title: Serum_control_rep2

city: Guangzhou

first: Shengli

address: No.58, Zhong Shan Er Lu.

department: Department of Spine Surgery

institute: The First Affiliated Hospital of Sun Yat-sen University

description: Circulting miRNA profiles of participants whose bone mineral density T-score > –2.5 (dual energy X-ray absorptiometry)

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity ＞ 10.0 pmol Cy3/μg cRNA) was fragmented at 60℃ for 30 minutes in a reaction volume of 22.5 μl containing 1 × Agilent fragmentation buffer and 2 × Agilent blocking agent following the manufacturers’ instructions. On completion of the fragmentation reaction, 22.5 μl of 2 × Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA Mircoarray (8 × 60K) for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 4 × 180K array slides (Scan Area 61 × 21.6 mm, Scan resolution 3 μm, Dye channel is set to Green and Green PMT is set to 100％)

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as “Detected” were maintained.

source_name: Serum

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS Kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n: AM1556) following the manufacturer’s instructions.

treatment_protocol: All participants were unrelated ethnic Han Chinese women who resided in South China. The inclusion criteria of participants were as follows: (1) age ≥ 50 years; (2) menopausal duration ≥ 1 year; and (3) signed an informed consent form before study entry. The exclusion criteria of participants were as follows: (1) any comorbidity that could significantly affect bone metabolism, e.g., thyroid disease, diabetes, cancer, kidney disease, or ankylosing spondylitis; (2) previous treatment with anti-osteoporosis drugs or hormones, e.g., estrogen or glucocorticoids; and (3) a history of tobacco smoking or alcohol dependence within the last year.

value: postmenopausal without osteoporosis

tag: menopausal duration


title: FFPE prostate_cancer_primary_7

status: Public on May 01 2022

type: RNA

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

country: USA

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

growth_protocol: Not Applicable

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

treatment_protocol: Not Applicable

tag: primary gleason

tag: secondary gleason

tag: pre-treatment psa (ng/ml)

tag: age

tag: race

value: Caucasian

tag: randomization arm

value: Placebo

tag: ecog3805 id


title: Serum_control_rep3

last: Zhao

state: Guangdong

country: China

tag: disease state


title: FFPE prostate_cancer_primary_9

value: Treatment


title: Orai1fl/fl Cd4Cre OTII CD4+ T Cells, Influenza A, rep 3

type: SRA

city: New York

first: Stefan

last: Feske

state: NY

address: 550 First Avenue

institute: New York University School of Medicine

library_source: transcriptomic

data_processing:
Reads-per-sample FASTQ files were generated using the bcl2fastq2 Conversion software (v2.20)
Adaptor sequences were trimmed using the Trimmomatic (v0.39) tool
Sequenced reads were mapped to the mm10 reference genome using STAR aligner (v.2.7.3a)
The read count matrix for the genomic features were generated using the R package Subread (Bioconductor v2.0.0).
The DESeq2 package (Bioconductor v3.10) was used for differential gene expression analysis among groups of samples with 3 replicates each and for principal component analysis (PCA).
Genome_build: mm10
Supplementary_files_format_and_content: TXT and CSV files containing the raw read counts matrix and filtered reads count for TPM < 5, respectively, for all features across all samples.

molecule: polyA RNA

organism: Mus musculus

source_name: FACS sorted CD4+ T cells

growth_protocol: N/A (ex vivo isolated CD4+ T cells were analyzed without cell culture)

extract_protocol:
RNA was extracted using the Quiagen MicroRNAeasy kit with Dnase I digestion
Automated Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat. No. RS-122-2101) was used with 100ng of input RNA for the construction of sequencing libraries

tag: strain

tag: cell type

value: CD4+ T cells

tag: genotype

value: Orai1fl/fl Cd4Cre OTII

tag: stress

value: Influenza A


title: Orai1fl/fl Cd4Cre OTII CD4+ T Cells, Influenza A, rep 2


title: Orai1fl/fl Cd4Cre OTII CD4+ T Cells, Influenza A, rep 1


title: Serum_patient_rep5

description: Circulting miRNA profiles of patients whose bone mineral density T-score ≤ –2.5 (dual energy X-ray absorptiometry)

value: postmenopausal osteoporosis


title: Serum_control_rep4


title: Serum_patient_rep6


title: Serum_control_rep1


title: CD45(-) cells from pancreatic cancer, run 3 [5_GEX_6]

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
raw base call files were demultiplexed with cellranger (v 3.1.0) pipeline
reads were aligned to the GRCh38-3.0.0 genome assembly using cellranger (v. 3.1.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix output from cellranger (v 3.1.0)

source_name: CD45(-) cells from pancreatic cancer

growth_protocol: Non-immune cells were sorted from single-cell suspensions obtained from pancreatic cancer tumor tissues by ARIA sorter

extract_protocol:
RNA was extracted from cells using 10x chromium single cell 5' V1.1 (Next GEM)
Chromium Next GEM Single Cell 5’ library v1.1 (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions
Single index kit T set A from 10x chromium single cell 5' V1.1 (Next GEM)

treatment_protocol: Untreated

tag: tissue

value: pancreas

value: CD45(-) cells

tag: tissue type

value: pancreatic cancer tumor tissue


title: FFPE prostate_cancer_primary_6


title: FFPE prostate_cancer_primary_8


title: CD45(-) cells from pancreatic cancer, run 2 [5_GEX_5]


title: WT OTII CD4+ T Cells, Influenza A, rep 3

value: WT OTII


title: FFPE prostate_cancer_primary_5


title: FFPE prostate_cancer_primary_4


title: WT OTII CD4+ T Cells, Influenza A, rep 2


title: Serum_patient_rep4


title: FFPE prostate_cancer_primary_3


title: Serum_patient_rep3


title: WT OTII CD4+ T Cells, Influenza A, rep 1


title: ChOR-seq_H1KO_T0_rep1

city: Beijing

first: Yu

last: Juan

address: 15 Datun Road, Chaoyang District

institute: Chinese Academy of Sciences

library_source: genomic

data_processing:
Library strategy: ChOR-seq
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS . Reads were normalized with fly reference as previous study
ChOR-seq: all sequencing data were mapped to the Mus musculus genome assembly (mm9) and D. melanogaster genome assembly (dm6) using bowtie2, with the default parameters. Low quality reads and PCR duplicates were removed by samtools and only uniquely mapped reads which mapping to a unique genomic location and strand were kept. Reads were normalized with fly reference as previous study. The enriched regions (peaks) were detected using MACS.
RNA-seq: the pair-end RNA-seq reads were mapped to the Mus musculus mm9 gene annotation model using Subread (Liao et al., 2013) with the default parameters, and the only uniquely mapped reads were used for further analysis. The differential expression between samples was performed with featureCounts (Liao et al., 2014) and R package DESeq2
Genome_build: mm9, dm6
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bedgraph
Supplementary_files_format_and_content: normalized counts

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.

extract_protocol:
Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
H3K27me3,V5-H1e Libraries(sample 6-21) were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.

value: mouse embryonic stem cells

tag: chip antibody


title: LTC34: IPF_02

city: Pittsburgh

first: Melanie

last: Königshoff

state: Pennsylvania

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing:
Following sequencing, the generation of count matrices was performed by using the Cellranger computational pipeline (v3.1.0, STAR v2.5.3a). The reads were aligned to the hg38 human reference genome (GRCh38.97)
Downstream analysis was performed using the Scanpy package (v1.8.0). The quality of the libraries were assessed and cropped away barcodes with either less than 400 genes detected and retained those with number of transcripts between 1000 to maximal 20 000. removed cells with high proportion (> 15%) of transcript counts derived from mitochondria-encoded genes were further removed. Genes were only considered if they were expressed in at least 3 cells in the data set.
R library SoupX was perfermed to mitigate effects of background mRNA contamination.
R library SoupX was perfermed to mitigate effects of background mRNA contamination. The contamination fraction was manually to 0.3.
The expression matrices were normalized with scran’s size factor based approach and log transformed via scanpy’s pp.log1p() function.
Genome_build: GRCh38.97
Supplementary_files_format_and_content: h5 file with annotated data; mtx/tsv file with raw counts

source_name: lung

extract_protocol:
Human lung tissue (IPF/age-matched donors, each n=3) was homogenized and 4 g of tissue were digested by dispase/collagenase (Collagenase: 0.1U/mL, Dispase: 0.8U/mL, Roche) for 1 hour at 37°C. Samples were successively filtered through nylon filters (100 µm and 20 µm) followed by a percoll gradient and MACS sorting with CD45 Microbeads (Miltenyi Biotec). Cells were stained with APC anti-human EpCAM antibody (Biolegend) and DAPI (ThermoFisher Scientific) and subjected to FACS.
Epcam+/DAPI- live single epithelial cell Single-cell suspensions were loaded onto a Chromium single cell chip (Chromium™ Single Cell 3' Reagent Kit, v2 Chemistry) to obtain single cell 3’ libraries for sequencing. cDNA obtained after droplet reverse transcription was amplified for 14 cycles and qualitied using Agilent Bioanalyzer. The barcoded libraries were sequenced using Illumina NovaSeq 6000HiSeq 4000 (Illumina, San Diego, CA, USA) aiming for 100,000 reads per cell and capturing 10,000 per library.

value: IPF

tag: Sex

value: male

value: lung


title: CD45(-) cells from pancreatic cancer, run 1 [5_GEX_4]


title: Orai1fl/fl Cd4Cre OTII CD4+ T Cells, HDM Asthma, rep 3

value: HDM Asthma


title: LTC52: IPF_03

value: female


title: Orai1fl/fl Cd4Cre OTII CD4+ T Cells, HDM Asthma, rep 2


title: HepG2 rep3

city: Shanghai

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

data_processing:
Raw reads were filtered by FastQC v0.11.8 and TrimGalore v0.6.2.
The clean reads were then mapped to Human genome (GRCh38) by STAR v2.6.1a.
Stringtie was used to calculate gene abundance.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM for each Sample ...

extract_protocol:
Total RNA was obtained from cells by standard TRIzol reagent (Invitrogen, 15596-018). cDNA was synthesized from 1000 ng total RNA in a 20 μl reaction using cDNA synthesis kit (11706, Accurate Biology) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: liver cancer cells

value: WT


title: HepG2 rep2


title: Serum_patient_rep2

tag: menopausal duration


title: LTC22: IPF_01


title: Retina, HIOP

city: NanChang

first: Lei

last: Shang

state: JiangXi

address: Donghu District Bayi Road #463

department: Affiliated Eye Hospital of Nanchang University

institute: NanChang University

data_processing:
Reference genome and gene model annotation files were downloaded from Ensembl.
Reads were mapped to Rattus genome (Rattus_norvegicus.Rnor_6.0.dna.toplevel) using STAR (2.5.4b) with --outFilterMultimapNmax 1 --quantMode GeneCounts --twopassMode Basic.
Counts were calculated using STAR with --quantMode GeneCounts. TPM values were calculated using RSEM (1.3.1) with --strandedness reverse.
Genome_build: Ensembl Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include count and TPM values for each Sample

organism: Rattus norvegicus

source_name: Retina

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Firstly, ribosomal RNA was removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA- depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: The rats were anesthetized with 10% chloral hydrate (0.2 ml/kg). A drop of chloramphenicol was administered to the conjunctive sac, and a 30-gauge needle connected to an instillation instrument filled with normal saline was inserted into the anterior chamber. The intraocular pressure (IOP) was elevated to 110 mmHg, maintained for 60 min, and then gradually lowered to normal. The rats were then allowed to survive for 12 hours before terminal use. For the sham surgery group, the needle was inserted into the anterior chamber without elevating the pressure (2.66 kPa), and rats were sacrificed after 12h. For GSK treatment group, the drug was inject into anterior chamber for 24h before retinal ischemia.

