title: DTRADQ, No DT, 4

description: dtr_con4.GTCTGAT.run_2891_s_*_withindex_sequence.txt_GTCTGAT

source_name: DTRADQ_No DT


title: DTRADQ, No DT, 2

status: Public on Nov 06 2020

type: SRA

first: Ruteja

middle: A

last: Barve

state: MO

address: 4515 McKinley Ave

department: Genetics

country: USA

institute: Washington University

description: dtr_con2.CGTCGCT.run_2891_s_*_withindex_sequence.txt_CGTCGCT

library_source: transcriptomic

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

molecule: total RNA

organism: Mus musculus

growth_protocol: iDTR mice are cross-mated with adiponectin-Cre tp generate DTRADQ mice

extract_protocol:
Total RNA of femur whole bone marrow were extracted with Trizole and cleaned-up with RNeasy mini kiy (Qiagen)
Clontech SMARTer v1

treatment_protocol: 2 months old DTRADQ mice and their Cre negative littermate control were IP injected with Diphtheria Toxin (100ng/mouse) daily for indicated days

tag: strain background

tag: genotype/variation

value: DTR flox, ADQ Cre+

tag: treatment/time point

value: No DT treatment

tag: tissue

value: whole bone marrow (femur)


title: TS-27 single cell RNA-seq

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
The raw fastq files were aligned to hg19 genome using tophat. The bam file acheived after alignment was used with cuffdiff to calculate FPKM of genes in every cell
Genome_build: hg19
Supplementary_files_format_and_content: Processed data is in text format. The processed data in every cell contains both both read-count and FPKM values for genes

molecule: polyA RNA

organism: Homo sapiens

source_name: Non small Lung cancer cell

growth_protocol: Cells derived from lung cancer patient were grown as Tumor sphere (TS) and maintained in medium with DMEM/F12 (US Biomedical),  4mg/ml Bovine Serum Albumin (Sigma), Non-essential amino acids, sodium pyruvate (Life Technologies) and 20ng/ml Epidermal Growth Factor, 4 ng/ml bovine Fibroblast Growth Factor and Insulin –Transferrin Selenium (Sigma). Tumor sphere derived adherent (Adh) cells were grown in the same media as above, without EGF, bFGF, ITS and BSA.  For Adh cell media was supplemented with 10% fetal bovine serum.

extract_protocol:
The single-cells were captured using C1 96 (large size) IFC using Fluidigm-C1 system. Reverse transcription and cDNA amplification were processed using SMART-seq2 script automatically in C1-Fluidigm machine.
The harvested single cell cDNA was barcoded in 96 well plate using Nextera XT Library Prep kit (Ilumina). Uniquely barcoded libraries from single cells pooled together and sequenced using a HiSeq-Hi-output sequencer (Illumina).

tag: cell type

value: Tumorosphere - TS

tag: sample type

value: Non adherant


title: Conventional TB infection mouse 6

type: RNA

city: Seattle

first: Kevin

last: Urdahl

state: Washington

address: 307 Westlake Ave N #500

department: Global Infectious Disease

institute: Seattle Children's Research Institute

hyb_protocol: standard Agilent protocol

scan_protocol: Agilent Technologies Scanner G2505C US93103711

data_processing: quantile normalized, duplicate probes averaged, log2 transformed

source_name: Whole blood

label_protocol: standard Agilent protocol

extract_protocol: none provided by the submitter

tag: infection group

value: HighDose

tag: day blood taken

tag: day cfu measured

tag: lung log10cfu


title: TS-28 single cell RNA-seq


title: DTRADQ, No DT, 3

description: dtr_con3.TTTTGTC.run_2891_s_*_withindex_sequence.txt_TTTTGTC


title: TS-26 single cell RNA-seq


title: Uninfected control mouse 7

value: Uninfected


title: Uninfected control mouse 6


title: K2

city: Jinan

first: Mei

last: Chen

state: Shandong

address: No.3501,Daxue Road

department: Qilu University of Technology

country: China

institute: Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Penicillium oxalicum 114-2 whole genome using SOAPaligner/SOAP2 v2.21 with parameters -m 0 -x 10000 -s 28 -l 32 -v 3 -p 3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Penicillium oxalicum 114-2 genome (NCBI accession: PRJNA60877)
Supplementary_files_format_and_content: One matrix table in Excel .xlsx format includes GeneID and RPKM values for each sample.

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: Freshly harvested conidia of the wild-type strain or mutants were inoculated with 106 conidia/mL into 100 mL Vogel’s medium that contained 2% glucose, and then grown for 22 hours at 30°C.

extract_protocol:
Total RNA was prepared from the mycelia by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mycelia were harvested via vacuum filtration, and then washed with Vogel’s medium without a carbon source, followed by 2 h growth in 100 mL Vogel’s medium without a carbon source. Subsequently, mycelia were harvested via vacuum filtration, and then transferred into Vogel’s medium that contained 2% cellulose for 4 hours.

tag: strain

tag: genetype


title: Uninfected control mouse 5


title: 114-2-C3

value: wild type


title: 114-2-C1


title: Uninfected control mouse 4


title: K1


title: TS-23 single cell RNA-seq


title: TS-25 single cell RNA-seq


title: Late CFU measument ULD mouse 15

value: Late


title: K3


title: 114-2-C2


title: DTRADQ, No DT, 1

description: dtr_con1.GAGGCGT.run_2891_s_*_withindex_sequence.txt_GAGGCGT


title: TS-22 single cell RNA-seq


title: TS-29 single cell RNA-seq


title: TS-19 single cell RNA-seq


title: Con, No DT, 4

description: wt_con4.TGAGGTT.run_2891_s_*_withindex_sequence.txt_TGAGGTT

source_name: Con_No DT

value: DTR flox, No Cre


title: TS-20 single cell RNA-seq


title: TS-21 single cell RNA-seq


title: TS-18 single cell RNA-seq


title: HBCx-10_AC_37

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: gene expression datas from tumors at the end of the experiment

hyb_protocol: Following fragmentation, 4,7 ug of cDNA were hybridized for 16 hr at 48°C onto Affymetrix Human Gene ST 2.1 array plate.  Array plate was hybridized,  washed and stained using an an Affymetrix Genetitan 4C device.

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

label: biotin

source_name: tumor

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Plus protocol from 100ng total RNA

growth_protocol: PDX models

extract_protocol: Total RNA extraction

value: Breast tumor xenograft

tag: treatment

value: AC chemotherapy

value: Nude mice


title: HBCx-10_DFX+AC_40

scan_protocol: Array plate was hybridized,  washed and stained using an an Affymetrix Genetitan 4C device.

value: iron chelator deferasirox (DFX) and AC chemotherapy


title: Late CFU measument ULD mouse 12


title: HBCx-10_DFX+AC_50


title: Late CFU measument ULD mouse 14


title: HBCx-10_DFX+AC_57


title: Late CFU measument ULD mouse 10


title: HBCx-10_DFX+AC_51


title: Late CFU measument ULD mouse 13


title: Late CFU measument ULD mouse 11


title: HBCx-10_AC_17


title: HBCx-10_AC_32


title: HBCx-10_DFX_47

value: iron chelator deferasirox (DFX)


title: TS-24 single cell RNA-seq


title: Late CFU measument ULD mouse 8


title: HBCx-10_DFX+AC_55


title: TS-17 single cell RNA-seq


title: Late CFU measument ULD mouse 9


title: TS-16 single cell RNA-seq


title: TS-15 single cell RNA-seq


title: HBCx-10_DFX_8


title: Late CFU measument ULD mouse 6


title: HBCx-10_DFX_25


title: HBCx-10_DFX_3


title: HBCx-10_DFX_24


title: HBCx-10_ctrl_13

value: control


title: HBCx-10_ctrl_5


title: HBCx-10_ctrl_58


title: TS-13 single cell RNA-seq


title: Late CFU measument ULD mouse 5


title: Late CFU measument ULD mouse 7


title: Late CFU measument ULD mouse 3


title: TS-11 single cell RNA-seq


title: Late CFU measument ULD mouse 4


title: placenta_normal_rep4

city: Shanghai

first: Lu

last: Gao

address: 800 Xiangyin Rd.

department: Physiology

institute: Second Military Medical University

description: lncRNA expression in human placenta

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Human LncRNA Array V2.0 (8x60, Arraystar) for 17 hours at 65C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325) and 1 minute with 37C Gene Expression Wash buffer 2 (Agilent p/n 5188-5326), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: placenta,normal,replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by purification using RNeasy Mini Kit (Qiagen p/n 74104). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from snap-frozen placenta tissues obtained from preeclampsia placenta patients and control patients using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instruction. The RNA integrity and concentration were evaluated using the NanoDrop ND-1000 spectrophotometer and 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA).

value: placenta

tag: maternal age

tag: diagnosis

value: normal control

tag: gestational age


title: placenta_normal_rep3

description: lncRNA expression in human placenta

source_name: placenta,normal,replicate 3


title: TS-14 single cell RNA-seq


title: TS-12 single cell RNA-seq


title: TS-10 single cell RNA-seq


title: TS-9 single cell RNA-seq


title: TS-8 single cell RNA-seq


title: placenta_preeclampsia_rep3

description: lncRNA expression in human placenta

source_name: placenta,preeclampsia,replicate 3

value: preeclampsia


title: Late CFU measument ULD mouse 2


title: placenta_normal_rep2

description: lncRNA expression in human placenta

source_name: placenta,normal,replicate 2


title: placenta_normal_rep1

description: lncRNA expression in human placenta

source_name: placenta,normal,replicate 1


title: placenta_preeclampsia_rep2

description: lncRNA expression in human placenta

source_name: placenta,preeclampsia,replicate 2


title: Zmat3 knockout 1

city: Stanford

first: Kathryn

last: Bieging-Rolett

state: California

address: CCSR-South, Rm 1240, 269 Campus Drive

department: Radiation Oncology

institute: Stanford University School of Medicine

data_processing:
RNA-seq reads were aligned to the mouse genome (mm10) and analyzed using the public server Galaxy (usegalaxy.org), which employs the STAR aligner.
DESeq2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Excel file contains the normalized counts for each sample

source_name: Mouse embryonic fibroblasts

extract_protocol:
RNA was extracted with na Rneasy Mini kit from QIAGEN.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: We used CRISPR/Cas9 to knockout Zmat3 in Cas9+ E1A;HrasG12V mouse embryonic fibroblasts (MEFs).  The sgRNAs were delivered to the cells using lentivirus.  After selection for Zmat3 or negative control sgRNAs, cells were cultured for 10 days, and then RNA was collected.

