title: TDCIPP_H2AZ_CUTTag_Rep2

description:
TDCIPP_H2AZ_CUTTag_RPKM.bw
TDCIPP_versus_DMSO_H2AZ.diffbind_all_consensus_peak.txt

data_processing:
Library strategy: CUT&Tag
Sequencing reads were aligned to zebrafish genome (GRCz11) using Bowtie2, and then PCR duplicates were marked and removed using Picard
Peak calling was performed using MACS2 with the following parameters: -f BAMPE --nomodel -broad using bam files of triplicates
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Differential peaks were identified by DiffBind using H2A.Z broadPeak and associated bam files for each replicate with default setting, using cutoff threshold of adjusted p-value < 0.05 and absolute value of log2FC at 0.5.
Genome_build: Zv11
Supplementary_files_format_and_content: bigWig files and txt files

extract_protocol: Around 10,000 cells from 6hpf embryos were used for CUT&Tag and library construction according to standard methods. Polyclonal H2A.Z antibody from Active Motif (Cat. 39113) was used.

treatment_protocol: Newly fertilized eggs were collected immediately after spawning, and placed around 50 per well in a 6 well plate. Embryos were treated with 5 mL of 3.12uM TDCIPP (treatment starts from 2-cell stage at 0.75hpf), 100uM 5-AzaC (treatment starts from 1-cell stage), or with 0.1% DMSO for control group.

value: 5 mL of 3.12uM TDCIPP


title: 5AzaC_H2AZ_CUTTag_Rep3

status: Public on Oct 23 2023

type: SRA

city: Rochester

first: Fanju

last: Meng

state: NY

address: 601 Elmwood Avenue

department: Biomedical Genetics

country: USA

institute: University of Rochester Medical Center

description:
5AzaC_H2AZ_CUTTag_RPKM.bw
5AzaC_versus_DMSO_H2AZ.diffbind_all_consensus_peak.txt

library_source: genomic

molecule: genomic DNA

organism: Danio rerio

source_name: zebrafish embryos

growth_protocol: Adult wild type AB/Tuebingen zebrafish were maintained on a 14h:10h light:dark cycle

tag: developmental stage

value: 6hour post fertilization

tag: treatment

value: 100uM 5-AzaC


title: DMSO_H2AZ_CUTTag_Rep2

value: DMSO


title: DMSO_H2AZ_CUTTag_Rep1


title: DMSO_H2AZ_CUTTag_Rep3


title: 5AzaC_H2AZ_CUTTag_Rep2


title: 5AzaC_H2AZ_CUTTag_Rep1


title: TDCIPP_H2AZ_CUTTag_Rep1


title: BAT RW 7d-2

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to the mouse genome (NCBI Build 38) using GSNAP (Wu and Nacu, 2010) version ‘2013-10-10’, allowing a maximum of two mismatches per 50 base pair sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap’).
Lastly, gene expression levels were quantified by calculating the number of reads mapped to the exons of each RefSeq gene using the HTSeqGenie R package.
Transcript annotation was based on the RefSeq database NCBI Annotation Releases 104 for mouse.
Read counts were scaled by library size, quantile normalized and precision weights calculated using the “voom” R package (Law et al., 2014).
Differential expression analysis on the normalized count data was performed using the “limma” R package (Ritchie et al., 2015) by contrasting treated samples with control samples, respectively. Gene expression was considered significantly different across groups if we observed an |log2-fold change| ≥ 1 (estimated from the model coefficients) associated with an FDR adjusted P-value ≤ 0.05. In addition, gene expression was obtained in the form of normalized Reads Per Kilobase gene model per Million total reads (nRPKM) as described previously (Srinivasan et al., 2016).
Assembly: mouse genome (NCBI Build 38)
Supplementary files format and content: csv (count and fpkm matrix)

molecule: total RNA

organism: Mus musculus

source_name: Brown adipose tissue

extract_protocol:
Total RNA was extracted from  tissues with Trizol (Invitrogen) following the provider’s recommendations. After adding isopropanol, the samples were transferred into RNAeasy extraction column (Qiagen), washed and eluded following the manufacturer protocol.
The libraries were sequenced on Illumina HiSeq 4000 (Illumina). We obtained on average 40 million single-end RNA-seq reads (50bp) per sample.

treatment_protocol: Male C57BL/6 mice at 10-14 weeks of age were obtained from Jackson Laboratories (strain ID: 00664). Mice were injected intraperitoneally with a single dose of blocking antibodies diluted in PBS at the following concentrations: anti-ragweed isotype control (40MPK); anti-Jag1+anti-jag2 (20MPK each); anti-Notch1+ anti-Notch2 (5MPK, 10MPK) , anti-Notch1+ anti-Notch2+ anti-Notch3 (5MPK, 10MPK, 20MPK). Exogenous administration of thyroxine (T4) and 3-Iodotrionine (T3) was performed daily starting at day 2 of the antibody treatment with a dose 1ug/g BW of T4 and 0.05μg/g BW T3.

tag: tissue

value: Brown adipose tissue

tag: strain

tag: diagnostics

value: Normal

value: RW 7 days


title: iWAT, lymph nodes removal, Cold 7days,  rep3 [LN_5]

city: Chicago

first: Jooman

last: Park

state: IL

address: 909 S Wolcott Ave COMRB 1120

department: Dept. of Physiology and Biophysics

institute: University of Illinois at Chicago

data_processing:
Raw data (raw reads) in fastq format was firstly processed through in-house perl scripts. In this step, clean data (clean reads) was obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and generate a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly use method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression[6] analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR[7] without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: inguinal white adipose tissue

extract_protocol:
RNA was extracted using Tri-Zol method following manufacturer's protocol.
RNA library for RNA seq were prepared using NEBNext Ultra™ II RNA Library Prep Kit following manufacturer's protocol.

value: inguinal white adipose tissue

value: lymph nodes removal

value: Cold exposue


title: iWAT, Sham, Cold 7days, rep3 [Sham_3]

value: Sham


title: iWAT, Sham, Cold 7days, rep2 [Sham_2]


title: iWAT, lymph nodes removal, Cold 7days,  rep2 [LN_2]


title: iWAT, Sham, Cold 7days, rep1 [Sham_5]


title: iWAT, lymph nodes removal, Cold 7days,  rep1 [LN_1]


title: iWAT, Sham, Cold 7days, rep4 [Sham_4]


title: BAT RW 7d-1


title: BAT aJ1aJ2 5d-9

value: anti-Jag1 and anti-Jag2 antibodies 5 days


title: BAT aJ1aJ2 5d-10


title: Differentiated BeWo b30 cell, replicate 1

status: Public on Oct 24 2023

type: RNA

city: Hamilton

first: Sonya

last: Kouthouridis

state: ON

address: 1280 Main St W

department: Chemical Engineering

country: Canada

institute: McMaster University

description: Gene expression data from BeWo b30 cells cultured in expansion medium for 2 days and differentiation medium for 2 more days.

hyb_protocol: Samples were hybridized for 16 hr at 45°C using Affymetrix WT PLUS Kit.

scan_protocol: Affymetrix GeneChip™ 3000 instrument system

data_processing: SST-RMA gene-level probeset summary with standard settings of the Transcriptome Analysis Console (TAC; version 4.0.3; Thermo Fisher Scientific)

label: biotin

organism: Homo sapiens

source_name: trophoblast cell line monolayer cultured 4 days

label_protocol: Total RNA was amplified using the WT PLUS Reagent Kit (Thermo Fisher Scientific Inc., Waltham, USA).

growth_protocol: Blastocyst-derived placental stem cells (PSCs, RCB-4940, female) were cultured in PSC expansion medium (PSCM) consisting of DMEM/F12 + GlutaMAX supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% penicillin-streptomycin, 0.3% BSA, 1% ITS media supplement, 1.5 ug/ml L-ascorbic acid, 50 ng/ml EGF, 2 uM CHIR99021, 0.5 uM A83-01, 1 uM SB431542, 0.8 mM VPA and 5 uM Y27632 or PSC differentiation medium consisting of DMEM/F12 + GlutaMAX supplemented with 0.1 mM 2-mercaptoethanol, 0.5% penicillin-streptomycin, 0.3% BSA, 1% ITS media supplement, 2.5 uM Y27632, 2 uM forskolin, and 4% KSR. BeWo 30 cells were cultured in expansion medium consisting of DMEM supplemented with 10% FBS and 1% penicillin-streptomycin and then differentiation medium consisting of DMEM supplemented with 10% FBS, 1% penicillin-streptomycin, 50 uM forskolin and 50 ng/mL of EGF.

extract_protocol: Samples were lysed and RNA extraction was performed using the PurelinkTM RNA Mini kit (Thermo Fisher Scientific, 12183018A) following the manufacturer’s instructions.

treatment_protocol: Cells were cultured according to their expansion or differentiation protocols.

tag: cell type

value: BeWo b30

tag: culture medium type

value: Differentiation

tag: culture days

tag: seeding density


title: LEW2 - TLH - scRNAseq

city: Toronto

first: Delaram

last: Pouyabahar

address: 160 College St

department: Molecular Genetics

institute: University of Toronto

description: 10x Genomics Single Cell 3’ v2

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger 3.1.0 pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Rattus_norvegicus.custom_6.0.98-
Supplementary files format and content: Matrix files (.mtx)

molecule: polyA RNA

organism: Rattus norvegicus

source_name: liver

growth_protocol: The animals were co-housed in the Animal Research Center facility at Princess Margaret Research Tower and were fed a standard diet of sterilized water and laboratory blocks.

