title: MT_APAP_10mM_with_LPS_24h_exp1

city: Maastricht

first: Jian

last: Jiang

address: Maastricht University

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: Individual samples were hybridized to an Agilent SurePrint G3 Human Gene Expression 8×60K v2 (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer'sin structions.

scan_protocol: Microarrays were scanned on an Agilent Microarray Scanner (Agilent Technologies, Amstelveen, The Netherlands). Pixel intensities were extracted as raw data from the scan images using Agilent Feature Extraction Software (Agilent).

data_processing: Quantile normalization and data processing were performed using an in house developed quality control pipeline in R as described before 66. Genes with less than 30% flagged were considered as bad spot and repeated identifiers mapping to the same gene were merged by the Babelomics 4.3 suite (http://v4.babelomics.org/).

label_protocol: A total amount of 200 µg RNA of each sample was used as input material for synthesizing dye labeled complimentary-RNA according to the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies).

growth_protocol: The human MTs were incubated in GravityTRAP™ plates with 90 μl 3D InSight™ Human Liver Maintenance Medium (InSphero AG) per well at 37 °C and 5% CO2.

extract_protocol: For the dose-finding study, the liver MTs were exposed to 0, 0.1, 1, 5, 10, 50 and 100 μg/ml LPS dissolved in culture medium for 24h. For the (co-)treatment experiment, the liver MTs were exposed to 0, 0.5, 5 or 10 mM APAP with or without 10 μg/ml LPS for 24h.

treatment_protocol: The liver MTs were exposed to 0, 0.5, 5 or 10 mM APAP with or without 10 μg/ml LPS for 24h.

tag: cell model

value: 3D-co-cultured microtissues (MTs), consisting of primary human hepatocytes (PHH) and Kupffer cells (KCs)

tag: co-treatment


title: MT_APAP_10mM_with_LPS_24h_exp3

status: Public on Oct 04 2020

type: RNA

molecule: total RNA

organism: Homo sapiens


title: TPC-1-shControl_rep3

city: Yiwu

first: Qiang

last: Sun

state: Zhejiang

address: No. N1, Shangcheng Avenue

country: China

institute: Zhejiang University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Robust multi-array average (RMA) using a non-linear correction based upon a convolution model.

label: biotin

source_name: cells transfected with control shRNA

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

growth_protocol: TPC-1 cells were maintained in RPMI1640.The media were supplemented with 10% fetal bovine serum in an incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA from control and RNAi DLD1 was prepared with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with control-shRNA-expressing lentivirus or SHCBP1-shRNA-expressing lentivirus.

tag: cell line

tag: treatment

value: transfected with control shRNA


title: MT_APAP_5mM_with_LPS_24h_exp3


title: TPC-1-shControl_rep2


title: Hippocampal cells DeltaCre-injected_biorep2

type: SRA

city: Boston

first: Michael

middle: E.

last: Greenberg

state: MA

address: 220 Longwood Ave

department: Neurobiology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
Data was processed using 10X Genomics Cell Ranger. Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: nuclear RNA

organism: Mus musculus

source_name: Hippocampal cells DeltaCre-injected

extract_protocol:
Mouse brain was sliced into 300-micron transverse sections on Leica VT1000. Hippocampal CA1 region was subdissected. Tissue was dounce homogenized and nuclei isolated with density gradient. Nuclei were then sorted using 10X Genomics platform.
Library preparation was performed according to the manufacturer’s instructions (10X Genomics). All samples were sequenced on a NextSeq 500 with 58 bp (read 1), 26 bp (read 2) and 8 bp (index).

tag: strain

tag: virus

value: deltaCre-GFP

value: 4-hour kainic acid

tag: tissue

value: CA1 region of hippocampus


title: TPC-1-shSHCBP1_rep2

source_name: cells transfected with SHCBP1 shRNA

value: transfected with SHCBP1 shRNA


title: TPC-1-shSHCBP1_rep1


title: CaMK2a_KA_input_biorep3

description:
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr_IP-vs-in__3-CaMKII.6hr_IP_vs_3-CaMKII.6hr_in__mm10.cd_f.ge.4__6470-UP
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr_IP-vs-in__3-CaMKII.6hr_IP_vs_3-CaMKII.6hr_in__mm10.cd_f.ge.4__7157-DN

data_processing:
Raw sequencing reads ≤ 75 bp in length were 3′-trimmed to a uniform 70 bp (ignoring the ~ 0.1% of reads that were shorter than this) and filtered for quality control. These were then mapped strand-nonspecifically to the mm10 genome (GRCm38) using the Burrows-Wheeler Aligner (bwa), allowing up to 2 mismatches and no gaps. In addition to the usual assembled chromosomes, alignment targets included mitochondrial DNA and a library of ~7 million short splice-junction sequences. Typically, 75–80% of reads were mappable; nonuniquely mapped reads were discarded, as were any that mapped to loci of rRNA genes (from RepeatMasker).
Genic features were based on exonic loci from the NCBI RefSeq annotation for mm10. Mean expression density across a gene’s exons was taken as a proxy for its expression level. (However, noncoding genes, some of which expressed quite highly and variably from one sample to the next, were excluded from these analyses.) The splice-junction target sequences for each gene comprised subsequences of minimal length of all possible concatenations of two or more ordered exons such that their boundaries would be crossed by 70 bp reads. This provided an exhaustive, nonredundant set of predictable exon-junction-spanning loci which typically accounted for ~ 20% of all exonic reads from mature messages.
Differential expression analyses employed edgeR to compare transcript levels in all biological-replicate samples at 6h of KA stimulation to the unstimulated samples. A gene’s expression level was flagged as significantly changed if (a) the Benjamini-Hochberg-corrected p value (q value) for the change, as calculated by edgeR, was consistent with a false discovery rate of 0.005, and (b) it passed a modest background filter (total number of reads ≥ 4 across all compared samples).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene for every sample with differential gene expression analyses (EdgeR)

molecule: cytoplasmic RNA

extract_protocol:
Hippocampal CA1 tissue was rapidly dissected from mice and subsequently Dounce homogenized; lysates were used directly for immunoprecipitation.
All RNA samples (20 ng for CaMK2a; 2.5 ng for PV) with sufficient integrity as analyzed by 2100 Bioanalyzer were SPIA-amplified with the Ovation RNA-seq System V2 (NuGEN). Subsequently, SPIA-amplified cDNA (1 ug) was fragmented to a length of ~400 bp using a Covaris S2 sonicator (Acoustic Wave Instruments). Fragmented cDNA (100 ng) was used to generate Illumina-compatible sequencing libraries using the Ovation Ultralow System V2 (NuGEN). Libraries were sequenced on a NextSeq 500 for 75 bp single-end reads to a depth of 20-40 million reads per sample.

tag: age

value: 3-4 weeks

tag: genotype

value: CaMK2a-Cre/+; LSL-Rpl22-HA/+

value: 6-hour kainic acid

tag: antibody


title: MT_APAP_10mM_with_LPS_24h_exp2


title: MT_APAP_5mM_with_LPS_24h_exp2


title: MT_APAP_5mM_with_LPS_24h_exp1


title: CaMK2a_KA_IP_biorep1

description:
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr.vs.0hr_in.IP__3-CaMKII.IP_6hr_vs_3-CaMKII.IP_0hr__mm10.cd_f.ge.4__6598-DN
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr.vs.0hr_in.IP__3-CaMKII.IP_6hr_vs_3-CaMKII.IP_0hr__mm10.cd_f.ge.4__6786-UP

value: anti-HA antibody (Sigma HA-7, H3663, 12 ug/IP)


title: MT_APAP_0.5mM_with_LPS_24h_exp3


title: Hippocampal cells Uninfected control_biorep2

source_name: Hippocampal cells Uninfected control

value: Non-transduced control for Del2


title: Hippocampal cells Uninfected control_biorep1

value: Non-transduced control for Del1


title: PBMC on visit 1 of the γδ HSTCL patient

status: Public on Oct 05 2020

type: genomic

city: Kiel

first: Jaydeep

last: Bhat

address: Arnold-Heller-Str.

country: Germany

institute: Institute of Immunology

description:
SAMPLE 1
6929689061_R06C02
PBMC isolated from patient blood.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450.

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

data_processing: GenomeStudio software v2011.1; methylation analysis module v1.9.0.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: ficoll-separated PBMC

label_protocol: Standard Illumina Protocol.

growth_protocol: Over the period of 20 months, γδ T-cell lymphoma patient visited 5 times and blood was collected on corresponding visits. PBMC were further isolated using ficoll-based density gradient method.

extract_protocol: Genomic DNA was extracted from isolated cells using Gentra purification Kit (Qiagen, Hilden, Germany) according to standard instructions.

treatment_protocol: A hepatosplenic γδ T-cell lymphoma was clinically on treatment with interferon-α2c dose of 1 million IU s.c. once daily.

tag: gender

value: Female

tag: cell type

value: PBMC

tag: disease state

value: Lymphoma

tag: time point

value: Visit 1


title: MT_APAP_0.5mM_with_LPS_24h_exp2


title: PBMC on visit 5 of the γδ HSTCL patient

description:
SAMPLE 5
6752625098_R04C01
PBMC isolated from patient blood.

value: Visit 5


title: Hippocampal cells DeltaCre-injected_biorep1


title: Hippocampal cells Cre-injected_biorep3

source_name: Hippocampal cells Cre-injected

value: Cre-GFP


title: Hippocampal cells WT non-transduced control_biorep3

value: Non-transduced control for Cre3


title: PBMC on visit 3 of the γδ HSTCL patient

description:
SAMPLE 3
6752625098_R02C01
PBMC isolated from patient blood.

value: Visit 3


title: Hippocampal cells Cre-injected_biorep2

value: 4-hour kainic acid


title: MT_APAP_0.5mM_with_LPS_24h_exp1

value: 3D-co-cultured microtissues (MTs), consisting of primary human hepatocytes (PHH) and Kupffer cells (KCs)


title: Hippocampal cells WT non-transduced control_biorep2

value: Non-transduced control for Cre1

value: CA1 region of hippocampus


title: SP15

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
We followed the procedures described previously (PMIDs: 31849962 and 32129527) for RNA-Seq data analysis: subread v2.0.0 (PMID: 23558742) for reads alignment (hg38), Rsubread v1.34.7 (PMID: 30783653) for calculation of number of reads for protein coding genes from RefSeq, and excel for calculation of Reads Per Kilobase of transcript, per Million mapped reads (RPKM) of exon model (PMID: 18516045), which measures gene expression from RNA-Seq.
Genome_build: hg38
Supplementary_files_format_and_content: XLS file, from left to right represent "Entrz ID", "Gene symbol", log2 RPKM values for group "CTR", "GFP", "SV40", "TCP", "CP5", "CP15", "SP5", and "SP15".

source_name: stem cells isolated from tissue

extract_protocol:
Total RNAs were isolated from cells using Trizol (Invitrogen) followed by additional purification using an RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
Following our previous practice (PMID: 31849962), RNA-Seq library were prepared by the Genomics Core of West Virginia University using using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA) and sequenced by the Genomics Core of Marshall University using HiSeq 2500.

value: infrapatellar fat pad

value: IPFSC

value: IPFSCs on dECM from passage 15 of SV40 transduced IPFSCs


title: PBMC on visit 4 of the γδ HSTCL patient

description:
SAMPLE 4
6752625098_R03C01
PBMC isolated from patient blood.

