title: WT_GF_231

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

data_processing:
The sequencing run was performed on a HiSeq 1000 instrument controlled by the HiSeq Control Software (HCS) 2.2.38, using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling were done by the Real Time Analysis Software (RTA) 1.18.61. The resulting .bcl files were converted into .fastq files with the CASAVA Software 1.8.2.
Fastq files were analysed for qualtiy using FastQC 0.11.8 and FastQScreen 0.14.0
Fastq files were aligned to the GRCh38.p12 assembly using STAR 2.7.2 with the following parameters STAR --runThreadN 10 --genomeDir x --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn x --readFilesCommand zcat –outFileNamePrefix x  --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10
Aligned BAM files were then used to generate a counts table with featureCounts v1.6.2 with the following paramters and using the Gencode Human annotation version 30: featurecounts -a gencode.v30.annotation.gtf-G GRCh38.p12.fasta -o counts.txt -F GTF -g gene_name -t exon -T 10 --largestOverlap
Diffrential gene expression analysis was performed using limma version 3.40.6 with the limma/voomWithQualityWeights pipeline as described in the limma vignette and using some commands from the edgeR package (version 3.26.7) . In short: a counts table was read into a DGEList object using the edgeR function DGEList and filtered for all genes with a counts of atleast 5 in 2 or more samples. Normalization factors were calculated using the edgeR function calcNormFactors. The DGEList object was then voom transformed using the voomWithQualityWeights function with standard settings. Fitting and Statistics were performed using the lmFit and eBayes function, again with standard settings.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: csv file containing raw counts for each sample.

source_name: brain

growth_protocol: Mice were housed under SPF or germ-free condiotions. Animals were 16 weeks old.

extract_protocol:
Adult microglia were harvested using density gradient separation. CD11b+CD45lo microglial cell populations were FACS-sorted and collected directly in cell lysis buffer.
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 300 pg total-RNA. Double stranded cDNA was amplified by LD PCR (13 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3.

treatment_protocol: One group of SPF mice was treated with a cocktail of antibiotics for 8 weeks prior to analysis.

value: GF

value: microglia

value: 16 weeks


title: WT_GF_229

status: Public on Jul 15 2020

type: SRA

city: Freiburg

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

value: WT

tag: tissue

tag: age


title: GXA_3036 Type: Patient derived Xenograft Passage: 12

type: genomic

first: Vincent

last: Vuaroqueaux

address: Am Flughafen 14

department: Bioinformatics

institute: 4HF Biotec

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Affymetrix Genome wide SNP6.0 CEL files were loaded into the Affymetrix Genotyping Console 4.1 Software (Affymetrix). After scanning, arrays were checked for quality using the Affymetrix Genotyping Console. In accordance with Affymetrix guidelines, SNP6.0 arrays with a Contrast QC value above 0.4 and MAPD below 0.35 were excluded from further analysis. Copy number variations were calculated using Affymetrix GTC v4.1 and PICNIC software provided by the Cancer Genome Project from the Welcome Trust Sanger Institute.   The PICNIC algorithm  (PICNIC - Predicting Integral Copy Numbers In Cancer) includes improved normalisation of the data together with determination of underlying copy numbers for each segment by genome wide analysis of allele ratio and signal strength data. The data was subsequently rescaled and plotted onto its predicted underlying integer value and segmentation was applied. This data analysis procedure also allowed for assignment of a genotype to each SNP. The PICNIC segment files were further compiled to generate a simplified gene matrix. A gene was assigned a deletion (CNV=0) if a deletion segment overlaps with the gene, otherwise the copy number of the most amplified segment overlapping with the gene was assigned.
PICNIC integer copy number score (0 is considered as a gene deletion, values between 1 and 7 are considered as a moderate gene copy alteration, values equal or greater than 8 are considered as a gene amplification)

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: patient-derived tumor xenograft

label_protocol: standard Affymetrix protocol

growth_protocol: PDX were passaged from mouse to mouse until DNA extraction

extract_protocol: DNA was extracted from snap frozen tumor xenografts, patient tumors or normal tissues. Samples were digested with proteinase K at 55°C overnight and the lysate was digested with DNAse-free RNAse (Qiagen). DNA was extracted with a mix of phenol:chloroform:isoamylalcohol and precipitated with ethanol. DNA pellets were washed and resuspended in Tris-EDTA buffer. Each DNA preparation was subjected to quality control using a 1.3% agarose gel and using NanoDrop 2000 to control for purity. Only DNA samples with no sign of degradation (a clearly defined high molecular weight band on the agarose gel) and the DNA was pure (260/280 nm and 260/230 nm close to 2.0), were used for the microarray analysis.

tag: passages


title: CPC5 rep14

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to miRbase 20
Expression levels are measured as Tags Per Million (TPM). The number of reads for a particular microRNA is divided by the total number of mapped reads and multiplied by 1 million (Tags Per Million). The differential expression analysis is done using the EdgeR statistical software package
Genome_build: miRbase 20
Supplementary_files_format_and_content: tsv (tab-separated values) text files contain counts and TPM of microRNAs for each sample

source_name: plasma

extract_protocol:
RNA was extracted from a total of 400 μl of plasma, then 6ul of total RNA was use to prepare short RNA NGS library using NEBNEXT library generation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: plasma

tag: cerebral performance category score


title: CPC5 rep15


title: CPC5 rep16


title: FAD_GF_201

value: FAD


title: WT_GF_199


title: CPC5 rep13


title: GXA_3036 Type: Patient derived Xenograft Passage: 2


title: GXA_3036 Type: Patient derived Xenograft Passage: 3


title: FAD_ABX_1151

value: ABX


title: GXA_3036 Type: Patient derived Xenograft Passage: 1


title: WT_SPF_936

value: SPF


title: FAD_ABX_1482


title: CPC5 rep10


title: FAD_SPF_1148


title: CPC5 rep12


title: GXA_3029 Type: Patient derived Xenograft Passage: 8; 11


title: FAD_ABX_1460


title: GXA_3036 Type: Patient Normal Passage: 0

source_name: normal tissue


title: CPC5 rep8


title: WT_ABX_932


title: GXA_3027 Type: Patient derived Xenograft Passage: 3N2


title: WT_GF_230


title: GXA_3027 Type: Patient derived Xenograft Passage: 3


title: Mammary tumor 95

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

country: USA

institute: BloodCenter of Wisconsin

description: Mammary tumor

data_processing:
Reads were aligned using Salmon V1.2.0 to mm9
Aligned reads were analyzed using DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated file containing gene level expression values for each gene and each sample in the data

molecule: polyA RNA

source_name: murine mammary gland tumor

growth_protocol: Both Cre- (control) and Cre+ mice were mated at 12 weeks of age to induce FBXW7 excision and monitored for tumor formation by weekly palpation. Mice were sacrificed upon tumor detection or at 40 weeks post pregnancy.

extract_protocol:
RNA was extracted using Trizol, processed through the Qiagen RNAeasy Mini Plus Kit
RNA-seq libraries were made using the NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Epithelial cells were extracted from homogenized glands and purified with mouse epithelial enrichement kit while whole glands and tissues were dissected and homogenized in TriZol.

tag: tissue type

value: mammary tumor tissue

value: 32 weeks

tag: cre status (pos or neg)

value: pos


title: FAD_ABX_1455


title: FAD_SPF_1146


title: CPC5 rep7


title: GXA_3027 Type: Patient derived Xenograft Passage: 2


title: FAD_SPF_1144


title: CPC5 rep5


title: CPC5 rep4


title: GXA_3027 Type: Patient Tumor Passage: 0

source_name: patient tumor


title: CPC5 rep11


title: GXA_3036 Type: Patient Tumor Passage: 0


title: WT_SPF_928


title: FAD_ABX_1453


title: GXA_3027 Type: Patient Normal Passage: 0


title: CPC5 rep9


title: FAD_ABX_1452


title: CPC5 rep2


title: CPC5 rep3


title: GXA_3023 Type: Patient derived Xenograft Passage: 15N7


title: CPC5 rep1


title: WT_SPF_925


title: GXA_3023 Type: Patient derived Xenograft Passage: 3


title: WT_SPF_926


title: GXA_3023 Type: Patient derived Xenograft Passage: 2


title: CPC1 rep25


title: CPC1 rep24


title: GXA_3023 Type: Patient derived Xenograft Passage: 1


title: WT_ABX_923


title: FAD_GF_185


title: CPC1 rep22


title: CPC1 rep23


title: GXA_3023 Type: Patient Tumor Passage: 0


title: FAD_GF_184


title: GXA_3027 Type: Patient derived Xenograft Passage: 1


title: CPC5 rep6


title: GXA_3013 Type: Patient derived Xenograft Passage: 4


title: WT_SPF_912


title: CPC1 rep20


title: FAD_GF_182


title: GXA_3012 Type: Patient derived Xenograft Passage: 4


title: WT_ABX_911


title: GXA_3011 Type: Patient derived Xenograft Passage: 3; 6N4


title: CPC1 rep19


title: GXA_3005 Type: Patient derived Xenograft Passage: 6; 3


title: CPC1 rep18


title: FAD_GF_181


title: CPC1 rep17


title: CPC1 rep16


title: WT_ABX_909


title: GXA_3023 Type: Patient Normal Passage: 0


title: CPC1 rep15


title: CPC1 rep14


title: Input-10wk-IUGR-4

city: Philadelphia

first: Paul

middle: Zhiping

last: Wang

state: pa

address: 3440 Market St

institute: Bioinformatics Core, IBI, UPen

library_source: genomic

data_processing:
Low quality reads were trimmed using Trimmomatic (v0.32) and mapped to rat genome rn6 using bowtie2. Mapped reads were further processed using samtools (v0.1.19) with -F 4 -q 10 parameters. Peak calling was performed using MACS (v2.1.0).
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: gene.diff.peak.annotation.csv: Annotated differential peaks among conditions in csv format.

organism: Rattus norvegicus

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with different antibodies.
Multiplexed libraries were created using the Illumina ChIP-seq DNA sample prep kit following manufacturer’s instructions.

tag: cell type

value: Pancreatic islets

tag: condition

value: IUGR

tag: time point

value: 10 weeks

tag: chip antibody


title: Input-10wk-IUGR-6


title: Input-10wk-IUGR-7


title: Input-10wk-IUGR-5


title: CPC1 rep21


title: CPC1 rep12


title: Input-10wk-IUGR-3


title: Input-10wk-IUGR-2


title: CPC1 rep9


title: WT_ABX_910


title: CPC1 rep11


title: Input-10wk-IUGR-1


title: Input-10wk-control-9

value: Control


title: CPC1 rep13


title: CPC1 rep7


title: GXA_3002 Type: Patient derived Xenograft Passage: 4


title: Input-10wk-control-8


title: CPC1 rep6


title: CPC1 rep8


title: Input-10wk-control-7


title: Input-10wk-control-6


title: CPC1 rep5


title: CPC1 rep10


title: Input-10wk-control-5


title: AGT2

type: RNA

city: Lubbock

first: Naima

last: Moustaid-Moussa

state: TX

address: 1301 Akron Street

department: Nutritional Sciences & Obesity Research Institute

institute: Texas Tech University

description:
SAMPLE 2
3824

hyb_protocol: The labeled cRNA was normalized at 1500 ng and hybridized on MouseRef-8 v2.0 according to Illumina’s Whole-Genome Gene Expression Direct Hybridization Assay Guide. The BeadChips were incubated in an Illumina Hybridization oven at 58°C for 16 hours at rocking speed of 5.