value: Sprague-Dawley

value: retina

value: post natal day 60

tag: treatment

value: Post retinal ischemia 12hr


title: Serum_patient_rep1

value: postmenopausal osteoporosis


title: Retina, HIOP_GSK

value: GSK treatment for 24hr before ischemia


title: Retina, CTL

value: Without treatment


title: mut_ind_rep3 [s11_mut_ind_3]

city: Ramat-Gan

first: Ilana

last: Lebenthal-Loinger

address: Bar-Ilan University

department: The Mina & Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

data_processing:
Reads were aligned to Pseudomonas aeruginosa 39016 strain  (refseq sequnces ID: NZ_CM001020) using the bowtie2 aligner software (version bowtie2-2.3.2) with default parameters.
Raw read counts for 6469  gene-level features were determined using HTSeq-count with the intersection-strict mode.
Normalized read counts were generated using  R Bioconductor package DESeq2
Genome_build: Assembly GCF_000148745.1 (refseq sequnces ID: NZ_CM001020)
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalized counts

organism: Pseudomonas aeruginosa 39016

source_name: prrA mutant strain with treatment

growth_protocol: Bacterial ON cultures were dilluted X100 and grown in M9+CA medium untill reaching the OD of 0.5 (595 nm)

extract_protocol:
Each sample was taken and incubated  with RNAprotect Bacteria Reagent (Qiagen). After incubation, the bacteria were centrifuged  and rinsed in Tris-EDTA buffer solution. Lysozyme (Roche),  Proteinase K (Qiagen), and  warm Tri-reagent 37°C (Sigma) were added to pelleted cells. After incubation at 65°C,  Chloroform was added. The solution was centrifuged  and the upper liquid phase was transferred into 80% ethanol. The RNA was then extracted using an RNeasy Mini Kit (Qiagen)
The library was constructed with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer instructions using 30 ng of depleted RNA.

treatment_protocol: 0.4mM of Norfloxacin was added to the treated samples. all the cultures were incubated for an additional 1 hour

tag: genotype/variation

value: prrA mutant

value: treated with 0.4mM Norfloxacin


title: HepG2 rep1


title: LTC50: Control_02

value: Healthy

tag: age


title: WT OTII CD4+ T Cells, HDM Asthma, rep 3

value: CD4+ T cells

value: WT OTII


title: WT OTII CD4+ T Cells, HDM Asthma, rep 2


title: RNA-seq_PANC1_2

first: hebing

last: chen

address: taiping road 27

institute: Institute of Health Service  and Transfusion Medicine

description: RNA-seq

data_processing:
Clean reads were mapped to the Homo Sapiens genome (hg19) using Bowtie2 (v2.3.4). An optimized and flexible pipeline filtered out unmapped, multi-mapped, or invalid paired-end reads by Hi-C Pro. Only uniquely valid paired-end reads were retained for analyses. The interaction matrices at various resolutions (i.e., with the genome partitioned into bins of different sizes were constructed using HiC-Pro software (v2.7.1) with default settings. Hi-C interaction matrices were constructed with bin sizes of 1mb,100kb,40kb,20kb,10kb,5kb at the genome-wide level following the methods of HiC-Pro software (v2.7.1) with default settings. Briefly, we utilized an improved computational efficiency ICE (Iterative Correction) method to remove potential Hi-C interaction bias. The genome-wide Hi-C resolutions were calculated based on the interaction maps according to previously published definitions.
We used NGMLR (https://github.com/philres/ngmlr) to do the Alignment with default parameters.  We used sniffles to find out structure variation by using default parameters and identify cancer-specific structure variation by BEDTools
Reads were aligned against the hg19 reference genome using HISAT2 with default parameters (v2.1.0), and the expression level of each gene was normalized by the method developed by Traver Hart which is based on the fragments per kilobase per million mapped fragments (FPKM) values
Genome_build: hg19
Supplementary_files_format_and_content: .hic
Supplementary_files_format_and_content: .vcf
Supplementary_files_format_and_content: fpkm.txt

source_name: human pancreatic carcinoma cells

growth_protocol: HPDE6-C7, PANC1 and BxPC3 were obtained from American Type Culture Collection (ATCC). All cell lines were cultured under recommended conditions (Furukawa, T. et al, Liu, N. et al).

extract_protocol: We used 40ml 2% formaldehyde solution to crosslink the tissue for 15mins at room temperature in vacuum. Then, we added 4.324ml 2.5M Gly to quench the cross-linking reaction. Remove the supernatant and tissues were in the precipitate. We kept the tissue in liquid nitrogen.  Tissues can be resuspended by 25ml extraction buffer (10 mM Tris-HCl at pH 8, 10 mM MgCl2,0.4 M sucrose, 0.1 mM phenylmethylsulfonyl fluoride [PMSF], 5 mM b-mercaptoethanol, and 13 protease inhibitor; Roche). Next filtered by miracloth (Calbiochem).  We then did the centrifugation at 4000rpm at 4℃ for 20mins. After that, resuspended the pellet by 1ml extraction II buffer (10 mM Tris-HCl pH8, 1% Triton X-100, 0.1mM PMSF, 0.25 M sucrose, 10mM MgCl2, 5mMb mercaptoethanol, 13 protease inhibitor). Later, the solution was centrifuged for 10 mins at 14000 rpm in 4℃. Resuspended the pellet by 300μl extraction buffer III (10mM Tris-HCl pH8, 1.7M sucrose, 2mM MgCl2, 1μL protease inhibitor, 0.1mM PMSF, 5mM b-mercaptoethanol, 0.15% Triton X-100). Afterwards, load another 300μl clean extraction buffer III and centrifuged at 14000rpm for 10mins. Removed the supernatant and then washed the pallet by 500ul ice-cold 1x CutSmart buffer, centrifuged at 2500g for 5mins each time. The remaining pallets were the nuclei. Hereafter, we used the restriction enzyme buffer to wash the pallet twice and moved to a safe-lock tube.  The next step has solubilized the chromatin with dilute SDS and incubated at 65℃ by 10mins. Then quenched SDS by Triton X-100 Overnight. Next, the nuclei were digested by 4 cutter restriction enzyme (400 units MboI) at 37℃ on a rocking platform. The next step was marked the DNA ends by biotin-14-dCTP and then did the blunt-end ligation between cross-linked fragments. Thus, the ligation enzyme could ligate the proximal chromatin DNA. We incubated the nuclear complexes with proteinase K at 65℃ and then the nuclear complexes were reversed cross-linked.  DNA was then purified by phenol-chloroform extraction. We used T4 DNA polymerase to remove the Biotin-C from non-ligated fragments. Next, we used sonication to shear the fragments to 200-600 base pairs and repair the fragments by the mixture of T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. Biotin-labeled DNA fragments were then enriched by streptavidin C1 magnetic beads. The Hi-C library from the beads was sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads.


title: RNA-seq_PANC1_3

description: RNA-seq


title: WT OTII CD4+ T Cells, HDM Asthma, rep 1


title: FFPE prostate_cancer_primary_2

tag: primary gleason

tag: secondary gleason

tag: pre-treatment psa (ng/ml)

tag: race

value: Caucasian

value: Treatment


title: mut_ind_rep2 [s11_mut_ind_2]


title: FoxP3 GFP+ lymph node - 7D after injury - TCR

city: Boston

first: James

last: Lederer

state: MA

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

description: 7D after injury TCR

data_processing:
Library strategy: TCR-seq
scRNA-seq reads were aligned to the mouse reference genome GRCm38 using Cell Ranger v3.1.0
Genome_build: GRCm38
Supplementary_files_format_and_content: cell ranger ".h5" file

source_name: lymph node

extract_protocol:
viable lymph node FoxP3 GFP+ cells were sorted from injured or uninjured Foxp3DTR mice at 7 days after injury. The sorted FoxP3 GFP+ cells were washed and resuspended in sorting buffer at a cell concentration of 1000 cells/µL. About 17,000 mouse cells were loaded onto a 10x Genomics ChromiumTM instrument (10x Genomics) according to the manufacturer’s recommendations.
The scRNAseq libraries were processed using ChromiumTM single cell 5’ library & gel bead kit (10x Genomics). Matched scTCRseq libraries were prepared using 2 µL of post cDNA amplification material and Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell. Quality controls for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The sequencing libraries for scRNAseq and scTCRseq were normalized to 4nM concentration and pooled using a volume ratio of 4:1. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform. The sequencing parameters were: Read 1 of 150bp, Read 2 of 150bp and Index 1 of 8bp.

value: FACS sorted viable lymph node FoxP3 GFP+ cells

tag: strain

value: Foxp3DTR (stock #01695.8)

tag: injury

value: 7D after injury


title: FFPE prostate_cancer_primary_1

tag: randomization arm

value: Placebo

tag: ecog3805 id


title: mut_ind_rep1 [s10_mut_ind_1]


title: mut_none_rep2 [s8_mut_none_2]

source_name: prrA mutant strain without treatment

value: untreated


title: RNA-seq_PANC1_1

description: RNA-seq


title: RNA-seq_HPDE6C7_3

description: RNA-seq

source_name: human pancreatic duct epithelial cells


title: FoxP3 GFP+ lymph node - uninjured - TCR

description: uninjured TCR

tag: cell type

value: uninjured


title: mut_none_rep3 [s9_mut_none_3]


title: FSHRdx2

city: Helsinki

first: Karolina

last: Lundin

address: Haartmaninkatu 8

department: Department of Obstetrics and Gynecology

country: Finland

institute: University of Helsinki

description:
Sample 2
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
filtered_normalized_data.csv.gz

data_processing:
Illumina NovaSeq 6000 was used for paired sequencing of the sample libraries resulting in R1 and R2 reads with lengths 28bp and 90bp respectively. The R1 read contains the 16bp cell barcodes and 12bp long UMIs, the R2 read contains the cDNA sequences for the mRNAs. 10x Genomics Cell Ranger v6.0.0 pipeline was used for filtering, barcode reading, alignment (against the human GRCh38 reference genome) and gene expression quantification. Cell Ranger aggr was then used to aggregate the gene expression data from the two samples into one experiment wide gene-cell barcode expression matrix.  This matrix was used in the downstream analyses using Seurat and Monocle3.
Genome_build: GRCh38
Supplementary_files_format_and_content: Final processed files from cell ranger aggr: barcodes.tsv.gz (Cellular Barcodes), features.tsv.gz (Gene names), matrix.mtx.gz (expression values in sparse matrix). The three files were read into and normalized in Seurat giving one gene expression matrix file (filtered_normalized_data.csv.gz)

source_name: FSHR expressing cells

growth_protocol: FSHR expressing cells were derived by differentiating 1.5 x10^6 hES cells on 0.5 ug/cm2 human Collagen I in DMEM/F12 + 2% B27 supplemented with 100 ng/ml Activin A +  5 uM CHIR-99021 + 10 uM Y-27632 for 24h, in 3 uM CHIR-99021 + 50 ng/ml BMP7 for 24 h, in 3 uM CHIR-99021 + 2 uM dorsomorphon for 48h and finally in plain DMEM/F12 + 2% B27 for 96h.

