title: A375 PRAME +/+ melanoma cells, rep3

value: WT - PRAME +/+


title: A375 PRAME +/+ melanoma cells, rep2

status: Public on Oct 16 2024

type: SRA

city: Oklahoma City

first: Jeffrey

middle: Don

last: McBride

state: OK

address: 1000 NE 13th St

department: Dermatology

country: USA

institute: University of Oklahoma

library_source: transcriptomic

data_processing:
Raw reads were cleaned using FastP (DOI: 10.1093/bioinformatics/bty560) program with the following parameters: -q 20 -l 30 -n 5 -e 25 –cut_front –cut_tail -M 30 -W 1 –trim_poly_g –trim_poly_x
Filtered reads were mapped to reference human genome (GRCh38), version 44 (Ensembl 110) using the STAR software v2.7.11b using default parameters
Gene counts were optained using STAR's option: --quantMode GeneCounts , and counts were taen from the 4th column: tail -n +5 5CP_S7.ReadsPerGene.out.tab | cut -f1 >> geneids.txt
Assembly: human genome (GRCh38), version 44 (Ensembl 110)
Supplementary files format and content: tab delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol:
Human melanoma cell lines A375 (ATCC) were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin, 50 µg/ml streptomycin. Primary epidermal melanocytes (ATCC) were cultured in dermal cell basal medium supplemented with Adult Melanocyte Growth Kit.  Primary dermal fibroblasts (ATCC)  were cultured in fibroblast basal medium supplemented with fibroblast growth kit.   Primary dermal microvascular endothelial cells were cultured in vascular cell basal medium supplemented with endothelial cell growth kit.
Cell cultures were maintained in a humidified atmosphere of 5% CO2 and 37 °C.

extract_protocol:
Qiagen Rneasy Mini kit
NEBNext Poly(A) mRNA Magnetic Isolation Module & IDT xGen Broad Range RNA Library Kit

treatment_protocol: Human melanoma A375 cells were cultured until they reached 80% confluency. The cells were then washed several times with PBS and switched to serum-free DMEM media for 72 hours to minimize protein contamination from serum. The medium was collected and centrifuged at 3,000 x g for 15 minutes to remove cellular debris, followed by ultrafiltration using 100 kDa filters (Amico Ultra-15, Millipore) at 4,000 x g for 15 minutes. PM, PF and EN cells were incubated with the collected condition medium for 72h respectively. Different groups of cells were collected separately and  performed RNAseq.

tag: cell line

tag: cell type

value: Human melanoma cell lines A375 (ATCC)

tag: genotype

tag: treatment

value: no treatment


title: Endothelial cells treated w/A375 PRAME +/+, rep1

source_name: HDMVEC

value: HDMVEC

value: Primary dermal microvascular endothelial cells

value: WT

value: Extracellular vesicle treatmant from A375 PRAME +/+


title: A375 PRAME +/- melanoma cells, rep3

value: WT - PRAME +/-


title: TT45RO_HU02

city: Erlangen

first: Krystelle

last: Nganou-Makamdop

address: Schlossgarten 4

department: Virology institute

country: Germany

institute: Universitätsklinikum Erlangen

data_processing:
Raw reads were trimmed for low-quality reads and miscalled nucleotides using Trimmomatic v. 0.36.
Reads that passed the trimming step were aligned to the human genome (Ensembl GRCh38 release 88) using the STAR aligner (version 2.5.3a).
Aligned reads were counted using HTSeq (version 0.9.1).
Read count files were merged and genes with mean of < 1 read per sample were excluded.
The expression and differential expression values were generated using DESeq2 in R
Assembly: hg38
Supplementary files format and content: excel file includes raw counts for each sample

source_name: Blood

growth_protocol: PBMC were stimulated with measles or tetanus antigens, or either left untreated and incubated at 37C 5% CO2.

extract_protocol:
RNA was extracted from sorted cells lysed in RNAzol RT (Molecular Research Center), according to the manufacturer’s instructions. Briefly, 0.4 volume of sterile water was added to each lysate to allow aqueous and organic phase separation. Total RNA was then extracted from the aqueous phase by isopropanol precipitation. RNA pellets were washed with 70% ethanol and resuspended in sterile water. Extracted RNA was stored at −80°C until preparation of mRNA libraries.
Messenger RNA libraries were constructed as described previously using the NEBNext Ultra RNA library preparation kit (New England Biolabs). Polyadenylated transcripts were purified with oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries. Libraries were validated by microelectrophoresis on a tapestation 4200 (Agilent), quantified with Kapa Library Quantification Kits (Roche), pooled and clustered on an Illumina S2 flow cell. Clustered flow cells were sequenced in 2x75 base paired-end runs.

treatment_protocol: 2 x 106 cells per well were seeded in R10 medium containing CD28/CD49d (BD; 1µg/ml each) with either SEB (0.25 ug/ml), TT protein (Tetanol, GSK—0.5 I.E), a MV 20-mer overlapping peptide pool corresponding to the measles virus hemagglutinin and fusion proteins (EMC, 2.5µg/ml) or left unstimulated. After 24 hours incubation at 37C in presence of 2nM monensin and CD154-PE (BD, clone TRAP), cells were stained for sort of T cell subsets.

tag: tissue

value: Blood

tag: disease state

value: HIV seronegative

value: CD4 T cells

value: tetanus toxoid antigen


title: MV154_HIV20

value: HIV seropositive

value: measles antigen


title: MV154_HIV19


title: MV154_HIV12


title: MV154_HIV18


title: MV154_HU06


title: Klebsormidium nitens, 72h Sucrose resupply to starved plants, Rep 2

city: Singapore

first: Yating

last: Dong

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
The raw sequence reads was mapped using STAR (v.2.7) with the reference genome
The raw readcounts were normalised using DeSeq2 package from R
The differentially expressed genes were used for downstream analysis
Assembly: M. polymorpha v5.1; K. nitens v1.1
Supplementary files format and content: comma-separated values file includes raw read counts for each sample

organism: Klebsormidium nitens

source_name: Whole plant

growth_protocol: Marchantia polymorpha L.  liverworts were axenically cultivated from gemmae on half-strength Gamborg’s B5 medium (hereafter 1⁄2 B5) containing 1% (w/v) plant agar under continuous white LED light (50-60 µmol m-2 s-1) at 22°C. Klebsormidium nitensalgae cultures were grown on C medium agar plates under continuous light (10 µmol m-2 s-1) at 22°C

extract_protocol:
RNA was extracted using the QIAGEN Plant RNeasy kit
Directional mRNA library preparation (poly A enrichment)

treatment_protocol: For nutrient treatment experiments, M. polymorpha gemmae and K. nitens were grown in axenic liquid culture with full Yamagami medium for seven days on an orbital shaker; afterwards, gemmalings were shifted into respective modified Yamagami media (nitrogen deprivation: 1% of the recommended concentrations of NaNO3 and KNO3, phosphate deprivation: 1% of recommended KH2PO4, sucrose deprivation: 0% of recommended sucrose). After five days of deprivation, culture media of M. polymorpha were replaced with full Yamagami medium for recovery periods for 6 h, 24 h, and 72 h, respectively.

value: Whole plant


title: MV154_HIV11


title: Klebsormidium nitens, 72h Sucrose resupply to starved plants, Rep 1


title: A375 PRAME +/+ melanoma cells, rep1


title: Klebsormidium nitens, 72h Sucrose resupply to starved plants, Rep 3


title: Klebsormidium nitens, 24h Sucrose resupply to starved plants, Rep 3


title: MV154_HIV09


title: Klebsormidium nitens, 24h Sucrose resupply to starved plants, Rep 2


title: MV154_HIV100


title: Klebsormidium nitens, 24h Sucrose resupply to starved plants, Rep 1


title: MV154_HIV10


title: Klebsormidium nitens,  6h Sucrose resupply to starved plants, Rep 3


title: MV154_HIV07


title: MV154_HIV06


title: MV154_HIV05


title: Klebsormidium nitens, 72h Phosphate resupply to starved plants, Rep 3


title: MV154_HIV04


title: Klebsormidium nitens,  6h Sucrose resupply to starved plants, Rep 1


title: Klebsormidium nitens, 72h Phosphate resupply to starved plants, Rep 2


title: MV154_HIV02


title: Klebsormidium nitens, 72h Phosphate resupply to starved plants, Rep 1


title: MV154_HIV01


title: Med45RO_HU24

value: Unstimulated


title: Med45RO_HU25


title: Med45RO_HU23


title: Klebsormidium nitens, 24h Phosphate resupply to starved plants, Rep 2


title: Klebsormidium nitens, 24h Phosphate resupply to starved plants, Rep 3


title: MV154_HIV08


title: Med45RO_HU21


title: Klebsormidium nitens, 24h Phosphate resupply to starved plants, Rep 1


title: Med45RO_HU22


title: Klebsormidium nitens,  6h Phosphate resupply to starved plants, Rep 2


title: Med45RO_HU20


title: Klebsormidium nitens,  6h Phosphate resupply to starved plants, Rep 3


title: Klebsormidium nitens,  6h Phosphate resupply to starved plants, Rep 1


title: Med45RO_HU19


title: Klebsormidium nitens, 72h Nitrate resupply to starved plants, Rep 3


title: Klebsormidium nitens,  6h Sucrose resupply to starved plants, Rep 2


title: Med45RO_HU18


title: Med45RO_HU15


title: Klebsormidium nitens, 72h Nitrate resupply to starved plants, Rep 1


title: Med45RO_HU17


title: Klebsormidium nitens, 72h Nitrate resupply to starved plants, Rep 2


title: Klebsormidium nitens, 24h Nitrate resupply to starved plants, Rep 3


title: Med45RO_HU12


title: Med45RO_HU13


title: Med45RO_HU10


title: Klebsormidium nitens, 24h Nitrate resupply to starved plants, Rep 1


title: Med45RO_HU06


title: BY4743 - replicate 1

city: Krakow

first: Hanna

last: Tutaj

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

data_processing:
Reads were aligned to the merged yeast R64-1-1 and ERCC reference fasta (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip) using hisat2 ( v2.1.) with the parameters --rna-strandness RF and -k 20. BAM files were sorted and indexed using samtools (1.9).
Transcript quantification was performed using featureCounts (2.0.6) with the following parameters: -F GTF -O -s 2 -t exon -p -R -T 8 --largestOverlap. The resulting files were then merged into one file using a custom script. The GTF file resulting from the concatenation of the GTF files downloaded from Ensembl and provided by the ERCC () was used in this step.
Assembly: R64-1-1 merged with ERCC fasta
Supplementary files format and content: RK-counts.tsv: TSV file with read counts per gene (or ERCC sequence).  The same amount of spike-in per cell number.
Supplementary files format and content: RK-counts-adj-vol.tsv:  TSV file with read counts per gene (or ERCC sequence). The counts for the ERCC transcripts were multiplied by adjustment factors (RK_02 - 8.40399; RK_03 - 2.72366, RK_04 - 3.58748, RK_01 - 1) to obtain the same amount of spike-in per given cell volume.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: WT diploid cell

growth_protocol: Individual monosomic strains were grown as replicate microcultures (5 to 100 μl) in YPD at 30°C to stationary phase. The latter were serially diluted and plated to test for the appearance of large colonies indicating the appearance of compensatory mutations. The microcultures in which more than 99% of the colonies were typical of a particular monosomic strain were pooled. Purity-tested cultures of monosomic cells were transferred to fresh YPD and incubated for 4 hours at 30°C with agitation. The density of the cultures was estimated by counting the cells in the Burker's chamber. The cells were also photographed under a light microscope and the long and short axes of the cells were measured for about 50 randomly selected cells. Using the formula for ellipsoids and assuming that the two shorter axes are equal, the volumes of individual cells and their sums were calculated.

