title: 3-NFL

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description:
SS34
BeWo_logCPM_exprTable.txt

data_processing:
Raw fastq was aligned to human reference genome GRCh38 with hisat2 v2.1.0.
Gene wise counts were generated with featureCounts from the subread package v1.5.1 for genes annotated by Ensembl GRCh38.92.
Counts from separate sequencing lanes for the same sample were summed.
Genes were filtered for at least 2 CPM in half the samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: *logCPM_exprTable.txt files contain counts normalized as log2 CPM for genes with at least 2 counts per million reads.

source_name: cell line

growth_protocol: BeWo cells were plated in DMEM/F12 supplemented with GlutaMAX plus 10% HI-FBS and penicillin/streptomycin at 5 x 10^4 cells/cm2 for fused, and 2.5 x 10^4 cells/cm2 for non-fused experimental conditions.

extract_protocol:
Cells were lysed in TRIzol reagent (Invitrogen). PureLink RNA extraction kit with on-column DNase treatment (Invitrogen) was used to isolate RNA. Input RNA integrity number (RIN) were all > 7 and concentration was >100 ng/µl RNA, as determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Qubit Fluorometer (Thermo Fisher).
RNA-seq libraries were generated with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB #E7760L) and NEBNext® rRNA Depletion Kit with sample purification beads (NEB #E6350) with an input amount of 200 ng total RNA per sample. Libraries were pooled and sequenced on an Illumina NovaSeq SP flowcell in paired-end 150 bp format (Illumina, San Diego, CA) to a read yield between 70-80 million reads (equivalent to 35- 40 million clusters).

treatment_protocol: PHT and BeWo cells were infected, or not, in 6 well-cell culture plates with 4 x 10^6 WT Lm /well for 1h followed by 30 min gentamicin, and 3.5 h in gentamicin-free medium (5 h samples). Cells were pulsed with gentamicin for 30 min after 5 hours infection, and incubated in gentamicin free medium for another 5 hours (10 hours samples).

value: DMSO

value: BeWo

value: trophoblast derived choriocarcinoma (epithelial)

tag: fused status

value: No

tag: batch

tag: listeria infection

value: Yes


title: Rep2_L771

status: Public on Jul 15 2021

type: SRA

city: San Francisco

first: Jason

last: Fernandes

state: CA

address: 600 16th Street, Genentech Hall, Room S574, MC 2280

country: USA

institute: UCSF

description:
HIV-1 RNA
Viral RNA harvested and sequenced after spread

library_source: transcriptomic

data_processing:
Library strategy: Amplicon-Sequencing
FASTQs were generated using bcl2fastq v2.17.1.14
Codons were counted using countDMS
Genome_build: HIV-1 NL4-3
Supplementary_files_format_and_content: tab

molecule: total RNA

organism: Human immunodeficiency virus 1

growth_protocol: SupT1 human T-cell lines were maintained in RPMI (supplemented with 25 mM HEPES pH 7.4, 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin) at 37°C and 5% CO2.

extract_protocol:
RNA was extracted from virions by ZR-96 Viral RNA extraction kits (Zymo) and eluted in 15 ul water. cDNA was amplified from 5uL of extracted RNA using the iScript Advanced (BioRad) cDNA synthesis.
PCR amplicons were made from DNA using primers specific to the Env LLP-2 region

treatment_protocol: We infected SupT1 cells at low MOI (multiplicity of infection) with each library individually and measured the change in allele frequencies after approximately 6 generations of viral spread (Figure 3A)

tag: source

value: SupT1 human T cell line

tag: strain

tag: treatment

value: Post-selection


title: PA-GFP Foxp3IRES-RFP_21

city: New York

first: Johanne

last: Jacobsen

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Raw FASTQ sequence files generated from Smartseq2 libraries were aligned to the mouse genome (v. mm10) with the annotated transcriptome (v. gencode M22) using STAR (v. 2.6). Subsequently, genome-mapped BAM files were processed using RSEM (v. 1.3.1) for gene quantification. The matrix of gene counts was used as input for analysis using the R package Seurat (v. 3.1.4.). To control unwanted sources of experimental variation, we eliminated any experiment-specific variables by regressing out the batch effect factors as described. Additionally, cells containing more than 10% of sequence reads aligned to mitochondrial genes were excluded before normalization.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contains RSEM results for each cell.

organism: Mus musculus

source_name: Germinal Centers

extract_protocol:
Single T cells were index-sorted into 96-well PCR plates containing 5 μl of TCL buffer (Qiagen) with 1% β-mercaptoethanol.
SmartSeq2: Libraries were prepared as previously described (Trombetta et al., 2014). Briefly, nucleic acids were extracted from sorted single cell using RNAClean XP SPRI beads (Beckman Coulter), and RNA was hybridized first using RT primer (/5BiosG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) then reverse-transcribed into cDNA using TSO primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG) and RT maxima reverse transcriptase (Thermo Fisher Scientific). cDNA was amplified using ISPCR primer (AAGCAGTGGTATCAACGCAGAGT) and KAPA HiFi HotStart ReadyMix (Fisher Scientific), cleaned up using RNAClean XP SPRI beads three times, and tagmented using Nextera XT DNA Library Preparation Kit (Illumina). For each sequencing batch, up to four plates were barcoded at a time with Nextera XT Index Kit v2 Sets A-D (Illumina). Finally, dual-barcoded libraries were pooled and sequenced using the Illumina Nextseq 500.

tag: sequencing plate

value: PA-GFP Foxp3IRES-RFP

tag: experiment

tag: cell annotation

value: CD4+ Resting


title: PA-GFP Foxp3IRES-RFP_23


title: 3-NFN

description:
SS33
BeWo_logCPM_exprTable.txt

organism: Homo sapiens

tag: cell line

tag: cell type


title: PA-GFP Foxp3IRES-RFP_22


title: Micro-C_∆YY1_UT_rep1

city: Berkeley

first: Xavier

last: Darzacq

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
Homozygous cell line with endogenous YY1 loci tagged with an auxin-inducible degron
YY1-UT_pool.mcool

library_source: genomic

data_processing:
Library strategy: Micro-C
ChIP-Seq quality check: FastQC
ChIP-Seq read alignment: Bowtie (-n 2, -m 1)
ChIP-Seq peak calling: MACS2 (--nomodel --extsize 300); merged inputs used as controls
ChIP-Seq heatmaps: deepTools (version 2.4.1) bamCoverage (--binSize 50 --normalizeTo1x 2150570000 --extendReads 300 --ignoreDuplicates -of bigwig) to normalize read numbers to 1x sequencing depth, obtaining read coverage per 50-bp bins across the whole genome (bigWig files). We then used the bigWig files to compute read numbers across 6 kb centered on  ChIP-Seq MACS2 peak summits (computeMatrix reference-point --referencePoint=TSS --upstream 3000 --downstream 3000 --missingDataAsZero --sortRegions=no). We sorted the output matrices by decreasing UT enrichment, calculated as the total number of reads within a MACS2 called ChIP-seq peak. Finally, heatmaps were created with the plotHeatmap tool (--averageTypeSummaryPlot=mean --colorMap='Blues' --sortRegions=no).
Micro-C allValidPairs were generated by HiC-Pro package (>2.10 version)
Micro-C mcool files were converted from allValidPairs by Cooler package
RNA-seq read alignment: STAR aligner
RNA-seq browser track: deepTools
mNET-seq read alignment: STAR aligner
mNET-seq browser track: deepTools
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq bigWig files: read coverage per 50-bp bins across the whole genome (read numbers normalized to 1x sequencing depth; merged duplicates)
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions
Supplementary_files_format_and_content: RNA-seq bigWig files: read coverage per 10-bp bins across the whole genome (read numbers normalized to TPM; merged duplicates; split strands)
Supplementary_files_format_and_content: mNET-seq bigWig files: read coverage per 10-bp bins across the whole genome (read numbers normalized to TPM; merged duplicates; split strands)

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: JM8.N4 mESCs were grown on gelatin-coated plates in knock-out DMEM supplemented with 15% FBS, non-essential amino acids, glutamax, Penicillin-streptomycin, 2-mercapoethanol and LIF. mES cells were fed daily and passaged every 2-3 days by trypsinization.

extract_protocol:
Micro-C protocol was performed as the following steps: 1) digest crosslinked chromatin by MNase; 2) Repair fragment ends with biotin-dNTP; 3) Proximal ligation and purge unligated ends; 4) Purify ligated dinucleosomal DNA.
Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1. Standard library preparation protocol including end-repair, A-tailing, and adapter ligation was performed on beads with individual enzymes purchased from Lucigen or NEBnext UltraII kit. Sequencing library was amplified by Kapa HiFi PCR enzyme with lowest possible cycles to reduce PCR duplicates. Sequencing library was sequenced paired-end 50x50 in Illumina HiSeq 4000 sequencer.

treatment_protocol: Degron cell lines were treated for 3 hours with either ethanol only (control, untreated) or with 500 uM, ethanol-dissolved auxin.

tag: genotype

value: mIAA7-mScarletI-YY1 / osTir

value: Ethanol, 3 hrs

tag: chip antibody


title: PA-GFP Foxp3IRES-RFP_20


title: Rep1_L771


title: PA-GFP Foxp3IRES-RFP_19


title: Rep6_R770


title: Rep5_R770


title: PA-GFP Foxp3IRES-RFP_18


title: Rep4_R770


title: PA-GFP Foxp3IRES-RFP_17


title: 2-NFN

description:
SS21
BeWo_logCPM_exprTable.txt


title: Rep3_R770


title: 2-NFL

description:
SS22
BeWo_logCPM_exprTable.txt


title: DCCO control rep1

city: Ste anne de bellevue

first: Jessica

last: Head

state: QC

address: 21111 Lakeshore Road

country: Canada

institute: McGill University

description: DCCO_KO_abundance_table_all_birds_Seq2Fun2.txt

data_processing:
Seq2Fun used for quantification of protein-coding genes
Seq2Fun starts the raw reads quality check and employs the translated search and does not require transcriptome de novo assembly. In brief, each pair of reads was first trimmed by both ends with an average base quality 20 in a sliding window size 4, followed by poly(G) trimming. The sequencing errors were corrected on the overlapped region of the read pair before ploy(A) removal. The overlapped read pair was joined to form a single end clean read. For the translated search, the clean read was translated to amino acid fragments using all possible reading frames from both directions. Length filtering was performed on the fragments and only the longest were kept for searching. The fragment homology searching was  performed using FMI based on Burrows-Wheeler transform data structure in Seq2Fun GREEDY mode. The gene abundance tables were generated by summarizing all the read-gene pairs. The protein sequences used by Seq2Fun for JQ and DCCO were retrieved from the KEGGREST database, consisting of 370644 protein sequences representing 36448 ortholog genes from 24 birds species (Tenenbaum and Maintainer 2020). The Gene Entrez IDs were used to retrieve Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog (KO) IDs.
Differential gene expression analysis was performed using EdgeR.
Genes were first filtered for low counts using minimum counts per million threshold of 0.5, then differentially expressed genes were identified between each treatment group (medium or high dose) and the control based on the combination of fold-change expression (log2FC ≥ 1) and adjusted p-value based on a false discovery rate (FDR < 0.05).
Genome_build: KEGGREST database with 24 bird species
Supplementary_files_format_and_content: tab delimited txt file with gene abundance counts for every gene and every sample

organism: Phalacrocorax auritus

source_name: embryonic liver

growth_protocol: Eggs were incubated at 37oC and 60% humidity

extract_protocol:
Individual liver samples were homogenized in buffer RLT using a TissueLyser II (Qiagen, Toronto, ON, CA), and RNA extracted using the RNeasy® Mini QIAcube Kit (Qiagen, Toronto, ON, CA) following the manufacturer’s protocol. An extra DNAse I digestion step was included in order to eliminate genomic DNA contamination. Total RNA concentration and purity was spectrophotometrically measured using the QIAxpert.
Library preparation and mRNA sequencing was performed by the Genome Quebec Innovation Centre (Montreal. QC). Libraries were sequenced to produce paired-end 101 bp reads using Illumina HiSeq 4000.