extract_protocol:
Cells were dissociated into single cell suspension using Trypsin-EDTA and TrypLE
Library preparations were done using the Chromium Next GEM Single Cell 3’Gene Expression version 3.1 Dual Index chemistry.

treatment_protocol: No treatment

value: ES-derived FSHR expressing cells

value: parental H9


title: LTC55: Control_03

tag: disease state

value: female

tag: tissue

value: lung


title: ChIP-seq_H1KO_H3K27me3_rep2

data_processing:
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS . Reads were normalized with fly reference as previous study
ChOR-seq: all sequencing data were mapped to the Mus musculus genome assembly (mm9) and D. melanogaster genome assembly (dm6) using bowtie2, with the default parameters. Low quality reads and PCR duplicates were removed by samtools and only uniquely mapped reads which mapping to a unique genomic location and strand were kept. Reads were normalized with fly reference as previous study. The enriched regions (peaks) were detected using MACS.
RNA-seq: the pair-end RNA-seq reads were mapped to the Mus musculus mm9 gene annotation model using Subread (Liao et al., 2013) with the default parameters, and the only uniquely mapped reads were used for further analysis. The differential expression between samples was performed with featureCounts (Liao et al., 2014) and R package DESeq2
Genome_build: mm9, dm6
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bedgraph
Supplementary_files_format_and_content: normalized counts

extract_protocol:
Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
H3K27me3,V5-H1e Libraries(sample 1-4, 5) were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.

value: mouse embryonic stem cells

tag: genotype

tag: chip antibody


title: mut_none_rep1 [s7_mut_none_1]

value: prrA mutant


title: RNA-seq_HPDE6C7_2

description: RNA-seq

tag: cell line


title: hCMEC1_RNA

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
For ATAC-seq results: Reads were mapped to the GRCh38 version of the human genome using Bowtie2 with default paired-end settings (Langmead and Salzberg, 2012). Mitochondrial reads, reads with a MAPQ < 10, and reads which did not align to the reference genome were removed using Samtools (version 1.13) (Danecek et al., 2021). Duplicated reads were then removed with Picard MarkDuplicates (Institute, 2019). Peak calling was carried out with MACS2 (callpeak  --nomodel –broad) (v2.2.7.1)(Zhang et al., 2008). Diffbind (version 3.2) (Ross-Innes et al., 2012; Stark R, 2011) was used to import peaksets (min.overlap= 0.66) into RStudio Server (version 1.4.1717, https://www.rstudio.com) using R (version 4.1 (Team, 4.1). dba.blacklist function was used to filter out peaks that overlap with the ENCODE blacklist. Consensus peaks were converted to mm10 using the liftOver tool available from the UCSC Genome Browser. A region was considered conserved if a minimum 0.95 ratio of bases remap. Selected regions were also examined using the ECR Browser (Ovcharenko et al., 2004) where the regions were analyzed using rVista 2.0 (Loots and Ovcharenko, 2004) in order to identify conserved transcription factor motifs. The TRANSFAC professional V10.2 vertebrate library was used with default parameters.
For RNA-seq results: Reads were first mapped to the human genome (GRCh38) using Salmon (version 1.5.1) (Patro et al., 2017). Transcript level quantification was then imported using txtimport (version 1.20.0) (Soneson et al., 2015) and analyzed using DESeq2 (Love et al., 2014). Genes were kept and considered actively expressed if they had more than 10 raw counts and >2 log2 fold change normalized expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig, bam and peak files for ATAC data. RNA-seq results contain sf abundance quantification file: Plain-text, tab-separated file with a single header line (which names all of the columns) that contains Name, Length, EffectiveLength, TPM and NumReads.

source_name: Brain microvascular cells

growth_protocol: Immortalized hCMEC/D3 (Millipore, SCC066) cells were grown to confluence using endothelial cell medium (ScienCell, #1001) on plates coated with Collagen Type I Rat Tail (Sigma-Aldrich, #C7661). Passages 4-6 were used for experiments.

extract_protocol:
RNA was extracted using Trizol reagent.
ATAC libraries were processed as previously described (Corces et al., 2017). The quality of purified DNA libraries was assessed using the Agilent High Sensitivity DNA kit (Agilent Technologies). Paired end, 2 x 75 bp sequencing was performed on an Illumina Nextseq 500 instrument. RNA from all samples was thawed and following confirmation of integrity and concentration using a Bioanalyzer, 100 ng was used for low-input library preparation using the NEBNext Ultra II RNA Library Prep kit for Illumina. The libraries were then quantified and sequenced using an Illumina NovaSeq 6000 at a depth of 20 million reads per sample.


title: RNA-seq_HPDE6C7_1

description: RNA-seq


title: Orai1fl/fl Cd4Cre OTII CD4+ T Cells, HDM Asthma, rep 1

value: Orai1fl/fl Cd4Cre OTII

tag: stress

value: HDM Asthma


title: wt_ind_rep3 [s6_wt_ind_3]

source_name: WT strain with treatment

tag: genotype/variation

value: wild type

tag: treatment

value: treated with 0.4mM Norfloxacin


title: LTC46: Control_01

value: Healthy

tag: Sex

value: male

tag: age


title: RNA-seq_BxPC3_3

description: RNA-seq

source_name: pancreatic cancer cells


title: FoxP3 GFP+ lymph node - 7D after injury - GEM

description: 7D after injury GEM

data_processing:
scRNA-seq reads were aligned to the mouse reference genome GRCm38 using Cell Ranger v3.1.0
Genome_build: GRCm38
Supplementary_files_format_and_content: cell ranger ".h5" file

value: FACS sorted viable lymph node FoxP3 GFP+ cells

value: Foxp3DTR (stock #01695.8)


title: FoxP3 GFP+ lymph node - uninjured - GEM

description: uninjured GEM


title: wt_none_rep3 [s4_wt_none_3]

source_name: WT strain without treatment


title: WT

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

description: 10x raw data contains cell barcode and UMI, cell barcode and UMI, cDNA reads

data_processing:
Chromium data was demultiplexed with cellranger mkfastq v3.0.1.
Gene-cell count matrix was generated by cellranger count v3.0.1 against Ensembl GRCm38.p5 reference genome.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Filtered count matrix from cellranger count is stored in three files: barcodes.tsv, features.tsv and matrix.mtx.

source_name: Hippocampus

extract_protocol:
Adult Wildttype hippocampal single cell suspensions were obtained by mechanical dissociation at 4°C and subsequent percoll-gradient centrifugation for debris and myealin removal. The sample loaded onto the 10x genomics chip is a pool of hippocampal cells from 3 adult mice.
10x Genomics Single Cell, V3

value: Brain

tag: developmental stage

value: 10 weeks old


title: FSHRdx1

description:
Sample 1
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
filtered_normalized_data.csv.gz


title: RNA-seq_BxPC3_1

description: RNA-seq


title: wt_none_rep2 [s3_wt_none_2]

value: untreated


title: RNA-seq Rad21-OE rep1

first: Wenxue

address: Yiheyuan Road

institute: Peking University

data_processing:
The raw sequences were cleaned using TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to human reference genome hg19 by STAR (v2.7.1a) with default parameter. All mapped bam files were converted to bigwig using bedtools (v2.24.0) (Quinlan, 2014). for visualization in IGV. High quality mapped reads were quantified using htseq -count (v0.11.3) (Anders et al., 2015). Differentially expressed genes were analyzed by DEseq2 (Love et al., 2014).
Hi-C data was processed by HiC-Pro (Servant et al., 2015). Briefly, reads were first aligned on the hg19 reference genome. Uniquely mapped reads were normalized using Iterative Correction and Eigenvector decomposition (ICE) and library size. For, compartment A/B analysis, HiTC (Servant et al., 2012) was used to visualize the interaction matrix and calculate the PC1 (at 150-kb resolution). And defining compartment switches by comparing the PC1 values between Rad-OE and control cell, using zero as PC1 cutoff. For TAD analysis, ICE-normalized 40-kb resolution matrices were used to detect TAD by script described by Crane et al. (https://github.com/dekkerlab/crane-nature-2015). Insulation scores were calculated for each 40-kb bin, and the valleys of insulation score curves were defined as TAD boundaries (Crane et al., 2015). CTCF annotation was generated by GENOVA (van der Weide et al., 2021). Aggregate TAD analysis was done by cooltools (v0.4.0) (Flyamer et al., 2020).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Hi-C interaction matrix

source_name: HeLa cells

growth_protocol: Human HeLa-S3 immortalized cell line (Catalog No. 30-2004) and human SK-BR-3 cell line (Catalog No. 30-2007) were grown at 37 °C with 5% CO2 in high-glucose DMEM (Gibco) contained 10% (v/v) fetal bovine serum (Gibco), 100 U/mL penicillin (Thermo Fisher), and 100 mg/mL streptomycin (Thermo Fisher).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN).
RNA sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina® (NEB England BioLabs). RNA-seq paired-end reads were sequenced on the Illumina NovaSeq 6000 platform.


title: hCMEC2_RNA


title: wt_none_rep1 [s2_wt_none_1]


title: Hi-C_PANC1_Lib2

description: HiC


title: Hi-C_PANC1_Lib3

description: HiC


title: RNA-seq_BxPC3_2

description: RNA-seq


title: wt_ind_rep1 [s1_wt_ind_1]


title: Scramble A549 cells

city: Edmonton

first: Evangelos

middle: D.

last: Michelakis

state: Alberta

department: Medicine

country: Canada

institute: University of Alberta

description: Gene Expression data from wild-type A549 cells

hyb_protocol: Following fragmentation, 10 ug of biotin-modified RNA were hybridized to the Affymetrix PrimeView Human Microarray in the Affymetrix GeneChip Hybridization Oven 645 set at 45 ˚C with 60 rpm for 16 h.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with the Transcriptome Analysis Console version 4.0.2 (TAC 4.0.2) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Scramble A549 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A549 cells were cultured in complete DMEM medium at 37˚C, 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: A549 cells were transfected with either a scramble or a CRMP2A siRNA. Following transfection, cells were allowed to grow for 72 hours before collection and RNA extraction.