extract_protocol:
Equal amounts of the mRNA spike ( 2 μl of 20x diluted ERCC RNA Spike-In Mix,TermoFisher per 10 million cells) were added to all samples. Total RNA was extracted using the FAE method followed by additional purification with RNAzol (as described in  Shedlovskiy et al. 2017).
Stranded RNAseq libraries were prepared by the Novogene company (DUTP method). For that, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. The second strand cDNA was synthesized using dUTP. The library was then subjected to end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification and purification.

tag: strain

value: WT diploid cell


title: Med45RO_HU09


title: Klebsormidium nitens,  6h Nitrate resupply to starved plants, Rep 3


title: Med45RO_HU03


title: Klebsormidium nitens,  6h Nitrate resupply to starved plants, Rep 2


title: Med45RO_HU02


title: BY4743 lacking one chromosome I - replicate 1

source_name: monosomic diploid cell

value: monosomic diploid cell

value: BY4743, monosomy chrI


title: BY4743 lacking one chromosome II - replicate 1

value: BY4743, monosomy chrII


title: Med45RO_HIV24


title: BY4743 lacking one chromosome XVI - replicate 3 [M16_3]

data_processing:
Illumina software used for basecalling
Reads aligned to the Saccharomyces cerevisiae genome using histat2 v. 2.1.0 with the following parameters: -t --dta-cufflinks -p 4 --new-summary
Alignment BAM files sorted and indexed with samtools (1.9)
Gene counts created with cuffquant with the following parameters: -v -p 4 --no-effective-length-correction and then normalized with cuffnorm with -p 4 -v -library-norm-method.classic-fpkm
Assembly: R64-1-1
Supplementary files format and content: tab-delimited text files include count values for each Sample

growth_protocol: Strains were cultured in YPD medium in 30˚C

extract_protocol:
Total RNA was extracted using RiboPure™ RNA Purification Kit
Non-paired RNA libraries were prepared for sequencing by Novagene Co., Ltd; Unstranded RNA-seq


title: Med45RO_HIV19


title: BY4743 lacking one chromosome XVI - replicate 2 [M16_2]


title: Klebsormidium nitens,  6h Nitrate resupply to starved plants, Rep 1


title: Med45RO_HU04


title: Med45RO_HIV12


title: Klebsormidium nitens, 0% Sucrose starvation, 5d, Rep 3

value: 0% Sucrose_5d


title: Klebsormidium nitens, 0% Sucrose starvation, 5d, Rep 2


title: Med45RO_HIV18


title: BY4743 lacking one chromosome XIV - replicate 3 [M14_3]


title: BY4743 lacking one chromosome XVI - replicate 1 [M16_1]


title: Med45RO_HIV100


title: Med45RO_HIV23


title: Med45RO_HIV10


title: Klebsormidium nitens, 0% Sucrose starvation, 5d, Rep 1


title: Med45RO_HIV11


title: Med45RO_HIV08


title: Med45RO_HIV07


title: Med45RO_HIV06


title: BY4743 lacking one chromosome XIV - replicate 1 [M14_1]


title: Med45RO_HIV09


title: BY4743 lacking one chromosome XIV - replicate 2 [M14_2]


title: Klebsormidium nitens, 1% Phosphate starvation, 5d, Rep 3

value: 1% Phosphate_5d


title: Klebsormidium nitens, 1% Phosphate starvation, 5d, Rep 2


title: BY4743 lacking one chromosome XI - replicate 3 [M11_3]


title: Med45RO_HIV04


title: Med45RO_HIV01


title: BY4743 lacking one chromosome XI - replicate 2 [M11_2]


title: Med45RO_HIV02


title: Klebsormidium nitens, 1% Nitrate starvation, 5d, Rep 3

value: 1% Nitrate_5d


title: COH-52-BCR [50046]

city: Duarte

first: Shiuan

last: Chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

description:
peripheral whole blood
scRNA-seq

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using CellRanger's default settings
Gene expression level of GENCODE coding genes were quantified using CellRanger's default settings
Assembly: GRCh38
Supplementary files format and content: text files containing the raw gene expression count

source_name: whole blood

extract_protocol:
Leukocyte cells were isolated from whole blood sample by using red cell  lysis buffer (10x Genomics protocoal CG000392)
10xGenomics Chromium single cell 5' Reagent kit s V2 was used for single cell gene expression, TCR and BCR sequencing library preperation

treatment_protocol: Paired whole blood samples of four patients from timepoint of baseline vs. 3 months treatment were collected and processed based single immune cell profiling protocol.

tag: library type

value: BCR

value: whole blood

value: leukocytes

tag: time point

value: 6 months

value: white button mushroom consumption in freeze-dried tablet form


title: COH-52-TCR [51242]

description:
peripheral whole blood
scRNA-seq

value: TCR


title: Med45RO_HIV05

value: Blood

value: HIV seropositive

value: CD4 T cells


title: COH-52-TCR [50045]

description:
peripheral whole blood
scRNA-seq


title: BY4743 lacking one chromosome XI - replicate 1 [M11_1]


title: COH-52-BCR [51243]

description:
peripheral whole blood
scRNA-seq


title: Klebsormidium nitens, 1% Nitrate starvation, 5d, Rep 1

value: Whole plant


title: BY4743 lacking one chromosome X - replicate 3 [M10_3]


title: Klebsormidium nitens, 1% Nitrate starvation, 5d, Rep 2


title: Klebsormidium nitens, untreated control, Rep 3

value: Full Yamagami


title: COH-52-GEX [51241]

description:
peripheral whole blood
scRNA-seq


title: COH-52-GEX [50044]

description:
peripheral whole blood
scRNA-seq


title: BY4743 lacking one chromosome X - replicate 2 [M10_2]

value: monosomic diploid cell


title: Klebsormidium nitens, 1% Phosphate starvation, 5d, Rep 1


title: BY4743 lacking one chromosome X - replicate 1 [M10_1]


title: Klebsormidium nitens, untreated control, Rep 2


title: COH-51-BCR [50049]

description:
peripheral whole blood
scRNA-seq

value: 5 months


title: BY4743 lacking one chromosome VIII - replicate 3 [M8_3]


title: COH-51-TCR [50048]

description:
peripheral whole blood
scRNA-seq


title: Klebsormidium nitens, untreated control, Rep 1


title: COH-51-GEX [51170]

description:
peripheral whole blood
scRNA-seq


title: BY4743 lacking one chromosome VIII - replicate 2 [M8_2]


title: COH-51-GEX [50047]

description:
peripheral whole blood
scRNA-seq


title: Input_PML-RARA (biological replicate 2)

city: Beijing

first: Feng

last: Wang

address: Tian Tan Xi Li 1

country: China

institute: Peking Union Medical College

library_source: genomic

data_processing:
Cutadapt (version 4.1) software were used to remove adapter and low quality reads
Then the reads were aligned to the human genome (hg38) using Bowtie 2 (version 2.2.9) to map the unique reads.
Duplicated reads from PCR amplification were further removed with Picard MarkDuplicates (version 1.119).
The sam files were converted to bam files and sorted with Samtools (version 1.3).
The bam files were converted to BW files by using Deeptools (version 3.5.1). MACS2 (version 2.2.7.1) was used to call peaks.
Assembly: Homo_sapiens.GRCh38.89.chr
Supplementary files format and content: We calculate the fragment sizes for read pairs given a BAM file from paired-end sequencing.
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: peripheral blood

extract_protocol:
hCD34+ cells with RARG fusions or PML-RARA overexpression were fixated with 1% formaldehyde for 10 min and incubated with glycine (50 mM final) 10 min and washed three times with PBS. After cell lysis and chromatin extraction, chromatin was sonicated to 100-500 bp using a Q800R3 Sonicator Chromatin and DNA Shearing System (Qsonica, USA).
The purified DNA was used to prepare ChIP-seq DNA libraries for Illumina sequencing using NEBNext Ultra II DNA Library Prep Kit (E7645).

value: peripheral blood

value: Human CD34+ cells

value: Hematopoietic stem cells


title: COH-46-TCR [50570]

description:
peripheral whole blood
scRNA-seq

value: 4 months


title: COH-46-BCR [49357]

description:
peripheral whole blood
scRNA-seq

value: BCR


title: Input_PML-RARG (biological replicate 2)


title: BY4743 lacking one chromosome VIII - replicate 1 [M8_1]


title: COH-46-TCR [49356]

description:
peripheral whole blood
scRNA-seq

value: whole blood


title: COH-46-GEX [50569]

description:
peripheral whole blood
scRNA-seq

value: leukocytes


title: COH-46-BCR [50571]

description:
peripheral whole blood
scRNA-seq


title: BY4743 lacking one chromosome III - replicate 1 [M3_1]


title: COH-44-BCR [50043]

description:
peripheral whole blood
scRNA-seq

value: 3 months


title: Input_NPM1-RARG (biological replicate 2)


title: COH-44-BCR [49172]

description:
peripheral whole blood
scRNA-seq

value: white button mushroom consumption in freeze-dried tablet form


title: COH-46-GEX [49355]

description:
peripheral whole blood
scRNA-seq


title: COH-51-BCR [51172]

description:
peripheral whole blood
scRNA-seq


title: COH-51-TCR [51171]

description:
peripheral whole blood
scRNA-seq

value: TCR


title: Input_NUP98-RARG  (biological replicate 2)


title: BY4743 lacking one chromosome II - replicate 3 [M2_3]


title: COH-44-TCR [50042]

description:
peripheral whole blood
scRNA-seq


title: E-17.5 HDAC2 ECKO cortical ECs-3 (biol rep 3)

city: Houston

first: Peeyush Kumar

last: Thankamani Pandit

state: TEXAS

address: 6431 Fannin St,

department: Neurosurgery

institute: University of Texas Health Science Center Houston

data_processing:
mRNA-seq reads were quality checked using FastQC [www.bioinformatics.babraham.ac.uk/projects/fastqc/] after removing adaptors with cutadapt. .
Raw reads were mapped with HISAT aligner and default parameters against build mm10 of the mouse reference genome and the latest annotation of mouse genome from the mouse GENCODE repository
We used featureCounts to count reads on each gene for gene expression quantification.
Differentially expressed genes were detected and ranked using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: CD31+ve FACS sorted endothelial cells

extract_protocol:
E17.5 WT and HDAC2 ECKO - The sorted cells were frozen on dry ice as soon as the sorting is done. Libraries were prepared with SMART-Seq V4 PLUS Kit (R400752, Takara Bio, Japan) following the manufacturer’s instructions
RNA with an integrity number of greater than 7 was used for library preparation. Libraries were prepared with KAPA mRNA HyperPrep (KK8581, Roche) and KAPA UDI Adapter Kit 15μM (KK8727, Roche) following the manufacturer’s instructions.
RNA-seq. For E-17.5 WT and HDAC2 ECKO - The libraries were pooled evenly and went for the paired-end 150-cycle sequencing on an Illumina NovaSeq X plus System

treatment_protocol: To conditionally KO HDAC2 E-17.5 endothelial cells we used tamoxifen-inducible Cdh5(PAC)-CreERT2 mice. HDAC2 flox/flox: mother was crossed with HDAC2flox/flox:Cdh5(PAC)-CreERT2 male. Tamoxifen was injected into the mother starting at E-12.5 and on alternate days until E-16.5. E-17.5 brain was harvested and cortex was isolated for Cd31+ve FACS sorting.