scan_protocol: BeadChips were washed according to Illumina’s protocol mentioned previously and scanned on an Illumina iScan Reader.

data_processing: The data were normalized using quantile normalization with lumi package in R.

source_name: Mouse epididymal adipose tissue

label_protocol: Double stranded cDNA was synthetized from 250 ng of total RNA, and in vitro transcription was performed to produce biotin-labeled cRNA using Illumina® TotalPrep RNA Amplification Kit, according to manufacturer’s instructions (Life Technologies).

extract_protocol: Epididymal adipose tissue was isolated after sacrifice, flash frozen in liquid nitrogen and stored in -80 degree Celsius. RNA was extracted with Trizol reagent, followed by clean-up and extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: strain

tag: genotype/variation

value: Angiotensinogen overexpression in white adipose tissue

tag: Sex

value: Male

value: 4 months

value: gonadal adipose tissue


title: CPC1 rep3


title: PAO1r_phage-0min_rep2

city: Chongqing,

first: Qiu

last: Zhong

address: Daping Changjiang street 10#

department: Department of Clinical Laboratory

country: China

institute: Third Military Medical University

description:
PAO1r2
GP-02

data_processing:
The sequenced libraries were mapped against predicted transcripts from the  Pseudomonas aeruginosa PAO1 genome using TopHat v2.0.4
The transcript  abundance (FPKM, Fragments Per Kilobase of exon per  Million fragments mapped) and significant changes in  transcript expression were estimated using Cufflinks  v2.0.2
Transcripts with p-values less than 0.05,  determined using CuffDiff
Genome_build: NC_002516.2 , KX074203.1,  KX074202.1and KX074201.1 were used as the reference genomes

organism: Pseudomonas aeruginosa

growth_protocol: PAO1r with or wihout phage infection was grown in Luria-Bertani (LB) broth medium aerobically.

extract_protocol: RNA extraction

treatment_protocol: Bacterial culture were infected with phage phiYY at MOI of 10 for 6min, 12min, 18min.The uninfected samples served as reference.

tag: treatment

value: without phiYY phage infection


title: PAO1r_phage-0min_rep3

description:
PAO1r3
GP-03


title: WT1

description:
SAMPLE 5
3820

value: WT


title: CPC1 rep4

value: plasma


title: Input-10wk-control-4


title: AGT4

description:
SAMPLE 4
3839


title: WT2

description:
SAMPLE 6
3829


title: CPC1 rep2


title: Input-10wk-control-3


title: AGT1

description:
SAMPLE 1
3821


title: PAO1r_phage-0min_rep1

description:
PAO1r1
GP-01


title: CPC1 rep1


title: AGT3

description:
SAMPLE 3
3836


title: WT4

description:
SAMPLE 8
3838


title: Input-10wk-control-2


title: T4_687

city: Houston

first: Huan

last: Meng

state: Texas

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

data_processing:
Fastq files containing raw RNA-seq reads were aligned to the human genome (hg38) using HISAT2. RNA-seq quantification was performed with htseq-count (default parameters). Protein-coding genes were quantified by iGenome annotation. Quantification values were normalized with DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: TRAF4-overexpressing castration-resistant xenograft tumors

growth_protocol: TRAF4 overexpressing or control LNCaP cells were injected into NOD/SCID mice subcutaneously. When tumors reach approximately 1cm in diameter, mice were were anesthetized using isoflourane and surgically castrated using standard surgical technique. For in vivo studies, 5-to 6-week-old male SCID mice (The Jackson Laboratory) were used for experimental castrate resistant prostate cancer study.

extract_protocol:
These RNA samples (200ng of total RNA for each sample) were converted into strand-specific total mRNA-seq libraries with the Universal Plus mRNA-seq kit (NuGen) per the manufacturer’s protocol.
The size selected libraries were analyzed for quality control with High Sensitivity DNA chip on a Bioanalyzer 2100 (Agilent), and the pooled libraries were sequenced with the NoveSeq 6000 (Illumina) using a 150-bp paired-end for an average of 40 million paired-end reads per sample at the Novogen Corporation (Beijing, China)

treatment_protocol: Total RNA from tumor tissues was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) per the manufacturer's instructions. The quantity and integrity of the total RNA were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and 1% agarose gel electrophoresis. Equal amounts of total RNA from each tissue was used for library preparation. Only the total RNA samples with RIN values ≥6.8 were used for constructing the cDNA libraries.

tag: host strain

value: NOD/SCID

tag: source cell type

value: LNCaP

tag: cell line source

value: 50 years adult

tag: genotype/sample type


title: fp_harr_07hr_2

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
The reads of the ribo-seq libraries was trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our our STAR runs.
The alignments above was made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
Genome_build: Host : Chlorosebus sabaeus genome and annotation ENSEMBL release 99. Virus Genebank NC_045512.2 with 3 changes to match the used strain, 241:C->T, 3037:C->T, 23403:A->G.
Supplementary_files_format_and_content: Wiggle files of the p site for each read of the ribo-seq samples, and the read p prime for the rna-seq samples. A tab delimited file of breakpoints from the STAR run on the rna-seq samples and the ribo-seq chx samples that appear in at least 2 different samples.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Calu 3 cells, ATCC HTB-55

extract_protocol:
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted, and poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239), along with any drugs used for sample treatment) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered.
RNA-seq: mRNA samplewas subjected to DNAseI treatment and 3’ dephpsphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp. Ribo-seq:
RNAseq and ribosome profiling

treatment_protocol: Cells were infected for 5 or 24 hours before treatment. For Ribo-seq libraries, cells were treated with either 50μM lactimidomycin(LTM) for 30 minutes or 2μg/mL Harringtonine (Harr) for 5 minutes, for translation initiation libraries (LTM and Harr libraries correspondingly), or left untreated for the translation elongation libraries (cycloheximide [CHX] library). All three samples were subsequently treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX.

tag: virus strain

tag: cell line

value: Calu 3 cells, ATCC HTB-55

tag: hours post infection


title: Input-10wk-control-1


title: fp_harr_07hr_1


title: H3K4me3-10wk-IUGR-3


title: WT3

description:
SAMPLE 7
3837

tag: age

tag: tissue


title: fp_ltm_07hr_2


title: TE-1 Cells with shGFP #2

city: Xi'an

first: Lili

last: Duan

state: Shaanxi

address: 169 Changle West Road

institute: Fourth military medical university

description: Gene expression data from EC109 cells with sgRNA-CON244

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: CEL files were processed using Affymetrix GCOS software and normalized with RMA method. RMA files were imported into GeneSpring 7.3 software (Agilent Technologies) and further analyzed.

source_name: TE-1 with sgRNA-CON244

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Cells were grown in RPMI 1640 with 10% FBS, 5% penicillin/streptomycin

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

treatment_protocol: No Chemicalls were treated

value: TE-1  Esophageal squamous cell carcinoma

tag: genotype

value: control


title: TE-1 Cells with LV-EI24-sgRNA #1

description: Gene expression data from EC109 cells with sgEI24

source_name: TE-1 with sgEI24

value: EI24 knockdown


title: TE-1 Cells with shGFP #1


title: TE-1 Cells with LV-EI24-sgRNA #3


title: EC109 Cells with shEI24 #3

description: Gene expression data from EC109 cells with shEI24

source_name: EC109 with shEI24

treatment_protocol: No Chemical treatment

value: EC109  Esophageal squamous cell carcinoma

value: EI24 overexpression


title: EC109 Cells with shEI24 #2


title: TE-1 Cells with LV-EI24-sgRNA #2


title: Ctrl_695

source_name: control castration-responsive tumors

value: control LNCaP xenograft tumors


title: H3K4me3-10wk-IUGR-2

tag: cell type

value: Pancreatic islets

tag: condition

value: IUGR

value: 10 weeks


title: T4_688

value: TRAF4-overexpressing castration-resistant xenograft tumors


title: TE-1 Cells with shGFP #3


title: H3K4me3-10wk-IUGR-1

tag: time point

tag: chip antibody


title: MDA-MB-231_siHPRT1-2 rep1 [MDA_S2_1]

city: El Paso

first: Shrikanth

last: Gadad

address: 5001 El Paso Drive

department: Department of Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

data_processing:
Adapters and low-quality bases were trimmed using Trim galore
Trimmed reads were aligned to hg38 using the hisat2 aligner
Read counts were generated using feature counts with gencode v28 as reference with "-p -t exon -g gene_id -s 2" as options.
Differential gene expression was determined using the DeSeq2 package in R
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited txt file with raw read counts for each sample

growth_protocol: MCF-7 was maintained in Eagle’s Essential Medium and supplemented with 5% Calf Serum. MCF-10A was grown on serum-free Mammary Epithelial Cell Growth Medium supplemented with Supplement Mix and 100 ng/ml cholera toxin. MDA-MB-231 was maintained in Dulbeccos Modified Medium – High Glucose with 10% Fetal Bovine Serum. All the cell lines were maintained with 5% CO2 at 37 degrees C.

extract_protocol:
Total RNA was extracted from cells 48 hours post siRNA transfection, using EZ-10 DNAaway RNA Miniprep kit.
Only samples with RIN values of >9 in agilent tapestation were included in subsequent analysis. Libraries were prepared by Novogene Corporation.
Strand-Specific (dUTP-based) paired end libraries

treatment_protocol: 10 nM siRNA was transfected using lipofectamine RNAiMax. Total RNA was extracted 48 hours after transfection using EZ-10 DNAaway RNA Miniprep kit.

tag: hormone status

value: Triple-negative

value: mammary epithelium

tag: genotype/variation


title: fp_chx_07hr_2


title: MDA-MB-231_siHPRT1-2 rep2 [MDA_S2_2]


title: Ctrl_699


title: MDA-MB-231_siHPRT1-1 rep2 [MDA_S1_2]


title: fp_chx_07hr_1


title: H3K4me3-10wk-control-3

value: Control


title: mrna_07hr_2


title: fp_ltm_07hr_1


title: H3K4me3-10wk-control-1


title: MDA-MB-231_siControl rep2 [MDA_c1_2]

value: siControl


title: MDA-MB-231_siHPRT1-1 rep1 [MDA_S1_1]


title: EC109 Cells with shEI24 #1

tag: treatment


title: H3K27me3-10wk-IUGR-2


title: MDA-MB-231_siControl rep1 [MDA_c1_1]


title: EC109 Cells with shGFP #1

description: Gene expression data from EC109 cells with shGFP

source_name: EC109 with shGFP

value: shGFP


title: mrna_07hr_1


title: H3K4me3-10wk-control-2


title: EC109 Cells with shGFP #2


title: H3K27me3-10wk-IUGR-3


title: EC109 Cells with shGFP #3


title: H3K27me3-10wk-IUGR-1


title: MDA-MB-231_Untreated rep 1 [MDA_1_1]

value: Untreated


title: TREM2_2

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 2

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for PrimeView Human Gene Expression Array

data_processing: The data were normalised using RMA normalisation from R/Bioconductor

source_name: iPSC-derived neuronal cultures

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

extract_protocol: RNA was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research, CA, USA) according to provider guidelines. After checking the quality of mRNA, 500 ng of RNA were used for complementary DNA synthesized with the TaqMan Reverse Transcription Kit (Applied Biosystems).