extract_protocol: Samples were prepared as outlined by the 10x Genomics Single Cell 3′ v2 Reagent Kit user guide. Briefly, the samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. Sample viability was assessed via Trypan Blue (Thermo Fisher) and using a haemocytometer (Thermo Fisher). Following counting, the appropriate volume for each sample was calculated for a target capture of 10,000 cells for TLH and 9000 cells for immune-enriched samples. Samples below the required cell concentration as defined by the user guide (i.e., <400 cells/µl) were pelleted and re-suspended in a reduced volume and counted again using a haemocytometer prior to loading onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen):cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′ Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).  The molarity of each library was calculated based on library size as measured using a bioanalyzer (Agilent Technologies) and qPCR amplification data (Kappa/Roche).  Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.1 N NaOH at equal volumes for 5 min at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 14 pM. 150 μl from the 14 pM pool was loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

value: liver

tag: cell dissociation

value: Total Liver Homogenate

value: Lewis

tag: Sex

value: M

tag: disease state

value: healthy


title: LSK ADT

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

library_source: other

data_processing:
The LSK CITE-Seq 10x Genomics library was sequenced at a depth 326 million and aligned to mouse genome (mm10), with unique molecular index quantified (UMI) gene counts obtained using the Cell Ranger workflow (version 3.1.0), considering both mRNAs and ADTs. Cell Ranger identified 12,391 filtered cell barcodes with >7,500 UMI per cell on average. Ambient RNAs were excluded in the mRNAs using SoupX and an ambient correction threshold of 10%. Using the default filtered cellular barcodes, the associated sparse-filtered SoupX corrected matrix files were converted to log 2 scaled normalized gene counts (counts per ten Thousand [CPTT] UMIs) using AltAnalyze’s Chromium Processing model and combined with ADT log2 scaled reads into a single flat matrix. This combined matrix was input to AltAnalyze and ICGS2 (Iterative Clustering and Guide-gene selection version 2). ICGS2 was run using the default options (cosine clustering) and exclusion with greater than 500 genes expressed (CPTT>1) per cell, were retained for further analysis (>90% of cell barcodes for all captures). This analysis autodetects ADTs with cell-barcode IDs in the name and forces the use of these ADTs as guide-genes in the iterative clustering analysis steps to prioritize markers for downstream sparse-NMF analysis.
Assembly: mm10
Supplementary files format and content: HDF5 sparse matrix RNA and ADT counts
Supplementary files format and content: CSV text file of ADT cell barcodes
Library strategy: CITE-Seq

molecule: other

source_name: Bone Marrow

extract_protocol:
20,000 LSK cells were sorted from a pool of four 2-months-old C57Bl/6J mice. The CITE-Seq protocol described in Muench et al. was applied to a LSK cells using a collection of 65 TotalSeq antibodies. For staining optimization, individual antibodies were titrated on ckit+ bone marrow cells by first conjugating the TotalSeq-A antibodies to an oligo-dT conjugated to Alexa Fluor 647 at a 1:1.5 molar ratio, before staining the cells at different dilutions. The prepared samples were washed and run on a BD LSRFortessa flow cytometer to determine optimal concentrations. For FACS-sorting total BM cells were collected from 3 C57/Bl6 male mice and enriched for ckit+ cells (Miltenyi). Cells were stained with fluorochrome-conjugated antibodies in staining buffer (1% FBS, PBS) for 30 minutes at 4C and washed three times in staining buffer at 4C. Cells were FACS-sorted and resuspended in 50uL of TotalSeq-A antibody cocktail for 30min at 4C and washed one time. Cells were resuspended at 1,000 cells/L, and 16,000 cells were loaded in 1 port of 10X Genomics Chromium Controller Instrument.
Genomics single-cell 3’ v3 assay protocol was performed according to manufacturer’s recommendation until the cDNA amplification step. The antibody derived tags (ADTs) were processed according to the CITE-Seq protocol detailed by BioLegend (Biolegend Inc, https://www.biolegend.com/en-us/protocols/totalseq-a-antibodies-and-cell-hashing-with-10x-single-cell-3-reagent-kit-v3-3-1-protocol).
The GEX library was generated following regular protocol of 10X Genomics. The final GEX library was sequenced at 50,000 reads per cell with paired-end 150 on Illumina NovaSeq platform (Novogene). The final ADT library was sequenced at 10,000 reads per cell with paired-end 50 on Illumina NovaSeq platform (Novogene).

value: Bone Marrow

tag: genotype

value: WT


title: LSK scRNA-Seq


title: Differentiated BeWo b30 cell, replicate 3


title: iWAT, lymph nodes removal, Cold 7days,  rep4 [LN_4]


title: LEW1 - TLH - scRNAseq

description: 10x Genomics Single Cell 3’ v2


title: BAT RW 5d-2

value: Brown adipose tissue

value: RW 5 days


title: BAT RW 5d-3

value: Normal


title: BAT aJ1aJ2 5d-7


title: BAT aJ1aJ2 5d-8


title: BAT aJ1aJ2 5d-6


title: BAT RW 5d-4


title: DA2 - TLH - scRNAseq

description: 10x Genomics Single Cell 3’ v2

value: Dark Agouti


title: BAT RW 5d-5


title: BAT aJ1J2 15h-10

value: anti-Jag1 and anti-Jag2 antibodies 15hours


title: BAT RW 5d-1


title: BAT aJ1J2 15h-9


title: TCR24h_KO2

city: London

first: Philip

last: East

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: quantifcation_exon_intron_mm10_ucsc_igenomes.xlsx

data_processing:
We generated BAM files using the nfcore/rnaseq version 3.5 pipeline with STAR and RSEM aligning against mm10 iGenome (UCSC)
We generated gene, exon and intron level quantifications using SummarizeOverlaps() from the GenomicAlignment Bioconductor package using RefSeq annotation GCF_000001635.26_GRCm38.p6
We generated bigwig coverage files using deeptools 3.3.1 with the per sample scaling factors reported.
Assembly: mm10 iGenome (UCSC)
Supplementary files format and content: bigwig coverage files normalised to the per sample scampling factors reported.
Supplementary files format and content: Excel spreadsheet containing gene, exon and intron level counts matrices.

source_name: lymph nodes

growth_protocol: OTI CD8+T cells are maintained in RPMI1640 10%FCS

extract_protocol:
RNA was harvested using Rneasy miniplus kit (Quiagen).A minimum of 1ng total RNA needed  to construct library
Nugen prep kit
Bulk RNA-seq

treatment_protocol: as described above

value: lymph nodes

value: CD8 T  lymphocytes

value: OTIMRTFABKO

tag: time


title: IL2stimulated_cells120min_KO2


title: RestedcellsIL12_KO2

value: Rested


title: IL2stimulated_cells60min_KO2


title: IL2stimulated_cells30min_KO2


title: naive_KO3

value: naive


title: RestedcellsIL12_KO3


title: IL2stimulatedcells60min_WT1

value: OTIWT


title: IL2stimulatedcells120min_WT1


title: TCR24h_WT2


title: naive_WT2


title: IL2stimulatedcells120min_KO3


title: IL2stimulatedcells30min_KO3


title: RestedcellsIL12_WT2


title: IL2stimulatedcells60min_KO3


title: Rested_cellsIL12_WT1


title: BAT aJ1J2 15h-8


title: TCR24h_KO3


title: DA1 - TLH - scRNAseq

description: 10x Genomics Single Cell 3’ v2

value: liver

value: Total Liver Homogenate


title: BAT aJ1J2 15h-7


title: IL2stimulated_cells120min_KO1


title: BAT RW 15h-5

value: RW 15 hours


title: top1_15min_treated_rep2

city: Barcelona

first: Montserrat

last: Vega

state: Barcelona

address: C/ Dr. Aiguader 88, lab 383

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra

description: each sample loaded in 4 lanes and 2 runs

data_processing:
Alignment using Bowtie2
BAM files, and quality aligment (supllementary, improper paired, non-primary alignments and reads with less than 20 of mapping quality) using SAMtools
Picard MarkDuplicated function employed to remove duplicated reads from BAM files
DANPOS2 was used to remove clonal reads, adjust read length, perfom quantile normalization and calculate differences in nucleosome occupancy
Assembly: Schizosaccharomyces pombe ASM294v2
Supplementary files format and content: BigWig files containing quantile normalization for each one of the samples

organism: Schizosaccharomyces pombe

growth_protocol: WT and top1 strain were grown in YE5S media at 30ºC at OD600 of 0.5

extract_protocol:
Micrococcal nuclease digestion
Roche Kapa Hyper Plus following manufacterer's instructions

treatment_protocol: 1mM H2O2 during 2, 5 and 15 minutes

value: 15 min 1mM H2O2


title: IL2stimulated_cells60min_KO1


title: BAT aJ1J2 15h-6


title: naive_KO2


title: top1_15min_treated_rep1


title: BAT RW 15h-4


title: BAT RW 15h-3


title: RestedcellsIL12_KO1


title: aJ1aJ2 thyroid 5 7 days [SAM24376384]

source_name: Thyroid

treatment_protocol: Male C57BL/6 mice at 10-14 weeks of age were obtained from Jackson Laboratories (strain ID: 00664). Mice were injected intraperitoneally with a single dose of blocking antibodies diluted in PBS at the following concentrations: anti-ragweed isotype control (40MPK); anti-Jag1+anti-jag2 (20MPK each); anti-Notch1+ anti-Notch2 (5MPK, 10MPK) , anti-Notch1+ anti-Notch2+ anti-Notch3 (5MPK, 10MPK, 20MPK).

value: Thyroid

value: anti-Jag1 and anti-Jag2 antibodies 7 days


title: BAT RW 15h-1

value: Brown adipose tissue


title: BAT RW 15h-2


title: top1_5min_treated_rep1

value: 5 min 1mM H2O2


title: IL2stimulated_cells30min_KO1


title: TCR24h_KO1


title: top1_5min_treated_rep2


title: aJ1aJ2 thyroid 2 7 days [SAM24376381]

value: Normal


title: aJ1aJ2 thyroid 4 7 days [SAM24376383]


title: top1_2min_treated_rep2

value: 2 min 1mM H2O2


title: aJ1aJ2 thyroid 3 7 days [SAM24376382]


title: TCR24h_WT1


title: IL2stimulated_cells120min_WT3


title: naive_KO1


title: aN1aN2aN3 thyroid 1 7 days [SAM24376400]

value: anti-Notch1, anti-Notch2 and anti-Notch3  antibodies 7 days


title: aJ1aJ2 thyroid 1 7 days [SAM24376380]


title: aN1aN2aN3 thyroid 3 7 days [SAM24376402]


title: aN1aN2aN3 thyroid 4 7 days [SAM24376403]


title: aN1aN2aN3 thyroid 2 7 days [SAM24376401]


title: aN1aN2 thyroid 5 5 days [SAM24398097]

value: anti-Notch1 and anti-Notch2 antibodies 5 days


title: top1_untreated_rep2

value: untreated


title: top1_untreated_rep1


title: IL2stimulated_cells60min_WT3

value: lymph nodes

value: CD8 T  lymphocytes


title: IL2stimulatedcells30min_WT1


title: aN1aN2 thyroid 4 5 days [SAM24398096]


title: IL2stimulatedcells30min_WT3


title: aN1aN2aN3 thyroid 5 7 days [SAM24376404]


title: top1_2min_treated_rep1


title: 972_15min_treated_rep1

source_name: WT

value: WT


title: 972_5min_treated_rep2


title: 972_15min_treated_rep2


title: 972_2min_treated_rep1


title: 972_2min_treated_rep2


title: 972_untreated_rep2


title: 972_untreated_rep1


title: 972_5min_treated_rep1


title: IL2stimulated_cells30min_WT2

value: OTIWT


title: sh.ctr_r2

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

data_processing:
The PEPATAC pipeline (version 0.10.3, Smith et al. 2021 NAR Genomics and Bioinformatics PMID: 34859208) with default settings was used for primary analysis and quality controls. Briefly, after adapter trimming with Skewer (PMID: 24925680) reads were  first pre-aligned with bowtie2 (PMID: 22388286) to the mouse_chrM2x mitochondrial genome (parameters: -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 ) to remove mitochondrial reads  and then mapped to the mm10 mouse genome (parameters: --very-sensitive -X 2000). Following alignment, reads with mapping quality scores below 10 and any residual mitochondrial reads were removed and read deduplication was carried out using Samblaster (PMID: 24812344).  Alignments were used to generate a signal track for visualization with IGV genome browser (https://doi.org/10.1038/nbt.1754).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: SV40 immortalized mouse kidney fibroblast

