title: ENL_L

city: Omaha

first: Shannon

last: buckley

state: Nebraska

address: 985805 Nebraska Medical Center

department: Genetics, Cell Biology, and Anatomy

institute: Unviversity of Nebraska Med Center

data_processing:
1. The original fastq format reads were trimmed by fqtirm tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30). The trimmed fastq files were processed by FastQC (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data; available online at:http://www.bioinformatics.babraham.ac.uk/projects/fastqc) for quality control. All FastQC results are in FastQC folder.
2. The trimmed fastq files were processed by our newly developed standard pipelines utilizing STAR  as the aligner and RSEM as the tool for annotation and quantification at both gene and isoform levels.
3. The trimmed fastq files were mapped to mm10 mouse reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Spleen

extract_protocol:
cryopreserved tumors were thawed and pelleted, followed by  RNA extraction using Monarch Total RNA Miniprep kit (NEB #T2010).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen

tag: cell selection

tag: strain

value: Untreated

tag: disease state

value: AML

tag: aml subtype

value: MLL-ENL


title: ENL_NO

status: Public on Jan 15 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment

tag: Sex

value: Female


title: small RNA selection, jird, 20 dpi immature male, b

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

data_processing:
Reads aligned to a combined A. aegypti, B. malayi, and wBm reference using BWA-ALN (v 0.7.12)
Aligned reads were used to predict microRNAs using mirDeep2 (v. 0.1.2) with nematode microRNAs from miRBase as a guide
MicroRNA reads were quantified using HTSEQ v0.5.3p9 with mode set to Union
TPM values were calculated from microRNA genes
Expression Modules for Differentially Expressed MicroRNA were identified for Brugia malayi using WGCNA v1.61
Protein-coding genes that contain microRNA targets were identified using Miranda v3.3
Differentially expressed protein-coding genes with inverse WGCNA modules to microRNAs that they have targets for were identified as putatively regulated gene clusters
Significantly over-represented functional terms were identified using Fisher's exact test for each putatively microRNA regulated protein coding WCGNA module
Genome_build: B. malayi WS259, wBm NC_006833.1, and A. aegypti AaegL3.3
Supplementary_files_format_and_content: tab-delimited files containing counts, TPM, WGCNA module assignments for differentially expressed genes, functional term enrichment analyses for WGCNA modules

organism:
Brugia malayi
Wolbachia endosymbiont of Brugia malayi

source_name: B. malayi immature males taken from jirds 20 dpi

extract_protocol:
For nematode samples, third stage larvae of Brugia malayi strain FR3 were isolated from infected mosquitoes 9-16 days post infection (dpi) using the NIAID/NIH Filariasis Research Reagent Resource Center (FR3) Research Protocol 8.4. Larvae were isolated in RPMI + P/S, enumerated, and either flash frozen in liquid nitrogen for storage at -80°C or used for the infection of male Mongolian gerbils (Meriones unguiculatus; Charles River, Wilmington, MA, USA). Gerbils were anesthetized with 5% isoflurane and infected by introducing 400 L3s into the peritoneal cavity using a butterfly catheter. Larvae, immature adults, and mature adults were recovered by peritoneal flush using a terminal procedure. Brugia malayi embryos were collected from live gravid females as previously described. For vector samples, the Aedes aegypti black-eyed Liverpool strain was obtained from FR3 and maintained in the Biosafety Level 2 Insectary at the University of Wisconsin Oshkosh. Desiccated mosquito eggs were hatched in deoxygenated water and the resulting larvae were maintained on a slurry of ground TetraMin fish food (Blacksburg, VA) at 27°C with 80% relative humidity. Female pupae were separated using a commercial larva pupa separator (The John Hock Company, Gainesville, FL), placed in mesh-covered paper soup cartons, and enclosed adults were fed with cotton pads soaked in sucrose solution. Females were deprived of sucrose approximately twelve hours prior to blood feeding. Mosquitoes were infected with the Brugia malayi FR3 strain by feeding microfilaremic cat blood (FR3) through Parafilm via a glass-jacketed artificial membrane feeder. When necessary microfilaremic cat blood was diluted with uninfected dog blood to achieve a suitable parasite density for infection (100-250 microfilariae/20 μL). Infected mosquitoes were collected at 18 hours post infection (hpi), 4 dpi, and 8 dpi. They were anesthetized with CO2 then transferred to chilled microscope slides where the legs, wings, heads and abdomens were removed. The thoraces with and without developing B. malayi larvae were flash frozen in liquid nitrogen and stored at -80 °C prior to RNA isolation. Vector-derived Infective B. malayi L3 were isolated from whole mosquitoes in bulk using the standard FR3 protocol. For RNA isolation, mosquito thoraces were combined with TRIzol (Zymo Research, Irvine, CA) at a ratio of 1 mL TRIzol per 50-100 mg mosquito tissue, while nematode samples were processed using a 3:1 volume ratio of TRIzol to sample. For both preparations, 1 µL β-mercaptoethanol was added for every 100 µL of sample. The tissues were homogenized using a bead beater and a TissueLyser (Qiagen, Germantown, MD) at 50 Hz for 5 min. The homogenate was then transferred to a new tube and centrifuged at 12,000g for 10 min at 4°C. After incubation at room temperature for 5 min, 0.2 mL chloroform was added for every 1 mL TRIzol. The samples were shaken by hand for 15 s, incubated at room temperature for 3 min, loaded into a pre-spun Phase Lock Gel heavy tube (5Prime, Gaithersburg, MD), and centrifuged at 12,000g for 5 min at 4°C. The upper phase was extracted, one volume of 100% ethanol was added, and then loaded onto a PureLink RNA Mini column (Ambion, Austin, TX). The samples were processed following manufacturer instructions, quantified using a Qubit fluorometer (Qiagen, Germantown, MD) and Nanodrop spectrometer (Nanodrop, Wilmington, DE), and sent to Institute for Genomic Sciences at the University of Maryland Baltimore for DNase treatment and library preparation.
Small RNA sequencing libraries were constructed using the CleanTag small RNA library prep kit (TriLink Biotechnologies) according to manufacturer’s protocol. Adapters were diluted 1:2 for sample input under 150ng. Samples with input over 150 ng Used 1X adapters. Post adapter annealing and cDNA synthesis samples were subject to 15 cycles of PCR. Following PCR, samples were evaluated and size selected via 3% agarose gel. Bands ~140 bp in size were excised and purified using a QIAquick gel extraction kit (Qiagen). Post purification samples were checked for sizing, quality, and quantity on the Perkin Elmer Gx. Using the GX quantification, samples were pooled in equimolar amounts. The sample pool was further quantified using the Kapa library quantification kit (Roche). The sample pool was diluted to 2 nM, denatured with 0.1N sodium hydroxide and loaded on a MiSeq sequencing system for 50 cycles of sequencing using an MiSeq reagent kit v2 (Illumina).

tag: b. malayi strain


title: ENL_RL


title: 33716

type: genomic

city: Bethesda

first: Heidi

middle: G

last: Parker

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: origin

value: Aysen region, Chile

tag: breed

value: Patagonian Ovejero Dog


title: small RNA selection, jird, 20 dpi immature male, a


title: AF9_42

tag: genotype

value: MLL-AF9 +/-

value: Male


title: AF9_47


title: small RNA selection, jird, 8 dpi, b

source_name: B. malayi taken from jirds 8 dpi


title: 34733

value: Magallenas region, Chile


title: 33723


title: AF9_2


title: 33711


title: 33709


title: small RNA selection, jird, 8 dpi, a


title: TS543_E2Fi_10uM_&_STAT3i_2

city: Singapore

first: Roberto

last: Tirado-Magallanes

email: e0056363@nus.edu.sg, rtmag4@gmail.com

state: Singapore

address: 14 Medical Dr

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads preprocessing was performed by Trimmomatic (version 0.36) with the parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50.
Mapping of RNA-seq reads was done using STAR (version 020201, Dobin et al., 2013) with default parameters for RNA-seq data; the human ENSEMBL gene annotation model (GRCh38).
RSEM software (Li and Dewey, 2011)  were used to quantify the gene-level expression.
Genome_build: hg38
Supplementary_files_format_and_content: txt format; TPM values for five experimental conditions with 3 replicates each.

organism: Homo sapiens

source_name: Cancer stem cells

growth_protocol: The GSCs were cultured in human neural stem cell Maintenance Media (Millipore), 1% Penicillin-Streptomycin (PS) supplemented with EGF and  FGF (20 ng/ml each) to maintain stemness.

extract_protocol:
Tree days after treatment, cells were harvested and total RNA were extracted with RNeasy® Micro Kit (Qiagen).
A modified NEBNext RNA Ultra protocol is used to prepare the libraries for mRNA sequencing. The first step is selectively purifying the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. Following purification, the mRNA is fragmented using divalent cations under elevated temperature. Next, the cDNA is synthesized using Reverse transcriptase and random hexamers in a first strand synthesis reaction. Subsequently, the cDNA is converted to double stranded cDNA in a DNA polymerase based reaction. These DNA molecules are then subjected to a series of enzymatic steps for end repair, A-Tailing and ligation with NEB adapters. Finally, these adapter ligated molecules are enriched in a limited cycle PCR with indexed primers and purified using AMPure beads to create final cDNA library for sequencing.

treatment_protocol: TS543 cells were treated with either DMSO, 10 uM of HLM006474, 15 uM of HLM006474, 75 uM of S3I-201 or 10 uM of HLM006474 with 75 uM of S3I-201.

tag: cell type

value: Glioblastoma patient derived cancer stem cell

tag: passage


title: TS543_E2Fi_10uM_&_STAT3i_1


title: TS543_E2Fi_10uM_&_STAT3i_3


title: INV16_27

value: cKit+

value: Mx+; Hygr+

value: Poly IC at post natal day 45

value: Inversion 16


title: small RNA selection, jird, 4 dpi, b

source_name: B. malayi taken from jirds 4 dpi


title: INV16_30


title: TS543_STAT3i_3


title: 33648


title: TS543_STAT3i_2


title: small RNA selection, jird, embryo, b

description: BmEm(b)

source_name: B. malayi embryos taken from jirds


title: 33713


title: 33667


title: WT_BM2

source_name: Bone Marrow

value: Bone Marrow

value: Wild Type


title: 33646


title: small RNA selection, jird, embryo, a

description: BmEm(a)


title: WT_BM1


title: TS543_STAT3i_1


title: small RNA selection, jird, adult male, a

description: BmAM(a)

source_name: B. malayi adult males taken from jirds


title: small RNA selection, jird, adult male, b

description: BmAM(b)


title: TS543_E2Fi_15uM_2


title: 33663


title: 33645


title: exosomes of normal H9c2  myocardial cells

city: Jinan

first: Zhenzhen

last: Hu

address: Lixia District

country: China

institute: Shandong University

data_processing:
Remove the reads without 3' adapter. Remove the reads without insert fragment. Remove the reads contain too much A/T. Remove the reads which length is out of range. Remove the low-quality reads. And then obtain the clean reads.
The clean reads were mapped to reference genome.
Map reads to mature miRNA and hairping which recorded in miRBase(release 21) to identiy known-miRNA.
DEGseq was used for differential gene expression analysis.
Genome_build: miRBase (release 21)
Supplementary_files_format_and_content: normalized_count

organism: Rattus norvegicus

source_name: H9c2  myocardial cells

growth_protocol: The H9c2 cells were cultured in Dulbecco’s modified eagle medium (DMEM) containing 10% fetal bovine serum (Hyclone, USA) supplemented with 1% penicillin/ streptomycin. The cultures were maintained at 37°C in 5% CO2.