tag: cells

value: NSCLC cells

tag: transfection

value: scramble


title: RNA-seq WT rep3

value: WT


title: RNA-seq WT rep2


title: RNA-seq Rad21-OE rep2


title: RNA-seq WT rep1


title: RNA-seq Rad21-OE rep3


title: Hi-C_PANC1_Lib1

description: HiC


title: OldTitan_5

city: Berlin

first: Anuroop

middle: Venkateswaran

last: Venkatasubramani

state: Berlin

address: Robert-Rössle-Straße 10

country: Germany

institute: MDC-Berlin

data_processing:
Read mapping of mouse tissue samples to the mouse genome (GRCm38) and counting of reads mapped to genes were performed using STAR v2.5.3a (Dobin and Gingeras, 2015) using parameters --quantMode GeneCounts and providing annotation –sjdbGTFfile Mus_musculus.GRCm38.97.gtf. Aligned reads were filtered for unmapped, multimapped and ambiguous reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-separated text file: read counts per gene

source_name: Liver

growth_protocol: The animals were maintained in a specific pathogen-free (SPF) environment with defined hygienic conditions at a temperature of 22.5±0.2°C, at least 40% humidity and a controlled light regime with a 12:12-h light-dark cycle. The mice were kept in Polysulfon-cages of 365 x 207 x 140 mm (H-Temp PSU, Type II L, Eurostandard, Tecniplast, Germany) and had free access to pellet concentrate and water. A standard breeding diet (SD) with 22% crude protein, 34% starch, 5% sugar, 4.5% crude fat, 3.9% crude fiber and 51.2% N free extracts (ssniff® M-Z autoclavable, Soest, Germany) were fed ad libitum.

extract_protocol:
50 mg of tissues were homogenized in Trizol (Thermo Fisher; cat. no. 15596026) and processed according to the manufacturer’s instructions. RNA concentration and A260/280 ratio was measured with NanoDrop, followed by Bioanalyzer using RNA pico assay kit using manufacturer’s protocol.
rRNA depletion was performed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) [NEB #E6310] and library preparation for RNA-sequencing was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina [NEB #E7760] following manufacturer’s protocol.

value: Liver

value: 19-21 weeks old

tag: selection

value: 45 years via weight-based breeding selection


title: Hi-C Rad21-OE

extract_protocol: The in situ Hi-C libraries was performed as previously described (Rao et al., 2014). Briefly, cells were grown to about 70%-80 % confluence, washed with PBS, fixed in 1% formaldehyde were suspended in Hi-C lysis buffer, to which 100 U MobI restriction enzyme (NEB, R0147) was added for overnight chromatin digestion. Free ends were labeled with biotin and then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500 bp and then biotinylated ligation junctions were recovered with streptavidin beads. Hi-C libraries were amplified using PCR and constructed according to the NEBnext library preparation protocol (NEB, E7335) and sequenced on the Illumina HiSeq X Ten platform.


title: OldTitan_4


title: CRMP2A siRNA A549 cells

description: Gene Expression data from CRMP2A KO A549 cells

source_name: CRMP2A siRNA A549 cells

value: CRMP2A siRNA


title: Wild-Type A549 cells

source_name: Wild-type A549 cells

growth_protocol: A549 cells (both cell types) were cultured in complete DMEM medium at 37˚C, 5% CO2.

treatment_protocol: Cells were allowed to grow for 2 passages before collection and RNA extraction. No treatments were applied.


title: RH41(48 hr) QC6352_3

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

description:
Rh41-QC6352-3
Rh41 cells treated with 200nM of QC6352 for 48hr biological replicate3

hyb_protocol: The WT Plus assay from Affymetrix fragments and labels 5.5 ug of ss-cDNA of which 2.3 ug is hybridized on the Clariom S human array with a constant temperature of 45° C for 16 hours while rotating at 60 rpm.

scan_protocol: The samples were the stained and washed using the Affymetrix Fluidics 450 stations and  recommended protocol. Then the Clariom Shuman arrays were then scanned by the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data from Affymetrix GeneChip arrays is acquired and analyzed using GeneChip Operating System (GCOS)

label: Biotin

label_protocol: The protocol used for the samples run on the Clariom S human arrays was the Whole Transcript Plus assay from Affymetrix.  The initial input of RNA was 125 ng.

growth_protocol: Rh30 or Rh41 cells were cultured in standard RMPI medium.

extract_protocol: RNA extraction by Rneasy kit (QIAGEN)

treatment_protocol: KDM4B shRNA knockdown or siKDM4C in Rh30 cells for 72hours.200nM QC6352 treatment of Rh30 or Rh41 cells for 48hours. Total RNA extracted for affymetrix analysis.

tag: tissue source

value: Rhabdomyosarcoma

value: 200nM of QC6352 for 48hr


title: CRMP2A KO A549 cells

source_name: CRMP2A KO A549 cells

value: CRMP2A KO


title: wt_ind_rep2 [s5_wt_ind_2]

value: wild type

value: treated with 0.4mM Norfloxacin


title: RH41(48 hr) QC6352_2

description:
Rh41-QC6352-2
Rh41 cells treated with 200nM of QC6352 for 48hr biological replicate2


title: F3_88

city: Hsinchu

first: Chia-Chan

last: Hsu

address: 101, Section2, Kuan-Fu Road

department: Institute of Biotechnology

country: Taiwan

institute: National Tsing Hua University

data_processing:
Illuminq Casava 1.8 was used for basecalling.
Sequenced reads were trimmed for sequence with adapter, N or low quality. Clean reads were mapped to GRCh38 using HISAT2.
The read numbers mapped to each gene was counted via featureCounts v 1.5.0-p3. Fragments Per Kilobase of transcript per Million (FPKM) was then calculated based on  the gene length and sequencing depth.
Genome_build: GRCh38
Supplementary_files_format_and_content: xls file contains raw count of each gene for every samples
Supplementary_files_format_and_content: The spreadsheet file with FPKM values for each gene and every samples

source_name: Lung; derived from metastatic site: liver

growth_protocol: NCI-H1688 cell line was subcultured evey 3 days and maintained in RPMI-1640 supplemented with 10% FBS, 2mM L-glutamine and 100U/ml Penicillin-Streptomycin.

extract_protocol:
Total RNAs were extracted using NucleoSpin RNA mini kit (#740955.5, MACHEREY-NAGEL) following the manufacturer's instruction.
Library construction was performed with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to Illumina's instruction.

treatment_protocol: Medium containing 0.1ug/ml Doxycycline was applied to NCI-H1688 to induce expression of shRNA for 48 hours.

value: Lung; derived from metastatic site:liver

value: SCLC


title: OldTitan_3


title: Hi-C_HPDE6C7_Lib3

description: HiC


title: Hi-C_BxPC3_Lib3

description: HiC


title: M3_88

value: shControl


title: Hi-C_HPDE6C7_Lib1

description: HiC


title: F2_88


title: M2_88


title: RH41(48 hr) QC6352_1

description:
Rh41-QC6352-1
Rh41 cells treated with 200nM of QC6352 for 48hr biological replicate1


title: YoungTitan_5

value: 11 weeks old


title: F1_88


title: Hi-C_BxPC3_Lib2

description: HiC


title: Hi-C_HPDE6C7_Lib2

description: HiC


title: Hi-C_BxPC3_Lib1

description: HiC


title: OldTitan_1


title: YoungTitan_4


title: RH41(48 hr) DMSO_3

description:
Rh41-DMSO-3
Rh41 cells treated with DMSO biological replicate3

source_name: Rh41 cells treated with DMSO

value: DMSO


title: Hi-C WT

last: Zhao


title: M1_88


title: OldTitan_2


title: RJLC18

first: Pengfei

last: Ma

address: Dongchuan Road 800

department: Renji Hospital

institute: School of Medicine, Shanghai Jiao Tong University

data_processing:
10X Genomics Cell Ranger 3.0 software was used for basecalling, cell count and matrix file.
batch effect correction with Combat.
Genome_build: hg38
Supplementary_files_format_and_content: lung_GGN_10x_raw_matrix.txt.gz file  with raw gene counts for every gene and every sample before batch effect correction with Combat.
Supplementary_files_format_and_content: lung_GGN_10x_combat_matrix.txt.gz file  with raw gene counts for every gene and every sample after batch effect correction with Combat.
Supplementary_files_format_and_content: lung_GGN_10x_barcode_cluster text file  with cell barcode and cluster information.

source_name: lung

extract_protocol:
Fresh tumors were cut into approximately 1 mm3 pieces in the RPMI-1640 medium (Gibico) with 10% fetal bovine serum (FBS; Gibico), and enzymatically digested with Liberase TL (0.1 mg/ml, Roche) and DNase I (0.02 mg/ml, Roche) for 30 mins on a rotor at 37°C. After filtered by 70 μm Cell-Strainer (BD) in the RPMI-1640 medium (Gibico), the suspended cells were centrifuged at 400 g for 5 min. After removing the supernatant, the pelleted cells were suspended in red blood cell lysis buffer (Invitrogen) and incubated on ice for 3 mins to lyse red blood cells. The cell pellets were re-suspended in PBS supplemented with 0.02% FBS after washing twice with PBS.
RNA libraries were prepared for sequencing using standard 10X Genomics protocols

value: lung tumor

tag: histology

value: IAC

tag: tumor stage

value: I A1


title: YoungTitan_3

value: Liver


title: RJLC17

value: I A2


title: FAC sorted GFP cells, 15 s Tg(fli1a:egfp), rep 2

city: Melbourne

first: Kelly

last: Smith

state: Victoria

address: Grattan Street

department: Department of Anatomy & Physiology

country: Australia

institute: The University of Melbourne

data_processing:
Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R
Library normalisation and differential expression analysis was performed using the limma package in R
Assembly: GRCz11
Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output

organism: Danio rerio

source_name: Endothelium

growth_protocol: Fish were allowed to lay eggs in a 30 minute window, fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage

extract_protocol:
Embryos were collected, deyolked, and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct-zol RNA MiniPrep kit (Zymo research)
2 ng of total RNA from each sample was used for the construction of sequencing libraries, libraries were prepared using the Smart-seq2 protocol as described by Picelli et al., 2014 (PMID:24385147)

value: Endothelium

tag: transgenic line

value: WT

value: 15 somite stage


title: YoungTitan_2

tag: tissue

value: 45 years via weight-based breeding selection


title: FAC sorted GFP cells, 15 s Tg(fli1a:egfp), rep 3

tag: genotype


title: YoungTitan_1


title: FAC sorted GFP cells, 15 s Tg(fli1a:egfp), rep 1


title: RH41(48 hr) DMSO_1

description:
Rh41-DMSO-1
Rh41 cells treated with DMSO biological replicate1

value: Rhabdomyosarcoma


title: YoungControl_5

value: Non-selected


title: RH41(48 hr) DMSO_2

description:
Rh41-DMSO-2
Rh41 cells treated with DMSO biological replicate2


title: RJLC15

value: AIS


title: RH30(48 hr) QC6352_3

description:
siRNA-KDM4C-2
Rh30 cells treated with 200nM of QC6352 for 48hr biological replicate3

value: 200nM of QC6352 for 48hr


title: YoungControl_3


title: YoungControl_4


title: RH30(48 hr) QC6352_2

description:
siRNA-KDM4C-1
Rh30 cells treated with 200nM of QC6352 for 48hr biological replicate2


title: FAC sorted GFP cells, 15 s Gt(endocard:egfp), rep 1

source_name: Endocardium

value: Endocardium

value: Gt(SAGFF27C); Tg(4xUAS:egfp)