treatment_protocol: Dosing solutions were injected into the air cell of fertilized, un-incubated eggs, and included DMSO control, medium dose, and high dose. The high dose was selected to result in <20% embryonic mortality based on preliminary species-specific data. Nominal doses of chlorpyrifos were 0.4, 4.0, and 40 µg/g egg for both species and injected doses were also analytically determined from egg samples.

tag: tissue

value: liver

tag: age

value: embryo development day 16


title: PA-GFP Foxp3IRES-RFP_16


title: 2-FL

description:
SS16
BeWo_logCPM_exprTable.txt

growth_protocol: BeWo cells were plated in DMEM/F12 supplemented with GlutaMAX plus 10% HI-FBS and penicillin/streptomycin at 5 x 10^4 cells/cm2 for fused, and 2.5 x 10^4 cells/cm2 for non-fused experimental conditions. Fusion was induced after 24 h of culture by daily addition of 20 µM forskolin (FSK, Sigma-Aldrich) for up to 72 h.

value: forskolin


title: 2-FN

description:
SS15
BeWo_logCPM_exprTable.txt


title: Rep2_R770


title: 1-NFL

description:
SS10
BeWo_logCPM_exprTable.txt


title: Rep6_H769


title: Rep1_R770


title: PA-GFP Foxp3IRES-RFP_14


title: 3-FL

description:
SS28
BeWo_logCPM_exprTable.txt


title: PA-GFP Foxp3IRES-RFP_13

value: Cycling


title: Rep4_H769


title: Rep5_H769


title: PA-GFP Foxp3IRES-RFP_12


title: 3-FN

description:
SS27
BeWo_logCPM_exprTable.txt


title: 1-NFN

description:
SS9
BeWo_logCPM_exprTable.txt


title: 1-FL

description:
SS4
BeWo_logCPM_exprTable.txt


title: mNET-seq_∆YY1_IAA_rep2

description: Homozygous cell line with endogenous YY1 loci tagged with an auxin-inducible degron

data_processing:
Library strategy: mNET-seq
ChIP-Seq quality check: FastQC
ChIP-Seq read alignment: Bowtie (-n 2, -m 1)
ChIP-Seq peak calling: MACS2 (--nomodel --extsize 300); merged inputs used as controls
ChIP-Seq heatmaps: deepTools (version 2.4.1) bamCoverage (--binSize 50 --normalizeTo1x 2150570000 --extendReads 300 --ignoreDuplicates -of bigwig) to normalize read numbers to 1x sequencing depth, obtaining read coverage per 50-bp bins across the whole genome (bigWig files). We then used the bigWig files to compute read numbers across 6 kb centered on  ChIP-Seq MACS2 peak summits (computeMatrix reference-point --referencePoint=TSS --upstream 3000 --downstream 3000 --missingDataAsZero --sortRegions=no). We sorted the output matrices by decreasing UT enrichment, calculated as the total number of reads within a MACS2 called ChIP-seq peak. Finally, heatmaps were created with the plotHeatmap tool (--averageTypeSummaryPlot=mean --colorMap='Blues' --sortRegions=no).
Micro-C allValidPairs were generated by HiC-Pro package (>2.10 version)
Micro-C mcool files were converted from allValidPairs by Cooler package
RNA-seq read alignment: STAR aligner
RNA-seq browser track: deepTools
mNET-seq read alignment: STAR aligner
mNET-seq browser track: deepTools
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq bigWig files: read coverage per 50-bp bins across the whole genome (read numbers normalized to 1x sequencing depth; merged duplicates)
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions
Supplementary_files_format_and_content: RNA-seq bigWig files: read coverage per 10-bp bins across the whole genome (read numbers normalized to TPM; merged duplicates; split strands)
Supplementary_files_format_and_content: mNET-seq bigWig files: read coverage per 10-bp bins across the whole genome (read numbers normalized to TPM; merged duplicates; split strands)

extract_protocol:
Nascent RNAs were extracted as the following steps: 1) Chromatin isolation; 2) Chromatin and RNA digestion; 3) Immunoprecipitation of Pol II complex; 4) RNA phosphorylation with T4 PNK; 5) RNA purification; 6) Size-selection for small RNAs.
mNET-seq RNA libraries were prepared according to protocol of NEBNext small RNA library prep kit (NEB, #E7330).

value: 500 mM auxin in ethanol, 3 hrs

value: Polymerase II (8WG16 antibody)


title: Rep3_H769


title: 1-FN

description:
SS3
BeWo_logCPM_exprTable.txt


title: mNET-seq_∆YY1_IAA_rep1


title: mNET-seq_∆YY1_UT_rep2


title: Rep6_Y768


title: mNET-seq_∆YY1_UT_rep1


title: Rep1_H769


title: PA-GFP Foxp3IRES-RFP_11


title: PA-GFP Foxp3IRES-RFP_15


title: PA-GFP Foxp3IRES-RFP_9


title: PA-GFP Foxp3IRES-RFP_8


title: Rep4_Y768


title: PA-GFP Foxp3IRES-RFP_5

value: Tfr


title: PA-GFP Foxp3IRES-RFP_6


title: Rep5_Y768


title: Rep3_Y768


title: PA-GFP Foxp3IRES-RFP_7


title: iAEC2-Lacto 500_3_RNA

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

description:
tpm.csv
raw.count.csv
SI_29340

data_processing:
Transcripts were quantified by alignment-free approach kallisto and then summarized to obtained gene level counts.
Genome_build: hg38
Supplementary_files_format_and_content: raw count and TPM in csv

source_name: iPSC (SPC2 iPSC line, clone SPC2-ST-B2, Boston University)-derived alveolar epithelial type 2 cells

growth_protocol: iPSC (SPC2 iPSC line, clone SPC2-ST-B2, Boston University) derived alveolar epithelial type 2 cells (iAEC2s) were differentiated and maintained as alveolospheres embedded in 3D Matrigel in "CK+DCI" media, as previously described (Jacob et al. 2019). iAEC2s were passaged approximately every two weeks by dissociation into single cells via the sequential application of dispase (2 mg/ml, Thermo Fisher Scientific, 17105-04) and 0.05% trypsin (Invitrogen, 25300054) and re-plated at a density of 400 cells/µl of Matrigel (Corning, 356231)

extract_protocol:
Cells were harvested in Trizol, and total cellular and viral RNA was extracted with the Direct-zol RNA extraction kit (Zymo Research).
Total RNA used the poly-A selection by Sera-Mag™ Oligo(dT)-Coated Magnetic Particles (Cat No. 38152103010150, GE Healthcare Life Sciences), and libraries were generated by KAPA RNA HyperPrep Kit (Cat No. KK8541, Roche Sequencing Solutions).

treatment_protocol: iAEC2 were seeded in a 24-well plate and treated with lactoferrin at the efficacious concentration of 6250 nM for 48 hrs.


title: Rep2_Y768


title: PA-GFP Foxp3IRES-RFP_4


title: PA-GFP Foxp3IRES-RFP_3


title: iAEC2-Lacto 500_2_RNA

description:
tpm.csv
raw.count.csv
SI_29339

value: treated with lactoferrin at the efficacious concentration of 6250 nM for 48 hrs.


title: Rep2_H769


title: PA-GFP Foxp3IRES-RFP_2


title: iAEC2-Lacto 500_1_RNA

description:
tpm.csv
raw.count.csv
SI_29338


title: iAEC2-NI_3_RNA

description:
tpm.csv
raw.count.csv
SI_29337

value: untreated


title: PA-GFP Foxp3IRES-RFP_10


title: PA-GFP Foxp3IRES-RFP_1


title: iAEC2-NI_2_RNA

description:
tpm.csv
raw.count.csv
SI_29336


title: Rep5_S767


title: Rep6_S767


title: Rep4_S767


title: Rep3_S767


title: Rep2_S767


title: Rapa/Veh 3

city: Memphis

first: Canan

last: Kuscu

address: 71 S Manassas St.

institute: University of Tennessee Health Science Center

data_processing:
Sequencing reads were first processed (trimming of 5 nt from 5’ end) and quality filtered (removal of reads with phred score < 28 in 80% of the read length) using fastx_toolkit.
Trimmed and filtered reads were aligned to mm38 reference genome using bowtie2.
Counts per gene were obtained with Htseq-count
DESeq2 was used to identify differentially expressed genes
Genome_build: mm38
Supplementary_files_format_and_content: csv files with base mean, log 2 fold change, pvalue and padj

source_name: Bone Marrow Dendritic cells

growth_protocol: freshly isolated BM was cultured with 6 ng/ml recombinant mouse GMCSF (total of 3 treatments) for 8 days in RPMI 1640 (Invitrogen).  80-90% of resulting cells were CD11c+ DCs as determined by flow cytometry with CD11c antibody.

extract_protocol:
RNA was extracted using Zymo Research RNA isolation kit.
400 ng of total RNA was used to generate libraries for RNA sequencing using NEB Next Ultra II-Dimensional RNA-seq library prep kit for Illumina

treatment_protocol: BMDC were treated with 10 ng/ml Rapamycin (Sigma, St. Louis, MO) for a total of 3 treatments for chronic treatment

value: BMDC

value: Rapamycin


title: iAEC2-NI_1_RNA

description:
tpm.csv
raw.count.csv
SI_29335


title: Rep1_S767

value: SupT1 human T cell line


title: Rapa/Veh 1


title: HUES21_Non_eroded_dKO_1

city: Isehara-shi

first: Atsushi

last: Fukuda

country: Japan

institute: Tokai University

data_processing:
Basecalls performed using bcl2fastq v2.20.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.38 tool.
The sequence reads were aligned to the Human reference genome (hg19) using STAR 2.7.1a.
The read counts allocated for each gene and transcript (Ensembl Genes 2014.01.02) were quantified using TPM (Transcripts Per Million) method using StrandNGS 3.4 software (Agilent Technologies, Santa Clara, CA).
Genome_build: hg19
Supplementary_files_format_and_content: An excel format file (XLSX) includes TPM quantification values and Ensembl gene annotations of all samples.

growth_protocol: Human pluripotent stem cells were cultured in mTeser1 (HUES21) and StemFlex (ADSC-iPS). For passage the cells, 1mM EDTA was used and Rock inhibitor was added to culture medium for 24 hours after passage.

extract_protocol:
Total RNA was extracted using RNeasy plus micro kit according to manufacturer's instructions
Total RNA obtained from each sample was subjected to a sequencing library construction using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA) according to the manufacturer’s protocols. Strand specific RNA-seq  (first strand).

treatment_protocol: Gene manupulated cell lines were generated by CRISPR-Cas9 system.