extract_protocol:
Exosomes were extracted from H9c2 cell culture medium by hypervelocity centrifugation.Total RNA was isolated using RNAiso Plus (code no. 9108, Takara).
Connecting the 3' adaptor to the total RNA. Connecting the 5' adaptor to the total RNA. RT-PCR. Recycling strips of 138-165bp (22-35nt RNA).

treatment_protocol: One sample was treated with 100mM alcohol for 24 hours.

tag: cell line

value: myocardial cells

value: untreated


title: small RNA selection, jird, adult female, b

description: BmAF(b)

source_name: B. malayi adult females taken from jirds


title: exosomes of alcohol-induced H9c2  myocardial cells

value: treated with 100mM alcohol for 24 hours


title: 33660


title: TS543_E2Fi_15uM_1


title: small RNA selection, jird, adult female, a

description: BmAF(a)


title: TS543_E2Fi_10uM_3


title: 33655


title: RNA-Seq_Empty-rep1 [G2021_53_1]

city: Grand Forks

first: Motoki

last: Takaku

state: North Dakota

address: 501 N Columbia Road,

institute: University of North Dakota

data_processing:
Base calling in illumina HiSeq X
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
reads mapping to annotated genes were counted using featureCounts
differential gene expression analysis using DESeq2
Reads were filtered based on a mean base quality score >20.
For ChIP-seq analysis, reads were mapped to hg19 genome using Bowtie 0.12.8. Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package. Paired-end reads were converted to a single fragment for metaplot analyses and visualization on the UCSC Genome Browser. After normalization within each data set, bigWig files were generated to visualize the genomic coverage. Peak calling was performed with HOMER v4.1 at default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cells were cultured in DMEM-F12 supplemented with 15% FBS, 2 mM L-glutamine, Insulin-transferrin-selenium (1x), 450 µM 1-Thioglycerol, and 50 µg/ml Ascorbic acid. Cells are maintained on Collagen-treated plates.

extract_protocol: RNAs from various cells were purified by the Direct-zol RNA kit (Zymo). RNA-seq libraries were prepared using NEBNext Ultra II RNA-Seq Kit (NEB) as per the manufacturer’s instruction with duel indexing. Quality of libraries was assessed in Tapestation (Agilent technologies) using D1000 Tape. Libraries were quantified using a well plate reader (Bio Tek) and pooled at a concentration of 12nM. Pooled libraries were quantified using the Droplet PCR system (Bio-Rad), and pooled libraries were sequenced in one lane Nova-Seq S4 as 150 bp Paired-end reads.

value: breast cancer

tag: cell subtype

value: luminal

tag: genotype/variation

value: Negative control

tag: passages


title: small RNA selection, jird, adult female, d

description: BmAF(d)


title: TS543_E2Fi_10uM_2


title: TS543_E2Fi_10uM_1


title: 33638

value: Aysen region, Chile

value: Patagonian Ovejero Dog


title: Cerebral cortex mTBI rep4

city: wuhan

first: Gang

last: Li

address: 169 Donghu Road, Wuchang District

institute: Zhongnan Hospital of Wuhan University

data_processing:
Trimmomatic 0.36 was used for quality control of reads
The identification of cicular RNA wad done by CIRI v2.0.3
FEELnc was used for the analysis of structure of circular RNA
DESeq was used for anlaysis of differnential expressed gene
The prediction of the relationship between circluar RNA and miRNA was finished by miranda.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: gene_RPM_matrix.txt

source_name: Cerebral cortex

extract_protocol:
At 24h after mTBI, animals were anesthetized and transcardially perfused with 100 ml of 4˚C isotonic saline. The ipsilateral cortex around the injury site was dissected rapidly in the mTBI group and the cerebral cortex at the same site was obtained in the sham group. And then they were placed immediately into liquid nitrogen and stored at -80 ˚C. Total RNA was isolated from eight ipsilateral cerebral cortex samples, including four mTBI samples and four control samples, using a miRNA Isolation Kit (Ambion, AM1560) following the manufacturer’s protocol. The samples with RIN ≥ 7, monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies, USA), were chosen for the following analysis.
TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, USA) was used for library construction.

value: Cerebral cortex

value: mTBI

tag: fraction

value: circular RNA


title: Cerebral cortex mTBI rep1


title: Cerebral cortex mTBI rep3


title: TS543_E2Fi_15uM_3

value: Glioblastoma patient derived cancer stem cell


title: Cerebral cortex mTBI rep2


title: RNAseq_mF1 rep2

city: Bunkyo-ku

first: Taiko

middle: Kim

last: To

state: Tokyo

address: 7-3-1 Hongo

department: Biological Science

country: Japan

institute: University of Tokyo

data_processing:
RNA-seq: The adaptor sequences and low quality regions were trimmed using Trimmomatic (Bolger et al. 2014). The quality filtered reads were mapped to genes (TAIR10) were counted through STAR algorithm (Dobin et al, 2013) and bedtools.
Genome_build: TAIR10
Supplementary_files_format_and_content: pergene

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Plants were grown on MS medium with 1% sucrose and 0.8% agar with 16h light / 8h dark.

extract_protocol:
Total RNAs were purified from 12-day-old plants grown on MS Agar plates using RNeasy Plant Mini Kit (QIAGEN), and then treated with DNase I (TaKaRa).
RNA Fragmentation was performed at 94°C for 7 min. Libraries were constructed using the KAPA Stranded RNA-seq Library Preparation Kit according to the manufacturer’s instruction.

value: seedling


title: Cerebral cortex sham rep4

value: sham


title: TS543_DMSO_3

value: DMSO


title: 33636


title: RNAseq_mF1 rep1


title: TS543_DMSO_2


title: 33643


title: TS543_DMSO_1


title: Cerebral cortex sham rep2


title: 33726


title: RNAseq_msss rep2

value: met1-1 suvh4 suvh5 suvh6


title: Cerebral cortex sham rep3


title: Cerebral cortex sham rep1


title: 33715


title: RNAseq_mcc rep2

value: met1-1 cmt2 cmt3


title: RNAseq_msss rep1


title: 33725


title: RNAseq_mcc rep1


title: small RNA selection, jird, adult female, c

description: BmAF(c)


title: RNAseq_met1 rep2


title: 33653


title: RNAseq_met1 rep1


title: 33724


title: 33712


title: RNAseq_F1 rep2


title: 24h_5mgYFSJ_75uMgefitinib [Y5_G75_2]

city: Guangzhou

first: Lizhu

last: Lin

address: 12 Jichang Street, Baiyun District

institute: Guangzhou University of Chinese Medicine

description: unstranded paired-end RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Low quality and adaptor sequences in raw reads were trimmed using Trim_galore (v0.4.2, Babraham Bioinformatics) with the following parameters: --stringency 6 --paired. Then cleaned reads were aligned to the reference genome (hg19, UCSC) using STAR_2.5.3a with the following parameters: --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --seedSearchStartLmax 30 –quantMode GeneCounts
Differential expression analysis was performed with edgeR and DE genes were selected with a False Discovery Rate (FDR) < 0.05.
Genome_build: hg19, UCSC
Supplementary_files_format_and_content: Tab delimited matrix showing raw counts of refGenes

growth_protocol: Human EGFR mutated NSCLC cell line H1975 was purchased from ATCC (HTB-22™, VA, USA) and were cultured in RPMI-1640 medium (Thermo Fisher Scientifc, MA, USA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientifc, MA, USA) at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated using PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
RNA libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Massachusetts, USA) according to the manufacturer's protocol.

treatment_protocol: Drug treatments were designed as follows: CKI in 2 doses (1.0 mg/mL and 2.0 mg/mL), YFSJ in 2 doses (2.5 mg/ml and 5 mg/ml) and  gefitinib in two doses (50 uM and 75 uM); Two doses of CKI combined with two doses of gefitinib; Two doses of YFSJ combined with two doses of gefitinib.

tag: tumor type

value: non-small cell lung cancer


title: 24h_5mgYFSJ_75uMgefitinib [Y5_G75_3]

description: unstranded paired-end RNA-seq


title: mitral valve endothelial cells (VECs) treated with naive plasma rep3

city: Boston

first: Ali

last: Hashemi Gheinani

address: 300 Longwood

department: Urology

institute: Boston Children's Hospital

data_processing:
Aligning reads using STAR (v2.5.2b) was performed in two steps: (i) creating genome indices using Ovis_aries.Oar_v3.1 genome assembly (GCA_000298735.1) and Ovis_aries.Oar_v3.1.99.gtf annotation. We obtained thereference genome and the reference annotation for the sheep from the Ensembl database. (ii) read alignment.
The alignments of fastq files produced   random order with respect to their position in the reference genome. The BAM files therefore were sorted using Samtools
Assessing alignment quality and mapping statistics were performed by ready Log.final.out files and uniquely mapped read, reads that mapped to mutliple locations and reads that were unmapped were defined. In addition to the STAR-specific summary we also obtain quality metrics using Qualimap and RNA-SeQC.
To perform subsetting and visualization of the alignment using a genome browser on the BAM file, an index was generated using Samtools  (v1.9) and Integrative Genomics Viewer (IGV) was used to assess the quality of the alignment.
The counts of reads that were mapped to a single location (uniquely mapping) were used as an input for featureCounts  (v2.0.0) tool to get the gene counts
featureCounts output file (count matrix) was then used to extract the read count, genomic coordinates and the length of the gene. Finally, multiQC (v1.5) was run on the files from (i) FastQC, .(ii) Log.final.out files from STAR and (iii) .summary file from featurecounts outputs from our workflow. This enabled us to  aggregate the results from several tools and generates a single HTML report with plots to visualize and compare various QC metrics between the samples.
DESeq2 (v1.26.0) was used for estimation of variance-mean dependence in count data and test for differential expression based on a model using the negative binomial distribution.The DESeq2 package was run using R program (Bioconductor version: Release (3.10)).
Genome_build: GCA_000298735.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Ovis aries

source_name: Mitral valve endothelial cells (VECs)

extract_protocol: library preparation was performed using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., Part# 15031047). Sequencing was performed on the Illumina HiSeq 2000 (paired-end 150 bp) using the TruSeq SBS Kit v3-HS (Illumina Inc.).