treatment_protocol: iPSC-derived neurons were differentiated for six weeks and then stimulated with 500 nM of oxidized Aß-S8C dimers for 72 h

tag: disease

value: AD (TREM2 mutation)


title: TREM2_1

description: replicate 1


title: H3K27me3-10wk-control-3


title: MCF-7_siHPRT1-2 rep2 [M7_S2_2]

value: Estrogen receptor positive


title: healthy_Abeta_1

description: replicate 1

value: healthy control

tag: agent

value: abeta


title: MDA-MB-231_Untreated rep 2 [MDA_1_2]


title: H3K27me3-10wk-control-2


title: S. aureus injection Biological Replicate 3

first: Aaron

middle: James

last: Forde

address: Breisacher Str. 115

institute: Medical Center University of Freiburg

description: Gene expression data of dermal macrophages sorted from CCR2-/- mice injected with S.aureus strain Newman

hyb_protocol: Purified ds cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the dUTP residues followed by a terminal labeling with biotin. 5,5 µg fragmented and labeled ds cDNA were hybridized to Affymetrix Clariom S mouse arrays for 16 h at 45 °C in a GeneChip hybridization oven 640.

scan_protocol: Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console v4.1.3 software.

data_processing:
Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software
After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated

label: Biotin

source_name: Dermal macrophages from mice injected with S.aureus

label_protocol: 1 ng of total RNA was used for reverse transcription to synthesize single-stranded (ss) cDNA with a T7 promoter sequence at the 5' end. Next a 3’ adaptor was added and the ss cDNA was converted to double-stranded cDNA, which acted as a template for a pre- in vitro transcription (IVT) amplification by a 9 cycle PCR

growth_protocol: Dermal macrophages were sorted from the ears of CCR2-/- mice

extract_protocol: Total RNA was extracted using the Qiagen RNeasy micro kit

treatment_protocol: The macrophages were sorted directly into lysis buffer (Qiagen RLT buffer supplemented with β-mercaptoethanol)


title: TREM2_Abeta_1

description: replicate 1


title: lung_and_liver HTO S4_L002

city: Los Angeles

first: Eun-Cheon

last: Lim

state: California

address: 116 N. Robertson Blvd., Pacific Theatres Building.Suite 903

department: Surgery

institute: Cedars-Sinai Medical Center

data_processing:
Cells were counted by cellranger version 3.1.0 with refdata-cellranger-mm10-3.0.0
RNA velocity was calculated using Velocyto version 0.17.17
Data normalization, PCA, UMAP were performed using Seurat 3.1.5
Differential expression analysis was done using MAST 1.14.0, and KEGG pathways were inferred using ClusterProfile version 3.17.0
Pseudotime was inferred using Moncle3 version 0.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Seurat object integrated with all gene symbols, raw count matrix, sample types, tissues, exp_types of all samples

extract_protocol:
Lung and liver were mechanically disrupted and passed through a 70 µm strainer to generate single-cell suspensions followed by percoll gradient centrifugation to enrich CD45+ immune cells. Bone marrows were flushed with buffer (DPBS with 1% BSA) and red blood cells were lysed at room temperature for 5 min. Blood was collected in EDTA tubes and immediately lysed at room temperature and quenched with buffer (DPBS with 1% BSA). The number of cells required from each tissue to give relatively equal numbers of Ly6G+ cells were determined a priori. Blood, bone marrow, liver and lung were labeled with hashing antibodies (Biolegend), pulled and stained with DAPI and Ly6G antibodies (Biolegend) for FACS sorting (BD Influx). 50,000 Ly6G+ cells were sorted with expected 15-30% contribution from each tissue. After FACS sorting, cells were further labeled with CXCR4 and CD62L CITE-seq antibodies (Biolegend) for 20 min on ice.
After washing with buffer, cells were counted and immediately processed for single-cell capture and library construction using 10× Genomics Chromium system and 3′ library and gel bead kit v2 (10× Genomics) following standard vendor-guided protocol.

treatment_protocol: Mice were untreated wild type controls.

value: lung, liver

tag: cell population

value: HTO

value: wildtype


title: MCF-7_siHPRT1-2 rep1 [M7_S2_1]


title: H3K27me3-10wk-control-1

value: Pancreatic islets


title: lung_and_liver HTO S4_L001


title: H3K27Ac-10wk-IUGR-3

value: IUGR


title: lung_and_liver ADT S6_L001

value: ADT


title: MCF-7_siHPRT1-1 rep2 [M7_S1_2]


title: PBS injection Biological Replicate 3

description: Gene expression data of dermal macrophages sorted from CCR2-/- mice injected with PBS

source_name: Dermal macrophages from mice injected with PBS


title: MCF-7_siHPRT1-1 rep1 [M7_S1_1]


title: PBS injection Biological Replicate 2


title: TREM2_Abeta_2

description: replicate 2


title: S. aureus injection Biological Replicate 1

description: Gene expression data of dermal macrophages sorted from CCR2-/- mice injected with S.aureus strain Newmann


title: healthy_1

description: replicate 1


title: MCF-7_siControl rep2 [M7_c1_2]


title: MCF-7_siControl rep1 [M7_c1_1]


title: healthy_2

description: replicate 2


title: H3K27Ac-10wk-control-3

value: 10 weeks


title: H3K27Ac-10wk-IUGR-1


title: MCF-7_Untreated rep 2 [M7_1_2]


title: H3K27Ac-10wk-control-2


title: blood_and_bone_marrow HTO S3_L002

value: blood, bone marrow


title: lung_and_liver gene expression S6_L001

value: gene expression


title: S. aureus injection Biological Replicate 2


title: H3K27Ac-10wk-IUGR-2


title: lung_and_liver ADT S6_L002


title: MCF-7_Untreated rep 1 [M7_1_1]

value: mammary epithelium


title: Uninfected Biological Replicate 2

description: Gene expression data of dermal macrophages sorted from uninfected CCR2-/- mice

source_name: Dermal macrophages from uninfected mice


title: Uninfected Biological Replicate 3


title: blood_and_bone_marrow HTO S3_L001


title: MCF-10A_siHPRT1-2 rep2 [M10_S2_2]

value: immortalized normal


title: PBS injection Biological Replicate 1


title: Uninfected Biological Replicate 1


title: Input-2wk-IUGR-5

value: 2 weeks


title: lung_and_liver gene expression S6_L002


title: MCF-10A_siHPRT1-2 rep1 [M10_S2_1]


title: blood_and_bone_marrow ADT S5_L002


title: blood_and_bone_marrow ADT S5_L001


title: MCF-10A_siHPRT1-1 rep2 [M10_S1_2]


title: Input-2wk-IUGR-4


title: Input-2wk-IUGR-2


title: Input-2wk-IUGR-3


title: MCF-10A_siHPRT1-1 rep1 [M10_S1_1]


title: H3K27Ac-10wk-control-1

value: Control


title: blood_and_bone_marrow gene expression S1_L001


title: MCF-10A_Untreated rep 2 [M10_1_2]

value: Untreated


title: blood_and_bone_marrow gene expression S1_L002


title: Input-2wk-control-5


title: Input-2wk-control-6


title: Input-2wk-IUGR-1


title: MCF-10A_siControl rep1 [M10_c1_1]

value: siControl


title: C2: NIH/3T3 were treated with TGFB1 (1ng/ml) and BI6727 (5μM) for 72h (rep 2)

city: Wuhan

first: Jie

last: Wu

state: Hubei

address: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1277

department: Department of Cardiovascular Surgery

data_processing:
Clean reads were mapped to the mm10 (UCSC) mouse genome with  subjunc (subread v1.6.4) with default parameters.
Transcripts were assembled Expression quantitation using featureCounts (subread v1.6.4) with mouse annotation (release_M20) from Gencode
Differential gene expression was calculated using the DESeq2 package (v1.22.2) package of the R (version 3.6.1) software
Genome_build: mm10
Supplementary_files_format_and_content: Comma-Separated counts for each sample

growth_protocol: In all three groups, NIH/3T3 was resuspended in DMEM complete medium and cultured at 37℃.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
DNase I was used to digest double-stranded and single-stranded DNA in total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI Shenzhen, China).

treatment_protocol: We designed the experiment to three groups,NIH/3T3 were treated with vehicle (PBS) for 72h (A1,A2),NIH/3T3 were treated with TGFB1 (1ng/ml) and  vehicle (DMSO) for 72h (B1,B2),NIH/3T3 were treated with TGFB1 (1ng/ml) and BI6727 (5μM) for 72h (C1,C2).

value: fibroblast


title: MCF-10A_siControl rep2 [M10_c1_2]


title: MS-8: Post-MPA Sensitive Inidividual 3 (Stim.1.MPA.S3)

city: Indianapolis

first: Kimberly

middle: S.

last: Collins

state: IN

address: 950 W Walnut Street E202

department: Medicine

institute: Indiana University School of Medicine

data_processing:
26 bp of cell barcode and UMI sequences, and  98 bp RNA reads were generated with Illumina NovaSeq 6000.
CellRanger (v2.1.0) mkfastq was used to convert raw base sequence calls and demultiplex sequence data into sample-specific FASTQ files.
Fastq files were aligned to the human reference genome GRCh38 with RNAseq aligner STAR
CellRanger (v2.1.0) was use to align the seqence data to human reference genome GRCh38.
The cell barcode-gene matrices generated from cellRanger were used for Seurat analysis.
Seurat v3 was used for pre-processing, feature selection, dimension reduction, identification of anchors between samples, and integration. We choose a dimensionality of 80 PCs for the integration of our 18 samples and a resolution of 0.8 for clustering analysis.
We manually classified clusters based on common gene expression markers identified in the literature for different lymphocyte subpopulations.
Genome_build: GRCh38
Supplementary_files_format_and_content: RDS file containing data from 120,194 cells and metadata.

source_name: Lymphocytes

extract_protocol:
No extraction occurred prior to submission for single cell sequencing. Cells were in suspension in RPMI media supplemented with 10% FBS.
Single cell capture and library preparation were carried out according to the Chromium Single cell 3’ Reagent kits V2 User Guide (10X Genomics PN-120267, PN-1000009, PN-120262). The resulting libraries were assessed with an Agilent Bioanalyzer 2100.

treatment_protocol: Baseline: Ficoll Isolation; Post-Stimulation: Anti-CD3/CD28; Post-MPA: 1 µg/mL MPA

value: Healthy

tag: Sex

value: Female

tag: race

value: Caucasian

value: Lymphocytes


title: C1: NIH/3T3 were treated with TGFB1 (1ng/ml) and BI6727 (5μM) for 72h (rep 1)

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

tag: cell line


title: A2: NIH/3T3 were treated with vehicle (PBS) for 72h (rep 2)


title: B1: NIH/3T3 were treated with TGFB1 (1ng/ml) and  vehicle (DMSO) for 72h (rep 1)


title: Input-2wk-control-3

value: Pancreatic islets


title: MCF-10A_Untreated rep 1 [M10_1_1]


title: Input-2wk-control-4


title: Input-2wk-control-1


title: A1: NIH/3T3 were treated with vehicle (PBS) for 72h (rep 1)


title: MS-11: Post-MPA Sensitive Inidividual 1 (Stim.1.MPA.S1)

value: Male

value: Asian


title: R-TEn-p1-Ebox_Mut_DP_H3K27ac

city: Kyoto

first: Kazuko

last: Miyazaki

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

country: Japan

institute: Institute for Life and Medical Sciences, Kyoto University

data_processing:
Illumina bcl2fastq software used for basecalling (HiSeq 2500, NovaSeq 6000,Illumina HiSeq X Ten).
ATAC-seq and ChIP-seq trimmed reads were mapped to the mm9 reference genome using Bowtie2 (version 1.2.7). Hi-C reads were trimmed from the 3’ end of sequences to GATC (MboI restriction enzyme site) and aligned to the mouse reference genome mm9 using bowtie2.
Tags mapped to unique DNA sequences of ATAC-seq, ChIP-seq and Hi-C were analyzed using HOMER (Lin et al., 2012, Heinz et al., 2018)
Genome_build: mm9
Supplementary_files_format_and_content: ATAC-seq and ChIP-seq : Tab-delimited BED files containing peak positions for each ATAC-seq or ChIP-seq experiment. Hi-C: Tab-delimited Text files containing PC1 values for each experiment.