extract_protocol:
Omni-ATAC was performed as previously described (Corces et al. 2017 Nat Methods PMID: 28846090) with minor modifications (Cernilogar et al. NAR 2019  PMID: 31350899) . Briefly, 50000 cells were washed in 1xPBS, resuspended in 50 μl of ATAC-seq resuspension buffer (RSB: 10 mM Tris-HCl, pH 7.4, 10 mM NaCl, and 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin (Promega) and were incubated on ice for 3 min. Following lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 was added, and nuclei were centrifuged at 500g (4 °C, 10 min). Pelleted nuclei were resuspended in 50 μl of transposition mix (25 μl 2 × TD buffer, 2.5 μl Tagment DNA enzyme (Illumina Tag DNA Enzyme and  Buffer Kit, cat. 20034197), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5.25 μl water) and incubated at 37 °C for 30 min in a thermomixer shaking at 1000 rpm. DNA was purified using Qiagen PCR clean-up MinElute kit (Qiagen).
The transposed DNA was subsequently amplified in 50ul reactions with custom primers as described (Mezeger et al., 2017 Nat Communications  PMID: 30194434  ). After 4 cycles libraries were then monitored with qPCR: 5 ul PCR sample in a 15 ul reaction with the same primers. qPCR output was monitored for the ΔRN; 0.25 ΔRN cycle number was used to estimate the number of additional cycles of the PCR reaction needed for the remaining PCR samples. Amplified libraries were purified with the Qiagen PCR clean-up MinElute kit (Qiagen) and size selected for fragments shorter than 600 bp using the Agencourt AMPure XP beads (Beckman Coulter). Libraries were quality controlled by Qubit and Agilent DNA TapeStation analysis

tag: cell line

value: fibroblasts

value: itgb1 KO

value: transduced with scramble shRNA


title: naive_WT3

value: naive


title: IL2stimulated_cells60min_WT2


title: aJ1aJ2 thyroid 3 5 days [SAM24398090]

value: Thyroid

value: anti-Jag1 and anti-Jag2 antibodies 5 days


title: aJ1aJ2 thyroid 4 5 days [SAM24398091]


title: aJ1aJ2 thyroid 5 5 days [SAM24398092]


title: aJ1aJ2 thyroid 2 5 days [SAM24398089]


title: ctr_r4

value: SV40 immortalized mouse kidney fibroblast


title: Gatad2ab-DKO_r3

value: itgb1 KO, Gatad2a/b double KO


title: Gatad2ab-DKO_r1


title: sh.ctr_r3


title: naive_WT1


title: Rested_cellsIL12_WT3

value: Rested


title: aN1aN2 thyroid 2 5 days [SAM24398094]

value: Normal


title: TCR24h_WT3


title: aN1aN2 thyroid 1 5 days [SAM24398093]


title: aN1aN2 thyroid 3 5 days [SAM24398095]


title: CHD4-KO_r1

value: itgb1 KO, CHD4 KO


title: Gatad2ab-DKO_r2


title: IL2stimulated_cells120min_WT2


title: CHD4-KO_r2


title: CHD4-KO_r3


title: CD4 T cells TCR_Library

city: Boston

first: Peter

last: Sage

address: 221 Longwood Ave

department: Medicine/Renal

institute: Brigham and Women's Hospital

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

source_name: CD4 T cells

extract_protocol:
Balb/c kidneys were transplanted into Il21CreRosa26Lox-STOP-Lox-YFP (IL21Fate Mapper) mice. 20 days post-transplantation, Tconventional (CD4+CXCR5-YFP-, LNTcon), Tfh21 (CD4+CXCR5+YFP+, LNTfh21) from dLN and graft infiltrating IL-21 producing cells (CD4+YFP+, Graft21) cells were sorted
Cells were resuspended in 0.4% BSA in PBS at a concentration of 2,000 cells per μl, then loaded onto a single lane (Chromium chip K, 10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 5′kit V2, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol. 5’ mRNA library was sequenced to an average of 50,000 reads per cell, V(D)J library and HTO (Cell Hashing antibodies) library sequenced to an average of 5,000 reads per cell, all using Illumina Novaseq.

value: CD4 T cells

value: Mouse CD4 T  cell

value: 6-8 weeks


title: CD4 T cells GEX_HTO_Library


title: aJ1aJ2 thyroid 1 5 days [SAM24398088]


title: sh.ctr_r1


title: T lymphocytes, scRNAseq, chip 5, transcriptome

city: Rotterdam

first: Amy

middle: Catharina Johanna

last: van der List

address: Wytemaweg 80

department: Internal Medicine

country: Netherlands

institute: Erasmus MC

description:
transcriptome
assembled.rds

data_processing:
The data was analyzed according to 'Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level' (Litjens, NHR et al. 2022) (PMID: 35622330)
Assembly: GRCh38 human reference genome
Supplementary files format and content: RData file containing barcodes as well as reads for TRA/TRB and RNA expression for each cell

source_name: T lymphocyte

extract_protocol:
Following stimulation and staining, 20-25 million cells/ml per sample were filtered through a 35 µm nylon mesh and sorted for alloreactive T cells were sorted by positive signal for CD3 and CD137 and negative signal for CD14 (monocytes), CD19 (B-cells), CD56 (natural killer cells) and FVS780 (dead cells). Sorted alloreactive T cells were stained with Hoechst and propidium iodide (PI) and 160 µl at a concentration of 20-50 thousand cells/mL were dispensed per sample onto a pre-printed and a Blanco chip using the ICELL8 Single-Cell System. CellSelect automated microscopy image analysis software (Takara Bio) selected wells containing a single viable cell for in-chip full-length copy DNA (cDNA) amplification using SMARTScribe reverse transcriptase (Takara Bio). The resulting barcoded amplicons were purified off-chip by NucleoSpin Gel and PCR Clean-up kit (Machery-Nagel, Düren, Germany) followed by an AMPure XP beads purification (Beckman Coulter, Brea, USA).
transcriptome: Prepared cDNA libraries according to Takara SMARTer 5-prime sequencing method. From the cells, mRNA was isolated and reverse transcribed to single-cell barcoded cDNA from the 5-prime ends of the transcripts and sequenced according to the Illumina TruSeq Rapid v2 protocol on Illumina HiSeq2500 sequencer resultingng in single-end reads with a specific barcode (reads of 50 bp in length with a single 8 bp index sequence)
TCR: Prepared cDNA libraries according to Takara SMARTer Human TCR a/b Profiling method. From the cells, mRNA was isolated and the full-length T-cell receptor alpha and beta transcripts were reverse transcribed to single-cell barcoded cDNA. These cDNAs were sequenced on an Illumina MiSeq sequencer resulting in paired-end 300 basepair reads with both a barcode and the transcribed TCR a/b sequences.
TAKARA ICELL8 Human TCR profiling and 5' DE scRNA-seq

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were stimulated with CD3-negative PBMCs of their donor or a third party control.

value: T lymphocyte


title: T lymphocytes, scRNAseq, chip 1, transcriptome

description:
transcriptome
assembled.rds


title: Sylvio_MNase_35U_Replicate2

city: Buenos Aires

first: Josefina

last: Ocampo

address: Vuelta de Obligado 2490

country: Argentina

institute: INGEBI-CONICET

description: Biological replicate 2

data_processing:
Sequences were aligned to Sylvio-X10 genome version 64 or CL Brener_all genome version 46  respectively using Bowtie2 with default settings.
Reads were size selected, and we kept all reads with the lengths between 120 and 180bp.
Genome-wide coverage profiles were computed with R, and they were normalized such that the average coverage for every chromosome is 1.
IGV tracks containing normalized nucleosome occupancy for reads from 120-180bp (bw files) were generated with R.
Assembly: Sylvio-X10 genome version 64 and Cl Brener _all, made from the combination Esmeraldo like haplotype reference genome (TriTrypDB-46_TcruziCLBrenerEsmeraldo-like_Genome.fasta), non Esmeraldo like haplotype reference genome(TriTrypDB-46_TcruziCLBrenerNon-Esmeraldo-like_Genome.fasta) and CL Brener genome (not included in the annotated haplotypes(TriTrypDB-46_TcruziCLBrener_Genome.fasta)
Supplementary files format and content: bw files containing the normalized occupancy profiles, for the IGV browser

organism: Trypanosoma cruzi

growth_protocol: Sylvio-X10  and CL Brener epimastigotes were grown at 28 °C in liver infusion tryptose (LIT) medium. Cell density was maintained between 1x106 and 1x108 cells.ml-1 by sub-culturing parasites every 6-7 days.

extract_protocol:
Late exponentially growing epimastigotes of the  Sylvio-X10 and CL Brener strains were collected and permeabilized as previously described with modifications (Leandro de Jesus et al., 2017).  Chromatin was digested with different amounts of MNase (units given in filenames)
The DNA was repaired using the DNA PreCR kit from New England Biolabs. Paired-end libraries were constructed and indexed using Illumina kits from NEB (E7370 and E7335). Agencourt AMPure XP beads (Beckman, A63880) were used to purify the DNA after adaptor ligation and PCR products before sequencing

treatment_protocol: no pre treatment

tag: life stage

value: exponentially growing epimastigotes

tag: mnase amount


title: PGDHi Sciatic nerve transection day 14 Muscle snRNA_sample 2

city: Stanford

first: Yu Xin

last: Wang

state: California

address: 269 Campus Dr

institute: Stanford University School of Medicine

description: 10x Multiome of single nuclei isolated from the injured legs of mice treated with a 15-PGDH inhibitor after sciatic nerve crush (14 days post injury)

data_processing:
CellRanger Arc
Assembly: mm10
Supplementary files format and content: h5ad annotated data format containing gene names, gene expression, indices, and gene IDs

source_name: Skeletal muscle

extract_protocol:
Skeletal muscles of the lower hindlimb were dissected, snap froze in lqN2, lysed and dounce homogenized to isolate nuclei, which were then FACS sorted for further enrichment
10x Chromium
10x Multiome Kit

treatment_protocol: Sciatic nerve on one leg of a C57BL6 mouse was surgically ressected, then mice were either treated with IP injection of a 15-PGDH inhibitor daily or vehicle

value: Skeletal muscle

value: all cells

value: SNT, IP PGDHi


title: PGDHi Sciatic nerve transection day 14 Muscle snRNA_sample 1


title: PGDHi Contralateral Muscle snRNA_sample 2

description: 10x Multiome of single nuclei isolated from contralateral legs of mice treated with a 15-PGDH inhibitor after sciatic nerve crush (14 days post injury)

value: CTL,IP PGDHi


title: CL_MNase_35U_Replicate2

description: Biological replicate 2

source_name: epimastigote

value: CL Brener


title: PGDHi Contralateral Muscle snRNA_sample 1

value: CTL, IP PGDHi


title: CL_MNase_70U_Replicate1

description: Biological replicate 1


title: Bristol N2_OP50_rep1

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Koyto Univ.