value: ovine naive plasma treated


title: mitral valve endothelial cells (VECs) treated with post-MI plasma rep1

value: ovine post-MI plasma treated


title: mitral valve endothelial cells (VECs) treated with post-MI plasma rep3


title: mitral valve endothelial cells (VECs) treated with post-MI plasma rep2


title: 24h_5mgYFSJ_75uMgefitinib [Y5_G75_1]

description: unstranded paired-end RNA-seq


title: 33710


title: mitral valve endothelial cells (VECs) treated with naive plasma rep1


title: RNAseq_F1 rep1


title: 24h_5mgYFSJ_50uMgefitinib [Y5_G50_2]

description: unstranded paired-end RNA-seq


title: 33719


title: RNAseq_sss rep1

value: suvh4 suvh5 suvh6


title: 33708


title: 33714


title: hPCEC_3

city: Shiga

first: RODI

middle: KADO

last: ABDALKADER

address: 1-1-1 Noji-Higashi, Kusatsu

institute: Ritsumeikan University

description: RNAseq data  from human primary corneal epithelial cells (hPCEpC), replicate 3

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated (FastQC v0.11.7)
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner (Trimmomatic 0.38, HISAT2 version 2.1.0, Bowtie2 2.3.5.1).
Transcript is assembled by StringTie with aligned reads. This process provides information of known transcripts, novel transcripts, and alternative splicing transcripts.
Expression profiles are represented as read count and normalization values which are calculated based on transcript length and depth of coverage (StringTie version 2.1.3b).
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalization values are provided as FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) and TPM(Transcripts Per Kilobase Million)

source_name: Cornea

growth_protocol:
Human embryonic stem cells KhES1(K1), KhES1-OCT4-EGFP (K1-OCT4-EGFP)  and human induced pluripotent stem cells 585A1 were used according to the guidelines of the ethnical committee of Kyoto University. Prior to inducing differentiation, a cell-culture dish was coated with Matrigel overnight at 4 ºC. Cultured cells were washed with PBS and treated with TryPLE Express at 37ºC for 5 min, followed by the addition of E8 medium  and transfer of the cell suspension into a 15-mL tube. Cells were centrifuged at 200 × g for 3 min and the supernatant was removed, resuspended in E8 basal medium supplemented with 10 µM Y27632 , and plated on Matrigel-coated culture dish, and cultured for 24 h in a humidified incubator at 37ºC with 5% CO2. The culturing medium was replaced with E8 basal medium daily.
[Differentation protocol]  When cells reached 30-40% of confluency, the E8 medium was replaced with chemical induction medium consisted of fresh E6 medium supplemented with Wnt pathway inhibitor (IWR-1 endo), TGFß kinase/activin receptor like kinase inhibitor (A83-01)  and human bFGF. These conditions were applied for four days. After that, cells were cultured with the maintenance medium consisting of E6 medium only. The medium was changed every day.

extract_protocol:
Total RNA was extracted from differentiated primary myoblasts using the RNeasy mini kit (QIAGEN).
RNA-seq library construction (TruSeq stranded mRNA LT Sample Prep Kit)

value: Mature corneal epithelial cells

tag: derived tissue

value: Cornea


title: hPCEC_2

description: RNAseq data  from human primary corneal epithelial cells (hPCEpC), replicate 2


title: hPCEC_1

description: RNAseq data  from human primary corneal epithelial cells (hPCEpC), replicate 1


title: RNAseq_cc rep2

value: cmt2 cmt3


title: 33718

value: Aysen region, Chile

value: Patagonian Ovejero Dog


title: mitral valve endothelial cells (VECs) treated with naive plasma rep2


title: RNAseq_cc rep1


title: 24h_2.5mgYFSJ_75uMgefitinib [Y2_5_G75_3]

description: unstranded paired-end RNA-seq


title: 33721


title: RNAseq_Col rep2

value: Wild-type


title: RNAseq_Col rep1


title: 24h_5mgYFSJ_50uMgefitinib [Y5_G50_3]

description: unstranded paired-end RNA-seq


title: 24h_2.5mgYFSJ_75uMgefitinib [Y2_5_G75_1]

description: unstranded paired-end RNA-seq


title: RNAseq_sss rep2


title: 24h_2.5mgYFSJ_50uMgefitinib [Y2_5_G50_3]

description: unstranded paired-end RNA-seq


title: BS_DDM1IBM1_rep2

library_source: genomic

data_processing:
The adaptor sequences and low quality regions were trimmed using Trimmomatic (Bolger et al. 2014). Mapping to the reference genome (TAIR10), deduplication, and methylation extraction were performed using Bismark version 0.10.1 (Krueger and Andrews, 2011). The parameters used for mapping is -n 1 –l 20 –e 90. Uniquely aligned reads were used and reads with more than one alignment with same read quality were removed.
Genome_build: TAIR10
Supplementary_files_format_and_content: CX_report file

source_name: Rosette leaves

extract_protocol:
Genomic DNA was isolated from rosette leaves using the Nucleon Phytopure genomic DNA extraction kit (GE Healthcare).
Genomic DNA was fragmented using Covaris S220, and the size between 300-450bp were gel-purified. The libraries were prepared using TruSeq DNA LT Sample Prep Kit (Illumina) and subjected to bisulfite conversion using MethylCode Bisulfite Conversion Kit (Life Technologies). Bisulfite-treated DNA were amplified with KAPA HiFi HotStart Uracil ReadyMix (Kapa Biosystems), and then purified with Agencourt AMPure XP (Beckman Coulter).
WGBS: Plants  were sown on MS medium with 1% sucrose and 0.8% agar and then  grown on soil  with 16h light / 8h dark.

value: DDM1 IBM1

value: Leaves


title: 33666


title: K1_CEC_D10_3

description: RNAseq data  from Human embryonic stem cells KhES1(K1) derived cornea epithelial cells  at day 10 post  differentiated condition, replicate 3

value: embryonic stem cell line KhES1

value: embryonic stem cells-derived corneal cells

tag: time

value: day 10


title: 33658


title: 24h_5mgYFSJ_50uMgefitinib [Y5_G50_1]

description: unstranded paired-end RNA-seq


title: 24h_2.5mgYFSJ_50uMgefitinib [Y2_5_G50_2]

description: unstranded paired-end RNA-seq


title: K1_CEC_D10_2

description: RNAseq data  from Human embryonic stem cells KhES1(K1) derived cornea epithelial cells  at day 10 post  differentiated condition, replicate 2


title: BS_DDM1IBM1_rep1

growth_protocol: Plants  were sown on MS medium with 1% sucrose and 0.8% agar and then  grown on soil  with 16h light / 8h dark.

tag: tissue


title: 24h_2.5mgYFSJ_50uMgefitinib [Y2_5_G50_1]

description: unstranded paired-end RNA-seq

tag: treatment


title: 33665


title: 24h_2.5mgYFSJ_75uMgefitinib [Y2_5_G75_2]

description: unstranded paired-end RNA-seq


title: 33657


title: K1_CEC_D20_3

description: RNAseq data  from Human embryonic stem cells KhES1(K1) derived cornea epithelial cells  at day 20 post  differentiated condition, replicate 3

value: day 20


title: K1_CEC_D10_1

description: RNAseq data  from Human embryonic stem cells KhES1(K1) derived cornea epithelial cells  at day 10 post  differentiated condition, replicate 1


title: 33659


title: 33668


title: K1_3

description: RNAseq data from Human embryonic stem cells KhES1(K1) , replicate 3

source_name: Embryo

value: embryonic stem cells

value: Embryo


title: K1_CEC_D20_2

description: RNAseq data  from Human embryonic stem cells KhES1(K1) derived cornea epithelial cells  at day 20 post  differentiated condition, replicate 2


title: K1_CEC_D20_1

description: RNAseq data  from Human embryonic stem cells KhES1(K1) derived cornea epithelial cells  at day 20 post  differentiated condition, replicate 1


title: BS_DDM1ibm1_rep1

value: DDM1 ibm1


title: 33664


title: 33656


title: BS_ddm1IBM1_rep2

value: ddm1 IBM1


title: BS_ddm1IBM1_rep1


title: K1_2

description: RNAseq data from Human embryonic stem cells KhES1(K1) , replicate 2


title: 24h_2.5mg_YFSJ [Y2_5_3]

description: unstranded paired-end RNA-seq

value: non-small cell lung cancer


title: 24h_5mg_YFSJ [Y5_1]

description: unstranded paired-end RNA-seq


title: 33662


title: K1_1

description: RNAseq data from Human embryonic stem cells KhES1(K1) , replicate 1


title: 24h_5mg_YFSJ [Y5_2]

description: unstranded paired-end RNA-seq


title: BS_ddm1ibm1_rep2

value: ddm1 ibm1


title: 24h_2.5mg_YFSJ [Y2_5_2]

description: unstranded paired-end RNA-seq


title: 24h_2.5mg_YFSJ [Y2_5_1]

description: unstranded paired-end RNA-seq


title: BS_DDM1ibm1_rep2


title: 33661


title: 24h_5mg_YFSJ [Y5_3]

description: unstranded paired-end RNA-seq


title: BS_Mi_rep2

value: MET1 ibm1-4


title: Renal Angiomyolipoma cells (10uM Imatinib) - rep3

city: New York

first: Uchenna

last: Unachukwu

state: New York

address: 630 West 168th Street, P&S 7-430

department: Anesthesiology

institute: Columbia University Medical Center

data_processing:
Base calling was performed using Real-Time Analysis (RTA) version 1.17
Bcl2fastq2 (v2.20) was used to convert base calls to fastq format coupled with adaptor trimming
Pseudoalignment was performed using a kallisto index created from human transcriptome (GRCh38) using kallisto (0.44.0).
Differential gene expression was performed using Sleuth in R
Pathway analysis was performed using Ingenuity Pathway Analysis (IPA)
Genome_build: NCBi GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts per sample

source_name: Renal Angiomyolipoma cells

growth_protocol: Renal AML cells were maintained in culture media containing Dulbecco's Modified Eagle Medium (DMEM) and 10% Fetal Bovine Serum

extract_protocol:
Adherent renal AML cells in culture were washed twice with phosphate buffered saline (PBS) before RNA isolation using the Rneasy mini kit (Qiagen) according to the manufacturer's instructions. RNA quality was electrophoretically assessed using a Bioanalyzer and only samples with RNA Integrity values greater than 8 were used for RNA sequencing.
Library preparation was performed using illumina TruSeq RNA prep kit according to the manufacturer's protocol.

treatment_protocol: Renal AML cells were serum starved overnight in culture media containing DMEM and 0.1% Fetal Bovine Serum. Thereafter, cells were incubated for 24hrs with complete media only, or complete media fortified with Rapamycin (0.05uM, 1uM) or Imatinib (1uM, 10uM) at 37℃ and 5% CO2 prior to RNA extraction.

