title: liver-alcohol-fed and abdominal cavity_MNA2

city: Hangzhou

first: Wenwen

last: Yang

address: No.548 Binwen Road, Binjiang District

department: School of Life Science

country: Zimbabwe

institute: Zhejiang Chinese Medical University

description:
Mice were fed for 5 weeks,and MNA was intraperitoneally injected daily at 50mg/kg mouse weight
1_genes_fpkm_expression.txt; 2_lncRNA_Prediction_expression.txt; 3_circRNA_Prediction_expression.txt

data_processing:
Firstly, cutadapt-1.9 was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC(http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used hisat2 (https://ccb.jhu.edu/software/hisat2) to map reads to the genome of mmu10. The mapped reads of each sample were assembled using stringtie-1.3.4 (http://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating FPKM.
First of all, transcripts that overlapped with known mRNAs and transcripts shorter than 200bp were discarded. Then we utilized CPC0.9-r2 (http://cpc2.cbi.pku.edu.cn) with default parameters(cpc2 -i novel.fa -o cpc2.out) and CNCI2.0 (http://wwww.bioinfo.org/software/cnci) with default parameters (CNCI.py -f novel.fa -o CNCI.result -p 1 -m ve -g novel.gtf -d genome.fa) to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed and remained transcripts were considered as lncRNAs.
StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM. The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >= 1 or log2 (fold change) <= -1 and with statistical significance p value <= 0.05 by R package edgeR  (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
We used hisat2 (https://ccb.jhu.edu/software/hisat2) to map reads to the genome of mmu10, Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion. CIRCExplorer2 and CIRI was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion. All samples were generated unique circular RNAs. Circular RNA expressions from different samples or groups were caculated by scripts in house. Only the comparisons with “pvalue”less than 0.05 were regarded as showing differential expression by R package-edgeR.
Genome_build: mmu10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and read counts for each Sample.

source_name: liver

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA). After the enriched circRNAs were fragmented into small pieces using divalent cations under high temperature. After removing ribosomal RNAs, the left RNAs were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single-or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs.The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Hiseq 4000 following the vendor's recommended protocol.

value: liver

value: post natal day 8 weeks

value: Lieber-DeCarli diet and at the same time, they were intraperitoneally injected with MNA at a dose of 50mg/kg


title: liver-alcohol-fed and abdominal cavity_MNA3

status: Public on Aug 18 2021

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: age

tag: treatment


title: Mother_Family6225

type: genomic

city: Leuven

first: Joris

middle: R.

last: Vermeesch

address: Herestraat 49 box 606

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

description:
Genomic DNA extracted from cow ovarian tissue was genotyped using BovineHD BeadChip arrays (Illumina).
Cow gDNA in the pedigree Family6225

hyb_protocol: According to the manufacturer's protocol of Infinium HD Assay for BovineHD BeadChip arrays.

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA) according to the manufacturer's protocol of BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA)

data_processing:
Samples were genotyped using the BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA. The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0,75. We subsequently analysed these data with haplarithmisis adapted for bovine (Zamani Esteki et al. 2015, AJHG).
Genotypes: AA,AB,BB or NC (No Call); BAF: B-allele frequency; logR: log2ratio

molecule: genomic DNA

organism: Bos taurus

source_name: Cow ovarian tissue pedigree Family6225

label_protocol: 200 ng of gDNA and 600 ng of whole-genome amplified DNA was used as input for processing the samples according to the manufacturer's protocol of BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA).

growth_protocol: Embryos were in vitro produced according to previously described methods (Catteeuw et al., 2017).

extract_protocol: Extraction of gDNA from sperm and ovarian tissue was performed using the Qiagen DNeasy Blood and Tissue kit according to the manufacturer's protocol (sperm: user-developed protocol for purification of total DNA from animal sperm using the DNeasy® Blood & Tissue Kit; protocol 2). Single blastomere and whole-embryo DNA was whole-genome amplified using the REPLI-g SC kit (Qiagen) according to the manufacturer's instructions with full or half reaction volumes and a 3 h incubation reaction.

treatment_protocol: Single blastomeres of bovine preimplantation embryos were dissociated and whole genome amplified as described previously (Destouni et al., 2016)). Briefly, zona pellucida was removed by pronase treatment and single blastomeres were disassociated and picked individually.

value: Ovarian


title: liver-alcohol-fed and abdominal cavity_MNA1


title: miR-150 fl/fl_LV_Sham_rep1

type: RNA

city: Indianapolis

first: Il-Man

last: Kim

state: IN

address: 635 Barnhill Drive, MS 346A

country: USA

institute: INDIANA UNIVERSITY SCHOOL OF MEDICINE

description:
MiR-150fl-Sham-1
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). Each labeled cRNA was then fragmented, and the mixture was heated at 60°C for 30min. Lastly, labeled cRNAs were loaded into gasket slides and assembled to microarray slides. The slides were then incubated for 17h at 65°C in the SureHyb Hybridization Chamber (Agilent Technologies).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: LV_Sham_4 week

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit).

extract_protocol: Total RNAs from LVs were prepared using Qiagen RNeasy Plus kit. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

tag: gender

value: male

tag: age upon harvesting

value: 14 week age

tag: genotype/variation

value: miR-150 floxed/floxed [miR-150 fl/fl]

value: sham

value: left ventricles (LVs)


title: miR-150 fl/fl_LV_MI_rep3

description:
MiR-150fl-Ml-3
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

source_name: LV_MI_4 week

value: female

value: myocardial infarction [MI]


title: Affected_Family6225

description:
WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).
Sibling embryo WGA product in the pedigree Family6225

source_name: Embryo

value: Embryonic


title: EY005_MPP3_ERlow_US

city: Yuseong-gu

first: Hyojung

last: Paik

state: Daejeon

address: 245 Daehak-ro

country: South Korea

institute: KISTI

data_processing:
All of droplet-based single-cell RNA seq data are processed using the Cell Ranger Single-Cell Software Suite (version 2.0, 10xGenomics) against the Mus musculus genome (GRCm38) provided by Cell Ranger.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count mtx

molecule: polyA RNA

source_name: Multipotent progenitor 3 ER volume low_6hr cultured_ w/o LPS and Pam3CSK4 stimulation

extract_protocol:
For bulk RNA-seq, cells (5,000 to 7,000 per sample) were directly sorted into 350 μl RLT lysis buffer containing 1% b-mercaptoethanol from the RNeasy Plus Micro Kit (Qiagen, 74034) and RNA was isolated according to the manufacturer’s instructions.
For bulk RNA-seq, libraries were prepared using Trio RNA-seq Library Preparation Kit (NuGen, 0507) and for single cell RNA-seq, libraries were prepared using a Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10X Genomics).

value: Bone marrow

value: 6hr cultured

tag: sequencing method

value: droplet-based sing-cell RNA seq (10X Genomics, Illumina Hiseq 4000)


title: miR-150 cKO_LV_MI_rep2

description:
MiR-150cko-Ml-2
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

value: 15 week age

value: alpha-MHC-Cre;miR-150 fl/fl [miR-150 cKO]


title: miR-150 cKO_LV_MI_rep1

description:
MiR-150cko-Ml-1
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.


title: Father

description:
Genomic DNA extracted from bull sperm was genotyped using BovineHD BeadChip arrays (Illumina).
Bull gDNA universal for both pedigrees

source_name: Semen

value: Sperm


title: miR-150 cKO_LV_Sham_rep2

description:
MiR-150cko-Sham-2
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.


title: miR-150 fl/fl_LV_MI_rep1

description:
MiR-150fl-Ml-1
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.


title: miR-150 cKO_LV_Sham_rep1

description:
MiR-150cko-Sham-1
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.


title: liver-alcohol-fed3

description:
Mice were fed for 5 weeks
1_genes_fpkm_expression.txt; 2_lncRNA_Prediction_expression.txt; 3_circRNA_Prediction_expression.txt

value: liver

value: post natal day 8 weeks

value: Lieber-DeCarli diet


title: miR-150 cKO_LV_Sham_rep3

description:
MiR-150cko-Sham-3
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.