data_processing:
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.6.5), Trimmomatic (ver. 0.39) and cutadapt (ver. 2.7) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.98) using STAR (ver. 2.7.2b).
The read count of gene features was performed with the featureCounts tool (ver. 1.6.4)
Supplementary files format and content: ce11
Supplementary files format and content: tab-delimited text files include featureCount values for each sample

organism: Caenorhabditis elegans

source_name: Whole

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Clontech)

treatment_protocol: Three-day-old worms were cultured for five days on mNGM plates covered with OP50 (control-fed group) or a mixture of OP50 and Lactococcus kimchii.

value: Whole

value: Bristol N2

value: hermaphrodite

value: wild-type

value: feeding OP50

value: three-day-old


title: Vehicle Sciatic nerve transection day 14 Muscle snRNA_sample 1

description: 10x Multiome of single nuclei isolated from the injured legs of mice treated with vehicle after sciatic nerve crush (14 days post injury)

value: SNT, IP Vehicle


title: Vehicle Sciatic nerve transection day 14 Muscle snRNA_sample 2


title: Vehicle Contralateral Muscle snRNA_samples 1&2

description: 10x Multiome of single nuclei isolated from contralateral legs of mice treated with vehicle after sciatic nerve crush (14 days post injury)

value: CTL, IP Vehicle


title: Bristol N2_OPLK_rep1

value: feeding OP50+L. kimchii


title: Sylvio_MNase_70U_Replicate1

description: Biological replicate 1


title: Bristol N2_OPLK_rep2


title: Bristol N2_OP50_rep2


title: heart, Ft1sm22ko, 1 week, rep4

city: Rome

first: Isabella

last: Saggio

address: p.le Aldo Moro, 5

department: Biology and Biotechnologies Charles Darwin

country: Italy

institute: Sapienza, University of Rome

description:
WTyoung_vs_SM22young_res.tsv
KOyoung_vs_SM22young_res.tsv

data_processing:
RNA samples were quantified, and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA)
Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or by Caliper LabChip GX (PerkinElmer, Waltham, MA).
Libraries were then prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeq 6000 (Illumina, San Diego, CA).
RNA-seq reads were analyzed via Illumina pipeline and then aligned on reference hg38 genome/transcriptome with STAR4 (default parameters).
Transcript count was done with Stringtie (default parameters). RSeqQC6 package was used to perform quality control.
Htseq-count7 was used to preprocess RNAseq data for differential expression analysis by counting the overlap of reads with genes
DESeq28,9 was then used to perform comparisons between expression levels of genes and transcripts by fitting a Generalized Linear Model (GLM) for each gene as previously described {Wang, 2012 #181} {Anders, 2015 #182} {Anders, 2010 #183} {Love, 2014 #184}.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw reads for each sample
Supplementary files format and content: comma-separated table with all the statistical testing for a given pairwise test

source_name: Heart

extract_protocol:
RNA was extracted using the TRIzol reagent (Invitrogen) following the manufacturer's instructions
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) was used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand).

value: Heart


title: heart, Ft1sm22ko, 1 week, rep2


title: heart, Ft1sm22ko, 1 week, rep3


title: heart, Ft1sm22ko, 1 week, rep1


title: heart, Ft1ko, 1 week, rep3

description:
WTyoung_vs_KOyoung_res.tsv
KOyoung_vs_SM22young_res.tsv


title: aJ1aJ2 thyroid 4 15 hours [SAM24388066]

value: Thyroid

value: Normal

value: anti-Jag1 and anti-Jag2 antibodies 15hours


title: aN1aN2 thyroid 3 15 hours [SAM24398070]

value: anti-Notch1 and anti-Notch2 antibodies 15 hours


title: RW thyroid 3 5 days [SAM24398075]

value: RW 5 days


title: aJ1aJ2 thyroid 3 15 hours [SAM24388065]


title: aN1aN2 thyroid 4 15 hours [SAM24398071]


title: RW thyroid 1 5 days [SAM24398073]


title: RW thyroid 2 5 days [SAM24398074]


title: RW thyroid 4 5 days [SAM24398076]


title: aN1aN2 thyroid 2 15 hours [SAM24398069]


title: aN1aN2 thyroid 1 15 hours [SAM24398068]


title: aN1aN2 thyroid 5 15 hours [SAM24398072]


title: aJ1aJ2 thyroid 5 15 hours [SAM24388067]


title: RW thyroid 5 5 days [SAM24398077]


title: T lymphocytes, scRNAseq, chip 2, transcriptome

description:
transcriptome
assembled.rds

value: T lymphocyte


title: T lymphocytes, scRNAseq, chip 0, transcriptome

description:
transcriptome
assembled.rds


title: RW thyroid 5 15 hours [SAM24388062]

value: RW 15 hours


title: heart, Ft1ko, 1 week, rep1


title: aJ1aJ2 thyroid 2 15 hours [SAM24388064]


title: aJ1aJ2 thyroid 1 15 hours [SAM24388063]


title: heart, WT, 1 week, rep2

value: WT


title: heart, Ft1ko, 1 week, rep2


title: heart, WT, 1 week, rep3


title: heart, WT, 1 week, rep1


title: CD21_CDX30_NNE_P

city: Manchester

first: Caroline

last: Dive

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road

institute: Cancer Research UK Manchester Institute

data_processing:
Data was aligned using STARto GRCH38 Ensembl version 99as part of the RNA-Seq pipeline from nf-core (Nextflow RNA-Seq v3.3 pipeline).
Aligned reads were filtered to remove mouse contamination reads using the bamcmp algorithmbefore being mapped to genomic annotation.
Supplementary files format and content: Gene-level raw counts generated by Salmon
Supplementary files format and content: Gene-level transcripts per million (TPM) generated by Salmon

source_name: circulating tumor cell-derived explant (CDX) model

growth_protocol: CDX NE and non-NE cells were cultured on plastic and Matrigel for 24 hours

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit, Qiagen (#74104)
For sequencing run CD21, Paired-end 75bp sequencing was performed by loading 2pM pooled libraries on a NextSeq 500 sequencer (Illumina inc.). For sequencing run CD25, Paired-end 100bp sequencing was performed by loading 400pM pooled libraries on a NovaSeq 6000 sequencer (Illumina inc.).

tag: cdx model

tag: patient

tag: diagnosis

value: SCLC

tag: plastic or_matrigel

value: P

tag: neuroendocrine or_non-neuroendocrine

value: Non-NE

tag: sequencing run

tag: age

tag: gender

value: Female

tag: sclc stage

value: Extensive


title: CD21_CDX30_NNE_M

tag: tissue

value: circulating tumor cell-derived explant (CDX) model

value: M


title: CD21_CDX30_NE_P

value: NE


title: cow 0036 after LPS tratment

city: Saint Genès-Champanelle

first: christine

last: Leroux

address: Route de Theix

country: France

institute: INRAE

description: 100 ng total RNA was labelled with Cy3 using the one-color Quick Amp Labeling Kit

hyb_protocol: The hybridizations were performed overnight to the microarrays using the High-RPM Gene Expression Hyb Kit (Agilent Technologies, Inc. Santa Clara, USA) following manufacturer’s instructions. After washing, microarrays were scanned using the Innoscan (Innopsys, France) and the resulting TIFF images were processed using Feature Extraction software Version 11 (Agilent Technologies, Inc. Santa Clara, USA).

data_processing: The resulting TIFF images were processed using Feature Extraction software Version 11 (Agilent Technologies, Inc. Santa Clara, USA).

organism: Bos taurus

source_name: Milk Fat miRNA

label_protocol: 100 ng of total RNA was labelled with Cy3 using the one-color Quick Amp Labeling Kit (Agilent Technologies, Inc. Santa Clara, USA) according to the manufacture's instructions

growth_protocol: 27±3 days in milk

extract_protocol: One g of MF was mixed with 2.0 mL of TRIzol LS solution (Invitrogen Life Technologies Inc.), then 600 µL of chloroform were added before centrifugation at 12,000 x g for 20 min at 4°C. The upper aqueous layer was precipitated using 500 µL of isopropanol

treatment_protocol: 50 µg of LPS injected in mammary gland

value: Milk Fat

tag: growth

value: 27±3 days in milk

tag: treatment

value: 50 ug of LPS injected in mammary gland


title: cow 0036 before LPS treatment

scan_protocol: After washing, microarrays were scanned using the Innoscan (Innopsys, France)

value: No LPS


title: cow 1076 before LPS treatment


title: cow 9040 after LPS treatment


title: RW thyroid 1 15 hours [SAM24388058]

value: Thyroid

tag: strain

tag: diagnostics

value: Normal


title: aJ1aJ2 thyroid 5 7 days [SAM24362525]

value: anti-Jag1 and anti-Jag2 antibodies 7 days


title: RW thyroid 3 15 hours [SAM24388060]

value: RW 15 hours


title: RW thyroid 4 15 hours [SAM24388061]


title: RW thyroid 2 15 hours [SAM24388059]


title: CD21_CDX30_NE_M


title: aJ1aJ2 thyroid 4 7 days [SAM24362524]


title: aJ1aJ2 thyroid 3 7 days [SAM24362523]


title: CD21_CDX17_NNE_M


title: aJ1aJ2 thyroid 2 7 days [SAM24362522]


title: cow 1024 after LPS treatment


title: cow 1024 before LPS treatment


title: CD21_CDX17_NNE_P


title: CD21_CDX17_NE_M


title: CD21_CDX17_NE_P


title: U87,circPLOD2a-NC, rep1

city: Wuhan

first: Yiqi

state: State...

address: Shizishan Street

country: China

institute: Huazhong Agricultural University, China

data_processing:
Quality control with data trimming, fastp version 0.21.0, default parameters
Use hisat2 to align reads to hg38 genome, HISAT2 version 2.1.0, default parameters
Use samtools to transfer sam to sorted bam, Version: 1.3.1, default parameters
mRNA and lncRNA used htcount to bam counts statistiction, Public License v3, htseq-count with default parameters ; circRNA applied CLEAR and CIRI2 pipeline analysing.
R library DESeq2 to obtain differential expression genes, R 4.1.2, pvalue<0.05, |log2FC|>1
Assembly: hg38
Supplementary files format and content: readCount

extract_protocol:
Human GBM cell U87knocking down of circPLOD2a and circPLOD2b were planted in 6-cm dish respectively and treated in normoxia  (21% O2, 74% N2 and 5% CO2) . 48 hours later, the DMEM medium was removed, and 1mL PBS buffer was added into each dish to wash medium residue. Remove all the PBS buffer from the dishes and add 1mL Trizol buffer. Solution from each dish was collected into 1.5mL EP tube, and stored in liguid nitrogon for further analysis.
RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). And, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following the manufacturer’s recommendations. The first-strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H– ). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for Illumina, and index (X) primer. PCR products were purified and harvested.