value: Visit 4


title: MT_medium_with_LPS_24h_exp3


title: SP5

value: IPFSCs on dECM from passage 5 of SV40 transduced IPFSCs


title: Hippocampal cells WT non-transduced control_biorep1


title: Hippocampal cells Cre-injected_biorep1


title: CP5

value: IPFSCs on dECM from passage 5 of SV40 non-transduced IPFSCs


title: MT_medium_with_LPS_24h_exp1


title: MT_APAP_5mM_without_LPS_24h_exp2


title: TCP

value: IPFSCs on tissue culture plastic (TCP)


title: SV40

value: IPFSCs transducted with SV40


title: MT_APAP_10mM_without_LPS_24h_exp2


title: sham-operated 5

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling. All 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the standard Ensembl gtf annotation and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs and human-Mfn2 cDNA), using tophat v2.1.1.
htseq-count (authored by Simon Anders) was used in union mode to assign tophat-aligned reads to gene entries in the standard Ensembl gtf annotation supplied with the bowtie2 iGenome.
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Genome_build: GRCm38 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file includes htseq-count values for each gene.  Depth-normalized values were calculated according to DESeq’s library normalization algorithm.

molecule: polyA RNA

source_name: heart, ventricles

extract_protocol:
Hearts were removed and ventricular tissue was dissected, frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per Methods Mol Biol. 2015;1299:27-49, PMID 25836573.
non-strand-specific, single-end RNA-Seq

tag: Sex

value: Male

tag: age (weeks)

value: heart, ventricles

value: sham operation for ischemia-reperfusion


title: CUTRUN_CA1_CaMK2a_KA2_Fos

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Sequencing reads were trimmed for quality and remaining adapter sequence using Trimmomatic v0.36 (settings: LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25) and kseq (default settings)
Trimmed reads were aligned to the mm10 genome using Bowtie2 v2.2.9 with the following parameters: --local --very-sensitive-local --no-unal --dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700. Trimmed reads were also aligned to the sacCer3 genome with the same parameters to recover reads corresponding to yeast spike-in DNA used in CUT&RUN.
Genome-wide coverage of CUT&RUN fragments was generated using Bedtools v2.27.1 genomecov, normalizing to the number of yeast spike-in reads obtained for each sample.
BigWigs representing the average coverage across the three replicates were generated by concatenating BAM alignments for each individual replicate for a given condition aligned to either the mm10 or sacCer3 genome (for spike-in reads), and calculating normalized genome-wide coverage as above.
Peaks were identified for Fos CUT&RUN using SEACR v.1.1 using the following parameters: norm, relaxed. CUT&RUN performed using rabbit IgG was used as the negative control sample for peak calling. Peaks were subsequently filtered to identify peaks found in all three biological replicates for each condition using Bedtools v2.27.1 intersect, creating a conservative set of Fos-bound sites. Peaks within 150 bp of each other were then merged using Bedtools v2.27.1 merge.
Genome_build: mm10
Supplementary_files_format_and_content: BigWigs represent spike-in normalized genome-wide CUT&RUN coverage for each individual replicate, as well as a "MergedReplicates" sample that represents the average signal across three replicates. BED files represent peaks identified in Fos CUT&RUN experiments that are enriched relative to IgG in the KA condition. The peaks are filtered to preserve only those peaks observed in all three biological replicates.

extract_protocol:
Hippocampal tissue from mice was rapidly dissected and dounce homogenized. Dounce homogenization was performed in Buffer HB (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, pH 7.8 supplemented with protease inhibitors, 1mM DTT, 0.15mM spermine and 0.5mM spermidine) with tight pestle for 20 strokes in a total of 1.5mL volume. Tissue was then supplemented with 96uL 5% IGEPAL CA-630 and dounced an additional 5 strokes with tight pestle. Homogenate was then filtered through a 40-micron strainer to remove large debris and collected in a 15mL conical. 3.5mL of Buffer HB and 5mL of working solution (50% iodixanol with 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH 7.8 supplemented with protease inhibitors, DTT, spermine and spermidine) was added. Homogenized tissue was underlaid with 1mL of 30% iodixanol and 1mL of 40% iodixanol (diluted from working solution) solutions. Samples were centrifuged at 10,000xg for 18 minutes. Nuclei were collected in a 250uL volume at the 30/40% iodixanol interface. Isolated nuclei were diluted two-fold with CUT&RUN wash buffer supplemented with 4mM EDTA and stained with DRAQ5 (Abcam ab108410) at a 1:500 dilution. CaMK2a+ (GFP+) nuclei, resulting from CaMK2a-Cre-mediated expression of Sun1-sfGFP-Myc, were isolated using flow cytometry using a Sony SH800Z Cell Sorter. Sorted nuclei were resuspended in 1 mL cold CUT&RUN wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.2% Tween-20, 1mg/mL BSA, 10mM sodium butyrate, and 0.5mM spermidine supplemented with protease inhibitors), using 50,000 nuclei for each reaction. Nuclei were bound to magnetic Concanavalin-A (ConA) beads (Bangs Laboratories) that had been washed with CUT&RUN binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2). ConA-bead-bound nuclei were then incubated overnight in cold CUT&RUN antibody buffer (CUT&RUN wash buffer supplemented with 0.1% Triton X-100 and 2mM EDTA) and an in-house polyclonal Fos antibody (affinity eluted #1096) or rabbit IgG antibody (Cell Signaling Technologies # 2729). After antibody incubation, ConA-bead-bound nuclei were washed with CUT&RUN antibody buffer, resuspended in CUT&RUN Triton-wash buffer (CUT&RUN wash buffer supplemented with 0.1% Triton X-100), and Protein-A-MNase was added at a final concentration of 700ng/mL. Samples were incubated at 4°C for 1h. The ConA-bead-bound nuclei were then washed twice with CUT&RUN Triton-wash buffer and ultimately resuspended in 100uL of CUT&RUN Triton-wash buffer. 3uL of 100mM CaCl2 was added to each sample and samples were incubated on ice for 30 min. The reaction was stopped by adding 100uL of 2x STOP buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.04% Triton X-100, 20pg/mL yeast spike-in DNA, and 0.1ug/mL RNase A) and incubation at 37°C for 20 min. After incubation, ConA beads were captured using a magnet and supernatants containing DNA fragments released by Protein-A-MNase were collected. Supernatants were then treated with 2uL of 10% SDS and 2uL of 20mg/mL Proteinase-K and incubated at 65°C with gentle shaking for 1h. DNA was then purified using standard phenol/chloroform extraction with ethanol precipitation. DNA was resuspended in 30uL of 0.1x TE buffer.
CUT&RUN sequencing libraries were generated essentially as previously described (Hainer and Fazzio, Curr. Protoc. Mol. Biol., 2019), with the following modifications: Adapter ligation to end-repaired, A-tailed DNA was performed using Rapid T4 DNA ligase (Enzymatics). PCR-amplified libraries were purified from adapter dimers using a 1.1x ratio of AMPure XP beads, eluting in 20uL of 10mM Tris pH 8.0.

value: 3-4 weeks

value: CaMK2a-Cre/+; LSL-Sun1-GFP/+

value: 2-3-hour kainic acid

value: c-Fos (in-house 1096AE)


title: CUTRUN_CA1_CaMK2a_KA2_IgG

value: Rabbit IgG (Cell Signaling Technologies 2729)


title: CUTRUN_CA1_CaMK2a_KA3_Fos

value: CA1 region of hippocampus


title: CP15

value: infrapatellar fat pad

value: IPFSCs on dECM from passage 15 of SV40 non-transduced IPFSCs


title: sham-operated 4


title: sham-operated 3


title: MT_APAP_10mM_without_LPS_24h_exp3

value: 3D-co-cultured microtissues (MTs), consisting of primary human hepatocytes (PHH) and Kupffer cells (KCs)


title: MT_APAP_10mM_without_LPS_24h_exp1


title: MT_APAP_5mM_without_LPS_24h_exp3


title: MT_APAP_5mM_without_LPS_24h_exp1


title: MT_medium_with_LPS_24h_exp2


title: CTR

value: IPFSC

value: IPFSCs without transduction


title: MT_APAP_0.5mM_without_LPS_24h_exp3


title: MT_medium_without_LPS_24h_exp3


title: MT_APAP_0.5mM_without_LPS_24h_exp1


title: MT_APAP_0.5mM_without_LPS_24h_exp2


title: CUTRUN_CA1_CaMK2a_KA1_IgG


title: MT_medium_without_LPS_24h_exp2


title: CUTRUN_CA1_CaMK2a_KA3_IgG


title: sham-operated 2


title: MT_medium_without_LPS_24h_exp1


title: GFP

value: IPFSCs transducted with GFP lentvirus vector


title: myelodysplastic syndrome MSC sample 4

city: Grenoble

first: Mathieu

last: Meunier

address: Boulevard de la Chantourne

department: Hematology

country: France

institute: CHU Grenoble Alpes

description:
SMD4
miRNA

hyb_protocol: The labeled RNA was heated to 99°C for 5 minutes and then incubated at 45°C for 5 minutes. RNA-array hybridization was performed with agitation at 60 rotations per minute for 16 to 18 hours at 48°C on an Affymetrix 450 Fluidics Station (Affymetrix)

scan_protocol: The chips were scanned with an Affymetrix GeneChip Scanner 3000 (Affymetrix)

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip Command Console Software (AGCC) (Affymetrix). All analyses and results were exported using Affymetrix Expression Console Software. Array data were filtered by probes annotated species. Then, the data were normalized between each chip using Robust Multichip Average (RMA) method. The comparative analysis between test sample and control sample was carried out using fold-change and independent T test in which the null hypothesis was that no difference existed between the 2 groups. The miRNAs not detected in any samples were excluded from analysis. miRNA not completely expressed in either group were also excluded. Significance of differential expression between two groups was estimated by t test for those miRNAs of at least a 2-fold reduced or increased mean expression between the 2 groups. All statistical tests of differentially expressed (DE) genes were conducted using the R statistical language v.3.2.2.

label: Biotin

source_name: MSC were selected from CD34+ negative fraction of total bone marrow

label_protocol: 100ng for each RNA samples were labeled with the Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kits

growth_protocol: Mesenchymal Stromal Cells (MSC) were obtained from total bone marrow or from the CD34 negative fraction. Cells were cultured on plastic with DMEM (Dulbecco’s modified eagle medium, Life technologies, Paisley, UK) plus Fetal Bovine Serum 10% , antibiotics (penicillin, streptomycin, L-glutamine at 1%).

extract_protocol: The mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific) was used to extract total RNA

treatment_protocol: After multiple washes with PBS, adherent MSC were recovered and their identity was assessed by flow cytometry using CD73 CD90, CD105 and CD45 . All MSC were positive > 95% for CD73, CD90 and C105 and were negative for CD45.