value: embryonic stem cell

value: DNMT3A and 3B deletion


title: Rapa/Veh 2


title: Input_L775

description:
provirus
Proviral Plasmid sequenced, randomized at specified position

value: Pre-selection


title: HUES21_Eroded_1

value: WT


title: HUES21_Non_eroded_dKO_2


title: RNA-seq_∆YY1_IAA_rep1

data_processing:
ChIP-Seq quality check: FastQC
ChIP-Seq read alignment: Bowtie (-n 2, -m 1)
ChIP-Seq peak calling: MACS2 (--nomodel --extsize 300); merged inputs used as controls
ChIP-Seq heatmaps: deepTools (version 2.4.1) bamCoverage (--binSize 50 --normalizeTo1x 2150570000 --extendReads 300 --ignoreDuplicates -of bigwig) to normalize read numbers to 1x sequencing depth, obtaining read coverage per 50-bp bins across the whole genome (bigWig files). We then used the bigWig files to compute read numbers across 6 kb centered on  ChIP-Seq MACS2 peak summits (computeMatrix reference-point --referencePoint=TSS --upstream 3000 --downstream 3000 --missingDataAsZero --sortRegions=no). We sorted the output matrices by decreasing UT enrichment, calculated as the total number of reads within a MACS2 called ChIP-seq peak. Finally, heatmaps were created with the plotHeatmap tool (--averageTypeSummaryPlot=mean --colorMap='Blues' --sortRegions=no).
Micro-C allValidPairs were generated by HiC-Pro package (>2.10 version)
Micro-C mcool files were converted from allValidPairs by Cooler package
RNA-seq read alignment: STAR aligner
RNA-seq browser track: deepTools
mNET-seq read alignment: STAR aligner
mNET-seq browser track: deepTools
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq bigWig files: read coverage per 50-bp bins across the whole genome (read numbers normalized to 1x sequencing depth; merged duplicates)
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions
Supplementary_files_format_and_content: RNA-seq bigWig files: read coverage per 10-bp bins across the whole genome (read numbers normalized to TPM; merged duplicates; split strands)
Supplementary_files_format_and_content: mNET-seq bigWig files: read coverage per 10-bp bins across the whole genome (read numbers normalized to TPM; merged duplicates; split strands)

extract_protocol:
RNAs were extracted using the standard TRIzol RNA extraction protocol and then depleted rRNA with NEBNext rRNA Depletion Kit (NEB, #E6310).
The rRNA-depleted RNAs were then subjected to the RNA-seq library construction using the protocol of NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (NEB, #E7765).

value: mIAA7-mScarletI-YY1 / osTir


title: Veh/Veh 3

value: Vehicle


title: Input_L776


title: Rep1_Y768

value: Post-selection


title: Veh/Veh 2


title: HUES21_Non_eroded_2


title: Veh/Veh 1


title: Input_L774


title: RNA-seq_∆YY1_UT_rep2

value: Ethanol, 3 hrs


title: Single cell measurements of RNA & nuclear proteins in adult mouse hippocampus (n=2 PBS, n=2 kainic acid) [inCITE]

city: Cambridge

first: Hattie

last: Chung

state: MA

address: 415 Main St

institute: Broad Institute

description: Mouse hippocampus nuclei from PBS (n=2) and kainic acid (KA; n=2) treated mice. One PBS and one KA were pooled as a single batch (with two total batches) using nucleus-hashing antibodies, loaded on a single 10x channel, and computationally demultiplexed as PBS vs. KA with DemuxEM

data_processing:
Raw bcl files were converted to fastq, and aligned to either hg19_premrna or mm10_premrna genomes using cellranger v4.0.0 running on Cumulus version 1.0
Genome_build: hg19_premrna or mm10_premrna
Supplementary_files_format_and_content: csv files for creating anndata object. Contains gene expression data, nucleus hashtag HTO counts, protein ADT counts, and pooled batches (if applicable). Load as anndata object.

source_name: Adult mouse hippocampus

extract_protocol:
nuclei extraction with EZ prep
3' polyA RNA seq
10X Genomics Chromium Prep V3 3'

treatment_protocol: 8-week-old male mice were acclimated into the procedure room for 1hr, then injected intraperotineally with PBS or 20 mg/kg kainic acid dissolved in PBS. After 2 hrs, mice were euthanized by CO2 and perfused through the left ventricle of the heart with 20mL PBS. The entire brain was removed, and the hippocampus was dissected on ice before freezing on dry ice. Nuclei extracted from one PBS and one KA treated mice were pooled together with nucleus-hashing antibodies.

value: mouse hippocampus tissue, all cell types

tag: mixed sample

value: (n=2 PBS treated, n=2 kainic acid treated)

tag: sample type

value: multiplexed p65, c-Fos, NeuN, and PU.1 protein


title: ADSC_iPS_Non_eroded_dKO_2

value: iPS


title: Input_D773


title: Input_R772


title: DKO_input_ChIPseq

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

data_processing:
Reads were aligned to mm9 using BWA (v. 0.7.17).
For peak calling MACS2 was used.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files generated using deeptools (v. 2.5.4)

source_name: DKO GEMM prostate cell line

growth_protocol: Cells were grown in prostatic epithelial (PrE) media (DMEM supplemented with 2.5% charcoal-stripped FBS, 5 ug/mL ITS, 10 ug/mL BPE, 10 ug/mL EGF)

extract_protocol:
Input DNA from sonicated nuclei
Libraries were constructed using the KAPA HyperPrep Kit (Roche, #KK8504) with Illumina TruSeq indexes.

value: DKO GEMM prostate cell line


title: DKO_EZH2_ChIPseq

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were constructed using the KAPA HyperPrep Kit (Roche, #KK8504) with Illumina TruSeq indexes.

value: EZH2 (Active Motif, #39933)


title: IR_d28

city: 武汉

first: 汉

last: 朱

state: 湖北

address: 1095 解放大道， 武汉 430030， 中国

country: China

institute: 肾

data_processing:
none provided by the submitter
Genome_build: mm10

source_name: Kidney

extract_protocol: The kidney was homogenized using 21G and 26 1/2G syringes. Up to 0.25 g of the tissue was digested with 50ul of Enzyme D, 25 μl of Enzyme R and 6.75 μl of Enzyme A in 1 ml of RPMI and incubated for 30mins at 37°C. The reaction was deactivated by adding 10% FBS. The solution was then passed through a 40 μm cell strainer. After centrifugation at 1,000 RPM for 5 mins, cell pellet was incubated with 1 ml of RBC lysis buffer on ice for 3 mins. Cell number and viability were analyzed using Countess AutoCounter (Invitrogen, C10227).

value: Kidney


title: ADSC_iPS_Non_eroded_dKO_1


title: Input_L771


title: HUES21_Eroded_2


title: RNA-seq_∆YY1_IAA_rep2

value: 500 mM auxin in ethanol, 3 hrs


title: DKO_AR_ChIPseq

value: AR (Millipore, #06-680)


title: ADSC_iPS_Eroded_2


title: Input_R770

value: SupT1 human T cell line


title: IR_Lac.z_d5

address: 1095 解放大道， 武汉 430030， 中国


title: ADSC_iPS_Eroded_1


title: TKO_ATACseq

source_name: TKO GEMM prostate cell line

extract_protocol:
Samples were processed for ATAC-seq as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015).
Tagmentation reaction was performed using 2.5 µl Illumina TDE1 in 50 µl Illumina TD buffer at 37°C for 30 min. The tagmented DNA library was purified using the QIAquick PCR Purification Kit. Library quantification and number of amplification cycles was determined as described (Buenrostro et al., 2015).

value: TKO GEMM prostate cell line


title: IR_d5

address: 1095 解放大道， 武汉 430030， 中国


title: DKO_ATACseq


title: HUES21_Non_eroded_1

value: embryonic stem cell


title: Input_Y768

value: Pre-selection


title: RNA-seq_∆YY1_UT_rep1

value: mIAA7-mScarletI-YY1 / osTir


title: SKO_ATACseq

source_name: SKO GEMM prostate cell line

value: SKO GEMM prostate cell line

value: PTENf/f


title: Input_S767


title: P6 testicular cells, Dis3 WT (scRNA-seq)

city: Bethesda

first: Zhengpin

last: Wang

state: MD

address: National Institutes of Health, 9000 Rockville Pike

department: Laboratory of Cellular and Developmental Biology

institute: NIDDK, NIH

data_processing:
Raw base call (BCL) files were demultiplexed with bcl2fastq; Cell Ranger (version 3.1) from 10x genomics was used to align reads, generate feature-barcode matrices for both Control and KO samples
cellranger mkfastq was used to generate FASTQ files
cellranger count performs alignment, filtering, barcode counting, and UMI counting
Genome_build: mm10
Supplementary_files_format_and_content: filtered_feature_bc_matrix

source_name: P6 Testis

growth_protocol: B6D2F1 mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Testes isolated from P6 aged control and knockout mice.

extract_protocol:
Single testicular cells were isolated from P6 control and knockout mice. Testes were digested into single cell suspensions with 0.25% trypsin/EDTA, stained with DAPI and DRAQ5 dye. Single and live cells were sorted by FACS.
scRNA-seq libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics) according to the manufacturer’s instructions at the NHLBI Core Facility. Briefly, cells obtained from FACS were mixed with a suspension containing barcoded beads and UMI (unique molecular identifier) elements that allow specific tagging of messenger RNA. After partitioning thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and barcoding, full-length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Libraries were constructed by fragmentation, end repair, A-tailing, adaptor ligation and index PCR. After ensuring adequate quality of the cDNA libraries, the samples were sequenced at the NHLBI Genomic Core Facility.

value: B6D2F1 inbred

value: Testis

value: Dis3 WT

value: postnatal day 6 (P6)


title: P6 testicular cells, Dis3 KO (scRNA-seq)

value: Dis3 KO


title: ADSC_iPS_Non_eroded_1

value: iPS

value: WT


title: IR_d14

address: 1095 解放大道， 武汉 430030， 中国

value: Kidney


title: LP08 V1-1

status: Public on Jul 14 2021

city: Anseong

first: Dong Hwan

last: Kim

state: Gyeonggi

address: 4726 Seodong-daero, Daedeok-myeon

department: Department of Plant science and Technology

country: South Korea

institute: Chung-Ang University

description: replicate 1

data_processing:
Quality of the RNA-seq reads were evaluated using the FastQC software
The raw reads were trimmed and quality-filtered before alignment, and those with more than 90 % threshold (Q>30) were used for mapping. B. rapa reference genome was obtained from Ensembl and were used using the TopHat2 software with default parameters
Aligned reads were converted to digital counts using HTseq-count and were analyzed using edgeR.
Differentially expressed genes (DEGs) were identified based on a 0.05 p-value and a cutoff of two-fold difference in expression.
Genome_build: B. rapa reference genome was obtained from Ensembl
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for individual samples

organism: Brassica rapa

source_name: Whole plant

growth_protocol: 3 weeks old B. rapa plants were grown in greenhouse prior to vernalization treatment

extract_protocol:
Total RNA was extracted from whole seedling samples using RNeasy Mini Kit (Qiagen, Germany) and treated with DNase I (New England Biolabs, USA) to remove genomic DNA contamination.
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA) according to the manufacturer’s instructions. Libraries were then sequenced on NovaSeq 6000 system (Macrogen Inc., South Korea)

treatment_protocol: NV: non-vernalized 3 weeks old seedling; V1; 1 day cold treated; V20: 20 days cold treated; V40: 40 days cold treated; V40T10; 40 days cold treated and then further grown in warm temperature for 10 days

tag: cultivar

tag: flowering

value: early

value: Whole plant

value: 1 day cold treated


title: LP08 V20-2

description: replicate 2

value: 20 days cold treated


title: LP08 V20-3

description: replicate 3


title: LP08 V40-2

description: replicate 2

value: 40 days cold treated


title: LP08 V40T10-3

description: replicate 3

value: 40 days cold treated, then followed by 10 days warm temperature


title: LP08 V40T10-2

description: replicate 2


title: LP08 V40T10-1

description: replicate 1


title: LP08 V1-3

description: replicate 3


title: LP08 V1-2

description: replicate 2


title: LP08 V20-1

description: replicate 1


title: Input_H769

value: SupT1 human T cell line

value: Pre-selection


title: ADSC_iPS_Non_eroded_2


title: LP08 NV-3

description: replicate 3

value: non-cold treated


title: LP08 V40-3

description: replicate 3


title: LP08 NV-2

description: replicate 2


title: Chiifu V40T10-3

description: replicate 3

value: Chiifu

value: late


title: Chiifu V40T10-1

description: replicate 1


title: Chiifu V40-3

description: replicate 3


title: Chiifu V40T10-2

description: replicate 2


title: Chiifu V40-1

description: replicate 1


title: Chiifu V40-2

description: replicate 2


title: Chiifu V20-2

description: replicate 2


title: Chiifu V20-3

description: replicate 3


title: Chiifu V20-1

description: replicate 1


title: Chiifu V1-2

description: replicate 2


title: Chiifu V1-3

description: replicate 3


title: Chiifu V1-1

description: replicate 1


title: LP08 V40-1

description: replicate 1


title: Chiifu NV-3

description: replicate 3


title: LP08 NV-1

description: replicate 1


title: Chiifu NV-2

description: replicate 2


title: CUT&RUN H3K18ac TSA-500K K562 cells

city: Durham

first: Bryan

middle: J

last: Venters

state: NC

address: 6 Davis Drive

institute: EpiCypher

data_processing:
Library strategy: CUT&RUN
Base-calling: illumina software
Adapter Trimming: none
Alignment: Paired-end fastq files were aligned to the hg19 reference genome using the Bowtie2 algorithm (PMID: 22388286).
Filtering: Only uniquely aligned reads were retained, and blacklist regions (PMID: 31249361) were filtered out for subsequent analyses.
Peak Calliing: Peaks were called using SEACR (Sparse Enrichment Analysis of CUT&RUN) (PMID: 31300027).
Genome_build: hg19
Supplementary_files_format_and_content: Musselman_Metadata.xlsx: contains one excel sheet