title: liver-pair-fed3

value: isocaloric control liquid diet


title: liver-alcohol-fed1


title: liver-pair-fed1


title: liver-pair-fed2


title: WT_TGFb_plus

city: Seoul

first: Ye Lin

last: Son

state: Seoul

address: Ewha womans university Science Building C 5th floor

institute: Ewha womans university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using MapSplice-v2.1.8 with parameters -p 5.
Transcript abundances are quantified to abundance estimates by RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include expected count values for each Sample. Matrix table with raw gene counts for every gene and every sample.

source_name: control B16F10 cells

growth_protocol: Ahnak-knockdown B16F10 stable cells and control B16F10 cells were prepared in 5x10^5 cells per mouse injections suspended in 100 μL of PBS. For tail vein injections, 6-to-8-wk-old male mice were restrained using a rodent restrainer. The mouse tail was kept in contact with a 40°C heat pad to relax the vein before injection. Cells were injected into the mouse using a 30.5-gauge needle. Fourteen days later, mice were sacrificed and perfused with PBS through the right ventricle until pulmonary blood was completely removed. Lung tissues were preserved in 10% neutral buffered formalin (NBF), and tumor colonies on the lung surface were counted. GraphPad Prism software was used for statistical assessments and graphical presentations of colony number. Median values and statistical significance were obtained with Student’s t-test and the Mann-Whitney U test. All animal studies were performed under guidance of the Institutional Animal Care and Use Committee (IACUC) and the ethical guidelines of Ewha Womans University.

extract_protocol:
Mouse pulmonary endothelial cells were isolated from the lungs of 6 to 8-wk-old WT or Ahnak-/- mice. Each mouse was sacrificed by CO2 inhalation. After reperfusion with PBS, the lungs were removed and digested in DMEM supplemented with 0.1% type I collagenase (Worthington) for 60 minutes at 37C. A total of 15 mL of collagenase solution was used per mouse, and the mixture was shaken vigorously during digestion before being titrated into the fixed cannula three times. The collagenase solution containing cells was then strained through a 70-μm strainer. The filtered cell suspension was centrifuged at 1300 rpm for 8 min. After removal of the supernatant, the cell pellet was resuspended twice in 20 mL of 10% DMEM and again centrifuged at 1300 rpm for 8 min. After the supernatant was removed, the cell pellet was resuspended in 4 mL of 10% DMEM, and Dynabeads (Invitrogen) coupled to an anti-ICAM-2 antibody were added to the cells. The Dynabeads/cell mixture was incubated for 30 minutes at 4C. The bead-bound cells were collected using a magnet, washed 5 times in 10% DMEM and once in serum-free DMEM, and digested for 8 minutes at 37C in 1 mL of trypsin/EDTA to release the beads from the cells. The bead-free cells in 10% DMEM were centrifuged, resuspended in 4 mL of EGM-2 culture medium (Lonza), plated onto a gelatin-coated 60mm culture dish, and left undisturbed for approximately 4-5 days.
cDNA libraries were constructed with the TruSeq mRNA library kit using 1 μg of total RNA. Paired end sequencing of 100-mers length was performed using an Illumina HiSeq4000 system.

value: 6 to 8-wk-old mice

tag: genotype

value: WT mice

tag: cell type

value: primary pulmonary endothelial cells (ECs)

value: TGFβ stimulation


title: liver-alcohol-fed2


title: WT_TGFb_minus


title: Ahnak_KO_TGFb_minus

source_name: Ahnak-knockdown B16F10 stable cells

value: Ahnak knockout (Ahnak-/-) mice


title: Ahnak_KO_TGFb_plus


title: Sample40: Ifnar1-/- infection 4

city: CHAPEL HILL

first: Jason

last: Whitmire

state: NC

address: 5062 Genetic Medicine Bldg

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

data_processing:
Illumina Casava software used for basecalling.
Sequencing reads were aligned to mouse genome mm10 with STAR2.6
Raw transcript counts were estimated with Salmon0.7
Normalized RNA counts were generated with DESeq2 package in R3.6.
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with normalized gene counts for every gene and every sample

extract_protocol:
Liver RNAs were extracted with mirVana miRNA Isolation Kit  (Thermo Fisher) using the total RNA extraction protocol.
Libraries were prepared with TruSeq Stranded Total RNA Library Prep Gold Kit ( Illumina )

treatment_protocol: Mice were intravenously inoculated with the HAV virus inocula or PBS control at 6-8 weeks of age.

tag: Sex

value: F

value: HAV infection 14 days

tag: sequencing batch


title: Sample39: Ifnar1-/- infection 3


title: Sample38: Ifnar1-/- infection 2

value: M


title: Sample37: Ifnar1-/- infection 1


title: miR-150 cKO_LV_MI_rep3

description:
MiR-150cko-Ml-3
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

value: female

value: myocardial infarction [MI]

value: left ventricles (LVs)


title: Whole embryo_Nicotine_11

city: Woolloongabba

first: Suyinn

last: Chong

state: QLD

address: 37 Kent St

country: Australia

institute: Mater Research Institute - The University of Queensland

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were processed using GenomeStudio (1.9.0) following the manufacturer's protocol.

source_name: Whole embryo

label_protocol: Standard Illumina Labelling protocol

extract_protocol: Total RNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN), as per the manufacturer's protocol.

treatment_protocol: Voluntary maternal consumption of either 10% (v/v) ethanol (ethanol-exposure) or 100 µg/ml freebase nicotine (nicotine-exposure) from fertilisation (0.5 days post coitum) to mid-gestation (8.5 days post coitum).

value: 9.5 days post coitum

value: Male

tag: treatment group

value: Nicotine


title: Whole embryo_Ethanol_12

value: Ethanol


title: Whole embryo_Control_11

value: Control


title: Whole embryo_Ethanol_10


title: Whole embryo_Nicotine_12


title: Whole embryo_Control_12


title: Whole embryo_Ethanol_11


title: Sample36: Irf3S1/S1Ifnar1-/- infection 4

value: liver


title: Sample35: Irf3S1/S1Ifnar1-/- infection 3


title: Sample34: Irf3S1/S1Ifnar1-/- infection 2


title: Sample33: Irf3S1/S1Ifnar1-/- infection 1


title: Sample31: Ifnar1-/- naïve 3

value: vehicle control 14 days


title: Sample30: Irf3S1/S1Ifnar1-/- naïve 4


title: Sample28: Ifnar1-/- naïve 2


title: Sample29: Irf3S1/S1Ifnar1-/- naïve 3


title: Whole embryo_Control_8


title: Whole embryo_Control_10


title: Sample27: Ifnar1-/- naïve 1


title: Whole embryo_Control_9


title: Whole embryo_Nicotine_9


title: Sample26: Irf3S1/S1Ifnar1-/- naïve 2


title: Sample32: Ifnar1-/- naïve 4


title: Sample25: Irf3S1/S1Ifnar1-/- naïve 1


title: Whole embryo_Nicotine_8


title: Whole embryo_Nicotine_7


title: Whole embryo_Nicotine_10


title: Whole embryo_Ethanol_9


title: Whole embryo_Ethanol_6


title: Whole embryo_Control_7


title: Whole embryo_Nicotine_5


title: Sample23: Ifnar1-/- HAV 5

value: HAV infection 7 days


title: Whole embryo_Control_6


title: Whole embryo_Ethanol_8


title: Whole embryo_Nicotine_6


title: Whole embryo_Ethanol_5


title: Whole embryo_Ethanol_4


title: Whole embryo_Ethanol_7


title: Sample24: Ifnar1-/- HAV 6


title: Sample20: Mavs-/- HAV 5

value: Mavs-/-


title: Sample19: Mavs-/- HAV 4


title: Sample18: Ifnar1-/- Mock 6

value: vehicle control 7 days


title: Whole embryo_Control_4


title: Whole embryo_Ethanol_3


title: Whole embryo_Nicotine_4


title: Whole embryo_Control_5


title: Sample17: Ifnar1-/- Mock 5


title: Sample16: Ifnar1-/- Mock 4


title: Sample15: Mavs-/- Mock 6


title: Sample21: Mavs-/- HAV 6


title: Sample14: Mavs-/- Mock 5


title: Sample13: Mavs-/- Mock 4


title: Sample12: Ifnar1-/- HAV 3


title: CT18_LP_SCN rep2

city: Shanghai

first: Chuanzhen

last: Zhu

address: 320 Yueyang Road

country: China

institute: Institude of Neuroscience

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw fastq data were preprocessed by FASTX_Toolkit. After low quality reads filtering and 3’ adapter clipping, the sequences that were unable to match 3’ adapter or with a length shorter than 17bp after clipping were discarded and the redundant sequences were collapsed as useful reads for small RNA mapping and annotation.
We used Bowtie (Bowtie options -best -strata -k 100 -v 0) to map useful reads to mouse genome (Mouse GRCm38/mm10). The reads were aligned sequentially to known miRNA (miRBase 18) and other small RNA sequences (tRNA: Genomic tRNA Database; rRNA: 18S and 28S from NCBI GenBank and 5S and 5.8S from Ensembl; snoRNA and snRNA from Ensembl) by Bowtie with no mismatching.
We defined the reads that exactly matched the 5’ start site of annotated miRNAs and matched the 3’ ends with at most 2-nt deletions and/or 2-nt additions derived from pre-miRNAs as valid miRNAs counts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include useful count of each miRNA.

