GGAGCGTC-GCACGGAC_S89_L008
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

tag: cell line

value: iPSC

tag: editing strategy

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

tag: parental cell_line


title: HAEC, RNA, IL1b, 14h, rep2

tag: cell type

tag: treatment


title: MESO-MOK20015P-C12, KO

description:
Library name: ISL1_ENDO_PTC_C12_GT24-12111_AAGATACT-ATGTAAGT_S87_L008
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to mesoderm

value: day 5


title: L68A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpc.4

tag: tissue

value: Lung

tag: genotype

value: WT

tag: vaccination status

tag: vaccine

tag: vaccine dose

value: subcutaneous

tag: challenge route

value: Intranasal

tag: disease

value: Tuberculosis

value: Early infection


title: HAEC, RNA, IL1b, 14h, rep1

tag: timepoint


title: IL4_GLS1_2

description: Library name: Sample 13

tag: cell line

value: Cell culture + interleukin-4 (IL-4)


title: IL4_GLS1_3

description: Library name: Sample 14


title: L67A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpc.3

value: Immunized

tag: vaccine route

tag: days post_immunization

tag: challenge

tag: challenge strain

tag: challenge dose

tag: disease stage


title: PrS-MOK20105_125_98_101-WT3-hyp, WT

description:
Library name: KOLF2_2J_3_O2_REP3_GT25-00024_ATGAGGCC-CAATTAAC_S721_L004
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: study8_featureCounts.csv study8_genesCounts.csv study8_genesRawCounts.csv study8_genesTPM.csv study8_stats.csv study8_txCounts.csv study8_txRawCounts.csv study8_txTPM.csv

extract_protocol:
Arcturus PicoPure RNA isolation Kit Applied biosystems
KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina NovaSeq X

tag: cell type

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

tag: condition

value: hypoxia

tag: parental cell_line


title: L66A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpc.2

tag: tissue

tag: genotype

tag: vaccination status

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

value: day 97

value: Yes

value: Mtb H37Rv

value: 500 cfu

tag: challenge route

tag: disease


title: IL4_GLS1_1

description: Library name: Sample 12

tag: cell line


title: PrS-MOK20105_125_98_101-WT2-hyp, WT

description:
Library name: KOLF2_2J_3_O2_REP2_GT25-00023_GCAGAATT-TGGCCGGT_S707_L004
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: iPSC


title: IL4_CTL_3

description: Library name: Sample 11


title: HAEC, RNA, IL1b, 8h, rep2

value: human aortic endothelial cells

tag: timepoint

value: 8 hours

tag: treatment


title: IL4.MSO_CTL3

description: Library name: Sample 17

tag: cell type


title: PrS-MOK20105_125_98_101-WT1-hyp, WT

description:
Library name: KOLF2_2J_3_O2_REP1_GT25-00022_AACGTTCC-AGTACTCC_S714_L004
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

tag: editing strategy

tag: altered gene_symbol


title: IL4_CTL_2

description: Library name: Sample 10


title: HAEC, RNA, IL1b, 8h, rep1


title: L65A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpc.1

value: Lung

value: WT

tag: vaccine route

value: subcutaneous

tag: days post_immunization

tag: challenge

tag: challenge strain

tag: challenge dose

value: Intranasal

tag: disease stage


title: PrS-MOK20101P-H01-hyp, KO

description:
Library name: ELF5_PTC_H01_3_O2_GT25-00021_GGTACCTT-GACGTCTT_S704_L004
KOLF2.2J derived knockout cell line, ELF5 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: Termination codon

tag: altered locus

tag: time

tag: model system

tag: condition

tag: parental cell_line


title: IL4_CTL_1

description: Library name: Sample 9

tag: cell line

value: Cell culture + interleukin-4 (IL-4)


title: HAEC, RNA, IL1b, 32h, rep1

tag: timepoint

value: 32 hours


title: L63A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpc.7

tag: tissue

tag: genotype

tag: vaccination status

value: Immunized

tag: vaccine

value: BCG

tag: vaccine dose

tag: challenge route

tag: disease

value: Tuberculosis

value: Early infection


title: MSO_GLS1_2

description: Library name: Sample 8

tag: cell type

value: Cell culture


title: PrS-MOK20101P-B06-hyp, KO

description:
Library name: ELF5_PTC_B06_3_O2_GT25-00020_GCACGGAC-TGCGAGAC_S731_L004
KOLF2.2J derived knockout cell line, ELF5 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