value: CD31+ve FACS sorted endothelial cells

value: Cortical endothelial cells

value: HDAC2 ECKO

value: Tamoxifen injection to mother-2mg/10g body weight.


title: E-17.5 HDAC2 ECKO cortical ECs-2 (biol rep 2)


title: BY4743 lacking one chromosome II - replicate 1 [M2_1]


title: COH-44-GEX [50041]

description:
peripheral whole blood
scRNA-seq


title: BY4743 lacking one chromosome II - replicate 2 [M2_2]


title: BY4743 lacking one chromosome III - replicate 2 [M3_2]


title: PML-RARA (biological replicate 2)


title: COH-44-TCR [49171]

description:
peripheral whole blood
scRNA-seq


title: E-17.5 HDAC2 ECKO cortical ECs-1 (biol rep 1)


title: E-17.5 WT cortical ECs-2 (biol rep 2)

value: WT


title: BY4743 lacking one chromosome III - replicate 3 [M3_4]

value: monosomic diploid cell


title: Input_HNRNPC-RARG (biological replicate 2)


title: BY4743 lacking one chromosome I - replicate 3 [M1_3]


title: COH-44-GEX [49170]

description:
peripheral whole blood
scRNA-seq


title: PML-RARG (biological replicate 2)


title: Endometrium_0316_HU2-22J0019_SPA1-81-G2-EPST261_Control_C12

city: Paterna

first: Raul

last: Pérez-Moraga

state: Valencia

address: Rda. de Narcís Monturiol, 11, Bloque C

country: Spain

institute: Carlos Simon Foundation, INCLIVA Health Research Institute

description: 10x Genomics

data_processing:
Raw sequences were demultiplexed, aligned, and counted using the CellRanger software suite (v 6.0.2) for whole cell gene expression calculations, which takes advantage of intronic reads to improve sensitivity and sequencing depth (human reference genome GRCh38-2020-A). Low-quality droplets and barcodes were filtered out in four quality control-based consecutive steps throughout the analysis: (i) low UMI-count barcode removal using an EmptyDrops-based method; (ii) cells marked as doublets by DoubletFinder (2.0.3) and scds (1.6.0) tools – the hybrid approach from the scds R package was used to avoid removing false-positive doublets; (iii) cells with median absolute deviation (MAD) > 3 in two of three basic quality control metrics: number of detected features, number of counts and mitochondrial ratio. These cell-to-count matrices were integrated and corrected using Seurat and scVI functions, as described below. A final filtering step, (iv), was applied alongside different rounds of clustering, where the obtained clustered cells with less than 750 features/cell, more than 25% mitochondrial ratio, and/or showing a pattern of high doublet-scoring plus no gene marker associated expression (during manual cell type annotations), were also removed. A total of 65,381 high quality cells were integrated within the uniform manifold approximation and projection (UMAP). From those 28,154 cells formed the sPE group and 37,227 cells the control group.
1) Raw count matrix: This contains the unfiltered count matrix generated by CellRanger. 2): Various h5ad files that contain the integrated cells of the dataset, along with zoomed views of different main cell populations.
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content: Different integrated h5ad files of the scRNA-seq data with annotated barcodes, UMAPs, and metadata, representing subsets from each main cell populations detected, along the all integrated cell populations
Supplementary files format and content: tar archive with filtered or raw count matrix data (MTX, TSV)

source_name: Endometrium

extract_protocol:
All human endometrial samples of this study were collected in University and Polytechnic La Fe Hospital, Valencia, Spain and pass their Clinical Research Ethics Committee. Samples were collected from women aged 18-40 without any medical condition who had been pregnant 1-8 years earlier. All donors had regular menstrual cycles (25-31 days) without underlying pathological condition and had no received hormonal therapy in the 3 months preceding sample collection. Endometrial biopsies were obtained by pipelle catheter (Genetics Hamont-Achel, Belgium) under sterile conditions and were maintained in a preservation solution HypoThermosol® FRS (Stemcell Techonologies) at 4°C until their processing.
Endometrial biopsies were washed with PBS and mince. Afterwards, samples were enzymatically digested with a solution containing 1 mg/mL Collagenase V (C9263, Sigma-Aldrich), 100 µg/mL DNase Type I. scRNA-seq analysis of the endometrial processed samples were performed using the 10X Chromium technology (10X Genomics, Pleasanton, CA, USA). As mentioned, 17,000 cells were loaded onto a 10X G Chip to obtain Gel Bead-in-emulsions (GEMs) containing an individual cell. GEMs were used to generate barcoded cDNA libraries following the manufacturer's intructions (Single Cell 3' Reagent Kit v3.1, 10X Genomics) and quantified using the TapeStation High Sensitivity D5000 kit (Agilent, Germany). Following, cDNA (1-100 ng) was obtained to construct gene expression libraries that were quantified using the TapeStation High Sensitivity D1000 kit (Agilent, Germany) determining the average fragment size and library concentration. Libraries were normalized, diluted, and sequenced on the Illumina NovaSeq 6000 system (Illumina, USA) according to the manufacturer's instructions.  (03724751103, Roche) and 10% inactivated FBS in RPMI media for 45 min at 37°C and 175 rpm. The enzymatical reaction was inactivated by adding 1 volume of 10% inactivated FBS in RPMI media (Complete medium), the solution filtered through a 100-µm cell strainer, and the strainer washed with 5 mL of complete medium. The flow-through solution contained the stromal fraction, whereas the undigested tissue retained in the cell strainer we the epithelial fraction of the endometrium.   The stromal fraction was centrifuged 5 min at 2000 rpm, and the pellet was wahed with PBS. 1x RBC Lysis Buffer (eBioscience, ThermoFisher Scientific) 5 min at RT was applied to eliminate blood from the sample following manufacturer recommendation. The cell fraction was washed  with PBS centrifuged 5 min at 2000 rpm and the pellet resuspended with 200 µL of 0.04% BSA in PBS (w/v). Finally, sample was filtered using a 40-µm flowmi filter (BAH136800040-50EA, Merk) to obtain a single cell suspension of the stromal fraction.   Regarding the epithelial fraction, the 100-µm cell strainer mentioned above contained the epithelial cells. They were recovered by flushing 15 mL PBS to the inverted cell strainer into a 50-mL falcon tube and centrifuged 5 min at 2000 rpm. For digestion of the epithelial tissue, the pellet was incubated with 5 mL of 100 µg/mL DNase Type I (03724751103, Roche) in 0.25% Trypsin-EDTA solution (25200072, Life Technologies) 10 min at 37°C and 175rpm shacking. After inactivation with complete media, the suspension was filtered through a 100-µm cell strainer, the filter was washed with 5 mL PBS and the solution centrifuged 5 min at 2000 rpm. If needed, the pellet was treated with RBC lysis solution as mentioned before, washed again with PBS, resuspended with 200 µL of 0.04% BSA in PBS (w/v) and filtered using 40-µm flowmi filter.   An aliquot of stromal and epithelial cell suspensions was stained with Tripan Blue dye and counted for alive cell concentration in an automatic cell counter (EVE™, NanoEnTek). Same number of both stromal and epithelial cells will be mixed and a total of 17,000 cells were loaded  a 10X Chromium as explained in the following section.

tag: biopsy origin

value: Endometrium

tag: seurat id

tag: experimental group

value: Control

tag: patient

tag: protocol

value: sc


title: NUP98-RARG (biological replicate 2)

value: peripheral blood

value: Human CD34+ cells

value: Hematopoietic stem cells


title: BY4743 lacking one chromosome I - replicate 2 [M1_2]


title: NPM1-RARG (biological replicate 2)


title: Endometrium_0316_HU2-22J0020_SPA1-82-G3-EPST262_sPE_sPE11

description: 10x Genomics

value: sPE


title: PhBPIC5

city: Chapel Hill

first: Claire

middle: M

last: Doerschuk

state: NC

address: 125 Mason Farm Rd.

institute: University of North Carolina

description:
grcm39gcM33_pHrodo_geneCount.txt
grcm39gcM33_pHrodo_geneTPM.txt

data_processing:
Raw data in fastq files were mapped to reference genome/transcriptome using STAR aligner to generate .BAM files.
Gene expression was estimated based on the BAM file with transcript assembler, StringTie v2, and saved as count and TPM values.
Assembly: GRCm39 and Gencode vM33
Supplementary files format and content: Estimated raw count in tab-delimited text.
Supplementary files format and content: Estimated TPM (transcripts per million mapped reads) in tab-delimited text.

source_name: Alveolar Macrophages

extract_protocol:
Total RNA was isolated from BAL cell pellets using the Quick-RNA Microprep kit (Zymo Research).
Standard RNA-seq with PolyA selection, 20M paired end reads per sample, Illumina, 2x150bp.

treatment_protocol: Female ICAM-1 null (Bullard DC. J Immunol. 2007. PMID: 17202346) or wild type (C57Bl/6J) mice between 7-8 weeks of age were utilized for all studies. Staphylococcus aureus pHrodo-labeled bioparticles (Thermo Fisher Cat: P35367) were reconstituted in PBS (2.27mg/mL) and evenly dispersed according to manufacturers recommendations. Animals were anesthetized using inhaled isoflurane, and 100uL of bioparticles were administered via oropharyngeal aspiration for 1 hour. At 1 hour post inoculation, animals were euthanized by isoflurane overdose immediately prior to bronchoalveolar lavage (BAL). BAL was performed with PBS containing 2mM EDTA. Cell pellets were flash frozen and stored at -80°C prior to RNA isolation.

value: Alveolar Macrophages

value: Primary

value: Alveolar macrophages

value: ICAM-1 null

value: 1 hour S. aureus-pHrodo


title: HNRNPC-RARG (biological replicate 2)


title: PhBPIC4


title: Input_CPSF6-RARG (biological replicate 2)


title: BY4743 lacking one chromosome I - replicate 1 [M1_1]


title: Klebsormidium nitens, 24h Nitrate resupply to starved plants, Rep 2

value: Whole plant


title: E-17.5 WT cortical ECs-3 (biol rep 3)

value: CD31+ve FACS sorted endothelial cells

value: Cortical endothelial cells


title: CPSF6-RARG (biological replicate 2)


title: BY4743 - replicate 2 [BY_2]

value: WT diploid cell


title: Endometrium_0307_HU2-22Y0011_SPA1-77-G2-EPST240_Control_C10

description: 10x Genomics


title: NUP98-RARG_2

data_processing:
Cutadapt (version 4.1) software were used to remove adapter and low quality reads
Then the reads were aligned to the human genome (hg38) using Bowtie 2 (version 2.2.9) to map the unique reads.
Duplicated reads from PCR amplification were further removed with Picard MarkDuplicates (version 1.119).
The sam files were converted to bam files and sorted with Samtools (version 1.3).
The bam files were converted to BW files by using Deeptools (version 3.5.1). MACS2 (version 2.2.7.1) was used to call peaks.
Assembly: Homo_sapiens.GRCh38.89.chr
Supplementary files format and content: We calculate the fragment sizes for read pairs given a BAM file from paired-end sequencing
Supplementary files format and content: bigWig

extract_protocol:
10,0000 hCD34+ cells with or without CPSF6::RARG or NUP98::RARG overexpression were harvested, centrifuged for 5 min at 2300 rpm at 4 °C, and the cell nuclei were extracted by  lysisi buffer.
The DNA fragmentation was performed by using Frafment Mix buffer, and DNA fragments were extracted by DNA Extract Beads following the manufacturer’s protocol. To amplify the libraries, 20 µL fragmented DNA was mixed with 30 µL 2× CAM buffer, 5  µL universal N5, and 5 µL uniquely barcoded N7 primer, using a different barcode for each sample. The sample was placed in a thermocycler with a heated lid using the following cycling conditions: 72 °C for 3 min, 95 °C for 30 min, 15 cycles of 98 °C for 10 s and 60 °C for 5 s, final extension at 72 °C for 1 min, and holding at 4 °C. Post-PCR clean-up was performed by using  DNA Clean Beads.