source_name: mouse brain tissue

extract_protocol:
SCN, hypothalamus or cortex was removed and immediately frozen in liquid nitrogen. Total RNA was extractted using Trizol reagent (Takara).
RNA libraries were prepared for sequencing according to Illumina protocols

value: suprachiasmatic nucleus


title: CT18_LP_SCN rep1


title: CT18_CTRL_SCN rep1


title: Whole embryo_Ethanol_2


title: CCK rep2

source_name: mouse SCN subtype neuron


title: Whole embryo_Control_2


title: Whole embryo_Nicotine_2


title: Whole embryo_Control_3


title: Sample11: Ifnar1-/- HAV 2

value: F


title: Whole embryo_Nicotine_1


title: Whole embryo_Control_1


title: CT18_CTRL_SCN rep2


title: Sample10: Ifnar1-/- HAV 1


title: Whole embryo_Ethanol_1


title: Sample8: Mavs-/- HAV 2


title: Sample9: Mavs-/- HAV 3


title: AVP rep1


title: Sample7: Mavs-/- HAV 1


title: VIP rep1


title: CCK rep1


title: AVP rep2


title: VIP rep2


title: Sample6: Ifnar1-/- Mock 3


title: ZT38_SCN


title: ZT42_SCN


title: ZT34_SCN


title: Sample3: Mavs-/- Mock 3


title: ZT30_SCN


title: ZT26_SCN


title: Sample1: Mavs-/- Mock 1


title: Sample5: Ifnar1-/- Mock 2


title: Sample2: Mavs-/- Mock 2


title: ZT22_SCN


title: ZT14_SCN


title: ZT6_SCN


title: ZT10_SCN


title: ZT2_SCN


title: Sample4: Ifnar1-/- Mock 1


title: Cortex rep2

value: cortex


title: Cortex rep1


title: Hypothalamus rep1

value: hypothalamus


title: ZT18_SCN


title: Hypothalamus rep2

value: hyothalamus


title: SCN rep2


title: SCN rep1


title: Sample_DR14_B_II_2

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: beginning of color production, around 1.5 cm in size

data_processing:
We used Trinity to De-novo assemble the Irus transcriptome (v. trinityrnaseq_r20140717, min_kmer_cov = 2, min_contig_length 200) from all 8 libraries. Quast (v. 3.2 ) had been used to estimate the assembly quality.
Using the align_and_estimate_abundance.pl script from trinity package, the reads from each sample were aligned to the irus transcriptom using Bowtie (v. 1.0.0) and the number of mapped reads per gene per sample was counted using RSEM (v. 1.2.25).
In order to annotate the genes we do BLASTX against UNIPROT database (2016-09-26). We set the e value cutoff to < 0.0001
freeBayes (v1.0.2,  default parameters) have been used to call the variants at the samples comparing to the reference transcriptom.
Genome_build: Denovo assembly. FASTA file with transcript sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Iris atropurpurea

source_name: Bud stage 2b

growth_protocol: Plants that were brought from a large I. atropurpurea population in Dora (32°17'N 34°50'E) in Israel and grew at the Tel Aviv university botanical garden.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany), according to manufacturer’s instructions.
RNA libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina), according to manufacturer’s instructions.

value: Bud

tag: developmental stage

value: stage 2b


title: Sample_DR14_L

description: young leaf

source_name: Leaf

value: Leaf


title: Sample_DR14_R

description: root

source_name: Root

value: Root


title: Sample_DR14_B_II_1

source_name: Bud stage 2a

value: stage 2a


title: Sample_DR8_B_IIa


title: Sample_DR8_B_I

description: early bud, no color

source_name: Bud stage 1

value: stage 1


title: Sample_DR14_B_III

description: full colored bud, over 2 cm in size

source_name: Bud stage 3

value: stage 3


title: Sample_DR14_B_I

description: early, no color


title: Ctrl-17(Sup)

city: Beijing

first: Jinghua

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10´ Blocking Agent and 1 μL of 25´ Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2´ Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 5 out of 10 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” analyses.

data_processing: “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed using the R software. GO analysis was performed using topGO package in R environment for statistical computing and graphics, and Pathway analysis was calculated by fisher's exact test.

organism: Rattus norvegicus

source_name: left ventricle tissue-Ctrl-17

label_protocol: The “IP” RNA and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific actitity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: control

value: heart - left ventricle

value: male

value: 8  week

tag: experimental

value: supernatant

value: Wistar


title: LPS-7(Sup)

source_name: left ventricle tissue-LPS-7

value: LPS


title: Ctrl-15(Sup)

source_name: left ventricle tissue-Ctrl-15


title: Ctrl-18(Sup)

source_name: left ventricle tissue-Ctrl-18


title: Ctrl-16(Sup)

source_name: left ventricle tissue-Ctrl-16


title: Ctrl-20(IP)

source_name: left ventricle tissue-Ctrl-20

value: immunoprecipitation


title: Ctrl-20(Sup)


title: LPS-6(Sup)

source_name: left ventricle tissue-LPS-6


title: LPS-5(Sup)

source_name: left ventricle tissue-LPS-5


title: LPS-3(IP)

source_name: left ventricle tissue-LPS-3


title: Ctrl-15(IP)


title: LPS-1(Sup)

source_name: left ventricle tissue-LPS-1


title: LPS-7(IP)


title: Ctrl-16(IP)


title: LPS-1(IP)


title: LPS-3(Sup)


title: LPS-5(IP)


title: Ctrl-17(IP)


title: Wt_AI_tot03_SC_SP_CTACAC

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

data_processing:
Library strategy: 5PSeq
Demultiplexing using bcl2fastq v2.20.0.422 at default settings, allowing one mismatch and minimum read length of 35nt
Quality control with FASTQC and MultiQC v1.9 at default parameters
Adapter trimming using cutadapt 2.3 with Python 3.7.2, options: --minimum-length 28; -e 0.2; -o 9; --nextseq-trim 20
Extraction of barcodes and UMI using umitools and options --bc-pattern CCCCCCNNNNNNNN, whitelist.txt file of barcodes was provided and fastq files where spitted according to barcode
Mapping of reads using STAR and options: --alignEndsType Extend5pOfRead1; --outFilterMatchNminOverLread 0.9; --outFilterMultimapNmax 3; --limitBAMsortRAM 100000000000; alignIntronMax 2500
Deduplication using UMIs was done with umitools
Count statistics on species and RNA composition were determined using bedtools intersect (aka intersectBed) Version: v2.29.2, bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>
Genome_build: Saccharomyces cerevisiae R64-1-1, Schizosaccharomyces pombe (ASM294v2)  and Schizosaccharomyces pombe: GCF_000002945.1_ASM294v2_genomic.fna; GCF_000002945.1_ASM294v2_genomic.gff was created and files were mapped using STAR
Supplementary_files_format_and_content: Bedgraphs of forward (fwd) and reverse (rev) 5P read positions were created using BEDTools genomecov program with options {-bg -strand [+/-] -5} of concatenated Saccharomyces cerevisiae and Schizosaccharomyces pombe genome

organism: Saccharomyces cerevisiae

source_name: cells

growth_protocol: Cells were grown in glucose rich medium (YPD) to exponential phase and for