value: Bone marrow mesenchymal stromal cells

value: myelodysplastic syndrome


title: CUTRUN_CA1_CaMK2a_KA1_Fos


title: T31_pMIR_ARN_long

data_processing:
a 3' adenylated DNA adaptor is ligated to the enriched sample in the absence of ATP preventing the self-ligation of miRNAs. Then a 5' RNA adaptor is ligated in the presence of ATP at the other end of the miRNAs. The RT primer complementary of the 3' adaptor is added at this stage with which it will form a duplex thereby reducing the ligation between adaptors. A reverse transcription is therefore perfomed from the RT primer and finally these captured miRNAs are amplified by PCR with primers complementary to the 3' and 5' adaptors. During this PCR, a specific barcode is incorporated allowing individualisation of each library. Each PCR is loaded on the Fragment Analyzer (AATI) for a precise quantification of each miRNA peak of interest. Based on these results, a equimolar pool of about ten of different samples are performed. Finally, the pooled PCR product is loaded on PAGE in order to excise the band of miRNA that is extracted and purified on a Qiagen MinElute column. Libraries produced are quantified by QPCR to load precisely reads quantity per line of HiSeq Flow-Cell. After the sequencing platform has generated the sequencing images, the data are analyzed in three steps: image analysis, base calling and bcl conversion. CASAVA demultiplexes multiplexed samples during the bcl conversion step and Convert *bcl files into compressed FASTQ files
genome build: hg19
Supplementary_files_format_and_content:raw counts

source_name: Hematopoietic stem cells

growth_protocol: Healthy donor HSPC (CD34+) cells were transfected by electroporation (Amaxa™ Human CD34 Nucleofector™ Kit V, Lonza) with Nucleofector II (Amaxa Biosystem, Lonza) with two different commercial plasmids : one expressing an irrelevant sequence (ref: CmiR0001-MR04, GeneCopoeia™)  and one expressing mir-486

treatment_protocol: Two days after electroporation, the transfected cells were harvested on the GFP expression by flow cytometry

value: Hematopoietic stem cells  (CD34+)

tag: condition

value: nucleofected with mir-486


title: sham-operated 1

value: Male

value: heart, ventricles

value: sham operation for ischemia-reperfusion


title: control (naive) 5

value: naïve, non-operated


title: T30_pMIR_ARN_long


title: CUTRUN_CA1_CaMK2a_PBS2_IgG

value: 3-4 weeks

value: CaMK2a-Cre/+; LSL-Sun1-GFP/+

value: 2-3-hour PBS


title: CUTRUN_CA1_CaMK2a_PBS3_Fos

value: c-Fos (in-house 1096AE)

value: CA1 region of hippocampus


title: control (naive) 4


title: CUTRUN_CA1_CaMK2a_PBS2_Fos


title: T30_pCTRL_ARN_long

value: nucleofected with an irrelevant sequence


title: control (naive) 2


title: T27_pMIR_ARN_long


title: T27_pCTRL_ARN_long


title: CUTRUN_CA1_CaMK2a_PBS1_IgG

value: Rabbit IgG (Cell Signaling Technologies 2729)


title: myelodysplastic syndrome MSC sample 3

description:
SMD3
miRNA


title: control (naive) 1


title: CUTRUN_CA1_CaMK2a_PBS1_Fos


title: CUTRUN_CA1_CaMK2a_PBS3_IgG


title: T31_pCTRL_ARN_long


title: myelodysplastic syndrome MSC sample 1

description:
SMD1
miRNA


title: Healthy donor MSC sample 3

description:
CTL3
miRNA

value: healthy control


title: myelodysplastic syndrome MSC sample 2

description:
SMD2
miRNA


title: Healthy donor MSC sample 1

description:
CTL1
miRNA


title: Healthy donor MSC sample 2

description:
CTL2
miRNA


title: control (naive) 3


title: TPC-1-shControl_rep1

value: transfected with control shRNA


title: M-4W-1

status: Public on Oct 03 2020

city: Philadelphia

first: Haoran

last: Zhang

state: Pennsylvania

address: 415 Curie Boulevard

institute: University of Pennsylvania

data_processing:
Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and removing low quality reads by cutadapt software (v1.9.3), the high-quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM.
The logFPKM of mRNA in different mouse groups was plotted and compared.
Genome_build: MM10
Supplementary_files_format_and_content: Excel files include FPKM values and annotations for each Sample ...

source_name: Muscle

extract_protocol:
Total RNA was collected from TA muscle and heart tissues of different mice (two replicates for each group) by trizol and the rRNAs were removed with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer’s instructions. Libraries were quality-controlled and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

treatment_protocol: Transgenic mice were constructed by linearized plasmids microinjection of UAA incorporation system into fertilized eggs. Trans/mdx mice were constructed by crossing transgenic and mdx mice and further genotype identification. Trans/mdx mice were treated with or without UAA (50 mg NAEK every 2-3 day, for 4 weeks).

value: Muscle

tag: genotypic/variation

value: trans/mdx

value: +UAA, 4 weeks


title: M-mdx-1

value: mdx

value: nonsense mutation in dmd gene


title: M-WT-2

value: wild-type


title: H-mdx-2

source_name: Heart

value: Heart


title: M-cross-2

value: transgenic

value: -UAA


title: M-WT-1


title: M-mdx-2


title: M-trans-2

value: UAA incorporation system


title: M-cross-1


title: H-WT-2


title: H-WT-1


title: H-trans-2


title: H-cross-1


title: H-cross-2


title: H-4W-2


title: H-4W-1


title: M-4W-2


title: Rh76.GABA.rna

city: Bronx

first: Stella

last: Dracheva

state: New York

address: James J. Peters VA Medical Center,130 W Kingsbridge Rd

department: Dept. of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description: RNA isolated from FANS-sorted nuclei

data_processing:
RNA-seq FASTQ files were pre-processed using tools: Scythe, Sickle, and seqtk (trimming 3 bp from the 5′ end of Read 1, in accordance with the SMARTer RNA-seq library kit protocol).
Reads were quantifiied using a transcript- quantification software tool Salmon (version 0.9.1), and aggregated by gene using the R package "tximport" (version 1.6.0)
Differential expression analysis was performed using DESeq2, with the settings: abs(fold change) > 2, FDR < 0.05
Genome_build: hg38, panTro5, rheMac8
Supplementary_files_format_and_content: diiferential expression comparison tables

organism: Macaca mulatta

source_name: brain

extract_protocol:
The dorsolateral prefrontal cortex (DLPFC) tissue specimens were sampled from frozen brains of macaque and chimpanzee subjects, in a region corresponding to human BA9.
Nuclei of glutamatergic or MGE-derived GABAergic neurons were isolated by flow cytometry, using antibodies against neuronal nuclei (anti-NeuN) and MGE-derived GABAergic neurons (anti-SOX6).
Total RNA was isolated from sorted nuclei, using PicoPure Kit (Thermo Fisher Scientific).
RNA-seq libraries were constructed using SMARTer Stranded Total Pico-Input RNA-seq kit (Clontech) and 10 ng RNA from each sample.
Sequencing was performed on an Illumina HiSeq 2500 instrument, using a paired-end 50 (PE50) protocol to an average of ∼50 million read pairs per sample.

value: MGE-dervied GABAergic neurons

tag: brain area

value: dorsolateral prefrontal cortex

value: Male

tag: age (years)

value: wild type


title: H-mdx-1

tag: treatment


title: clone_EE_mRNA_seq

city: Kumamoto-shi

first: Manabu

last: Maeshiro

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Molecular Laboratory Medicine

country: Japan

institute: Kumamoto University

data_processing:
We used FASTQC v0.11.8 software for an initial quality assessment and to detect common issues in RNA-seq data.
Adaptor sequences and low-quality ends were removed with Trimmomatic (v0.38). Trimmed reads were aligned to a combined human (GRCh38) reference by using HISAT2 (v2.1.0).
The expression level of each gene was quantified as fragments per kilobase of exons per million mapped reads (FPKM) by using both StringTie (v1.3.6) and Ballgown (v2.12.0) with default parameters.
Genome_build: human reference genome GRCh38

source_name: head and neck squamous cell carcinoma cells

growth_protocol: SAS cells were routinely grown by re-plating in RPMI1640 supplemented with 10% heat-inactivated FBS in 5% CO2 at 37  ℃.

extract_protocol:
Total RNA was prepared from exponentially growing cells by using Isogen (Nippon Gene, Toyama, Japan) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: clone H and EE cells were barcoded by lentiviral infection at a multiplicity of infection of 0.1, and infected cells were selected with puromycin.

value: SAS cells

value: DNA barcoded


title: clone_H_mRNA_seq


title: Rh75.GABA.rna

description: RNA isolated from FANS-sorted nuclei


title: Rh74.GABA.rna

description: RNA isolated from FANS-sorted nuclei


title: Rh36.GABA.rna

description: RNA isolated from FANS-sorted nuclei


title: dox_hu_gh2ax_2

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

data_processing:
The 3' end of the sequences were trimmed for Illumina adapters, for ambiguous nucleotides (N's), and for artificial poly G's using cutadapt.
ChIP-seq reads were aligned to the mouse mm10 genome assembly using Bowtie2 wit hthe following configurations:
ChIP-seq peaks were called using the SICER algorithm on EPIC software platform.
Quantile normalization of V3C-seq and ChIP-seq datasets were performed on Rstudio using the preprocessCore package.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Processed files are uploaded as bed and bedgraph files

source_name: Fibroblast

growth_protocol: Murine A9 fibroblasts containing a lentivirally integrated NS1 expression cassette generated using pInducer20 system were parasynchronized in Isoleucine-deficient DMEM media containing 5 percent FBS for 36-42 hours. Upon release into complete DMEM media, cells were induced with Doxycycline for 24 hours before being harvested and processed for ChIP-seq analysis. 1 mM HU treatment was started in the indicated cells at 8 hours post Dox induction, and continued for 16 hours.

extract_protocol:
For ChIP assays, Cell were crosslinked with 1% formaldehyde for 10 minutes at room temperature and then quenched in 0.125> glycine for 5 minutes. Cells were collected, lysed in ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8, protease inhibitors) and sonicated using a Diagenode Bioruptor for 60 cycles (30 seconds on; 30 secoonds off). The lysate was immunoprecipitated overnight with antibody-conjugated Dynabeads (Protein A; ThermoScientific). lysates were clarified from sonicated nuclei (Diagenode), and DNA-protein complexes were immunoprecipitated using antibodies conjugated to Dynabeads (ThermoScientific). Samples were washed, eluted, reverse crosslinked, Proteinase K treated and purified using PCR purification kit (Qiagen) and eluted in 50 microliters of buffer EB.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (cat # E7645L) according to manufacturer's instructions. Nine samples were pooled in one run and samples were analyzed by 75 bp single-end sequencing on the NextSeq 500 (Illumina).

treatment_protocol: Murine A9 fibroblasts treated with 1 mM Hydroxyurea for 16 hours before being harvested for chromatin immunoprecipitation.

value: Subcutaneous connective tissue

value: Doxycycline (24 hrs) + Hydroxyurea (16 hrs)

tag: strain

tag: chip antibody

value: Millipore #05-636 (5 ug)


title: Rh76.GLU.rna

description: RNA isolated from FANS-sorted nuclei

value: glutamatergic neurons


title: Parental_mRNA_seq

value: untreated


title: PBMC on visit 2 of the γδ HSTCL patient

description:
SAMPLE 2
6752625098_R01C01
PBMC isolated from patient blood.

value: Female

value: PBMC

value: Lymphoma

value: Visit 2


title: dox_hu_ns1_2

description: Mouse Anti-NS1 antibody was generated at the MU Hybridoma core (Salome and Pintel, unpublished) and was purified using HiTrap Protein G columns (GE Lifesciences). Anti-NS1 antibody was validated using western blots, immunofluorescense and immunoprecipitation.