title: BY4743 - replicate 1 [BY_1]


title: E-17.5 WT cortical ECs-1 (biol rep 1)

value: WT

value: Tamoxifen injection to mother-2mg/10g body weight.


title: PhBPIC3


title: Endometrium_0307_HU2-22Y0004_SPA1-75-G2-EPST232_Control_C09

description: 10x Genomics

value: Endometrium

value: Control


title: IBD_308858, colon

first: Terrence

last: Furey

address: 120 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description: IBD tissue

data_processing:
STAR v2.7.9a using --WaspOutputMode
Read counts quantified using QTLtools v1.3.1
Read counts were normalized using edgeR TMM and rank inverse normal transformed using R v4.1.3
Assembly: hg38, GENCODE v39
Supplementary files format and content: tab-delimited text file includes normalized count data for each sample
Supplementary files format and content: tab-delimited text file includes eQTL covariates for each sample

source_name: colon

extract_protocol:
Tissue was digested with TRIzol and RNA was extracted using chloroform. RNA was isolated using Norgen Biotek Total RNA Isolation Plus Kit (cat#48400).
Libraries were constructed using the Kapa Total RNA Stranded with Ribo Erase.

value: colon

tag: disease

value: IBD

tag: gender

value: Male

tag: batch


title: NUP98-RARG_1

value: peripheral blood

tag: cell line

value: Human CD34+ cells

value: Hematopoietic stem cells


title: PhBPIC1

value: Alveolar Macrophages

value: Primary

tag: cell type

value: Alveolar macrophages


title: PhBPIC2

tag: genotype

value: ICAM-1 null

value: 1 hour S. aureus-pHrodo


title: Endometrium_0281_HU2-22M0037_SPA1-73-G2-EPST230_Control_C08

description: 10x Genomics

value: sc


title: IBD_627183, colon

description: IBD tissue

value: Female


title: CPSF6-RARG_1


title: BY4743 - replicate 3 [BY_3]

value: WT diploid cell


title: Endometrium_0316_HU2-22J0014_SPA1-79-G2-EPST254_Control_C11

description: 10x Genomics


title: Endometrium_0271_HU2-22M0014_SPA1-70-G2-EPST207_Control_C07

description: 10x Genomics


title: PhBPW5

tag: treatment


title: IBD_417916, colon

description: IBD tissue

tag: tissue


title: PhBPW4


title: Endometrium_0269_HU2-22M0012_SPA1-68-G3-EPST205_sPE_sPE09

description: 10x Genomics

value: sPE


title: CON_2


title: PhBPW3


title: IBD_440319, colon

description: IBD tissue


title: CON_1


title: Endometrium_0269_HU2-22M0011_SPA1-67-G3-EPST204_sPE_sPE08

description: 10x Genomics

value: Endometrium


title: IBD_654735, colon

description: IBD tissue


title: Endometrium_0269_HU2-22M0003_SPA1-65-G2-EPST196_Control_C06

description: 10x Genomics

value: Control


title: PhBPW2


title: pLKO-shPRCAT71-2#

city: Chicago

first: Yongyong

last: Yang

state: IL

address: 303 E Superior ST

department: Department of Urology

institute: Northwestern University

data_processing:
The strand-specific paired-end reads were inspected for sequencing and data quality. Adaptor-trimmed reads were aligned to the human reference genome (GRCh38) and assigned to the reference genes using HISAT2 v2.1.0. Read counts for each gene were calculated by featureCounts v1.6.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each group.

source_name: LNCaP

extract_protocol:
Total RNAs were extracted using RNeasy Plus Kit (74134, Qiagen, Germantown, MD).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library prep kit following manufacturer's protocols.

value: LNCaP

value: PRCAT71 knockdown


title: CPSF6-RARG_2


title: PhBPW1


title: Input_PML-RARG


title: IBD_995536, colon

description: IBD tissue

value: colon

value: IBD

value: Male


title: Endometrium_0271_HU2-22M0013_SPA1-69-G3-EPST206_sPE_sPE10

description: 10x Genomics


title: pLKO-shPRCAT71-1#


title: Endometrium_0269_HU2-22M0002_SPA1-64-G2-EPST195_Control_C05

description: 10x Genomics


title: Endometrium_0269_HU2-22M0001_SPA1-63-G2-EPST194_Control_C04

description: 10x Genomics


title: PhBNIC5

value: Naïve


title: Endometrium_0239_HU2-21D0057_SPA1-62-G3-EPST193_sPE_sPE07

description: 10x Genomics


title: Input_NUP98-RARG

value: peripheral blood

value: Human CD34+ cells

value: Hematopoietic stem cells


title: Input_HNRNPC-RARG


title: pLKO-shNC

value: WT


title: shKHSRP-2#

value: KHSRP knockdown


title: Endometrium_0237_HU2-21D0038_SPA1-61-G3-EPST192_sPE_sPE06

description: 10x Genomics

value: sc


title: PhBNIC4

value: Alveolar Macrophages

value: Primary

value: Alveolar macrophages

value: ICAM-1 null


title: PhBNIC2


title: Input_CPSF6-RARG


title: Input_PML-RARA


title: Input_CON


title: Endometrium_0237_HU2-21D0037_SPA1-60-G2-EPST191_Control_C03

description: 10x Genomics

value: Endometrium

value: Control


title: shKHSRP-1#


title: PhBNIC1


title: Endometrium_0237_HU2-21D0036_SPA1-59-G3-EPST190_sPE_sPE05

description: 10x Genomics

value: sPE


title: shNC


title: Input_NPM1-RARG


title: BY4743 lacking one chromosome III - replicate 1

value: monosomic diploid cell

value: BY4743, monosomy chrIII


title: PML-RARG


title: PhBNW4


title: Endometrium_0192_ASH-21G0010_SPA1-40-G3-EPST108_sPE_sPE04

description: 10x Genomics


title: IBD_407896, colon

description: IBD tissue

value: colon

value: IBD

value: Male


title: PhBNW3

value: Naïve


title: PhBNIC3


title: IBD_734301, colon

description: IBD tissue

value: Female


title: IBD_165328, colon

description: IBD tissue


title: PhBNW2


title: HNRNPC-RARG

value: peripheral blood

value: Human CD34+ cells

value: Hematopoietic stem cells


title: NPM1-RARG


title: IBD_564226, colon

description: IBD tissue


title: Endometrium_0184_HUT-21L0020_SPA1-36-G3-EPST104_sPE_sPE02

description: 10x Genomics

value: sc


title: Endometrium_0156_HUT-21A0011_SPA1-28-G3-EPST80_sPE_sPE01

description: 10x Genomics


title: S-C4

city: Maastricht

first: Bart

last: Spronck

address: Universiteitssingel 40

department: Dept. of Biomedical Engineering

country: Netherlands

institute: Maastricht University

data_processing:
Differentially expressed genes (DEGs) were obtained from raw gene counts using DESeq2 v1.26.0 in R v3.6.2.
Assembly: GRCm38/mm10
Supplementary files format and content: Comma-separated values file contains raw gene counts for each sample.

source_name: descending thoracic aorta

extract_protocol:
Crushed whole descending thoracic aorta (DTA) tissue was immersed in RLT lysis buffer (Qiagen N.V., Venlo, The Netherlands) and vigorously vortexed. Total RNA was isolated using a RNeasy Mini Kit and DNase Digestion Set (Qiagen) according to the manufacturer’s protocol.
RNA-Seq reads were aligned to a reference genome (GRCm38/mm10) with Gencode annotation using HISAT2 for alignment, and StringTie for transcript abundance estimation.

value: descending thoracic aorta

value: control


title: Endometrium_0156_HUT-21A0010_SPA1-25-G2-EPST77_Control_C02

description: 10x Genomics


title: IBD_165321, colon

description: IBD tissue


title: PhBNW1

value: Alveolar Macrophages

value: Primary

value: Alveolar macrophages


title: CPSF6-RARG


title: IBD_332149, colon

description: IBD tissue


title: Endometrium_0156_HUT-21A0006_SPA1-19-G2-EPST63_Control_C01

description: 10x Genomics

value: Endometrium

value: Control


title: S-C3


title: PML-RARA


title: IBD_213942, colon

description: IBD tissue


title: CAST-seq on HSCs treated with Cas12a targeting NCF1B and NCF1C, technical replicate 3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq pipelines with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: Matrix table of translocation sites detected with the CAST pipeline. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.
Library strategy: CAST-seq

source_name: human hematopoietic stem cells (HSCs).

growth_protocol: Human healthy CD34+ cells from mobilized peripheral blood were purchased (Lonza Group AG, Basel, Switzerland). CD34+ cells were cultured in X-VIVO 20 (Lonza), supplemented with 1% (v/v) human albumin (CSL Behring AG, Bern, Switzerland), 300 ng/mL stem cell factor (SCF), 300 ng/mL FMS-like tyrosine kinase-3 ligand (Flt3-L) and 100 ng/mL thrombopoietin (TPO) (CellGenix GmbH, Freiburg, Germany). CD34+ cells were expanded for 7 days before genomic DNA isolation by column purification using QIAamp DNA Blood Mini Kit.

extract_protocol:
Genomic DNA was extracted by column purification using QIAamp DNA Blood Mini Kit according to manufacturer's recommendation. Genomic DNA was eluted from the column in DNAse/RNAse free water.
CAST-Seq was performed as previously described (Klermund et al. 2024. Mol Ther. doi: 10.1016/j.ymthe.2024.03.006.)
A third PCR introduced the barcoded Illumina adapter for sequencing (NEB, NEBNext Multiplex Oligos for Illumina, Cat.# E7335, E7500, E7710, E7730). Libraries were sequenced by Azenta Life Sciences using the Illumina NovaSeq platform with a 2 x 150 bp configuration.

treatment_protocol: RNPs were formed by complexing Cas protein (Cas9 or Cas12a) with gRNAs at 1:1.2 molar ratio and delivered to the cells with the Neon™ Transfection System (Thermo Fisher Scientific). 100,000 cells were electroporated in Buffer T (1400 V, 10 ms, 3 pulses) with 7.2 µM of RNP complexes and 2.5 µM single-stranded oligodeoxynucleotide.

value: human hematopoietic stem cells (HSCs).

value: CD34+ cells


title: NUP98-RARG_H3K27ac_1


title: S-C1


title: CAST-seq on HSCs treated with Cas12a targeting NCF1B and NCF1C, technical replicate 2


title: Endometrium_0192_ASH-21G0009_SPA1-39-G3-EPST107_sPE_sPE03

description: 10x Genomics

value: sPE


title: CPSF6-RARG_H3K27ac_1


title: IBD_838352, colon

description: IBD tissue

value: colon

value: IBD


title: CON_H3K27ac


title: S-A5

value: AngII


title: CAST-seq on HSCs treated with Cas12a targeting NCF1B and NCF1C, technical replicate 1


title: IBD_212365, colon

description: IBD tissue

value: Male


title: IBD_605026, colon

description: IBD tissue

value: H


title: S-A4


title: CAST-seq on HSCs treated with Cas9 targeting NCF1B and NCF1C, technical replicate 3


title: NUP98-RARG

value: peripheral blood

value: Human CD34+ cells

value: Hematopoietic stem cells


title: CPSF6-RARG_H3K4me3


title: S-A2

value: descending thoracic aorta


title: IBD_130170, colon

description: IBD tissue


title: S-A1


title: IBD_827477, colon

description: IBD tissue


title: CON_H3K4me3


title: CAST-seq on HSCs treated with Cas9 targeting NCF1B and NCF1C, technical replicate 2


title: CAST-seq on HSCs treated with Cas9 targeting NCF1B and NCF1C, technical replicate 1


title: S-C2

value: control


title: NUP98-RARG-RARG_H3K4me1


title: C-C5


title: Untreated sample used as control

description:
use as un-treated control
NCF1-Cas9_FINAL.xlsx
NCF1-Cpf1_FINAL.xlsx

value: No treatment


title: CPSF6-RARG_H3K4me1


title: NUP98-RARG_H3K4me3


title: C-C3


title: Hep3B_PELPsh1-3

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using HiSAT2 default settings. The aligned BAM files sorted (SAMTools) and then processed using FeatureCounts to obtain the counts per gene
Gene count measurements were obtained using FeatureCounts
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format, which contains geneid, chromosome location (chr, start, end, strand), gene length, and read counts.