tag: genotype

tag: sgrna

value: sgZmat3 52.6

value: embryonic fibroblasts


title: placenta_preeclampsia_rep4

description: lncRNA expression in human placenta

source_name: placenta,preeclampsia,replicate 4


title: Zmat3 knockout 3

value: sgZmat3 54.8


title: TS-7 single cell RNA-seq

value: Tumorosphere - TS

value: Non adherant


title: Conventional TB infection mouse 4

value: HighDose


title: Late CFU measument ULD mouse 1

value: Late


title: Conventional TB infection mouse 5


title: placenta_preeclampsia_rep1

description: lncRNA expression in human placenta

source_name: placenta,preeclampsia,replicate 1


title: Control 2

value: sgNegative control SPA


title: Control 3

value: sgNegative control ACOCA


title: Zmat3 knockout 2

value: sgZmat3 51.5


title: TS-6 single cell RNA-seq


title: Conventional TB infection mouse 2


title: Conventional TB infection mouse 3


title: TS-5 single cell RNA-seq


title: Nko3R

city: Heidelberg

first: Carine

last: Legrand

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

description: long RNA fraction (>200 nt)

data_processing:
Reads were trimmed with a quality cutoff of 30 for each base (corresponding to a confidence level of 99.9%) and aligned using BSMAP (Xi and Li 2009), which allows C-T base modifications without flagging them as mismatches.
We used 3% mismatch rate, and full sequence usage in BSMAP (parameters: -s 12 -v 0.03 -g 0 -w 1000 -S 0 -p 1 -V 1 -I 1 -n 0 -r 2 -u -m 15 -x 1000).
Resulting aligned reads were kept only if their length was 25 nt or more, if they aligned uniquely, and if both forward and reverse pairs were located at the same positions.
Reads containing more than 3 adjacent non-converted cytosines (rRNA and mRNA), or more than 6 adjacent non-converted cytosines (tRNA) were interpreted as non-converted reads resulting from RNA folding or bound proteins and were thus discarded. The presence of Nsun2- and Dnmt2-dependent methylation at C38, C48 and C49 in some tRNAs made it necessary to raise this threshold from 3 to 6 in tRNAs. (2.) Mismatches apart from C/T, occurring consistently at a specific position indicate the existence of a distinct subset of reads (as caused by RNA editing or single-nucleotide polymorphisms). If such a subset additionally correlates with the presence or absence of a converted cytosine, we discarded the mismatched subsets of reads to avoid confounding errors (upon significance of a Fisher exact test between reads with converted cytosines or not, compared to reads with a mismatch or not, Bonferroni-adjustment for multiple testing, significance cutoff ). We permitted an exception for tRNA(Val), which is known to be subject to RNA editing at position 34.
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include  non-conversion ratio at each cytosine

organism: Caenorhabditis elegans

source_name: whole organisms

growth_protocol: C. elegans strains were grown and maintained at 20°C and HB101 strain Escherichia coli was used as food source.

extract_protocol:
RNA extraction was performed according to the TRIsure RNA isolation protocol (Bioline). The nucleic acid concentrations and purity were analyzed on the NanoDrop ND-1000 Spectrophotometer. RNA integrity was measured on a TapeStation 2200 (Agilent). Samples were stored at -80 °C.
RNA was fractionated into <200 nt and >200 nt using a modified mirVana miRNA isolation kit (AM1560) protocol. Briefly, 50 μg of RNA in a volume of 80 μl were mixed with 400 μl of mirVana lysis/binding buffer and 48 μl of mirVana homogenate buffer and incubated for 5 min at room temperature. Next, 1/3 volume (176 μl) of 100% ethanol was added and thoroughly mixed by inversion, and the mixture was incubated for 20 min at room temperature. After addition of 0.8 μg of Glycoblue, the samples were spun down at 2,500 x g for 8 min at 21°C for precipitation of long RNAs. The supernatant containing the short fraction was transferred to a fresh tube and the RNA pellet was washed in 1 ml of cold 75% ethanol before centrifugation at maximum speed for at least 20 min at 4°C. The pellet was finally air-dried and resuspended in DEPC-treated water. For short fraction RNA precipitation, 800 μl of isopropanol were added to the supernatant and the mixture was incubated at -80°C for at least 20 min. Next, 20 μg of Glycoblue were added and the mixture was spun down at maximum speed for at least 20 min at 4°C. The pellet was washed with cold 70% ethanol and air dried before resuspension in DEPC-treated water. Depletion of ribosomal RNA was performed on the short fractions and on half of the long fractions using a Ribo-zero rRNA removal kit (Illumina), according to the supplier’s instructions. The other half of long fractions was processed as Ribo+ samples. RNA was stored at -80°C until the moment of use. The long fractions (with and without rRNA depletion) were further processed with the NEBNext Magnesium RNA Fragmentation Module (NEB), as described in the manual. 3 min of fragmentation at 94°C has been established to lead to a peak at approximately 250 nt, appropriate for the final 100 bp paired-end sequencing. The fragmented RNA was precipitated using ethanol with 20 μg GlycoBlue at -80°C for at least 10 min. Samples were treated with TURBO DNase (Ambion) in a final volume of 20 μl, according to the manufacturer’s instructions. DNase-treated samples were bisulfite-converted using an EZ RNA Methylation Kit (Zymo Research), following the manufacturer’s manual. As a final step before library preparation, a stepwise RNA end repair was carried out using T4 polynucleotide kinase (TaKaRa). A 3′-dephosphorylation and 5′- phosphorylation reaction was performed using T4 PNK enzyme (TaKaRa). The enzyme was removed by phenol-chloroform purification. Library preparation was done using a NEBNext Small RNA Library Prep Set, according to the manufacturer’s protocol. cDNA was amplified with 12 cycles of PCR and purified using the QIAquick PCR Purification Kit (Qiagen). The libraries were size-selected on a 6% polyacrylamide gel. Compatible barcodes were selected, and samples were pooled in equimolar ratios on multiple lanes in an Illumina HiSeq 2000 platform. A 100 bp paired-end sequencing approach was used.
RNA Bisulfite seq

treatment_protocol: The strains of interest (N2 and noNSUN) were grown in 90 mm plates until gravid adult stage, washed 3 times with M9 and pelleted by centrifugation at 2000 rpm for 2 minutes. Gravid adults were resuspended in 4 ml of bleaching solution (final concentration 177 mM NaOH, 177 mM NaOCl solution - free chlorine 4–4.99%) and vortexed vigorously for 7 minutes. Recovered embryos were washed 4 times to remove any traces of bleach and left to hatch in ml of M9 for 24 h at 20°C in a rotating wheel. Synchronised L1 starved larvae were used for RNA extraction. Independent triplicates were obtained from three different generations.

tag: background

value: N2 Bristol

value: Nsun-/-

tag: developmental stage


title: Nko2R

description: long RNA fraction (>200 nt)


title: TS-3 single cell RNA-seq


title: Nko1R

description: long RNA fraction (>200 nt)


title: Group F4 - patient 100

city: Rio de Janeiro

first: Turan

middle: Peter

last: Urmenyi

address: Av Carlos Chagas Filho 373

country: Brazil

institute: Universidade Federal do Rio de Janeiro

data_processing:
The first stage of analysis was performed by the Torrent Suite software version 5.1. After base calling, sequences smaller than 8 bp were discarded.
The sequences were exported in FASTQ format for further analysis using the CLC Genomics Workbench software version 8.5.
The transcripts were trimmed - so that only those between 15 bp and 30 bp in size were kept, compatible with mature miRNAs-, and then annotated by comparing sequence similarity to miRBASE
After identification of mature miRNAs, differential expression analysis of miRNAs between the mild fibrosis and cirrhosis groups was performed using Empirical Analysis of Differential Gene Expression (EDGE), considering significant transcripts that varied at least twice (fold-change ≥ 2 and ≤ ������ 2), with pvalue ≤ 0.05, present in at least two of the samples from each sample group
To verify the potential target genes regulated by the differentially expressed miRNAs identified between the two groups studied, the miRnet tool version 2.0 was applied to identify the regulatory networks in which the miRNAs are involved
Supplementary_files_format_and_content: Tab-delimited text files with normalized counts and miR regions for each sample
Supplementary_files_format_and_content: Tab-delimited text file containing raw gene counts for every gene and every sample

source_name: Human serum

extract_protocol:
Small RNA isolated from 200 μl of serum using silica column filtration and the miRNeasy Serum/Plasma Kit isolation kit
Library preparation for sequencing was performed using the Total Ion RNA-Seq kit v2, the Ion Xpress RNA - Seq Barcode 01–16 kit, and the Magnetic Bead Clean Up Module according to the manufacturer’s instructions

tag: Sex

value: Male

tag: age

tag: hcv genotype

tag: degree of fibrosis

tag: treatment outcome peg-ifn + rbv

value: sustained viral responder

tag: follow up (years)

tag: degree of fibrosis/chc at the end of follow up

value: hepatocellular carcinoma


title: TS-4 single cell RNA-seq

tag: cell type

tag: sample type


title: TS-2 single cell RNA-seq


title: Nko3L

description: long RNA fraction (>200 nt) Ribo-


title: Control 1

value: sgNegative control EV


title: Conventional TB infection mouse 1

tag: infection group

tag: day blood taken

tag: lung log10cfu


title: ETMR1_case_#9

type: genomic

city: Vienna

first: Johannes

last: Gojo

address: Währinger Gürtel 18-20

department: Department of Pediatrics and Adolescent Medicine

country: Austria

institute: Medical University of Vienna

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

source_name: human tumor

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a ReliaPrep gDNA Tissue Miniprep System (Promega, Madison, Wisconsin, USA) after milling of the frozen sample in a Precellys 24 Lyse & homogenization system (Bertin Technologies, Montigny-le-Bretonneux, France).