tag: disease

value: Tuberous Sclerosis

value: Treated with 10uM Imatinib for 24hrs

tag: drug

value: Imatinib (Novartis)

value: UMB1949 (ATCC, #CRL-4004; RRID:CVCL_C471)


title: Renal Angiomyolipoma cells (10uM Imatinib) - rep2


title: 24h_2mgCKI_75uMgefitinib [C2_G75_3]

description: unstranded paired-end RNA-seq


title: Renal Angiomyolipoma cells (10uM Imatinib) - rep1


title: 33652

tag: origin

value: Aysen region, Chile

value: Patagonian Ovejero Dog


title: 24h_2mgCKI_75uMgefitinib [C2_G75_2]

description: unstranded paired-end RNA-seq


title: BS_Mi_rep1

value: Leaves


title: 33651

tag: breed


title: BS_mi_rep2

tag: genotype

value: met1-1 ibm1-4


title: Renal Angiomyolipoma cells (1uM Imatinib) - rep3

value: Treated with 1uM Imatinib for 24hrs


title: Renal Angiomyolipoma cells (1uM Imatinib) - rep2


title: 33641


title: Renal Angiomyolipoma cells (1uM Imatinib) - rep1


title: BS_mi_rep1


title: 33650


title: 24h_2mgCKI_75uMgefitinib [C2_G75_1]

description: unstranded paired-end RNA-seq


title: 33654


title: 33640


title: BS_ddm1ibm1_rep1


title: 24h_2mgCKI_50uMgefitinib [C2_G50_2]

description: unstranded paired-end RNA-seq


title: 24h_2mgCKI_50uMgefitinib [C2_G50_3]

description: unstranded paired-end RNA-seq


title: Renal Angiomyolipoma cells (1uM Rapamycin) - rep2

value: Treated with 1uM Rapamycin for 24hrs

value: Rapamycin (#R-5000; LC Laboratories)


title: Renal Angiomyolipoma cells (1uM Rapamycin) - rep3


title: 33649


title: 24h_2mgCKI_50uMgefitinib [C2_G50_1]

description: unstranded paired-end RNA-seq


title: BS_ibm1_1st_rep2


title: BS_ibm1_2nd


title: BS_ibm1_1st_rep1


title: Renal Angiomyolipoma cells (1uM Rapamycin) - rep1


title: 24h_1mgCKI_75uMgefitinib [C1_G75_3]

description: unstranded paired-end RNA-seq


title: 33647


title: Renal Angiomyolipoma cells (0.05uM Rapamycin) - rep3

value: Treated with 0.05uM Rapamycin for 24hrs


title: BS_mF1(msss X mcc)_rep4


title: 24h_1mgCKI_75uMgefitinib [C1_G75_2]

description: unstranded paired-end RNA-seq


title: BS_mF1(mcc X msss)_rep3


title: 24h_1mgCKI_75uMgefitinib [C1_G75_1]

description: unstranded paired-end RNA-seq


title: Renal Angiomyolipoma cells (0.05uM Rapamycin) - rep2


title: 33637


title: 24h_1mgCKI_50uMgefitinib [C1_G50_3]

description: unstranded paired-end RNA-seq


title: BS_mF1(msss X mcc)_rep2


title: Renal Angiomyolipoma cells (0.05uM Rapamycin) - rep1


title: 33644


title: BS_mF1(mcc X msss)_rep1


title: 33635


title: Renal Angiomyolipoma cells (untreated) - rep3

value: Untreated


title: 24h_1mgCKI_50uMgefitinib [C1_G50_2]

description: unstranded paired-end RNA-seq


title: 33642


title: Renal Angiomyolipoma cells (untreated) - rep2


title: BS_msss_rep2

value: met1-1 suvh4 suvh5 suvh6


title: BS_msss_rep1


title: 24h_2mg_CKI [C2_3]

description: unstranded paired-end RNA-seq

value: non-small cell lung cancer


title: 24h_1mgCKI_50uMgefitinib [C1_G50_1]

description: unstranded paired-end RNA-seq


title: BS_mcc_rep2

value: met1-1 cmt2 cmt3


title: 33639


title: AN 2 [DC-22208_S14]

city: Houston

first: John

middle: Morgan

last: Knight

state: TX

address: One Baylor plaza, M917

department: Pathology and Immunology

institute: Baylor College of Medicine

data_processing:
Paired-end Fastq reads were filtered with Fastp (v0.21.0) set at minimum length of 50bp and Phred score of 15
Reads mapped to mouse genome (Genecode release M25) with STAR aligner (v2.7.7a) with RSEM (v1.3.3) with default settings
Differential expressed gene analysis with DESeq2 (v1.30.1) with consideration for batch effects and PBS group as reference
Genome_build: Genecode release M25
Supplementary_files_format_and_content: raw counts

source_name: Sinus Tissue

extract_protocol:
Sinus tissue was extracted by scraping the sinus cavity and total RNA isolated by Qiagen RNeasy Mini Kit according to manufactures protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were intranasally challenged with 50uL of PBS or 400k Aspergillus niger conidia 3x/wk for 12 wks.

tag: strain

tag: disease state

value: Infected/CRS

value: Aspergillus niger

value: Sinus

tag: batch

value: B


title: 24h_2mg_CKI [C2_2]

description: unstranded paired-end RNA-seq

tag: cell line


title: AN 3 [DC-22209_S15]


title: BS_mcc_rep1


title: 24h_2mg_CKI [C2_1]

description: unstranded paired-end RNA-seq


title: AN 1 [DC-21956_S11]

value: A


title: BS_met1-1


title: 24h_1mg_CKI [C1_3]

description: unstranded paired-end RNA-seq


title: PBS 3 [DC-22207_S13]

value: Control

value: PBS


title: Pulmonary LAM Tumor cells  (10uM Imatinib) - rep1

data_processing:
Base calling was performed using Real-Time Analysis (RTA) version 1.17
Bcl2fastq2 (v2.20) was used to convert base calls to fastq format coupled with adaptor trimming
Pseudoalignment was performed using a kallisto index created from human transcriptome (GRCh38) using kallisto (0.44.0).
Differential gene expression was performed using Sleuth in R
Pathway analysis was performed using Ingenuity Pathway Analysis (IPA)
Genome_build: NCBI GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts per sample

source_name: Pulmonary LAM Tumor Biopsy

growth_protocol: Pulmonary LAM tumor cells were maintained in DF8 complete culture media containing DMEM/F12 (1:1), 10% Fetal Bovine Serum (FBS), 5 x 10-8 M sodium selenite, 1.2 x 10-8 M vasopressin, 1 x 10-8 M cholesterol, 2 x 10-7 M hydrocortisone, 10μg/mL transferrin, 1 x 10-9 M triiodothyronine (T3), 0.025mg/mL insulin, and freshly prepared 1.6 x 10-6M ferrous sulfate

extract_protocol:
Adherent pulmonary LAM tumor cells in culture were washed twice with phosphate buffered saline (PBS) before RNA isolation using the Rneasy mini kit (Qiagen) according to the manufacturer's instructions. RNA quality was electrophoretically assessed using a Bioanalyzer and only samples with RNA Integrity values greater than 8 were used for RNA sequencing.
Library preparation was performed using illumina TruSeq RNA prep kit according to the manufacturer's protocol.

treatment_protocol: Pulmonary LAM tumor cells were serum starved overnight in DF8 complete culture media supplemented with 0.1% Fetal Bovine Serum. Thereafter, cells were incubated for 24hrs with DF8 complete media only, or DF8 complete media fortified with Rapamycin (0.05uM, 1uM) or Imatinib (1uM, 5uM, 10uM) at 37℃ and 5% CO2 prior to RNA extraction.

value: Lymphangioleiomyomatosis

value: Treated with 10uM Imatinib for 24hrs

value: Imatinib (Novartis)


title: Pulmonary LAM Tumor cells  (10uM Imatinib) - rep2


title: PBS 2 [DC-22206_S12]


title: 24h_1mg_CKI [C1_2]

description: unstranded paired-end RNA-seq


title: BS_Col_Wild-type

value: Wild-type

value: Leaves


title: Pulmonary LAM Tumor cells  (5uM Imatinib) - rep1

value: Treated with 5uM Imatinib for 24hrs


title: RNA_cpsf70_rep2

city: Beijing

first: Peizhe

last: Song

state: Beijing

address: Chengfu Road CCME B234

institute: Peking University

data_processing:
Reads were trimmed by pair-end model of cutadapt (v1.18) software.
Trimmed reads were aligned to TAIR10 genome assembly by hisat2 (v2.1.0) software using the default parameter for pair-end model
CLIP Peakcalling were performed by macs2 (v2.2.5), the enrichment fold threshold is 2, p threshold is 0.01
A-seq2 were performed by Aseq2 pipeline (https://git.scicore.unibas.ch/zavolan_public/A-seq2-processing).
m6A-seq Peakcalling were performed by macs2 (v2.2.5), the enrichment fold threshold is 5, FDR threshold is 0.05
RNA-seq were performed by R package ballgown, fold change threshold is 1.5, p threshold is 0.01
Genome_build: TAIR10
Supplementary_files_format_and_content: xls files include peak coordination, enrichment, p-value, q-value, TPM. Change of enrichment and gene id are also included in sig_diff.xls

molecule: polyA RNA

source_name: 12-day seedlings

growth_protocol: All plants germination and growth were under the conditions: 16 h light/8 h dark at 22 °C with a light intensity of 90 to 120 mE m-2 s-1

extract_protocol:
Total RNA was first extracted  by Trizol reagent, The polyA RNA was then purified with oligo d(T)25 magnetic beads
For m6A-Seq, polyA RNA was fragmented by NEBNext Magnesium RNA Fragmentation Module. A portion of fragmented RNA was reserved as m6A input, others were incubated with anti-m6A antibody and eluted as the m6A IP. Both m6A input and IP samples were prepared for next-generation sequencing library by standard protocol of NEBNext Ultra II RNA Library Prep Kit for Illumina; For A-Seq2, poly(A) RNA was fragmented by alkaline hydrolysis and performed with 5’ ends phosphorylation and DNase treatment. 3’ ends were blocked by cordycepin triphosphate and 5’ endwere ligated with 3’ adaptor.  Reverse transcription (Superscript IV, Invitrogen) was carried out using BiodUdT25, then the USER enzyme and RNase H (NEB) was added to get the first strand cDNA. After 5’ adaptor ligation, cDNA was amplified and sequenced with Illumina HiSeq X Ten; For FA-CLIP, formaldehyde cross-linked samples were harvested and lysated, and the lysates were treated with Turbo DNase and RNase T1 and incubated with pre-washed Anti-Flag M2 magnetic beads. After washed by low-salt wash buffer, beads was suspended into low-slat wash buffer and digested with RNaseT1. Beads was incubated with T4 PNK and ATP orderly to end repair. Using protease K digestion and phenol/chloroform extraction, the recovered RNA were prepared for next-generation sequencing followed by standard protocol of NEB Next Multiplex Small RNA Library Prep Kit for illumina; For RNA-Seq, RNA libraries were prepared for next-generation sequencing using standard protocol of NEBNext Ultra II RNA Library Prep Kit for Illumina

value: cpsf70 mutant

value: 12-day seedlings

tag: rip antibody


title: 24h_1mg_CKI [C1_1]

description: unstranded paired-end RNA-seq

value: non-small cell lung cancer


title: Pulmonary LAM Tumor cells  (1uM Imatinib) - rep2

value: Treated with 1uM Imatinib for 24hrs


title: PBS 1 [DC-21955_S10]


title: RNA_cpsf70_rep1


title: 24h_75uM_gefitinib [G75_3]

description: unstranded paired-end RNA-seq


title: Pulmonary LAM Tumor cells  (1uM Imatinib) - rep1


title: Renal Angiomyolipoma cells (untreated) - rep1

value: Tuberous Sclerosis

value: Untreated

value: UMB1949 (ATCC, #CRL-4004; RRID:CVCL_C471)