source_name: Liver

growth_protocol: Hep3B cells were cultured in RPMI medium

extract_protocol:
Total cellular RNA was isolated using TRIzol reagent (Invitrogen).
Total RNA samples were used for sequencing library preparation with KAPA RNA HyperPrep kit with RiboErase (HMR) following KAPA RNA library preparation protocol. Each library was bar-coded and then pooled for sequencing run paired-end sequencing protocol.

treatment_protocol: PELP1 knockdown (KD) HEP3B cells were generated using human specific PELP1-shRNA1 (TRCN0000159883; Sigma) and PELP1-shRNA2 (TRCN0000159673; Sigma) lentiviral particles. Control cells were created using non-targeted shRNA (SHC016-1EA; Sigma) lentiviral particles. PELP1 knockdown  HEP3B cells were selected using puromycin (1mg/ml) selection to produce stable clones, and pooled clones were selected.

value: Liver

value: Hep3B cell line

value: Hepatocellular Carcinoma

value: PELP1 KD


title: IBD_469904, colon

description: IBD tissue


title: C-C2


title: CON_H3K4me1


title: IBD_651640, colon

description: IBD tissue

value: Female


title: Hep3B_PELPsh1-2


title: IBD_117528, colon

description: IBD tissue


title: C-C1


title: IBD_204164, colon

description: IBD tissue


title: Hep3B_C3

value: shRNA control


title: Hep3B_PELPsh1-1


title: C-A3


title: C-A5


title: IBD_322211, colon

description: IBD tissue

value: colon


title: Hep3B_C2


title: IBD_203023, colon

description: IBD tissue

value: IBD


title: Mouse, 24h, rep3

city: Wuhan

first: Hao

last: Cui

address: Wuhan University, 299 Bayi Road, Wuchang District, Wuhan, Hubei, P.R. China

institute: Wuhan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to ASM1011175v1 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction 0.8 similarty fractior 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: ASM1011175v1
Supplementary files format and content: list file includes raw counts for each Sample
Supplementary files format and content: list file includes FPKM values for each Sample

organism: Nakaseomyces glabratus

source_name: kidney

growth_protocol: Candida glabrata were grown in the kidney of mice

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). A total amount of 1 μg RNA per sample was used as input material for library construction.
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: kidney

value: WT

value: post infection 24h


title: Mouse, 48h, rep2

value: post infection 48h


title: Mouse, 48h, rep1


title: Mouse, 48h, rep3


title: C-A2

value: AngII


title: Hep3B_C1


title: IBD_255857, colon

description: IBD tissue

value: H


title: C-A1

value: descending thoracic aorta


title: Mouse, 24h, rep2


title: NC3

city: Zhenjiang

first: Zhongqun

address: Jiefang road 438

institute: Affiliated Hospital of Jiangsu University

data_processing:
The sequencing platform is novaseq 6000. After the data is off the machine, RTA (real time analysis) is used to convert it into the original BCL file, and the version is v3.4.4; It is split by bcl2fastq (btq) software and converted into FQ, version v2.19. Fastp software is used for quality control, version 0.19.7, involving the parameter fastp-G-Q5-U50-N 15-L150.
Assembly: hg38
Supplementary files format and content: Fastq

source_name: Anterior tibial artery

extract_protocol:
1. Prepare enzyme digestion solution according to 2mg/ml collagenase I, 1mg/ml collagenase II, 0.04 mg/ml DNase I, 60 U/ml hyaluronidase and HBSSand filter it;2. Pour the sample tissue into the petri dish, place it on the ice plate, record the number, take pictures for retention, add the cleaning solution, and clean it twice with the cleaning solution;3. After discarding the cleaning solution, add a small amount of digestive solution to the petri dish and cut the sample tissue with scissors;4. After the tissue is cut, rinse the scissors with 1ml digestive liquid, collect and transfer to a suitable centrifuge tube, and add appropriate amount of enzyme liquid.5. 20μl digestive suspension was taken for Trypan blue staining microscopy.6. Seal the centrifuge tube with a sealing film and place the sample in a shaking table at 37ºC for 1h digestion;7. Blow the digestive fluid after digestion for 30 minutes, observe the digestive effect, and find that the tissue is basically digested8. After digestion, 20μl digestive suspension was taken for Trypan blue staining microscopy.9. Transfer the digestive fluid through the 100μm and 40μm filter to a 50ml centrifuge tube and centrifuge 300×g for 5min;10. Discard the upper liquid, add 1ml erythrocyte lysate to gently blow the cells, leave for 3min, transfer to 15ml tube;11. Add cleaning solution to 10ml to stop cracking red, centrifuge 300×g for 5min;12. The supernatant was discarded, the cleaning solution was added and re-mixed, and 20μl was taken respectively for AO/PI counting and Trisan blue microscopy. The results were reported.
Sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions.

value: Anterior tibial artery

tag: group

value: non-calcified


title: C2C12, dC1, clone D5

city: San Francisco

first: Ross

last: Okimoto

address: 513 Parnassus Ave

institute: University of California, San Francisco

description: Column name in processed data: dC1_D5

data_processing:
FASTQ files were aligned to GRCm39 using STAR (version 2.7.11b).
Gene counts were extracted during alignment using STAR parameter --quantMode GeneCounts
Differental expression analysis was performed in R (version 4.2.2) with edgeR (version 3.40.2).
Log2(cpm) data were obtained from TMM-normalized data using edgeR with the cpm function (log = T) which with this version of edgeR adds an average prior count of 2.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file, STAR gene counts for all samples, data taken from column 4 of STAR output due to the strandedness of the library prep kit used. File name = counts_C2C12_dC1.txt.
Supplementary files format and content: Tab-delimited text file, log2(counts per million) measurements for all samples after edgeR processing. File name = C2C12_log2_of_cpm.txt.

growth_protocol: Transduced and clonally selected C2C12 cells were maintained in DMEM (high glucose, +L-Glutamine, +Sodium Pyruvate) with 10% fetal bovine serum (FBS) and 1% Pen-Strep (100 U/mL Penicillin, 100 ug/mL Streptomycin) at 37C in a 5% CO2 humidified incubator.

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen) including an on-column Dnase digest (Qiagen). Samples were also cleaned up with Monarch RNA Cleanup Kit (NEB) and checked for integrity on a TapeStation (Agilent).
Libraries were constructed by Novogene by polyA-enriching RNA and then using the NEBNext Ultra II Directional Library Prep Kit for Illumina (NEB).

treatment_protocol:
C2C12 cells were transduced with ecotropic retrovirus encoding a gene-IRES-EGFP construct where the gene was one of the following: empty (empty vector), full-length CIC::DUX4, or C1-deleted CIC::DUX4.
Clonal populations were derived by sorting EGFP+ cells via FACS into single wells of 96 well plates, expanding, and validating transgene expression by Western blot.
Cell lines were seeded at 75,000 cells in a single well of a 6-well plate, allowed to grow for approximately 48 hours, and harvested for RNA.

value: myoblast

tag: genetic modification

value: C1-deleted CIC::DUX4 transduced


title: IBD_980747, colon

description: IBD tissue


title: C2C12, dC1, clone C5

description: Column name in processed data: dC1_C5


title: IBD_780248, colon

description: IBD tissue


title: Mouse, 0h, rep3

value: post infection 0h


title: IBD_304272, colon

description: IBD tissue

value: Male


title: Mouse, 0h, rep2


title: NC2


title: C2C12, CIC::DUX4, clone D6

description: Column name in processed data: CD4_D6

value: full length CIC::DUX4 transduced


title: C2C12, CIC::DUX4, clone C9

description: Column name in processed data: CD4_C9


title: CA3

value: calcified


title: Mouse, 0h, rep1


title: IBD_418271, colon

description: IBD tissue

value: colon


title: IBD_592152, colon

description: IBD tissue

value: IBD

value: Female


title: CA2


title: C2C12, EV, clone G4

description: Column name in processed data: EV_G4

value: EV transduced


title: IBD_750138, colon

description: IBD tissue


title: C2C12, EV, clone C7

description: Column name in processed data: EV_C7


title: IBD_676592, colon

description: IBD tissue


title: KO_2

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

library_source: other

data_processing:
Data analysis performed according to scripts used in https://doi.org/10.1038/s41587-023-01743-6
Assembly: A. fumigatus (A1163, assembly GCA_000150145.1)
Supplementary files format and content: The processed data files contain the adjusted total counts of tRNAs for abundance and the sum of errors identified in Nano-tRNAseq in tsv file format.

molecule: other

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: To perform Nano-tRNAseq, CEA17 ∆akuBKU80 and ∆mod5 fungal samples (5x107 spores) were cultured for 24 h in Aspergillus minimal media.

extract_protocol:
tRNA isolation from A. fumigatus strains CEA17 ∆akuBKU80 and ∆mod5 1x108 spores were cultured for 24 h in AMM at 37°C, 200 rpm. The mycelia were harvested using Miracloth (EMD Millipore Corp., USA) and crushed with mortar and pestle under constant treatment with liquid nitrogen. Approximately 0.8 mL of mycelium was transferred into a 2-mL Safe-Lock tube, mixed with the same volume TRIzol, and snap frozen in liquid nitrogen. The samples were left on ice to thaw, mixed again, and incubated for 5 min first on ice and afterwards at room temperature. After addition of 0.2 volumes of chloroform per vol. of TRIzol, the samples were vortexed and centrifuged at full speed for 5 min, 4°C. The upper aqueous phase containing RNA (ca. 600 µL) was transferred into a new tube and centrifuged again (15000 rpm, 30 min, 4°C) resulting in a supernatant that was collected in a new tube (ca. 500 µL). For subsequent total tRNA precipitation, 3/4 vol. 8 M LiCl was added to the samples and incubated for 2 h (or longer) at -20°C. Samples were centrifuged (14000 rpm, 15 min, 4°C) to separate larger RNA molecules and the supernatant containing small RNAs was transferred into a new tube. The precipitation was repeated once to improve purification. The supernatant was mixed with 1/10 vol. ammonium acetate, pH 7.0 and 2.5 vols. of ice-cold 100% EtOH p.a. to be incubated overnight at -20°C. Precipitated tRNA was collected by centrifugation (14000 rpm, 30 min, 4°C). The pellet was washed twice briefly with 75% (v/v) EtOH and vacuum-dried (8 min, 60°C, 1 bar) in a vacuum concentrator centrifuge. The dried RNA was resuspended in 50 µL DEPC-H2O. The tRNA samples were quantified with QubitTM RNA BR Assay kit (Thermo Fisher Scientific) on the Qubit Flex Fluorometer (Thermo Fisher Scientific) and stored at -80°C.
At least 20 µg per extracted RNA samples were subsequently submitted to IMMAGINA Biotechnology S.r.l. (Italy) for quality control, library preparation, and nanopore sequencing. The company performed sequencing and bioinformatic assessment according to  https://doi.org/10.1038/s41587-023-01743-6 with slight modifications to facilitate sample multiplexing.
Direct RNA Sequencing using a MinION device.