extract_protocol:
Total RNA was prepared by adding acid phenol (200 ul) on the cell pellet together with 200 ul of TES (Tris/EDTA/SDS) (Current Protocols in Molecular Biology (1993)), soluble RNA was prepared by lysing the cell pellet as for polysome profiling (Panasenko and Collart, 2012, doi:10.1111/j.1365-2958.2011.07957.x), and addition of an equal volume of hot acid phenol to the lysis buffer.
HT-5PSeq libraries were generated as reported (Zhang and Pelechano, doi: https://doi.org/10.1101/2020.06.22.165134) with minor modifications.   In brief, 15µg total RNA, containing 5% total RNA from Schizosaccharomyces pombe as spike-in, was used. Each sample was spited in two. One part was used for preparing conventional HT-5PSeq libraries and the other part for was random fragmented prior to the preparation of HT-5PSeq libraries (negative control).  For random fragmented samples: 7.5ug RNA was fragmentation at 80 ̊C for five minutes in fragmentation buffer (40mM Tris Acetate pH 8.1, 100mM KOAc and 30mM MgOAc). Samples were purified using 1.8x volumes of RNACleanXP beads (Beckman Coulter) following re-phosphorylation of 5’OH sites at 37 ̊C for 60 minutes with 5 Units of T4 Polynucleotide kinase (PNK, NEB). Subsequent, reaction was purified using Phenol:Chloroform: Isoamyl Alcohol (24:25:1), followed by sodium acetate-ethanol precipitation. From this step forward, experimental pipelines for random fragmented and HT-5PSeq library preparation merge.   For HT-5PSeq Libraries: 7.5 µg RNA was ligated over night at 16˚C to r5P_RNA_MPX oligo (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN). Ligase was deactivated using 5mM EDTA and heat at 65˚C for 10 minutes (up to X individual barcoded RNA ligations were pooled) and subsequent purified using 1.8x volumes of RNAClean XP beads (Beckman Coulter). Ligated RNA was then reverse transcribed using random hexamer (5Pseq-RT, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN, 20µM) and oligo-dT (5Pseq-dT, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTTTTTTTTTT at 0.05µM) oligos to prime. After, remaining RNA was degraded using NaOH. Ribosomal RNA was removed using previously descrived rRNA DNA oligo depletion mixes, following a duplex-specific nuclease (DSN, Evrogen) digestion. rRNA depleted cDNA was amplified by PCR (17 cycles) and final product was enriched for fragments with the range of 300-500nt using Ampure XP.   Size selected HT-5P Libraries were quantified by fluorescence (Qubit, Thermo Fisher), size estimated using an Agilent Bioanalyzer and sequenced using a NextSeq500 Illumina sequencer (75cycles High output kit).  Sequencing files were demultiplexed using bcl2fastq v2.20.0.422 (one mismatch, minimum length 35nt), and adapters were trimmed using cutadapt 2.3.  at default settings, allowing one mismatch and minimum read length of 35nt. In addition to standard illumine dual index (i5, i7), the inline sample and UMI barcode was analyzed using Umitools. Reads were mapped to the concatenated genome of S. cervisiae (R64-1-1) and S. pombe (ASM294v2) using STAR.  Second read enables to splits reads between oligo-dT or random primer. That information was not used in the current analysis.

treatment_protocol: Strains with a degron were additionally treated for 15 min at 1 mM final.

value: ADH1p-TIR1::URA3 leu2 trp1 ura3

tag: culture conditions

value: YPD exponential growth, 15 min auxin 1mM final

tag: library protocol

value: HT-5PSeq Multiplexed RNA ligation

tag: molecule

value: total RNA


title: Wt_AI_tot01_SC_SP_ CGTGCA


title: Wt_AI_tot02_SC_SP_TAATGT


title: Wt_AI_sol03_SC_SP_GTGATC

value: soluble RNA


title: Ctrl-18(IP)

tag: tissue

tag: strain


title: Wt_AI_sol02_SC_SP_ACGCTG


title: Sample22: Ifnar1-/- HAV 4

source_name: liver

value: F

value: liver

tag: treatment

value: HAV infection 7 days


title: Not1p_AI_tot02_SC_SP_CTACAC

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not1::NOT1-AID-Myc9-NATMX4


title: Wt_AI_sol01_SC_SP_GACTAG


title: Not1p_AI_sol03_SC_SP_ACTGGT


title: Not1p_AI_sol02_SC_SP_GTGATC


title: Not1p_AI_tot03_SC_SP_GACTAG


title: Not1p_AI_sol01_SC_SP_ACGCTG


title: Not1p_AI_tot01_SC_SP_TAATGT


title: Whole embryo_Nicotine_3

source_name: Whole embryo

tag: age

value: 9.5 days post coitum

tag: gender

value: Male

value: Nicotine


title: Wt_tot03_SC_SP_ACTGGT

value: MAT[alpha] his3 leu2 ura3 lys2

value: YPD exponential growth


title: Wt_tot02_SC_SP_GTGATC


title: LPS-6(IP)

value: heart - left ventricle

value: male

value: 8  week

value: Wistar


title: Wt_tot01_SC_SP_ACGCTG


title: Wt_sol03_SC_SP_CTACAC


title: Wt_sol02_SC_SP_TAATGT


title: Wt_sol01_SC_SP_CGTGCA


title: not5∆_tot03_SC_SP_TAATGT

value: MAT[alpha] his3 leu2 ura3 lys2 not5::KanMX


title: genomic DNA from umbilical cord bood 470

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

description: 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

label: Cy5 and Cy3

organism: Homo sapiens

source_name: umbilical cord blood 470

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: sample type

value: Umbilical cord blood


title: not5∆_tot02_SC_SP_CGTGCA

value: HT-5PSeq Multiplexed RNA ligation

value: total RNA


title: genomic DNA from umbilical cord bood 469

description: umbilical cord blood sample

source_name: umbilical cord blood 469

value: Female


title: genomic DNA from umbilical cord bood 460

description: umbilical cord blood sample

source_name: umbilical cord blood 460


title: not5∆_tot01_SC_SP_ ACTGGT


title: genomic DNA from umbilical cord bood 464

description: umbilical cord blood sample

source_name: umbilical cord blood 464


title: genomic DNA from umbilical cord bood 468

description: umbilical cord blood sample

source_name: umbilical cord blood 468


title: genomic DNA from umbilical cord bood 454

description: umbilical cord blood sample

source_name: umbilical cord blood 454


title: not5∆_sol02_SC_SP_GACTAG

value: soluble RNA


title: genomic DNA from umbilical cord bood 462

description: umbilical cord blood sample

source_name: umbilical cord blood 462


title: genomic DNA from umbilical cord bood 449

description: umbilical cord blood sample

source_name: umbilical cord blood 449


title: genomic DNA from umbilical cord bood 459

description: umbilical cord blood sample

source_name: umbilical cord blood 459


title: genomic DNA from umbilical cord bood 461

description: umbilical cord blood sample

source_name: umbilical cord blood 461


title: genomic DNA from umbilical cord bood 456

description: umbilical cord blood sample

source_name: umbilical cord blood 456


title: genomic DNA from umbilical cord bood 455

description: umbilical cord blood sample

source_name: umbilical cord blood 455


title: genomic DNA from umbilical cord bood 458

description: umbilical cord blood sample

source_name: umbilical cord blood 458


title: not5∆_sol01_SC_SP_CTACAC


title: genomic DNA from umbilical cord bood 450

description: umbilical cord blood sample

source_name: umbilical cord blood 450


title: genomic DNA from umbilical cord bood 466

description: umbilical cord blood sample

source_name: umbilical cord blood 466


title: genomic DNA from umbilical cord bood 467

description: umbilical cord blood sample

source_name: umbilical cord blood 467


title: genomic DNA from umbilical cord bood 451

description: umbilical cord blood sample

source_name: umbilical cord blood 451


title: genomic DNA from umbilical cord bood 447

description: umbilical cord blood sample

source_name: umbilical cord blood 447


title: genomic DNA from umbilical cord bood 465

description: umbilical cord blood sample

source_name: umbilical cord blood 465


title: genomic DNA from umbilical cord bood 452

description: umbilical cord blood sample

source_name: umbilical cord blood 452


title: not4∆_tot03_SC_SP_CGTGCA

source_name: cells

value: MAT[alpha] his3 leu2 ura3 lys2 not4::KanMX


title: genomic DNA from umbilical cord bood 457

description: umbilical cord blood sample

source_name: umbilical cord blood 457


title: not4∆_tot01_SC_SP_GTGATC


title: not4∆_sol03_SC_SP_GACTAG


title: not4∆_sol02_SC_SP_CTACAC


title: not4∆_sol01_SC_SP_TAATGT


title: not4∆_tot02_SC_SP_ACTGGT


title: TNL8

first: Chaolu

last: Chen

address: Xueshi Road

institute: Women’s Hospital, School of Medicine, Zhejiang University

data_processing:
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Then these libraries were sequenced on the Illumina sequencing platform ( Illumina HiSeq 4000) and 150bp paired-end reads were generated.
Raw data(raw reads)were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: myometrium

growth_protocol: Tissues were snap-frozen in liquid nitrogen and preserved at -80℃ until use.