tag: cell line

tag: genotype


title: U87,circPLOD2a-NC, rep2


title: U87,circPLOD2b-KD, rep3


title: U87,circPLOD2a-NC, rep3


title: U87,circPLOD2b-NC, rep3


title: U87,circPLOD2b-KD, rep2


title: U87,circPLOD2b-KD, rep1


title: U87,circPLOD2b-NC, rep2


title: aJ1aJ2 thyroid 1 7 days [SAM24362521]

city: South San Francisco

first: Robert

address: 1 DNA Way

institute: Genentech Inc.

data_processing:
Sequencing reads were aligned to the mouse genome (NCBI Build 38) using GSNAP (Wu and Nacu, 2010) version ‘2013-10-10’, allowing a maximum of two mismatches per 50 base pair sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap’).
Lastly, gene expression levels were quantified by calculating the number of reads mapped to the exons of each RefSeq gene using the HTSeqGenie R package.
Transcript annotation was based on the RefSeq database NCBI Annotation Releases 104 for mouse.
Read counts were scaled by library size, quantile normalized and precision weights calculated using the “voom” R package (Law et al., 2014).
Differential expression analysis on the normalized count data was performed using the “limma” R package (Ritchie et al., 2015) by contrasting treated samples with control samples, respectively. Gene expression was considered significantly different across groups if we observed an |log2-fold change| ≥ 1 (estimated from the model coefficients) associated with an FDR adjusted P-value ≤ 0.05. In addition, gene expression was obtained in the form of normalized Reads Per Kilobase gene model per Million total reads (nRPKM) as described previously (Srinivasan et al., 2016).
Assembly: mouse genome (NCBI Build 38)
Supplementary files format and content: csv (count and fpkm matrix)

extract_protocol:
Total RNA was extracted from  tissues with Trizol (Invitrogen) following the provider’s recommendations. After adding isopropanol, the samples were transferred into RNAeasy extraction column (Qiagen), washed and eluded following the manufacturer protocol.
The libraries were sequenced on Illumina HiSeq 4000 (Illumina). We obtained on average 40 million single-end RNA-seq reads (50bp) per sample.


title: RW thyroid 5 7 days [SAM24362520]

value: RW 7 days


title: sg34,Rep3

city: Hangzhou

first: Xiaoli

last: Jin

state: Zhejiang

address: Yuhangtang road 866

institute: Zhejiang University

data_processing:
The clean reads were mapped to the reference genome of Nipponbare (MSU7.v7.0) using the Bowtie 2 (Cock et al. 2010; Langmead et al. 2009) in HISAT2 version 2.1.0 (Kim et al. 2015)
The isoforms of the same gene were decided using the RSEM software (Li and Dewey 2011). The transcript abundance was measured in terms of Transcripts Per Million (TPM) in the StringTie software.
Gene co-expression analysis was carried out using WGCNA.
Deseq2 (version 1.12.4) was used for differentially expressed gene (DEG) analysis with q-value < 0.001 and |Fold Change| > 2.
Assembly: Reference sequnce usded for read alignment
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: Grains

extract_protocol: RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Grains

value: Grain cells

tag: cell type

value: mutant

value: Treatment

value: Mature period


title: cow 1076 after LPS treatment


title: RW thyroid 4 7 days [SAM24362519]

last: Piskol


title: RW thyroid 3 7 days [SAM24362518]


title: sg34,Rep1


title: Zhenong 34,Rep3

value: Wild type

value: Control


title: sg34,Rep2


title: U87, hypoxia, 24h rep2

extract_protocol:
Human GBM cell U87-wt were planted in six 6-cm dish. Three dishes of cells were cultured in hypoxia (1% O2, 94% N2 and 5% CO2) and another three dishes treated in normoxia  (21% O2, 74% N2 and 5% CO2) respectively. 24 hours later, the DMEM medium was removed, and 1mL PBS buffer was added into each dish to wash medium residue. Remove all the PBS buffer from the dishes and add 1mL Trizol buffer. Solution from each dish was collected into 1.5mL EP tube, and stored in liguid nitrogon for further analysis.
RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). And, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following the manufacturer’s recommendations. The first-strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H– ). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for Illumina, and index (X) primer. PCR products were purified and harvested.

value: wild type

value: hypoxia


title: U87, hypoxia, 24h rep3


title: U87, normoxia, 24h rep3

value: normoxia


title: U87, normoxia, 24h rep2


title: U87, hypoxia, 24h rep1


title: RW thyroid 2 7 days [SAM24362517]


title: RW thyroid 1 7 days [SAM24362516]


title: U87, normoxia, 24h rep1


title: cow 8027 after LPS treatment

value: Milk Fat

value: 27±3 days in milk

value: 50 ug of LPS injected in mammary gland


title: Zhenong 34,Rep2


title: Unwounded Dorsal Skin scRNA-seq

city: Los Angeles

first: Hans I-Chen

last: Harn

address: 2011 Zonal Ave. HMR304

institute: University of Southern California

data_processing:
Data were analyzed using Partek Flow; cells with fewer than 5% mitochondrial reads were included in the analysis. tSNE and UMAP plots were created with default settings.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Sparse matrix files with genes in columns and cells in rows

source_name: Dorsal skin

extract_protocol:
Single cells were isolated from excised tissue from naïve animals (pooled from 3 wounds) using a collagenase/dispase digestion. Cells were stained with antibodies against CD45 (hematopoietic), CD31 (endothelial) and Ter119 (red blood cells); live cells were discriminated with DAPI. At least 100,000 live, CD45-CD31-Ter119- cells were subjected to single cell capture and droplet formation following instructions in the online Drop-seq protocol v.3.1 (http://mccarrolllab.org/download/905/) and those published in the original Drop-seq paper. In brief, cells at 150,000 cells/ml, barcoded beads at 175,000 beads/ml and droplet generation oil were co-flowed at a rate of 4, 4, and 15 ml/hour, respectively, in a PDMS microfluidics chip to generate oil droplets containing beads and lysed cells. Post flow, droplets were broken and reverse transcription performed. Complementary DNA was PCR amplified, magnetically cleaned up and subjected to tagmentation and sequencing library construction. Prepared libraries were cleaned up and sequenced via Illumina HiSeq4000 or NovaSeq.
Drop-seq protocol v.3.1; uses Illumina reagents

value: Dorsal skin


title: Zhenong 34,Rep1


title: U87,circPLOD2a-KD, rep3


title: U87,circPLOD2b-NC, rep1


title: U87,circPLOD2a-KD, rep2


title: U87,circPLOD2a-KD, rep1


title: Multiplexing Capture of negative controls

first: Seong Won

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: 10X Genomics

data_processing:
Demultiplexing, barcode processing, and aligning to the reference genome were done using CellRanger Software (ver 6.1.0)
Assembly: hg38
Supplementary files format and content: Tab separated matrix file, barcodes file, and feature files.
Supplementary files format and content: List of demultiplexed CellRanger barcodes and Genotype assignment

extract_protocol:
hiPSC-CMs were dissociated with Accutase and snap-frozen for snRNAseq
3' CellPlex Kit was used to barcode cell pellets. Nuclei was extracted, washed and pooled at equal amount. Library was constructed according to the manufacturer's instruction for Chromium 3’ v3.1 dual index kit.

tag: sample type

value: Cell Multiplex Barcodes


title: Pooled Gene Expression of hiPSC-CM with negative controls

description: 10X Genomics

value: hiPSC derived cardiomyocytes

value: snRNAseq


title: N6_10xBulge_RNAseq

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

data_processing:
Reads from small RNA libraries were sorted into individual libraries based on the barcodes and the 3′ adapter sequences were clipped from the reads using cutadapt (DOI:http://dx.doi.org/10.14806/ej.17.1.200) with only sequences of at least 15 nucleotides left for further analysis (cutadapt parameters: -a AGATCGGAAGAGCACACGTCT -m 15 -e 0.2 -O 4 -q 10 --match-read-wildcards).  The reads were then mapped to the mouse genome (GRCm38: Ensembl release 95) using STAR(Dobin et al., 2013) (with parameters: --runThreadN 10 -outFilterType BySJout --limitOutSJcollapsed 50000000 --limitIObufferSize 1500000000) and length distributions of the reads were plotted. Read counts were normalized to library sizes.  To see whether any piRNAs are produced from the reporters, the reads were mapped by bowtie(Langmead et al., 2009) (with parameters: -v 0 -a --best --strata) to the Ythdc2 transcript sequence containing individual reporters: 1xPerf,1xBulge,10xPerf,10xBulge.
Reads from long RNA-seq libraries were mapped to the mouse genome (GRCm39 - Ensembl release 104) using salmon(Patro et al., 2017) (salmon quant with options -l A –validateMappings–gcBias). Further analysis was performed using R(R Core Team, 2017) and Bioconductor(Huber et al., 2015). The DESeq2(Love et al., 2014) package was used to obtain normalized read counts for individual genes.
Assembly: GRCm38(small RNA libraries) and GRCm39 (total RNA libraries)
Supplementary files format and content: The bigwig files contain piRNA coverages along the genome. The csv file contains gene expression data.

source_name: Testes

growth_protocol: The reporters were created by inserting one or ten complementary binding sites for piR-A in the 3ʹ UTR of the Ythdc2 gene (MGI: 2448561; NCBI Gene: 240255). Binding sites were perfectly complementary or contained two mismatches at the 10th and 11th position relative to the guide RNA. Mismatched sites are referred to bulges. The first line contains one perfect complementary binding site (1XPerf), the second line contains one bulge binding site (1xBulge), the third line contains ten perfect complementary binding sites (10xPerf) and the fourth line contains ten bulge binding sites (10xBulge). Ythdc2 locus of the B6D2F1/J hybrid line (also called B6D2; The Jackson Laboratory, stock no. 100006) was targeted using CRISPR/Cas9 system.

extract_protocol:
Total RNA was extracted from adult testes using TRIzol™ Reagent (Thermo Scientific, Cat. No.  15596026).   Immunoprecipitation was conducted with Mili (PMID: 19465913) or Miwi antibodies (PMID: 22121019) and Protein G Sepharose® 4 Fast Flow beads (GE Healthcare, No. 17-0618-01) and Mili and Miwi loaded piRNAs were extracted using phenol-chloroform.
piRNA sequencing libraries were prepared with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs, Ref. E7300L) and sequenced by NextSeq 500 platform (Illumina) in GeneCore(Heidelberg).   The Stranded Total RNA Ribo-Zero Plus kit from Illumina was used for the library preparation from total RNA with 500 ng of total RNA as input. Library molarity and quality were assessed with the Qubit and Tapestation (DNA High sensitivity chip). Libraries were sequenced on a NovaSeq 6000 Illumina sequencer for SR100 reads (iGE3 Genomics Platform, University of Geneva).