source_name: K562 cells

growth_protocol: K562 cells were maintained (1–10 × 10^5 cell/ml) in T25 flasks in IMDM + 10% FBS  +  1% Pen/Strep

extract_protocol:
CUTANA protocol v1.5.1; optimized version of PMID: 29651053
NEBNext Ultra II DNA Library Prep kit (New England Biolabs #E7645S)

treatment_protocol: Native cells unless otherwise specified. For H3K18ac sample, 500K cells were crosslinked with 0.1% formaldehyde for 1 minute at room temperature, and then quenched with 125 mM glycine. For TSA experiments, native cells were harvested and during CUT&RUN all buffers were supplemented with 1uM TSA to prevent acetyl degradation.

value: K562 human immortalised myelogenous leukemia cell line

value: 1 uM Trichostatin A (TSA) in wash buffer

tag: antibody

value: anti-H3K18ac Invitrogen #PA5-85523, lot UG2799523D


title: CUT&RUN GST-BPTF TSA-500K K562 cells

description: GST-BPTF (peptide)

value: this study


title: CUT&RUN H3K4me3 TSA-500K K562 cells

value: anti-H3K4me3 ThermoFisher #PA5-27029, lot SG2419844A


title: VivoMacrophage_Ctrl3 [NBM3_S22]

city: Lund

first: Pablo

last: Peña-Martínez

address: Klinikgatan 28

department: Clinical Genetics

country: Sweden

institute: Lund University

description:
NBM3_S22
processed data file: MFsVivo_IL4vsCtrl_PvalFC.txt

data_processing:
Bcl2FastQ software was used for basecalling.
Sequenced reads were mapped to the mm10 referece genome using Tophat 2.0.13 with parameters -p 2 --keep-fasta-order --no-coverage-search
BAM files were imported to the Qlucore Omics Explorer 3.0 software and normalized using the TMM (Trimmed Mean of M-values) method. Features with less than 10 reads in at least 5 samples were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited .txt file of TMM values, fold change and p-values of t-test between control and treated cells for every gene. A rank was created for each gene based on the log10 of the p-value and the direction of the fold change.

growth_protocol: In vitro: monocytes were purified from bone marrows of C57BL/6 mice and put in culture for 7 days in RPMI 10% heat inactivated FBS in the presence of 25 ng/mL CSF1. Half of the media was changed every 2-3 days. In vivo: mice were transplanted with AML cells expressing an IL4 cDNA or an empty control vector. After 12 days, F4(80+ cells were sorted from the bone marrows of these mice.

extract_protocol:
RNA was extracted using the QIAshredder and RNeasy Microkit (QIAgen, Hilden, Germany).
Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: In vitro: the IL4 group was cultured in the presence of 20 ng/mL of murine IL4 for 7 days.

tag: collection method

value: In vivo

value: BM

value: Sorted murine bone marrow macrophages

value: control

tag: protocol


title: VivoMacrophage_Ctrl2 [NBM2_S21]

description:
NBM2_S21
processed data file: MFsVivo_IL4vsCtrl_PvalFC.txt

tag: strain

tag: treatment


title: CUT&RUN BPTF TSA-500K K562 cells

description: BPTF (antibody)

value: anti-FALZ/BPTF Bethyl #A300-973A, lot 2


title: 3xTg-AD cultured ILC2

city: Albany

first: Ivan Ting Hin

last: Fung

address: 47 New Scotland Ave

institute: Albany Medical College

description: in vitro cultured

data_processing:
Library was generated using chromium 5' gene expression kit (10Xgenomincs).
Reference genome mouse (mm10) was used for read alignment and gene expression quantification using Cellranger v3.1.0 pipelines.
The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines.
These pipelines combine Chromium specific algorithms with the RNA-seq aligner STAR.
Genome_build: mm10
Supplementary_files_format_and_content: mtx and tsv for processed data, bam for each sample

source_name: 3xTg-ADl ILC2 purified from whole brain tissue

extract_protocol:
Cultured ILC2 from the whole brain tissue were sorted based on their surface marker expressions. Total RNA extracted following the instructions of the 10X genomics kit
scRNA-seq libraries were prepared using the 5’ single cell gene expression kit  (10x Genomics) accoding to the manufacturer’s instruction

treatment_protocol: 7 months old 3xTg-AD and Control ILC2 from whole brain tissue was pruified and cultured with stimulatory cytokines for 8 days

value: 7 months


title: VivoMacrophage_IL4_1 [IL4BM1_S1]

description:
IL4BM1_S1
processed data file: MFsVivo_IL4vsCtrl_PvalFC.txt

value: IL4-secreting AML cells


title: VivoMacrophage_IL4_3 [IL4BM3_S3]

description:
IL4BM3_S3
processed data file: MFsVivo_IL4vsCtrl_PvalFC.txt


title: VivoMacrophage_Ctrl1 [NBM1_S20]

description:
NBM1_S20
processed data file: MFsVivo_IL4vsCtrl_PvalFC.txt


title: VitroMacrophage_IL4_4 [FAIL44_S19]

description:
FAIL44_S19
processed data file: MFsVitro_IL4vsCtrl_PvalFC.txt

value: In vitro

value: Monocyte derived

value: Murine monocyte-derived macrophages


title: VivoMacrophage_IL4_2 [IL4BM2_S2]

description:
IL4BM2_S2
processed data file: MFsVivo_IL4vsCtrl_PvalFC.txt


title: CUT&RUN IgG negative control TSA-500K K562 cells

description: IgG

value: CUTANA™ Rabbit IgG CUT&RUN Negative Control Antibody EpiCypher 13-0042, lot 20036001-52


title: CUT&RUN GST antibody only negative control TSA-500K K562 cells

description: GST (antibody)

value: GST antibody Bethyl #190-122A lot 11


title: VitroMacrophage_IL4_2 [FAIL42_S17]

description:
FAIL42_S17
processed data file: MFsVitro_IL4vsCtrl_PvalFC.txt


title: Chiifu NV-1

description: replicate 1

value: Chiifu

value: late

value: Whole plant

value: non-cold treated


title: VitroMacrophage_IL4_1 [FAIL41_S16]

description:
FAIL41_S16
processed data file: MFsVitro_IL4vsCtrl_PvalFC.txt


title: VitroMacrophage_Ctrl4 [FA4_S15]

description:
FA4_S15
processed data file: MFsVitro_IL4vsCtrl_PvalFC.txt


title: VitroMacrophage_Ctrl3 [FA3_S14]

description:
FA3_S14
processed data file: MFsVitro_IL4vsCtrl_PvalFC.txt


title: VitroMacrophage_Ctrl2 [FA2_S13]

description:
FA2_S13
processed data file: MFsVitro_IL4vsCtrl_PvalFC.txt


title: VitroMacrophage_Ctrl1 [FA1_S12]

description:
FA1_S12
processed data file: MFsVitro_IL4vsCtrl_PvalFC.txt


title: HOM-44

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) RNAseq raw reads were aligned to mouse genome (mm10) using STAR v2.5.2b.
2) Gene read coverages were computed with featureCounts v1.5.2 using GENCODE annotation release M13
3) Differential expression analysis was performed using edgeR v3.22.0
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts

source_name: SMNKO_Wk8_gastrocnemius muscle

extract_protocol:
Qiagen RNeasy mini kit
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold
38-bp paired-end RNA-sequencing

value: SMNKO

tag: Sex

value: M

value: gastrocnemius muscle

tag: sequencing pool

value: B


title: HOM-42


title: HOM-43


title: HOM-41

value: A


title: HOM-40


title: HOM-39


title: Control culutred ILC2

description: in vitro cultured

source_name: Control ILC2 purified from whole brain tissue


title: VitroMacrophage_IL4_3 [FAIL43_S18]

description:
FAIL43_S18
processed data file: MFsVitro_IL4vsCtrl_PvalFC.txt


title: WT-38

source_name: WT_Wk8_gastrocnemius muscle

value: WT


title: WT-37


title: WT-35

value: F


title: WT-36


title: WT-34


title: WT-32

source_name: WT_Wk2_gastrocnemius muscle

value: not collected


title: HOM-31

source_name: SMNKO_Wk2_gastrocnemius muscle


title: HOM-30


title: HOM-28


title: HOM-20

source_name: SMNKO_Wk6_gastrocnemius muscle


title: WT-23


title: WT-21


title: HOM-29


title: WT-26


title: WT-24


title: HOM-22


title: WT-25


title: HOM-19


title: WT-17

source_name: WT_Wk6_gastrocnemius muscle


title: WT-16


title: HOM-7

source_name: SMNKO_Wk4_gastrocnemius muscle


title: WT-6

source_name: WT_Wk4_gastrocnemius muscle


title: HOM-12


title: HOM-10


title: WT-5


title: HOM-8


title: HOM-11


title: WT-2


title: WT-3


title: WT-1


title: Gli2A Tg CD8-Rep2

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

description:
N22-CD8
NM0434_10--(N22-CD8)

data_processing:
Base Calling was done using RTA v(2.4.1.1)
Alignment was done using TopHat v(2.0.7)
Peak Calling was performed using Picard
The Bioconductor package DESeq2 was used to generate normalised estimates of transcript abundance
Genome_build: mm10
Supplementary_files_format_and_content: comma separated file including RPKM values for each Sample.

source_name: Skin CD8+ Cells

extract_protocol:
WT, Gli2ΔN2 and Gli2ΔC2 mice (6 from each strain) were sensitised on the shaved abdomen with 3% of the hapten 4-ethoxymethylene-2-phenyloxazolin-5-one (Oxazolone, Sigma), and then challenged topically on the ears with five doses of 0.6% Oxazolone on days 5, 7, 9, 11 and 13 and sacrificed and analysed on day 14. To release leukocytes from the whole ear tissue, ears were split into dorsal and ventral halves and digested for 30min at 37°C with 1mg/ml Collagenase D (Roche) and 0.5mg/ml DNase I (Roche) in RPMI (Life Technologies) containing 2% FCS (Life Technologies) and 2% Penicillin/Streptomycin (Life Technologies). Tissues were filtered through a 70μm cell strainer (VWR) and washed in RPMI containing 10% FCS and 5% Pen/Strep, spun at 1400rpm for 10min and counted with haemocytometer (Hawksley). Skin cell suspensions from two groups of three mice each from WT, Gli2ΔN2 and Gli2ΔC2 mice were obtained. Cells were stained and live (ZA-) CD4 T cells (CD45+CD3+γδTCR-CD4+CD8-) and CD8 T cells (CD45+CD3+γδTCR-CD4-CD8+) were sorted into Trizol LS reagent (Thermo Fisher Scientific). RNA was extracted from these cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

value: CD8+ T cells

tag: developmental stage

value: Adult


title: Gli2R Tg CD4-Rep1

description:
C21-CD4
NM0429_5--(C21-CD4)

source_name: Skin CD4+ Cells

tag: cell type

value: CD4+ T cells


title: Gli2R Tg CD8-Rep1

description:
C21-CD8
NM0431_7--(C21-CD8)

tag: genotype


title: WT-4


title: Gli2R Tg CD4-Rep2

description:
C22-CD4
NM0430_6--(C22-CD4)


title: WildType CD8-Rep1

description:
WT1-CD8
NM0427_3--(WT1-CD8)

value: WildType


title: control_2

city: Chongqing

first: zhuyan

last: jiang

state: Shapingba

address: 30 Gaotanyan Zhengjie, Shapingba District, Chongqing, China

institute: Army Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HiSat2 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: PBMCs

growth_protocol: The study included 7 samples, of which 4 were RA samples and 3 were normal controls (The data has been uploaded).