extract_protocol:
total RNA was extracted by TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: condition

value: TNL

value: myometrium


title: genomic DNA from umbilical cord bood 453

description: umbilical cord blood sample

source_name: umbilical cord blood 453


title: genomic DNA from umbilical cord bood 463

description: umbilical cord blood sample

source_name: umbilical cord blood 463

value: Male


title: TNL7


title: TNL5


title: TNL4


title: TNL3


title: genomic DNA from umbilical cord bood 443

description: umbilical cord blood sample

source_name: umbilical cord blood 443


title: genomic DNA from umbilical cord bood 445

description: umbilical cord blood sample

source_name: umbilical cord blood 445


title: TNL2


title: genomic DNA from umbilical cord bood 442

description: umbilical cord blood sample

source_name: umbilical cord blood 442


title: not5∆_sol03_SC_SP_ACGCTG

tag: genotype


title: TNL1


title: genomic DNA from umbilical cord bood 448

description: umbilical cord blood sample

source_name: umbilical cord blood 448


title: TL8

value: TL


title: TL7


title: TL6


title: TNL6


title: TL5


title: TL4


title: genomic DNA from umbilical cord bood 439

description: umbilical cord blood sample

source_name: umbilical cord blood 439


title: TL3


title: genomic DNA from umbilical cord bood 444

description: umbilical cord blood sample

source_name: umbilical cord blood 444


title: TL2


title: TL1


title: genomic DNA from umbilical cord bood 437

description: umbilical cord blood sample

source_name: umbilical cord blood 437


title: genomic DNA from umbilical cord bood 446

description: umbilical cord blood sample

source_name: umbilical cord blood 446


title: sh3

first: Shuchen

last: Gu

state: Shanghai

institute: Shanghai Ninth People's Hospital

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: FPKM

source_name: fibroblast

extract_protocol:
fresh frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

treatment_protocol: The short hairpin RNA (shRNA) targeting CSMD1 was synthetized and the recombinant lentiviral vectors (Lenti-shRNA-CSMD1) were generated by Zorin Co. Ltd. (Shanghai, China). The RNA interference target was 5’-GCATACAACCCACCTGCATTG-3’. Lentiviral vector carrying green fluorescent protein without target genes (Lenti-GFP) was constructed as negative control. The fibroblast cell line was transfected with Lenti-shRNA-CSMD1 (shCSMD1) and Lenti-GFP (shNC) respectively at MOI of 30 in 6-well dishes for 24h, with the assistance of 6μg/ml polybrene.

value: skin

tag: cell type

value: skin fibroblast

value: CSMD1 knockdown by shRNA


title: genomic DNA from umbilical cord bood 438

description: umbilical cord blood sample

source_name: umbilical cord blood 438


title: genomic DNA from umbilical cord bood 441

description: umbilical cord blood sample

source_name: umbilical cord blood 441


title: genomic DNA from umbilical cord bood 433

description: umbilical cord blood sample

source_name: umbilical cord blood 433


title: genomic DNA from umbilical cord bood 440

description: umbilical cord blood sample

source_name: umbilical cord blood 440


title: K43R-ZVNGET-T3

city: Heidelberg

first: Karsten

last: Rippe

address: Im Neuenheimer Feld 280

department: Chromatin Networks

country: Germany

institute: German Cancer Research Center

data_processing:
10x genomics CellRanger 3.01
Removal of Immunoglobulin genes (n=410)
Quality filtering (mitochondrial reads/detected genes per cell)
Doublet removal (Scrublet Python tool, sim_doublet_ratio = 2; n_neighbors = 30; expected_doublet_rate = 0.1. All cells with a doublet score > 0.4 were discarded + manual curation)
Removal of low-quality clusters (high percentages of mitochondrial gene counts, low housekeeping signature scores and/or low numbers of detected genes as well as no expression of biologically relevant cell type or cell state specific genes)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw UMI count table (cell x gene)

source_name: Bone marrow aspirate

extract_protocol:
Bone marrow aspirate; Ficoll gradient, magnetic sorting (CD138)
10x genomics chromium scRNA-seq 3´ (v2)

tag: tumor stage

value: refractory multiple myeloma

value: bone marrow

tag: cell fraction

value: Whole bone marrow - buffy coat (arm)


title: genomic DNA from umbilical cord bood 429

description: umbilical cord blood sample

source_name: umbilical cord blood 429


title: shNC

value: negative control


title: K43R-ZVNGET-T2

value: Whole bone marrow - buffy coat (shoulder)