title: RNA_Col0_rep2

value: wild type


title: Pulmonary LAM Tumor cells  (1uM Rapamycin) - rep2

value: Treated with 1uM Rapamycin for 24hrs

value: Rapamycin (#R-5000; LC Laboratories)


title: RNA_Col0_rep1


title: Pulmonary LAM Tumor cells  (1uM Rapamycin) - rep1


title: 24h_75uM_gefitinib [G75_2]

description: unstranded paired-end RNA-seq


title: 24h_75uM_gefitinib [G75_1]

description: unstranded paired-end RNA-seq


title: 24h_50uM_gefitinib [G50_3]

description: unstranded paired-end RNA-seq


title: Pulmonary LAM Tumor cells  (5uM Imatinib) - rep2


title: CLIP_Col0_rep2

data_processing:
Library strategy: CLIP
Reads were trimmed by pair-end model of cutadapt (v1.18) software.
Trimmed reads were aligned to TAIR10 genome assembly by hisat2 (v2.1.0) software using the default parameter for pair-end model
CLIP Peakcalling were performed by macs2 (v2.2.5), the enrichment fold threshold is 2, p threshold is 0.01
A-seq2 were performed by Aseq2 pipeline (https://git.scicore.unibas.ch/zavolan_public/A-seq2-processing).
m6A-seq Peakcalling were performed by macs2 (v2.2.5), the enrichment fold threshold is 5, FDR threshold is 0.05
RNA-seq were performed by R package ballgown, fold change threshold is 1.5, p threshold is 0.01
Genome_build: TAIR10
Supplementary_files_format_and_content: xls files include peak coordination, enrichment, p-value, q-value, TPM. Change of enrichment and gene id are also included in sig_diff.xls

value: ANTI-FLAG M2 Magnetic Beads (Sigma, M8823, Lot# SLBS8760)


title: CLIP_OE_rep2

value: CPSF70 overexpression line


title: Pulmonary LAM Tumor cells (0.05uM Rapamycin) - rep2

value: Lymphangioleiomyomatosis

value: Treated with 0.05uM Rapamycin for 24hrs


title: Pulmonary LAM Tumor cells  (0.05uM Rapamycin) - rep1


title: 24h_50uM_gefitinib [G50_2]

description: unstranded paired-end RNA-seq


title: CLIP_Col0_rep1


title: 24h_50uM_gefitinib [G50_1]

description: unstranded paired-end RNA-seq


title: Pulmonary LAM Tumor cells  (untreated) - rep2


title: Pulmonary LAM Tumor cells (untreated) - rep1


title: 24h_untreated [UT24_3]

description: unstranded paired-end RNA-seq


title: WT TEC

first: Zhaoqi

last: Zhang

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

institute: University of Chinese Academy of Sciences

description: A sample from WT mice TECs

data_processing:
The Cell Ranger software pipleline (Version 3.0) provided by 10x Genomics used to demultiplex cellular barcodes, map reads to the mm10 genome.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: WT TEC

extract_protocol:
Single-cell thymic stromal suspensions were isolated from 2-week-old WT and TEC-specific Furin knockout mice, then TECs (CD45-EpCAM+) were sorted by FACS. Barcoded single cells were captured using the 10X Genomics.
RNA libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

tag: age

tag: cell type

value: TEC

value: WT


title: Furin cKO TEC

description: A sample from Furin KO mice TECs

source_name: Furin cKO TEC

value: Furin cKO


title: Control

city: Durham

first: Purushothama Rao

last: Tata

email: pt93@duke.edu, tata.lab@yahoo.com

state: NC

address: 303 Research Dr., Alexander Sands Building, Room- 451, BOX 3709

department: Department of Cell Biology

institute: Duke University School of Medicine

data_processing:
FASTQ files were processed using Cell Ranger (10x Genomics) and mapped to the GRCh38 reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: expression matrix

source_name: Human lung

extract_protocol:
Organoids from control (day21) or EGF depletion (day21) or ADM (day10) condition were incubated with TrypLE select enzyme at 37ºC for 10min. After 10 min, organoids were scooped out using cell scraper (VWR, # 734-2978) and matrigel was disrupted by pipetting. Organoids were again incubated at 37ºC for 10 min followed by TrypLE inactivation using DMEM/F-12 containing 10% FBS medium. Single cell suspension was filtered through 40 µm strainer and dead cells were removed using dead cell removal kit (Miltenyi biotech, #130-090-101) according to manufacturer’s instructions. Single cells were resuspended in 0.04% BSA at 1000 cells/µl concentration and used for gel bead emulsion (GEM) generation in 10x chromium instrument.
Followed the protocol of 10x Genomics Chromium v3.1 chemistry

value: Cultured lung cells

value: Adult

value: Normal


title: 24h_untreated [UT24_2]

description: unstranded paired-end RNA-seq

tag: tumor type

value: non-small cell lung cancer


title: CLIP_OE_rep1

value: 12-day seedlings


title: 24h_untreated [UT24_1]

description: unstranded paired-end RNA-seq


title: APA_cpsf70_rep2

data_processing:
Library strategy: A-seq2
Reads were trimmed by pair-end model of cutadapt (v1.18) software.
Trimmed reads were aligned to TAIR10 genome assembly by hisat2 (v2.1.0) software using the default parameter for pair-end model
CLIP Peakcalling were performed by macs2 (v2.2.5), the enrichment fold threshold is 2, p threshold is 0.01
A-seq2 were performed by Aseq2 pipeline (https://git.scicore.unibas.ch/zavolan_public/A-seq2-processing).
m6A-seq Peakcalling were performed by macs2 (v2.2.5), the enrichment fold threshold is 5, FDR threshold is 0.05
RNA-seq were performed by R package ballgown, fold change threshold is 1.5, p threshold is 0.01
Genome_build: TAIR10
Supplementary_files_format_and_content: xls files include peak coordination, enrichment, p-value, q-value, TPM. Change of enrichment and gene id are also included in sig_diff.xls

value: cpsf70 mutant


title: APA_Col0_rep2


title: SUMOi

city: Berlin

first: Schayan

last: Yousefian

address: Hannoversche Str. 28

country: Germany

institute: Berlin Institute of Health at Charité Berlin

data_processing:
bcl2fastq Conversion Software (Illumina) was used to generate demultiplexed fastq files
Cell Ranger (v. 6.0.1):  "cellranger count" was run per sample
Genome_build: Mouse GRCm38 (mm10)
Supplementary_files_format_and_content: Barcode filtered matrix containing raw gene expression counts (UMIs)

source_name: Spleen

extract_protocol:
10x Genomics Chromium Next GEM Single Cell 3ʹ v3.1 with Feature Barcoding technology for Cell Surface Protein
3' end mRNA + oligo-conjugated antibodies (surface marker & TotalseqB  hashtag antibodies)

treatment_protocol: mice were treated with 7.5 mg/kg SUMOi on day 1 and day 4. Analysis was on day 5.

value: SUMOi

value: mouse1; mouse2; mouse3


title: Serum treatement


title: 0h_untreated [UT0_3]

description: unstranded paired-end RNA-seq


title: APA_cpsf70_rep1


title: control

value: control

value: mouse4; mouse5; mouse6


title: Distal lung

data_processing:
FASTQ files were processed using SpaceRanger (10x Genomics) and mapped to the GRCh38 reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: expression matrix and H E images

extract_protocol:
Spatial transcriptomics was performed using Visium Spatial Gene Expression assay (10x Genomics) as per manufacturer’s recommendation. Briefly, small pieces of the human lung were incubated in OCT at 4°C for 30 min and frozen in OCT and stored at -80°C.  10 µm sections were placed onto Visium Gateway gene expression slide and stored with desiccants at -80°C until staining and library preparation. Prior to the main experiment, permeabilization time for spatial transcriptomics assay was calculated to be 30 min using the Visium Spatial Tissue Optimization slide by Duke University’s Molecular Genomics core facility. H&E staining was performed on the Visium slide and imaged using 10x objective on Keyence BZX800 microscope. Tissue sections were permeabilized immediately to capture RNA molecules onto barcoded spots on the slide. Libraries were then prepared and sequenced (150 bp paired-end) using NovaSeq S4 flow cell.
Followed the protocol of 10x Genmics Visium spatial gene expression assay for spatial RNA-seq (3' enrichment)

value: lung tissue


title: APA_Col0_rep1

value: wild type


title: EGF depletion


title: 0h_untreated [UT0_2]

description: unstranded paired-end RNA-seq


title: RNA-seq of BAT about F2

city: Nanning City

first: Wang

last: Peng

address: Nanning City College Road and XiXiangTang District

institute: Guangxi University

data_processing:
Illumina Casava1.7 software used for basecalling.
The high-quality sequences filtered by fastp were mapped to the mouse reference genome (mm10) by Bowtie2 (v2.0.0.5) and Tophat (v2.0.0).
Then, the mapping readings were assembled and GTF files were generated by StringTie (v2.2.0). The GTF files were then merged into one file by Cuffmerge, from which the counts of each gene were extracted.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BAT(Brown Adipose Tissue)

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: BAT(Brown Adipose Tissue)

value: Fetal mouses on the last day of gestation + High fructose

tag: Sex

value: male


title: RNA-seq of BAT about F1


title: m6A_Col0_rep2

data_processing:
Library strategy: m6A-seq
Reads were trimmed by pair-end model of cutadapt (v1.18) software.
Trimmed reads were aligned to TAIR10 genome assembly by hisat2 (v2.1.0) software using the default parameter for pair-end model
CLIP Peakcalling were performed by macs2 (v2.2.5), the enrichment fold threshold is 2, p threshold is 0.01
A-seq2 were performed by Aseq2 pipeline (https://git.scicore.unibas.ch/zavolan_public/A-seq2-processing).
m6A-seq Peakcalling were performed by macs2 (v2.2.5), the enrichment fold threshold is 5, FDR threshold is 0.05
RNA-seq were performed by R package ballgown, fold change threshold is 1.5, p threshold is 0.01
Genome_build: TAIR10
Supplementary_files_format_and_content: xls files include peak coordination, enrichment, p-value, q-value, TPM. Change of enrichment and gene id are also included in sig_diff.xls

source_name: 14-day seedlings

value: 14-day seedlings


title: 0h_untreated [UT0_1]

description: unstranded paired-end RNA-seq


title: Cartilaginous airway


title: RNA-seq of BAT about C2

value: Fetal mouses on the last day of gestation


title: m6A_Col0_rep1


title: 5

status: Public on Jan 14 2022

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

institute: Fourth Military Medical University

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2 v2.0.13 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_exp.xls: Excel file includes RPKM values and counts for each Sample.

source_name: liver sinusoidal endothelial cells

extract_protocol:
Liver sinusoidal endothelial cells were isolated from wild type and RBPjcKO mice. Total RNA was isolated from the cells using the Trizol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0 (Life Technologies, USA) and then diluted to 10pM for cluster generation in situ on the HiSeq3000 pair-end flow cell followed by sequencing (2×150bp) on HiSeq 3000.

treatment_protocol: Wild type and RBPjcKO mice were injected intraperitoneally with Tamoxifen to induce Notch signaling inactivation.