value: Doxycycline (24 hrs)

value: mouse anti-NS1 monoclonal (10ug)


title: H-trans-1

tag: tissue

value: Heart

value: transgenic

value: UAA incorporation system


title: Rh75.GABA.input

description: MNase-digested genomic DNA

data_processing:
Paired-end reads were aligned using Bowtie (version 1.1.2) with the following settings: chunkmbs 512 -S -q -l 40 -n 1 -phred33-quals -p 7 -m 1
H3K27ac-enriched regions (peaks) were called using MACS2 (2.1.1.20160309) using an input control (MNase-digested chromatin) for each sample with the following settings: callpeak -B -f BAMPE –broad –broad-cutoff 0.00001
Peaks coordinates were converted between species using the liftOver tool.
Differentially acetylated H3K27ac peaks were detected with DESeq2 by comparing the sets of biological replicates between cell types or species, using the following criteria: FDR < 0.05, Log2(FC) > 1.
Genome_build: hg38, panTro5, rheMac8
Supplementary_files_format_and_content: H3K27ac ChIP-seq signal traces in BigWig format, constructed using a normalization to 1,000,000 reads in each sample.
Supplementary_files_format_and_content: Peak coordinate files; differentially acetylated analysis tables, in TXT format

extract_protocol:
The dorsolateral prefrontal cortex (DLPFC) tissue specimens were sampled from frozen brains of macaque and chimpanzee subjects, in a region corresponding to human BA9.
Nuclei of glutamatergic or MGE-derived GABAergic neurons were isolated by flow cytometry, using antibodies against neuronal nuclei (anti-NeuN) and MGE-derived GABAergic neurons (anti-SOX6).
Histone modification ChIP-seq was performed using anti-H3K27ac antibodies, and a native MNase-digestion-based protocol.
ChIP-seq libraries were constructed using NEBNext Ultra DNA Library Prep kit.
Sequencing was performed on an Illumina HiSeq 2500 instrument, using a paired-end 50 (PE50) protocol to an average of ∼40 million read pairs per sample.

value: MGE-dervied GABAergic neurons

value: dorsolateral prefrontal cortex

value: Male

value: wild type

value: input control chromatin


title: Rh74.GLU.rna

description: RNA isolated from FANS-sorted nuclei


title: Rh75.GLU.rna

description: RNA isolated from FANS-sorted nuclei


title: Rh76.GABA.input

description: MNase-digested genomic DNA


title: Input

value: Subcutaneous connective tissue


title: Liver, JT003-Fibrosis

city: guangzhou

first: Xianxing

state: guangdong

address: 132 east outer ring road

institute: Sun Yat-Sen University

description: CCl4-VS-JT003.DEGseq_Method.GeneDiffExp.txt

data_processing:
Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value,28S/18S and the fragment length distribution
internal software SOAPnuke to filter reads, followed as:
1) Remove reads with adaptors;
2) Remove reads in which unknown bases(N) are more than 10%;
3) Remove low quality reads (we define the low quality read as the percentage of base which
quality is lesser than 15 is greater than 50% in a read).
Use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2, and then calculate gene expression level with RSEM
We detect DEGs with PossionDis as requested.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Liver were removed, flash frozen on liquid nitrogen , and RNA was harvested using Trizol reagent. TransGen Biotech RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

tag: age

value: 6-8 weeks

value: male

value: Post-treatment fibrosis

value: liver


title: dox_ns1_2


title: Rh74.GABA.input

description: MNase-digested genomic DNA

tag: genotype


title: Rh36.GLU.rna

description: RNA isolated from FANS-sorted nuclei

value: glutamatergic neurons


title: dox_gh2ax_1

value: Doxycycline (24 hrs) + Hydroxyurea (16 hrs)

value: Millipore #05-636 (5 ug)


title: dox_hu_ns1_1

value: Doxycycline (24 hrs)

value: mouse anti-NS1 monoclonal (10ug)


title: dox_gh2ax_2


title: Liver, JT003-HFD

description: HFD-VS-JT003.PossionDis_Method.GeneDiffExp.txt

value: Post-treatment NASH


title: Liver, Oil

description: Oil-VS-CCl4_2.PossionDis_Method.GeneDiffExp.txt

value: Normal control

value: Oil


title: Rh76.GLU.input

description: MNase-digested genomic DNA

value: dorsolateral prefrontal cortex

tag: antibody


title: Liver, HFD

tag: gender

value: NASH


title: Rh75.GLU.input

description: MNase-digested genomic DNA

tag: cell type

value: Male

value: wild type


title: DAOY_ZNF521_DMSO

city: San Giovanni rotondo

first: Valentina

last: Melocchi

state: Foggia

address: Viale Padre Pio 7

department: ISBReMIT - Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies

country: Italy

institute: Casa Sollievo della Sofferenza Hospital - IRCCS

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using STAR v2.7.0e with parameters  --runThreadN 8 --outFilterMultimapNmax 20 --alignIntronMax 500000 --quantMode TranscriptomeSAM GeneCounts --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate
Raw counts were determined by STAR v2.7.0e. For each sample raw reads coming from two different RNA-Seq experiments were summed.
STAR gene counts were normalized applying the median of ratios method implemented in DESeq2 R package
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with DESeq normalized reads for every gene and every sample

source_name: DAOY cell line

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer’s protocol and quantified using the 2100 Bioanalyzer (Agilent).
Poly-A-enriched strand-specific ribosomal RNA-depleted libraries were generated with the Illumina TruSeq Stranded Total RNA Library Prep Gold, according to the manufacturer’s instructions.

tag: cell line

value: DAOY

value: brain/cerebellum

value: medulloblastoma


title: dox_hu_gh2ax_1

value: Subcutaneous connective tissue


title: DAOY_ZNF521_SAG


title: Liver, CD

description: SD-VS-HFD.PossionDis_Method.GeneDiffExp.txt

value: 6-8 weeks

value: male

tag: disease state

value: Chow diet Control

value: liver


title: Rh74.GLU.input

description: MNase-digested genomic DNA

value: glutamatergic neurons

tag: Sex

value: input control chromatin


title: Rh36.GLU.input

description: MNase-digested genomic DNA


title: dox_ns1_1

value: Doxycycline (24 hrs)

value: mouse anti-NS1 monoclonal (10ug)


title: DAOY_CTL_DMSO


title: Rh36.GABA.input

description: MNase-digested genomic DNA

value: MGE-dervied GABAergic neurons


title: 32h Hippo-IR rep3

city: Milan

first: Fabio

last: Marchiano

address: Via Alessandro Manzoni 56

institute: Humanitas

description: flight muscle from 32h pupae APF

data_processing:
BRB-seqTools was used for reads demultiplexing
STAR (version 020201) was used to map sequenced reads to dm6 whole genome
HTSeq (version 0.9.1) for features count and raw count matrices generation
DESeq2 (version 1.22.2) to produce normalized (RLE) counts tables and differential expression analysis
Genome_build: BDGP6.23 (dm6)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample in excel format (xls)
Supplementary_files_format_and_content: Matrix table with normalised (RLE) gene counts for every gene and every sample in excel format (xls)
Supplementary_files_format_and_content: Matrix table containing the differential expression analysis results for each pairwise comparison. It contains also the normalised (RLE) gene counts for every gene and every sample, and in add the mean count of the biological replicated of the two condition taken in account for the statistical test. In excel format (xls) and for both the time points taken in account (24h and 32h)

organism: Drosophila melanogaster

source_name: Indirect flight muscle

extract_protocol:
For each replicate flight muscles from seven Mef2-GAL4, UAS-GMA-GFP pupae at 24 h and 32 h APF were dissected in ice-cold PBS treated with DEPC using a fluorescent binocular. Flight muscles were collected in an Eppendorf tube and centrifuged at 2000g for 5 min. The flight muscle pellet was re-suspended in TRIzol™, shock-frozen in liquid nitrogen and kept at -80°C. RNA was isolated directly from the TRIzol muscle samples using a 96 well plate extraction kit (Direct-zol™-96 RNA, Zymo Research, #R2054): after thawing to room temperature in 1,5ml Eppendorf tubes, the tissue samples were homogenized using a small pestle, followed by nucleic acid precipitation with 100% ethanol. The pellet was dissolved and transferred to the 96 well plate containing the purification columns. DNA digestion was performed in columns according to the kit instructions. Total RNA was eluted with 25 μl of RNase-free water and was quantified using the Quantifluor RNA System (Promega, #E3310).
RNA sequencing libraries were prepared using 20 ng of total RNA following the BRB-sequencing protocol. Briefly, each RNA sample was reverse transcribed in a 96-well plate using SuperScriptTM II Reverse Transcriptase (Lifetech 18064014) with individual barcoded oligo-dT primers (Microsynth, Switzerland). Next, the samples were split into 3 pools, purified using the DNA Clean and Concentrator kit (Zymo Research #D4014), and treated with exonuclease I (New England BioLabs, NEB #M0293S). Double-stranded cDNA was generated by the second strand synthesis via the nick translation method. For that, a mix containing 2 μl of RNAse H (NEB, #M0297S), 1 μl of E. coli DNA ligase (NEB, #M0205 L), 5 μl of E. coli DNA Polymerase (NEB, #M0209 L), 1 μl of dNTP (0 .2 mM), 10 μl of 5x Second Strand Buffer (100 mM Tris, pH 6.9, AppliChem, #A3452); 25 mM MgCl2 (Sigma, #M2670); 450 mM KCl (AppliChem, #A2939); 0.8 mM β-NAD Sigma, N1511); 60 mM (NH4)2SO4 (Fisher Scientific Acros, #AC20587); and 11 μl of water was added to 20 μl of ExoI-treated first-strand reaction on ice. The reaction was incubated at 16 °C for 2.5 h. Full-length double-stranded cDNA was purified with 30 μl (0.6x) of AMPure XP magnetic beads (Beckman Coulter, #A63881) and eluted in 20 μl of water. The Illumina compatible libraries were prepared by tagmentation of 5 ng of full-length double-stranded cDNA with 1 µl of in-house produced Tn5 enzyme (11 μM). After tagmentation the libraries where purified with DNA Clean and Concentrator kit (Zymo Research #D4014) eluted in 20 µl of water and PCR amplified using 25 μl NEB Next High-Fidelity 2x PCR Master Mix (NEB, #M0541 L), 2.5 μl of P5_BRB primer (5 μM, Microsynth), and 2.5 μl of Illumina index adapter (Idx7N5 5 μM, IDT) following program: incubation 72 °C—3 min, denaturation 98 °C—30 s; 15 cycles: 98 °C—10 s, 63 °C—30 s, 72 °C—30 s; final elongation at 72 °C—5 min. The fragments ranging 200–1000 bp were size-selected using AMPure beads (Beckman Coulter, #A63881) (first round 0.5x beads, second 0.7x). The libraries were profiled with High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, #DNF-474) and measured with Qubit dsDNA HS Assay Kit (Invitrogen, #Q32851) prior to pooling and sequencing using the Illumina NextSeq 500 platform using a custom primer and the High Output v2 kit (75 cycles) (Illumina, #FC-404-2005). The library loading concentration was 2.2 pM and sequencing configuration as following: R1 6c / index 8c / R2 78c.