title: genomic DNA from umbilical cord bood 436

description: umbilical cord blood sample

source_name: umbilical cord blood 436

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 432

description: umbilical cord blood sample

source_name: umbilical cord blood 432


title: genomic DNA from umbilical cord bood 430

description: umbilical cord blood sample

source_name: umbilical cord blood 430


title: genomic DNA from umbilical cord bood 427

description: umbilical cord blood sample

source_name: umbilical cord blood 427


title: K43R-ZPMZFJ-T3

value: Tumor - bone marrow CD138+


title: K43R-ZPMZFJ-N2

value: Normal - bone marrow CD138-


title: genomic DNA from umbilical cord bood 434

description: umbilical cord blood sample

source_name: umbilical cord blood 434


title: K43R-ZPMZFJ-N1


title: K43R-ZPMZFJ-T2


title: genomic DNA from umbilical cord bood 424

description: umbilical cord blood sample

source_name: umbilical cord blood 424

value: Female


title: genomic DNA from umbilical cord bood 421

description: umbilical cord blood sample

source_name: umbilical cord blood 421


title: genomic DNA from umbilical cord bood 428

description: umbilical cord blood sample

source_name: umbilical cord blood 428


title: genomic DNA from umbilical cord bood 435

description: umbilical cord blood sample

source_name: umbilical cord blood 435


title: K43R-YK554L-F2

value: Whole bone marrow - buffy coat


title: K43R-YK554L-N2


title: genomic DNA from umbilical cord bood 425

description: umbilical cord blood sample

source_name: umbilical cord blood 425


title: genomic DNA from umbilical cord bood 422

description: umbilical cord blood sample

source_name: umbilical cord blood 422


title: genomic DNA from umbilical cord bood 426

description: umbilical cord blood sample

source_name: umbilical cord blood 426


title: genomic DNA from umbilical cord bood 420

description: umbilical cord blood sample

source_name: umbilical cord blood 420


title: K43R-ZPMZFJ-N3


title: genomic DNA from umbilical cord bood 431

description: umbilical cord blood sample

source_name: umbilical cord blood 431


title: K43R-YK554L-N1


title: genomic DNA from umbilical cord bood 417

description: umbilical cord blood sample

source_name: umbilical cord blood 417


title: K43R-YK554L-T2

source_name: Bone marrow aspirate


title: genomic DNA from umbilical cord bood 418

description: umbilical cord blood sample

source_name: umbilical cord blood 418


title: genomic DNA from umbilical cord bood 423

description: umbilical cord blood sample

source_name: umbilical cord blood 423


title: K43R-ZPMZFJ-T1


title: K43R-XF2DTB-N2


title: genomic DNA from umbilical cord bood 416

description: umbilical cord blood sample

source_name: umbilical cord blood 416


title: genomic DNA from umbilical cord bood 415

description: umbilical cord blood sample

source_name: umbilical cord blood 415


title: K43R-VP6CSY-N2


title: K43R-VP6CSY-T2


title: K43R-VP6CSY-N1


title: K43R-VP6CSY-T1


title: genomic DNA from umbilical cord bood 414

description: umbilical cord blood sample

source_name: umbilical cord blood 414


title: K43R-TS6ZX9-N2


title: K43R-YK554L-T1


title: K43R-XF2DTB-T2


title: K43R-TS6ZX9-T1


title: K43R-R1V8RN-N2


title: genomic DNA from umbilical cord bood 410

description: umbilical cord blood sample

source_name: umbilical cord blood 410


title: genomic DNA from umbilical cord bood 409

description: umbilical cord blood sample

source_name: umbilical cord blood 409


title: K43R-TS6ZX9-T2


title: K43R-R1V8RN-T2


title: genomic DNA from umbilical cord bood 413

description: umbilical cord blood sample

source_name: umbilical cord blood 413


title: K43R-R1V8RN-N1


title: genomic DNA from umbilical cord bood 412

description: umbilical cord blood sample

source_name: umbilical cord blood 412


title: genomic DNA from umbilical cord bood 411

description: umbilical cord blood sample

source_name: umbilical cord blood 411


title: genomic DNA from umbilical cord bood 408

description: umbilical cord blood sample

source_name: umbilical cord blood 408


title: K43R-TS6ZX9-N1


title: K43R-R1V8RN-T1


title: K43R-R1H4HE-N2


title: genomic DNA from umbilical cord bood 404

description: umbilical cord blood sample

source_name: umbilical cord blood 404


title: genomic DNA from umbilical cord bood 419

description: umbilical cord blood sample

source_name: umbilical cord blood 419


title: K43R-R1H4HE-N1


title: genomic DNA from umbilical cord bood 406

description: umbilical cord blood sample

source_name: umbilical cord blood 406


title: genomic DNA from umbilical cord bood 405

description: umbilical cord blood sample

source_name: umbilical cord blood 405


title: genomic DNA from umbilical cord bood 402

description: umbilical cord blood sample

source_name: umbilical cord blood 402


title: K43R-R1H4HE-T1

source_name: Bone marrow aspirate


title: K43R-PUVQFD-F1-H02


title: K43R-PUVQFD-N1-H02


title: genomic DNA from umbilical cord bood 397

description: umbilical cord blood sample

source_name: umbilical cord blood 397


title: K43R-PUVQFD-T1-H02


title: genomic DNA from umbilical cord bood 403

description: umbilical cord blood sample

source_name: umbilical cord blood 403


title: K43R-PUVQFD-F1-H01


title: K43R-PUVQFD-N1-H01


title: genomic DNA from umbilical cord bood 398

description: umbilical cord blood sample

source_name: umbilical cord blood 398


title: genomic DNA from umbilical cord bood 395

description: umbilical cord blood sample

source_name: umbilical cord blood 395


title: genomic DNA from umbilical cord bood 407

description: umbilical cord blood sample

source_name: umbilical cord blood 407


title: genomic DNA from umbilical cord bood 393

description: umbilical cord blood sample

source_name: umbilical cord blood 393


title: genomic DNA from umbilical cord bood 399

description: umbilical cord blood sample

source_name: umbilical cord blood 399


title: K43R-NUL141-N1


title: genomic DNA from umbilical cord bood 400

description: umbilical cord blood sample

source_name: umbilical cord blood 400


title: genomic DNA from umbilical cord bood 394

description: umbilical cord blood sample

source_name: umbilical cord blood 394


title: K43R-NUL141-T2


title: genomic DNA from umbilical cord bood 387

description: umbilical cord blood sample

source_name: umbilical cord blood 387


title: genomic DNA from umbilical cord bood 396

description: umbilical cord blood sample

source_name: umbilical cord blood 396


title: K43R-N7ZK3L-N2


title: genomic DNA from umbilical cord bood 401

description: umbilical cord blood sample

source_name: umbilical cord blood 401


title: genomic DNA from umbilical cord bood 390

description: umbilical cord blood sample

source_name: umbilical cord blood 390


title: K43R-N7ZK3L-T2


title: K43R-NUL141-T1


title: K43R-PUVQFD-T1-H01


title: K43R-N7ZK3L-N1


title: K43R-N7ZK3L-T1


title: genomic DNA from umbilical cord bood 391

description: umbilical cord blood sample

source_name: umbilical cord blood 391


title: genomic DNA from umbilical cord bood 389

description: umbilical cord blood sample

source_name: umbilical cord blood 389


title: K43R-N5CC3E-Z2


title: genomic DNA from umbilical cord bood 384

description: umbilical cord blood sample

source_name: umbilical cord blood 384


title: K43R-NUL141-N2

source_name: Bone marrow aspirate


title: genomic DNA from umbilical cord bood 392

description: umbilical cord blood sample

source_name: umbilical cord blood 392


title: K43R-R1H4HE-T2


title: K43R-N5CC3E-T2


title: K43R-N5CC3E-T1


title: K43R-N5CC3E-Z1


title: K43R-E79WZA-F1-H02


title: genomic DNA from umbilical cord bood 386

description: umbilical cord blood sample

source_name: umbilical cord blood 386


title: K43R-E79WZA-T1-H02


title: K43R-E79WZA-N1-H02


title: K43R-E79WZA-N1-H01


title: K43R-E79WZA-F1-H01


title: genomic DNA from umbilical cord bood 383

description: umbilical cord blood sample

source_name: umbilical cord blood 383


title: genomic DNA from umbilical cord bood 381

description: umbilical cord blood sample

source_name: umbilical cord blood 381


title: genomic DNA from umbilical cord bood 378

description: umbilical cord blood sample

source_name: umbilical cord blood 378


title: genomic DNA from umbilical cord bood 377

description: umbilical cord blood sample

source_name: umbilical cord blood 377


title: K43R-CSU6UB-Z3


title: genomic DNA from umbilical cord bood 382

description: umbilical cord blood sample

source_name: umbilical cord blood 382


title: K43R-CSU6UB-T3


title: genomic DNA from umbilical cord bood 388

description: umbilical cord blood sample

source_name: umbilical cord blood 388


title: K43R-CSU6UB-Z2


title: K43R-CSU6UB-T2


title: K43R-8YGUU8-F4


title: K43R-E79WZA-T1-H01


title: genomic DNA from umbilical cord bood 380

description: umbilical cord blood sample

source_name: umbilical cord blood 380


title: genomic DNA from umbilical cord bood 369

description: umbilical cord blood sample

source_name: umbilical cord blood 369


title: genomic DNA from umbilical cord bood 379

description: umbilical cord blood sample

source_name: umbilical cord blood 379


title: K43R-8YGUU8-Z4


title: genomic DNA from umbilical cord bood 376

description: umbilical cord blood sample

source_name: umbilical cord blood 376


title: genomic DNA from umbilical cord bood 371

description: umbilical cord blood sample

source_name: umbilical cord blood 371


title: genomic DNA from umbilical cord bood 385

description: umbilical cord blood sample

source_name: umbilical cord blood 385


title: K43R-8YGUU8-T4


title: K43R-8YGUU8-Z3


title: genomic DNA from umbilical cord bood 375

description: umbilical cord blood sample

source_name: umbilical cord blood 375


title: K43R-8YGUU8-T3


title: genomic DNA from umbilical cord bood 367

description: umbilical cord blood sample

source_name: umbilical cord blood 367


title: genomic DNA from umbilical cord bood 373

description: umbilical cord blood sample

source_name: umbilical cord blood 373