tag: immunoprecipitation

tag: mouse


title: N2_WT_RNAseq

value: WT


title: N4_10xPerf_RNAseq


title: N3_10xPerf_RNAseq


title: N5_10xBulge_RNAseq


title: Exosomes, derived from H2O2-treated HaCaT, biol rep3 [Exo04_4]

city: Xi'an

first: Jingjing

last: Ma

address: No. 127 Changlexi Road

institute: Fourth Military Medical University

data_processing:
bcl2fastq
quality assessment using FastQC
Sequence reads were trimed for adaptor sequence using cutadapt-1.7.1and fastx-toolkit-0.0.14.
Trimed sequences were subjected to length distribution statistic analysis and rRNA、tRNA、snRNA and ncRNA were filtered using bowtie-1.1.1 and R language.
Read counts extraction and normalization were performed using program of CapitalBio Corporation (Beijing, China).
Assembly: miRBase
Supplementary files format and content: Excel file includes reads for each sample.
Supplementary files format and content: Excel file includesTPM (Total Mapped Reads) for each sample.

source_name: Skin

extract_protocol:
Total RNA was extracted using Trizol reagent (Life Technologies, Carlsbad, CA) according to manufacturer’s protocol.
Exosomal RNA of each sample was used to construct small RNA libraries with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, Ipswich, MA).

value: Skin

value: HaCaT

value: Keratinocyte

value: With type


title: Exosomes, derived from H2O2-treated HaCaT, biol rep1 [Exo04_2]


title: Exosomes, derived from H2O2-treated HaCaT, biol rep2 [Exo04_3]


title: N1_WT_RNAseq


title: Exosomes, derived from H2O2-untreated HaCaT, biol rep2 [Exo0_3]

value: untreated


title: cow 8027 before LPS treatment

value: No LPS


title: cow 9066 before LPS treatment


title: G39_TAS120_rep1

city: Washington

first: Nagi

last: Ayad

state: DC

address: 3800 Reservoir Rd NW

institute: Georgetown University

description:
TAS120_869
BETi_FGFRi_invivo-logCPM.csv
BETi_FGFRi_invivo-rawdata.csv

data_processing:
FastQ files were aligned to the human genome and raw gene counts were determined
Trimmed Mean of M-values (TMM) normalization was performed using edgeR.
TMM values were used as input into the NOISeqBIO R-package for differential gene analysis. Genes with low counts across all samples were excluded, samples were normalized to the DMSO control, and differentially expressed genes were detected.
Assembly: hg19
Supplementary files format and content: comma-deliminated file contains raw counts for each gene for each sample
Supplementary files format and content: comma-deliminated file contains logCPM values for each gene for each sample

source_name: PDX G39

growth_protocol: PDX GBM6, GBM22, GBM39, GBM76, and GBM150 cells were obtained from the Brain Tumor PDX national resource at the Mayo Clinic31. Nu/nu mice were implanted with 300,000 PDX GBM39 cells. Following a 10 day recovery period post-surgery, animals were assigned to treatment groups and treatment was initiatied.

extract_protocol:
Mice were anesthetized with tribromoethanol (avertin, 250 mg/kg Sigma-Aldrich) intraperitoneally prior to transcardial perfusion. Once the mouse showed signs of proper depth of anesthesia (lack of reflex response to hind paw withdrawal or ocular stimulation), the chest cavity was opened and the heart was exposed. A cut was made in the right atrium to prevent blood recirculation and a 28 G butterfly needle attached to a syringe was inserted into the left ventricle to perfuse the circulatory system with PBS After perfusion, mice were rapidly decapitated and tumors were isolated from the brain. Tumors were dissociated using a mortar and pestle, followed by a QIAshredder column. RNA was extracted from the lysate per manufacturer instructions using a AllPrep DNA/RNA mini kit (Qiagen, Valencia, CA, USA).
Ribo-Depletion of 900-1000ng total RNA was performed using the Epicentre Ribo-Zero Gold Kit (part# RZHM11106) followed by library construction of samples using the Epicentre ScriptSeq v2 RNA-Seq Library Preparation Kit (part# SSV21124 ) according to manufacturers protocols (12-16 cycles PCR). Samples were barcoded to allow for multiplexing

treatment_protocol: Mice were treated with DMSO, 50 mg/kg/day birabresib, 12.5 mg/kg/day futibatinib, or 50 mg/kg/day birabresib + 12.5 mg/kg/day futibatinib. Compounds were dissolved in DMSO and diluted to a final concentration of 10% DMSO, 40% PEG400, 50% PBS. Compounds were injected intraperitoneally 5 days per week on alternating sides, with a final volume of 10 µl/g body weight. Drug treatment was administered for a duration of 2 weeks.

value: PDX G39

value: Glioblastoma patient derived xenograft, G39

value: Futibatinib


title: WT

city: Beijing

first: Jianchen

last: Wu

address: Medical Building, c304

institute: Tsinghua University

data_processing:
CellRanger software was applied to demultiplex the Illumina BCL output into FASTQ files. The Cell Ranger count was then applied to each FASTQ file to align reads to the reference genome and generate barcode and unique molecular identifier counts. We followed the Seurat integrated analysis and comparative analysis workflows to do all scRNA-seq analyses (Stuart et al., 2019). For quality control and filtering out low quality cells, only cells expressing more than 200 genes (defined as genes detected in at least 3 cells) and fewer than 20% mitochondrial genes were selected. All single cells passed quality control for further batch correction and unbiased clustering.
Supplementary files format and content: Homo_sapiens.GRCh38.93.chr
Supplementary files format and content: Tab-separated values and matrix files

extract_protocol:
The cells were digested for 10 min at 37 ℃ temperature in the enzyme solution(TrypLE). After collection of cells, centrifuge at a speed not exceeding 400rcf. Carefully discard the supernatant and retain the cell precipitation. The cell pellet was resuspended by 1mL 1X PBS containing 0.04% BSA and the washing procedure was repeated twice. After washing, appropriate volume PBS was added to the cell precipitation to obtain single-cell dispersion suspension with a concentration close to the goal number. A type of wide-bore pipette tip was used in cell resuspension for a lower cell damage. Cell filter was applied to remove cell debris and clusters by 30µm MACS SmartStrainers and 40µm FlowmiTM Cell Strainer. Automatic cytometry was used to determine the cell concentration ((Thermo fisher scientific; AMAQAF1000). And the sample volume was calculated based on the optimal cell sampling concentration supplied by 10X official website and the target capture number. Once the desired cell suspension was obtained, immediately place the samples on ice for subsequent GEMs preparation and reverse transcription by Annoroad Gene Tech. (Beijing) Co., Ltd.
scRNA-seq libraries were prepared according to manufacturer protocol of Chromium Next GEM Automated Chip G Single Cell Kit (10x Genomics, PN-1000146). Briefly, the cells、the Beads and partitioning Oil was loaded onto a Chromium Chip G. Resulting single-cell GEMs were collected and linear amplification was conducted in a C1000 Touch Thermal cycler as 72℃ for 5 min, 98℃ for 30 s, cycled 12X: 98℃ for 10 s, 63℃ for 30 s and 72 ℃ for 1 min. Emulsions were then coalesced using the Recovery Agent and cleaned up using Dynabeads. Indexed sequencing libraries were then constructed, purified and sequenced on an Illumina NovaSeq instrument at Annoroad Gene Tech. (Beijing) Co., Ltd.

value: hPSCs-derived Beta cells


title: KO


title: HET


title: Exosomes, derived from H2O2-untreated HaCaT, biol rep1 [Exo0_2]


title: G39_MK8628_rep1

description:
MK8628_855
BETi_FGFRi_invivo-logCPM.csv
BETi_FGFRi_invivo-rawdata.csv

value: Birabresib


title: G39_TAS120_rep2

description:
TAS120_890
BETi_FGFRi_invivo-logCPM.csv
BETi_FGFRi_invivo-rawdata.csv


title: G39_DMSO_rep3

description:
DMSO_872
BETi_FGFRi_invivo-logCPM.csv
BETi_FGFRi_invivo-rawdata.csv

value: DMSO


title: Exosomes, derived from H2O2-untreated HaCaT, biol rep3 [Exo0_4]


title: G39_MK8628_rep2

description:
MK8628_879
BETi_FGFRi_invivo-logCPM.csv
BETi_FGFRi_invivo-rawdata.csv


title: cow 9066 after LPS treatment

value: Milk Fat

value: 27±3 days in milk

value: 50 ug of LPS injected in mammary gland


title: G39_DMSO_rep2

description:
DMSO_865
BETi_FGFRi_invivo-logCPM.csv
BETi_FGFRi_invivo-rawdata.csv


title: adipose stromal cells, untreated - input, Rep 4 [CR_KDM6B_19]

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

institute: INSERM U1236-MOBIDIC

data_processing:
Illumina software used for basecalling.
FastQC control quality.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie 2.
Peaks were identified with MACS2, using input as background. Only peaks with a minimum FDR < 10-5 were kept.
The R package ChIPseeker64 (v4.1) with the function annotatePeak() was then used to annotate peaks with their genomic locations and to associate them to the closer gene.
Differential peak binding was then performed with DESeq2 algorithm (v1.22.2). Significant peaks were defined as p < 0.05 after adjustment for false discovery by Benjamini-Hochberg correction.
Assembly: hg19
Supplementary files format and content: matrix_table.csv: Comma-separated text file includes raw count values for each Sample.
Library strategy: CUT&RUN-seq

source_name: adipose stromal cells, input

growth_protocol: Adipose stromal cells (ASC) were obtained from the stromal vascular fraction of adipose tissue and were maintained in a modified Minimum Essential Medium Eagle (Gibco) supplemented with 10% fetal calf serum (FCS) (Biosera) and 1 ng/mL of basic fibroblast growth factor (bFGF) (Cellgenix). These cells were used between passages 1 and 3 for experiments in the same medium without supplementation in bFGF.

extract_protocol:
After treatment, KDM6B binding was performed using the CUT&RUN methods: Briefly, Cells (1.103) were bound to Concanavalin A beads (Polysciences) and incubated with 1 μl of anti-KDM6B (Abcam, ab38113) antibodies, overnight at 4°C. pA/G-MNase (0.89 ng/μl) was bound to antibodies and activated with CaCl2 to digest chromatin during 30 min at 0°C. Enzymatic reaction was stopped and chromatin fragments were released by an incubation of 10 min at 37°C. Chromatin sonication was performed with the EpiShearTM Probe Sonicator (Active Motif). DNA was purified with MinElute PCR Purification Kit (Qiagen).
Libraries were prepared by Integragen, with the CUTANA CUT&RUN Library Prep Kit and accordingly to manufacturer recommendation.
Paired-end.

treatment_protocol: ASC were treated by using tumor necrosis factor alpha (TNFα) (5 ng/mL) / lymphotoxin αlpha1 beta2 (LTα1β2) (50 ng/mL) (R&D Systems) and collected 6 hours after treatment.