value: liver sinusoidal endothelial cells

value: 7-8 weeks

value: RBPjcKO


title: 6


title: 4


title: 3


title: 2


title: RNA-seq of BAT about C1


title: 1


title: RCD080 205045560006_R06C01

first: Ze

state: MA

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

institute: Harvard Medical School

description:
RCD080
clear cell renal cell carcinoma

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R studio
SeSAMe Processed Average Beta

label: Cy5 and Cy3

source_name: clear cell renal cell carcinoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen AllPrep kit (#80224), Blood & Tissue Kit, CelProgen or  Zymo Quick-DNA Miniprep Plus Kit according to standard instructions

value: oxBS

tag: dna extraction kit

value: AllPrep kit (#80224)

tag: arraytypes

value: IlluminaHumanMethylationEPIC


title: RCD080 205045560006_R05C01

description:
RCD080
clear cell renal cell carcinoma

tag: treatment

value: BS


title: RCD078 205051010114_R07C01

description:
RCD078
clear cell renal cell carcinoma


title: RCD078 205051010114_R08C01

description:
RCD078
clear cell renal cell carcinoma


title: RCD074 205045560006_R02C01

description:
RCD074
clear cell renal cell carcinoma

value: Blood & Tissue Kit


title: RCD074 205045560006_R01C01

description:
RCD074
clear cell renal cell carcinoma


title: RCD072 205051010114_R02C01

description:
RCD072
clear cell renal cell carcinoma


title: RCD072 205051010114_R01C01

description:
RCD072
clear cell renal cell carcinoma


title: RCD062 205051010007_R08C01

description:
RCD062
clear cell renal cell carcinoma


title: RCD060 205045550131_R04C01

description:
RCD060
clear cell renal cell carcinoma


title: RCD058 205051010029_R06C01

description:
RCD058
clear cell renal cell carcinoma


title: RCD058 205051010029_R05C01

description:
RCD058
clear cell renal cell carcinoma


title: RCD060 205045550131_R03C01

description:
RCD060
clear cell renal cell carcinoma


title: RCD047 205051010029_R08C01

description:
RCD047
clear cell renal cell carcinoma


title: RCD062 205051010007_R07C01

description:
RCD062
clear cell renal cell carcinoma


title: RCD047 205051010029_R07C01

description:
RCD047
clear cell renal cell carcinoma


title: Epithelium from mouse M3

city: Philadelphia

first: Kelly

middle: A

last: Whelan

state: PA

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

description: Illumina sequenced bulk RNA-Seq data

data_processing:
bcl2fastq
Genome alignment and gene-level count summarization was done with Cell Ranger (v6)
Genome_build: GRCm38
Supplementary_files_format_and_content: cell x gene matrix in txt with transcript counts

source_name: Esophageal Epithelium

extract_protocol:
Sinlge cell droplet was generated by 10X Genomics Chromium, and cDNAs with UMIs were generated at single-cell level.
Illumina adapters with unique index were added to the cDNAs of each sample with Chromium Next GEM Single Cell 3’ mRna Library Construction Kit v3.1

tag: tissue

value: Esophageal Epithelium

value: M


title: Epithelium from mouse F2

description: Illumina sequenced bulk RNA-Seq data

value: F


title: Epithelium from mouse F6

description: Illumina sequenced bulk RNA-Seq data


title: RCD008_rep 205051010014_R02C01

description:
RCD008_rep
clear cell renal cell carcinoma


title: RCD008_rep 205051010014_R01C01


title: RCD008 204949780073_R03C01

description:
RCD008
clear cell renal cell carcinoma


title: Young mouse young6F index c

description: 10X Chromium sequenced single cell RNA-Seq data

value: Young


title: RCD008 204949780073_R05C01

description:
RCD008
clear cell renal cell carcinoma


title: RCD007_rep 205051010014_R08C01

description:
RCD007_rep
clear cell renal cell carcinoma


title: Young mouse young6F index b


title: RCD007_rep 205051010014_R07C01


title: Young mouse young5M index d


title: Young mouse young5M index c


title: Young mouse young6F index a


title: Young mouse young5M index a


title: RCD006 204949780073_R04C01

description:
RCD006
clear cell renal cell carcinoma


title: Young mouse young4M index d


title: RCD007 204949780073_R02C01

description:
RCD007
clear cell renal cell carcinoma


title: RCD005_rep 205051010007_R04C01

description:
RCD005_rep
clear cell renal cell carcinoma


title: RCD006 204949780073_R06C01

description:
RCD006
clear cell renal cell carcinoma


title: Young mouse young4M index c


title: Young mouse young4M index b


title: RCD013 205051010140_R04C01

description:
RCD013
clear cell renal cell carcinoma


title: RCD013 205051010140_R03C01

description:
RCD013
clear cell renal cell carcinoma


title: RCD005 204963470080_R03C01

description:
RCD005
clear cell renal cell carcinoma


title: RCD005 204963470080_R08C01

description:
RCD005
clear cell renal cell carcinoma


title: RCD005_rep 205051010007_R03C01


title: RCD004 204963470080_R05C01

description:
RCD004
clear cell renal cell carcinoma


title: Young mouse young3F index d


title: Young mouse young3F index c


title: Young mouse young6F index d


title: Young mouse young3F index a


title: Young mouse young3F index b


title: RCD004 204963470080_R04C01

description:
RCD004
clear cell renal cell carcinoma


title: Young mouse young2F index d


title: RCD003_rep 205051010140_R01C01

description:
RCD003_rep
clear cell renal cell carcinoma


title: RCD003_rep 205051010140_R02C01


title: Young mouse young2F index c


title: RCD007 204949780073_R07C01

description:
RCD007
clear cell renal cell carcinoma


title: RCD003 204963470080_R01C01

description:
RCD003
clear cell renal cell carcinoma


title: RCD003 204963470080_R02C01

description:
RCD003
clear cell renal cell carcinoma


title: Young mouse young5M index b


title: Young mouse young2F index b


title: RCD002_rep 205051010029_R04C01

description:
RCD002_rep
clear cell renal cell carcinoma


title: Aged mouse old6F index d

value: Aged


title: Aged mouse old6F index c


title: RCD002_rep 205051010029_R03C01


title: RCD002 204963470080_R06C01

description:
RCD002
clear cell renal cell carcinoma


title: Young mouse young4M index a


title: RCD002 204963470080_R07C01

description:
RCD002
clear cell renal cell carcinoma


title: Aged mouse old6F index a


title: RCD001 204949780073_R01C01

description:
RCD001
clear cell renal cell carcinoma


title: RCD001 204949780073_R08C01

description:
RCD001
clear cell renal cell carcinoma


title: HFO018 205051010029_R02C01

description:
HFO018
human fetal oligodendrocyte replicate

source_name: human fetal oligodendrocyte replicate

value: CelProgen


title: Aged mouse old6F index b


title: HFO018 205051010029_R01C01


title: Aged mouse old5M index d


title: HFO017 205051010014_R06C01

description:
HFO017
human fetal oligodendrocyte replicate


title: Aged mouse old5M index a


title: Aged mouse old5M index b


title: Aged mouse old5M index c


title: HFO017 205051010014_R05C01


title: HFO016 205045560065_R06C01

description:
HFO016
human fetal oligodendrocyte replicate


title: Aged mouse old4F index c


title: Aged mouse old4F index d


title: HFO016 205045560065_R05C01


title: Aged mouse old4F index a


title: HFO015 205051010019_R08C01

description:
HFO015
human fetal oligodendrocyte replicate


title: Aged mouse old3 index d


title: Aged mouse old3 index c


title: Aged mouse old4F index b


title: HFO015 205051010019_R07C01


title: Young mouse young2F index a


title: Aged mouse old3 index b


title: HFO014 205045560065_R07C01

description:
HFO014
human fetal oligodendrocyte replicate


title: HFO013 205045550131_R02C01

description:
HFO013
human fetal oligodendrocyte replicate


title: Aged mouse old3 index a


title: Aged mouse old2 index d


title: HFO012 205051010140_R06C01

description:
HFO012
human fetal oligodendrocyte replicate


title: Aged mouse old2 index c


title: Aged mouse old2 index b


title: HFO012 205051010140_R05C01


title: Aged mouse old2 index a


title: HFO011 205051010019_R06C01

description:
HFO011
human fetal oligodendrocyte replicate


title: HFO011 205051010019_R05C01


title: HFO010 205051010140_R07C01

description:
HFO010
human fetal oligodendrocyte replicate


title: HFO010 205051010140_R08C01


title: HFO008 205045560065_R02C01

description:
HFO008
human fetal oligodendrocyte replicate


title: BM-GOM-2-RNAseq

city: Chengdu

first: jin

last: long

address: Hui ming

institute: Sichuan Agricultural University

data_processing:
Contacts matrix were generated by using juicer tools.
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Tpm and counts matrixs were generated using R vresion 3.6.1.
TADs were identified using DomainCaller and Insulation Score.
Compartment A/B were defined by principal component analysis.
Genome_build: Susscrofa11.1
Supplementary_files_format_and_content: binned raw and normalized 2D contact matrices text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: genes expression level (TPM) and counts text file
Supplementary_files_format_and_content: TAD files
Supplementary_files_format_and_content: ABindex files

organism: Sus scrofa

source_name: greater omentum fat

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 49 million 150-bp paired-end raw reads and ~ 48 million high-quality reads for each library.

value: Bama pig

tag: developmental stage

value: Adult

value: greater omentum fat


title: BM-GOM-2-hic

extract_protocol:
The 1g adipose tissue were cross-linked with a final concentration of 4% freshly made formaldehyde for 30min at room temperature and followed by quenching with glycine in a final concentration of 0.25 mol/L. After lysis of cells, DNA was digested with 200 units of MboI enzyme (NEB, Cat.N: R0543S) at 37°C for 1h, 65°C for 20min and 25°C for 5min. The restriction fragments were filled and labeled by biotinylated nucleotides and then ligated with T4 DNA ligase (Enzymatics, Cat.N: L6030-HC-L) at 20°C for 30 min
After crosslink reversal, ligated DNA was purified and sheared to a length of 300–500 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina NovaSeq 6000 sequencing.