value: indirect flight muscle

tag: developmental stage

value: 32h APF

value: Hippo-IR


title: Rh76.GABA

description: MNase-digested genomic DNA

value: dorsolateral prefrontal cortex

value: Male

value: wild type

value: anti-H3K27ac-precipitated chromatin


title: Rh75.GABA

description: MNase-digested genomic DNA


title: Liver, CCl4

value: Liver Fibrosis


title: 32h Hippo-IR rep2

description: flight muscle from 32h pupae APF


title: OP-3

city: WuHan

first: Guosong

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Transcript_FPKM.xls [L300]

data_processing:
Illumina Casava  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp software with default parameters
clean reads were mapped to hg38  genome using tophat2 and new transcripts were assembled by  cufflinks with default parameters
lncRNA filtered by following steps : transcripts length > 200 bp , exon num >= 2 ,FPKM > 0.5 , using CNCI,CPC,PFAM,phyloCSF software to predict coding potential ,then take the intersection of four software results as the final lncRNA
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample  and lncRNA fasta file

source_name: serum exosome

extract_protocol:
Blood samples were centrifuged at 1,500 g for 15 minutes at 4 °C. The collected supernatant (2.5 mL plasma) were then centrifuged at 12,000 g for 30 minutes at 4 °C. The supernatant was collected and ultra-centrifuged at 100,000 g for 2 hours at 4 °C to pellet the exosomes. Exosome pellets were then washed in filtered PBS and re-centrifuged at 100,000 g, the supernatant was removed and the final exosomal pellet was re-suspended in 200 µl PBS. The size distribution of exosomes was examined using a NanoSight Tracking Analysis LM20 System (NanoSight Ltd). Total RNA in exosomes were isolated using TRIzol (Invitrogen) reagent as per manufacturer’s instructions. To remove DNA, the RNA was treated with RQ1 DNase (Promega, Madison, WI, USA) for 20 minutes at 37°C. The quality and quantity of the purified RNA were confirmed by measuring the absorbance at 260 and 280 nm (A 260 and A 280) using a SmartSpec Plus Spectrophotometer (Bio-Rad Laboratories, Inc., Hercules, CA, USA). RNA integrity was further verified by electrophoresis using a 1.5% agarose gel. All RNA samples were stored at -80°C for future use.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: with osteoporosis

value: Peripheral blood


title: OP-2

description: Transcript_FPKM.xls [L21]


title: 32h Yorkie-CA rep3

description: flight muscle from 32h pupae APF

value: Yorkie-CA


title: 32h Yorkie-CA rep2

description: flight muscle from 32h pupae APF


title: OP-1

description: Transcript_FPKM.xls [L16]


title: Rh74.GABA

description: MNase-digested genomic DNA


title: Rh36.GABA

description: MNase-digested genomic DNA


title: 32h Yorkie-CA rep1

description: flight muscle from 32h pupae APF


title: RNA-seq of mus musculus: 3-week old male and female aorta4

city: Nanjing

first: Lisha

last: Wei

email: 278530660@qq.com, weils@nicemice.cn

address: Xuefu Road 12#

institute: Nanjing University

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis was performed using the DESeq2 R package (1.16.1)
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: aorta

extract_protocol:
RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer(Life Technologies, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: 3 weeks old

value: KO


title: RNA-seq of mus musculus: 3-week old male and female aorta1

value: WT


title: RNA-seq of mus musculus: 3-week old male and female aorta2


title: RNA-seq of mus musculus: 3-week old male and female aorta3


title: NC-3

description: Transcript_FPKM.xls [s3]

value: without osteoporosis


title: DAOY_CTL_SAG

value: DAOY

value: brain/cerebellum

value: medulloblastoma


title: 32h wild type rep6

description: flight muscle from 32h pupae APF

value: indirect flight muscle

value: 32h APF


title: 32h wild type rep5

description: flight muscle from 32h pupae APF


title: 32h Hippo-IR rep1

description: flight muscle from 32h pupae APF

value: Hippo-IR


title: Rh75.GLU

description: MNase-digested genomic DNA

value: glutamatergic neurons

value: dorsolateral prefrontal cortex

value: Male


title: 32h wild type rep4

description: flight muscle from 32h pupae APF

value: wild type


title: NC-2

description: Transcript_FPKM.xls [s2]


title: NC-1

description: Transcript_FPKM.xls [s1]


title: Rh36.GLU

description: MNase-digested genomic DNA

value: anti-H3K27ac-precipitated chromatin


title: Rh74.GLU

description: MNase-digested genomic DNA


title: 32h wild type rep3

description: flight muscle from 32h pupae APF


title: 32h wild type rep2

description: flight muscle from 32h pupae APF


title: CFBE RPF enriched for CFTR

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

description: Ribosme protected

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-2: -v 2 --best --strata -m 1
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-2 the middle nucleotide of each read was taken.
Read counts were normalized by million mapped reads and transcript length for each nucleotide

source_name: CFBE cells 48h after transfection with wild-type CFTR

growth_protocol: Cystic Fibrosis Bronchial Epithelial cells were grown at 37°C to 70% confluency in Eagle's MEM, transfected with wild-type CFTR vector and incubated for 48h prior to harvesting

extract_protocol:
Cells were harvested in ice-cold polysome lysis buffer and CFTR transcripts were enriched using specific biotin-labeled oligos. CFTR enriched, dephosphorylated RPFs were then subjected to denaturating PAGE for size exclusion
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009}

value: Cystic Fibrosis Bronchial Epithelial (CFBE) cells

tag: transfected with

value: wild-type CFTR

tag: time point

value: 48h after transfection


title: 32h wild type rep1

description: flight muscle from 32h pupae APF


title: ChHER.GABA.rna

description: RNA isolated from FANS-sorted nuclei

organism: Pan troglodytes

value: MGE-dervied GABAergic neurons

tag: brain area

tag: age (years)


title: CD4 T cell Ang3

city: Tucson

first: Heddwen

last: Brooks

state: Arizona

address: 1656 E Mabel St, RM 413

department: Physiology

institute: University of Arizona

data_processing:
Sequences were trimmed using trimmomatic (v0.32) with the following parameters: TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20.
Trimmed reads were aligned to the whole mouse genome (GRCm38.p3) using TopHat (v2.1.1).
Genome_build: whole mouse genome (version GRCm38.p3)
Supplementary_files_format_and_content: CSV matrix table includes cuffdiff output for group comparisons
Supplementary_files_format_and_content: CSV matrix tables include FPKM values for each identified gene for each sample

source_name: Splenic CD4 T cells

extract_protocol:
CD4 T cells were isolated from single cell suspensions of spleen using StemCell EasySep Mouse CD4+ T cell Isolation Kit (Cat# 19852). RNA was extracted from cell lysates according to instructions included in the Qiagen RNeasy Micro Kit (Cat# 74004)
RNA libraries were prepared for sequencing using standard Illumina RNA Truseq protocols

treatment_protocol: Angiotensin II treatment (800 ng/kg/min) via osmotic minipump for 2 weeks

tag: strain

value: Splenic CD4+ T cells

tag: agent

value: Ang II

value: 10 weeks old pre 2 weeks Ang II


title: CD4 T cell Ang2

tag: tissue


title: CD4 T cell Ang1

tag: age


title: Rh76.GLU

description: MNase-digested genomic DNA

tag: genotype


title: ChBR.GABA.rna

description: RNA isolated from FANS-sorted nuclei


title: 24h Hippo-IR rep2

description: flight muscle from 24h pupae APF

value: 24h APF


title: 24h Hippo-IR rep3

description: flight muscle from 24h pupae APF


title: CD4 T cell Con3

value: untreated

value: 10 weeks old pre 2 weeks control


title: ChBB.GABA.rna

description: RNA isolated from FANS-sorted nuclei


title: ChHER.GLU.rna

description: RNA isolated from FANS-sorted nuclei


title: CD4 T cell Con2


title: CD4 T cell Con1


title: ChBR.GLU.rna

description: RNA isolated from FANS-sorted nuclei


title: 24h Hippo-IR rep1

description: flight muscle from 24h pupae APF

value: indirect flight muscle


title: 24h Yorkie-CA rep2

description: flight muscle from 24h pupae APF

value: Yorkie-CA


title: Ppara -/- MLL-AF9_Rep1

first: Leinal

middle: Alen

last: Sejour

address: 58 Lonsdale St.

department: Pathology

institute: Beth Israel Deaconess medical center

hyb_protocol: Total RNA was extracted using Triazol reagent (Invitrogen) and retro-transcribed to cDNA using iScript cDNA Synthesis kit (Bio-Rad). Samples for qPCR were run in triplicate in a Lightcycler 480 (Roche) using SYBR Green I Master Mix (Roche). Values were normalized by mouse Actin levels.

scan_protocol: Affymetrix protocol

data_processing: RMA and limma

source_name: BM-MNCs, secondary recipient of Ppara -/- MLL-AF9, first replicate

label_protocol: 293T cells were transfected using Lipofectamine 2000 (ThermoFisher catalog # 11668019), pCL-Eco, and  MSCV-MLL-AF9-IRES-GFP, both of which were a kind gift from the lab of Dr. Scott Armstrong. Supernatant was changed one day following transfection, collected at 48 hours post-infection, and concentrated using a 100K centrifuge column (Millipore-Sigma catalog # UFC910008). Cells were spin-infected with concentrated retrovirus and 8 g/mL polybrene. Following infection, cells were washed twice with PBS before being counted and injected into recipients.

growth_protocol: BM-MNCs were isolated from secondary recipients of Ppara +/+ MLL-AF9 or Ppara -/- MLL-AF9 leukemia and FAC-sorted based on te expression of GFP.

extract_protocol: Trizol

value: Murine, GFP-positive, sorted MLL-AF9 leukemia


title: 24h Yorkie-CA rep1

description: flight muscle from 24h pupae APF


title: ChHER.GABA.input

description: MNase-digested genomic DNA

value: dorsolateral prefrontal cortex

tag: antibody

value: input control chromatin


title: Sorted microglia from pooled P0 brain of WT mice, treated with LPS+interferon b, replica 3

city: New york

first: Yurii

last: Chinenov

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description:
Neonatal microglia
invitro_microglia_summary_table_2019-12-03.xls

data_processing:
Pair-end and single-end sequencing was performed at the Weill Cornell Epigenomics Core using HiSeq2500 at the depth of ~30 million reads per sample. Read quality was assessed and adapters trimmed using fastp
50bp Reads were then mapped to the mm10 and reads in exons were counted against Gencode v27 with STAR Aligner
Differential gene expression analysis was performed in R with edgeR using LRT framework. Genes with low expression levels ( < 3 counts per million in at least one group ) were filtered from all downstream analyses.
Genes with unadjusted P-value less than 0.01 and log2 fold change greater than 1 were considered differentially expressed.
Surogate variable analysis (R sva package) was used to correct for an unknown sex ratio of pooled mouse embryos
Genome_build: mm10
Supplementary_files_format_and_content: Xlsx tables with raw feature counts, log-transformed normalized feature counts and edgeR LRT differential expression statistics

source_name: P0 Neonatal mouse microglia

growth_protocol: 1. Neonatal microglia:P0 mice were decapitated, olfactory nerves were cut, cerebellum, midbrain and meninges were carefully removed under the microscope. Meninges-free brains were pooled, washed and digested in 0.25% Trypsin – 10 mg/ml DNAse I (Roche) for 10’ at RT. Then, cells were carefully homogenized with a 1000 μl pipette to break up tissue without killing cells, filtered through 100-μM cell strainer (BDTM) and placed into DMEM - 10% FBS in presence of 20% L-Cell conditioned media (LCCM). 24 h after, cells were washed and observed, changing media every 3-4 days, until a large number of MG started to appear on top of the astrocyte monolayer. At day 14-20, cells were trypsinized and MG was isolated by Cd11b Microbeads (Miltenyi Biotec) selection. MG were plated at the density of 50,000 cells/cm2 in DMEM - 10% FBS - 1% Pen/Strep in flasks pre-coated with 0.01% poly-L-lysine (Sigma) for a minimum of 2 h.