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 ml of peripheral blood was centrifuged in700x g at room temperature. Removing the plasma, then dilute it by volume with precooled PBS 1 to 1, then add it slowly to the lymphocyte isolate at room temperature, and centrifuge it in 700x g. Carefully absorb the middle layer of white membrane with straw and wash it 2 times with pre cooled PBS at room temperature.The ratio of serum and DMSO to volume ratio was 9 to 1, and suspended cells were frozen with liquid nitrogen.

tag: diagnosis

value: normal control

value: Peripheral blood

value: PBMCs


title: control_3

tag: tissue


title: WildType CD4-Rep1

description:
WT1-CD4
NM0425_1--(WT1-CD4)


title: WildType CD8-Rep2

description:
WT2-CD8
NM0428_4--(WT2-CD8)


title: Gli2A Tg CD8-Rep1

description:
N21-CD8
NM0433_9--(N21-CD8)


title: Gli2A Tg CD4-Rep2

description:
N22-CD4
NM0436_12--(N21-CD4)


title: Gli2R Tg CD8-Rep2

description:
C22-CD8
NM0432_8--(C22-CD8)


title: Gli2A Tg CD4-Rep1

description:
N21-CD4
NM0435_11--(N21-CD4)


title: WildType CD4-Rep2

description:
WT2-CD4
NM0426_2--(WT2-CD4)


title: RA-1

value: RA patient


title: control-N3

growth_protocol: The study included 7 samples, of which 4 were SLE samples and 3 were normal controls (The data has been uploaded).


title: control-N2


title: RA-3


title: RA-2


title: RA-C


title: SLE-yuanxu

value: SLE patient


title: SLE-zouhang


title: control-N1


title: SLE-songmeng


title: control_1


title: SLE-liumin


title: Non-Angiogenesis_CSF_10

city: Guangzhou

first: Gang

state: Guangdong

address: 1023 Guangzhou Avenue North

department: Neurosurgery

institute: Nanfang Hospital of Southern Medical University

description: MiRNA expression in cerebrospinal fluid of angiogenesis or non-angiogenesis after Encephalo-myo-synangiosis in patients with moyamoya disease

data_processing:
Small RNA sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). The basic reads were converted into sequence data (also called raw data/reads) by base calling. Low-quality reads were filtered,  and the reads with 5’ primer contaminants and poly (A) were removed. The reads without 3’adapter and insert tag, the reads shorter than 15 nt and longer than 41nt from the raw data were filtered, and the clean reads were  obtained
For primary analysis, the length distribution of the clean sequences in the reference genome was determined. Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and small nucleolar RNAs  (snoRNAs). These RNAs were aligned and then subjected to the BLAST search against Rfam v.10.1 (http://www.sanger.ac.uk/software/Rfam) and GenBank databases (http://www.ncbi.nlm.nih.gov/genbank/). The known miRNAs were identified by aligning against miRBase v.21 database (http://www.mirbase.org/), and the known miRNA expression patterns in different samples were analyzed. Unannotated small RNAs were analyzed by mirdeep2 to predict novel miRNAs. Based on the hairpin structure of a pre-miRNA and the miRBase database, the corresponding miRNA star sequence was also identified.
Differentially expressed miRNAs were identified with the threshold of p value < 0.05. While the p value was calculated with DEG algorithm in the R package for experiment with biological replicates, and with Audic Claverie statistic for experiment without biological replicates
The targets of differentially expressed miRNAs were predicted by using software miranda in animal, with the parameter as follows: S ≥ 150 ΔG ≤ −30 kcal/mol and demand strict 5' seed pairing. And targetfinder was used for miRNA target prediction in plant
GO enrichment and KEGG pathway enrichment analysis of different expressed miRNA-target-Gene were respectively performed using R based on the hypergeometric distribution
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw counts for every miRNA and every sample

source_name: cerebrospinal fluid

extract_protocol:
Total RNA from CSF was extracted using the miRNeasy Serum/Plasma Kit (QIAGEN, NO. 217184) according to the manufacturer’s protocol. Quantitation of total RNA was performed using an Agilent 2100 Bioanalyzer (Agilent Technology, USA)
Total RNA was ligated to adapters at each end. Next, the adapter-ligated RNA was reverse-transcribed to cDNA, and PCR amplification was performed. PCR products ranging from 140 to 160 bp were isolated and purified as small RNA libraries. Library quality was assessed with the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips. The libraries were finally sequenced using the Illumina HiSeq X Ten platform.

treatment_protocol: Book with patients signed the informed consent of patients with lumbar puncture cerebrospinal fluid, each patient get 10 ml of cerebrospinal fluid, follow the principle of aseptic throughout the whole process, get as quickly as possible after placing it on - 80 ° C to save

value: cerebrospinal fluid

tag: gender

value: female

tag: age


title: Non-Angiogenesis_CSF_07


title: Non-Angiogenesis_CSF_08

value: male


title: Non-Angiogenesis_CSF_09


title: Non-Angiogenesis_CSF_03


title: Non-Angiogenesis_CSF_04


title: Non-Angiogenesis_CSF_02


title: Non-Angiogenesis_CSF_05


title: Angiogenesis_CSF_10


title: Angiogenesis_CSF_09


title: Angiogenesis_CSF_07


title: Angiogenesis_CSF_04


title: Angiogenesis_CSF_03


title: Angiogenesis_CSF_08


title: Liver_BSO+RGZ_6 hr_pooled

type: RNA

city: Nagoya

first: Ru

last: JIA

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Drug Safety Sciences

institute: Nagoya University Graduate School of Medicine

description: After data processing, probes that have positive and certain signal intensity (gIsFeatNonUnifOL = 0, gIsBGPopnOL = 0, gIsPosAndSignif = 0, gIsWellAboveBG = 1, ) are used in enrichment analysis described in this paper.

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit (Agilent) according to manufacturer's instructions.

scan_protocol: Slides were scanned using Agilent Technologies Microarray Scanner (Scan Resolution 3um,TIFF file dynamic range, 20bit).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (Agilent).  All raw signal intensities were normalized by 75 percentile-shift and log-2-transformed and then fold changes to the vehicle control group were calculated using Subio Platform ver. 1.22 (Subio, Kagoshima, Japan).

source_name: Liver, 700 mg/kg BSO plus 300 mg/kg RGZ, i.p., 6 hr, pooled

label_protocol: Labelling of cRNA was performed using Low Input Quick Amp Labeling Kit (Agilent) according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from each liver sample collected at 6 hr after the administration of TGZ, RGZ or vehicle using an RNeasy Mini kit according to manufacturer’s instructions.

value: BALB/c

value: Liver

value: 6 weeks old


title: Angiogenesis_CSF_06


title: Liver_RGZ_6 hr_pooled

source_name: Liver, 300 mg/kg RGZ, i.p., 6 hr, pooled

value: 300 mg/kg RGZ, i.p., 6 hr


title: Angiogenesis_CSF_01


title: Liver_TGZ_6 hr_pooled

source_name: Liver, 300 mg/kg TGZ, i.p., 6 hr, pooled

value: 300 mg/kg TGZ, i.p., 6 hr


title: Liver_Vehicle_6 hr_pooled

source_name: Liver, Vehicle, i.p., 6 hr, pooled

value: Vehicle, i.p., 6 hr


title: Liver_BSO+TGZ_6 hr_pooled

source_name: Liver, 700 mg/kg BSO plus 300 mg/kg TGZ, i.p., 6 hr, pooled


title: 3622 Arcuate nucleus

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description:
Moderate-plane of nutrition
Arcuate_merged_counts.txt

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (UMD3.1) using STAR (v2.6.1), incorporating the quantmode function to determine the number of mapped reads.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Tab delimited txt file of merged gene read counts

molecule: polyA RNA

organism: Bos taurus

source_name: Arcuate nucleus

growth_protocol: Angus X Holstein-Friesian heifer calves were fed differentially either a High plane of nutrition (n=14) or a Moderate plane of nutrition (n=15)  from 2-21 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.2 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.

extract_protocol:
RNA was  precipitated and purified from arcuate nucleus tissue samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks.

tag: diet

value: Moderate

value: Arcuate nucleus

tag: breed

value: Holstein-Friesian X Angus


title: 250 g/l, high glucose stress L214V rep1

city: Tianjin

first: Qinhong

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to reference genome using Bowtie2 with default parametres
Abundance measurements by RSEM
Differential gene expression by R package DESeq2, a p-value cutoff of 0.05 or less and an absolute fold-change threshold of 2.0 or greater.
Genome_build: R64
Supplementary_files_format_and_content: gene expression Raw counts file gene_Raw_counts.txt: text file include all expression gene list with Raw counts

organism: Saccharomyces cerevisiae

source_name: Early-log phase cells

extract_protocol:
Sample were grown on YP medium containing 200 g/l glucose at 30ºC at 200 rpm for 10 h to the early-log phase, and harvested in Falcon tubes precooled in liquid N2 by centrifuging for 5 minutes at 4000 rpm (3220 × g). The supernatant was discarded, and the pellet was stored at −80°C until further use. Total RNA extraction, library construction and sequencing were conducted by Novogene Bioinformatics Technology Co., Ltd (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: phenotype

value: Stress senstive

tag: culture conditions

value: 250 g/l, high glucose stress

tag: growth phase

value: early log


title: Non-Angiogenesis_CSF_06


title: 250 g/l, high glucose stress S118L rep2


title: 250 g/l, high glucose stress R238K rep2

value: Stress tolerant


title: 250 g/l, high glucose stress S118L rep1


title: Angiogenesis_CSF_02


title: 3620 Arcuate nucleus

description:
High-plane of nutrition
Arcuate_merged_counts.txt

value: High


title: Non-Angiogenesis_CSF_01

value: cerebrospinal fluid


title: 250 g/l, high glucose stress R238K rep1


title: 2537 Arcuate nucleus


title: 2551 Arcuate nucleus


title: 2535 Arcuate nucleus


title: 2570 Arcuate nucleus


title: 2532 Arcuate nucleus


title: 2528 Arcuate nucleus


title: 250 g/l, high glucose stress A140G rep1


title: 2346 Arcuate nucleus


title: 250 g/l, high glucose stress P169A rep2


title: 250 g/l, high glucose stress P169A rep1


title: 250 g/l, high glucose stress A140G rep2


title: 250 g/l, high glucose stress CK rep2

value: Wild type

value: CK


title: 250 g/l, high glucose stress L214V rep2


title: 250 g/l, high glucose stress CK rep1


title: 40℃ high tempeature stress condition L214V rep2

value: 40 degrees C high tempeature stress condition


title: 1707 Arcuate nucleus


title: 1690 Arcuate nucleus


title: 40℃ high tempeature stress condition L214V rep1


title: 2120 Arcuate nucleus


title: 3148 Arcuate nucleus


title: 1689 Arcuate nucleus


title: 40℃ high tempeature stress condition R238K rep2


title: 1395 Arcuate nucleus


title: 1531 Arcuate nucleus


title: 40℃ high tempeature stress condition R238K rep1


title: 40℃ high tempeature stress condition P169A rep2


title: 1388 Arcuate nucleus


title: 1392 Arcuate nucleus


title: 40℃ high tempeature stress condition P169A rep1


title: 1082 Arcuate nucleus


title: 40℃ high tempeature stress condition CK rep1


title: 1089 Arcuate nucleus


title: Normal condition L214V rep2

value: Normal condition


title: 1057 Arcuate nucleus


title: 1050 Arcuate nucleus


title: 40℃ high tempeature stress condition A140G rep1


title: Normal condition L214V rep1


title: 991 Arcuate nucleus


title: 981 Arcuate nucleus


title: 986 Arcuate nucleus


title: Normal condition S118L rep1


title: Normal condition R238K rep2


title: 975 Arcuate nucleus


title: Normal condition R238K rep1


title: Normal condition P169A rep2


title: Normal condition P169A rep1


title: 40℃ high tempeature stress condition A140G rep2


title: 40℃ high tempeature stress condition CK rep2


title: Normal condition A140G rep2


title: 553 Arcuate nucleus


title: 2535 Hypothalamus

description:
High-plane of nutrition
Hypothalamus_merged_counts.txt

source_name: Hypothalamus

extract_protocol:
RNA was  precipitated and purified from hypothalamus samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