title: HFO008 205045560065_R01C01


title: BM-GOM-1-RNAseq


title: BM-ULB-2-RNAseq

source_name: upper layer of backfat

value: upper layer of backfat


title: WB-ULB-2-hic

value: wild boar


title: HFO007 205051010014_R04C01

description:
HFO007
human fetal oligodendrocyte replicate


title: HFO009 205045560006_R07C01

description:
HFO009
human fetal oligodendrocyte replicate


title: BM-ULB-2-hic


title: HFO014 205045560065_R08C01


title: HFO007 205051010014_R03C01


title: WB-ULB-1-hic


title: HFO006 205051010114_R04C01

description:
HFO006
human fetal oligodendrocyte replicate


title: WB-ULB-1-RNAseq


title: WB-ULB-2-RNAseq


title: WB-GOM-2-hic


title: HFO013 205045550131_R01C01


title: HFO005 205045550131_R08C01

description:
HFO005
human fetal oligodendrocyte replicate


title: HFO006 205051010114_R03C01


title: WB-GOM-2-RNAseq


title: WB-GOM-1-hic


title: WB-GOM-1-RNAseq


title: HFO005 205045550131_R07C01


title: HFO004 205045560006_R04C01

description:
HFO004
human fetal oligodendrocyte replicate


title: HFO004 205045560006_R03C01


title: HFO009 205045560006_R08C01


title: berghia_rhinophore_ganglion

city: Amherst

first: Paul

last: Katz

state: Massachusetts

address: 611 North Pleasant Street, 221 Morrill Science Center III

department: Biology

institute: University of Massachusetts Amherst

data_processing:
Paired-end reads, with read 1 containing the cellular barcodes and read 2 containing the cDNA sequence, were loaded into HTStream to trim off unwanted sequences from reads (i.e., adapters, primer sequences, poly-A tails), merge short overlapping paired-end reads, remove quality bases or N characters, and remove PCR duplicates, junk reads, and contamination.
Clean reads were indexed based on the reference transcriptome generated by the Lyons's lab in the alevin pipeline. Alevin extracts a transcript-id-to-gene-id tab-separated file from the transcript FASTA file to map the reads.
Alevin uses the read 1 file containing the cell barcodes (CB) and the UMI information to generate a frequency distribution of all the observed CB and correct the CB. Then, alevin aligns the sequences in the read 2 FASTA file to the reference transcriptome, annotates the sequences with barcode information, identifies potential PCR/sequencing errors in the UMIs, and de-duplicates UMIs due to PCR amplification while also accounting for UMI collisions.
Finally, alevin generates an estimated whitelist of correct CB and a gene-by-cell matrix for each sample containing information about the expression level of all genes in rows and all cells in columns.
Genome_build: N/A
Supplementary_files_format_and_content: The processed data files contain a matrix where rows are genes and columns are cells, and each slot contains the number of UMIs assigned to each gene for each cell of the sample.

organism: Berghia stephanieae

source_name: whole cells from 18 pairs of rhinophore ganglia

growth_protocol: 25oC in artificial sea water at salinity 1.022

extract_protocol:
the brains were treated in a mixture of pronase and liberase and dissociated by pipetting. The cells were fixed in methanol.
10X Genomics' Chromium Single Cell 3' Gene Expression v3 protocol

value: brain

tag: tissue region

value: rhinophore ganglion

tag: fixation method

value: methanol

value: adult


title: BM-GOM-1-hic

tag: breed


title: HFO003 205051010007_R06C01

description:
HFO003
human fetal oligodendrocyte replicate

value: oxBS

value: IlluminaHumanMethylationEPIC


title: HFO003 205051010007_R05C01

value: BS


title: HFO002 205051010007_R02C01

description:
HFO002
human fetal oligodendrocyte replicate


title: HFO001 205045550131_R06C01

description:
HFO001
human fetal oligodendrocyte replicate


title: HFO001 205045550131_R05C01


title: HFO002 205051010007_R01C01


title: C4-2-tet-shRB-Dox-GSK_rep1

first: Changmeng

last: Cai

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

description:
C42shRB_Dox_GSK_count_table.txt.gz
C42shRB_DOXGSK_1_S7_L001

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (version 1.6.4) from GRCh37 Ensembl reference.
Genome_build: hg19
Supplementary_files_format_and_content: txt file forraw counts of sequence reads

source_name: C4-2 cell

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
RNA-seq libraries of both C4-2-tet-shRB (DHT) and LNCaP cells were performed by using TruSeq® Strnd Total RNA LT (Illumina). RNA-seq libraries of VCaP cells and C4-2-tet-shRB (GSK) were performed by using TruSeq® Stranded mRNA (Illumina).

value: prostate cancer cell line

tag: medium condition

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)

value: 0.05ug/ml doxycycline for 3 days, then treat 10uM GSK2879552 for 24 hours


title: GR4-2 DEX 204221240068_R02C01

description:
GR4-2 DEX
glioma patients treated with Dexamethasone

value: Zymo Quick-DNA Miniprep Plus


title: C4-2-tet-shRB-Dox-GSK_rep2

description:
C42shRB_Dox_GSK_count_table.txt.gz
C42shRB_DOXGSK_2_S8_L001


title: GR4-2 DEX 204221240068_R01C01

source_name: glioma patients treated with Dexamethasone


title: C4-2-tet-shRB-GSK_rep2

description:
C42shRB_Dox_GSK_count_table.txt.gz
C42shRB_GSK_2_S4_L001

value: 10uM GSK2879552 for 24 hours


title: GR4-18 DEX 204221240031_R06C01

description:
GR4-18 DEX
glioma patients treated with Dexamethasone


title: C4-2-tet-shRB-GSK_rep1

description:
C42shRB_Dox_GSK_count_table.txt.gz
C42shRB_GSK_1_S3_L001


title: GR4-2 Con 204221240068_R05C01

description:
GR4-2 Con
glioma patients treated without Dexamethasone


title: VCaP-siRB_rep2

description:
VCaP_samples_count_table.txt.gz
VCaP_CSS_siRb_2

source_name: VCaP cell

value: In DMEM medium with 10% FBS

value: VCaP

value: transfected with 20nM siRNA of RB1 for 2 days


title: GR4-18 DEX 204221240031_R05C01


title: C4-2-tet-shRB-Dox-DMSO_rep2

description:
C42shRB_Dox_GSK_count_table.txt.gz
C42shRB_DOX_2_S6_L001

value: 0.05ug/ml doxycycline for 3 days


title: GR4-18 Con 204221240032_R04C01

description:
GR4-18 Con
glioma patients treated without Dexamethasone


title: GR4-18 Con 204221240032_R03C01

source_name: glioma patients treated without Dexamethasone


title: C4-2-tet-shRB-Dox-DMSO_rep1

description:
C42shRB_Dox_GSK_count_table.txt.gz
C42shRB_DOX_1_S5_L001


title: HT29 CD26+, biological rep2

type: RNA

city: Pokfulam

first: Lui

last: Ng

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

hyb_protocol: The cRNAs were hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix GeneChip System.

data_processing: Data generated was analyzed using Genespring GX 350

label: biotin

source_name: HT29 cell-line FACS sorted CD26+

label_protocol: As per manufacturer (Affymetrix 3'-IVT Kit)

growth_protocol: All cell lines are maintain at 37oC incubator with 5% CO2 with DMEM supplement with 10% FBS

extract_protocol: Total RNA were extracted by Trizol reagent accroding to manufacturer's protocol

value: human colorectal cell-line


title: HT29 CD26-, biological rep2

source_name: HT29 cell-line FACS sorted CD26-


title: C4-2-tet-shRB-DMSO_rep2

description:
C42shRB_Dox_GSK_count_table.txt.gz
C42shRB_2_S2_L001

value: untreated


title: berghia_main_brain

source_name: whole cells from 20 pairs of cerebropleural and pedal ganglia  and around 5 pairs of buccal ganglia

value: brain

value: main brain


title: GR3-2 DEX 204221240032_R08C01

description:
GR3-2 DEX
glioma patients treated with Dexamethasone


title: GR3-2 Con 204221240043_R02C01

description:
GR3-2 Con
glioma patients treated without Dexamethasone


title: HT29 CD26+, biological rep1


title: C4-2-tet-shRB-DMSO_rep1

description:
C42shRB_Dox_GSK_count_table.txt.gz
C42shRB_1_S1_L001


title: VCaP-siNTC_rep1

description:
VCaP_samples_count_table.txt.gz
VCaP_CSS_siNCT_1

value: transfected with 20nM siRNA of non-target control (NTC) for 2 days


title: GR4-2 Con 204221240068_R06C01

value: oxBS


title: VCaP-siRB_rep3

description:
VCaP_samples_count_table.txt.gz
VCaP_CSS_siRb_3


title: LNCaP-GSK-1uM-2D_rep2

description:
LNCaP_samples_count_table.txt.gz
GSK2DVEH_ACAGTG_L002

source_name: LNCaP cell

value: LNCaP

value: 1uM GSK2879552 for 2 days


title: GR3-18 DEX 204221240043_R08C01

description:
GR3-18 DEX
glioma patients treated with Dexamethasone

value: IlluminaHumanMethylationEPIC


title: GR3-18 Con 204221240068_R08C01

description:
GR3-18 Con
glioma patients treated without Dexamethasone


title: GR3-18 Con 204221240068_R07C01

value: BS


title: LNCaP-GSK-1uM-2D_rep1

description:
LNCaP_samples_count_table.txt.gz
GSK2DVEH_ACAGTG_L001

value: prostate cancer cell line

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)


title: VCaP-siRB_rep1

description:
VCaP_samples_count_table.txt.gz
VCaP_CSS_siRb_1


title: SMC1A_KD#1_HCT116

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

data_processing:
Sequenced reads were aligned to Ensemble database with STAR.
Gene expression values were normalized to obtain RPKM values using RSEM.
Overlap differentially expressed genes in WT /KO HCT-116 and CT26  cells.
Genome_build: Ensemble
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample .

extract_protocol:
Cells were lysed in Trizol reagent and total RNA was extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal cancer cell line

tag: genotype


title: GR2-2 Con 204221240031_R04C01

description:
GR2-2 Con
glioma patients treated without Dexamethasone

value: Zymo Quick-DNA Miniprep Plus


title: GR2-2 DEX 204221240032_R06C01

description:
GR2-2 DEX
glioma patients treated with Dexamethasone


title: VCaP-siNTC_rep3

description:
VCaP_samples_count_table.txt.gz
VCaP_CSS_siNCT_3

value: In DMEM medium with 10% FBS

value: VCaP


title: LNCaP-Veh_rep2

description:
LNCaP_samples_count_table.txt.gz
LNVEH_CGATGT_L002


title: NIPBL_KO#2_HCT116


title: HT29 CD26-, biological rep1


title: GR2-2 Con 204221240031_R03C01


title: GR2-18 DEX 204221240068_R04C01

description:
GR2-18 DEX
glioma patients treated with Dexamethasone


title: VCaP-siNTC_rep2

description:
VCaP_samples_count_table.txt.gz
VCaP_CSS_siNCT_2


title: NIPBL_KO#1_HCT116


title: GR3-2 DEX 204221240032_R07C01


title: C4-2-tet-shRB-Dox30d-DHT_rep2

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRBDOX1MDHT_GTGAAA_L002

value: In RPMI 1640 medium with reduced steroid hormone [8% charcoal-stripped FBS (CSS) plus 2% regular FBS]

value: 0.05ug/ml doxycycline for 30 days, then treat 10nM dihydrotestosterone (DHT) for 24 hours