extract_protocol:
2. Macrophages, microglia from healthy and EAE mice: Total immune cells were isolated from spinal cords following tissue digestion and following a classic Percoll gradient protocol. Next, they were incubated with fluorochrome coupled antibodies for leukocytes (anti-CD45 FITC), T-cells (anti-CD3 APC), myeloid cells (anti-Cd11b PE and F4/80 PE-Cy7) and DAPI for dead cells. Live CD45+Cd11b+ cells were sorted in RLT lysis buffer and RNA were extracted using RNAeasy Plus Micro Kit (QIAGEN), Quality control (QC) of extracted RNA were performed and high quality ones were sequenced.
Total RNA from sorted myeloid CD45+Cd11b+ cells from WT and KO spinal cords of EAE mice was polyA enriched using  Illumina TrueSeq2.0 kit

treatment_protocol: 1. Neonatal microglia: 24 hours after plating, MG were treated for 2 h with LPS±100 nM Dex or LPS±500 U/ml IFNβ, RNA was extracted using RNAeasy Plus Mini Kit (QIAGEN)and profiled by RNAseq

value: Microglia

value: wild type

tag: treatment

value: LPS+interferon b

value: microglia

tag: desease state

value: healthy

value: pooled embryos


title: Sorted microglia from pooled P0 brain of WT mice, treated with LPS, replica 3

value: LPS

tag: cell type


title: 24h Yorkie-IR rep3

description: flight muscle from 24h pupae APF

value: Yorkie-IR


title: Sorted microglia from pooled P0 brain of WT mice, treated with interferon b, replica 3

value: interferon b


title: ChET.GABA.input

description: MNase-digested genomic DNA

value: MGE-dervied GABAergic neurons

value: Male


title: 24h Yorkie-CA rep3

description: flight muscle from 24h pupae APF

value: 24h APF


title: 24h Yorkie-IR rep2

description: flight muscle from 24h pupae APF

value: indirect flight muscle


title: Ppara -/- MLL-AF9_Rep2

city: Boston

source_name: BM-MNCs, secondary recipient of Ppara -/- MLL-AF9, second replicate


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with LPS, replica 3


title: ChBB.GLU.rna

description: RNA isolated from FANS-sorted nuclei

value: glutamatergic neurons


title: Ppara -/- MLL-AF9_Rep3

source_name: BM-MNCs, secondary recipient of Ppara -/- MLL-AF9, third replicate

value: Murine, GFP-positive, sorted MLL-AF9 leukemia


title: BEAS-2B cells, replicate 3-exposed to PM2.5

city: Freiburg

first: Stefan

last: Günther

department: Institute of Pharmaceutical Sciences

institute: Albert-Ludwigs University Freiburg

description: BEAS-2B cells in the presence of PM2.5

hyb_protocol: 50 μg/mL of biotinylated and fragmented cRNA was hybridized to HG-U133 Plus 2.0 arrays. After washing and fluorescence labeling (GeneChip Hybridization, Wash & Stain Kit, Affymetrix, #900720), arrays were scanned (Affymetrix GeneChip Scanner 3000, Affymetrix).

scan_protocol: Arrays were scanned by the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed using the R package ‘simpleaffy’ using RMA normalization.

source_name: BEAS-2B bronchial epithelial cell line

label_protocol: Biotinylated cRNA probes were prepared using the 3'IVT Plus Amplification Kit, Affymetrix, according to the standard Affymetrix protocol.

growth_protocol: Beas-2B cells were plated at a density of 70000 cells per 75 cm2 flask in DMEM/F12 medium containing 5% FBS and split twice a week

extract_protocol: RNA extraction was performed by the RNeasy Plus Mini Kit, Qiagen, according to the manufacturer's instructions.

treatment_protocol: BEAS-2B cells were repeatedly exposed to 100 mg/ml PM2.5 every first day after each passage for 5 weeks before RNA extraction; control cells were similarly treated, but without addition of PM2.5.

tag: tissue type

value: cell line, immortalized primary cells

tag: cell line

value: bronchial epithelial

value: exposed to PM2.5


title: BEAS-2B cells, replicate 2-exposed to PM2.5

description: BEAS-2B cells in the presence of PM2.5


title: 24h Yorkie-IR rep1

description: flight muscle from 24h pupae APF

tag: developmental stage


title: Ppara +/+ MLL-AF9_Rep1

source_name: BM-MNCs, secondary recipient of Ppara +/+ MLL-AF9, first replicate


title: Ppara +/+ MLL-AF9_Rep2

source_name: BM-MNCs, secondary recipient of Ppara +/+ MLL-AF9, second replicate


title: BEAS-2B cells, replicate 1-exposed to PM2.5

description: BEAS-2B cells in the presence of PM2.5


title: BEAS-2B cells, replicate 2-control

description: BEAS-2B cells in the absence of PM2.5

value: control


title: Ppara +/+ MLL-AF9_Rep3

source_name: BM-MNCs, secondary recipient of Ppara +/+ MLL-AF9, third replicate


title: 24h Slmap-IR rep3

description: flight muscle from 24h pupae APF

value: Slmap-IR


title: ChBB.GABA.input

description: MNase-digested genomic DNA

source_name: brain

value: dorsolateral prefrontal cortex

tag: Sex

value: wild type

value: input control chromatin


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with interferon b, replica 3

value: Microglia

value: microglia

value: healthy

value: pooled embryos


title: ChHER.GLU.input

description: MNase-digested genomic DNA

value: Male


title: 24h Slmap-IR rep2

description: flight muscle from 24h pupae APF

value: 24h APF


title: CR TR CR_D3

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent G2534A Microarray Hybridization Chamber. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G4900DA SureScan Microarray Scanner System.Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Microarray Scan Control Software 9.1 was used for background subtraction and LOWESS normalization.

source_name: T cell, cultures

label_protocol: 200ng of total RNA were used and follow agilent Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions  miRNA Easy Kit (Qiagen, Germantown, MD,USA)

value: cell line

tag: group

value: Cultured PBMCS-Cryo--Cryo

source_name: universal human reference RNA

tag: sample type

value: pooled whole huam RNA


title: ChBR.GABA.input

description: MNase-digested genomic DNA

value: MGE-dervied GABAergic neurons

tag: brain area


title: Sorted microglia from pooled P0 brain of WT mice, untreated, replica 2

value: untreated


title: ChET.GLU.input

description: MNase-digested genomic DNA

value: glutamatergic neurons

tag: age (years)


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with LPS+interferon b, replica 3

tag: strain

value: LPS+interferon b


title: 24h Slmap-IR rep1

description: flight muscle from 24h pupae APF

value: indirect flight muscle

value: Slmap-IR


title: Sorted microglia from pooled P0 brain of WT mice, untreated, replica 1

value: wild type


title: ChBR.GLU.input

description: MNase-digested genomic DNA

value: dorsolateral prefrontal cortex

value: input control chromatin


title: ChBB.GLU.input

description: MNase-digested genomic DNA


title: 24h Dlg5-IR rep3

description: flight muscle from 24h pupae APF


title: Sorted microglia from pooled P0 brain of WT mice, treated with LPS, replica 2

value: Microglia

value: LPS

value: microglia


title: 24h Dlg5-IR rep2

description: flight muscle from 24h pupae APF


title: Sorted microglia from pooled P0 brain of WT mice, treated with interferon b, replica 1

value: interferon b

value: healthy

value: pooled embryos


title: Sorted microglia from pooled P0 brain of WT mice, treated with LPS, replica 1


title: ChHER.GABA

description: MNase-digested genomic DNA

value: Male

value: anti-H3K27ac-precipitated chromatin


title: 24h wild type rep3

description: flight muscle from 24h pupae APF

value: 24h APF


title: BEAS-2B cells, replicate 3-control

description: BEAS-2B cells in the absence of PM2.5

value: cell line, immortalized primary cells

value: bronchial epithelial

value: control


title: BEAS-2B cells, replicate 1-control

description: BEAS-2B cells in the absence of PM2.5


title: ChBR.GABA

description: MNase-digested genomic DNA

value: MGE-dervied GABAergic neurons


title: FR UTR CR_D3

value: cell line

value: Cultured PBMCS-Fresh--Cryo

value: pooled whole huam RNA


title: FR TR CR_D3


title: Sorted microglia from pooled P0 brain of WT mice, treated with Dex, replica 2

value: wild type

value: Dex


title: CR UTR FR_D3

value: Cultured PBMCS-Cryo--Fresh


title: FR TR FR_D3

value: Cultured PBMCS-Fresh--Fresh


title: CR TR FR_D3


title: ChET.GABA

description: MNase-digested genomic DNA

value: dorsolateral prefrontal cortex


title: 24h wild type rep2

description: flight muscle from 24h pupae APF

value: indirect flight muscle


title: FR_D3

value: Uncultured PBMCS--Control(Fresh)


title: FR UTR FR_D3


title: CR UTR CR_D3

value: Cultured PBMCS-Cryo--Cryo


title: CR_D3

value: Uncultured PBMCS--Control(Cryo)


title: 24h wild type rep1

description: flight muscle from 24h pupae APF

value: 24h APF


title: CR UTR CR_D2


title: Sorted microglia from pooled P0 brain of WT mice, treated with LPS+interferon b, replica 1

value: Microglia

value: LPS+interferon b

value: microglia

value: healthy

value: pooled embryos


title: Sorted microglia from pooled P0 brain of WT mice, treated with Dex, replica 1


title: CR TR CR_D2

value: cell line


title: 24h Dlg5-IR rep1

description: flight muscle from 24h pupae APF


title: Sorted microglia from pooled P0 brain of WT mice, treated with LPS+Dex, replica 2

value: LPS+Dex


title: ChET.GLU

description: MNase-digested genomic DNA

value: glutamatergic neurons

value: Male

value: wild type

value: anti-H3K27ac-precipitated chromatin


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, untreated, replica 2

value: C57BL/6:LysM-Cre:GRIP1 fl/fl

value: GRIP1 -/-

value: untreated


title: ChBR.GLU

description: MNase-digested genomic DNA

value: dorsolateral prefrontal cortex


title: Sorted microglia from pooled P0 brain of WT mice, treated with LPS+Dex, replica 1


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, untreated, replica 1


title: ChBB.GLU

description: MNase-digested genomic DNA


title: Spleen_TCR_2

city: Wuhan

first: Muyang

last: Gu

address: 1277 Jiefang Road, Jianghan District

institute: Union Hospital, Tongji Medical College, Huazhong   University of Science and Technology

data_processing:
Library strategy: TCR-Seq
Raw sequencing files were filtered for sequence quality, low-quality cells with <200~300 genes expressed or with high mitochondrial gene content were identified and removed from the datasets, and doublets with relatively high library size were also removed from the analysis.
Reads were then mapped to mm10 using Hisat2 (http://ccb.jhu.edu/software/hisat2；Kim D et al., 2015).
When clustering multiple samples, we aggregated the multiple runs together to normalize the sequencing depth and recomputed the gene-barcode matrices.
Raw readcount tables were provided to the unsupervised clustering pipeline Seurat, and for each cell, the counts were normalized by the total counts and then multiplied by a scale factor of 100,000 before transforming to the log2 scale.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized gene expression for every single cell
Supplementary_files_format_and_content: Matrix table with tSNE cluster information for every single cell
Supplementary_files_format_and_content: Comma-Separated Values files include V(D)J sequences for every single cell

source_name: Spleen CD4 TCR

extract_protocol:
approximately 12,000 CD4+ T cells from 7-day post-MI heart and spleen of the C57BL/6J mice were double-sorted by magnetic-activated cell sorting (MACS) and fluorescence activated cell sorting (FACS) (90% viability) and encapsulated into droplets at a concentration of 700 cells/μL, which resulted in expected mRNA barcoding of ~6,000 single cells with a multiplet rate of 5.4%. After the RT step, the droplets were broken, and barcoded cDNA was purified with DynaBeads, followed by 14 cycles of PCR amplification. The resulting amplified cDNA was sufficient to construct 5’ gene expression libraries and T cell receptor-enriched libraries. The cDNA of single-cell transcriptomes was fragmented, double-sized selected with SPRI beads, and sequenced on an Illumina NextSeq platform. The cDNA encoding the TCR library was amplified by PCR using DNA primers provided in the kit.
The cDNA of single-cell transcriptomes was fragmented, double-sized selected with SPRI beads, and sequenced on an Illumina NextSeq platform. The cDNA encoding the TCR library was amplified by PCR using DNA primers provided in the kit. After library construction, V(D)J region-enriched libraries were size selected with SPRI beads and sequenced on an Illumina NovaSeq 6000 instrument.