value: Hypothalamus


title: 2537 Hypothalamus

description:
Moderate-plane of nutrition
Hypothalamus_merged_counts.txt


title: 2532 Hypothalamus


title: 2528 Hypothalamus


title: 1360 Arcuate nucleus


title: Normal condition S118L rep2


title: Normal condition CK rep2


title: Normal condition CK rep1


title: 2346 Hypothalamus


title: NPN-2

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

data_processing:
The Fastq files were evaluated for read quality using FastQC 0.11.4
Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using STAR 2.5.3a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEG) between groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.05 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: Normalized abundance measurements- Cufflink Gene.FPKM.Tracking

organism: Equus caballus

source_name: Uterus

extract_protocol:
Total RNA was isolated from all CA samples using RNeasy Mini Kit (#74104; Qiagen), and DNA digestion was performed on-column using RNase-free DNase I (#79254: Qiagen), followed by cleanup procedures. All procedures were performed according to the manufacturer’s instructions. After extraction, RNA concentration and quality were analyzed using Nanodrop 2000 spectrophotometer (#ND-2000; Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer® (Agilent, Santa Clara, CA, USA). All samples had a 260/280 ratio >2.0 and RNA integrity number (RIN) > 8.0.
A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads.

treatment_protocol: Chorioallantois (CA) samples were collected from the margin of the NP lesion (NPL, n=4) and grossly normal region (NPN, n=4). Additionally, CA samples were collected from normal postpartum mares (Control; CRL, n=4).

value: Chorioallantois

tag: group

value: Nocaridioform Placentitis normal-appearing region


title: NPN-4


title: 2120 Hypothalamus


title: NPN-3


title: Normal condition A140G rep1

tag: strain


title: 1707 Hypothalamus


title: 911 Arcuate nucleus


title: 1690 Hypothalamus


title: NPN-1


title: 1689 Hypothalamus


title: NPL-4

value: Nocaridioform Placentitis Lesion


title: 1531 Hypothalamus


title: NPL-3


title: NPL-2


title: 1395 Hypothalamus

value: Moderate


title: 1392 Hypothalamus


title: NPL-1


title: 1388 Hypothalamus


title: 1360 Hypothalamus


title: CRL-3

value: Control


title: CRL-4


title: CRL-2


title: TC48_7 (cep135 null E11.5 cortex)

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

description:
sacrifice at embryonic day E11.5
TL48_7

data_processing:
Read adapters and polyA tails were removed with bbduk.sh, following the Lexogen recommendations. Processed reads were analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19 (--library-type fr-secondstrand in TopHat), allowing three mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1 (--stranded=yes), using the mouse gene annotation from GENCODE (gencode.vM20.GRCm38.Ensembl95). Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2

source_name: Dorsal telencephalon from E11.5 embryonic cortex

growth_protocol: All mice were generated and maintained at the Animal Facility of the Spanish National Cancer Research Centre (CNIO) under specific pathogen-free conditions in accordance with the recommendation of the Federation of European Laboratory Animal Science Associations (FELASA)

extract_protocol: Total RNA samples were used (300 ng on average, with five samples under 60 ng). Sample RNA Integrity numbers were 9.4 on average (range 8.6-9.4) when assayed on an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: no pharmacological treatment

value: Dorsal telencephalon (tissue)

tag: culture time (hours)


title: 1082 Hypothalamus

value: Holstein-Friesian X Angus


title: 1050 Hypothalamus


title: TC48_4 (cep135 null E11.5 cortex)

description:
sacrifice at embryonic day E11.5
TL48_4


title: 1057 Hypothalamus


title: TC48_2 (cep135 wt E11.5 cortex)

description:
sacrifice at embryonic day E11.5
TC48_2


title: 1089 Hypothalamus


title: 986 Hypothalamus


title: 981 Hypothalamus


title: TC48_1 (cep135 wt E11.5 cortex)

description:
sacrifice at embryonic day E11.5
TC48_1


title: 975 Hypothalamus


title: 911 Hypothalamus


title: TBI180_6 12h (cep135 null neurospheres 12h)

description:
sacrifice at embryonic day E14.5
TBI180_6_12h

source_name: Dorsal telencephalon from E14.5 embryonic cortex (cells)

value: Cortical Neural Progenitors


title: TBI180_6 (cep135 null E14.5 cortex)

description:
sacrifice at embryonic day E11.5
TBI180_6

source_name: Dorsal telencephalon from E14.5 embryonic cortex


title: TBI189_1 (cep135 null E11.5 cortex)

description:
sacrifice at embryonic day E11.5
TBI189_1


title: TBI180_6 24h (cep135 null neurospheres 24h)

description:
sacrifice at embryonic day E14.5
TBI180_6_24h


title: 3620 Hypothalamus


title: 3148 Hypothalamus


title: TBI180_5 (cep135 wt E14.5 cortex)

description:
sacrifice at embryonic day E14.5
TBI180_5


title: TBI180_5 24h (cep135 wt neurospheres 24h)

description:
sacrifice at embryonic day E14.5
TBI180_5_24h


title: 2570 Hypothalamus


title: TBI180_5 12h (cep135 wt neurospheres 12h)

description:
sacrifice at embryonic day E14.5
TBI180_5_12h


title: 2551 Hypothalamus


title: TBI180_4 (cep135 wt E14.5 cortex)

description:
sacrifice at embryonic day E14.5
TBI180_4


title: CRL-1


title: 991 Hypothalamus


title: TBI180_4 24h (cep135 wt neurospheres 24h)

description:
sacrifice at embryonic day E14.5
TBI180_4_24h


title: TBI189_2 (cep135 wt E11.5 cortex)

description:
sacrifice at embryonic day E11.5
TBI189_2


title: Week1_sham WRE1.5R

city: La Jolla

first: Samuel

middle: Richard

last: Ward

address: 9500 Gilman Drive (0863)

department: Orthopaedic Surgery, Radiology, and Bioengineering

institute: University of California San Diego

data_processing:
quality control on raw fastq uisng FASTQC
aligned to rabbit genome
read quanitification using RSEM and Ensembl Orycun annotation
edgeR, limma-voom, followed by empirical bayes, TMM applied
design (Tenotomy - Sham)
Genome_build: Orycun2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryctolagus cuniculus

source_name: supraspinatus

extract_protocol:
muscle was extracted and flash frozen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: tenotomy, or a sham were performed(cut of the skin)

tag: time post-tenotomy

value: sham


title: TBI180_4 12h (cep135 wt neurospheres 12h)

description:
sacrifice at embryonic day E14.5
TBI180_4_12h


title: Week1_tenotomy WRE1.6L

value: tenotomy


title: TBI180_3 (cep135 wt E14.5 cortex)

description:
sacrifice at embryonic day E14.5
TBI180_3


title: TBI180_3 24h (cep135 wt neurospheres 24h)

description:
sacrifice at embryonic day E14.5
TBI180_3_24h


title: Week1_sham WRE1.4R


title: TBI180_2 (cep135 null E14.5 cortex)

description:
sacrifice at embryonic day E14.5
TBI180_2


title: Week1_tenotomy WRE1.5L


title: Week1_sham WRE1.6R


title: 3622 Hypothalamus


title: TBI180_2 24h (cep135 null neurospheres 24h)

description:
sacrifice at embryonic day E14.5
TBI180_2_24h


title: TBI180_3 12h (cep135 wt neurospheres 12h)

description:
sacrifice at embryonic day E14.5
TBI180_3_12h


title: Week1_tenotomy WRE1.3L


title: Week1_tenotomy WRE1.4L


title: 553 Hypothalamus

description:
High-plane of nutrition
Hypothalamus_merged_counts.txt

value: High


title: TBI180_1 (cep135 null E14.5 cortex)

description:
sacrifice at embryonic day E14.5
TBI180_1


title: Week1_sham WRE1.3R


title: Week1_tenotomy WRE1.2L


title: TBI180_2 12h (cep135 null neurospheres 12h)

description:
sacrifice at embryonic day E14.5
TBI180_2_12h


title: Week1_sham WRE1.1R


title: TBI180_1 12h (cep135 null neurospheres 12h)

description:
sacrifice at embryonic day E14.5
TBI180_1_12h


title: Week1_tenotomy WRE1.1L


title: TBI180_1 24h (cep135 null neurospheres 24h)

description:
sacrifice at embryonic day E14.5
TBI180_1_24h


title: Week8_sham WRC_rep_20


title: Week8_tenotomy WRC_rep_20


title: Week16_sham WRC_rep_16


title: Week16_tenotomy WRC_rep_16


title: Week2_sham WRC_rep_04


title: Week2_sham WRC_rep_03


title: Week8_tenotomy WRC_rep_01


title: Week2_tenotomy WRC_rep_03


title: Week16_tenotomy WRC_24


title: Week4_sham WRC_22


title: Week16_sham WRC_23


title: Week16_tenotomy WRC_23


title: Week4_tenotomy WRC_22


title: TNBC T194

city: Daejeon

first: Seon-Kyu

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Arrays were scanned on an Affymetrix GeneChip 3000 7G scanner according to the manufacturer’s instructions.

data_processing: We normalized gene expression data using GCRMA, log2 transformation, and quantile normalization.

label: biotin

source_name: Tripple negative breast cancer

label_protocol: Approximately two micrograms of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.