tag: editing strategy

tag: altered gene_symbol

value: day 6

value: primitive syncytium

value: hypoxia


title: L62A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpc.6

value: 10e6 cfu

tag: vaccine route

tag: days post_immunization

value: day 97

tag: challenge

value: Yes

tag: challenge strain

value: Mtb H37Rv

tag: challenge dose

value: 500 cfu

tag: disease stage


title: PrS-MOK20101P-A04-hyp, KO

description:
Library name: ELF5_PTC_A04_3_O2_GT25-00019_ATGTAAGT-CATAGAGT_S725_L004
KOLF2.2J derived knockout cell line, ELF5 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

tag: cell line

value: iPSC

tag: altered locus

tag: time

tag: model system

tag: condition

tag: parental cell_line


title: L61A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpc.5

tag: tissue

value: Lung

tag: genotype

value: WT

tag: vaccination status

tag: vaccine

tag: vaccine dose

value: subcutaneous

tag: challenge route

value: Intranasal


title: MSO_GLS1_1

description: Library name: Sample 7

tag: cell type


title: HAEC, RNA, IL1b, 2h, rep1

value: human aortic endothelial cells

tag: timepoint

value: 2 hours

tag: treatment


title: HAEC, RNA, IL1b, 2h, rep3


title: HAEC, RNA, IL1b, 8h, rep3

value: 8 hours


title: PrS-MOK20098P-E05-hyp, KO

description:
Library name: ASCL2_PTC_E05_3_O2_GT25-00018_CGGCGTGA-ACAGGCGC_S723_L004
KOLF2.2J derived knockout cell line, ASCL2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

tag: editing strategy

value: Termination codon

tag: altered gene_symbol


title: HAEC, RNA, control, rep3

value: 0 hours

value: Control


title: L60A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpc.4

value: Immunized

value: BCG

tag: vaccine route

tag: days post_immunization

tag: challenge

tag: challenge strain

tag: challenge dose

tag: disease

value: Tuberculosis

tag: disease stage

value: Early infection


title: PrS-MOK20098P-D02-hyp, KO

description:
Library name: ASCL2_PTC_D02_3_O2_GT25-00017_TAATACAG-GTGAATAT_S719_L004
KOLF2.2J derived knockout cell line, ASCL2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

tag: cell line

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

tag: condition

value: hypoxia

tag: parental cell_line


title: MSO_CTL_1

description: Library name: Sample 5

tag: cell type

value: Cell culture


title: HAEC, RNA, control, rep2

tag: timepoint

tag: treatment


title: L59A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpc.3

tag: tissue

value: Lung

tag: genotype

value: WT

tag: vaccination status

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

value: day 97

value: Yes

value: Mtb H37Rv

value: 500 cfu

tag: challenge route


title: PrS-MOK20098P-B06-hyp, KO

description:
Library name: ASCL2_PTC_B06_3_O2_GT25-00016_TGACGAAT-GCCTACTG_S712_L004
KOLF2.2J derived knockout cell line, ASCL2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: iPSC

tag: editing strategy

value: Termination codon

tag: altered gene_symbol


title: Basal_GLS1_2

description: Library name: Sample 4

tag: cell line


title: L64A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpc.8

value: Immunized

tag: vaccine route

value: subcutaneous

tag: days post_immunization

tag: challenge

tag: challenge strain

tag: challenge dose

value: Intranasal

tag: disease

tag: disease stage


title: HAEC, RNA, control, rep1

tag: cell type

value: human aortic endothelial cells

tag: timepoint

value: 0 hours

tag: treatment

value: Control


title: L58A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpc.2

tag: tissue

tag: genotype

tag: vaccination status

value: BCG

value: Tuberculosis

value: Early infection


title: Basal_GLS1_1

description: Library name: Sample 3

value: Cell culture


title: HAEC, RNA, IL1b, 2h, rep2

value: 2 hours


title: PrS-MOK20125P-C07-hyp, KO

description:
Library name: TP63_PTC_C07_3_O2_GT25-00014_TTGGACTC-CTGCTTCC_S717_L004
KOLF2.2J derived knockout cell line, TP63 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

tag: condition

value: hypoxia

tag: parental cell_line


title: L57A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpc.1

value: Lung

value: WT

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

tag: vaccine route

tag: days post_immunization

value: day 97

value: Yes

value: Mtb H37Rv

value: 500 cfu

tag: challenge route