title: RJLC14

value: MIA


title: RH30(48 hr) QC6352_1

description:
siRNA-control-2
Rh30 cells treated with 200nM of QC6352 for 48hr biological replicate1


title: RJLC13-2


title: YoungControl_2

value: 11 weeks old


title: RJLC16

value: lung tumor


title: MT-F7 rep3

city: Hohhot

first: wen

middle: qiang

last: xu

state: Inner Mongolia autonomous region

address: Yuquan District

institute: Inner Mongolia University

data_processing:
The RNA sequencing library was prepared using Illumina’s NEBNext® UltraTM RNA Library Prep Kit (NEB, USA) according to the manufacturer’s protocols.
the library quality was assessed and 150 bp paired-end reads were generated by Illumina sequencing.
The image data from the sequenced fragments was processed through a high-throughput sequencer and converted into sequence data in the fastq format (reads).
High quality data was obtained after filtering. The reference genome and gene model annotation files were downloaded from the open genome website (Ensembl).
Hisat2 v2.0.5. software  (http://daehwankimlab.github.io/hisat2/) was used to build the index of the reference genome. The clean paired end reads were aligned to the reference genome. The read numbers mapping to each gene were calculated using the Feature Counts v1.5.0-p3 software. TMM (Trimmed Mean of M-values) was employed to standardize the counting data of the reads. EdgeR was used to analyze the differentially Expressed genes (DEGs). P-values were adjusted for the false discovery rate (FDR). The genes with fold changes greater than 1 and P-value < 0.05 were marked as differentially expressed. Cluster Profiler was used for Gene Ontology (GO) and KEGG enrichment analysis of differentially expressed genes. The RNA-seq data was converted into TPM and used for analysis of relative gene expression.
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: Pluripotent stem cells

extract_protocol:
The dissociated cells were placed in a 100-mm gelatin-coated petri dish for 25 minutes. The floating cells were collected for RNA-seq experiments.Total RNA was extracted by the Arcturus™ PicoPure™ RNA Isolation Kit (Applied Biosystems by Thermo Fisher Scientific, Lithuania) according to the provided procedure. NanoDrop 2000c Spectrophotometer (Thermo Fisher Scientific) was exploited to determine the quality and quantity of RNA. 1 mg of total RNA and the PrimeScript™ RT Reagent Kit with gDNA Eraser (Takara) were applied to reverse transcription and cDNA synthesis. The RNA sequencing library was prepared using Illumina’s NEBNext® UltraTM RNA Library Prep Kit (NEB, USA) according to the manufacturer’s protocols.
The sequencing library was prepared using Illumina’s NEBNext UltraTM RNA Library Prep Kit (NEB, USA) according to the manufacturer’s protocols.

tag: breed

value: Holstein Friesian

tag: cell type

value: Pluripotent stem cells from IVF

tag: cultured on

value: MT-MEFs


title: YoungControl_1

value: Liver


title: MT-F7 rep2

tag: cell line


title: OldControl_5

value: 19-21 weeks old


title: RH30(48 hr) DMSO_2

description:
Rh30-QC6352-3
Rh30 cells treated with DMSO biological replicate2

source_name: Rh30 cells treated with DMSO

tag: treatment

value: DMSO


title: FAC sorted GFP cells, 15 s Gt(endocard:egfp), rep 2

value: WT

value: 15 somite stage


title: RH30(48 hr) DMSO_3

description:
siRNA-control-1
Rh30 cells treated with DMSO biological replicate3

value: Rhabdomyosarcoma


title: RJLC12

value: IAC

value: I A2


title: RJLC11

value: I A1


title: 1M-F7 rep3


title: RJLC13-1


title: RH30 (72 hr) siRNA_KDM4C_1

description:
Rh30-DMSO-3
Rh30 transduced with siKDM4C  for 72h biological replicate 1

source_name: Rh30 transduced with siKDM4C  for 72h

value: siKDM4C  for 72h


title: RH30 (72 hr) shRNA_KDM4C_2

description:
Rh30-QC6352-1
Rh30 transduced with siKDM4C  for 72h biological replicate 2


title: FAC sorted GFP cells, 15 s Gt(endocard:egfp), rep 3

value: Endocardium

value: Gt(SAGFF27C); Tg(4xUAS:egfp)


title: RH30(48 hr) DMSO_1

description:
Rh30-QC6352-2
Rh30 cells treated with DMSO biological replicate1


title: 1M-F7 rep2


title: OldControl_3

value: Non-selected


title: MT-F7 rep1


title: OldControl_4


title: 1M-F7 rep1


title: RJLC8

value: lung tumor

value: MIA


title: RJLC10


title: RJLC9


title: OldControl_2


title: Macro 3

status: Public on Apr 29 2022

city: Saint Louis

first: Christopher

middle: A

last: Miller

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St Louis

data_processing:
We used Partek® Flow® software, version 7.0 (Partek) to analyze all RNA sequencing data
Reads were aligned to the mm10 mouse reference genome by STAR (v. 2.5.3a) and normalized CPM values were determined using Partek E/M (mm10 Ensembl Transcripts release 88).
Assembly: mm10
Supplementary files format and content: CPM normaliized RNA expression in an excel spreadsheet

source_name: bone marrow

extract_protocol:
Bone marrow from Cx3Cr1gfp/+ mice was collected and the following cell populations flow sorted: 1) DCs: CX3CR1-GFPhigh MHCIIhigh CD11chigh Gr-1- B220- cells; 2) macrophages: CX3CR1-GFP- MHCIIhigh CD169+ Gr-1- B220- cells; and 3) monocytes: CX3CR1-GFPhigh CD115+, B220- (both Gr1-low and -high) cells.  RNA was purified  using the Qiagen RNeasy Micro Kit (74004, Qiagen).
Libraries were generated using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) based on manufacturer’s protocol

value: bone marrow

value: Macrophages

value: Baseline


title: DC2 PAM3

value: Dendritic cells

value: Treated with PAM3CSK4


title: DC2 CTRL

value: Treated with vehicle alone


title: Macro 2


title: DC1 PAM3


title: Macro 1


title: DC4 CTRL


title: RH30 (72 hr) siRNA_Ctrl_2

description:
Rh30-DMSO-2
Rh30 transduced with siRNA control for 72h biological replicate 2

value: siRNA control for 72h


title: Mono 3

value: Monocytes


title: RH30 (72 hr) shRNA_KDM4B_2

description:
sh-kdm4b-2
Rh30 transduced with KDM4B shRNA  for 72h biological replicate 2

value: Rhabdomyosarcoma

value: KDM4B shRNA  for 72h


title: OldControl_1

value: Liver

value: 19-21 weeks old


title: DC4 PAM3


title: RH30 (72 hr) shRNA_Ctrl_2

description:
sh-Control-2
Rh30 transduced with shRNA control for 72h biological replicate 2

value: shRNA control for 72h


title: RH30 (72 hr) siRNA_Ctrl_1

description:
Rh30-DMSO-1
Rh30 transduced with siRNA control for 72h biological replicate 1


title: DC3 PAM3


title: ZL_4w

status: Public on Apr 27 2022

first: Ning

last: Yu

state: Shanghai

address: Baode Road 1278

institute: Shanghai Skin Disease Hospital

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
The read counts of each gene were obtained by htseq-count.
Supplementary files format and content: tab-delimited text files include gene read count for Samples in processed_data.txt

source_name: Blood

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Blood

tag: disease status

value: Psoriasis vulgaris

value: Peripheral blood mononuclear cell (PBMC)

tag: time point

value: week 4

value: guselkumab


title: ZL_0w

value: week 0


title: RH30 (72 hr) shRNA_Ctrl_1

description:
sh-Control-1
Rh30 transduced with shRNA control for 72h biological replicate 1


title: DC3 CTRL

value: bone marrow


title: DC1 CTRL

value: Dendritic cells


title: Mono 2

value: Baseline


title: RH30 (72 hr) shRNA_KDM4B_1

description:
sh-kdm4b-1
Rh30 transduced with KDM4B shRNA  for 72h biological replicate 1


title: XYC_4w


title: Mono 1


title: WWZ_4w


title: SYJ_0w


title: WWZ_0w


title: WJJ_4w


title: XJ_0w


title: SYJ_4w


title: WJJ_0w


title: GWL_4w


title: LLZ_4w


title: LSX_4w


title: PLY_4w


title: XJ_4w


title: LSX_0w


title: PLY_0w


title: WYZ_0w


title: XYC_0w


title: HF_0w


title: KO_CSPG_D

status: Public on Apr 25 2022

city: Vienna

first: Vanja

last: Nagy

address: Lazarettgasse 14

country: Austria

institute: LBI-RUD

data_processing:
Galaxy DESeq2
Assembly: mm10
Supplementary files format and content: Galaxy DESeq2 output file for each sample compiled into one tab-delimited file

source_name: hippocampus

extract_protocol:
Qiagen RNeasy Mini Kit following manufacturer's protocol
NEBNext Ultra RNA library prep kit, following manufacturer's protocl

value: hippocampus

value: neuron

value: fibcd1 -/-

value: Stimulation with CSPG


title: KO_CSPG_B


title: KO_CSPG_C


title: HF_4w


title: LLZ_0w


title: KO_C


title: KO_CSPG_A


title: KO_D


title: KO_A


title: WT_CSPG_E

value: wt


title: KO_B


title: GWL_0w


title: WYZ_4w


title: WT_CSPG_B


title: WT_D


title: WT_B


title: WT_CSPG_D


title: WT_CSPG_C


title: WT_CSPG_A


title: WT_E


title: 6perACSH Xylose Rep 1

status: Public on Apr 24 2022

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

data_processing:
For RNA-seq analysis, the paired-end FASTQ files were were trimmed using Trimmomatic version 0.3 with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3,  SLIDINGWINDOW of 3:30, and MINLEN of 36. After trimming the reads were aligned to the Z. mobilis (ZM4, 8b) genome using BWA-mem version 0.7.12-r1039 with default settings. Aligned reads were mapped to gene locations using HTSeq version 0.6.0 using default settings. Raw sequencing reads were normalized using the reads per kilobase per million mapped reads (RPKM).
Assembly: GCA_003052025.1
Supplementary files format and content: Zhang_RPKM_data.txt - RPKM normalized read count values from RNA-seq, linear format
Supplementary files format and content: Zhang_RawCounts_data.txt - Raw read count values from RNA-seq, linear format

organism: Zymomonas mobilis

source_name: bacteria

growth_protocol: Z. mobilis was grown in bioreactors as described in Yang, S., et al., Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. Biotechnol Biofuels, 2018. 11: p. 125.

extract_protocol:
RNA was extracted from cultures using a phenol-chloroform method as described in Rhodius, V.A. and C.A. Gross, Using DNA microarrays to assay part function. Methods Enzymol, 2011. 497: p. 75-113.
Illumina Low Input RNASeq w/rRNA Depletion: rRNA was removed from 100 ng of total RNA using Ribo-Zero rRNA Removal Kit (Illumina). Stranded cDNA libraries were generated using the Illumina Truseq Stranded mRNA Library Prep kit. The rRNA depleted RNA was fragmented and reversed transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with end-pair, A-tailing, adapter ligation, and 10 cycles of PCR. The prepared library was quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. The quantified library was then multiplexed with other libraries, and the pool of libraries was then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v4, and Illumina’s cBot instrument to generate a clustered flow cell for sequencing. Sequencing of the flow cell was performed on the Illumina HiSeq 2500 sequencer using HiSeq TruSeq SBS sequencing kits, v4, following a 2x100 indexed run recipe.