tag: sp142 pd-l1

value: negative

tag: ajcc stage

tag: vital status

value: death


title: TNBC T193

value: alive


title: Week2_tenotomy WRC_rep_04


title: Week8_sham WRC_rep_01


title: TNBC T196


title: TNBC T186

value: positive


title: TNBC T190


title: TNBC T192


title: Week1_sham WRE1.2R


title: TNBC T181


title: TNBC T184


title: Week8_sham WRC_21


title: TNBC T189


title: TNBC T182


title: TNBC T188


title: TNBC T179


title: TNBC T187


title: TNBC T183


title: Week16_sham WRC_24


title: TNBC T185


title: TNBC T177


title: Week8_tenotomy WRC_18


title: Week8_sham WRC_18


title: Week4_tenotomy WRC_19


title: Week4_sham WRC_19


title: Week8_tenotomy WRC_21


title: Week4_sham WRC_17


title: Week4_tenotomy WRC_15


title: Week16_sham WRC_14


title: Week16_tenotomy WRC_14


title: Week2_sham WRC_13


title: TNBC T174


title: Week2_tenotomy WRC_13


title: TNBC T176


title: TNBC T172


title: TNBC T166


title: TNBC T162


title: TNBC T175


title: TNBC T165


title: TNBC T163


title: TNBC T160


title: TNBC T159


title: TNBC T170


title: TNBC T171


title: Week4_sham WRC_15


title: Week4_tenotomy WRC_17


title: Week4_tenotomy WRC_12


title: Week16_tenotomy WRC_11


title: TNBC T158


title: Week4_sham WRC_10


title: Week2_sham WRC_09


title: Week4_tenotomy WRC_10


title: Week16_sham WRC_11


title: TNBC T180


title: TNBC T152


title: Week8_sham WRC_07


title: TNBC T153


title: TNBC T154


title: TNBC T157


title: TNBC T149


title: Week8_tenotomy WRC_07


title: Week2_sham WRC_06


title: Week4_sham WRC_12


title: Week16_sham WRC_05


title: TNBC T147


title: Week16_tenotomy WRC_05


title: TNBC T142


title: Week2_tenotomy WRC_02


title: Week2_sham WRC_02


title: Week2_tenotomy WRC_09


title: OML1R_olap_4Gy_2

city: Chiayi County

first: Jie Ting

last: Low

state: Minxiong Township

address: No. 168, Daxue Road, Section 1

country: Taiwan

institute: National Chung Cheng University

data_processing:
Fastq files were imported to CLC Genomic Workbench v.10
The raw data was Q20 trimmed
reads shorter than 100 was discarded
filtered reads were mapped to hg19
Genome_build: hg19
Supplementary_files_format_and_content: CNV files were exported from CLC Genomic Workbench v.10

growth_protocol: OML1 and OML1R cells were grown in RPMI medium containing 10% FBS, and supplemented with 1% penicillin-streptomycin, and 2 mM L-glutamine. Cells were cultured at 37°C under a humidified atmosphere of 5% CO2 and 95% air.

extract_protocol:
We used TRIZOL to isolate total RNAs according to the manufacturer's instructions (Invitrogen, Carlsbad, CA).
RNA libraries were prepared using Agilent SureSelect strand-specfic RNA preparation kit. Manufacturer's protocol was followed.
PolyA RNA was selected using oligo-dT beads, followed by random fragmentation. Fragmented RNA was reverse transcribed using random primers. cDNA was then end-repaired, single A base addition, and ligated to index-adaptor. The ligated libraries were amplified and polished to remove primer dimer.

treatment_protocol: control:untreatrment,olap:olaparib 12uM treat for 72hrs,4Gy:cells stress by irradiated 4Gy single fraction,olap_4Gy: combiant cells stress by irradiated 4Gy single fraction and olaparib 12uM

value: tumor

tag: cell type

value: Buccal mucosa squamous carcinoma

tag: treatment

value: OML1 R traeted olaparib 12uM 72hrs and 4Gy irradiation


title: OML1R_olap_4Gy_1

tag: tissue


title: OML1_olap_4Gy_2

value: OML1  traeted olaparib 12uM 72hrs and 4Gy irradiation


title: OML1_olap_4Gy_1


title: TNBC T139


title: TNBC T133


title: TNBC T135


title: TNBC T140


title: OML1_olap_2

value: OML1  traeted olaparib 12uM 72hrs


title: OML1R_olap_2

value: OML1 R traeted olaparib 12uM 72hrs


title: OML1R_olap_1


title: OML1_olap_1


title: TNBC T143


title: TNBC T138


title: TNBC T141


title: TNBC T134


title: TNBC T126


title: TNBC T132


title: OML1R_4Gy_1

value: OML1R traeted 4Gy irradiation


title: OML1R_4Gy_2

value: OML1 R traeted 4Gy irradiation


title: TNBC T129


title: TNBC T130


title: TNBC T127


title: TNBC T128


title: TNBC T124


title: TNBC T125


title: OML1_4Gy_2

value: OML1 traeted 4Gy irradiation


title: OML1_4Gy_1


title: TNBC T122


title: TNBC T123


title: OML1R_Control_2

value: Radioresistant oral cancer cell line, Untreated


title: OML1R_Control_1


title: OML1_Control_1

value: parent oral cancer cell,Untreated


title: OML1_Control_2


title: miRNA_Submucosa_05

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

country: Germany

institute: Ludwig-Maximilians-University Munich

data_processing:
Fastq-files were generated using Illumina bcl2fastq (v2.20.0.422).
Bioinformatic analyses were performed according to Stokowy et al. (Stokowy T, Eszlinger M, Swierniak M, Fujarewicz K, Jarzab B, Paschke R, Krohn K. Analysis options for high-throughput sequencing in miRNA expression profiling. BMC research notes. 2014;7:144).
Mapping against miRBase release 22 reference sequences was done using Bowtie2.
Differential expression was analyzed using DESeq2.
Genome_build: miRBase (release 22)
Supplementary_files_format_and_content: CSV-files (comma-separated values) containing differential expression datasets.

source_name: Colonic biopsy

extract_protocol:
Biopsies of the in the sigmoid colon were taken during colonoscopy and subsequently cryoconserved. In order to assess tissue-specific miRNA expression, the biopsies were micro-dissected prior to preservation. Total RNA was extracted using TRIzol reagent according to the instructions of the manufacturer.
Sequencing libraries were prepared using NEXTflex Small RNA Seq Kit v 3 (Bio Scientific) according to the small RNA protocol of the manufacturer.

value: Submucosal tissue biopsy


title: TNBC T119


title: miRNA_Submucosa_04


title: miRNA_Submucosa_03


title: TNBC T116


title: miRNA_Mucosa_03

value: Mucosal tissue biopsy


title: miRNA_Mucosa_01


title: miRNA_Mucosa_02


title: TNBC T120

value: negative


title: miRNA_CTR_17

value: Healthy control

tag: disease


title: TNBC T117

tag: age

value: alive


title: TNBC T121

value: death


title: miRNA_CTR_15


title: miRNA_CTR_14


title: miRNA_CTR_16


title: TNBC T114

value: positive


title: miRNA_CTR_13


title: TNBC T111


title: TNBC T113


title: TNBC T109


title: miRNA_CTR_12


title: TNBC T107


title: TNBC T112


title: TNBC T106


title: miRNA_CTR_11


title: miRNA_CTR_10


title: TNBC T104


title: miRNA_CTR_09


title: miRNA_CTR_08


title: miRNA_CTR_07


title: miRNA_CTR_06


title: TNBC T102


title: TNBC T115


title: TNBC T103


title: TNBC T064


title: TNBC T074


title: TNBC T080


title: miRNA_CTR_05


title: TNBC T108


title: TNBC T169


title: miRNA_CTR_04


title: KP.2622_000_WT_000_LPS_3h_Rep.1

city: New York

first: Kyung-Hyun

last: Park-Min

email: ParkminK@HSS.EDU, parkmink@gmail.com

address: 535 East 70th Street

institute: Hospital for Special Surgery

data_processing:
Basecalling was performed using bcl2fastq (version bcl2fastq-1.8.4)
Sequenced reads were preprocessed with fastp (with parameters fastp -q 15 -n 10 -l 20)
After preprocessing, sequenced reads were mapped to mm10 whole genome using STAR v2.7.3a (with parameters --outFilterMultimapNmax 1  --outSAMstrandField intronMotif --quantMode GeneCounts), using gencode mm10 annotation
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts, filtered gene counts (min expression cutoff of 5 CPM) and log CPMs from edgeR for every gene and every sample

source_name: Control macropahges stimulated with LPS rep1

growth_protocol: For the generation BMDMs, bone marrow cells were flushed from femurs and tibias of mice and cultured at 37oC, 5% CO2 in complete α-MEM medium (10% heat-inactivated defined FBS (HyClone Fisher), penicillin-streptomycin (Invitrogen), and L-glutamine (Invitrogen)) with 5% L929 cell supernatant as conditioned medium (CM) as a source of M-CSF (Englen et al., 1995) after lysis of RBCs using ACK lysis buffer (Invitrogen). Then, the non-adherent cell population was recovered the next day and cultured for three additional days. Final concentration of M-CSF in our culture was 23.3 ng/ml. Cells that remained in suspension were removed by aspiration and attached cells were washed twice with PBS, then re-plated and cultured with complete α-MEM medium with 20 ng/ml human M-CSF.

extract_protocol:
RNA from the cultures was extracted using a RNeasy Plus Mini Kit (Qiagen) according to the manufacturers instructions.
Libraries were prepared following the manufacturer's procotols for the Illumina TruSeq Stranded mRNA library preparation kit (part # 20020595). Purified mRNA was isolated from total RNA using oligo-dT beads then converted into double stranded cDNA. Fragmented cDNA libraries were individually indexed and properly ligated molecules were PCR enriched to generate final library.

treatment_protocol: Cells were stimulated with or without LPS (10ng/ml) for 3hr

value: LysM cre

value: Bone marrow-derived macrophages

tag: genotype

value: WT

value: LPS

tag: Sex

value: female


title: KP.2622_000_WT_000_CTRL_0h_Rep.1

source_name: Conrol M0 macrophages rep1

value: MCSF


title: KP.2622_000_KO_000_LPS_3h_Rep.1

source_name: MYC deficient  macrophages stimulated with LPS  rep1

value: MYC f/fLysM cre

value: MYC cKO


title: miRNA_CTR_01


title: TNBC T118


title: TNBC T030


title: TNBC T105


title: miRNA_PD_13

value: Patient with Parkinson's disease


title: miRNA_CTR_03


title: Col-0_rep1

city: Pohang

first: Ildoo

last: Hwang

state: Kyungbuk

address: 77 Cheongam-Ro, Hyoja-dong, Nam-gu,

department: Department of Life Sciences

institute: POSTECH

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: The data were treated using MATLAB 7.13.0 (R2011b)

organism: Arabidopsis thaliana

source_name: Col-0, cotyledon, replicate 1

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: 7-day-old seedlings were grown under the longday light condition (16h/8h)

extract_protocol: TriZol (Invitrogen) total RNA extraction protocol,

value: cotyledon

tag: genotype/variation


title: TNBC T032


title: ckg_rep2

source_name: ckg, cotyledon, replicate 2

value: cgr mutant


title: miRNA_PD_12


title: ckg_rep3

description: Gene expression in the cgr mutant cotyledons

source_name: ckg, cotyledon, replicate 3


title: ckg_rep1

source_name: ckg, cotyledon, replicate 1


title: TNBC T083


title: NHA shNT Rep3

city: Tempe

first: Christopher

middle: L

last: Plaisier

state: Arizona

department: SBHSE

institute: Arizona State University

data_processing:
Adapter trimming using cutadapt
Alignment using STAR
Counts tabulated using ht-seq-count
Genome_build: GRCh38 V2.7.1a
Supplementary_files_format_and_content: raw counts for all genes across all samples

source_name: Normal Human Astrocytes (NHA)

growth_protocol: ihNPCs, hGSCs and mGSCs, were cultured as spheres on non- tissue culture-treated 10cm plates or as adherent cultures on laminin on tissue culture-treated 10cm plates (ThermoFisher Scientific). ihNPCs and hGSCs were grown in DMEM/F12 media, supplemented with B27 and N2 (Invitrogen, ThermoFisher Scientific) in the presence of 20 ng/ml epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF) (MilliporeSigma). Primary Human Astrocytes (NHA; ScienCell) were grown in Astrocyte Media (5% FBS, Astrocyte Growth Supplement, 1% penn-strep) on Poly-L Lysine coated plates according to manufacturer recommendations.

extract_protocol:
72 hours post-selection, total RNA was extracted from cells using the PureLink RNA Mini Kit (Ambion) in accordance to the manufacturerÕs instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GSCs, hNPCs and NHAs transduced with either shNT or shHDAC1 shRNAs at a MOI of 3 were selected with 2 _g/mL puromycin 72 hours post-transduction.

value: Primary human astrocytes

value: NHA

value: shNonTargeting

value: Control

tag: replicate


title: NHA shNT Rep2


title: miRNA_CTR_02

value: Healthy control


title: 22000

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and quantile-quantile normalised using MBCB

source_name: Liver

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Bio-rad Experion System.