source_name: DP cells purified by MACS (CD4+CD8+CD69–TCRb– )

growth_protocol: For proB cell culture, B cells were enriched by B220-MACS column from total bone marrow cells. Then, B cells were cultured in PRMI 1640 with 10% fetal bovine serum, 2mg/ml sodium bicarbonate, 1 mM sodium pyruvate, 0.1mM nonessential amino acid solution, 5x10-5M 2-Mercaptoethanol, 100µg/ml streptomycine and 100U/ml penicillin in the presence of IL-7 and stem cell factor.

extract_protocol: ATAC-seq : ATAC-seq was performed as described (Buenrostro et al., 2013) with modifications. Cells were lysed, then treated with Tn5 transposase (Nextera DNA Sample Preparation Kit). After the treatment, the tagmentated DNA was cleaned up and purified with DNA Clean & Concentrator kit (Zymo Research).  The purified DNA were amplified with determined cycles of PCR based on the amplification curve, then were size-selected using Ampure XP beads. Hi-C : in situ Hi-C was performed as described (Rao et al., 2014).  DP and cultured proB cells from control and deletion mutant mice were fixed with 1% formaldehyde/FACS buffer for 10 minutes at room temperature. Cells were lysed and chromatin was digested overnight using MboI. The fragment overhangs generated by the restriction enzyme were filled in with biotin-14-dATP by Klenow fragment, then proximity ligation was performed.  Biotinylated DNA was sonicated to 300-500 bp on a Covaris M220. The biotinylated DNA was captured on Dynabeads MyOne Streptavidin T1 beads. After washing the beads, ends of sheared DNA were repaired and added A-tail according to the protocol. NEBNext Multiplex Oligos for Illumina (NEB) were ligated and the beads were washed.  Libraries were amplified by PCR and size selected using ProNex (Promega). As to CD4SP cells, Tethered Conformation Capture (TCC) was performed as described (Kalhor et al. 2012).  CD4SP cells were fixed with 1% formaldehyde/FACS buffer for 10 minutes at room temperature. Cells were lysed and chromatin was digested overnight using MboI.  ChIP-seq : Cells were fixed in 1% formaldehyde/PBS . The reactions were quenched by 1.5M glycine and cells were washed with PBS and pelleted. Pelleted cells were lysed and chromatin was sonicated by Covaris M220.  Diluted sheared chromatin was immunoprecipitated with each antibody which is pre-bound to Dynabead Protein G magnetic microbeads overnight at 4 °C. Samples were washed, eluted and reverse cross-linked  65°C overnight. Samples were next treated with RNase A and proteinase K and purified using DNA Clean & Concentrator kit (Zymo Research). Samples were ligated to NEBNext Multiplex Oligos for Illumina (NEB) and multiplex amplified by PCR. Amplified ChIP DNA was selected by size.

tag: strain

tag: cell

value: DP cells purified by MACS

value: Thymus

value: anti-H3K27ac (abcam:# ab4729)


title: MR-36: Post-MPA Resistant Individual 3 (Stim.1.MPA.R3)

tag: age

tag: tissue


title: MR-35: Post-MPA Resistant Individual 2 (Stim.1.MPA.R2)


title: B6_DP_H3K27ac

tag: genotype

value: Wild type


title: H3K4me3-2wk-IUGR-3

tag: cell type

tag: condition

value: IUGR


title: B2: NIH/3T3 were treated with TGFB1 (1ng/ml) and  vehicle (DMSO) for 72h (rep 2)


title: R-TEn-p1-Ebox_Mut_DP_H3K27me3

tag: chip antibody

value: anti-H3K27me3 (Milipore:# ab07-499)


title: B6_DP_H3K27me3


title: MR-14: Post-MPA Resistant Individual 1 (Stim.1.MPA.R1)


title: SS-11: Post-Stimulation Sensitive Individual 1 (Stim.0.MPA.S1)


title: H3K4me3-2wk-IUGR-1

tag: time point

value: 2 weeks


title: H3K4me3-2wk-IUGR-2


title: H3K4me3-2wk-control-2

value: Control


title: SS-8: Post-Stimulation Sensitive Individual 3 (Stim.0.MPA.S3)


title: SR-36: Post-Stimulation Resistant Individual 3 (Stim.0.MPA.R3)


title: SS-4: Post-Stimulation Sensitive Individual 2 (Stim.0.MPA.S2)


title: H3K4me3-2wk-control-1


title: B6_DP_H3K4me1

value: anti-H3K4me1 (abcam:# ab8895)


title: SR-35: Post-Stimulation Resistant Individual 2 (Stim.0.MPA.R2)


title: MS-4: Post-MPA Sensitive Inidividual 2 (Stim.1.MPA.S2)


title: H3K27me3-2wk-control-3


title: H3K27me3-2wk-control-2


title: B6_DP_H3K27me3_2

description: ChIP-seq

data_processing:
Illumina bcl2fastq software used for basecalling (HiSeq 2500, NovaSeq 6000,Illumina HiSeq X Ten ).
ATAC-seq and ChIP-seq trimmed reads were mapped to the mm9 reference genome using Bowtie2 (version 1.2.7). Hi-C reads were trimmed from the 3’ end of sequences to GATC (MboI restriction enzyme site) and aligned to the mouse reference genome mm9 using bowtie2.
Tags mapped to unique DNA sequences of ATAC-seq, ChIP-seq and Hi-C were analyzed using HOMER (Lin et al., 2012, Heinz et al., 2018)
Genome_build: mm9
Supplementary_files_format_and_content: ATAC-seq and ChIP-seq : Tab-delimited BED files containing peak positions for each ATAC-seq or ChIP-seq experiment. Hi-C: Tab-delimited Text files containing PC1 values for each experiment.

source_name: DP cells purified by MACS (CD4+CD8+CD69-TCRb-)


title: H3K27me3-2wk-control-1


title: BS-8: Baseline Sensitive Individual 3 (Baseline.S3)


title: R-TEn-p1-Ebox_Mut_DP_H3K27ac_2

description: ChIP-seq


title: B6_DP_H3K27ac_2

description: ChIP-seq


title: R-TEn-p1-Ebox_Mut_DP_H3K4me1


title: BS-4: Baseline Sensitive Individual 2 (Baseline.S2)


title: R-TEn-p1-Ebox_Mut_DP_H3K27me3_2

description: ChIP-seq


title: BS-11: Baseline Sensitive Individual 1 (Baseline.S1)


title: H3K27Ac-2wk-IUGR-3


title: H3K27me3-2wk-IUGR-4


title: R-TEn-p1-Ebox_Mut_DP_Smc3_2

description: ChIP-seq

value: anti-SMC3 (abcam:# ab9263)


title: R-TEn-p1-Ebox_Mut_DP_H3K4me1_2

description: ChIP-seq


title: H3K27Ac-2wk-IUGR-1


title: H3K27Ac-2wk-IUGR-2


title: H3K27me3-2wk-IUGR-3


title: BR-35: Baseline Resistant Individual 2 (Baseline.R2)

value: Healthy


title: BR-36: Baseline Resistant Individual 3 (Baseline.R3)

value: Female


title: H3K27Ac-2wk-control-3


title: BR-14: Baseline Resistant Individual 1 (Baseline.R1)


title: WT_DP_Smc3_2

description: ChIP-seq


title: R-TEn-p1-Ebox_Mut_DP_CTCF_2

description: ChIP-seq

value: anti-CTCF (Milipore:# 07-729)


title: H3K27Ac-2wk-control-2


title: SR-14: Post-Stimulation Resistant Individual 1 (Stim.0.MPA.R1)

value: Lymphocytes


title: A5006_1

city: Bethesda

first: Igor

last: Panyutin

state: MD

address: 10 Center DR., room 1C401

department: Radiology Imaging Sciences

institute: NIH/CC

data_processing:
Base Calling by CASAVA base recognition.
Alignment with STAR (Spliced Transcripts Alignment to a Reference) a fast NGS read aligner of RNA-seq data.
HTSeq used to assess gene expression levels expressed as FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced).
Genome_build: hg19
Supplementary_files_format_and_content: FPKM/gene of all samples in .txt format

source_name: WA09 hESC

growth_protocol: H9 hESCs (WiCell, Madison, WI, USA, passage 21) were cultured in feeder-free complete mTeSR-1 culture medium (STEMCELL Technologies, B.C., Canada) in Matrigel (Corning, NY, USA) coated flasks. After irradiation and 24-hour recovery, hESCs were directed to differentiate into neuronal lineages via embryoid bodies using STEMdiff Neural Induction Protocol.

extract_protocol:
Total RNA was extracted and purified using the PureLink RNA Mini Kit (Invitrogen), and DNA-free™ DNA Removal Kit (Invitrogen) to remove genomic DNA.
Libraries were prepared with NEBNext Library prep kit (NEB, Ipswich, MA).

treatment_protocol: Cell irradiations were performed using a single X-ray tube of a dual-source CT scanner (SOMATOM Definition Flash, Siemens Healthcare, Forchheim, Germany).

value: hESC-derived neural progenitor cells

tag: day/ir dose

tag: biological replicate


title: H3K27Ac-2wk-control-1

value: Pancreatic islets


title: WT_DP_CTCF_2

description: ChIP-seq

value: anti-CTCF (Milipore:#07-729)


title: virion.Vero6

organism: Severe acute respiratory syndrome coronavirus 2

source_name: virus

tag: virus strain


title: B6_DP_H3K4me1_2

description: ChIP-seq

value: DP cells purified by MACS


title: virion.Calu3


title: X6

city: Hefei

first: Shihai

last: Xing

state: Anhui

address: No.1 Qianjiang Road, Xinzhan District

institute: Anhui University of Chinese Medicine

data_processing:
Raw reads were filtered via SOAPnuke (v1.4.0) by removing reads containing adaptors, poly-N or low quality, and then clean reads were obtained.
Trinity (v2.0.6) was used to assemble the clean reads and Tgicl (v2.0.6) to perform clustering and eliminate redundant data in the assembled transcripts to obtain unique genes. The assembled transcripts were processed for further expression analysis and functional annotation.
Clean reads were mapped to the assembled unique genes by Bowtie2 (v2.2.5)and the expression level of genes were calculated by RSEM (v1.2.8) and normalized to FPKM (Fragments per kilo base of transcript per million mapped reads). Functional annotation of genes was achieved by mapping genes to different databases (NT, NR, KOG, KEGG) using the software BLAST (v2.2.23). GO annotation was performed by Blast2GO (v 2.5.0) with NR annotations. DEseq2 was used to detect DEGs (Different expressed genes), and DEGs with fold change > 2 or <-2 and adjusted P value <= 0.001 were considered to be significantly different expressed genes. GO enrichment analysis and KEGG enrichment analysis were performed using Phyper, a function of R. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value < 0.05).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Platycodon grandiflorus

source_name: calli

growth_protocol: The leaves are derived from the original plant. The callus induction of Platycodon grandiflorum is based on stem with nodes as explants, and the formula is MS + NAA 1.0 mg / L + 6-BA 0.5 mg / L.