title: genomic DNA from umbilical cord bood 366

description: umbilical cord blood sample

source_name: umbilical cord blood 366


title: K43R-8YGUU8-T2

source_name: Bone marrow aspirate


title: genomic DNA from umbilical cord bood 374

description: umbilical cord blood sample

source_name: umbilical cord blood 374


title: K43R-6KLSUS-F2-H02


title: genomic DNA from umbilical cord bood 363

description: umbilical cord blood sample

source_name: umbilical cord blood 363


title: genomic DNA from umbilical cord bood 364

description: umbilical cord blood sample

source_name: umbilical cord blood 364


title: genomic DNA from umbilical cord bood 372

description: umbilical cord blood sample

source_name: umbilical cord blood 372


title: genomic DNA from umbilical cord bood 368

description: umbilical cord blood sample

source_name: umbilical cord blood 368


title: K43R-6KLSUS-T2-H02


title: K43R-6KLSUS-N2-H02


title: K43R-6KLSUS-F2-H01


title: genomic DNA from umbilical cord bood 361

description: umbilical cord blood sample

source_name: umbilical cord blood 361


title: K43R-8YGUU8-Z2


title: genomic DNA from umbilical cord bood 360

description: umbilical cord blood sample

source_name: umbilical cord blood 360


title: K43R-6KLSUS-T2-H01


title: K43R-6K8YTY-F3


title: genomic DNA from umbilical cord bood 370

description: umbilical cord blood sample

source_name: umbilical cord blood 370


title: genomic DNA from umbilical cord bood 362

description: umbilical cord blood sample

source_name: umbilical cord blood 362


title: K43R-6K8YTY-Z2


title: K43R-6K8YTY-Z3


title: K43R-6KLSUS-N2-H01


title: genomic DNA from umbilical cord bood 365

description: umbilical cord blood sample

source_name: umbilical cord blood 365


title: genomic DNA from umbilical cord bood 357

description: umbilical cord blood sample

source_name: umbilical cord blood 357


title: K43R-6K8YTY-T2


title: K43R-37A66E-N2


title: K43R-37A66E-T2


title: K43R-37A66E-N1


title: genomic DNA from umbilical cord bood 355

description: umbilical cord blood sample

source_name: umbilical cord blood 355


title: genomic DNA from umbilical cord bood 358

description: umbilical cord blood sample

source_name: umbilical cord blood 358


title: genomic DNA from umbilical cord bood 351

description: umbilical cord blood sample

source_name: umbilical cord blood 351


title: K43R-6K8YTY-T3


title: K43R-37A66E-T1


title: genomic DNA from umbilical cord bood 359

description: umbilical cord blood sample

source_name: umbilical cord blood 359


title: genomic DNA from umbilical cord bood 354

description: umbilical cord blood sample

source_name: umbilical cord blood 354


title: K43R-32ARQL-N2

source_name: Bone marrow aspirate


title: genomic DNA from umbilical cord bood 352

description: umbilical cord blood sample

source_name: umbilical cord blood 352


title: K43R-32ARQL-T2


title: genomic DNA from umbilical cord bood 347

description: umbilical cord blood sample

source_name: umbilical cord blood 347


title: genomic DNA from umbilical cord bood 356

description: umbilical cord blood sample

source_name: umbilical cord blood 356


title: K43R-2FTMUU-N2


title: K43R-2FTMUU-T2


title: K43R-2FTMUU-N1


title: genomic DNA from umbilical cord bood 350

description: umbilical cord blood sample

source_name: umbilical cord blood 350


title: ChIPseq_Histones_PC3_input

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

institute: University of Zurich

library_source: genomic

data_processing:
ChIPseq reads from Ilumina HiSeq to the human hg38 reference genome using Bowtie2 (version 2.2.5). Duplicated sequences were removed with samtools-1.9. Read counts were computed and normalized using “bamCoverage” from deepTools (version 2.0.1; (Ramirez et al., 2014)) using a bin size of 50bp in order to generate bigwig files. Enriched regions (peaks) were calulated with MACS 2.0 (default settings). For HA-TIP5 ChIPs, enriched regions were calcutated with p-val <0.01. Genomic annotation of ChIPseq peaks was done with ChIPseeker (Yu et al., 2015). Genome_build: GRCh38/hg38
Genome_build: GRCh38/hg38

source_name: PC3 cells

growth_protocol: PC3 cells were cultured in RPMI 1640 medium and Ham's F12 medium (1:1; Gibco) containing 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco). PCa spheres were cultured in serum free DMEM/F12 medium (1:1, Gibco) supplemented with 20ng/ml of basic human FGF (Sigma), 20ng/ml of EGF (Sigma), 3μg/ml of Insulin (Sigma) and 1x B-27 (Gibco). 1x104 cells were seeded in low adhesion petri dishes (Greiner) and cultured for 6 to 8 days. About 20% of media was changed every 2 days. All cells were regularly tested for mycoplasma contamination.

extract_protocol: ChIP experiments were performed as previously described (Leone et al., 2017). Briefly, 1% formaldehyde was added to cultured cells to cross-link proteins to DNA. Isolated nuclei were then lysed (50 mM Tris-HCl pH 8.1, 10 mM EDTA and 1% SDS) and sonicated using a Bioruptor ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin was diluted tenfold with ChIP buffer (16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS and 1.1% Triton X-100) and precleared for 2h with 10ul of packed Sepharose beads for at least 2h at 4°C. Immunoprecipitation was done overnight with the indicated antibodies. Pulldowns were done with Dynabeads protein-A (or -G, Millipore) for 4h at 4°C. For HA-TIP5 ChIPs, preclearing and pulldowns were done with beads block with BSA (50μg) and ytRNA (50μg), per 400ul of Dynabeads protein-A. After washing, elution and reversion of cross-links, eluates were treated with RNAse A (1μg). DNA was purified with phenol-chloroform, ethanol precipitated and quantified by quantitative PCR. The quantity and quality of the isolated DNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The NEBNext® Ultra™ II DNA Library Prep Kit from NEB (New England Biolabs, Ipswich, MA) was used in the succeeding steps. ChIP samples (1ng) were end-repaired and adenylated.  Adapters containing the index for multiplexing were ligated to the fragmented DNA samples. Fragments containing adapters on both ends were enriched by PCR.  The quality and quantity of the enriched libraries were measured using Qubit® (1.0) Fluorometer and the Tapestation (Agilent, Waldbronn, Germany). The product is a smear with an average fragment size of approximately 300 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina HiSeq 2500 ot Hiseq 4000 single end 125 bp using the TruSeq SBS Kit v4-HS (Illumina, Inc, California, USA).

tag: cancer status

value: Metastatic

value: Prostate

value: PC3 cells

value: ChIPseq

tag: chip antibody

value: none (input)


title: genomic DNA from umbilical cord bood 349

description: umbilical cord blood sample

source_name: umbilical cord blood 349

value: Male


title: ChIPseq_H3K27ac_PC3

value: H3K27ac (Abcam ab4729)


title: ChIPseq_H3K14ac_PC3

value: H3K14ac (Active Motif 61433)


title: genomic DNA from umbilical cord bood 346

description: umbilical cord blood sample

source_name: umbilical cord blood 346


title: genomic DNA from umbilical cord bood 339

description: umbilical cord blood sample

source_name: umbilical cord blood 339


title: ChIPseq_H3K27me3_PC3

value: H3K27me3 (Active Motif 39155)


title: ChIPseq_H3K4me3_PC3

value: H3K4me3 (Millipore 07-473)


title: genomic DNA from umbilical cord bood 343

description: umbilical cord blood sample

source_name: umbilical cord blood 343


title: genomic DNA from umbilical cord bood 345

description: umbilical cord blood sample

source_name: umbilical cord blood 345


title: genomic DNA from umbilical cord bood 342

description: umbilical cord blood sample

source_name: umbilical cord blood 342


title: genomic DNA from umbilical cord bood 353

description: umbilical cord blood sample

source_name: umbilical cord blood 353


title: genomic DNA from umbilical cord bood 348

description: umbilical cord blood sample

source_name: umbilical cord blood 348


title: genomic DNA from umbilical cord bood 340

description: umbilical cord blood sample

source_name: umbilical cord blood 340


title: genomic DNA from umbilical cord bood 334

description: umbilical cord blood sample

source_name: umbilical cord blood 334


title: genomic DNA from umbilical cord bood 337

description: umbilical cord blood sample

source_name: umbilical cord blood 337


title: K43R-2FTMUU-T1

source_name: Bone marrow aspirate

value: refractory multiple myeloma

value: bone marrow


title: genomic DNA from umbilical cord bood 344

description: umbilical cord blood sample

source_name: umbilical cord blood 344

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 332

description: umbilical cord blood sample

source_name: umbilical cord blood 332


title: Sample 213

city: Syracuse

first: Vladimir

middle: A

last: Kuznetsov

state: NY

address: 750 E Adams St

department: Urology / Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

description: human breast tumor RNA

hyb_protocol: standard

scan_protocol: Labelled cRNAs were fragmented to an average size of approximately 50–100 nucleotides by heating at 60 °C in the presence of 10 mM ZnCl2, added to a hybridization buffer containing 1 M NaCl, 0.5% sodium sarcosine, 50 mM MES, pH 6.5, and formamide to a final concentration of 30%, final volume 3 ml at 40 °C. Hu25K microarrays represented the 24,479 biological oligonucleotides plus 1,281 control probes. Sequences for microarrays were selected from RefSeq (a collection of non-redundant mRNA sequences; http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html) and from expressed sequence tag (EST) contigs (http://www.phrap.org/est_assembly/human/gene_number_methods.html). Each mRNA or EST contig was represented on the Hu25K microarray by a single 60-polymer oligonucleotide chosen by the oligonucleotide probe design programme. After hybridization, slides were washed and scanned using a confocal laser scanner (Agilent Technologies). Fluorescence intensities on scanned images were quantified, corrected for background noise and normalized.