treatment_protocol: Samples were left untreated

value: mycelium

tag: strain

tag: time

value: untreated


title: KO_3


title: CA1


title: NC 3

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings.Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings.
Assembly: hg38
Supplementary files format and content: Fastq
Library strategy: Spatial Transcriptomics

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries w ere prepared w ith 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction


title: Mouse, 24h, rep1

value: kidney

value: WT

value: post infection 24h


title: IBD_388822, colon

description: IBD tissue

value: H


title: KO_1


title: WT_3


title: IBD_189841, colon

description: IBD tissue


title: NC 2

value: Anterior tibial artery

value: non-calcified


title: NC1


title: WT_2


title: 50 μM Glutamine

city: Philadelphia

first: Graham

last: Lobel

address: 421 Curie Blvd

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made by using the Cell Ranger software v3.1.0
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: DCs

extract_protocol:
cDCs differentiated in vitro using FLT3L were scraped out of 6 well plates and resuspended in scRNA-seq analysis buffer.
Library was constructed using the manufacturer's instructions (Single Cell 3' v3)

value: DCs

value: 50 μM Glutamine


title: IBD_856637, colon

description: IBD tissue

value: Male


title: WT_1


title: NC 1


title: cKOHet_liver_iNKT1-H4

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

data_processing:
Raw sequence reads were trimmed using Trimmomatic v0.33
aligned to the mm10 genome assembly from iGenomes using STAR
Aligned reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78
DESeq2 was used to normalize the gene counts and to calculate differential expression statistics for each gene for each pairwise comparison of sample groups within an nf-Core Differential Abundance workflow
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

extract_protocol:
RNA isolation was performed using  RNeasy mini kits (QIAGEN) following the manufacturer’s protocol.
RNA-seq libraries were constructed using Nugen’s Ovation Ultralow Library systems following the manufacturer's protocol

value: liver

value: primary cells

value: CD1d-Tetramer+ YFP+ iNKT1 cells

value: Tbx21Cre Ets1F/F Tbx21F/+  Rosa26-YFP+


title: IBD_159242, colon

description: IBD tissue

value: colon

value: IBD


title: IBD_682714, colon

description: IBD tissue

value: Female


title: cKOHet_liver_iNKT1-H2


title: IBD_549590, colon

description: IBD tissue


title: 1 uM DON

description: 10x Genomics

value: 1 μM DON


title: CA 1

value: calcified


title: Control_liver_iNKT-W4

value: Tbx21Cre Rosa26-YFP+


title: CA 2


title: Dentate gyrus, Subject 4

city: Montreal

first: Naguib

last: Mechawar

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics pipeline spaceranger to generate FASTQ files
Sequences were aligned to the GRCh38-2020-A genome to gene expression count using spaceranger's default settings
Gene expression level of Refseq coding genes were quantified using spaceranger's default settings
Space Ranger outputs of each sample were read into R (v. 4.1.0) in a customized structure using the Seurat R package (V4)
Spots with very high molecular counts were filtered out for two of the samples
The samples were then combined into a single Seurat object.
The data was normalized using the log-normalization procedure with NormalizeData function with Seurat.
Variable genes were identified using the FindVariableFeatures function (with the selection method set to vst and the number of features set to 2000) with Seurat.
The normalized dataset was next scaled using the ScaleData function with Seurat.
The top 50 principal components (PCs) were computed with the RunPCA function with Seurat.
The merged Seurat object was converted into a SingleCellExperiment (v.1.16.0) object for batch correction with the R package Harmony (v.0.1.0) and for spot clustering.
The first 15 PCs were used for downstream clustering using the BayesSpace (t-distributed error model) clustering algorithm (v. 1.4.1) with the SpatialCluster (nrep = 50 000) BayesSpace function.
Assembly: GRCh38
Supplementary files format and content: CombinedSeuratObject_HPC.rds: combined seurat object with all 4 subjects and containing BayesSpace (t-distributed error model) clustering data and tSNE (after batch correction with the R package Harmony) cell embeddings
Supplementary files format and content: A1_raw_feature_bc_matrix.h5: unfiltered feature-barcode matrix for library A1
Supplementary files format and content: B1_raw_feature_bc_matrix.h5: unfiltered feature-barcode matrix for library B1
Supplementary files format and content: C1_raw_feature_bc_matrix.h5: unfiltered feature-barcode matrix for library C1
Supplementary files format and content: D1_raw_feature_bc_matrix.h5: unfiltered feature-barcode matrix for library D1
Supplementary files format and content: spatial_A1.tar.gz: contains the spatial outputs of space ranger for library A1 (tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json and tissue_positions.csv)
Supplementary files format and content: spatial_B1.tar.gz: contains the spatial outputs of space ranger for library B1 (tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json and tissue_positions.csv)
Supplementary files format and content: spatial_C1.tar.gz: contains the spatial outputs of space ranger for library C1 (tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json and tissue_positions.csv)
Supplementary files format and content: spatial_D1.tar.gz: contains the spatial outputs of space ranger for library D1 (tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json and tissue_positions.csv)
Library strategy: Spatial Transcriptomics

source_name: Dentate gyrus

extract_protocol:
Fresh frozen tissue were OCT embedded and 10µm sections were cut with the cryostat
Spatial transcriptome sequencing libraries were prepared with the 10x Genomics Spatial Gene Expression slides and Reagent Kit according to the manufacturer's instructions

value: Dentate gyrus

tag: Sex

tag: age

value: 21 years old


title: IBD_602882, colon

description: IBD tissue


title: cKOHet_liver_iNKT-H1


title: Dentate gyrus, Subject 3

value: 26 years old


title: Control_liver_iNKT1-W2


title: Dentate gyrus, Subject 2

value: 43 years old


title: Control

description: 10x Genomics

value: DCs

value: WT

value: 2 mM Glutamine


title: IBD_434298, colon

description: IBD tissue

value: Male


title: Control_liver_iNKT1-W1

value: liver

value: primary cells


title: Dentate gyrus, Subject 1

value: 42 years old


title: CA 3

value: Anterior tibial artery


title: IBD_996969, colon

description: IBD tissue

value: colon

value: IBD


title: MDA-MB-231 siRagC2 BioRep6

city: Paris

first: Philippe

last: Chavrier

address: 12 rue Lhomond

country: France

institute: Institut curie

data_processing:
bioinfo-pf-curie/RNA-seq: v4.0.0
Sequence reds were trimmed from adapter sequences, primers and poly-A tails using Cutadapt Tool (v0.6.2, parameter - Min quality: 20)
Trimmed sequences were mapped to GRCh37/hg19 using STAR alignment tool (v2.7.6a) included in the analysis pipeline
Read count extraction and normalization were performed using Institut Curie NGS/Bioinformatics core facilities RNA-seq analysis pipeline (v4.0.1)
Assembly: GRCh37/hg19
Supplementary files format and content: comma-delimited text file (.csv) includes raw counts for each sample

growth_protocol: MDA-MB-231 cells were maintained in L-15 medium supplemented with 15% FBS and 2mM L-glutamine in a humidified 37°C 1% CO2 atmosphere.

extract_protocol:
RNA was harvested using RNEasy Kit (Sigma).
500 ng of total RNA per sample was ued for construction of library

treatment_protocol: Gene knock-down was induced with lipofection of siRNA (Lullaby, OZ Biosciences) in OPTI-MEM for 72 hrs.

value: breast cancer cells

value: RagC knock-down

value: siRNA


title: 273-untreated

type: RNA

city: Macau

first: Ning-Yi

last: Shao

address: University of Macau

department: Faculty of Health Sciences

institute: University of Macau

hyb_protocol: 1 μg of each labeled cRNA was fragmented and heated followed by addition of hybridization buffer to dilute the labeled cRNA.  Hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner.

scan_protocol: The profiling of lncRNAs and the entire set of protein-coding mRNAs were performed using Arraystar Human LncRNA Arrays V5.0 (Arraystar Inc.). The acquired array images scanned by the Alilent Scanner G2505C.

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

source_name: iPSC-ECs

label_protocol: mRNA was purified from the total RNA after removal of rRNA. Each sample was amplified and transcribed into fluorecent cRNA (pmol Cy3/ugcRNA) along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit).

growth_protocol: iPSCs were differentiated into endothelial cells using a monolayer chemically-defined methods.

extract_protocol: RNA was extrated using the a Direct-zol RNA Kit with DNA digestion, and collected total RNA was used for microarray.

treatment_protocol: iPSC-ECs were seeded into 6 well plates and once they reached 60-70% confluency, cells were treated with and without e-cigarette extraction for 24 hours.

value: Vehicle


title: 273-e-cig

value: e-cig extraction


title: C15-e-cig


title: 78-untreated


title: flu_D20_all_cells_rep1

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Read alignment and cell calling using STAR-solo (velocyto output)
Ambient-RNA correction using scvi-tools scAR
h5ad file creation using anndata
h5ad file creation using anndata
Assembly: GRCm39
Supplementary files format and content: .h5ad

source_name: lung

extract_protocol:
Primary mouse lung tissue was dissociated into single-cell suspensions and subjected to FACS.
10X Genomics 3’-biased gene expression library construction (v3.1)

value: lung

tag: time post_treatment

tag: lineage sort

value: influenza


title: IBD_422479, colon

description: IBD tissue

value: Female


title: 78-e-cig


title: MDA-MB-231 siRagC1 BioRep6


title: flu_D20_tdTomato_neg_rep1


title: IBD_299477, colon

description: IBD tissue


title: IBD_309068, colon

description: IBD tissue

value: H


title: flu_D20_tdTomato_pos_rep1


title: IBD_421195, colon

description: IBD tissue


title: MDA-MB-231 siRagC2 BioRep5


title: flu_D10_all_cells_rep1


title: MDA-MB-231 siCtrl BioRep6

value: WT


title: RNA parthenote2

city: Columbus

first: Jinsoo

last: Ahn

address: 2029 Fyffe Rd

institute: Ohio State Univesity

data_processing:
To remove adapters and low-quality reads from the raw RNA-seq data, we utilized Trimmomatic (v0.39), applying parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Using the STAR aligner (v2.7.9a), the cleaned reads were aligned to the reference genome (Sscrofa11.1/susScr11) with default parameters.
Uniquely mapped reads were retrieved with SAMtools and were subsequently deduplicated using Picard MarkDuplicate.
Assembly: susScr11
Supplementary files format and content: Quantification files in plain-text format (.sf)

organism: Sus scrofa

source_name: whole embryo

growth_protocol: After electric stimulation of oocytes followed by 2 h of stabilization period, parthenogenetic embryos were placed into oviducts of each of the two surrogate gilts aged 12 months at onset of estrus to produce developed parthenogenetic embryos.

extract_protocol:
From the whole collected embryos of CN and PA, total RNA was isolated and fragmented.
To select poly-A tails and construct cDNA libraries, 1 µg of total RNA was used with the TruSeq RNA Sample Prep Kit v.2.

treatment_protocol: In a fusion chamber with 250 µm diameter wire electrodes, selected oocytes were placed and fusion was achieved by two DC pulses (1 sec interval) of 1.2 kV/cm for 30 µs using an LF101 Electro Cell Fusion Generator.