extract_protocol:
CTAB-PBIOZOL reagent was used as extraction solution for the purification of total RNA from leaves and calli of P. grandiflorus. The leaves and the calli materials were washed with ultrapure water and immersed in liquid nitrogen immediately after drying on sterilized filter paper. Grinded tissue samples of leaves and calli at about 80 mg with liquid nitrogen into powder and transferred the milled powder samples to 1.5 mL tubes with preheated at 65 °C by extraction solution. The samples were incubated by Solarbio mixer for 15 min at 65 °C to make the nucleoprotein complexes in the samples completely dissolved. After 5 min centrifuge at 12000 × g at 4 °C, the supernatants were added 400 uL of chloroform per 1.5 mL of extraction solution and centrifuged at 12000 × g for 10 min at 4°C. After centrifuge, each supernatant was transferred to a new 2.0 mL test tube that added 700 uL acidic phenol and 200 uL chloroform followed by centrifuging at 12000 × g for 10 min at 4°C. Subsequently, the aqueous phase was added with its’ equal volume of chloroform and centrifuged at 12000 × g for 10 min at 4°C. The supernatant was added with equal volume of isopropyl alcohol and placed at -20°C for 2 hours for precipitation. After precipitating, each of the mix was centrifuged at 12000 × g for 20 min at 4°C and then removed the supernatant. After washed with 1 mL of 75% ethanol 2 times, the RNA pellet was air-dried in the bio-safety cabinet and was dissolved with 50 µL of sterilized DEPC-treated water. Finally, total RNA was qualified and quantified by a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT) attached magnetic beads were used to purified mRNA with eliminating rRNA and tRNA in the total RNA. Purified mRNA of leaves and calli of P. grandiflorus were fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated by random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. After that, RNA Index Adapters and A-Tailing Mix were added by incubating to end repair. The fragments of cDNA obtained from previous steps were amplified by PCR, and the PCR products were purified by Ampure XP Beads firstly, dissolved in EB solution. The products were validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products obtained from previous steps were heated to denature and circularized by the splint oligo sequence to get the final library, and the single stranded circular DNA (ssCir DNA) was formatted as the final library.
The constructional final library was further amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of each molecular, DNBs were loaded into the patterned nano-array and single end of 50 bases reads were generated on BGIseq 500 platform (BGI-Shenzhen, China).

treatment_protocol: The culture conditions of the tissue culture room were 12 h/d, the illuminance was 1600 lx, the culture temperature was (25 ± 1) °C, and the culture was carried out for 50 d.

value: calli


title: ATAC_R1pro_Ebox_mut_proB_2

description: ATAC-seq

source_name: DP cells (CD4+CD8+CD5–CD69–TCRb– )

value: DP cells

value: Bone marrow


title: A50010_1


title: ATAC_R1pro_Ebox_mut_DN3_2

description: ATAC-seq

source_name: DN3a cells (CD4–CD8–LinnegCD44–CD25+CD28– )

value: DN3a cells

value: Thymus


title: A50010_3


title: Lig4-/- CH12F3 RNA-seq

city: Dalian

first: Weifeng

last: Mao

address: 9 Lvshun South Rd,

institute: Dalian Medical University

description: gene.fpkm.matrix

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence ( SeqPrep ), and masked for low-complexity or low-quality sequence ( Sickle ) , then mapped to GRCh38 using TopHat with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Lig4-/- CH12F3 cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 5 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: B cell lymphoma


title: ATAC_R1pro_Ebox_Cont_DN3_2

description: ATAC-seq

value: Wild type


title: ATAC_R1pro_Ebox_Cont_proB_2

description: ATAC-seq


title: A5006_3


title: A5000_1

value: hESC


title: A50010_2


title: A5000_3


title: X5


title: HepG2 EFTUD2 overexpression rep2

city: Guangzhou

first: Chen

last: Qu

state: Guangdong

address: #601 West Huangpu Road

institute: Jinan University

data_processing:
Basescaling was performed by BGI
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 with default parameters.
Bowtie2 was applied to align the clean reads to the reference coding gene set. Then expression level of gene was calculated by RSEM. Differential expression analysis was performed using the DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: hepatocellular carcinoma

extract_protocol:
The total RNA was immediately isolated from the cells using Trizol Reagent (Invitrogen, Waltham, MA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the standard BGI protocols

value: Hep G2

value: hepatocellular carcinoma

tag: transfected with

value: EFTUD2 gene


title: A5000_2


title: A5006_2


title: HepG2 EFTUD2 overexpression rep1


title: DNM_3

city: Stellenbosch

first: Pieter

middle: Herodus

last: du Preez

state: Western Cape

address: LAB239, JC Smuts Building, Van der Bijl Street

department: Genetics

country: South Africa

institute: University of Stellenbosch

description: Bisulfite treated

data_processing:
Quality check with FastQC
Trimming, using Trimmomatic, HEADCROP:10 SLIDINGWINDOW:15:20 MINLEN:40 ILLUMINACLIP
Bismark genome preparation
Bismark allignment, implementing Bowtie2 -L,-0.6,-0.8
Bismark methylation extraction, -p --no_overlap --ignore 2 --ignore_3prime 5 --no_header --cutoff 10 --gazillion
Genome_build: GCA_001465515.1
Supplementary_files_format_and_content: tab-delimited text files with 8 columns, 1:gene/intergenic, 2:gene/intergenic number, 3:contig #, 4:base position on contig, 5:total calls, 6:methylated call, 7:strandedness, 8:context

organism: Diuraphis noxia

source_name: Whole organism

growth_protocol: Both biotypes were maintained on a susceptible wheat cultivar "SST362" prior to extraction

extract_protocol:
DNeasy Blood & tissue Kit with recomended protocol for insect DNA
Bisulfite conversion, using EZ DNA Methylation Lightning kit (Zymo Research), followed by Accel-NGS Methyl-Seq (Swift bioscience)

tag: biotype

value: SAM


title: A156_3


title: HepG2 control rep3

value: empty vector


title: CH12F3 RNA-seq

description: gene.fpkm.matrix

source_name: CH12F3 cells


title: X4


title: X3

source_name: Leaves

value: Leaves


title: X1


title: HepG2 EFTUD2 overexpression rep3


title: A156_1

value: hESC-derived neural progenitor cells


title: A1510_1


title: DNM_2

description: Bisulfite treated


title: HepG2 control rep2


title: DN1_2

description: Bisulfite treated


title: X2


title: DN1_1

description: Bisulfite treated

data_processing:
Quality check with FastQC
Trimming, using Trimmomatic, HEADCROP:10 SLIDINGWINDOW:15:20 MINLEN:40 ILLUMINACLIP
Bismark genome preparation
Bismark allignment, implementing Bowtie2 -L,-0.6,-0.6
Bismark methylation extraction, -p --no_overlap --ignore 2 --ignore_3prime 5 --no_header --cutoff 10 --gazillion
Genome_build: GCA_001465515.1
Supplementary_files_format_and_content: tab-delimited text files with 8 columns, 1:gene/intergenic, 2:gene/intergenic number, 3:contig #, 4:base position on contig, 5:total calls, 6:methylated call, 7:strandedness, 8:context

extract_protocol:
DNeasy Blood & tissue Kit with recomended protocol for insect DNA
Bisulfite conversion, using EZ DNA Methylation Lightning kit (Zymo Research), followed by TruSeq DNA Methylation Library Kit (Illumina)


title: DNM_1

description: Bisulfite treated


title: DN1_3

description: Bisulfite treated


title: A150_1


title: A1510_2


title: A1510_3


title: A150_3


title: A150_2


title: hy5_5

city: Shanghai

first: hongtao

last: LIU

address: #300 Fenglin Road

institute: CAS center for excellence in Molecular plant sciences

data_processing:
Illumina software used for basecalling.
Sequenced reads were processed using Trimmomatic(Version0.36), The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2(Version2.2.1.0).
Then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks TopHat（version:2.2.1）
FPKM and read counts valueof each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(Version1.18.0)(2012) functions estimateSizeFactors and nbinomTest.
Genome_build: TAIR10.1_NCBI
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
RNA was extracted from 7 day old seedlings grown in Short Day conditions at ZT20 with using a RNAiso Plus kit (Takara Bio, Shiga, Japan)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: seedling

value: 7 DAY OLD

value: hy5-215  mutant


title: hy5_6


title: A06_1


title: hy5_4

value: hy5-215 mutant


title: human Serum (hSerum-27)

city: Columbus

first: NADUPARAMBIL

middle: Korah

last: JACOB

state: Ohio

address: 410 W 12th Ave

department: Radiation Oncology

institute: The Ohio State University

description:
miRNA profiling
Serum was isolated from volunteer' whole blood. Total miRNA was extracted using Qiagen miRNAeasy kit and counts were measured by nanoString

hyb_protocol: Label protocol was performed following manufacturer's standard protocol

data_processing: Raw data was technically normalized using positive and negative hybridization controls and ligase controls on  nanoString nCounter system. The technical normalized data was further biologically normalized to geometric means of top 100 miRNAs by nSolver software (Nanostring technologies, Seattle, WA).

label: nanoString Dye

source_name: Healthy Volunteer -3

extract_protocol: RNA was extracted using Qiagen miRNAeasy Kit

value: whole blood

tag: disease state

value: Healthy

tag: total mirna

tag: sample type

value: Serum


title: A06_3


title: human Serum (hSerum-25)

scan_protocol: Label protocol was performed following manufacturer's standard protocol

source_name: Healthy Volunteer -1


title: human Serum (hSerum-26)

source_name: Healthy Volunteer -2

label_protocol: Label protocol was performed following manufacturer's standard protocol


title: human Platelets (hPLT-23)

description:
miRNA profiling
Whole blood was collected in the form of leukopak (American Redcross). Total miRNA was extracted using Qiagen miRNAeasy kit and counts were measured by nanoString

source_name: Healthy Leukopak (American Red Cross) -2

value: Platelets


title: A06_2


title: HepG2 control rep1

tag: cell line


title: human Platelets (hPLT-22)

source_name: Healthy Leukopak (American Red Cross) -1


title: Col_0_2

value: Wild-type


title: Red Blood Cells (RBC-21)

source_name: Healthy Leukopak (American Red Cross) -3

value: Red Blood Cells


title: A010_1

source_name: WA09 hESC


title: A010_2


title: A010_3


title: Col_0_1


title: cor27cor28SD3

value: cor27cor28 mutant


title: cor27cor28SD1


title: cor27cor28SD2


title: A00_1

value: hESC


title: Red Blood Cells (RBC-19)


title: Red Blood Cells (RBC-20)


title: A00_3


title: A00_2


title: cop1SD3

value: cop1-6 mutant


title: Col_0_3


title: Hematopoetic Stem Cells (HSCs-16)

value: Hematopoetic Stem Cells


title: Hematopoetic Stem Cells (HSCs-17)