treatment_protocol: Samples for RNA-seq were collected by mixing 10 mL of culture with 1.25 mL ice-cold unbuffered phenol and ethanol mixture (5:95, vol/vol) as described in chwalbach, M.S., et al., Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen. Appl Environ Microbiol, 2012. 78(9): p. 3442-57.

tag: strain

value: Z. mobilis 2032

value: bacteria

value: 6perACSH Xylose


title: WT_C


title: WT_A


title: 6perACSH Xylose Rep 2


title: 6perACSH Xylose Rep 4


title: 6perACSH Xylose Rep 3


title: heart_517s_N21

status: Public on Apr 21 2022

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the mouse reference genome (GRCm38 / mm10) using TapHat2, Bowtie1 or Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the sample-plates were combined into one expression matrix file
counts data was processed and analyzed using SingleCellExperiment, pagoda2 and monocle packages in R-software
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

source_name: male mouse

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse heart in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using standard SmartSeq2 protocol

value: heart

tag: age

value: 10-20 weeks

tag: Sex

value: male

tag: mouse id


title: heart_517s_N12


title: heart_517s_N23


title: heart_517s_M8


title: heart_517s_O22


title: heart_517s_M7


title: heart_517s_N16


title: heart_517s_M19


title: heart_517s_M13


title: heart_517s_N14


title: heart_517s_M18


title: heart_517s_M15


title: heart_517s_M3


title: heart_517s_L8


title: heart_517s_L3


title: heart_517s_L24


title: heart_517s_K14


title: heart_517s_K24


title: heart_517s_K12


title: heart_517s_K2


title: heart_517s_L17


title: heart_517s_K18


title: heart_517s_L1


title: heart_517s_J22


title: heart_517s_J19


title: heart_517s_J15


title: heart_517s_J11


title: heart_517s_J13


title: heart_517s_F7


title: heart_517s_E19


title: heart_517s_D7


title: heart_517s_D3


title: heart_517s_F16


title: heart_517s_D6


title: heart_517s_E10


title: heart_517s_G14


title: heart_517s_D24


title: heart_517s_D4


title: heart_517s_D21


title: heart_517s_D23


title: heart_517s_D8


title: heart_517s_G7


title: heart_517s_E11


title: heart_517s_D19


title: heart_517s_D22


title: heart_517s_C24


title: heart_517s_D17


title: heart_517s_C20


title: heart_517s_C19


title: heart_517s_C17


title: heart_517s_C18


title: heart_517s_C11


title: heart_517s_D18


title: heart_517s_D16


title: heart_517s_D15


title: heart_517s_C14


title: heart_517s_C13


title: heart_517s_D1


title: heart_517s_C23


title: heart_517s_D14


title: heart_517s_D5


title: heart_517s_D13


title: heart_517s_D11


title: heart_517s_D10


title: heart_517s_D20


title: heart_517s_C22


title: heart_517s_C21


title: heart_517s_C8


title: heart_517s_C9


title: heart_517s_C10


title: heart_517s_C12


title: heart_517s_B22


title: heart_517s_B9


title: heart_517s_B19


title: heart_517s_B8


title: heart_517s_B24


title: heart_517s_B7


title: heart_517s_B14


title: heart_517s_B17


title: heart_517s_B4


title: heart_517s_B16


title: heart_517s_C1


title: heart_517s_B5


title: heart_517s_B3


title: heart_517s_C16


title: heart_517s_B13


title: heart_517s_B6


title: heart_517s_B20


title: heart_517s_A9


title: heart_517s_B12


title: heart_517s_B11


title: heart_517s_B23


title: heart_517s_B1


title: heart_517s_B10


title: heart_517s_B18


title: heart_517s_A5


title: heart_517s_A7


title: heart_517s_B21


title: heart_517s_A8


title: heart_517s_A2


title: heart_517s_A6


title: heart_517s_B2


title: heart_517s_A19


title: heart_517s_A18


title: heart_517s_A20


title: heart_517s_A13


title: heart_517s_A15


title: heart_517s_A24


title: heart_517s_A14


title: heart_316s_P7


title: heart_320s_C4

value: PdgfrbGFP


title: heart_320s_P6


title: heart_320s_O1


title: heart_316s_P8


title: heart_320s_G24


title: heart_517s_A11


title: heart_517s_A10


title: heart_316s_P2


title: heart_316s_P5


title: heart_316s_P12


title: heart_316s_N17


title: heart_316s_M17


title: heart_316s_J22


title: heart_316s_M4


title: heart_316s_P17


title: heart_316s_K15


title: heart_316s_I19


title: heart_316s_I15


title: heart_316s_J2


title: heart_316s_J19


title: heart_316s_I6


title: heart_316s_K22


title: heart_316s_G19


title: heart_316s_I10


title: heart_316s_G15


title: heart_316s_F22


title: heart_316s_H17


title: heart_316s_O10


title: heart_316s_E21


title: heart_316s_E17


title: heart_316s_C9


title: heart_316s_C5


title: heart_316s_C7


title: heart_316s_C8


title: heart_316s_D23


title: heart_316s_C6


title: heart_316s_C3


title: heart_316s_C22


title: heart_316s_C23


title: heart_316s_C24


title: heart_316s_C21


title: heart_316s_C20


title: heart_316s_C2


title: heart_316s_C17


title: heart_316s_C19


title: heart_316s_C11


title: heart_316s_C12


title: heart_316s_C14


title: heart_316s_C16


title: heart_316s_B3


title: heart_316s_C10


title: heart_316s_B7


title: heart_316s_B8


title: heart_316s_B24


title: heart_316s_B22


title: heart_316s_B23


title: heart_316s_B21


title: heart_316s_B20


title: heart_316s_B18


title: heart_316s_B19


title: heart_316s_C1


title: heart_316s_B15


title: heart_316s_C18


title: heart_316s_C15


title: heart_316s_B10


title: heart_316s_A9


title: heart_316s_B12


title: heart_316s_A8


title: heart_316s_C13


title: heart_316s_A7


title: heart_316s_A3


title: heart_316s_A5


title: heart_316s_A24


title: heart_316s_A21


title: heart_316s_B2


title: heart_316s_A23


title: heart_316s_A20


title: heart_316s_A16


title: heart_316s_A17


title: heart_316s_A19


title: heart_316s_A18


title: heart_316s_B14


title: heart_316s_A15


title: heart_316s_A14


title: heart_316s_A1


title: heart_316s_B13


title: heart_316s_A12


title: heart_316s_A13


title: heart_316s_A11


title: heart_316s_A10


title: heart_204s_P9


title: heart_204s_P3


title: heart_204s_P6


title: heart_204s_P24


title: heart_204s_P5


title: heart_204s_P19


title: heart_204s_P21


title: heart_204s_P18


title: heart_316s_A2


title: heart_204s_P11


title: heart_204s_P1


title: heart_204s_P12


title: heart_204s_P17


title: heart_204s_O8


title: heart_204s_O5


title: heart_204s_O9


title: heart_204s_P10


title: heart_204s_O20


title: heart_204s_O6


title: heart_204s_O18


title: heart_204s_O17


title: heart_204s_P4


title: heart_204s_O22


title: heart_204s_O2


title: heart_204s_O4


title: heart_204s_O16


title: heart_204s_O15


title: heart_204s_P15


title: heart_204s_O21


title: heart_204s_O13


title: heart_204s_N9


title: heart_204s_O1


title: heart_204s_O7


title: heart_204s_O19


title: heart_204s_O11


title: heart_204s_N5


title: heart_204s_N23


title: heart_204s_N3


title: heart_204s_O14


title: heart_204s_N22


title: heart_204s_O12


title: heart_204s_N8


title: heart_204s_P14


title: heart_204s_N19


title: heart_204s_N17


title: heart_204s_N16


title: heart_204s_N15


title: heart_204s_N4


title: heart_204s_O10


title: heart_204s_N14


title: heart_204s_N7


title: heart_204s_N13


title: heart_204s_N18


title: heart_204s_N21


title: heart_204s_O3


title: heart_204s_N2


title: heart_204s_M4


title: heart_204s_M5


title: heart_204s_N12


title: heart_204s_M8


title: heart_204s_M19


title: heart_204s_M24


title: heart_204s_M15


title: heart_204s_N11


title: heart_204s_M6


title: heart_204s_M2


title: heart_204s_M14


title: heart_204s_M22


title: heart_204s_M17


title: heart_204s_M21


title: heart_204s_M13


title: heart_204s_M1


title: heart_204s_N1


title: heart_204s_M3


title: heart_204s_M18


title: heart_204s_L9


title: heart_204s_M11


title: heart_204s_L7


title: heart_204s_L8


title: heart_204s_L24


title: heart_204s_L23


title: heart_204s_M7


title: heart_204s_L6


title: heart_204s_L2


title: heart_204s_L22


title: heart_204s_L16


title: heart_204s_L5


title: heart_204s_L19


title: heart_204s_L18


title: heart_204s_L14


title: heart_204s_L11


title: heart_204s_L13


title: heart_204s_L10


title: heart_204s_K6


title: heart_204s_L3


title: heart_204s_K4


title: heart_204s_L17


title: heart_204s_K5


title: heart_204s_M23


title: heart_204s_M12


title: heart_204s_K8


title: heart_204s_L1


title: heart_204s_L15


title: heart_204s_K9


title: heart_204s_K3


title: heart_204s_K24


title: heart_204s_L21


title: heart_204s_K23


title: heart_204s_K22


title: heart_204s_L12


title: heart_204s_K21


title: heart_204s_J9


title: heart_204s_J19


title: heart_204s_K15


title: heart_204s_K18


title: heart_204s_K13


title: heart_204s_P8


title: heart_204s_J4


title: heart_204s_K11


title: heart_204s_J17


title: heart_204s_K19


title: heart_204s_K17


title: heart_204s_J3


title: heart_204s_K20


title: heart_204s_J13


title: heart_204s_J8


title: heart_204s_K16


title: heart_204s_K1


title: heart_204s_J20


title: heart_204s_J11


title: heart_204s_J6


title: heart_204s_J14


title: heart_204s_J16


title: heart_204s_K2


title: heart_204s_J2


title: heart_204s_J22


title: heart_204s_J15


title: heart_204s_J23


title: heart_204s_J7


title: heart_204s_J10


title: heart_204s_J1


title: heart_204s_I7


title: heart_204s_I6


title: heart_204s_I5


title: heart_204s_I22


title: heart_204s_I23


title: heart_204s_I20


title: heart_204s_I3


title: heart_204s_I17


title: heart_204s_I19


title: heart_204s_I13


title: heart_204s_I1


title: heart_204s_I2


title: heart_204s_I14


title: heart_204s_I15


title: heart_204s_H7


title: heart_204s_I4


title: heart_204s_H9


title: heart_204s_I11


title: heart_204s_H3


title: heart_204s_H4


title: heart_204s_H8


title: heart_204s_H6


title: heart_204s_I21


title: heart_204s_I10


title: heart_204s_H24


title: heart_204s_H23


title: heart_204s_I8


title: heart_204s_I12


title: heart_204s_I16


title: heart_204s_H5


title: heart_204s_H21


title: heart_204s_H12


title: heart_204s_H10


title: heart_204s_H1


title: heart_204s_H20


title: heart_204s_H19


title: heart_204s_H22


title: heart_204s_G5


title: heart_204s_H17


title: heart_204s_E5


title: heart_204s_G3


title: heart_204s_H15


title: heart_204s_H16


title: heart_204s_E4


title: heart_204s_H11


title: heart_204s_H2


title: heart_204s_G8


title: heart_204s_G21


title: heart_204s_G6


title: heart_204s_G9


title: heart_204s_G7


title: heart_204s_E18


title: heart_204s_E16


title: heart_204s_E19


title: heart_204s_H14


title: heart_204s_G23


title: heart_204s_E12


title: heart_204s_E24


title: heart_204s_E11


title: heart_204s_E20


title: heart_204s_E23


title: heart_204s_D6


title: heart_204s_G24


title: heart_204s_D5


title: heart_204s_G22


title: heart_204s_E14