tag: tissue preparation

value: Frozen

tag: tumor subgroup

value: ETMR


title: Group F4 - patient 77

value: Female


title: Uninfected control mouse 3

value: Uninfected


title: Uninfected control mouse 1


title: Group F4 - patient 48

value: non-responder


title: Uninfected control mouse 2


title: Nko2L

description: long RNA fraction (>200 nt) Ribo-

tag: genotype


title: ETMR1_case_#8


title: Mouse 4 Cheek Wound [M4CW]

city: London

first: Tanya

middle: J

last: Shaw

address: Guy's Campus, New Hunt's House, Great Maze Pond

department: Centre for Inflammation Biology & Cancer Immunology

country: United Kingdom

institute: King's College London

data_processing:
Sequencing Reads Filtering: Removed low quality reads (more than 20% of the bases qualities are lower  than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to  get the clean reads. Used BGI internal software SOAPnuke versions v1.5.2, parameters: -l 15 -q 0.4 -n 0.01 -A 0.25, website: https://github.com/BGI-flexlab/SOAPnuke
Mapping: HISAT2 (version v2.0.4) was used to map clean reads onto reference genome mm10 (parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Gene Expression Analysis: Clean reads were mapped to reference using Bowtie2 (v2.2.5), and then calculate gene  expression level with RSEM (v1.2.12).
Differentially expressed genes (DEGs): DEGs were identified with DEseq2.DEseq2 is based on the negative binomial  distribution, performed as described at Love, M. I., Huber, W. & Anders, S. Genome Biol. 15, 550  (2014).
Genome_build: mm10
Supplementary_files_format_and_content: Format: tab-delimited text; Content: Rows=genes, Columns=GeneID, TranscriptID, Symbol, Description, and all 24 Samples
Supplementary_files_format_and_content: Format: tab-delimited text; Content: Rows=genes, Columns=9 pair-wise comparisons [log2 fold change (left column) and adjusted pvalue (right column)]

source_name: Cheek Skin Wound

growth_protocol: All experiments were conducted according to UK Home Office regulations. CD1 mice from an in-house colony were maintained with free access to food and water and a 12h light-dark cycle.

extract_protocol:
Whole tissue (flash frozen in liquid nitrogen upon harvest) was first homogenised in lysis buffer with the help of a QIAshredder. Total RNA was then extracted from whole tissue using a Qiagen RNeasy Total RNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols (performed by BGI)

treatment_protocol: For wound experiments, age-matched mice (7 weeks, coordinated in telogen) were anaesthetised and provided analgesic, and then shaved and subjected to one (cheek) or two (abdomen/back) 2mm (diameter)-thickness excisional wounds at a single site. After 3 days, mice were sacrificed and wound (or adjacent healthy control) tissue was collected using a 2mm punch biopsy.

tag: strain

tag: tissue

value: Skin

tag: anatomical site

value: Cheek

tag: treatment

value: Wound


title: TS-1 single cell RNA-seq

source_name: Non small Lung cancer cell

value: Tumorosphere - TS

value: Non adherant


title: ETMR1_case_#5


title: Mouse 4 Cheek Control [M4CC]

source_name: Cheek Skin Control

value: Control


title: Nko1L

description: long RNA fraction (>200 nt) Ribo-

tag: background

value: N2 Bristol

tag: developmental stage


title: ETMR1_case_#4


title: ETMR1_case_#1


title: ETMR1_case_#3


title: MS 4883 D

city: San Juan

first: Carmen

middle: Lydia

last: Cadilla

state: PR

address: University of Puerto Rico Medical Sciences Campus, Area of Medical Center

department: Biochemistry

country: Puerto Rico

institute: University of Puerto Rico School of Medicine

hyb_protocol: Hybridization of labeled cDNAs was caried out with the Hybridization, wash and stain kit, as recommended by the manufacturer

scan_protocol: We used the AGCC software to scan the arrays.

data_processing: The TAC 4.0 software was used to analyze the .CEL files and generate the .CHP files. We used Gene level - Core: RMA-sketch.

source_name: lymphoblastoid cells

label_protocol: After the reduction of rRNA step was carried out using the RiboMinusTM Human/Mouse Transcriptome Isolation Kit from Invitrogen, the GeneChip WT Sense Target Labeling Assay was used to carry out the cDNA synthesis and amplification steps and the WT Terminal labeling kit for labeling, as recommended by the manufacturer.

growth_protocol: Cells were grown in RPMI 1640 media supplemented with 10% fetal bovine serum and L-glutamine

extract_protocol: total RNA was extracted from exponentially growing cells using the Qiagen RNAEasy kit. Each sample represents cells from a different passage.

tag: disease state

value: Setleis Syndrome

value: TWIST2 Q119X

value: lymphoblastoid cells


title: Nko1S

description: small RNA fraction (<200 nt) Ribo-

value: Nsun-/-


title: ETMR1_case_#7


title: ETMR1_case_#2


title: ETMR1_case_#6


title: Group F1/F2 - patient 73

tag: Sex

value: Male

tag: age

tag: hcv genotype

tag: degree of fibrosis

tag: treatment outcome peg-ifn + rbv

tag: follow up (years)


title: Group F1/F2 - patient 57

tag: degree of fibrosis/chc at the end of follow up


title: Mouse 4 Back Wound [M4BW]

source_name: Back Skin Wound

value: Back


title: Mouse 4 Back Control [M4BC]

source_name: Back Skin Control


title: Group F4 - patient 22

value: hepatocellular carcinoma


title: wt3R

description: long RNA fraction (>200 nt)

value: wild type


title: Nko2S

description: small RNA fraction (<200 nt) Ribo-


title: wt1R

description: long RNA fraction (>200 nt)


title: MS 4883 C

tag: cell type


title: Group F1/F2 - patient 15

value: relapser


title: MS 4883 A


title: wt3L

description: long RNA fraction (>200 nt) Ribo-


title: K1_static [FL_static_S4]

city: HELSINKI

first: Emmi

last: Helle

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
FastQ data quality analysis (FastQC)
Analysis summarization with MultiQC
Light quality trimming with Trimmomatic
Alignment of the sample reads against the human gencode Release 30 (GRCh38.p12) reference with STAR, Spliced Transcripts Alignment to a Reference
Mapping quality assessment with Qualimap
Read quantification (featureCounts)
Differential expression incl.normalization (DESeq2)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Csv: DSeq2 normalized counts / sample

growth_protocol: The cells were grown in either static cell culture conditions (static) or in laminar 15 dyn flow for 24 hours (flow)

extract_protocol:
Total RNA from the lysed cells was extracted with Nucleospin RNA II Kit (Macherey-Nagel).
NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to generate cDNA libraries for next generation sequencing.

value: iPS-derived endothelial cells (iPS-EC)

tag: culture condition

value: static


title: Group F1/F2 - patient 17

value: non-responder


title: Mouse 4 Abdomen Control [M4AC]

source_name: Abdomen Skin Control

value: Skin

value: Abdomen


title: Mouse 3 Cheek Wound [M3CW]

value: Cheek

value: Wound


title: wt2R

description: long RNA fraction (>200 nt)

value: N2 Bristol

tag: genotype


title: MS4881 A

value: control


title: K1_flow [FL_flow_S12]

value: in laminar 15 dyn flow for 24 hours (flow)


title: Mouse 3 Cheek Control [M3CC]

tag: strain

value: Control


title: MS4881 J

value: lymphoblastoid cells


title: Mouse 4 Abdomen Wound [M4AW]

source_name: Abdomen Skin Wound

tag: tissue


title: wt2L

description: long RNA fraction (>200 nt) Ribo-


title: wt1L

description: long RNA fraction (>200 nt) Ribo-


title: MS4881 E


title: HEL24_3_flow [FF_flow_S11]


title: Mouse 3 Back Wound [M3BW]

tag: anatomical site


title: Nko3S

description: small RNA fraction (<200 nt) Ribo-

value: Nsun-/-


title: HEL24_3_static [FF_static_S3]


title: HEL47_2_static [EC_static_S2]


title: Mouse 3 Back Control [M3BC]

value: Back

tag: treatment


title: wt3S

description: small RNA fraction (<200 nt) Ribo-

tag: background


title: Mouse 3 Abdomen Wound [M3AW]


title: Mouse 3 Abdomen Control [M3AC]


title: HEL47_2_flow [EC_flow_S10]


title: HEL46.11_static [DZ_static_S1]


title: wt1S

description: small RNA fraction (<200 nt) Ribo-

tag: developmental stage


title: wt2S

description: small RNA fraction (<200 nt) Ribo-


title: HEL46.11_flow [DZ_flow_S9]


title: Mouse 2 Cheek Control [M2CC]


title: 48h NHEK cells transfected with miR-378 inhibitor transfection 3

city: Bangkok

first: Pattarin

last: TANGTANATAKUL

state: กรุงเทพมหานคร

address: Thoethai Road

country: Thailand

institute: Chulalongkorn University

data_processing:
The quality control of the sequenced raw reads was analyzed.
low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed
Trimmed reads are mapped to reference genome (UCSC hg19) with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads.
Gene differential expression analysis was performed with edgeR Bioconductor statistical library version 3.81,2 on RStudio.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Primary Human keratinocytes cells

growth_protocol: Normal human epidermal keratinocyte (NHEK; ATCC® PCS-200-010™) was purchased from ATCC. NHEK was maintained in Dermal Cell Basal Medium supplemented with keratinocyte growth kit (ATCC; 0.4% bovine pituitary extract (BPE), 0.5 ng/mL rh TGF-a, 6 mM L-glutamine, 100 ng/ml hydrocortisone hemisuccinate, 5 mg/ml rh insulin, 1.0 mM epinephrine, 5 mg/ml apo-transferrin, 33 µM phenol red and penicillin-streptomycin-amphotericin B Solution) and was incubated at 37 ºC in humidified incubator containing 5% CO2. NHEK (passage 3) was seeded at 5 x 104 cells per well of a 12-well plate for 6 hours and then were transiently transfected with 100 nM mirVana® miRNA hsa-miR-378a-3p mimic (MC10049), mirVana® miRNA negative control mimic (4464058), 100 nM mirVana® miRNA hsa-miR-378a-3p inhibitor (MH11360) or mirVana® miRNA negative control inhibitor (4464076). Transient transfections were performed using Lipofectamine RNAi Max Reagent according to the manufacturer’s instructions (Invitrogen).