tag: radiation

value: Low-LET

tag: dose

tag: pathology

value: HCC


title: KP.2622_000_KO_000_CTRL_0h_Rep.1

state: NY

source_name: MYC deficient M0 macrophages rep1

tag: strain

value: Bone marrow-derived macrophages


title: miRNA_PD_11

tag: group


title: 24408

value: High-LET


title: TNBC T008

last: Kim

tag: sp142 pd-l1

value: negative

value: death


title: miRNA_PD_10


title: 22066


title: NHA shNT Rep1

value: WT


title: 24111


title: 20743


title: NHA shHDAC1 Rep3

value: Knock-down


title: 23761

value: Normal


title: 20860


title: 23941

value: non-IR


title: miRNA_PD_09

value: Patient with Parkinson's disease


title: 23644


title: 23641


title: 21368


title: NHA shHDAC1 Rep2


title: Week2_tenotomy WRC_06

state: CA

tag: time post-tenotomy

value: tenotomy


title: miRNA_PD_07


title: GB3 shNT Rep3

source_name: GB3 GSC

value: Brain tumor

value: GBM

value: IV


title: 23762


title: GB3 shNT Rep2

value: shNonTargeting

value: Control


title: miRNA_PD_06


title: 23766


title: miRNA_PD_05


title: GB3 shNT Rep1


title: GB3 shHDAC1 Rep3


title: miRNA_PD_08


title: miRNA_PD_04


title: 23645


title: 23769


title: miRNA_PD_02


title: GB3 shHDAC1 Rep2


title: 23936


title: 21390

value: Low-LET


title: 23945


title: 21392


title: 23937


title: 24717


title: 21393


title: 21394


title: 23939


title: 23763


title: 23646


title: GB3 shHDAC1 Rep1


title: miRNA_PD_03


title: 20717

value: HCC


title: CC24 shNT Rep3

source_name: CS14iCTR-nxx (ihNPC)

value: Human fibroblast-derived induced pluripotent stem cells


title: miRNA_PD_01


title: 21171


title: Tamm-3 [RNA-seq]

city: Harbin

first: Xu

last: Enshuang

address: NO.600 Changjiang Road, Xiangfang District

institute: Northeast Agricultural University

description:
R20004784-NBC20200225-A-Tamm-3_combined
processed data file: All_Counts.txt

data_processing:
RNA-seq:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
miRNA-seq:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Dog miRNA database and Dog genome.
count counting
Genome_build: CanFam3.1
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Canis lupus familiaris

source_name: tamoxifen-resistant canine mammary gland tumor metastatic cell line

growth_protocol: The cells were cultured to contain phenol-red-free DMEM medium containing 10% charcoalstripped, steroid-depleted FBS (Sigma-Aldrich), antibiotics, and amphotericin.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification or cDNA library construction. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
Hiseq Sequencing Protocol

treatment_protocol: Drug resistant cell lines were constructed by concentration gradient method at 10 months until the cells could normally proliferate in 10 μM TAM medium, then culture at 10 uM for 1 month . To avoid the influence of the experiment, the medium was changed without drugs for 1 week.

tag: cell line


title: 21109


title: CC24 shNT Rep2


title: GC087304: BMDM_phl_LPS_Rep5

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

country: Belgium

description: Replicate 5

data_processing:
Quality of raw sequence reads was checked using FastQC version 0.11.8, and nucleotide calls with a quality score of 28 or higher were considered high quality. Adapters were removed using cutadapt v.2.4. Reads were aligned to the hg19 genome reference, using STAR (2.5.0e) and amaximum of five mismatches were allowed.
the raw counts were imported to R/Bioconductor package DESeq2 v.3.9 to identify differentially expressed genes among samples. The default DESeq2 options were used, including log fold change shrinkage.
Genome_build: mm9

source_name: BMDMs

extract_protocol:
RNA was extracted with QIAzol reagent, followed by RNA extraction with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 23 weeks

tag: gender

value: Female

tag: cell type

value: bone-marrow-derived macrophage (BMDMs)


title: Tamm-2 [RNA-seq]

description:
R20004784-NBC20200225-A-Tamm-2_combined
processed data file: All_Counts.txt

value: tamoxifen-resistant canine mammary gland tumor metastatic cell line


title: GC087298: BMDM_phl_LPS_Rep4

description: Replicate 4

value: 22 weeks


title: 21276


title: GC087292: BMDM_phl_LPS_Rep3

description: Replicate 3

value: 21 weeks


title: GC087286: BMDM_phl_LPS_Rep2

description: Replicate 2

value: 20 weeks


title: 20501

value: High-LET


title: Chmm-3 [RNA-seq]

description:
R20004784-NBC20200225-A-Chmm-3_combined
processed data file: All_Counts.txt

source_name: canine mammary gland tumor metastatic cell line


title: GC087303: BMDM_LPS_Rep5

description: Replicate 5

value: 18 weeks


title: GC087280: BMDM_phl_LPS_Rep1

description: Replicate 1

value: 19 weeks


title: CC24 shNT Rep1

tag: tissue

value: WT

tag: treatment


title: GC087297: BMDM_LPS_Rep4

description: Replicate 4

tag: age

value: 17 weeks


title: CC24 shHDAC1 Rep2

tag: disease

value: Knock-down


title: CC24 shHDAC1 Rep3


title: Tamm-1 [RNA-seq]

description:
R20004784-NBC20200225-A-Tamm-1_combined
processed data file: All_Counts.txt


title: Chmm-2 [RNA-seq]

description:
R20004784-NBC20200225-A-Chmm-2_combined
processed data file: All_Counts.txt

value: canine mammary gland tumor metastatic cell line


title: GC087291: BMDM_LPS_Rep3

description: Replicate 3

value: 16 weeks


title: CC24 shHDAC1 Rep1


title: GC087279: BMDM_LPS_Rep1

description: Replicate 1

value: 14 weeks


title: 21119

value: non-IR

value: HCC


title: GC087285: BMDM_LPS_Rep2

description: Replicate 2

value: 15 weeks

value: Female


title: Chmm-1 [RNA-seq]

description:
R20004784-NBC20200225-A-Chmm-1_combined
processed data file: All_Counts.txt


title: BT187 shNT Rep3

source_name: BT187 GSC

value: Brain tumor

value: GBM

value: IV

value: mut/loss

value: shNonTargeting

value: Control


title: GC087305: BMDM_phl_Rep5

description: Replicate 5

value: 13 weeks

value: bone-marrow-derived macrophage (BMDMs)


title: Tamm-3 [miRNA-seq]

description:
R20003495-NBC20200212-Tamm-3_combined
processed data file: All.miRNA.Counts.txt

value: tamoxifen-resistant canine mammary gland tumor metastatic cell line

tag: molecule subtype

value: microRNA


title: GC087299: BMDM_phl_Rep4

description: Replicate 4

value: 12 weeks


title: BT187 shNT Rep2


title: Tamm-2 [miRNA-seq]

description:
R20003495-NBC20200212-Tamm-2_combined
processed data file: All.miRNA.Counts.txt


title: GC087293: BMDM_phl_Rep3

description: Replicate 3


title: GC087281: BMDM_phl_Rep1

description: Replicate 1


title: GC087287: BMDM_phl_Rep2

description: Replicate 2


title: GC087294: BMDM_ctrl_Rep4

description: Replicate 4


title: BT187 shNT Rep1


title: Tamm-1 [miRNA-seq]

description:
R20003495-NBC20200212-Tamm-1_combined
processed data file: All.miRNA.Counts.txt


title: BT187 shHDAC1 Rep2

value: Knock-down


title: BT187 shHDAC1 Rep3


title: Chmm-3 [miRNA-seq]

description:
R20003495-NBC20200212-Chmm-3_combined
processed data file: All.miRNA.Counts.txt

value: canine mammary gland tumor metastatic cell line


title: GC087282: BMDM_ctrl_Rep2

description: Replicate 2


title: GC087300: BMDM_ctrl_Rep5

description: Replicate 5


title: GC087288: BMDM_ctrl_Rep3

description: Replicate 3


title: GC087276: BMDM_ctrl_Rep1

description: Replicate 1


title: BT187 shHDAC1 Rep1


title: Chmm-1 [miRNA-seq]

description:
R20003495-NBC20200212-Chmm-1_combined
processed data file: All.miRNA.Counts.txt


title: BT145 shNT Rep3

source_name: BT145 GSC

value: WT


title: Chmm-2 [miRNA-seq]

description:
R20003495-NBC20200212-Chmm-2_combined
processed data file: All.miRNA.Counts.txt


title: Synovial tisssue from Pigmented villonodular synovitis joint [zxs140611A]

city: Beijing

first: Dai

last: Hui

address: Xue Yuan Road 28, Haidian District

institute: Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University

data_processing:
Raw data were cleaned via fastp.
Cleaned reads were aligned to human genome (GRCh38) by hisat2.
Aligned reads were counted by Htseq.
fpkm of 6 samples were produced via DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: raw and fpkm

extract_protocol:
Total cellular RNA of synovial tissues was isolated using a RNeasy Mini kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by the Agilent2200 (Agilent, USA).
The sequencing library of each RNA sample was prepared by using Ion Total RNA-Seq Kit v2 according to the protocol provided by manufacturer (Life technologies, USA). Briefly, poly(A)-containing mRNA was purified from 5 ug total RNA with Dynabeads (Life technologies, USA). The mRNA was fragmented using RNaseIII and purified. The fragmented RNA was hybrized and ligated with Ion adaptor. The RNA fragments were reverse- transcribed and amplified to double-stranded cDNA. Then, the amplified cDNA was purified by magnetic bead-based method, and the molar concentration was determined for each cDNA library.

tag: subject status

value: Pigmented villonodular synovitis

value: Synovial tisssue


title: BT145 shNT Rep2

tag: replicate


title: Synovial tisssue from Pigmented villonodular synovitis joint [zxs140525A]


title: NHA shHDAC1 Rep1

value: Primary human astrocytes

value: NHA


title: Stat3_KO_Test-2

city: Boston

first: Prem

middle: Swaroop

last: Yadav

state: MA

address: 118 Longwood Medical Area

department: HSDM

institute: Harvard University

data_processing:
Thermo Fisher Torrent Suite V5.10 used for basecalling
Thermo Fisher Torrent Suite V5.10 used for alignment
Thermo Fisher ampliSeqRNA V5.10 in Torrent Suite V5.10 used for reads counting and normalization
Genome_build: AmpliSeq_Mouse_Transcriptome_v1
Supplementary_files_format_and_content: tab-delimited text file include RPM values for each Sample

source_name: humerus shaft

growth_protocol: E16.5 humerus shaft was used to isolate total RNA. RNA was isolated using Trizol reagent.

extract_protocol:
RNA samples were prepared using TRIZOL reagent from Sigma.
cDNA was synthesized using SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). Libraries were prepared using Ion AmpliSeq Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit on Ion Chef (Thermo Fisher Scientific) according to the manufacturer’s instructions.

treatment_protocol: Total six sample i.e. three samples from Ctrl (Stat3C/+) and three sample Test (Prrx1Cre; Stat3C/C) were used.

value: Long bone

tag: genotype

value: Prrx1Cre; Stat3C/C

value: Stat3 KO


title: Stat3_KO_Test-1


title: Stat3_KO_Test-3


title: WT_Ctrl-3

value: WT Ctrl


title: BT145 shNT Rep1

value: Brain tumor

value: GBM

value: IV

value: shNonTargeting

value: Control


title: WT_Ctrl-2


title: BT145 shHDAC1 Rep2


title: BT145 shHDAC1 Rep1


title: WT_Ctrl-1


title: Synovial tisssue from osteoarthritis joint [OAA]

value: osteoarthritis


title: Synovial tisssue from osteoarthritis joint [OA1A]