value: adipose stromal cells

tag: cut&run antibody

value: none (input)

tag: subject

value: healthy donor 2


title: Ad_KLK8_4

city: Shanghai

first: xiaoyan

last: Zhu

address: NO.800 Xiangyin Road

institute: The Second Military Medical University

data_processing:
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads   were generated.
Raw data (raw reads) of   fastq format were firstly processed using Trimmomatic and the low quality reads were removed   to obtain the clean reads.
The clean reads were mapped to the human genome (GRCh38) using HISAT2  .  FPKM  of each   gene was calculated using Cufflinks  , and the read counts of each gene were obtained by HTSeqcount  .  Differential expression analysis was performed using the DESeq (2012) R package  .
ASprofile was used to analyse the alternatively splicing of differentially regulated transcripts   isoforms or exons.  SNPs and InDels were called using SAMtools and BCFtools
Assembly: GRCh38
Supplementary files format and content: .rpkm

source_name: lung

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA   purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo   Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent   Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using TruSeq Stranded   mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s   instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd.   (Shanghai, China).

value: lung

value: pulmonary endothelial cells


title: Ad_KLK8_3


title: Ad_KLK8_2


title: G39_DMSO_rep1

description:
DMSO_854
BETi_FGFRi_invivo-logCPM.csv
BETi_FGFRi_invivo-rawdata.csv


title: Ad_KLK8_1


title: adipose stromal cells, TNFLT-treated - KDM6B, Rep 4 [CR_KDM6B_18]

source_name: adipose stromal cells, cultured

value: treated with TNFLT


title: Ad_con_4

value: Ad-control


title: G39_COMBO_rep2

description:
COMBO_883
BETi_FGFRi_invivo-logCPM.csv
BETi_FGFRi_invivo-rawdata.csv

value: Futibatinib+Birabresib


title: adipose stromal cells, TNFLT-treated - input, Rep 4 [CR_KDM6B_20]


title: 192_IF: ECFC1_IFN_treatment

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

institute: Hospital San Raffaele

hyb_protocol: Microarray preparation and analysis performed by Arraystar Inc

source_name: ECFC exposed to Interferon-β

growth_protocol: ECFCs were grown in EGM-2 (Lonza) supplemented with 10% FBS (Invitrogen) and allowed to reach confluency before treatment. Cells were passaged following defined treatment protocols to allow senescence induction to take hold, before cells were lysed and homogenised using 700uL of Qiazol (Qiagen)

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (Qiagen) following manufacturers protocol.

treatment_protocol: Confluent ECFCs were exposed to one of the following treatments: A. 10gy X-ray, four days recovery, passaging, RNA extraction 4 days post-passage. B. 1uM Etoposide for four days, four days recovery, passaging, RNA extraction 4 days post-passage. C. ECFCs were passaged until Hayflick limit was reached/cells exhausted their replicative potential, RNA was then extracted. D. ECFCs were treated with 100 IU/ml Interferon-β for 24 h. RNA was then extracted.

value: Umbilical Cord Blood

value: 100 IU/ml Interferon-β for 24 h

value: ECFCs


title: Ad_con_3


title: adipose stromal cells, untreated - KDM6B, Rep 4 [CR_KDM6B_17]

value: untreated


title: G39_COMBO_rep1

description:
COMBO_875
BETi_FGFRi_invivo-logCPM.csv
BETi_FGFRi_invivo-rawdata.csv

value: PDX G39

value: Glioblastoma patient derived xenograft, G39


title: adipose stromal cells, TNFLT-treated - input, Rep 3 [CR_KDM6B_16]

value: healthy donor 1


title: Ad_con_2


title: adipose stromal cells, untreated - input, Rep 3 [CR_KDM6B_15]


title: Ad_con_1


title: CD25_CDX31_NNE_M

tag: cdx model

tag: patient

value: circulating tumor cell-derived explant (CDX) model

tag: diagnosis

value: SCLC

tag: plastic or_matrigel

value: M

tag: neuroendocrine or_non-neuroendocrine

value: Non-NE

tag: sequencing run

value: Female

value: Extensive


title: CD25_CDX31_NNE_P

tag: tissue

value: P

tag: age

tag: gender

tag: sclc stage


title: SCC2_3

city: Zhengzhou

first: gangyu

last: Chen

state: He Nan

address: No 127  Dongming Road

institute: The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: LLC1、SCC1 and SCC2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Using limiting dilution, we established the SCDCLs(SCC1 and SCC2) from LLC1.SCC1 and SCC2 were cultured under the same conditions and passaged at least five but no more than eight times.

value: lung

tag: cell line

tag: cell subline

value: tumor cells

tag: genotype

value: WT

tag: treatment


title: CD25_CDX31_NE_M

value: NE


title: adipose stromal cells, untreated - input, Rep 2 [CR_KDM6B_08]

tag: cell type

value: adipose stromal cells

value: none (input)

value: healthy donor 2


title: CD25_CDX31_NE_P


title: adipose stromal cells, TNFLT-treated - KDM6B, Rep 3 [CR_KDM6B_14]

value: treated with TNFLT

tag: cut&run antibody


title: SCC2_1

value: untreated


title: SCC2_2


title: adipose stromal cells, untreated - KDM6B, Rep 3 [CR_KDM6B_13]

tag: subject

value: healthy donor 1


title: CD25_CDX19_NNE_M

tag: cdx model

value: circulating tumor cell-derived explant (CDX) model


title: SCC1_3


title: CD25_CDX19_NNE_P

tag: patient

value: SCLC


title: SCC1_2


title: adipose stromal cells, TNFLT-treated - input, Rep 2 [CR_KDM6B_07]


title: adipose stromal cells, TNFLT-treated - KDM6B, Rep 2 [CR_KDM6B_06]


title: CD25_CDX19_NE_M

tag: diagnosis

value: M


title: adipose stromal cells, untreated - KDM6B, Rep 2 [CR_KDM6B_05]


title: SCC1_1


title: adipose stromal cells, TNFLT-treated - input, Rep 1 [CR_KDM6B_04]


title: CD25_CDX19_NE_P

tag: plastic or_matrigel


title: LLC1_3


title: adipose stromal cells, untreated - input, Rep 1 [CR_KDM6B_03]


title: VAMP3

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human.GRCh38 whole genome using hisat2-2.0.1.
Fragments Per Kilo bases per Million reads (FPKM) were calculated using a protocol from Mortazavi et al., 2008.
Assembly: human.GRCh38
Supplementary files format and content: .txt files contain FPKM values

source_name: SK-N-SH cells

extract_protocol:
Total RNA was harvested using Trizol reagent.
1 μg total RNA was used for library preparation. Poly(A) mRNA was isolated using oligo(dT) beads.  mRNA was fragmented with divalent cations and high temperature. Random Primers were used to prime cDNA synthesis, and first strand cDNA and the second-strand cDNA synthesized. Double-stranded cDNA was treated to repair both ends and add a dA-tail, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. .Each sample was amplified by PCR using adapter sequence primers at both ends.  Libraries were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions

treatment_protocol: Cells were co-transfected with RNA and DNA using Lipofectamine 2000.

value: SK-N-SH cells

value: Overexpressing VAMP3


title: LLC1_2


title: miR-124

value: Overexpressing miR-124


title: LLC1_1


title: Control

value: Control


title: adipose stromal cells, untreated - KDM6B, Rep 1 [CR_KDM6B_01]


title: adipose stromal cells, TNFLT-treated - KDM6B, Rep 1 [CR_KDM6B_02]


title: HiChIP of H3K27ac in Homo sapiens: U87-H3K27ac-HiChIP-Rep2

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

data_processing:
Clean reads of RNA-seq were mapped to hg38 using HISAT2(2.1.0)
Expression levels of all genes were count.txted and expression profile matrix was constructed with featureCounts (2.0.4)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with padj < 0.05 and fold change > 2 or < 1/2
Clean reads of ChIP-seq were mapped to hg38 using Bowtie2(2.3.1)
Peak calling using MACS2(2.2.7.1)
Clean reads of HiChIP were mapped to hg38 with HIC-Pro (2.11.4)
HiChIP loops was called by hichipper(0.7.7)
Assembly: hg38
Supplementary files format and content: gene count text files; chip peak bigwig files; HiChIP interaction matrix files
Library strategy: HiChIP

source_name: brain

growth_protocol: The glioma cell lines U87 was cultured in DMEM (GIBCO), supplemented with 10% fetal bovine serum (BI) and 1% penicillin/streptomycin (GIBCO).

extract_protocol:
1. For RNA-seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions.  2. For Chip-seq: Cells were cross-linked with 1% formaldehyde at RT for 10 min and quenched in 125 mM glycine for 5 min. Cells were resuspended in SDS lysis buffer for 5 min and sonicated to generate DNA fragments averaging 100–500 bp in length. After centrifugation, chromatin fragments were immunoprecipitated with antibodies overnight (H3K27ac, H3K4me1, Abcam). The precipitated DNA and input DNA were purified and then sequenced at Novogene (Tianjin city, China).                                                                                3. For HiChIP: Briefly,  cells were cross-linked and chromatin was digested using MboI restriction enzyme (NEB). Then biotin-14-dATP was used to fill in the restriction fragment overhangs and mark the DNA ends. After ligation and sonication, the genomic DNA was incubated with H3K27ac antibody at 4 °C overnight. Immunocomplexes were captured by protein A magnetic beads. Beads were subsequently washed three times with low salt wash buffer, high salt wash buffer and LiCl wash buffer. DNA was eluted and purified with AMPure XP Beads (Beckman). Biotinylated DNA beads were captured by Streptavidin C-1. QIAseq FX DNA Library Kits (QIAGEN) was used to generate the sequencing library according to the manufacturer’s protocol. The libraries were validated for size distribution of 300–700 bp using AMPure XP beads (Beckman). The DNA was subjected to 2 × 150 bp paired-end sequencing at Novogene (Tianjin city, China).
RNA-seq Library: Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Then 3 µl USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.                                                                                2. ChIP-seq:  DNA libraries were generated using a FS DNA Library Prep Kit (QIAGEN). The precipitated DNA and input DNA were purified and then sequenced on Illumina HiSeq XTen sequencer. Bowtie2 was used to map ChIP-seq raw reads to the hg38 human reference genome. MACS2 program was used to call peaks of ChIP-seq data with the corresponding input data as control with default parameters. 3. HiChIP: QIAseq FX DNA Library Kits (QIAGEN) was used to generate the sequencing library according to the manufacturer’s protocol. The libraries were validated for size distribution of 300–700 bp using AMPure XP beads (Beckman). The DNA was subjected to 2 × 150 bp paired-end sequencing. The respective paired-end reads were aligned to the hg38 genome by HiC-Pro pipeline. Default settings were used for removal of duplicated reads, assignment to MboI restriction fragments and filtering for valid interactions. For each cell type, we merged the valid read pairs of individual samples. Hichipper was applied to call loops with default parameter. Loops with FDR < 0.1 and supported by at least 2 paired-end tags (PETS) were kept for further analysis. HiC-Pro was used to generate the HiChIP interaction maps. HiChIP interaction maps was then visualized by JuicerBox software at 50, 10 and 5 kb resolution as indicated.