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Ambion) in accordance with the manufacturer’s instruction.
Libraries for high throughput sequencing were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit. The cDNA was checked for quality and quantity on an Agilent 2100 Bioanalyzer. Libraries sequencing was carried on using NovaSeq 6000 System (Illumina Inc., San Diego, CA, USA) with 100 bp paired-end reads.

treatment_protocol: The keratinocytes were transfected with either miR-378a mimic or miR-378a inhibitor at 24 and 48 hours.

value: Normal human epidermal keratinocyte

tag: treatment duration

value: 48 hours

value: miR-378 inhibitor transfection

tag: group

value: test


title: 48h NHEK cells transfected with miR-378 inhibitor transfection 2

state: กรุงเทพมหานคร


title: Mouse 2 Back Wound [M2BW]


title: 48h NHEK cells transfected with miR-378 inhibitor transfection 1

state: กรุงเทพมหานคร


title: SET-2 OTX P/R BRD4 ChIP Seq

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

library_source: genomic

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ChIP-Seq reads were mapped to the human genome build UCSC hg19 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq tracks represented normalized to reads per million mapped in WIG and TDF format

source_name: Drug resistant sAML cell line

growth_protocol: HEL92.1.7, HEL-OTX P/R, SET-2 and SET-2-OTX P/R cells were cultured in 20% FBS containing RPMI1640 media.

extract_protocol:
sAML cells (10 million) were treated with 1% formaldehyde for 10 minutes with rotation. The crosslinking reaction was quenched with 2.5 M Glycine for 5 minutes. Chromatin lysates were clarified from ultra-sonicated nuclei and histone-DNA complexes or BRD4-containing complexes were isolated with H3K27Ac or BRD4 antibody, respectively. Following ChIP washes, the  immunoprecipitated DNA fragments were treated with mutant Tn5 transposase for 10 minutes at 37°C to attach sequencing adapters to the DNA. Tagmented DNA was eluted and formaldehyde-induced crosslinks were reversed. Tagmented, eluted DNA was purified over a column and utilized for library preparation.
Libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Library Prep Kit (Cat. No. FC-121-1030). After adapter ligation, DNA was PCR amplified with Illumina universal primer for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated utilizing AMP-XP beads. The purified DNA was captured on an Illumina NExt-Seq 500 flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

tag: cell line

value: leukemia blast cells

tag: phenotype

value: Drug resistant sAML cell line

tag: chip antibody

value: BRD4 rabbit monoclonal [ clone BL-149-2H5] (Bethyl Labs)  catalog #A700-004


title: epididyme_52ans_section8-replicat 3

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation. After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files. Microarray hybridization was carried out at the Microarrays Facility of the Research Center of Laval University CRCHUL.

data_processing: Background subtraction and normalization of probe set intensities were performed using the method of Robust Multiarray Analysis (RMA) described by Irizarry et al. (Irizarry et al, 2003).

label: Biotin

source_name: Cauda segment

label_protocol: For each sample, 400 ng of total RNA were labeled with the FlashTag Biotin HSR Labeling Kit (Affimetrix, Santa Clara, USA). Microarray analyses were carried out using an Affymetrix GeneChip Human Clariom S array (Affymetrix, CA, USA).

extract_protocol: Total RNA was isolated from each segment of caput, corpus and the cauda epididymal regions of human epidydimis from 3 healthy patients. Frozen tissues were powdered with a pestle and mortar on dry ice, and homogenized in RLT lysis buffer (Qiagen). RNA was purified with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol, and potential genomic DNA contamination was eliminated with the RNase-free DNase set (Qiagen). Total RNA was eluted in RNAse-free water and its concentration was quantified with a NanoDrop 1000 microvolume spectrophotometer (Thermo Scientific). RNA quality was assessed with the Agilent RNA 6000 pico and Agilent RNA nano kits on a 2100 Bioanalyzer from the transcriptomic Core facility of the CHUQ (Agilent). Samples were stored at −80°C until use.

value: Cauda segment

tag: donor number

tag: donor age


title: epididyme_52ans_section7-replicat 3

source_name: Corpus segment

value: Corpus segment


title: epididyme_52ans_section4-replicat 3

source_name: Caput proximal segment

value: Caput proximal segment


title: epididyme_52ans_section5-replicat 3

source_name: Caput intermediate segment

value: Caput intermediate segment


title: epididyme_52ans_section6-replicat 3

source_name: Caput distal segment

value: Caput distal segment


title: 48h NHEK cells transfected with microRNA inhibitor control 3

state: กรุงเทพมหานคร

value: miRNA inhibitor control transfection

value: controls


title: epididyme_52ans_section3-replicat 3

source_name: Efferent duct distal segment

value: Efferent duct distal segment


title: epididyme_52ans_section2-replicat 3

source_name: Efferent duct intermediate segment

value: Efferent duct intermediate segment


title: Mouse 2 Back Control [M2BC]

value: Skin

value: Back

value: Control


title: SET-2 BRD4 ChIP Seq

source_name: sAML cultured cell line

value: sAML cultured cell line


title: 48h NHEK cells transfected with microRNA inhibitor control 2

state: กรุงเทพมหานคร

value: Normal human epidermal keratinocyte

value: 48 hours


title: epididyme_52ans_section1-replicat 3

source_name: Efferent duct proximal segment

value: Efferent duct proximal segment


title: Mouse 2 Abdomen Wound [M2AW]

value: Abdomen

value: Wound


title: SET-2-OTX P/R input DNA

value: leukemia blast cells

value: Drug resistant sAML cell line


title: Mouse 2 Cheek Wound [M2CW]

source_name: Cheek Skin Wound

value: Cheek


title: 48h NHEK cells transfected with miR-378 mimic transfection 3

state: กรุงเทพมหานคร

value: miR-378 mimic transfection

value: test


title: 48h NHEK cells transfected with microRNA inhibitor control 1

state: กรุงเทพมหานคร

value: miRNA inhibitor control transfection

value: controls


title: Mouse 2 Abdomen Control [M2AC]


title: epididyme_50ans_section8-replicat 2

value: Cauda segment


title: 48h NHEK cells transfected with miR-378 mimic transfection 2

state: กรุงเทพมหานคร


title: SET2 parental H3K27Ac ChIP Seq

value: H3K27Ac (Active Motif) RRID:AB_2793305


title: Mouse 1 Cheek Wound [M1CW]

value: Skin


title: epididyme_50ans_section7-replicat 2

value: Corpus segment


title: epididyme_50ans_section6-replicat 2

value: Caput distal segment


title: 48h NHEK cells transfected with miR-378 mimic transfection 1

state: กรุงเทพมหานคร

value: Normal human epidermal keratinocyte


title: HEL OTX P/R H3K27Ac ChIP Seq


title: epididyme_50ans_section5-replicat 2

value: Caput intermediate segment


title: 48h NHEK cells transfected with microRNA mimic control 3

state: กรุงเทพมหานคร

value: 48 hours

value: miRNA mimic controls transfection


title: Mouse 1 Back Wound [M1BW]

value: Back

value: Wound


title: Mouse 1 Abdomen Wound [M1AW]

value: Abdomen


title: 48h NHEK cells transfected with microRNA mimic control 2

state: กรุงเทพมหานคร


title: HEL92.1.7 parental input DNA

value: leukemia blast cells

value: sAML cultured cell line


title: HEL92.1.7 parental H3K27Ac ChIP Seq


title: SET-2-OTX P/R H3K27Ac ChIP Seq

value: Drug resistant sAML cell line


title: Mouse 1 Abdomen Control [M1AC]

value: Control


title: epididyme_50ans_section2-replicat 2

value: Efferent duct intermediate segment


title: epididyme_50ans_section3-replicat 2

value: Efferent duct distal segment


title: epididyme_50ans_section1-replicat 2

value: Efferent duct proximal segment


title: Mouse 1 Cheek Control [M1CC]

source_name: Cheek Skin Control

value: Skin

value: Cheek


title: Control-B4

first: Bin

last: Zhou

state: Shanghai

address: No.150, Jimo Road, Pudong

department: Vascular Surgery

institute: Shanghai East Hospital affiliated to Tongji University School of Medicine

description:
level of C3
4B

data_processing:
The raw sequencing data was used to filter low quality reads and short reads (<15 nt).
All small RNA clean reads were aligned to the miRBase database (http://www.mirbase.org/).
Unmapped reads with miRBase database were aligned to Genomic tRNA database (http://gtrnadb.ucsc.edu/) before  they were aligned to tRFdb (http://genome.bioch.virginia.edu/trfdb/) and MintBase.
Ultimately, tRFs were obtained by mapping of these databases. Unmapped reads with Genomic tRNA database were aligned to other corresponding databases of small RNA (piRNA, small nuclear RNA, small nucleolar RNA etc.).
The tRFs whose expression was significantly different between VVs patients and healthy controls were selected by criterion (Log2FC>1 or <-1, FDR<0.05) using EBSeq.
Genome_build: As Human NCBI genome build 36
Supplementary_files_format_and_content: tab-delimited text files include Read count for each Sample.

source_name: Human veins

extract_protocol:
Total RNA was isolated from vascular tissue with Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Small RNA (135-170bp) were obtained by standard denaturing by 1% agarose gel electrophoresis. Purified small RNA was then sent to Yingbio (Shanghai, China) for construction of small RNA libraries using NEBNext® Multiplex Small RNA Library Prep Kit (NEB #E7560S) and for small RNA sequencing analysis
The total RNA was removed from rRNA. Thereafter, cDNA constructs were created using RT-PCR. Next, the dA-tailing reagent was added and 3’- and 5’- adapters were purified. Finally, RNA libraries were sequenced on an Illumina NextSeq 500.