value: whole embryo

value: parthenogenesis


title: MDA-MB-231 siRagC1 BioRep5


title: flu_D10_all_cells_rep1_resequenced


title: flu_D10_tdTomato_neg_rep1


title: IBD_906136, colon

description: IBD tissue

data_processing:
STAR v2.7.9a using --WaspOutputMode
Read counts quantified using QTLtools v1.3.1
Read counts were normalized using edgeR TMM and rank inverse normal transformed using R v4.1.3
Assembly: hg38, GENCODE v39
Supplementary files format and content: tab-delimited text file includes normalized count data for each sample
Supplementary files format and content: tab-delimited text file includes eQTL covariates for each sample

extract_protocol:
Tissue was digested with TRIzol and RNA was extracted using chloroform. RNA was isolated using Norgen Biotek Total RNA Isolation Plus Kit (cat#48400).
Libraries were constructed using the Kapa Total RNA Stranded with Ribo Erase.

value: I


title: IBD_647871, colon

description: IBD tissue


title: RNA parthenote3


title: RNA parthenote1


title: MDA-MB-231 siCtrl BioRep5


title: RNA control6

value: untreated


title: C15-untreated


title: C2-untreated


title: C2-e-cig


title: flu_D10_tdTomato_pos_rep1


title: IBD_965724, colon

description: IBD tissue


title: IBD_933581, colon

description: IBD tissue

value: Male


title: RNA control5


title: flu_D00_all_cells_rep1


title: MDA-MB-231 siRagC2 BioRep4


title: flu_D00_tdTomato_neg_rep1


title: RNA control4


title: RNA control3


title: IBD_112415, colon

description: IBD tissue

value: colon


title: IBD_618849, colon

description: IBD tissue

value: IBD


title: RNA control2


title: flu_D00_tdTomato_pos_rep1


title: IBD_949169, colon

description: IBD tissue


title: IBD_727829, colon

description: IBD tissue


title: MDA-MB-231 siRagC2 BioRep3

value: breast cancer cells


title: flu_D30_tdTomato_pos_rep1


title: MDA-MB-231 siRagC1 BioRep3

value: RagC knock-down


title: IBD_955826, colon

description: IBD tissue


title: RNA control1


title: MDA-MB-231 siCtrl BioRep3

value: siRNA


title: basal CK5eYFP, 2m, mouse 2, plate 3

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
Data were analyzed using the Seurat package v.4.0. 6. Cell QC filtering was done using the following thresholds: nCount > 500, nCount < 40000, nFeature > 300 percent.mito < 20, log10GenesPerUMI > 0.8 percent.spike_in < 30.
AddModuleScore from the Seurat package was used for inferring the activity of gene-sets of interest.
Assembly: mm10
Supplementary files format and content: Raw and filtered Seurat RDS objects

source_name: prostate

extract_protocol:
Whole mouse prostates were harvested and digested to single cell solution using 5mg/mL collagenase in advanced DMEM (+/+/+) for 1 hour of shaking at 37 degrees Celsius. This was followed by medium washes and 15-minute incubation with TrypLE at 37 degrees Celsius then the digest solution was passed through a 70uM filter. Cells treated with DAPI for live/dead stain were sorted at the Department of BioMedical Research FACs Core facilities in a solution of PBS with 0.2% fetal bovine serum. Protocols for sorting single eYFP+ cells into wells of 384-well SORT-Seq plates were conducted under the recommendations of Single Cell Discoveries (https://www.scdiscoveries.com/). eYFP positive control prostates were used to adjust A488 gating settings for each sort. Two animals and three 96-well plates were collected as single cells for each group, centrifuged at 4 degrees Celsius, snap-frozen on dry ice, and then stored at -80 degrees Celsius until transport to sequencing facilities
The SORT-seq protocol (a partially robotized method based on the CEL-Seq2 protocol) was used to generate libraries for scRNA-Seq

treatment_protocol: The luminal model eYFP+ selected cells were collected from prostates with a Probasin (PB) -Cre (PB-Cre) recombinase system, referred here as PBeYFP. Basal cells were labeled in vivo using a tamoxifen-inducible cytokeratin 5 (Krt5)- specific Cre recombinase system paired with a Rosa26eYFP reporter gene, referred here as CK5eYFP. To directly test the impact of downregulating PI5P4Kα in basal cell populations, we crossed CK5-eYFP animals with a GEMM that is homozygote for floxed Pip4k2a alleles, referred here as CK5PIP. Cre activation occurs by 8 weeks of age, and eYFP+ cells were collected with FACs two weeks and two months later for PBeYFP and CK5eYFP, and two months later for CK5PIP.

value: prostate

value: 2 months


title: MDA-MB-231 siRagC1 BioRep4


title: flu_D00_tdTomato_pos_rep1_resequenced

value: lung


title: basal CK5eYFP, 2m, mouse 2, plate 2


title: MDA-MB-231 siRagC2 BioRep2


title: mock_D30_tdTomato_pos_rep1


title: IBD_420609, colon

first: Terrence

address: 120 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description: IBD tissue


title: MDA-MB-231 siCtrl BioRep4


title: MDA-MB-231 siRagC1 BioRep2


title: IBD_564849, colon

description: IBD tissue


title: mock_D30_tdTomato_neg_rep1


title: IBD_845356, colon

description: IBD tissue


title: MDA-MB-231 siCtrl BioRep2


title: basal CK5PIP, 2m, mouse 2, plate 1


title: MDA-MB-231 siRagC2 BioRep1


title: p53ERTAM_p53IP_repeat1

city: houston

first: Longyong

last: Xu

state: TX

address: SCRB4, 1901 East Road

department: ET

institute: University of Texas MD Anderson Cancer Center

data_processing:
Cutadapt (version 3.7) was used to cut contaminating adaptor and polyA sequences from the ChIP-Seq reads and to remove low-quality reads (quality score<30), with parameters ‘-a "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT;max_error_rate=0.1;min_overlap=10" -A "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT;max_error_rate=0.1;min_overlap=10" -q 30 -m 40 -G "A(150);max_error_rate=0.1;min_overlap=3" --max-n 15 --trim-n’. BWA (version 0.7.15) was then applied to map the obtained high-quality reads to the mouse reference genome (mm10), with parameters ‘-t 10 -k 32 -M’. Uniquely mapped reads with mismatch base number lower than 8 (~5% mismatch rate for 150-bp reads) were retained from aligned read pairs. Filtered high-quality alignments were sorted by coordinates and duplicates were removed using Samtools (version 0.1.19). Alignments were further sorted by read name and MACS2 (version 2.1.1.20160309) was applied to identify peak regions, with parameters ‘--SPMR --bdg --treatment=treat.rmdup.sort.bam --control=control.rmdup.sort.bam --keep-dup=all --pvalue=0.05 --format=BAMPE --gsize=1870000000’.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: breast

growth_protocol: DMEM/F12 1:1 Media (Cytiva HyClone™) supplemented with 10% FBS (GIBCO), insulin (5 ng/ml), EGF (10 ng/ml), hydrocortisone (1 µg/ml), penicillin (100 U/ml) and streptomycin (100 μg/ml). Cells were grown at 37 °C in a 5% CO2 incubator and were tested to be mycoplasma-negative by the standard PCR method.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature. Reaction was quenched with 125 mM glycine. Chromatin extracts were sonicated to obtain DNA fragments with an average size of 400 bp and were immunoprecipitated by using the p53 antibody (clone DO-1) at 4 °C overnight.
The ChIP-seq libraries were generated by DNA SMART™ ChIP-Seq Kit (Takara, 634865) according to the manufacture’s instruction.

treatment_protocol: 4-OH tamoxifen, 100 nM, 48 hours

value: breast

value: 2153L GEM tumor derived primary cell

value: TNBC

value: 4-OH tamoxifen, 100 nM, 48 hours


title: basal CK5PIP, 2m, mouse 2, plate 2


title: IBD_187482, colon

description: IBD tissue


title: p53ERTAM_P53IP_repeat2


title: IBD_346821, colon

description: IBD tissue


title: p53ERTAM_Input_repeat1


title: basal CK5PIP, 2m, mouse 1, plate 1


title: MDA-MB-231 siCtrl BioRep1

value: WT


title: cell, THZ531_Endo,4h,rep2

city: Helsinki

first: Harri

last: Itkonen

address: Haartmaninkatu

country: Finland

institute: University of Helsinki

data_processing:
Sequence reads were mapped to hg38 using Bowtie2  (Version:2.3.4.1).
Samtools 1.6 converted SAM to BAM files, sorted, and built BAM index.
TCReads counts extraction was performed using Slamdunk 0.4.3
Alternative splicing events were indetified using rmats (v4.1.2).
SummarizeOverlaps function from GenomicAlignments (v1.34.0) and DEseq2 (1.38.2) were used to generate differentially expression genes for RNA-seq analysis.
Assembly: hg38
Supplementary files format and content: TC-reads counts file is a TSV format file
TSV column headers: Chromosome, Start, End, Name, Length, Strand, ConversionRate, ReadsCPM, Tcontent, CovereageOnTs, ConversionsOnTs, ReadCount, TcReadCount, multimapCount, ConversionRateLower, ConversionRateUppe
Library strategy: SLAM-seq

extract_protocol:
RNA was harvested using the following kit: Amersham RNAspin Mini Kit 50 preps Cytiva (25050071).
Library preparation from 300 ng of total RNA was performed according to Lexogen QuantSeq 3’ mRNA kit manual (Lexogen, Vienna, Austria), protocol version 015UG009V0251. Dual indexing and UMI modules were used in the library construction process. Library quality check was performed using LabChip GX Touch HT High Sensitivity assay (PerkinElmer, Hopkinton, MA, USA) and libraries were pooled based on the concentrations acquired from the assay. The library pool was quantified using Collibri Library Quantification kit (Thermo Fisher Scientific, Waltham, MA, USA) and then sequenced on the Illumina NovaSeq6000 system using S1 flow cell (Illumina, San Diego, CA, USA) with v1.5 reagents. Read length for the single-end run was 101 bp.

value: THZ531 and SCO101


title: basal CK5PIP, 2m, mouse 1, plate 2


title: cell, THZ531_Endo,4h,rep1


title: Combo

description: 10 x genomics

data_processing:
Raw reads were mapped to mouse genome mm10 and counted using CellRanger. Then the UMI counts were imported to R and processed with R package Seurat (4.0.1). Default pamameters were used to filter cells with low qualities. DoubletFinder (v2.0) was used to remove doublets detected in scRNA-seq (Assume 7.5% doublet formation rate). Data normalization and analysis were performed with R package Seurat according to its instructions. UMI counts were normalized using function SCTransform with the regression of mitochondria genes and cell cycle genes. PCA was run based on the SCT-normalized data and clusters were called with FindNeighbors and FindClusters using the top 20 PCs and resolution set to 0.3 for all CD45+ cells, 0.7 for T cells and 0.5 for monocytic lineage derived cells. Marker genes for each cluster were called with FindMarkers. Heatmaps showed top 5 differentially expressed genes of monocytic lineage derived cell clusters and top 10 differentially expressed genes of T cell clusters. Dimension reduction and visualization were performed with UMAP. Macrophage signatures were calculated using function AddModuleScore. Gene signatures of T cells were evaluated with VISION (2.1.0). Pseudotime analysis and trajectory inference was performed using slingshot (2.4.0). Then Tradeseq (1.10.0) was used to call the differentially expressed genes along pseudotime and between different T cell activation lineages.
Assembly: mm10
Supplementary files format and content: mtx for matrix
Supplementary files format and content: tsv for barcodes and features

source_name: Breast

growth_protocol: 2153L GEM tumor transplated into the mammary fat pad of female Balbc mice

extract_protocol:
CD45+ immune cells were isolated by fluorescence-activated cell sorting from fresh digested tumors with indicated treatment.
single-cell suspension was loaded on a Chromium controller to obtain single cell GEMS (Gel Beads-In-Emulsions) for the reaction. The library was prepared with Chromium Next GEM single cell 3’ kit V2 (10X Genomics)

treatment_protocol: Tumors bearing mice were treated with vehicle, ORIN1001, docetaxel or combo (ORIN1001, 150 mg/kg; docetaxel 20 mg/kg) for 8 days before harvest the tumor.