title: heart_204s_E13


title: heart_204s_D3


title: heart_204s_D24


title: heart_204s_E2


title: heart_204s_E15


title: heart_204s_E17


title: heart_204s_E10


title: heart_204s_D8


title: heart_204s_D4


title: heart_204s_D15


title: heart_204s_E1


title: heart_204s_D20


title: heart_204s_D14


title: heart_204s_D17


title: heart_204s_D19


title: heart_204s_D9


title: heart_204s_D10


title: heart_204s_D16


title: heart_204s_D21


title: heart_204s_D1


title: heart_204s_D2


title: heart_204s_D13


title: heart_204s_C6


title: heart_204s_C4


title: heart_204s_D11


title: heart_204s_C21


title: heart_204s_C9


title: heart_204s_C7


title: heart_204s_C24


title: heart_204s_C3


title: heart_204s_D12


title: heart_204s_D18


title: heart_204s_C8


title: heart_204s_C22


title: heart_204s_C5


title: heart_204s_C20


title: heart_204s_C19


title: heart_204s_D23


title: heart_204s_C17


title: heart_204s_C10


title: heart_204s_C1


title: heart_204s_C11


title: heart_204s_B8


title: heart_204s_B9


title: heart_204s_B5


title: heart_204s_B7


title: heart_204s_C2


title: heart_204s_C23


title: heart_204s_B3


title: heart_204s_B20


title: heart_204s_C12


title: heart_204s_B19


title: heart_204s_B18


title: heart_204s_B16


title: heart_204s_C14


title: heart_204s_B23


title: heart_204s_C15


title: heart_204s_B22


title: heart_204s_B12


title: heart_204s_C18


title: heart_204s_A9


title: heart_204s_B21


title: heart_204s_B14


title: heart_204s_A7


title: heart_204s_B15


title: heart_204s_A8


title: heart_204s_B6


title: heart_204s_B17


title: heart_204s_C13


title: heart_204s_A24


title: heart_204s_B4


title: heart_204s_C16


title: heart_204s_B13


title: heart_204s_A6


title: heart_204s_B11


title: heart_204s_A18


title: heart_204s_A5


title: heart_204s_A3


title: heart_204s_A10


title: heart_204s_A16


title: heart_204s_A17


title: heart_204s_A15


title: heart_204s_A4


title: heart_204s_A23


title: heart_203s_J2


title: heart_203s_G20


title: heart_204s_A11


title: heart_204s_B10


title: P10STZn6S1

status: Public on Apr 20 2022

city: Cambridge

first: Wenjun

last: Yan

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

description: JAX P10stz omega6 #3

data_processing:
For Nextseq 75 bp run, Read 1 (61 bp) is transcript
Index read 1 (8 bp): barcode 1
Index read 2 (8 bp): Library index
Read 2 (14 bp): 8 bp barcode 2 and 6bp UMI
The basecall files were demultiplexed through the Harvard BPF Genomics Core's pipeline. Reads were processed using the inDrop v3 pipeline implemented in bcbio-nextgen version 1.2.4-76d5c4b.  Briefly, dual cellular barcodes, sample barcodes and UMIs were detected using umis (Svensson et al., 2017). Cells with fewer than 500 total reads assigned to them were discarded. Reads were assigned to Mus musculus transcripts (GRCm38 (mm10) release M23) using Rapmap (Srivastava et al., 2016) and counts of reads per transcript per unique UMI were generated for each cell. The generated gene count matrix was used for subsequent analysis.
Assembly: Release M23 (GRCm38.p6)
Supplementary files format and content: Count matrix in the format of .csv

source_name: retina

extract_protocol:
Single-cell suspensions were prepared from mouse retinas by using Worthington papain dissociation system.
inDrop protocol

treatment_protocol: P10PBS and P10STZ mice were littermates. P10stz omega3 and P10stz omega6 were littermates and split into 2 cages with nursing dams fed on either omega3- or omega6 enriched diets

value: retina

tag: condition

value: hyperglycemia-assoicated retinopathy

value: STZ, omega6

value: postnatal day 10


title: P10STZn6S2

description: JAX P10 omega6 #4


title: P10STZS1

description: P10STZ #4

value: STZ


title: P10STZn3S1

description: JAX P10stz omega3 #1

value: STZ, omega3


title: P10STZn6S3

description: JAX P10 omega6 #5


title: P10PBSS3

description: P10 PBS #3

value: control, normal condition

value: PBS


title: P10PBSS2

description: P10 PBS #2


title: P10PBSS1

description: P10 PBS #1


title: heart_204s_A13


title: P10STZS3

description: P10STZ #6


title: CON1

status: Public on Apr 18 2022

city: Shanghai

value: Blood

value: Healthy donor

value: Normal-density neutrophil (NDN)


title: NDN4

value: Generalized pustular psoriasis (GPP)


title: LDN4

value: Low-density neutrophil (NDN)


title: CON3


title: NDN2


title: LDN1


title: NDN1


title: P10STZS2

description: P10STZ #5


title: LDN3


title: P10STZn3S2

description: JAX P10stz omega3 #2


title: LDN2


title: NDN3


title: CON2


title: Normal, Early tumors, and Late tumors 2

status: Public on Apr 06 2022

first: Jonathan

middle: M

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Raw sequencing data were demultiplexed, aligned to the mouse genome mm10 using bcbio-nextgen single-cell RNA-seq pipeline (https://bcbio-nextgen.readthedocs.io/en/latest/).
We select cells by removing small outliers of library size and feature number, and large outliers of mitochondrial genes using a median absolute deviation (MAD)-based threshold of 2, 3 and 4 respectively.
Genome_build: mm10
Supplementary_files_format_and_content: CSV table of counts

source_name: brain

extract_protocol:
Mice were perfused with 10ml PBS, brain was harvested, and cerebellum removed. Brain was minced and resuspended in 1.5mg/ml Collagenase in HBSS with calcium and magnesium. Mixture was incubated rotating at 37°C for 30 minutes, with gentle dissociation using a P1000 pipette halfway through to break apart large pieces. Dissociated cell mixture is filtered through a 100μm filter and diluted with HBSS. All washes are pelleted at 400g for 5min. Mixture is resuspended in 30% Percoll in PBS for myelin removal at 700g for 15min with brake on low. Myelin layer is removed, and mixture is diluted and pelleted at 400g for 5min. Red blood cells are lysed using Biolegend RBC lysis buffer according to manufacturer protocol. sample was stained with CD45 and Zombie Yellow fixable viability dye. Cells were washed with RNAse free PBS with 0.1% BSA and immediately sorted on a FACs Aria Cell Sorter for viable CD45+ and CD45- populations into ice cold RNAse free PBS with 0.1% BSA. A minimum of 1 million CD45+ and CD45- cells were harvested when possible to account for the low capture rate of InDrop system.
Cells were then filtered through a 70um filter before being given to the Harvard Medical School Single Cell Sequencing core where they were run on the InDrop system with the goal of encapsulating 10k cells per sample. Following encapsulation, the reverse transcription reaction was performed, and libraries were made, full protocol has been described previously. As per core recommendation, 4 libraries per 10k cells were made. Following harvest of all three samples, libraries were sequenced using the NextSeq system with 16 libraries per sequencing run, so that the depth of sequencing was calculated to be 25,000 genes per cell.

tag: sorting


title: Normal, Early tumors, and Late tumors 1


title: Liver, CDE, 3 weeks, replicate 3

status: Public on Apr 12 2022

city: Bentley

first: Rodrigo

last: Carlessi

state: WA

address: Kent St

department: Curtin Medical School

institute: Curtin University

description: 10x Genomics 3’v3

data_processing:
BCL files were demultiplexed and converted into FASTQ using bcl2fastq utility of Illumina BaseSpace Sequence Hub. FASTQ files were processed using Cell Ranger 3.0.2. Both intronic and exonic reads were counted towards gene expression using a custom pre-mRNA reference built as described in (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.0/advanced/references#premrna) from mm10-2.1.0 Cell Ranger reference.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Hepatic nuclei were isolated from flash frozen liver chunks. Briefly, tissue samples were cut into pieces of approximately 25 mg and immediately homogenized using a Kimble Dounce tissue grinder (Sigma-Aldrich, D8938) by performing 15 strokes with pestle A in 2 mL of ice-cold nuclei lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL ® CA-630). Then, another 2 mL of nuclei lysis buffer were added to each sample and lysis proceeded on ice for 10 min followed by straining the lysates through 40 µm cell strainers (Falcon, Corning). Lysates were centrifuged at 500 g for 5 min at 4°C and resuspended in 4 mL of nuclei wash buffer (PBS supplemented with 1% BSA and 0.2U/µL RNasin® Plus Ribonuclease Inhibitor (Promega, N2615). Following another round of centrifugation, nuclei were resuspended in 700 µL of nuclei wash buffer, stained with 4’,6-Diamidine-2’-phenylindole dihydrochloride (DAPI) at 0.1 µg/mL and propidium iodide (PI) at 2.5 µg/mL. Nuclei preparations were strained through 70 µm cell strainers prior to fluorescence-activated cell sorting (FACS) sorting with a two-laser configuration (488nm 80mW and 640nm 50mW) BD FACSJazz™ stream-in-air cell sorter (BD Biosciences), equipped with a 100 µm nozzle operating at a sheath pressure of 27 psi. Machine calibration was performed by flow cytometry facility staff before each sort using Sphero™ 8-peak rainbow calibration beads (BioLegend) to achieve optimal stream alignment, laser alignment and target mean fluorescence intensities for each detector. The drop delay was determined by setting a value that resulted in total side-stream deflection of Accudrop Beads (BD Biosciences) sorted through a 640nm 5mW laser that bisected center and side streams. Nuclei were identified through an initial FSC-H/SSC-H gate, followed by the discrimination of single events exhibiting proportional FSC-W/FSC-H profiles. Within single events, nuclei were identified as PI positive events. Two peaks of PI-positive events were visualized corresponding to 2n and 4n nuclei; both peaks were pooled together for sorting and downstream 10x Genomics analysis to maintain hepatic cell representation unaltered. 50,000 PI-positive events were sorted per sample, then post-sort nuclei concentration and quality were checked using a fluorescence microscope and hemocytometer.
For the construction of snRNA-seq libraries, 10x Genomics Chromium Single Cell 3’v3 Reagent Kits were used according to manufacturer’s instructions. 10,000 freshly sorted nuclei were loaded onto a 10x Genomics Chromium Single Cell 3ʹ v3 chip B and processed immediately in a 10x Chromium controller. Specifically, we utilized 19 PCR cycles for cDNA amplification. Libraries were quantified with qPCR using the NEBnext Library Quant Kit for Illumina and fragment size assessed with TapeStation D1000 kit (Agilent). Libraries were pooled in equimolar concentration and sequenced using an Illumina NovaSeq 6000 and S2 flow cells (100 cycle kit) with a read one length of 28 cycles, and a read two length of 94 cycles.
snRNA-seq