treatment_protocol: Primary VVs were obtained from patients who underwent open surgery or endovenous treatment

tag: diagnosis

value: Normal Veins

value: veins

tag: tissue source


title: 24h NHEK cells transfected with miR-378 inhibitor transfection 2

state: กรุงเทพมหานคร

tag: cell type

value: Normal human epidermal keratinocyte

value: 24 hours

value: miR-378 inhibitor transfection

value: test


title: HEL OTX P/R input DNA


title: 24h NHEK cells transfected with miR-378 inhibitor transfection 3

state: กรุงเทพมหานคร


title: BS18

city: Planegg-Martinsried

first: Nikolaos

last: Papaioannou

address: Großhaderner Straße 9

institute: Biomedical Center

data_processing:
Sequencing reads were aligned to mm10 mouse genome using STAR
Gene expression in transcripts per kilobase million (TPM) was calculated with RSEM
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file  contains TPM values for each sample

source_name: spleen

extract_protocol:
RNA isolation with PicoPure Kit according to protocol. Cells were sorted directly in lysis buffer supplied with the kit
cDNA creation with SMARTseq v4 Kit (Takara), library creation with MicroPlex Library Preparation Kit v2 (Diagenode)

value: spleen

tag: age

value: 8 weeks

tag: genotype

value: Clec9a-Cre/Cre Rosa-tdTomato/tdTomato

tag: celltype

value: TOM+ cDC2

tag: sorting strategy

value: Live Single Autofluorescence- MHCII+ CD11c+ CD11b+ TOM+


title: Mouse 1 Back Control [M1BC]

source_name: Back Skin Control

tag: strain

tag: tissue

tag: anatomical site

value: Back

tag: treatment

value: Control


title: epididyme_50ans_section4-replicat 2

value: Caput proximal segment


title: 24h NHEK cells transfected with miR-378 inhibitor transfection 1

state: กรุงเทพมหานคร

tag: treatment duration

tag: group


title: Control-B3

description:
level of C4b
3B

value: underwent open surgery or endovenous treatment


title: SET2 parental input DNA

tag: cell line

value: leukemia blast cells

tag: phenotype

value: sAML cultured cell line


title: BS17


title: Control-B2

description:
level of C4b
2B

value: Normal Veins


title: 48h NHEK cells transfected with microRNA mimic control 1

state: กรุงเทพมหานคร

value: 48 hours

value: miRNA mimic controls transfection

value: controls


title: BS16

value: 9 weeks


title: 24h NHEK cells transfected with microRNA inhibitor control 3

state: กรุงเทพมหานคร

value: Normal human epidermal keratinocyte

value: 24 hours

value: miRNA inhibitor control transfection


title: Control-B1

description:
level of C4a
1B

value: Varicose veins

value: veins


title: BS15

value: spleen

value: postnatal day 8

value: Clec9a-Cre/Cre Rosa-tdTomato/tdTomato

value: TOM- DC2

value: Live Single Autofluorescence- MHCII+ CD11c+ CD11b+ TOM-


title: epididyme_37ans_section7-replicat 1

value: Corpus segment

tag: donor number


title: epididyme_37ans_section6-replicat 1

value: Caput distal segment

tag: donor age


title: epididyme_37ans_section5-replicat 1

value: Caput intermediate segment


title: Case-A4

description:
level of C3
4A

tag: diagnosis

value: underwent open surgery or endovenous treatment


title: epididyme_37ans_section8-replicat 1

value: Cauda segment


title: 24h NHEK cells transfected with microRNA inhibitor control 2

state: กรุงเทพมหานคร

value: controls


title: 24h NHEK cells transfected with microRNA inhibitor control 1

state: กรุงเทพมหานคร


title: BS13


title: epididyme_37ans_section3-replicat 1

value: Efferent duct distal segment


title: Case-A3

description:
level of C4b
3A

tag: tissue source


title: BS11


title: Case-A2

description:
level of C4b
2A


title: BS14

value: TOM+ cDC2

value: Live Single Autofluorescence- MHCII+ CD11c+ CD11b+ TOM+


title: 24h NHEK cells transfected with miR-378 mimic transfection 3

state: กรุงเทพมหานคร

tag: cell type

value: Normal human epidermal keratinocyte

value: 24 hours

value: miR-378 mimic transfection

value: test


title: 24h NHEK cells transfected with miR-378 mimic transfection 2

state: กรุงเทพมหานคร


title: BS12

value: spleen

tag: age

value: postnatal day 8


title: Case-A1

description:
level of C4a
1A

value: Varicose veins

value: veins


title: 24h NHEK cells transfected with miR-378 mimic transfection 1

state: กรุงเทพมหานคร


title: sRNA-Dep-2 [D2]

city: Nanjing

first: Zhen

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

data_processing:
RNA-sequencing reads were aligned to the mouse genome GRChM38 (mm10) using HISAT2 (Kim et al., 2015). The gene expression profile was generated by Cufflinks 2.2.1 (Trapnell et al., 2010). Low and non-expressed genes with less than an average of 10 fragments per kilobase of exon model per million mapped reads (FPKM) in all samples were omitted from the analysis.
Differential analysis was performed using Student’s t test. Significance was set at an uncorrected p < 0.05 for broad pattern identification. A fold-change threshold was set at > 1.3. Heatmaps were generated using pheatmap R package and GO analysis was performed using DAVID Bioinformatics Resource 6.8 (Huang et al., 2009a, b).
Genome_build: GRChM38 (mm10)
Supplementary_files_format_and_content: processed_data.csv

source_name: A single blastocyst-stage embryo_Dep

extract_protocol:
The collected single blastocyst-stage embryos (E3.5) were lysed to release all RNAs, which were then reverse transcribed into first strands cDNA using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Clontech, Mountain View, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: E3.5 day

tag: genotype/tissue

value: Blastocyst-stage embryo from zygotes which were injected with sperm sRNAs from depressive male mice


title: I3hG17012(I3)

city: Xi'an

first: Qiang

last: Lyu

address: No169 Changle Road

department: Department of Aerospace Physiology

institute: Fourth Military Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: Expression_Transcript.xlsx

organism: Rattus norvegicus

source_name: lung

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: SD

value: lung

tag: developmental stage

value: adult


title: I3hG17011(I3)

tag: strain


title: epididyme_37ans_section2-replicat 1

tag: tissue

value: Efferent duct intermediate segment


title: I3hG17013(I3)


title: NP_scRNAseq

data_processing:
Sequencing reads were mapped to the mouse genome (mm10) using STAR after spiking in the sequences of iCRE (GenBank iD: AY056050.1), the predicted transcript of the unrecombined Rosa locus and Tomato sequence (GenBank ID: AY678269.1).
Cell Ranger’s count pipeline was run under default parameters. The output of Cell Ranger’s count pipeline was a gene-barcode matrix consisting of approximately 1,788 cellular barcodes with 179,245 mean reads per barcode.
This matrix was inserted to the R (Version 3.5.3) software package Seurat (v3.0.2)83,84 for all downstream analyses.
Cells expressing less than 200 genes, having more than 7.5% of mitochondrial associated genes and genes detected in less than 3 cells were removed from further analysis according to the software suggestions. In addition, cells were scored based on their cell cycle score and the differences between G2M and S phase cells were regressed.
The SCtransform package was used to normalize, scale and find the variable features of the dataset before principal component (PC) analysis. Genes associated with the top 40 PCs were used for graph-based cluster identification (resolution 1.3) and subsequent dimensionality reduction using Uniform Manifold Approximation and Projection (UMAP).
Genome_build: mm10
Supplementary_files_format_and_content: filtered_feature_RNAseq_matrix.txt file contaimns the matrix used to construct the initial Seurat object for all downstream analyses

extract_protocol:
After sorting, cells were counted and resuspended at a concentration of 1000 cells/uL. Samples were processed for single-cell encapsulation and cDNA library generation using the Chromium Single Cell 3’ v3 Reagent Kits
Library construction was performed according to the manufacturer's protocol
scRNAseq using the 10x genomics technology. The constructed library was sequenced on an Illumina HiSeq1500 (Rapid Run) sequencer with 28 (read 1) + 91(read 2) base pair paired-end reads and a sequencing depth of 320 million reads in total

value: postnatal day 9

tag: genotype

value: Clec9a-Cre/Cre Rosa-tdTomato/tdTomato

value: MHCII+ cells

tag: sorting strategy

value: Live Single Autofluorescence- CD19-MHCII+


title: BS10

tag: celltype

value: TOM+ cDC2

value: Live Single Autofluorescence- MHCII+ CD11c+ CD11b+ TOM+


title: 24h NHEK cells transfected with microRNA mimic control 3

state: กรุงเทพมหานคร

source_name: Primary Human keratinocytes cells

value: Normal human epidermal keratinocyte

tag: treatment duration

value: 24 hours

tag: treatment

value: miRNA mimic controls transfection

tag: group

value: controls


title: 24h NHEK cells transfected with microRNA mimic control 2

state: กรุงเทพมหานคร


title: sRNA-Dep-1 [D1]


title: Intervention DY131-treatment 3

first: Ma

last: Yang

address: No. 140 Hanzhong Rd

institute: Department of Nephrology

data_processing:
Sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s protocol.
The quality of the constructed libraries was assessed on the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).
Qualified libraries were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
The raw reads were processed under quality control before they were aligned to the reference genome using Hisat2 v2.0.5.
The gene expression was measured in units of fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: all_compare.txt reports counts, fpkms, DEGs in all three groups

source_name: liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Intervention group refers to mice pretreated with DY131 before LPS challenge.

value: liver

value: 8-9 weeks

value: Intervention DY131


title: C3hG17013(C3)

value: SD


title: 24h NHEK cells transfected with microRNA mimic control 1

state: กรุงเทพมหานคร


title: C3hG17012(C3)

value: lung


title: epididyme_37ans_section4-replicat 1

value: Caput proximal segment

tag: donor number


title: Intervention DY131-treatment 2


title: cc03-20mock2

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
Raw reads were aligned using Star aligner 2.6.1 (8)/RSEM 1.2.28
Genome_build: using a custom human GRCh38  transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein  5 coding and long non-coding RNA genes based on human GENCODE version 33 annotation with  SARS-Cov2 virus genome MT246667.1 https://www.ncbi.nlm.nih.gov/nuccore/MT246667.1.
Supplementary_files_format_and_content: count and TPM

source_name: Organoid

extract_protocol:
Total RNA was extracted from mock and SARS-CoV-2 infected alveolar organoid cultures lysed in Trizol (Thermo Fisher Scientific) using the chloroform-iso-propanolethanol method.
Library construction was performed by the Cedars-Sinai Applied Genomics, Computation and Translational Core using the Lexogen RiboCop rRNA Depletion kit and Swift Biosciences RNA Library Sciences

value: lung organoid

value: mock


title: sRNA-Ctl-2 [C2]

source_name: A single blastocyst-stage embryo_Ctrl

value: E3.5 day

value: Blastocyst-stage embryo from zygotes which were injected with sperm sRNAs from normal male mice


title: C3hG17011(C3)

value: adult


title: HG17013(H)