value: Breast

value: CD45+ immune cells

value: Combo


title: IBD_631005, colon

city: Chapel Hill

last: Furey

description: IBD tissue

source_name: colon

value: colon

value: Female

value: I


title: basal CK5eYFP, 2m, mouse 2, plate 1


title: basal CK5eYFP, 2m, mouse 1, plate 3


title: p53ERTAM_Input_repeat2


title: basal CK5eYFP, 2m, mouse 1, plate 2


title: Docetaxel

description: 10 x genomics

value: Docetaxel


title: IBD_268458, colon

description: IBD tissue

value: IBD


title: basal CK5eYFP, 2m, mouse 1, plate 1

value: prostate


title: IBD_301690, colon

description: IBD tissue


title: MDA-MB-231 siRagC1 BioRep1

value: breast cancer cells

value: RagC knock-down

value: siRNA


title: IBD_850257, colon

description: IBD tissue


title: cell, Endovion,4h,rep2


title: Hepatoblast, Myh9 siRNA-transfected, replicate 4

city: Dresden

first: Marino

last: Zerial

address: Pfotenhauerstr. 108

institute: MPI-CBG

description:
siMyh9_m8
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.

data_processing:
Adapter removal with cutadapt v1.16 with arguments: --nextseq-trim=20 -e 0.05 –match-read-wildcards --minimum-length 15 -a AGATCGGAAGAG -A AGATCGGAAGAG
Aligning reads to genome with STAR v2.7.1a with arguments: --alignSJDBoverhangMin 5 --alignSJoverhangMin 8 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignMatesGapMax 200000 –seedSearchStartLmax  25 --chimSegmentMin 20 --twopassMode Basic --alignIntronMin 20 --alignIntronMax 200000 --readFilesCommand zcat --quantMode GeneCounts --runMode alignReads
Assembly: GRCm39
Supplementary files format and content: secondstrand.tab.gz: Tabulator separated gzipped text file that contains a table with read counts as output by STAR mapper with rows=genes and columns=samples

growth_protocol: Hepatoblast isolation from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequent in vitro differentiation toward hepatocytes was performed as described in Belicova et al. (2021). In brief, embryonic livers were fragmented in Liver Perfusion Medium (Thermo Fisher Scientific; 17701–038) and subsequently digested in Liver Digest Medium (Thermo Fisher Scientific; 17703–034) supplemented with 10 µg/ml DNase I (Sigma-Aldrich; DN25). Erythrocytes were lysed in red blood cell lysis buffer: 155 mM NH4Cl, 10 mM KHCO3, and 0.1 mM EDTA, pH 7.4. Next, the cells were blocked with anti-mouse CD16/CD32 blocking antibody (BD Biosciences; 553142; Rat) and Dlk1+ hepatoblasts were labelled with anti-Dlk mAb-FITC (MBL; D187-4; Rat) and anti-FITC MicroBeads (Miltenyi Biotec; 130–048-701). Labelled Dlk + hepatoblasts were isolated using a magnetic column (Miltenyi Biotec; 130–024-201) according to the manufacturer’s protocol. Isolated hepatoblasts were seeded in 96-well cell culture microplates (Greiner; 655090) coated with Matrigel (Corning; 356231) at a density of 13,000 cells/well in expansion media: DMEM/F-12, GlutaMAX supplement (Thermo Fisher Scientific; 31331028), 10% FBS, 1 × insulin-transferrin-selenium-ethanolamine (Gibco; 51500–056), 0.1 µM dexamethasone (Sigma-Aldrich; D1756), 10 mM nicotinamide (Sigma-Aldrich; N0636), 10 ng/ml human hepatocyte growth factor (in-house production), and 10 ng/ml mouse epidermal growth factor (in-house production). After 24 h, the cells were overlaid with differentiation media: MCDB131 (Thermo Fisher Scientific; 10372019), 2 mM L-glutamine (Thermo Fisher Scientific; M11-004) 0.25 × insulin-transferrin-selenium-ethanolamine, and 0.1 µM dexamethasone, containing Matrigel to a final concentration of 5% vol/vol. Cells were cultured in a humidified incubator with 5% CO2 at 37°C for 5 days.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen; 74104) including the DNase I (Qiagen; 79254) treatment. Cells were lysed with RNeasy lysis buffer supplemented with DTT.
mRNA was isolated from the total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s instructions, fragmented to 350 nt, and libraries were prepared using the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina. For Illumina flowcell production, samples were equimolarly pooled and distributed on all lanes for 100bp paired-end sequencing on Illumina NovaSeq 6000.

treatment_protocol: For the PEG950 treatment, the culture medium of the cells was replaced at day 3 with differentiation medium containing 10 mM PEG950 (Merck; P3515). For the siRNA transfections: Cells were reverse transfected with siRNAs upon plating using Lipofectamine RNAiMAX (Thermo Fisher Scientific; 13778075) according to the manufacturer’s protocol. The final siRNA concentration per well was 10 nM at a concentration of 0.1 vol/vol % Lipofectamine RNAiMAX. siRNAs used: siLuciferase (sense 5′-cuuAcGcuGAGuAcuucGAdTsdT-3′, antisense 5′-UCGAAGuACUcAGCGuAAGdTsdT-3′), siNMIIA (siMyh9) (Thermo Fisher Scientific; MSS237342).

value: Liver

value: Hepatoblast

value: Reverse transfection with 10 nM siMyh9 siRNA upon plating


title: Hepatoblast, Myh9 siRNA-transfected, replicate 3

description:
siMyh9_m4
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: cell, SRPIN340,4h,rep2


title: IBD_560473, colon

description: IBD tissue

value: Male


title: cell, SRPIN340,4h,rep1


title: Hepatoblast, Myh9 siRNA-transfected, replicate 2

description:
siMyh9_m16
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: G_aCD4_3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Lung

extract_protocol:
Total RNA was extracted from each lung tissue sample using a QuickGene-Auto12S machine and a QuickGene-AutoS RNA Cultured Cell Kit (Kurabo Industries Ltd.).
RNA libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: BALB/c mice were vaccinated with PBS or 1 µg of G protein on days 0 and 21, and challenged with 1.0 × 10⁵ PFU of RSV on day 31. To deplete CD4+ T cells, mice received an intraperitoneal injection of 100 µg of rat anti-mouse CD4 antibody (Bio X Cell) or rat IgG2b isotype control (Bio X Cell) on day 30. Five days post-challenge, mice were euthanized, and their lungs were collected.

value: Lung

value: Vaccination with G protein and treatment with anti-CD4 antibody


title: IBD_954059, colon

description: IBD tissue


title: IBD_193721, colon

description: IBD tissue


title: cell, THZ531,4h,rep2


title: Hepatoblast, Myh9 siRNA-transfected, replicate 1

description:
siMyh9_m12
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: G_aCD4_2


title: cell, THZ531,4h,rep1


title: IBD_135118, colon

description: IBD tissue

value: H


title: Hepatoblast, luciferase siRNA-transfected, replicate 4

description:
siLuc_m7
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.

value: Reverse transfection with 10 nM siLuciferase siRNA upon plating


title: IBD_839147, colon

description: IBD tissue

value: colon


title: Hepatoblast, luciferase siRNA-transfected, replicate 3

description:
siLuc_m3
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: G_isotype_4

value: Vaccination with G protein and treatment with IgG2b isotype control


title: cell, Endovion,4h,rep1


title: Vehicle

description: 10 x genomics

value: Breast

value: CD45+ immune cells

value: Vehicle


title: IBD_484581, colon

description: IBD tissue

value: IBD


title: Hepatoblast, luciferase siRNA-transfected, replicate 2

description:
siLuc_m15
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: ORIN1001

description: 10 x genomics


title: cell, control,rep1


title: IBD_118727, colon

description: IBD tissue

value: Female

value: I


title: G_isotype_3


title: G_aCD4_4


title: G_isotype_2


title: Hepatoblast, luciferase siRNA-transfected, replicate 1

description:
siLuc_m11
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: HEC1A SMIP-3

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

institute: UT Health Science Center at San Antonio

description: HEC-1-A cells incubated with McCoy's 5A media+SMIP34 20µM 24 hours

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using HISAT2 default settings. The aligned BAM files sorted (SAMTools) and then processed using FeatureCounts to obtain the counts per gene
gene count measurements were obtained using FeatureCounts
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format generated by FeatureCounts. Seven (7) columns are: Geneid; Chr; Start; End; Strand; Length; bamFileName

source_name: Endometrial cancer cell line-HEC-1-A

growth_protocol: HEC-1-A cells were cultured in McCoy's 5A media supplemented with 10% FBS

extract_protocol:
Total RNA from HEC-1-A control and SMIP34-treated cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the NEB stranded mRNA sample preparation guide

treatment_protocol: HEC-1-A cells were incubated in 10% FBS McCoy's 5A medium with or without SMIP34 for 24 hrs.

tag: cell-line


title: HEC1A SMIP-2


title: G_isotype_1


title: Hepatoblast, PEG950-treated, replicate 4

description:
PEG950_m6
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.

value: Treated between day 3 and day 5 in vitro with 10 mM PEG950


title: G_aCD4_1


title: cell, control,rep2


title: IBD_919154, colon

description: IBD tissue

tag: disease


title: IBD_794755, colon

description: IBD tissue

tag: gender


title: PBS_aCD4_4

value: Vaccination with PBS and treatment with anti-CD4 antibody


title: Hepatoblast, PEG950-treated, replicate 3

description:
PEG950_m18
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.

value: Liver

value: Hepatoblast


title: HEC1A SMIP-1


title: HEC1A C3

description: HEC-1-A cells incubated with McCoy's 5A media

value: Control


title: IBD_396332, colon

description: IBD tissue

value: Male

tag: batch


title: PBS_aCD4_3

value: Lung


title: Hepatoblast, PEG950-treated, replicate 2

description:
PEG950_m14
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: IBD_467982, colon

description: IBD tissue

value: H


title: Hepatoblast, PEG950-treated, replicate 1

description:
PEG950_m10
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: PBS_aCD4_2


title: PBS_aCD4_1


title: Hepatoblast, non-treated control, replicate 4

description:
Ctrl_m9
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.

value: Non-treated control


title: Hepatoblast, non-treated control, replicate 3

description:
Ctrl_m5
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: HEC1A C1


title: IBD_816534, colon

description: IBD tissue

value: colon


title: PBS_isotype_4

value: Vaccination with PBS and treatment with IgG2b isotype control


title: IBD_602009, colon

description: IBD tissue


title: IBD_328631, colon

description: IBD tissue


title: Hepatoblast, non-treated control, replicate 1

description:
Ctrl_m13
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: Hepatoblast, non-treated control, replicate 2

description:
Ctrl_m17
Hepatoblast isolated from embryonic livers (E13.5, male and female embryos) of C57BL/6JOlaHsd mice and subsequently in vitro differentiated toward hepatocytes, RNA isolation at day 5 in vitro.


title: PBS_isotype_2


title: PBS_isotype_3


title: PBS_isotype_1