title: cop1SD2


title: HepG2 si-importin8-miR-552-3p-1

first: Jing

last: Chen

state: Shanghai

address: 501 Haike Road

department: Center for Drug Safety Evaluation and Research

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

data_processing:
raw data were filtered to clean data by SOAPnuke: v1.5.2 parameter v1.5.2
HISAT v2.0.4 was used for mapping clean reads to human genome Vesion 38 with parameter --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Bowtie2 ( v2.2.5  -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200) was used for gene alignment and RSEM(v1.2.8, parament default) was used for gene quantificaition
different expresion genes were calculated by DEGseq with  Fold Change >= 2.00 and Adjusted Pvalue <= 0.001
Genome_build: GCF_000001405.38_GRCh38.p12

source_name: human liver

extract_protocol:
HepG2 cells total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBseq platform

value: hepatocellular carcinoma


title: cop1SD1


title: HepG2 si-importin8-NC-2


title: Natural Killer Cells (NK cells-15)

value: Natural Killer Cells


title: Col_0SD2


title: Natural Killer Cells (NK cells-14)


title: HepG2 si-importin8-NC-1


title: Hematopoetic Stem Cells (HSCs-18)


title: B-lymphocytes (B cells-12)

value: B- lymphocytes


title: Natural Killer Cells (NK cells-13)


title: Col_0SD1

value: seedling


title: HepG2 miR-552-3p-2


title: HepG2 miR-552-3p-1


title: PAO1r_phage-18min_rep3

city: Chongqing,

first: Qiu

last: Zhong

address: Daping Changjiang street 10#

institute: Third Military Medical University

description:
PAO1r12
GP-12

data_processing:
The sequenced libraries were mapped against predicted transcripts from the  Pseudomonas aeruginosa PAO1 genome using TopHat v2.0.4
The transcript  abundance (FPKM, Fragments Per Kilobase of exon per  Million fragments mapped) and significant changes in  transcript expression were estimated using Cufflinks  v2.0.2
Transcripts with p-values less than 0.05,  determined using CuffDiff
Genome_build: NC_002516.2 , KX074203.1,  KX074202.1and KX074201.1 were used as the reference genomes

organism:
Pseudomonas aeruginosa
Pseudomonas phage phiYY

extract_protocol: RNA extraction

tag: strain

tag: treatment

value: after phiYY phage infection of 18min


title: B-lymphocytes (B cells-11)

tag: tissue


title: HepG2 NC-2


title: PAO1r_phage-18min_rep2

description:
PAO1r11
GP-11


title: PAO1r_phage-18min_rep1

description:
PAO1r10
GP-10


title: T-lymphocytes (T cells-9)

value: T- lymphocytes


title: HepG2 NC-1


title: PAO1r_phage-12min_rep3

description:
PAO1r9
GP-09

value: after phiYY phage infection of 12min


title: HepG2 si-importin8-miR-552-3p-2


title: T-lymphocytes (T cells-8)

value: whole blood


title: PAO1r_phage-12min_rep2

description:
PAO1r8
GP-08


title: Tn-Seq Mac24

city: Boston

first: Simon

middle: L

last: Dove

state: MA

address: 300 Longwood Ave

department: Division of Infectious Diseases

institute: Boston Children's Hospital and Harvard Medical School

description:
Transposon-genomic DNA junctions amplified from transposon mutant library gDNA
Mac_24_output2_TnOnly_HighConfCounts.wig
AllInput2_TnOnly_HighConfCounts.wig

data_processing:
Cutadapt (version 1.16; Martin, 2011) used to demultiplexed
Cutadapt (version 1.16; Martin, 2011) used trim adapters (cutadapt -a ACAGGTTGGATGATAAGTCCCCGGTCTTCGTATGCCGTCTTCTGCTTG --no-indels --discard-untrimmed )
reads mapped to genome (NC_007880.1) using bowtie (version 1.2; Langmead et al., 2009) with a seed length of 16 and zero mismatches allowed (bowtie --best -k 1 --fullref -v 0 -l 16)
Custom scripts were used to identify reads corresponding to insertions in TA sites and tally only those insertions with reads mapping from both ends of the transposon
Datasets were normalized for positional bias using Matlab
EL-ARTIST (Pritchard et al., 2014, PMID: 25375795) was used to identify genes essential for in vitro growth
CON-ARTIST (Pritchard et al., 2014, PMID: 25375795) was used to identify genes critical for survival in media and in macrophage
Genome_build: NC_007880.1
Supplementary_files_format_and_content: wig files with value representing the number of high-confidence transposon insertions at TA sites (arbitrarily placed at the T of the TA dinucleotide)

organism: Francisella tularensis subsp. holarctica LVS

source_name: Bacterial cells grown in J774A.1 murine macrophage-like cells

extract_protocol:
gDNA extraction ws performed with Epicentre MasterPure Complete DNA and RNA Purification Kit
Libraries were prepared as in Goodman et al., 2001 (PMID: 22094732), starting with  linear PCR. Custom adapters were used as per protocol.

tag: sample name

value: Sample 5

tag: transposon library

value: Complex transposon mutant library

value: sample recovered after 24 hours of growth in J774A.1 murine macrophage-like cells

tag: library pairs

value: Output library for sample 3

tag: analysis groups

value: all in vitro critical genes, intramacrophage growth


title: T-lymphocytes (T cells-7)

value: Healthy

tag: cell type


title: Col_0SD3

tag: age

value: 7 DAY OLD

tag: genotype

value: Wild-type


title: human Peripheral Blood Mononuclear Cells (hPBMC-6)

value: Peripheral Blood Mononuclear Cells


title: Tn-Seq MHB

description:
Transposon-genomic DNA junctions amplified from transposon mutant library gDNA
MH_output2_TnOnly_HighConfCounts.wig
AllInput2_TnOnly_HighConfCounts.wig

source_name: Bacterial cells grown in supplemented Mueller-Hinton broth

value: Sample 4

value: sample recovered after growth in supplemented Mueller-Hinton broth

value: Output library for sample 1

value: all in vitro critical genes, in vitro growth


title: PAO1r_phage-12min_rep1

description:
PAO1r7
GP-07


title: Input-2wk-control-2

city: Philadelphia

first: Paul

last: Wang

address: 3440 Market St

institute: Bioinformatics Core, IBI, UPen

data_processing:
Low quality reads were trimmed using Trimmomatic (v0.32) and mapped to rat genome rn6 using bowtie2. Mapped reads were further processed using samtools (v0.1.19) with -F 4 -q 10 parameters. Peak calling was performed using MACS (v2.1.0).
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: gene.diff.peak.annotation.csv: Annotated differential peaks among conditions in csv format.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with different antibodies.
Multiplexed libraries were created using the Illumina ChIP-seq DNA sample prep kit following manufacturer’s instructions.

value: Pancreatic islets

tag: condition

value: Control

tag: time point

value: 2 weeks

tag: chip antibody


title: Tn-Seq CHAH B

description:
Transposon-genomic DNA junctions amplified from transposon mutant library gDNA
Mac_0_input2_TnOnly_HighConfCounts.wig
AllInput2_TnOnly_HighConfCounts.wig

source_name: Bacterial cells grown on CHAH, resuspended in DMEM + 10% FBS

value: Sample 2

value: sample taken after growth on CHAH and resuspended in DMEM + 10% FBS

value: Unpaired

value: all in vitro critical genes


title: PAO1r_phage-6min_rep3

description:
PAO1r6
GP-06

value: after phiYY phage infection of 6min


title: B-lymphocytes (B cells-10)

value: whole blood

tag: disease state

value: B- lymphocytes


title: human Whole Blood (hWB-3)

value: Healthy

tag: total mirna


title: SJPB42

status: Public on Jul 14 2020

city: Memphis

first: Anthony Pak-Yin

last: Liu

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using iSCAN BeadArray reader

data_processing: R library minfi

label: Cy5, Cy3

source_name: pineal parenhchymal tumors

label_protocol: Standard Illumina protocol

extract_protocol: DNA isolation using DNA QIAamp FFPE Tissue Kit

tag: tumor

value: pineal parenchymal


title: SJPB41


title: SJPB40


title: human Whole Blood (hWB-1)


title: SJPB39


title: human Whole Blood (hWB-2)


title: SJPB43


title: SJPB38


title: SJPB37


title: SJPB36


title: SJPB34


title: SJPB31


title: SJPB32


title: SJPB35


title: SJPB33


title: human Peripheral Blood Mononuclear Cells (hPBMC-5)

value: Peripheral Blood Mononuclear Cells


title: SJPB30


title: SJPB29


title: human Peripheral Blood Mononuclear Cells (hPBMC-4)


title: Tn-Seq CHAH C

description:
Transposon-genomic DNA junctions amplified from transposon mutant library gDNA
Mac_24_input2_TnOnly_HighConfCounts.wig
AllInput2_TnOnly_HighConfCounts.wig

value: Sample 3

value: Complex transposon mutant library

value: Input library for sample 5

value: all in vitro critical genes, intramacrophage growth


title: PAO1r_phage-6min_rep2

description:
PAO1r5
GP-05


title: SJPB27


title: SJPB25


title: Tn-Seq CHAH A

description:
Transposon-genomic DNA junctions amplified from transposon mutant library gDNA
MH_input2_TnOnly_HighConfCounts.wig
AllInput2_TnOnly_HighConfCounts.wig

source_name: Bacterial cells grown on CHAH, resuspended in supplemented Mueller-Hinton broth

value: Sample 1

value: sample taken after growth on CHAH and resuspended in supplemented Mueller-Hinton broth

value: Input library for sample 4

value: all in vitro critical genes, in vitro growth


title: SJPB26


title: PAO1r_phage-6min_rep1

description:
PAO1r4
GP-04


title: SJPB23


title: SJPB24


title: SJPB22


title: SJPB21


title: SJPB20


title: SJPB19


title: SJPB18


title: SJPB17


title: SJPB16


title: SJPB28


title: SJPB15


title: SJPB13


title: SJPB14


title: SJPB12


title: SJPB11


title: SJPB06


title: SJPB08


title: SJPB10


title: SJPB03


title: SJPB07


title: SJPB04


title: SJPB05


title: U3196MG cells

city: Uppsala

first: Sven

last: Nelander

address: Rudbecklab

country: Sweden

institute: Uppsala Universitet

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Expression levels were RMA-normalized employing the Affymetrix Expression Console software.

source_name: U3196MG cells

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA extracted from GC lines using the RNeasy Mini kit (Qiagen) was labeled and hybridized on Affymetrix Human Transcriptome 2.0 arrays.