treatment_protocol: Six-week-old male C57BL/6J mice were housed in individually ventilated cages and kept on 12-hour light/dark cycles. Mice were randomly grouped into three experimental groups (healthy, CDE and TAA). Healthy animals received normal chow and drinking water ad libitum; CDE animals received a choline-deficient diet with drinking water that contained 0.15% dl-ethionine; and TAA mice received normal chow with water that contained 300 mg/L of TAA. Animals were culled three weeks after the commencement of the protocol, liver was perfused with saline, harvested, and flash frozen with liquid nitrogen.

value: All liver cells

value: Liver

value: 9 weeks

value: CDE


title: Liver, healthy, 3 weeks, replicate 1

description: 10x Genomics 3’v3

value: healthy control


title: Liver, CDE, 3 weeks, replicate 1

description: 10x Genomics 3’v3


title: Liver, CDE, 3 weeks, replicate 2

description: 10x Genomics 3’v3


title: Liver, TAA, 3 weeks, replicate 2

description: 10x Genomics 3’v3

value: TAA


title: Liver, TAA, 3 weeks, replicate 3

description: 10x Genomics 3’v3


title: Liver, healthy, 3 weeks, replicate 2

description: 10x Genomics 3’v3


title: Liver, TAA, 3 weeks, replicate 1

description: 10x Genomics 3’v3


title: Liver, healthy, 3 weeks, replicate 3

description: 10x Genomics 3’v3


title: mpra_let-7a_rep2

status: Public on Mar 31 2022

first: Sean

middle: E.

last: McGeary

address: 455 Main St.

department: Biology

institute: Whitehead Institute / MIT

data_processing:
Each read was used if it satisfied the following criteria: 1) it passed the Illumina chastity filter, as indicated by the presence of the number 1 rather than 0 in the final position of the fastq header line, 2) it did not contain any “N” base calls, 3) it did not contain any positions with a Phred quality score (Q) of B or lower, 4) the sequenced 6-nt sample-multiplexing barcode associated with the read was identical to one of the barcodes used when generating the sequencing library, and 5) it did not match either strand of the phi-X genome.
Reads were queried against a list of the 120-nt sequences downstream of the sequencing-primer site in the reporter mRNA 3′ UTR, requiring a perfect match.
Counts were normalized to the total number of perfectly matching reads to obtain counts-per-million (cpm) values.
Genome_build: NA
Supplementary_files_format_and_content: A tab delimited text file containing the site-architecture information and the counts-per-million (cpm) values corresponding to the abundance within each of the 8 samples, for each of the 532 designed reporter variants.

growth_protocol: For each sample, 3 million F9 cells were plated in a 10 cm dish supplied with 10 mL of media (DMEM + 10% FBS) and grown for 24 hours.

extract_protocol:
RNA was extracted according to the methods.
Small RNA-seq libraries were prepared according to the methods.
small RNA-seq

treatment_protocol: After 24 h of culture, the cells were supplied with fresh media and were transfected with 5.8 µg of the plasmid library diluted with 28.9 µg of pUC19 carrier plasmid using Lipofectamine 2000 (Thermo Fisher, 11668019) and Opti-MEM (Thermo Fisher 31985062), and either let-7a duplex, let-7a-21nt duplex, miR-1 duplex, or no duplex (mock) at a final duplex concentration of 25 nM, according to the manufacturer’s protocol.

tag: miRNA

tag: rep


title: mpra_mock_rep2

value: mock


title: mpra_miR-1_rep2


title: mpra_miR-1_rep1


title: mpra_let-7a-21nt_rep1


title: mpra_let-7a-21nt_rep2


title: mpra_mock_rep1


title: HK-2 cells, CSE, t24h, control sample, rep2

status: Public on Mar 16 2022

city: Taipei

first: Yung-Li

last: Wang

address: 250 Wu-Hsing Street

institute: Graduate Institute of Clinical Medicine, Taipei Medical University

data_processing:
The original data obtained by high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format. FastQC and MultiQC were used to check fastq files for quality.
The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1) without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 (v1.22.1) with biological duplicate.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human kidney

growth_protocol: HK-2 cells were maintainedkept in Keratinocyte-serum-free medium (K-SFM) with bovine pituitary extract and human recombinant EGF (Invitrogen, CA), cultured at 37 °C/5% CO2

extract_protocol:
Total RNA was isolated using the EasyPrep Total RNA Kit (Cat:TB-DPT-BD19).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded 24 hours before treatment on 6-cm dish at a density of 6x10^5 cells per well with 4 ml of medium per dish. Cells were treated at ~90% confluency with the required doses for the required timepoints. Control cells were exposed to an appropriate concentration of the control vehicle.

value: immortalized human renal proximal tubular epithelial cells

value: untreated


title: HK-2 cells, CSE, t24h, control sample, rep1


title: boron application 2

status: Public on Mar 08 2022

city: 扬州

first: 东贺

last: 刘

address: wenhuilu

department: Yuanzhi College

institute: yzau

data_processing:
Illumina Novaseq 6000 platform used for basecalling.
Clean reads were obtained by removing adapters, high contents of unknown bases reads and low quality reads
Gene expression levels were estimated according to Fragments Per Kilobase of transcript sequence per Millions (FPKM)
The clean reads were mapped to the reference genome of Chinese white pear deposited in the NCBI database (ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Pyrus_x_bretschneideri/) using Hisat2
Genome_build: Pyrus x bretschneideri (assembly Pbr_v1.0)
Supplementary_files_format_and_content: Excel files include genes read count and FPKM values for each sample (.xls)

organism: Pyrus pyrifolia

source_name: Aikiba

growth_protocol: Akibae pear in the orchards of the Yangzhou University, Jiangsu Province, China

extract_protocol:
Total RNA was extracted by the Trizol Kit (Promega, USA) following the manufacturers instructions, using pulp collected from fruits.
RNA-Seq library was generated with NEB Next® UltraTM RNA Library Prep Kit for Illumina (NEB, USA) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Boron application treatment on the fruit, or control

value: boron application

tag: tissue

value: fruit


title: CK 2

value: CK


title: boron application 3


title: boron application 1


title: FSCN1_input_2

status: Public on Mar 05 2022

city: jilin

first: Hongfei

last: cai

address: No.1 Xinmin Street, Chaoyang District, Changchun City, Jilin Province

department: Ddepartment of Thoracic Surgery

institute: The First Hospital of Jilin University

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of FSCN1 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

growth_protocol: Eca-109 cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from FSCN1-RNA complexes and another for the western blotting assay for FSCN1 immunoprecipitation.The FSCN1-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

tag: antibody


title: CK 3


title: FSCN1_IP_1

value: FSCN1 monoclonal antibody


title: FSCN1_input_1


title: mpra_let-7a_rep1


title: Infected with Lso haplotype A, rep 2 [J4-2_S59]

status: Public on Feb 20 2022

city: College Station

first: Kyle

last: Harrison

address: 2475 TAMU

department: Entomology

institute: Texas A&M University

data_processing:
cDNA libraries were developed using the TruSeq RNA Library Prep Kit v2 following the manufacturer's protocol
Libraries were multiplexed and sequenced on the Illumina PE HiSeq 2500 v4 platform
Sequence cluster identification, quality prefiltering, base calling, and uncertainty assessment were done in real time using Illumina’s HCS 2.2.38 and RTA 1.18.61 software with default parameter settings
bioinformatic analysis was performed using the HISAT2-StringTie-Ballgown RNA-Seq workflow
Genome_build: Libraries reads were mapped to the S. lycopersicum genome (vSL3.0) using HISAT2; StringTie assembled hits to known transcripts based on the vITAG3.2 annotation
Supplementary_files_format_and_content: Matrix table with fpkm (Fragments Per Kilobase of transcript per Million mapped reads) values for every gene and every sample

organism: Solanum lycopersicum

source_name: leaf tissue

extract_protocol:
Plant RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf

tag: variety

value: Moneymaker

value: Infected with Lso haplotype A


title: HK-2 cells, CSE, t24h, control sample, rep3

tag: cell type


title: Infected with Lso haplotype A, rep 1 [J4-1_S58]


title: FSCN1_IP_2


title: Uninfested control, rep 2 [C2_S50]

value: Uninfested control


title: Infected with Lso haplotype A, rep 3 [J4-3_S60]


title: Infected with Lso-free psyllids, rep 3 [J1-3_S54]

value: Infected with Lso-free psyllids


title: Infected with Lso haplotype B, rep 2 [J3-2_S56]

value: Infected with Lso haplotype B


title: Infested with Lso-free psyllids, rep 1 [J1-1_S52]

value: 9 weeks

value: Infested with Lso-free psyllids


title: Infested with Lso-free psyllids, rep 2 [J1-2_S53]


title: 25B

status: Public on Feb 16 2022

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

data_processing:
trimomatic
gSNAP
cufflinks
R programming environment (ver 4.0.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files

source_name: vastus lateralis skeletal muscle biopsy

growth_protocol: Randomized cross-over treatment design of individuals who were seditary, had small bouts, or one continuous bout of moderate intensity walking

extract_protocol:
RNA was isolated using Trizol from Ambion according to instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
NuGEN universal Plus mRNA SEQ protocol part no. 9133

treatment_protocol: Interventions were given for 4-days and vastus lateralis skeltal muscle was biopsied

value: vastus lateralis skeletal muscle biopsy

value: ONE

tag: treatment id

value: B


title: 26B


title: 25A

value: SED

value: A


title: Uninfested control, rep 1 [C1_S49]


title: 18C

value: MICRO

value: C


title: 26C


title: Infected with Lso haplotype B, rep 3 [J3-3_S57]


title: 30B


title: 18A


title: 17C


title: CK 1

value: CK

value: fruit


title: Infected with Lso haplotype B, rep 1 [J3-1_S55]

value: leaf


title: 8B


title: 30C


title: Uninfested control, rep 3 [C5_S51]

value: Moneymaker


title: 18B


title: 25C


title: 17A