value: H


title: cc03-20mock1


title: sRNA-Dep-3 [D3]

value: Blastocyst-stage embryo from zygotes which were injected with sperm sRNAs from depressive male mice


title: Model LPS 3

value: Model LPS


title: cc03-19mock1


title: Intervention DY131-treatment 1


title: sRNA-Ctl-1 [C1]


title: F1_C3_hippocampus_normal_offspring

data_processing:
RNA-sequencing reads were aligned to the mouse genome GRChM38 (mm10) using HISAT2 (Kim et al., 2015). The gene expression profile was generated by Cufflinks 2.2.1 (Trapnell et al., 2010). Low and non-expressed genes with less than an average of 10 fragments per kilobase of exon model per million mapped reads (FPKM) in all samples were omitted from the analysis.
Differential analysis was performed using tximport. Significance was set at an adiusted P value < 0.1 for broad pattern identification.  Heatmaps were generated using pheatmap R package and GO analysis was performed using DAVID Bioinformatics Resource 6.8 (Huang et al., 2009a, b).
Genome_build: GRChM38 (mm10)
Supplementary_files_format_and_content: processed_data.csv

extract_protocol:
Hippocampal samples collected from 3 independent mice of the F0-Ctl, F0-Dep,F1-Ctl and F1-Dep groups were processed for RNA extraction. Transcriptome libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 8 week

value: offspring born to normal male mice

value: hippocampus


title: HG17011(H)


title: Model LPS 1

value: liver


title: NG17013(N)

value: N


title: F1_C2_hippocampus_normal_offspring


title: Model LPS 2

value: 8-9 weeks


title: cc01-20mock2


title: epididyme_37ans_section1-replicat 1

value: Efferent duct proximal segment

tag: donor age


title: cc01-20mock1


title: F1_C1_hippocampus_normal_offspring


title: sRNA-Ctl-3 [C3]


title: NG17012(N)

value: SD

value: lung


title: NG17011(N)


title: Control saline 3

value: Control saline


title: Mock3

data_processing:
Star aligner 2.6.1 (8)/RSEM 1.2.28
Genome_build: hg38/GRCh38 with SARS-COVID 19 genome MT246667.1

source_name: Mock group

extract_protocol:
Total RNA was extracted from mock and SARS-CoV-2 infected proximal airway ALI and alveolar organoid cultures lysed in Trizol (Thermo Fisher Scientific) using the chloroform-iso-propanolethanol method.
Lexogen RiboCop rRNA Depletion kit and Swift Biosciences RNA Library Sciences
sequenecd by NovaSeq 6000 (Illumina) with single-end 75bp sequencing chemistry

value: lung organoid

value: Mock


title: Control saline 2


title: Mock2


title: DD_C6DD

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

data_processing:
Adapter and Quality trimming with trim_galore (phred33)
Alignment to reference with hisat2
FPKM calling with Cufflinks (max-bundle-length 10000000; max-bundle-frags 10000000)
Genome_build: mm10
Supplementary_files_format_and_content: excel spreadsheet include FPKM values for each Sample

source_name: Pancreatic islets

extract_protocol: Isolation of total RNA from islets of Langerhans was performed with the Micro RNA Isolation RNAqueous® Kit (Life Technologies™, Darmstadt, Germany).

treatment_protocol: Pancreatic islets were isolated from 6-week old mice, mice were kept under chow diet

value: Pancreatic islets

value: NZO/HIBomDife x DBA/2J

tag: locus


title: Control saline 1


title: HG17012(H)

value: adult

value: H


title: Mock1


title: val1 val2 rep3

city: guangzhou

first: Liang

middle: Bing

last: Yuan

state: Guangdong

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: Life of Science

institute: Sun Yat-Sen University

data_processing:
tophat v2.1.1; cufflinks v2.2.1; cuffmerge; cuffdiff
• Extract unique mapped no-duplicated reads; • Use MACS2 (gsize=1.35e8, bw=300, q=0.05, Do not Build shift model, extsize= 100) to call peaks;
Genome_build: Tair 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM and RPKM values for each Sample; bed files were generated using macs2

organism: Arabidopsis thaliana

source_name: Young seedlings

growth_protocol: For seed germination, sterilized seeds were stratified for 3 days at 4℃ in darkness; seeds were then sown on Murashige and Skoog (MS) plates containing 1% sucrose and 0.6% agar. Seedlings were grown in growth rooms with 16-h light/8-h dark cycles at 22℃.

extract_protocol:
Total RNA was isolated from about 100 milligrams of 14-day-old seedlings using the RNAprep pure Plant Kit (Tiangen) according to supplier’s instruction.
RAN libaries and ChIP-seq libraries were prepared for sequencing using standard illumina protocols
RNA-seq; ChIP-seq

value: seedling

value: 14 days old


title: DD_C17DD


title: val1 val2 rep2


title: DD_C1DD


title: CoV2-3

source_name: infected group

value: infected with SARS-CoV2


title: Hivep3-/- Thymic iNKT cells_Mouse1

city: Aurora

first: Laurent

last: Gapin

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical campus

data_processing:
Fastq files were aligned to the mm10 genome (v1.2.0) and feature reads were quantified simultaneously using Cell Ranger (v3.1.0) count for feature barcoding to generate filtered barcode.tsv, feature.tsv and matrix.mtx files
Filtered barcode.tsv, feature.tsv and matrix.mtx files were read using Seurat v.3.1.4. Low-quality cells were filtered using the cutoffs nFeature_RNA >= 500 & nFeature_RNA < 4100 & nCount_RNA >=1000 & percent.mt < 6.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data contain matrix.mtx; features.tsv; barcodes.tsv

source_name: iNKT cells

extract_protocol: Libraries were prepared according to standard protocols produced by 10X Genomics for sequencing using Chromium Single Cell 5' V2 chemistry. Briefly, cell suspensions loaded onto the 10x chromium controller were mixed with reagents from the Chromium Single Cell 5ʹ GEM, Library & Gel Bead Kit v2 according to the manufacturers instructions and libraries were sequenced using a NovaSeq sequencer (Illumina)

value: thymocytes

value: Hivep3 KO mice

value: 8-9 week old

value: untreated


title: val1 val2 rep1


title: Hivep3-/- Thymic iNKT cells_Mouse2


title: CoV2-2


title: C57BL/6 Thymic iNKT cells_Mouse2

value: wildtype


title: val2 rep3


title: val2 rep2


title: C57BL/6 Thymic iNKT cells_Mouse1


title: NN_C16NN


title: CoV2-1


title: val2 rep1


title: NN_C10NN


title: DD_C5DD


title: HEL47_2_iPS_EC_flow [SI-GA-H4]

description: processed data file: HEL47_gene_matrix

data_processing:
Data processing and analysis were performed using 10x Genomics Cell Ranger v2.1.1 pipelines
The “cellranger mkfastq” was used to produce FASTQ (raw data) files and “cellranger count” to perform alignment, filtering and UMI counting.
mkfastq was run using the Illumina bcl2fastq v2.2.0 and alignment was done against human genome GRCh38.
Cellranger aggr pipeline was used to combine data from multiple samples into an experiment-wide gene-barcode matrix and analysis.
Analyses were performed with Seurat R package version 3.0.1 (Butler et al., 2018).
Genome_build: GRCh38
Supplementary_files_format_and_content: Aggregated MatrixMarket file (matrix.mtx) and two tab separated metadata files (barcodes.tsv, genes.tsv).

source_name: IPS-EC

growth_protocol: iPS-ECs and iPS-CMs were grown either alone in monoculture or together in  cocultue for 48hours. The flow exposed iPS-ECs cells were grown in laminar 15 dyn flow for 24 hours (flow).

extract_protocol:
The cells were detached using Accutase (A6964, Sigma) and their concentration was measured. The cells were washed once with PBS containing 0.04% BSA, and then resuspended in PBS with 0.04% BSA to a concentration of 0.79-1.0 x 10^6 cells/ml. The cells were passed through a 35 µm strainer (352235, Corning) and placed on ice until continuation of the 10X Genomics Single Cell Protocol
The Chromium Single Cell 3’RNAseq run and library preparation were done using the Chromium™ Single Cell 3' Reagent version 2 chemistry

tag: cell line

value: iPSC-Derived Endothelial Cells (iPS-EC)

tag: culture type

value: flow


title: HEL24_3_iPS_EC_CM_cooculture [13_HA_GT]

description: processed data file: HEL24_3_gene_matrix

source_name: IPS-EC and iPS-CM

tag: cell type

value: IPS-EC and iPS-CM

value: coculture


title: HEL24_3_iPS_EC_monoculture [11_HA]

value: monoculture


title: HEL47_2_iPS_CM_monoculture [SI-GA-C5]

description: processed data file: HEL47_gene_matrix

source_name: IPS-CM

value: iPSC-Derived Cardiomyocytes (iPS-CM)


title: val1 rep2

tag: age


title: val1 rep1


title: WT rep3


title: val1 rep3


title: HEL47_2_iPS_EC_CM_cooculture [SI-GA-B5]

description: processed data file: HEL47_gene_matrix


title: HEL47_2_iPS_EC_monoculture [SI-GA-A5]

description: processed data file: HEL47_gene_matrix


title: WT rep1


title: WT rep2


title: NN_C7NN

value: Pancreatic islets

value: NZO/HIBomDife x DBA/2J


title: NN_C8NN


title: HEL24_3_iPS_CM_monoculture [12_GT]


title: Day_10B3_5hmC

status: Public on Nov 05 2020

city: Stanford

first: Nidhi

last: Bhutani

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery

institute: Stanford University

data_processing:
QC and filtering: An iterative quality check (FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and filtering procedure (Cutadapt http://code.google.com/p/cutadapt/) was performed to obtain good quality reads after trimming of the initial 7 bases.
Alignment: The Burrows-Wheeler Aligner, version 0.7.5a-r405 (http://bio-bwa.sourceforge.net/) (Li and Durbin 2009), was used with default parameters to align the filtered and trimmed reads to the mouse reference genome (GRCm38/mm10 http://genome.UCSC.edu) and alignments with a MAPQ score of greater than 5 were used for downstream analyses.
QC: MEDIPS (Lienhard et al. 2014) was used to assess the sequencing depth and coverage across the genome.
Peak calling: MACS version 1.4.2 (http://liulab.dfci.harvard.edu/MACS/) (Zhang et al. 2008), was used to call peaks using default settings. The MACS peaks annotated with Cisgenome version 2.0 (http://www.biostat.jhsph.edu/~hji/cisgenome/) (Ji et al. 2008), are based on the GRCm38/mm10 (http://genome.UCSC.edu) annotation file.
Data visualizaiton: To identify the distribution of 5mC/5hmC throughout the gene body and around the TSS, ngs.plot (Shen et al. 2014) was used with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: All processed data files contain peak calls generated using MACS and are in .txt files.