treatment_protocol: For Erastin treatment, U87 cells were treated with 10 μM Erastin for 72 h.

value: brain

value: Normal growth condition


title: T lymphocytes, scRNAseq, chip 5, TCR

city: Rotterdam

first: Amy

last: van der List

address: Wytemaweg 80

institute: Erasmus MC

description:
TCR
assembled.rds

data_processing:
The data was analyzed according to 'Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level' (Litjens, NHR et al. 2022) (PMID: 35622330)
Assembly: GRCh38 human reference genome
Supplementary files format and content: RData file containing barcodes as well as reads for TRA/TRB and RNA expression for each cell

source_name: T lymphocyte

extract_protocol:
Following stimulation and staining, 20-25 million cells/ml per sample were filtered through a 35 µm nylon mesh and sorted for alloreactive T cells were sorted by positive signal for CD3 and CD137 and negative signal for CD14 (monocytes), CD19 (B-cells), CD56 (natural killer cells) and FVS780 (dead cells). Sorted alloreactive T cells were stained with Hoechst and propidium iodide (PI) and 160 µl at a concentration of 20-50 thousand cells/mL were dispensed per sample onto a pre-printed and a Blanco chip using the ICELL8 Single-Cell System. CellSelect automated microscopy image analysis software (Takara Bio) selected wells containing a single viable cell for in-chip full-length copy DNA (cDNA) amplification using SMARTScribe reverse transcriptase (Takara Bio). The resulting barcoded amplicons were purified off-chip by NucleoSpin Gel and PCR Clean-up kit (Machery-Nagel, Düren, Germany) followed by an AMPure XP beads purification (Beckman Coulter, Brea, USA).
transcriptome: Prepared cDNA libraries according to Takara SMARTer 5-prime sequencing method. From the cells, mRNA was isolated and reverse transcribed to single-cell barcoded cDNA from the 5-prime ends of the transcripts and sequenced according to the Illumina TruSeq Rapid v2 protocol on Illumina HiSeq2500 sequencer resultingng in single-end reads with a specific barcode (reads of 50 bp in length with a single 8 bp index sequence)
TCR: Prepared cDNA libraries according to Takara SMARTer Human TCR a/b Profiling method. From the cells, mRNA was isolated and the full-length T-cell receptor alpha and beta transcripts were reverse transcribed to single-cell barcoded cDNA. These cDNAs were sequenced on an Illumina MiSeq sequencer resulting in paired-end 300 basepair reads with both a barcode and the transcribed TCR a/b sequences.
TAKARA ICELL8 Human TCR profiling and 5' DE scRNA-seq

value: T lymphocyte


title: 2MC3T3

city: Toledo

first: Shang

last: Su

state: Ohio

address: 3000 Transverse Dr

department: Cell and Cancer Biology

institute: The University of Toledo

data_processing:
We applied a customed species-specific pipeline by integrating three different methods, Xenome, Xenofilter, and Kallisto, to extract human- and mouse- specific reads from the RNA-Seq data from the mixed co-culture samples. For Xenome and Xenofilter, read alignment was performed based on reference genome (GRCh38 for human and GRCm38 for mouse) and human/mouse-only reads were sorted with default settings and the species-specific reads were used for downstream differential expression (DE) analyses. For Kallisto, a combined human-mouse transcriptome was created by joining human transcriptome and mouse transcriptome (downloaded from Gencode) and then the FastQ reads were mapped to the joint transcriptome. Human/mouse-specific transcript counts were extracted for downstream DE analyses. DE analyses were performed with DESeq2 in R and DE gene thresholds were set at |log2FC| >=1 & padj < 0.05.
Assembly: GRCh38/GRCm38
Supplementary files format and content: CSV file containing log2FC results from DESeq2

source_name: cell line

growth_protocol: All the cells were maintained in alpha-MEM supplemented with 10% FBS.

extract_protocol:
Total RNAs were extracted from cells cultured alone or the mixed co-culture using RNeasy kit and were decontaminated of the DNA using RNase-Free DNase Set (Qiagen, Hilden, Germany). 500 ng of total RNA was used for the construction of sequencing libraries.
Libraries were prepared by the Van Andel Institute Genomics Core from 500 ng of total RNA using the KAPA stranded mRNA kit (v4.16) (Kapa Biosystems, Wilmington, MA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina UDI adapters (IDT, Coralville, IA). Quality and quantity of the libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Santa Clara, CA) and QuantiFluor® dsDNA System (Promega). Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq 6000 sequencer using 100 cycle sequencing kit (Illumina Inc., San Diego, CA) to a minimum read depth of 40 M reads/library.

value: cell line

value: mouse osteoblasts

value: WT

value: Cultured alone


title: 3MC3T3


title: HiChIP of H3K27ac in Homo sapiens: U87-H3K27ac-HiChIP-Rep1


title: T lymphocytes, scRNAseq, chip 1, TCR

description:
TCR
assembled.rds


title: 1MC3T3


title: HiChIP of H3K27ac in Homo sapiens: U87-Erastin 10 μM 72 h-H3K27ac-HiChIP-Rep2

value: 10 microM Erastin treated 72 h


title: Mus15

city: Cincinnati

first: Mike

last: Adam

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Raw sequencing data was processed through 10X Genomics CellRanger v2.2.0 using default parameters to obtain the gene expression matrices.
Genome_build: mm10 or Aco_one
Supplementary_files_format_and_content: mtx matrix files

source_name: ear

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: Adult

value: ear

value: macrophages


title: T lymphocytes, scRNAseq, chip 0, TCR

description:
TCR
assembled.rds


title: HiChIP of H3K27ac in Homo sapiens: U87-Erastin 10 μM 72 h-H3K27ac-HiChIP-Rep1


title: T lymphocytes, scRNAseq, chip 2, TCR

description:
TCR
assembled.rds


title: gastroc normoxia replicate 12

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. All arrays were included for data processing and normalization. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: gastroc, normoxia

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7).

growth_protocol: Male C57BL/6JOlaHsd mice arrived at 10 weeks of age and were individually housed and maintained under environmentally controlled conditions (21 ± 1ºC, 12 h/12 h light–dark cycle, 50 ± 10% humidity) and had ad-libitum access to feed and water. During the first three weeks of the study, mice could adapt to the new environment and received a purified low-fat diet that contained 10% energy from fat (Hoevenaars et al., Genes & Nutr 2012). Thereafter, mice received a purified high-fat diet that contained 40% energy from fat for the remaining 6 weeks of the study.

extract_protocol: Total RNA was isolated from the gastrocnemius muscle using RNeasy Mini columns (Qiagen) according to the manufacturer’s instruction, quantified using Nanodrop (IsoGen Life Science) and qualified using Experion Automated Electrophoresis System (BioRad).

treatment_protocol: After the 6 weeks of high-fat feeding, mice were fasted and were either exposed to hypoxia (12% oxygen) or remained under normoxia (20.9% oxygen) for a duration of 6 hours, according to Duivenvoorde et al., (J Gerontol A Biol Sci Med Sci. 2014). Mice were decapitated directly after the exposure and the gastrocnemius muscle was removed and snap-frozen in liquid nitrogen.

tag: strain

value: male

value: gastrocnemius

tag: stress

value: normoxia

source_name: gastroc, reference pool of all samples

tag: sample type

value: reference pool of all samples


title: cow 9040 before LPS treatment

city: Saint Genès-Champanelle

first: christine

last: Leroux

address: Route de Theix

institute: INRAE

data_processing: The resulting TIFF images were processed using Feature Extraction software Version 11 (Agilent Technologies, Inc. Santa Clara, USA).

source_name: Milk Fat miRNA

extract_protocol: One g of MF was mixed with 2.0 mL of TRIzol LS solution (Invitrogen Life Technologies Inc.), then 600 µL of chloroform were added before centrifugation at 12,000 x g for 20 min at 4°C. The upper aqueous layer was precipitated using 500 µL of isopropanol

tag: tissue

value: Milk Fat

tag: growth

value: 27±3 days in milk

value: No LPS


title: gastroc hypoxia replicate 10

source_name: gastroc, hypoxia

tag: gender

value: hypoxia


title: 193F_IF: ECFC2_IFN_treatment

scan_protocol: Microarray preparation and analysis performed by Arraystar Inc

value: Umbilical Cord Blood

value: 100 IU/ml Interferon-β for 24 h

value: ECFCs


title: healthy donor - adipose stromal cells, Rep 4

data_processing:
Illumina software used for basecalling.
FastQC control quality.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR with parameters : --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
The read counts were called using featureCounts from Subread package.
Differential gene expression analysis was performed using DESeq2 in R Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts values for each Sample.

source_name: healthy donor, fat tissue

growth_protocol: not applicable

extract_protocol:
Lipoaspiration from 4 healthy donors were collected and enzymatically dissociated. After depletion of hematopoietic cells (Dynal, Dynabeads CD45) stromal cells were sorted by FACS based on their phenotype and RNA extraction (Macherey-Nagel, NucleoSpin RNA XS) was performed. Quality control was performed using the Agilent RNA 6000 Pico Kit.
RNA libraries were prepared (with 10ng of total RNA) for sequencing using standard Illumina protocols.

treatment_protocol: not applicable

value: native adipose stromal cells

value: healthy donor


title: ChIP-seq of H3K27ac in Homo sapiens: U87-input1

data_processing:
Clean reads of RNA-seq were mapped to hg38 using HISAT2(2.1.0)
Expression levels of all genes were count.txted and expression profile matrix was constructed with featureCounts (2.0.4)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with padj < 0.05 and fold change > 2 or < 1/2
Clean reads of ChIP-seq were mapped to hg38 using Bowtie2(2.3.1)
Peak calling using MACS2(2.2.7.1)
Clean reads of HiChIP were mapped to hg38 with HIC-Pro (2.11.4)
HiChIP loops was called by hichipper(0.7.7)
Assembly: hg38
Supplementary files format and content: gene count text files; chip peak bigwig files; HiChIP interaction matrix files

tag: cell line

value: brain

value: Normal growth condition


title: Mus10

tag: age

value: Adult

value: ear


title: gastroc hypoxia replicate 12

value: male


title: Mus05

value: macrophages


title: gastroc hypoxia replicate 09

value: gastrocnemius


title: gastroc hypoxia replicate 01

value: reference pool of all samples


title: B2_IF: ECFC3_IFN_treatment

data_processing: Microarray preparation and analysis performed by Arraystar Inc


title: gastroc normoxia replicate 06

value: normoxia


title: gastroc normoxia replicate 02


title: gastroc hypoxia replicate 11


title: gastroc hypoxia replicate 02


title: gastroc hypoxia replicate 03


title: gastroc hypoxia replicate 05


title: gastroc hypoxia replicate 04