value: spleen

value: CD4+T cells

value: 8 weeks

tag: disease state

value: 7 days post-MI


title: Spleen_CD4_3_4

data_processing:
Raw sequencing files were filtered for sequence quality, low-quality cells with <200~300 genes expressed or with high mitochondrial gene content were identified and removed from the datasets, and doublets with relatively high library size were also removed from the analysis.
Reads were then mapped to mm10 using Hisat2 (http://ccb.jhu.edu/software/hisat2；Kim D et al., 2015).
When clustering multiple samples, we aggregated the multiple runs together to normalize the sequencing depth and recomputed the gene-barcode matrices.
Raw readcount tables were provided to the unsupervised clustering pipeline Seurat, and for each cell, the counts were normalized by the total counts and then multiplied by a scale factor of 100,000 before transforming to the log2 scale.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized gene expression for every single cell
Supplementary_files_format_and_content: Matrix table with tSNE cluster information for every single cell
Supplementary_files_format_and_content: Comma-Separated Values files include V(D)J sequences for every single cell

source_name: Spleen CD4+T cells

tag: tissue


title: FR TR CR_D2

value: Cultured PBMCS-Fresh--Cryo

value: pooled whole huam RNA


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with LPS, replica 2

value: Microglia

tag: age

value: LPS

value: microglia

value: healthy

value: pooled embryos


title: ChHER.GLU

description: MNase-digested genomic DNA

value: glutamatergic neurons

value: Male

tag: genotype

value: wild type


title: skin_8am.D

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

description:
CountTable.GEO.csv
XMA.w_M24mo_S_8AM_GW_2016-10-13_pe

data_processing:
Short sequencing reads were filtered using an in-house data processing pipeline [58]. Briefly, sequencing adaptors, if detected, were first removed from sequencing reads. Processed sequencing reads were subsequently trimmed and filtered based on quality scores by using a filtration algorithm that removed low-scoring sections of each read and preserved the longest remaining fragment.  Processed sequencing reads were subsequently mapped to X. maculatus genome version 5.0 using Tophat2, and gene expression of gene models annotated by Ensembl database (Release 94) was quantified using FeatureCount.
Genome_build: X. maculatus v5.0
Supplementary_files_format_and_content: expression profile in .csv format

organism: Xiphophorus maculatus

source_name: Xiphophorus skin

growth_protocol: X. maculatus Jp 163 A in the 116th inbred generation (i.e., sibling mating) were provided by the Xiphophorus Genetic Stock Center (http://www.xiphophorus.txstate.edu/). Mature male X. maculatus were maintained in separate 38-liter aquaria filled with filtered aquifer water from San Marcos, TX on a 13 hr light/11 hr dark cycle under 10,000 K fluorescent light (Coralife T8 Lamp 10,000 K, 32 W). All fish utilized were co-adapted to the same conditions for at least two weeks prior to the experiment. Fish were fed with flake food precisely at 8 a.m. and brine shrimp at 3 p.m. during this adaptive synchronizing periods.

extract_protocol:
Skin samples were dissected into separate 2.5 ml microcentrifuge tubes filled with RNAlater (Ambion Inc.) for RNA isolation.RNAlater was removed from respective microcentrifuge tubes followed by addition of 750 μL of QIAzol (Qiagen) in 2.0 mL collection tubes designed for automated tissue homogenization and RNA isolation stations. Skin were homogenized using the TisseLyser II (Qiagen) facilitated by stainless beads (Qiagen) for 10 min at 25 Hz. RNA isolation was subsequently performed using a QIAcube HT (Qiagen) automated bio-sample isolation system. The isolation system is equipped with a robotic arm with 8 pipettes. Each pipette is able to pick and eject pipette tips, self-clean, and transfers liquids between well/columns, or between reagent reservoirs and well/columns in standard 96-well plate formats. Each sample was independently maintained throughout the isolation process. Briefly, 150 µL of chloroform was added to each isolation tube and the samples were vigorously shaken for 15 sec and then phases partitioned by centrifugation (12,000×g for 15 min at 4°C).  The aqueous phase containing nucleic acids was transferred to a new sample tube by a rack of automated pipettors. After extraction, nucleic acids were precipitated with 500 µL 70% ethanol. RNA was then purified using a Qiagen RNeasy mini RNA kit (96-well plate) and eluted following the manufacturer’s protocol.
Each RNA sample was used to construct an independent sequencing library using Illumina TruSeq library preparation kit (Illumina, Inc., San Diego, CA, USA).

treatment_protocol: no treatment

tag: organ

value: skin

value: male

tag: time


title: ChBB.GABA

description: MNase-digested genomic DNA

value: MGE-dervied GABAergic neurons

value: dorsolateral prefrontal cortex

tag: antibody

value: anti-H3K27ac-precipitated chromatin


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with LPS, replica 1

value: C57BL/6:LysM-Cre:GRIP1 fl/fl

value: GRIP1 -/-

tag: treatment

tag: cell type

tag: desease state


title: FR UTR CR_D2

value: cell line

value: Cultured PBMCS-Fresh--Cryo


title: Spleen_CD4_3_3

value: spleen

value: CD4+T cells

value: 8 weeks

value: 7 days post-MI


title: CR_D2

value: Uncultured PBMCS--Control(Cryo)

value: pooled whole huam RNA


title: CR TR FR_D2

value: Cultured PBMCS-Cryo--Fresh


title: Spleen_CD4_3_1


title: skin_2am.D

description:
CountTable.GEO.csv
XMA.u_M24mo_S_2AM_GW_2016-10-13_pe


title: CR UTR FR_D2


title: Spleen_TCR_1


title: Spleen_TCR_3


title: CR UTR CR_D1

value: Cultured PBMCS-Cryo--Cryo


title: skin_2am.C

description:
CountTable.GEO.csv
XMA.s_M24mo_S_2AM_GW_2016-10-13_pe

value: skin


title: skin_8am.C

description:
CountTable.GEO.csv
XMA.v_M24mo_S_8AM_GW_2016-10-13_pe

value: male


title: Spleen_CD4_2_2


title: Spleen_CD4_2_4


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with Dex, replica 2

value: Microglia

value: Dex

value: microglia

value: healthy

tag: developmental stage

value: pooled embryos


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with interferon b, replica 1

value: C57BL/6:LysM-Cre:GRIP1 fl/fl

value: GRIP1 -/-

value: interferon b


title: CR UTR FR_D1

value: cell line


title: skin_8pm.D

description:
CountTable.GEO.csv
XMA.r_M24mo_S_8PM_GW_2016-10-13_pe

tag: Sex


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with LPS+Dex, replica 1

value: LPS+Dex


title: M-trans-1

city: Philadelphia

first: Haoran

institute: University of Pennsylvania

data_processing:
Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and removing low quality reads by cutadapt software (v1.9.3), the high-quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM.
The logFPKM of mRNA in different mouse groups was plotted and compared.
Genome_build: MM10
Supplementary_files_format_and_content: Excel files include FPKM values and annotations for each Sample ...

source_name: Muscle

extract_protocol:
Total RNA was collected from TA muscle and heart tissues of different mice (two replicates for each group) by trizol and the rRNAs were removed with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer’s instructions. Libraries were quality-controlled and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: Muscle

tag: genotypic/variation

value: transgenic

value: UAA incorporation system


title: Spleen_CD4_2_3

value: spleen

value: CD4+T cells

value: 8 weeks

value: 7 days post-MI


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with Dex, replica 1

value: Microglia


title: skin_8pm.C

description:
CountTable.GEO.csv
XMA.p_M24mo_S_8PM_GW_2016-10-13_pe

value: skin

value: male


title: FR UTR CR_D1

tag: group

value: Cultured PBMCS-Fresh--Cryo

tag: sample type

value: pooled whole huam RNA


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with LPS+interferon b, replica 1

value: C57BL/6:LysM-Cre:GRIP1 fl/fl

value: LPS+interferon b

value: microglia

value: healthy

value: pooled embryos


title: FR UTR FR_D1

value: cell line

value: Cultured PBMCS-Fresh--Fresh


title: CR TR CR_D1

value: Cultured PBMCS-Cryo--Cryo


title: skin_2pm.D

description:
CountTable.GEO.csv
XMA.o_M24mo_S_2PM_GW_2016-10-13_pe


title: Spleen_CD4_1_2

value: spleen


title: Spleen_CD4_2_1

value: CD4+T cells


title: Sorted microglia from pooled P0 brain of GRIP1 KO mice, treated with LPS+Dex, replica 2

value: GRIP1 -/-

value: LPS+Dex


title: Sorted spinal cord microglia from healthy WT mice, replica 4

description:
Homeostatic microglia
SM-homeo_edgeR_DEGs_2019-05-03.xlsx

source_name: Spinal cord

value: Spinal cord

value: wild type

value: untreated

value: female


title: Spleen_CD4_1_3

value: 8 weeks

value: 7 days post-MI


title: skin_11pm.B

description:
CountTable.GEO.csv
XMA.ak_M24mo_S_11PM_GW_2016-10-13_pe

value: skin

value: male


title: skin_2pm.C

description:
CountTable.GEO.csv
XMA.m_M24mo_S_2PM_GW_2016-10-13_pe


title: Sorted spinal cord microglia from healthy WT mice, replica 3

value: microglia

value: healthy


title: skin_5pm.B

description:
CountTable.GEO.csv
XMA.ah_M24mo_S_5PM_GW_2016-10-13_pe


title: skin_11pm.A

description:
CountTable.GEO.csv
XMA.aj_M24mo_S_11PM_GW_2016-10-13_pe


title: CR TR FR_D1

value: cell line

value: Cultured PBMCS-Cryo--Fresh

value: pooled whole huam RNA


title: CR_D1

value: Uncultured PBMCS--Control(Cryo)


title: FR TR CR_D1

value: Cultured PBMCS-Fresh--Cryo


title: FR TR FR_D1

value: Cultured PBMCS-Fresh--Fresh


title: Spleen_CD4_1_4

value: spleen

value: CD4+T cells


title: Sorted spinal cord microglia from healthy GRIP1 KO mice, replica 4

value: C57BL/6:LysM-Cre:GRIP1 fl/fl

value: Spinal cord

value: GRIP1 -/-


title: skin_5pm.A

description:
CountTable.GEO.csv
XMA.ag_M24mo_S_5PM_GW_2016-10-13_pe


title: Spleen_CD4_1_1

value: 8 weeks


title: Sorted spinal cord microglia from healthy GRIP1 KO mice, replica 3

value: untreated

value: female


title: Spheroid4_Neg_

first: Christina

last: Annunziata

state: Maryland (MD)

address: 10 center drive, Building 10, room 12N226

institute: National Cancer Institute

description:
Ovarian cancer cell line without siRNA construct, spheroid growth condition, replicate 4
voomNormalizedCountsMatrix.txt

data_processing:
Adapter trimming: Cutadapt
Alignment: STAR
Normalization: RSEM
Normalization and differential expression: Limma voom
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.RSEM.genes.results: Tab-separated text files include RSEM gene counts results.