tag: cell line

value: U3196MG cells


title: U3201MG cells

source_name: U3201MG cells

value: U3201MG cells


title: U3202MG cells A

source_name: U3202MG cells

value: U3202MG cells


title: SJPB01


title: U3198MG cells

source_name: U3198MG cells

value: U3198MG cells


title: U3189MG cells

source_name: U3189MG cells

value: U3189MG cells


title: U3191MG cells

source_name: U3191MG cells

value: U3191MG cells


title: SJPB02


title: U3180MG cells A

source_name: U3180MG cells

value: U3180MG cells


title: U3181MG cells

source_name: U3181MG cells

value: U3181MG cells


title: U3177MG cells

source_name: U3177MG cells

value: U3177MG cells


title: U3185MG cells

source_name: U3185MG cells

value: U3185MG cells


title: U3183MG cells

source_name: U3183MG cells

value: U3183MG cells


title: U3175MG cells

source_name: U3175MG cells

value: U3175MG cells


title: U3173MG cells A

source_name: U3173MG cells

value: U3173MG cells


title: SJPB09

value: pineal parenchymal


title: U3164MG cells A

source_name: U3164MG cells

value: U3164MG cells


title: U3169MG cells A

source_name: U3169MG cells

value: U3169MG cells


title: U3167MG cells A

source_name: U3167MG cells

value: U3167MG cells


title: U3163MG cells

source_name: U3163MG cells

value: U3163MG cells


title: U3165MG cells

source_name: U3165MG cells

value: U3165MG cells


title: U3160MG cells

source_name: U3160MG cells

value: U3160MG cells


title: U3159MG cells

source_name: U3159MG cells

value: U3159MG cells


title: U3172MG cells A

source_name: U3172MG cells

value: U3172MG cells


title: U3149MG cells

source_name: U3149MG cells

value: U3149MG cells


title: U3146MG cells A

source_name: U3146MG cells

value: U3146MG cells


title: U3151MG cells

source_name: U3151MG cells

value: U3151MG cells


title: U3155MG cells

source_name: U3155MG cells

value: U3155MG cells


title: U3140MG cells A

source_name: U3140MG cells

value: U3140MG cells


title: U3137MG cells A

source_name: U3137MG cells

value: U3137MG cells


title: U3139MG cells

source_name: U3139MG cells

value: U3139MG cells


title: U3138MG cells

source_name: U3138MG cells

value: U3138MG cells


title: U3134MG cells B

source_name: U3134MG cells

value: U3134MG cells


title: U3132MG cells C

source_name: U3132MG cells

value: U3132MG cells


title: U3132MG cells B


title: U3134MG cells C


title: U3129MG cells A

source_name: U3129MG cells

value: U3129MG cells


title: U3121MG cells

source_name: U3121MG cells

value: U3121MG cells


title: U3118MG cells

source_name: U3118MG cells

value: U3118MG cells


title: U3115MG cells

source_name: U3115MG cells

value: U3115MG cells


title: U3112MG cells

source_name: U3112MG cells

value: U3112MG cells


title: U3117MG cells

source_name: U3117MG cells

value: U3117MG cells


title: U3110MG cells

source_name: U3110MG cells

value: U3110MG cells


title: U3158MG cells

source_name: U3158MG cells

value: U3158MG cells


title: U3104MG cells

source_name: U3104MG cells

value: U3104MG cells


title: U3102MG cells A

source_name: U3102MG cells

value: U3102MG cells


title: U3106MG cells

source_name: U3106MG cells

value: U3106MG cells


title: U3097MG cells B

source_name: U3097MG cells

value: U3097MG cells


title: U3101MG cells

source_name: U3101MG cells

value: U3101MG cells


title: U3093MG cells

source_name: U3093MG cells

value: U3093MG cells


title: U3097MG cells C


title: U3094MG cells

source_name: U3094MG cells

value: U3094MG cells


title: U3088MG cells

source_name: U3088MG cells

value: U3088MG cells


title: U3091MG cells

source_name: U3091MG cells

value: U3091MG cells


title: U3086MG cells

source_name: U3086MG cells

value: U3086MG cells


title: U3084MG cells

source_name: U3084MG cells

value: U3084MG cells


title: U3073MG cells

source_name: U3073MG cells

value: U3073MG cells


title: U3085MG cells

source_name: U3085MG cells

value: U3085MG cells


title: U3123MG cells A

source_name: U3123MG cells

value: U3123MG cells


title: human Platelets (hPLT-24)

source_name: Healthy Leukopak (American Red Cross) -3

value: whole blood

value: Healthy

value: Platelets


title: U3078MG cells

source_name: U3078MG cells

value: U3078MG cells


title: U3075MG cells

source_name: U3075MG cells

value: U3075MG cells


title: U3070MG cells

source_name: U3070MG cells

value: U3070MG cells


title: U3082MG cells

source_name: U3082MG cells

value: U3082MG cells


title: U3068MG cells

source_name: U3068MG cells

value: U3068MG cells


title: U3067MG cells

source_name: U3067MG cells

value: U3067MG cells


title: U3060MG cells

source_name: U3060MG cells

value: U3060MG cells


title: U3057MG cells

source_name: U3057MG cells

value: U3057MG cells


title: U3062MG cells

source_name: U3062MG cells

value: U3062MG cells


title: U3071MG cells

source_name: U3071MG cells

value: U3071MG cells


title: U3051MG cells

source_name: U3051MG cells

value: U3051MG cells


title: U3096MG cells

source_name: U3096MG cells

value: U3096MG cells


title: U3054MG cells

source_name: U3054MG cells

value: U3054MG cells


title: U3056MG cells

source_name: U3056MG cells

value: U3056MG cells


title: U3047MG cells

source_name: U3047MG cells

value: U3047MG cells


title: U3045MG cells

source_name: U3045MG cells

value: U3045MG cells


title: U3046MG cells

source_name: U3046MG cells

value: U3046MG cells


title: U3042MG cells

source_name: U3042MG cells

value: U3042MG cells


title: U3041MG cells

source_name: U3041MG cells

value: U3041MG cells


title: U3040MG cells C

source_name: U3040MG cells

value: U3040MG cells


title: U3039MG cells

source_name: U3039MG cells

value: U3039MG cells


title: U3053MG cells

source_name: U3053MG cells

value: U3053MG cells


title: U3048MG cells

source_name: U3048MG cells

value: U3048MG cells


title: U3037MG cells

source_name: U3037MG cells

value: U3037MG cells


title: U3040MG cells B


title: U3035MG cells

source_name: U3035MG cells

value: U3035MG cells


title: U3034MG cells

source_name: U3034MG cells

value: U3034MG cells


title: U3033MG cells

source_name: U3033MG cells

value: U3033MG cells


title: U3031MG cells

source_name: U3031MG cells

value: U3031MG cells


title: U3029MG cells

source_name: U3029MG cells

value: U3029MG cells


title: U3028MG cells

source_name: U3028MG cells

value: U3028MG cells


title: U3027MG cells

source_name: U3027MG cells

value: U3027MG cells


title: U3024MG cells

source_name: U3024MG cells

value: U3024MG cells


title: U3019MG cells

source_name: U3019MG cells

value: U3019MG cells


title: U3017MG cells

source_name: U3017MG cells

value: U3017MG cells


title: U3021MG cells

source_name: U3021MG cells

value: U3021MG cells


title: U3065MG cells

source_name: U3065MG cells

value: U3065MG cells


title: U3009MG cells

source_name: U3009MG cells

value: U3009MG cells


title: U3013MG cells

source_name: U3013MG cells

value: U3013MG cells


title: U3008MG cells

source_name: U3008MG cells

value: U3008MG cells


title: U3005MG cells

source_name: U3005MG cells

value: U3005MG cells


title: U3002MG cells

source_name: U3002MG cells

value: U3002MG cells


title: human astrocytes

source_name: human astrocytes

value: human astrocytes


title: U3299MG cells

source_name: U3299MG cells

value: U3299MG cells


title: U3291MG cells

source_name: U3291MG cells

value: U3291MG cells


title: U3289MG cells

source_name: U3289MG cells

value: U3289MG cells


title: U3279MG cells

source_name: U3279MG cells

value: U3279MG cells


title: U3274MG cells

source_name: U3274MG cells

value: U3274MG cells


title: U3275MG cells

source_name: U3275MG cells

value: U3275MG cells


title: U3263MG cells

source_name: U3263MG cells

value: U3263MG cells


title: U3257MG cells

source_name: U3257MG cells

value: U3257MG cells


title: U3265MG cells

source_name: U3265MG cells

value: U3265MG cells


title: U3243MG cells

source_name: U3243MG cells

value: U3243MG cells


title: U3272MG cells

source_name: U3272MG cells

value: U3272MG cells


title: U3245MG cells

source_name: U3245MG cells

value: U3245MG cells


title: U3020MG cells

source_name: U3020MG cells

value: U3020MG cells


title: U3226MG cells

source_name: U3226MG cells

value: U3226MG cells


title: U3220MG cells

source_name: U3220MG cells

value: U3220MG cells


title: U3230MG cells

source_name: U3230MG cells

value: U3230MG cells


title: U3083MG cells

source_name: U3083MG cells

value: U3083MG cells


title: U3235MG cells

source_name: U3235MG cells

value: U3235MG cells


title: U3217MG cells

source_name: U3217MG cells

value: U3217MG cells


title: U3016MG cells

source_name: U3016MG cells

value: U3016MG cells


title: U3212MG cells

source_name: U3212MG cells

value: U3212MG cells


title: U3213MG cells

source_name: U3213MG cells

value: U3213MG cells


title: U3214MG cells

source_name: U3214MG cells

value: U3214MG cells


title: U3206MG cells

source_name: U3206MG cells

value: U3206MG cells


title: U3205MG cells

source_name: U3205MG cells

value: U3205MG cells


title: U3187MG cells

source_name: U3187MG cells

value: U3187MG cells


title: U3281MG cells

source_name: U3281MG cells

value: U3281MG cells


title: U3182MG cells

source_name: U3182MG cells

value: U3182MG cells


title: U3253MG cells

source_name: U3253MG cells

value: U3253MG cells


title: U3180MG cells

source_name: U3180MG cells

value: U3180MG cells


title: U3202MG cells

source_name: U3202MG cells

value: U3202MG cells


title: U3164MG cells

source_name: U3164MG cells

value: U3164MG cells


title: U3167MG cells

source_name: U3167MG cells

value: U3167MG cells


title: U3233MG cells

source_name: U3233MG cells

value: U3233MG cells


title: U3172MG cells

source_name: U3172MG cells

value: U3172MG cells


title: U3242MG cells

source_name: U3242MG cells

value: U3242MG cells


title: U3169MG cells

source_name: U3169MG cells

value: U3169MG cells


title: U3140MG cells

source_name: U3140MG cells

value: U3140MG cells


title: U3123MG cells

source_name: U3123MG cells

value: U3123MG cells


title: U3221MG cells

source_name: U3221MG cells

value: U3221MG cells


title: U3137MG cells

source_name: U3137MG cells

value: U3137MG cells


title: U3173MG cells

source_name: U3173MG cells

value: U3173MG cells


title: U3102MG cells

source_name: U3102MG cells

value: U3102MG cells


title: G1_10A input

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description: MCF10A breast epithelial cells were treated with Nocodazole for 16hrs, media replaced for 3hrs for uniform release of cells from mitotic arrest, harvested, and subjected to RUNX1 ChIP-Seq

data_processing:
Remove adapter reads (Cutadapt v1.6)
Trim low quality base calls from both ends. Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
Align reads with STAR v2.4 to hg38+U13369.1 rDNA*, splicing disabled with '--alignIntronMax 1'.
Call peaks and generate .bdg with MACS2, p-value e-5. (MACS2 v2.1.0.20140616)
Compare treatment bedgraph to input with MACS2 bdgcmp in FE mode.
Convert FE.bdg to bigwig with UCSC's bedGraphToBigWig v4
Refine peaks by individual strand cross-correlation at unshifted (read_corr) and shifted by observed fragment size (180 bp) minus read size (101 bp) (frag_corr). frag_corr of > .7 and frag_corr - read_corr > .1 required.
*Creating custom hg38+U13369.1 rDNA
Download U13369.1 rDNA sequence from GenBank
Align 50bp in-silico reads from U13369.1 to hg38 and generate bed of multi-aligning regions
Add sequence U13369.1 from GenBank to hg38 .fasta.
bedtools maskfasta using multi-aligning regions and modified .fasta to create final .fasta
Genome_build: hg38 plus rDNA as chrU13369.1
Supplementary_files_format_and_content: macs2_peaks_filtered.bed; narrowPeak files with strand cross-correlation metrics added.  Additional columns are read correlation, fragment correlation, and fragment minus read correlation.
Supplementary_files_format_and_content: FE.bw; bigwig of fold-enrichment of pull-down over input containing hg38 chromosomes with the addition of U13369.1 from GenBank as chrU13369.1.