source_name: ATDC5 chondrogenic cell line D10 (replicate) enriched for hydroxymethylated DNA

growth_protocol: ATDC5 chondroprogenitor cells were maintained in DMEM/F12, 5% fetal bovine serum, 2mM L-Glutamine, 1x Antibiotic-Antimycotic (all Fisher Scientific) and 12.5μg/mL ascorbic acid (Eastman). To differentiate the cells into chondrocytes, 1x Insulin-Transferrin-Selenite (Invitrogen) was added to the basal media for 20 days.

extract_protocol:
Total DNA was extracted at appropriate timepoint. Extracted DNA was enriched for either 5mC (MIRA-base enrichment -  MethylCollector Ultra, Active Motif) or 5hmC (Hydroxymethyl Collector, Active Motif).
Libraries were prepared using enrichmed DNA and the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB) as per manufacturers guidelines.  200-500ng of enriched DNA was used for each library.

value: Differentiating chondrocyte

tag: enrichment type

tag: method for enrichment

value: Hydroxymethyl Collector (Active Motif) as per manufacturer's guidelines.


title: CHBP+ M-MDSC

city: Shanghai

first: Jiawei

last: Li

address: 180 Fenglin Road

institute: Fudan University Zhongshan Hospital

data_processing:
Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
Obtained clean reads were mapped to the mouse mm10 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: GRCm38

source_name: monocyte myeloid-derived suppressor cells

growth_protocol: MDSCs were isolated from C57/B6 mice bone marrow and induced in vitro. After 7 days, cells were harvested and seperated by flow cytometry.

extract_protocol:
The Raw Reads obtained by sequencing may contain unqualified Reads with low overall quality, sequencing primers, low end quality, etc. These unqualified Reads are likely to have a certain impact on the analysis quality, so they must be filtered to obtain Clean Reads that can be used for data analysis, apply Seqtk to filter, the main steps are as follows:  1. Remove the linker sequence contained in reads;  2. Remove the bases whose 3'end quality Q is less than 20, that is, the base error rate is less than 0.01, where Q=-10logerror_ratio;  3. Remove reads whose length is less than 25;  4. Remove the ribosome RNA reads of the species.
The Raw Reads obtained by sequencing may contain unqualified Reads with low overall quality, sequencing primers, low end quality, etc. These unqualified Reads are likely to have a certain impact on the analysis quality, so they must be filtered to obtain Clean Reads that can be used for data analysis, apply Seqtk to filter, the main steps are as follows:  1. Remove the linker sequence contained in reads;  2. Remove the bases whose 3'end quality Q is less than 20, that is, the base error rate is less than 0.01, where Q=-10logerror_ratio;  3. Remove reads whose length is less than 25;  4. Remove the ribosome RNA reads of the species.

treatment_protocol: CHBP- group used GM-CSF and CHBP+ group used CHBP+GM-CSF to induce MDSC in vitro.

value: monocyte myeloid-suppressor cells

tag: strain

value: GM-CSF+CHBP


title: CHBP- M-MDSC

value: GM-CSF


title: Day_5B3_5hmC

source_name: ATDC5 chondrogenic cell line D5 (replicate) enriched for hydroxymethylated DNA

tag: developmental stage


title: D10mDNA

source_name: ATDC5 chondrogenic cell line D10 enriched for methylated DNA

value: MethylCollector Ultra (Active Motif) as per manufacturer's guidelines.


title: Day_5B1_5hmC

source_name: ATDC5 chondrogenic cell line D5 enriched for hydroxymethylated DNA


title: Ctrl erythroblasts

city: San Francisco

first: Giorgio

last: Lagna

state: CA

address: 555 Mission Bay Blvd South

department: CVRI

institute: UCSF

source_name: CD71+Ter119 high cells from ctrl embryos

extract_protocol:
erythroblasts were sorted from E10.5 peripheral blood
described in Supplementary Information 2

value: erythroblast

tag: genotype

value: Drosha fl/fl or Drosha fl/+

tag: drosha abundance

value: WT


title: Drosha cKO-1 erythroblasts

data_processing: described in Supplementary Information 2

source_name: CD71+Ter119 high cells from cKO embryos

value: Drosha fl/fl;cdh5-cre+


title: Day_10B1_5hmC

source_name: ATDC5 chondrogenic cell line D10 enriched for hydroxymethylated DNA


title: Drosha cKO-2 erythroblasts

source_name: CD71+Ter119 low cells from cKO embryos

value: abundant as WT


title: D0mDNA

source_name: ATDC5 chondrogenic cell line D0 enriched for methylated DNA

value: Chondroprogenitor


title: D0input

source_name: ATDC5 chondrogenic cell line input DNA


title: R738 GBM HOT ASCL1 ChIP

city: Dallas

first: Jane

middle: E

last: Johnson

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Reads were mapped to hg19 assembly using bowtie2
Low quality reads were filtered using samtools
Removed duplicates using picard
Bigwig files contain ChIP signal normalized to 10M reads
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq signal in bigwig format

source_name: PDX-GBM

growth_protocol: PDX-GBMs were briefly passaged then propagated in brains of NOD-SCID mice

extract_protocol:
PDX-GBMs were dissected from the brain and dissociated for ChIP experiments
Library preparation was done by the UTSW Next Generation Sequencing Core

value: gliomas

tag: host mouse tissue

value: NOD-SCID mouse brain

tag: antibody

value: Anti-Mash1 (ASCL1) antibody (BD Biosciences, 556604)


title: ATDC5 day 15 Tet1sh2 shRNA

description: Sample name: Tet1sh2

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45C at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing:
Data were processed using dChip software. Background correction was applied and normalization to the median array intensity was performed, gene level expression were summarized from the corrected intensities.
MoGene-1_0-st-v1.r3.cdf
MoGene-1_0-st-v1.na32.mm9.transcript.csv

source_name: ATDC5 day 15 cultured with Tet1sh2 shRNA

label_protocol: Ambion WT Expression kit  was used to generate ssDNA targets. Fragmentation and biotin-labeling were performed using Afymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: ATDC5 cells cultured in the presence of Insulin-Transferrin-Selenium (ITS) for 15 days to induce chondrogenic differentiation

extract_protocol: QIAGEN Rneasy

treatment_protocol: Lentiviral shRNA knockdown, transduction at day 0

value: ATDC5 chondroprogenitor cell line

tag: genotype/variation

value: wild-type

tag: treatment

value: Tet1sh2 shRNA

tag: time

value: Day 15


title: R548 GBM HOT ASCL1 ChIP


title: Genomic DNA from umbilical cord blood buffycoat 557

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

institute: University of Oxford

description:
U610
Umbilical cord blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

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

data_processing:
R v3.4.2
Beta_for_GEO.txt includes Beta-mixture Quantile (BMIQ) normalized Beta Values.

label: Cy5 and Cy3

source_name: umbilical cord blood buffy coat 557

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from cord blood samples using QIAamp Blood DNA mini kit according to standard instructions.

tag: gender

value: Male

tag: tissue

value: Umbilical cord blood buffy coat

tag: maternal gdm status

value: No GDM


title: R738 GBM HOT Input

value: none (input)


title: R548 GBM HOT Input


title: ATDC5 day 15 Tet1sh1 shRNA

description: Sample name: Tet1sh1

source_name: ATDC5 day 15 cultured with Tet1sh1 shRNA

tag: cell line

value: Tet1sh1 shRNA


title: Genomic DNA from umbilical cord blood buffycoat 554

description:
U606
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 554

value: GDM


title: T72

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

institute: University Hospital Heidelberg

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw-intensity data were obtained after image analysis of the fluorescent spot intensity reads. All preprocessing and normalization steps were performed in the R programming environment [www.r-project.org]. Inter-array normalization was conducted using vsn normalization in the vsn package.

source_name: meningioma tissue

label_protocol: Standard labeling protocol of Genomic Core Facility of the German Cancer Research Center (DKFZ, Heidelberg, Germany)

growth_protocol: Cells were grown as floating neurospheres in DMEM/F-12 medium containing 20% BIT serum-free supplement, basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) at 20ng/ml each (all Provitro, Berlin, Germany). To study expression changes, IDH1mut and IDH1wt GSCs were grown under normoxic and hypoxic conditions. Hypoxic conditions (1.5% O2, 5% CO2, 93.5% N2) were established in an O2- and CO2-controlled tissue culture incubator (Nunc, Langenselbold, Germany) as previously described.

extract_protocol: Total RNA was extracted from tissue using the AllPrep Kit (Qiagen) according to manufacturer's instructions. RNA integrity was assessed by the Agilent 2100 Bioanalyzer.