title: GR2-18 Con 204221240043_R05C01

description:
GR2-18 Con
glioma patients treated without Dexamethasone


title: GR3-18 DEX 204221240043_R07C01


title: C4-2-tet-shRB-Dox30d-DHT_rep1

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRBDOX1MDHT_GTGAAA_L001


title: GR1-2 DEX 204221240043_R04C01

description:
GR1-2 DEX
glioma patients treated with Dexamethasone


title: SMC1A_KD#2_HCT116


title: GR3-2 Con 204221240043_R01C01

description:
GR3-2 Con
glioma patients treated without Dexamethasone


title: C4-2-tet-shRB-Dox30d-Veh_rep2

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRBDOX1M_GTCCGC_L002

value: 0.05ug/ml doxycycline for 30 days


title: pK27R_2_H3-3

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

data_processing:
Concatenated fastq files were processed in a Galaxy environment with standard parameters for adaptor trimming using the Trimmomatic (v0.38) including initial Illumina CLIP step for TruSeq3 (Single-ended, for MiSeq and HiSeq) and sliding window trimming
Trimmed fastq files were mapped using bowtie2 (v2.3.4.1) using standard settings to both mm10(patch4) and dm6 genomes. The reads mapping exactly one time (unique) were noted for each genome to generate scaling factor for downstream normalization purposes
the mm10 mapped bam files were filtered for unique reads using Rmdup (v1.3.1) using standard settings. This downstream bam file containing unique reads were converted to 6-column BED files using bedtools (v2.29.2).
BED files were then uploaded onto EaSeq (v1.111) software usign standard import settings for ChIPSeq (see https://easeq.net) and each file was newly describe to include the spike-in normalization factor in addition to standard FPKM normalization (automatic in EaSeq). No peak-calling was performed for these datasets
Further details are found in the associated methods section of the manuscript
Genome_build: mm10 (patch4), dm6 (spike-in)

source_name: mESCs

growth_protocol: mESCs were grown in feeder-free standard naïve pluripotent growth conditions including LIF and 2i (GSK3 and MEK1 inhibitors) and 2 million mESCs were plated in each human plasma fibronectin coated 10cm tissue culture dish and subjected to a 48 hour EpiLC differentiation protocol with media change after 24 hours prior to harvesting chromatin at 48 hours

extract_protocol:
Chromatin was extracted from crosslinked cells using "SDS lysis" buffer containing (100mM NaCl, 50mM Tris-Cl pH8, 5mM EDTA pH8, 0.2% sodium azide and 0.5% SDS). Chromatin was then pelleted and resuspended on ice in sonication/IP buffer that is a 2:1 mix of "SDS lysis" buffer and cold "Triton dilution" buffer (100mM Tris-Cl pH8.6, 100mM NaCl, 5mM EDTA pH8, 0.2% sodium azide, and 5% Triton X-100), prior to sonication using a Diagenode Bioruptor Pico.
ChIP libraries were prepared using the NEBNext Ultra II DNA library preparation kit (Catalog E7645S/L) according to manufacturers guidelines including the recommended size selection step

treatment_protocol: For all ChIPs, cells were crosslinked in 1% formaldehyde for 10 minutes and quenched with 0.125M glycine before cell lysis for chromatin preparation.

value: mESCs

tag: chip antibody

value: Millipore (Catalog 09-838, Lot:3310680)

tag: strain background

value: Knockout with K27R mutant addback_clone2


title: GR1-2 DEX 204221240043_R03C01


title: GR1-2 Con 204221240032_R02C01

description:
GR1-2 Con
glioma patients treated without Dexamethasone

value: oxBS


title: pK27R_1_H3-3

tag: cell line

value: Knockout with K27R mutant addback_clone1


title: GR1-2 Con 204221240032_R01C01


title: C4-2-tet-shRB-Dox30d-Veh_rep1

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRBDOX1M_GTCCGC_L001


title: GR1-18 DEX 204221240031_R02C01

description:
GR1-18 DEX
glioma patients treated with Dexamethasone


title: GR1-18 DEX 204221240031_R01C01


title: GR2-2 DEX 204221240032_R05C01


title: pK27WT_2_H3-3

value: Knockout with wildtype addback_clone2


title: C4-2-tet-shRB-Dox3d-DHT_rep2

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRBDOX3DDHT_CCGTCC_L002

value: 0.05ug/ml doxycycline for 3 days, then treat 10nM dihydrotestosterone (DHT) for 24 hours


title: GR1-18 Con 204221240031_R08C01

description:
GR1-18 Con
glioma patients treated without Dexamethasone

value: IlluminaHumanMethylationEPIC


title: pK27WT_1_H3-3

value: Knockout with wildtype addback_clone1


title: GR1-18 Con 204221240031_R07C01

value: BS


title: C4-2-tet-shRB-Dox3d-DHT_rep1

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRBDOX3DDHT_CCGTCC_L001

value: prostate cancer cell line


title: H3-3KO_H3-3

value: H3.3 Knockout


title: LNCaP-Veh_rep1

description:
LNCaP_samples_count_table.txt.gz
LNVEH_CGATGT_L001

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)

value: LNCaP

value: untreated


title: GR2-18 DEX 204221240068_R03C01

value: Zymo Quick-DNA Miniprep Plus


title: C4-2-tet-shRB-Dox3d-Veh_rep2

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRBDOX3D_ATGTCA_L002

value: In RPMI 1640 medium with reduced steroid hormone [8% charcoal-stripped FBS (CSS) plus 2% regular FBS]

value: 0.05ug/ml doxycycline for 3 days


title: WT_HCT116

value: colorectal cancer cell line


title: GR2-18 Con 204221240043_R06C01


title: NPWT-1 [miRNA]

first: Yunshu

last: Yang

state: Shaanxi

address: Changle West Road

institute: Air Force Medical University

data_processing:
RNA-Seq
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
Unmapped reads were collected to identify the circRNA utilizing ACFS
count counting
miRNA-Seq
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 33bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to mature miRNAs with annotation from miRBase(v.21).
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: dermal wound tissues

growth_protocol: A third-degree scald of 2 cm diameter was generated on the shaved back of each mouse using water vapor by continuous scalding for 4 s; the wound occupied approximately 6–8% of the body surface area. Subsequently, 50 μl of fluorescently labeled P. aeruginosa (1.0 × 106 colony-forming units/ml) was inoculated onto the eschar. When the bacteria solution was completely absorbed, the mice were allowed to recover.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: The wounds were covered with polyurethane foam and blocked with a biologic semi-permeable membrane. In the NPWT group, the wounds were subjected to NPWT with continuous negative pressure suction of –120 mmHg. In the control group, the wounds were cleaned with a sterile saline solution, and the dressing was changed once every 24 h. Tissue samples were collected on days 3.

value: dermal wound tissues

tag: protocol

value: negative pressure wound therapy

tag: strain

tag: age

value: Eight- to twelve-week-old


title: NPWT-2 [miRNA]


title: C4-2-tet-shRB-Dox3d-Veh_rep1

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRBDOX3D_ATGTCA_L001

tag: cell type


title: Control-1 [miRNA]

value: control


title: Control-2 [miRNA]


title: C4-2-tet-shRB-DHT_rep2

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRBDHT_AGTTCC_L002

value: 10nM dihydrotestosterone (DHT) for 24 hours


title: Day 21 GVHD CD4 T cells scTCR-seq

city: Milwaukee

first: Clint

middle: T

last: Piper

state: WI

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

description: scTCR-seq

data_processing:
Reads were aligned to mouse reference genome mm10
Matrix files were generated using Cell Ranger (10x Genomics).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: Colon T cells

extract_protocol:
At 21 days post transplantation, cells were extracted from the colons of 5 mice using a lamina propria dissociation kit (Miltyeni).  Cells from all colons were pooled and donor T cells (H2-Kb+, TCR-B+) were FACS-sorted.  Following sorting, cells were kept on ice and immediately processed for single cell RNA sequencing.
Libraries for transcriptome sequencing were constructed using 10x Chromium v2 5' reagents using standard protocols. Libraries for TCR sequencing were prepared from the same cDNA used in transcriptome sequencing using nested PCR as described in the associated publication.

treatment_protocol: Lethally irradiated Balb/c mice underwent transplantation with B6 bone marrow (5*10^6 cells) and splenocytes (adjusted to yield an alpha beta T cell dose of 8x10^5 cells)

value: C57BL/6 donor mouse, Balb/c recipient mouse

tag: time point

value: 21 days post transplantation

value: Colon


title: Day 21 GVHD CD4 T cells scRNA-seq

description: scRNA-seq


title: C4-2-tet-shRB-Veh_rep2

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRB_AGTCAA_L002

value: prostate cancer cell line


title: BATF_KO_mILC2_Rep2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10 using Bowtie2.
Reads were then filtered using SAMtools (-F1796).
Peaks were called using MACS2 (--no model --shift -100 --ext size 200 -q 0.01) (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

extract_protocol:
ATAC-seq was performed according to a published protocol (Buenrostro et al., 2015) with minor modification.
ATAC-seq was performed according to a published protocol (Buenrostro et al., 2015) with minor modification.

treatment_protocol: mILC2s were sorted from the lungs of Batffl/fl ERT2CreRosamTmG mice and cultured in vitro in RPMI-1640 medium (Invitrogen) with 10% heat-inactivated FBS, 100 U/mL penicillin, 0.1 mg/mL streptomycin, 50 μM 2-mercaptoethanol, 10 ng/mL of IL-2, 10 ng/mL of IL-7, and 0.04 ng/mL of 4-Hydroxytamoxifen (4-OHT) for conditional inactivation of Batf. Two days after 4-OHT treatment, IL-33 (10 ng/mL) was added for expansion and cells were cultured continuously in the presence of 4-OHT. After 6-7 days expansion, cells were collected and stained with the indicated antibodies for flow cytometry analysis, or GFP- and GFP+ ILC2s were FACS sorted to perform ATAC-sequence analysis.

value: small intestine


title: BATF_KO_mILC2_Rep1


title: ABE_7_10_H3-3

value: mESCs

value: Millipore (Catalog 09-838, Lot:3310680)

value: Wildtype


title: WT_mILC2_Rep1


title: V5-C4-2-tetE2F1K185R-Dox-GSK_rep2

city: Boston

description:
V5_C42_E2F1_K185R_siRB_GSK.bw
V5_C42_E2F1_K185R_siRB_GSK_peaks.narrowPeak.gz

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.9a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS2 (version 2.1.0) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 369).
Genome_build: hg19
Supplementary_files_format_and_content: bw, narrowPeak

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)

value: 0.25ug/ml doxycycline for 3 days, then treat 50uM GSK2879552 for 24 hours

value: anti-V5 (Thermo Scientific)


title: C4-2-tet-shRB-DHT_rep1

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRBDHT_AGTTCC_L001

value: In RPMI 1640 medium with reduced steroid hormone [8% charcoal-stripped FBS (CSS) plus 2% regular FBS]


title: C4-2-tet-shRB-Veh_rep1

description:
C42shRB_Dox_DHT_count_table.txt.gz
C42SHRB_AGTCAA_L001

value: untreated


title: WT_mILC2_Rep2


title: V5-C4-2-tetE2F1K185R-Dox-GSK_rep1


title: V5-C4-2-tetE2F1K185R-GSK_rep2

description:
V5_C42_E2F1_K185R_siNTC_GSK.bw
V5_C42_E2F1_K185R_siNTC_GSK_peaks.narrowPeak.gz

value: 50uM GSK2879552 for 24 hours


title: scRNAseq_Day10_Lung_ILC

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: ILC

extract_protocol: 10x Genomics

treatment_protocol: Pulmonary ILCs were FACS-sorted from influenza-infected mice on day 5 and day 10 post infection and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles)

value: C57BL/6 mice

tag: infection

value: influenza A/PR8/34

value: Lung


title: scRNAseq_Day5_Lung_ILC