source_name: MCF10A breast epithelial cells

growth_protocol: MCF10A cells were cultured in DMEM/F12 50:50 media, supplemented with 5% horse serum, 10ug/mL human Insulin, 20ng/mL hEGF, 100ng/mL Cholera toxin, 0.5ug/mL Hydrocortisone, 100U/mL Penicillin-Streptomycin, and 2mM L-Glutamine

extract_protocol:
Harvested lysates were fixed in 1% MeOH formaldehyde and sonicated. Following sonication, samples were incubated with RUNX1 ab for ChIP reaction. Ab-DNA complex isolated using Protein A/G beads and magnets. DNA was purified from solution and subject to library construction
ChIP libraries were generated using Accel-NGS® 2S Plus DNA Library kit (Swift Biosciences, Ann Arbor, MI) following manufacturers protocol. Input and RUNX1 ChIP samples were normalized to 1ng prior to library generation. Libraries were amplified in an optional PCR step for 12 total cycles. Finalized libraries were double size selected using AMPure XP beads (0.8X and 0.2X volume ratios to sample), resulting in the majority fragments sized between 250-400bp.

treatment_protocol: DMSO (Asynchronous MCF10A population was treated with DMSO [equal volume as Nocodazole treatment] for 16hr). BLOCKED (Mitotic MCF10A population was treated with Nocodazole 50ng/mL for 16hr). RELEASED (G1 MCF10A population was treated with Nocodazole 50ng/mL for 16hrs and media was replaced with fresh media lacking Nocodazole for 3hrs).

value: Breast epithelium

tag: phenotype

value: normal-like

tag: chip-antibody


title: U3146MG cells

source_name: U3146MG cells

value: U3146MG cells


title: Asynch_10A input

description: MCF10A breast epithelial cells were treated with DMSO for 16hrs, harvested, and subjected to RUNX1 ChIP-Seq

tag: tissue


title: Mitotic_10A input

description: MCF10A breast epithelial cells were treated with Nocodazole for 16hrs, harvested, and subjected to RUNX1 ChIP-Seq


title: Mitotic_10A RUNX1 ChIP

value: Runx1 (CST 4336BF) - Lot #2


title: G1_10A RUNX1 ChIP


title: Asynch_10A RUNX1 ChIP


title: U3179MG cells

source_name: U3179MG cells

value: U3179MG cells


title: U3129MG cells

source_name: U3129MG cells

value: U3129MG cells


title: p10wtE

city: Tucson

first: Martha

last: Bhattacharya

state: AZ

address: 1040 E 4th Street

department: Neuroscience

institute: University of Arizona

data_processing:
Alignment to mouse genome using Salmon (salmon-0.11.1-linux_x86_64) for single end reads.
Trim first column of Salmon output data to contain ENSMUST transcript identifiers. This was done using the Galaxy platform.
Created a file to convert ENSMUST identifiers to GeneID using Galaxy
Normalize count values and idnetify differentially expressed genes using DeSeq2. This was done using the Galaxy Platform.
Export Data and evaluate in R to create visuals.
Genome_build: mm10
Supplementary_files_format_and_content: salmon_outputs.xlsx

source_name: Dorsal Root Ganglia

growth_protocol: DRGs were isolated from mice of the appropriate embryonic or postnatal age. Entire ganglia were included with no dissociation.

extract_protocol:
Total RNA was extracted using Trizol according to the Invitrogen protocol.
250-300bp insert cDNA library

tag: strain

value: Wild type control

value: Dorsal Root Ganglia


title: p10wt1


title: P0mu2

value: C57BL/6 background

value: Tmem184b gene trap homozygous


title: P0wtD


title: p10wtC


title: Vhc2

city: Montreal

first: Hadla

last: Hariri

state: Quebec

address: 1003 Decarie Boulevard, Shriners Hospital For Children

department: Human Genetics

country: Canada

institute: Shriners Hospital for Children, Canada-Montreal, Department of Human Genetics, McGill University, Montreal,Quebec,Canada

description: Extracted by TRIzol method

data_processing:
The Cufflinks program was used to assemble aligned RNA-Seq reads into transcripts and to estimate their abundance (FPKM).
Pair-end reads of 100 base pairs were obtained by Illumina HiSeq 2000 PE100 sequncing.Sequenced reads were trimmed for adaptor sequence and mapped to whole mouse genome mm10.
Illumina TrueSeq RNA adaptor was used.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all samples

source_name: MC3T3-E1 cells

growth_protocol: MC3T3-E1 cells (subclone 4) were mantained in minimumessential medium alpha (αMEM;Invitrogen, Waltham, MAsupplemented with 10% fetal bovine serum (FBS) from HyClone (Logan, UT).

extract_protocol:
Prior to RNA isolation, cells were washed 3 times with cold PBS. RNA was isolated using 1 ml of TRIzol reagent following the manufacturer's instructions(Thermo Fisher Scientific, Mississauga, ON).
RNA-Seq libraries were built with TruSeq Stranded mRNA Library Prep Kit from Illumina following the manufacturer's instructions. Pair-end reads of 100 base pairs were obtained on a HiSeq 2000 sequencing system (Illumina). The Cufflinks program was used to assemble aligned RNA-Seq reads into transcripts and to estimate their abundance (FPKM).

treatment_protocol: Cells were treated with Vehicle or parathyroid hormone PTH(1-34) recombinant protein for 2 h prior to extraction. PTH(1–34) (catalog no. H4835) was purchased from Bachem (Torrance, CA)

value: MC3T3-E1 cells

tag: source

value: Calvaria

value: Osteoblast-like cells

tag: treatment

value: Vehicle, 30min


title: p10mu3


title: PTH2

description: Extracted by TRIzol method


title: p10mu1


title: Vhc1

description: Extracted by TRIzol method


title: P0mu3


title: P0mu4


title: E13mu3


title: E13mu1


title: P0wtB


title: PTH3

description: Extracted by TRIzol method


title: E13WTA


title: P0wtC


title: E13WTB


title: E13WC


title: E13mu2


title: PTH1

description: Extracted by TRIzol method


title: p10mu2


title: WT Striatum male ZT9 miRNA rep5

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
561562_CRM57
561562_CRM57_WT_STRR_26WKS_M_ZT9_L4.LB21
miRNA
processed data file: Striatum-counts.csv

data_processing:
Libraries for miRNA-seq were sequenced using an Illumina HiSeq 2000.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.3a with default parameter settings.
Raw counts were obtained with HTSeq 0.10.0 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Genome_build: Genome version Mouse GRCm38 (mm10)
Supplementary_files_format_and_content: *-counts.csv: Comma-separated text files include count values for each Sample.

source_name: Striatum right hemisphere

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Corpus Striatum

value: Wild type

tag: strain/background

value: 26 weeks

tag: Sex

value: male

tag: zt group

value: 9 hrs


title: WT Striatum male ZT9 miRNA rep9

description:
561694_CR88
561694_CR88_WT_STRR_26WKS_M_ZT9_L7.LB16
miRNA
processed data file: Striatum-counts.csv

tag: genotype

tag: age

value: 33 hrs


title: WT Striatum male ZT9 miRNA rep8

description:
561658_CRM36
561658_CRM36_WT_STRR_26WKS_M_ZT9_L6.LB16
miRNA
processed data file: Striatum-counts.csv

tag: time point


title: WT Striatum male ZT9 miRNA rep6

description:
561589_CRM5
561589_CRM5_WT_STRR_26WKS_M_ZT9_L5.LB12
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT9 miRNA rep4

description:
561545_CRM35
561545_CRM35_WT_STRR_26WKS_M_ZT9_L3.LB4
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT9 miRNA rep2

description:
561522_CRM95
561522_CRM95_WT_STRR_26WKS_M_ZT9_L2.LB17
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT9 miRNA rep7

description:
561641_CRM86
561641_CRM86_WT_STRR_26WKS_M_ZT9_L3.LB34
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 miRNA rep3

description:
561560_CRM97
561560_CRM97_WT_STRR_26WKS_M_ZT6_L4.LB19
miRNA
processed data file: Striatum-counts.csv

value: 6 hrs

value: 30 hrs


title: WT Striatum male ZT21 miRNA rep2

description:
561543_CRM103
561543_CRM103_WT_STRR_26WKS_M_ZT21_L3.LB2
miRNA
processed data file: Striatum-counts.csv

value: 21 hrs


title: WT Striatum male ZT21 miRNA rep3

description:
561582_CRM83
561582_CRM83_WT_STRR_26WKS_M_ZT21_L4.LB5
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 miRNA rep3

description:
561592_CRM3
561592_CRM3_WT_STRR_26WKS_M_ZT3_L5.LB15
miRNA
processed data file: Striatum-counts.csv

value: 3 hrs


title: WT Striatum male ZT3 miRNA rep6

description:
561657_CRM59
561657_CRM59_WT_STRR_26WKS_M_ZT3_L6.LB15
miRNA
processed data file: Striatum-counts.csv

value: 27 hrs


title: WT Striatum male ZT9 miRNA rep1

description:
561520_CRM96
561520_CRM96_WT_STRR_26WKS_M_ZT9_L2.LB15
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 miRNA rep6

description:
561618_CRM34
561618_CRM34_WT_STRR_26WKS_M_ZT6_L3.LB11
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT21 miRNA rep4

description:
561613_CRM73
561613_CRM73_WT_STRR_26WKS_M_ZT21_L2.LB6
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 miRNA rep1

description:
561521_CRM66
561521_CRM66_WT_STRR_26WKS_M_ZT6_L2.LB16
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 miRNA rep4

description:
561616_CRM16
561616_CRM16_WT_STRR_26WKS_M_ZT3_L3.LB9
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT9 miRNA rep3

description:
561529_CRM99
561529_CRM99_WT_STRR_26WKS_M_ZT9_L2.LB24
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT21 miRNA rep5

description:
561698_CRM72
561698_CRM72_WT_STRR_26WKS_M_ZT21_L7.LB20
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 miRNA rep4

description:
561584_CRM93
561584_CRM93_WT_STRR_26WKS_M_ZT6_L5.LB7
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT18 miRNA rep2

description:
561631_CRM76
561631_CRM76_WT_STRR_26WKS_M_ZT18_L3.LB24
miRNA
processed data file: Striatum-counts.csv

value: 18 hrs


title: WT Striatum male ZT6 miRNA rep7

description:
561642_CRM98
561642_CRM98_WT_STRR_26WKS_M_ZT6_L3.LB35
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 miRNA rep1

description:
561513_CRM2
561513_CRM2_WT_STRR_26WKS_M_ZT3_L2.LB8
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 miRNA rep2

description:
561517_CRM62
561517_CRM62_WT_STRR_26WKS_M_ZT3_L2.LB12
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 miRNA rep2

description:
561526_CRM89
561526_CRM89_WT_STRR_26WKS_M_ZT6_L2.LB21
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 miRNA rep8

description:
561664_CRM94
561664_CRM94_WT_STRR_26WKS_M_ZT6_L6.LB22
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 miRNA rep5

description:
561655_CRM112
561655_CRM112_WT_STRR_26WKS_M_ZT3_L6.LB13
miRNA
processed data file: Striatum-counts.csv