source_name: ovarian tumor

growth_protocol: Adherent OV90 cells were grown in RPMI 1640 medium supplemented with Tetracycline-free Fetal Calf Serum (10%) and 1% penicillin/streptomycin. Spheroids were grown in ultra-low attachment plates or flasks in DMEM-F12 media supplemented with 1% KnockOut serum replacement, 1% penicillin/streptomycin, 0.1% insulin-transferrin-selenium, and 0.4% bovine serum albumin and growth factors EGF 20 ng/mL and FGF 10 ng/mL.

extract_protocol:
Total RNA was collected from cells according to the manufacturer's instructions using the RNeasy Mini Kit (Qiagen 74104).
Libraries were prepared according to the manufacturer's instructions using TruSeq Stranded mRNA library kit (Illumina 20020594).

treatment_protocol: 6 days growth in each condition, fresh medium was supplemented after 72 hours.

tag: cell line

value: ovarian cancer cell line

tag: growth condition

value: Spheroid


title: Spheroid3_Neg_

description:
Ovarian cancer cell line without siRNA construct, spheroid growth condition, replicate 3
voomNormalizedCountsMatrix.txt


title: Sorted spinal cord microglia from healthy WT mice, replica 1

tag: strain

value: wild type

value: microglia

value: healthy


title: Heart_TCR_3

source_name: Heart CD4 TCR

tag: tissue

value: heart

tag: disease state

value: 7 days post-MI


title: Spheroid2_Neg_

description:
Ovarian cancer cell line without siRNA construct, spheroid growth condition, replicate 2
voomNormalizedCountsMatrix.txt


title: Heart_TCR_2

tag: age


title: skin_11am.B

description:
CountTable.GEO.csv
XMA.ae_M24mo_S_11AM_GW_2016-10-13_pe

tag: organ

value: skin

value: male


title: skin_11am.A

description:
CountTable.GEO.csv
XMA.ad_M24mo_S_11AM_GW_2016-10-13_pe

tag: time


title: Heart_TCR_1


title: Sorted spinal cord microglia from healthy GRIP1 KO mice, replica 1

tag: genotype


title: skin_5am.B

description:
CountTable.GEO.csv
XMA.ac_M24mo_S_5AM_GW_2016-10-13_pe


title: skin_5am.A

description:
CountTable.GEO.csv
XMA.ab_M24mo_S_5AM_GW_2016-10-13_pe


title: Spheroid1_Neg_

description:
Ovarian cancer cell line without siRNA construct, spheroid growth condition, replicate 1
voomNormalizedCountsMatrix.txt


title: Heart_CD4_3_4

source_name: Heart CD4+T cells


title: AD4_Neg_

description:
Ovarian cancer cell line without siRNA construct, adherent growth condition, replicate 4
voomNormalizedCountsMatrix.txt

value: Adherent


title: Heart_CD4_3_3

value: CD4+T cells


title: Sorted spinal cord microglia from the WT mice with EAE, replica 4

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

tag: treatment

value: EAE


title: AD2_Neg_

description:
Ovarian cancer cell line without siRNA construct, adherent growth condition, replicate 2
voomNormalizedCountsMatrix.txt

tag: cell type


title: Sorted spinal cord microglia from the WT mice with EAE, replica 3

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

value: Spinal cord

tag: desease state


title: Sorted spinal cord macrophages from the WT mice with EAE, replica 4

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

value: macrophages


title: skin_8am.B

description:
CountTable.GEO.csv
XMA_116.c_M12mo_8AM_day1_S_GW_2018-11-29_pe


title: Heart_CD4_3_1

value: 8 weeks


title: Heart_CD4_2_4


title: FR_D1

value: cell line

value: Uncultured PBMCS--Control(Fresh)

value: pooled whole huam RNA


title: AD3_Neg_

description:
Ovarian cancer cell line without siRNA construct, adherent growth condition, replicate 3
voomNormalizedCountsMatrix.txt

value: ovarian cancer cell line


title: Sorted spinal cord macrophages from the WT mice with EAE, replica 3

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

value: wild type

value: untreated


title: Heart_CD4_3_2


title: skin_2pm.B

description:
CountTable.GEO.csv
XMA_116.c_M12mo_2PM_day1_S_GW_2018-11-29_pe


title: Heart_CD4_2_3


title: AD1_Neg_

description:
Ovarian cancer cell line without siRNA construct, adherent growth condition, replicate 1
voomNormalizedCountsMatrix.txt


title: skin_2am.B

description:
CountTable.GEO.csv
XMA_116.c_M12mo_2AM_day1_S_GW_2018-11-29_pe


title: skin_8pm.B

description:
CountTable.GEO.csv
XMA_116.b_M12mo_8PM_day1_S_GW_2018-11-29_pe


title: skin_8pm.A

description:
CountTable.GEO.csv
XMA_116.a_M12mo_8PM_day1_S_GW_2018-11-29_pe


title: skin_2am.A

description:
CountTable.GEO.csv
XMA_116.b_M12mo_2AM_day1_S_GW_2018-11-29_pe


title: Sorted spinal cord microglia from the WT mice with EAE, replica 2

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

value: microglia

value: female


title: Heart_CD4_2_2

value: heart

value: 7 days post-MI


title: Sorted spinal cord macrophages from the GRIP1 KO mice with EAE, replica 3

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

value: C57BL/6:LysM-Cre:GRIP1 fl/fl

value: GRIP1 -/-


title: Spleen_CD4_3_2

value: spleen

value: CD4+T cells


title: Heart_CD4_2_1


title: skin_8am.A

description:
CountTable.GEO.csv
XMA_116.a_M12mo_8AM_day1_S_GW_2018-11-29_pe

value: skin

value: male


title: skin_2pm.A

description:
CountTable.GEO.csv
XMA_116.a_M12mo_2PM_day1_S_GW_2018-11-29_pe


title: Heart_CD4_1_4

value: 8 weeks


title: Sorted spinal cord macrophages from the WT mice with EAE, replica 2

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

value: Spinal cord

value: macrophages

value: EAE


title: Sorted spinal cord microglia from GRIP1 KO mice with EAE, replica 2

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx


title: Heart_CD4_1_2


title: cryolesioned floxed mice rep 4 VS cryolesioned microglia-derived il6 deficient mice rep 2

city: Bellaterra

first: Paula

last: Sanchis

state: Barcelona

address: calle de la vall moronta s/n

department: Department of Cellular Biology, Physiology and Immunology, and Institute of Neurosciences

country: Spain

institute: Universitat Autònoma de Barcelona

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

source_name: right fronto-parietal cortex

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

extract_protocol: Total RNA was collected from brain tissue using Qiagen RNeasy Mini Kit

treatment_protocol: Ipsilateral cortex was dissected, snap-frozen in liquid nitrogen and stored at -80 ºC

value: cryolesioned floxed

value: cryolesioned microglia-derived Il6 deficient


title: Sorted spinal cord microglia from GRIP1 KO mice with EAE, replica 3

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

value: untreated


title: control floxed mice rep 3 VS cryolesioned microglia-derived il6 deficient mice rep 3

value: control floxed


title: cryolesioned microglia-derived il6 deficient mice rep 4 VS control floxed mice rep 4


title: Heart_CD4_1_3


title: Sorted spinal cord microglia from GRIP1 KO mice with EAE, replica 1

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

value: microglia


title: Heart_CD4_1_1

value: heart


title: cryolesioned microglia-derived il6 deficient mice rep 1 VS cryolesioned floxed mice rep 3


title: Sorted spinal cord macrophages from the WT mice with EAE, replica 1

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

value: wild type

value: female


title: Sorted spinal cord macrophages from the GRIP1 KO mice with EAE, replica 1

description:
EAE
EAE_edgeR_DEGs_2019-06-10.xlsx

value: C57BL/6:LysM-Cre:GRIP1 fl/fl

value: GRIP1 -/-


title: 16030X4_HJTWLDMXX

city: Baltimore

first: Lukas

middle: M

last: Weber

address: 615 N Wolfe St

department: Biostatistics

institute: Johns Hopkins University

data_processing:
Cell Ranger (cellranger count version 4.0.0) was used to generate single-cell feature counts for each sample.
Genome_build: GRCh38 (refdata-gex-GRCh38-2020-A provided with Cell Ranger)
Supplementary_files_format_and_content: gene count matrix (matrix_XXX.mtx.gz), features table (features_XXX.tsv.gz), barcodes table (barcodes_XXX.tsv.gz)

extract_protocol:
De-identified HGSOC samples were processed after cryopreservation in liquid nitrogen where tissue chunks were stored in RPMI media with 10% fetal bovine serum and 10% DMSO. Samples were thawed and dissociated to single cells using the Miltenyi Human Tumor Dissociation Kit and the GentleMACS dissociator. Samples were incubated on the GentleMACS at 37°C for 1 hour with the setting of 1,865 rounds per run. A 70 µm MACS smart strainer was used to deplete cell doublets before loading onto the 10x Genomics Chromium Controller.
Library preparation was performed using the 10x Genomics 3’ Gene Expression Library Prep v3 and libraries were sequenced on an Illumina NovaSeq instrument.

value: ovarian tumor


title: 16030X2_HJVMLDMXX


title: J82 tet-ZFP36L1 24 hour

status: Public on Oct 02 2020

city: Singapore

first: Pushkar

last: Dakle

address: 14 Medical Drive, #12-01,

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Paired end fastq files were pseudoaligned to Ensembl (hg19, v82) transcripts using Kallisto.
Transcript level abundances and counts were summarized to gene level using the TxImport bioconductor package.
Differential expression analysis was performed with DESeq2 bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited output files - abundance.tsv generated by kallisto

source_name: Human Bladder cancer cell line J82

growth_protocol: J82 cells (control or overexpressing) were grown until 90% confluent, and then treated with doxycycline (6 hours and 24 hours) or without doxycycline (1ug/mL).

extract_protocol:
RNA was harvested using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard BGISEQ500 protocols

tag: genotype/variation

value: tet-ZFP36L1 overexpressing cells with doxycycline treatment of 24 hours

value: Human Bladder cancer cell line


title: 16030X3_HJTWLDMXX


title: cryolesioned floxed mice rep 1 VS control microglia-derived il6 deficient mice rep 3

value: control microglia-derived Il6 deficient


title: control microglia-derived il6 deficient mice rep 4 VS cryolesioned floxed mice rep 2


title: J82 siNT

data_processing:
fastq aligned to hg19 reference genome using HISAT.
Gene expression level quantified by featurecounts.
Genome_build: hg19
Supplementary_files_format_and_content: raw gene counts from featurecounts

growth_protocol: J82 cells were grown until 90% confluent.

treatment_protocol: J82 cells were grown until 90% confluent, and then they were knockdown with NT or ZFP36L1 siRNA for 48 hourrs.

value: J82 cells treated with non-targeting siRNAs


title: J82 tet-control 0 hour

treatment_protocol: J82 cells (control or overexpressing) were grown until 90% confluent, and then treated with doxycycline (6 hours and 24 hours) or without doxycycline (1ug/mL).

value: tet-control cells without doxycycline treatment


title: J82 tet-control 6 hour

value: tet-control cells with doxycycline treatment of 6 hours