value: meningioma

tag: who grade

value: III


title: ATDC5 day 15 NT shRNA

description: Sample name: NT1

source_name: ATDC5 day 15 cultured with non-target shRNA

value: non-target shRNA


title: Genomic DNA from umbilical cord blood buffycoat 553

description:
U605
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 553


title: Genomic DNA from umbilical cord blood buffycoat 555

description:
U608
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 555


title: Genomic DNA from umbilical cord blood buffycoat 551

description:
U603
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 551


title: T66


title: T70


title: T71


title: T65


title: Genomic DNA from umbilical cord blood buffycoat 548

description:
U599
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 548

value: Female


title: Genomic DNA from umbilical cord blood buffycoat 549

description:
U600
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 549


title: T68


title: Genomic DNA from umbilical cord blood buffycoat 552

description:
U604
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 552


title: Genomic DNA from umbilical cord blood buffycoat 556

description:
U609
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 556


title: Genomic DNA from umbilical cord blood buffycoat 550

description:
U601
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 550


title: T63


title: Genomic DNA from umbilical cord blood buffycoat 545

description:
U596
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 545


title: Genomic DNA from umbilical cord blood buffycoat 546

description:
U597
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 546


title: Genomic DNA from umbilical cord blood buffycoat 547

description:
U598
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 547


title: T64


title: T67


title: Genomic DNA from umbilical cord blood buffycoat 543

description:
U594
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 543


title: Genomic DNA from umbilical cord blood buffycoat 544

description:
U595_rep1
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 544


title: T69


title: Genomic DNA from umbilical cord blood buffycoat 540

description:
U590
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 540


title: Genomic DNA from umbilical cord blood buffycoat 539

description:
U589
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 539


title: Genomic DNA from umbilical cord blood buffycoat 538

description:
U588
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 538


title: Genomic DNA from umbilical cord blood buffycoat 542

description:
U593
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 542


title: Genomic DNA from umbilical cord blood buffycoat 541

description:
U592
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 541


title: Genomic DNA from umbilical cord blood buffycoat 534

description:
U584
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 534


title: Genomic DNA from umbilical cord blood buffycoat 533

description:
U583
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 533


title: Genomic DNA from umbilical cord blood buffycoat 532

description:
U582
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 532


title: Genomic DNA from umbilical cord blood buffycoat 528

description:
U578
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 528


title: Genomic DNA from umbilical cord blood buffycoat 525

description:
U575
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 525


title: Genomic DNA from umbilical cord blood buffycoat 536

description:
U586_rep1
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 536


title: Genomic DNA from umbilical cord blood buffycoat 522

description:
U572
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 522


title: Genomic DNA from umbilical cord blood buffycoat 524

description:
U574
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 524


title: Genomic DNA from umbilical cord blood buffycoat 531

description:
U581
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 531


title: Genomic DNA from umbilical cord blood buffycoat 526

description:
U576
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 526


title: Genomic DNA from umbilical cord blood buffycoat 520

description:
U570
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 520


title: Genomic DNA from umbilical cord blood buffycoat 529

description:
U579
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 529


title: Genomic DNA from umbilical cord blood buffycoat 517

description:
U567
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 517


title: Genomic DNA from umbilical cord blood buffycoat 519

description:
U569
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 519


title: Genomic DNA from umbilical cord blood buffycoat 523

description:
U573
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 523


title: Genomic DNA from umbilical cord blood buffycoat 527

description:
U577
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 527


title: Genomic DNA from umbilical cord blood buffycoat 518

description:
U568
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 518


title: Genomic DNA from umbilical cord blood buffycoat 521

description:
U571
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 521


title: Genomic DNA from umbilical cord blood buffycoat 516

description:
U566
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 516


title: Genomic DNA from umbilical cord blood buffycoat 515

description:
U565_rep2
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 515


title: Genomic DNA from umbilical cord blood buffycoat 514

description:
U564
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 514


title: Genomic DNA from umbilical cord blood buffycoat 513

description:
U563
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 513


title: Genomic DNA from umbilical cord blood buffycoat 537

description:
U587
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 537


title: Genomic DNA from umbilical cord blood buffycoat 535

description:
U585
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 535


title: Genomic DNA from umbilical cord blood buffycoat 511

description:
U560
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 511


title: Genomic DNA from umbilical cord blood buffycoat 512

description:
U561
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 512


title: Genomic DNA from umbilical cord blood buffycoat 510

description:
U559
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 510


title: Genomic DNA from umbilical cord blood buffycoat 509

description:
U558
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 509


title: Genomic DNA from umbilical cord blood buffycoat 530

description:
U580
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 530


title: Genomic DNA from umbilical cord blood buffycoat 508

description:
U557
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 508


title: Genomic DNA from umbilical cord blood buffycoat 502

description:
U551
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 502


title: Genomic DNA from umbilical cord blood buffycoat 503

description:
U552
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 503


title: Genomic DNA from umbilical cord blood buffycoat 500

description:
U549
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 500


title: Genomic DNA from umbilical cord blood buffycoat 504

description:
U553
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 504


title: Genomic DNA from umbilical cord blood buffycoat 499

description:
U547
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 499


title: Genomic DNA from umbilical cord blood buffycoat 505

description:
U554
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 505


title: Genomic DNA from umbilical cord blood buffycoat 498

description:
U546
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 498


title: Genomic DNA from umbilical cord blood buffycoat 495

description:
U543
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 495


title: Genomic DNA from umbilical cord blood buffycoat 494

description:
U542
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 494


title: Genomic DNA from umbilical cord blood buffycoat 497

description:
U545
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 497


title: Genomic DNA from umbilical cord blood buffycoat 492

description:
U540
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 492


title: Genomic DNA from umbilical cord blood buffycoat 493

description:
U541
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 493


title: Genomic DNA from umbilical cord blood buffycoat 490

description:
U538
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 490


title: Genomic DNA from umbilical cord blood buffycoat 491

description:
U539
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 491


title: Genomic DNA from umbilical cord blood buffycoat 489

description:
U537
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 489


title: Genomic DNA from umbilical cord blood buffycoat 487

description:
U535
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 487


title: Genomic DNA from umbilical cord blood buffycoat 486

description:
U534
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 486


title: Genomic DNA from umbilical cord blood buffycoat 488

description:
U536
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 488


title: Genomic DNA from umbilical cord blood buffycoat 485

description:
U533
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 485


title: Genomic DNA from umbilical cord blood buffycoat 484

description:
U532
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 484


title: Genomic DNA from umbilical cord blood buffycoat 483

description:
U531
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 483


title: Genomic DNA from umbilical cord blood buffycoat 482

description:
U530
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 482


title: Genomic DNA from umbilical cord blood buffycoat 507

description:
U556
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 507


title: Genomic DNA from umbilical cord blood buffycoat 479

description:
U526
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 479


title: Genomic DNA from umbilical cord blood buffycoat 480

description:
U527
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 480


title: Genomic DNA from umbilical cord blood buffycoat 481

description:
U529_rep1
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 481


title: Genomic DNA from umbilical cord blood buffycoat 478

description:
U525
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 478


title: Genomic DNA from umbilical cord blood buffycoat 506

description:
U555
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 506


title: Genomic DNA from umbilical cord blood buffycoat 501

description:
U550
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 501


title: Genomic DNA from umbilical cord blood buffycoat 496

description:
U544
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 496


title: Genomic DNA from umbilical cord blood buffycoat 473

description:
U520
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 473


title: Genomic DNA from umbilical cord blood buffycoat 476

description:
U523
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 476


title: Genomic DNA from umbilical cord blood buffycoat 477

description:
U524
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 477


title: Genomic DNA from umbilical cord blood buffycoat 470

description:
U517
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 470


title: Genomic DNA from umbilical cord blood buffycoat 472

description:
U519
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 472


title: Genomic DNA from umbilical cord blood buffycoat 475

description:
U522
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 475


title: Genomic DNA from umbilical cord blood buffycoat 468

description:
U515
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 468


title: Genomic DNA from umbilical cord blood buffycoat 469

description:
U516
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 469


title: Genomic DNA from umbilical cord blood buffycoat 467

description:
U514
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 467


title: Genomic DNA from umbilical cord blood buffycoat 466

description:
U513
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 466


title: Genomic DNA from umbilical cord blood buffycoat 463

description:
U510
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 463


title: Genomic DNA from umbilical cord blood buffycoat 464

description:
U511
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 464


title: Genomic DNA from umbilical cord blood buffycoat 465

description:
U512
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 465


title: Genomic DNA from umbilical cord blood buffycoat 461

description:
U508
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 461


title: Genomic DNA from umbilical cord blood buffycoat 460

description:
U507
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 460


title: Genomic DNA from umbilical cord blood buffycoat 457

description:
U504
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 457


title: Genomic DNA from umbilical cord blood buffycoat 459

description:
U506
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 459


title: Genomic DNA from umbilical cord blood buffycoat 455

description:
U501
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 455


title: Genomic DNA from umbilical cord blood buffycoat 456

description:
U502
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 456


title: Genomic DNA from umbilical cord blood buffycoat 453

description:
U498
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 453


title: Genomic DNA from umbilical cord blood buffycoat 451

description:
U496
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 451


title: Genomic DNA from umbilical cord blood buffycoat 458

description:
U505
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 458


title: Genomic DNA from umbilical cord blood buffycoat 450

description:
U494
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 450


title: Genomic DNA from umbilical cord blood buffycoat 474

description:
U521
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 474


title: Genomic DNA from umbilical cord blood buffycoat 454

description:
U500
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 454


title: Genomic DNA from umbilical cord blood buffycoat 471

description:
U518
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 471


title: Genomic DNA from umbilical cord blood buffycoat 452

description:
U497_rep2
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 452


title: Genomic DNA from umbilical cord blood buffycoat 449

description:
U493
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 449


title: Genomic DNA from umbilical cord blood buffycoat 447

description:
U491
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 447


title: Genomic DNA from umbilical cord blood buffycoat 448

description:
U492
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 448


title: Genomic DNA from umbilical cord blood buffycoat 444

description:
U488
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 444


title: Genomic DNA from umbilical cord blood buffycoat 446

description:
U490
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 446


title: Genomic DNA from umbilical cord blood buffycoat 442

description:
U486
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 442


title: Genomic DNA from umbilical cord blood buffycoat 441

description:
U485
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 441


title: Genomic DNA from umbilical cord blood buffycoat 445

description:
U489
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 445


title: Genomic DNA from umbilical cord blood buffycoat 439

description:
U483
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 439


title: Genomic DNA from umbilical cord blood buffycoat 440

description:
U484
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 440


title: Genomic DNA from umbilical cord blood buffycoat 462

description:
U509
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 462


title: Genomic DNA from umbilical cord blood buffycoat 438

description:
U482
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 438


title: Genomic DNA from umbilical cord blood buffycoat 437

description:
U481
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 437


title: Genomic DNA from umbilical cord blood buffycoat 434

description:
U478
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 434


title: Genomic DNA from umbilical cord blood buffycoat 436

description:
U480
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 436


title: Genomic DNA from umbilical cord blood buffycoat 435

description:
U479
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 435


title: Genomic DNA from umbilical cord blood buffycoat 433

description:
U477
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 433


title: Genomic DNA from umbilical cord blood buffycoat 432

description:
U476
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 432


title: Genomic DNA from umbilical cord blood buffycoat 430

description:
U474
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 430


title: Genomic DNA from umbilical cord blood buffycoat 427

description:
U471
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 427