data_processing:
Normalization between the channels was accomplished by normalizing each channel to the mean intensities of all genes.
Batch effect correction using the Kolmogorov-Smirnov weighted mean method was used to reduce variability between patients. Patients were first categorized into batches. Then, for each probe, Kolmogorov-Smirnov statistics were calculated for every batch permutation. Weights were calculated by using the sum normalized sums of the KS distance matrix. Weights were used to calculate the weighted mean expression value of the given probe. Weighted average mean correction was then performed on each batch.

source_name: pool of individual breast tumors

label_protocol: cRNA was generated by in vitro transcription using T7 RNA polymerase on 5 µg total RNA and labelled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech). Five micrograms of Cy-labelled cRNA from one breast cancer tumour was mixed with the same amount of reverse colour Cy-labelled product from a pool, which consisted of an equal amount of cRNA from each individual sporadic patient

extract_protocol:
The criteria for the sporadic patients (n = 97) were: primary invasive breast carcinoma less than 5 cm (T1 or T2), no axillary metastases (N0), age at diagnosis less than 55 years, calendar year of diagnosis 1983–1996, no previous malignancies; all patients were treated by modified radical mastectomy (n = 35) or breast-conserving treatment (n = 62), including axillary lymph node dissection followed by radiotherapy. Five patients of the metastases group received adjuvant systemic therapy consisting of chemotherapy (n = 3) or hormonal therapy (n = 2), all other patients did not receive additional treatment. All patients were followed at least annually for a period of at least 5 years. The criteria for hereditary patients (n = 20) were: carriers of a germline mutation in BRCA1 or BRCA2, and primary invasive breast carcinoma; no other selection criterion was applied. This study was approved by the Medical Ethical Committee of the Netherlands Cancer Institute.
Tumour material was snap-frozen in liquid nitrogen within 1 h after surgery. A haematoxylin and eosin stained section was prepared before and after cutting slides for RNA isolation for assessment of the percentage of tumour cells. Only samples with greater than 50% tumour cells were selected, mean 67% and median 70% for all groups studied. Formalin-fixed, paraffin-embedded tumour tissue was used to evaluate the following: tumour type (according to the World Health Organisation classification), histological grade (grade 1–3), and the presence of angioinvasive growth and extensive lymphocytic infiltrate. ER expression was determined by immunohistochemical staining (negative when less than 10% of the nuclei showed staining, all others ER positive).
We used 30 sections of 30-µm thickness for total RNA isolation. Total RNA was isolated with RNAzolB, and finally dissolved in RNase-free H2O. Twenty-five micrograms of total RNA was treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns. Total RNA treated with DNase was dissolved in RNase-free H2O to a final concentration of 0.2 µg µl-1.

value: breast tumor

source_name: patient sample

tag: lypmph-nodes

value: LN+

tag: metastatis

value: Meta+

tag: death

value: Dead

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER+

tag: nih

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 331

description: umbilical cord blood sample

source_name: umbilical cord blood 331

tag: gender

tag: sample type


title: genomic DNA from umbilical cord bood 341

description: umbilical cord blood sample

source_name: umbilical cord blood 341


title: Sample 210

description: human breast tumor RNA

tag: tissue

value: Meta-

value: Alive


title: genomic DNA from umbilical cord bood 336

description: umbilical cord blood sample

source_name: umbilical cord blood 336

value: Female


title: Sample 208

description: human breast tumor RNA


title: Sample 207

description: human breast tumor RNA

value: LN-


title: genomic DNA from umbilical cord bood 329

description: umbilical cord blood sample

source_name: umbilical cord blood 329


title: Sample 212

description: human breast tumor RNA

value: ER-


title: Tau+UNC0642_2_PFC

city: Buffalo

first: Zhen

last: Yan

address: 955 Main St

institute: SUNY Buffalo

data_processing:
The RNA sequencing libraries was constructed by TruSeq stranded total RNA plus Ribo-zero kits (Illumina) then sequencing was carried out with the HiSeq 2500 platform (Illumina)
RNA-seq tags reads were aligned to the mouse RefSeq mRNAs using TopHat2 with default parameters. Alignments with a mapping score <10 were discarded using SAMtools.
Feature Counts was used to generate a matrix of mapped fragments per USCS RefSeq known annotated gene, from which genes annotated by RefSeq as rRNA were discarded.
Analysis for differential gene expression was performed using the edgeR package with the default setting.
Genome_build: mm10
Supplementary_files_format_and_content: bam file with genome alignment to mm10 genome

source_name: PFC

extract_protocol:
RNA extraction from PFC samples of biological duplicates in each group used the RNAeasy Mini kit (Qiagen), coupled to an RNase-free DNase step (Qiagen). The strand-specific RNA sequencing libraries were generated from 1 μg purified RNA using TruSeq stranded total RNA plus Ribo-zero kits (Illumina).
The RNA sequencing libraries was constructed by TruSeq stranded total RNA plus Ribo-zero kits (Illumina). Sequencing was carried out with the HiSeq 2500 platform (Illumina) at the Genomics and Bioinformatics Core of State University of New York at Buffalo.Reads were first trimmed using Cutadapt to remove the 3’ end adapters and trailing sequences, followed by aligning to mouse RefSeq mRNAs using TopHat2 with default parameters.

value: PFC

tag: cell type

value: Total cell lysate (bulk)

tag: genotype

tag: treatment


title: genomic DNA from umbilical cord bood 330

description: umbilical cord blood sample

source_name: umbilical cord blood 330


title: genomic DNA from umbilical cord bood 327

description: umbilical cord blood sample

source_name: umbilical cord blood 327


title: genomic DNA from umbilical cord bood 325

description: umbilical cord blood sample

source_name: umbilical cord blood 325

value: Male


title: genomic DNA from umbilical cord bood 333

description: umbilical cord blood sample

source_name: umbilical cord blood 333


title: Sample 209

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

tag: death


title: genomic DNA from umbilical cord bood 338

description: umbilical cord blood sample

source_name: umbilical cord blood 338


title: genomic DNA from umbilical cord bood 328

description: umbilical cord blood sample

source_name: umbilical cord blood 328


title: Sample 202

description: human breast tumor RNA

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)


title: genomic DNA from umbilical cord bood 326

description: umbilical cord blood sample

source_name: umbilical cord blood 326


title: Sample 205

description: human breast tumor RNA

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: Tau+UNC0642_1_PFC


title: Tau_1_PFC

value: Vehicle


title: genomic DNA from umbilical cord bood 335

description: umbilical cord blood sample

source_name: umbilical cord blood 335


title: Sample 201

description: human breast tumor RNA

tag: estrogen-receptor

tag: nih

tag: stgallen


title: Sample 203

description: human breast tumor RNA

tag: conservflag


title: genomic DNA from umbilical cord bood 324

description: umbilical cord blood sample

source_name: umbilical cord blood 324

tag: gender

tag: sample type


title: Sample 200

description: human breast tumor RNA

tag: tissue


title: genomic DNA from umbilical cord bood 320

description: umbilical cord blood sample

source_name: umbilical cord blood 320


title: Tau_2_PFC

tag: cell type

tag: genotype

tag: treatment


title: genomic DNA from umbilical cord bood 321

description: umbilical cord blood sample

source_name: umbilical cord blood 321


title: WT_2_PFC


title: genomic DNA from umbilical cord bood 323

description: umbilical cord blood sample

source_name: umbilical cord blood 323


title: Sample 199

description: human breast tumor RNA

source_name: pool of individual breast tumors

source_name: patient sample

tag: lypmph-nodes

tag: metastatis

tag: death


title: WT_1_PFC


title: genomic DNA from umbilical cord bood 322

description: umbilical cord blood sample

source_name: umbilical cord blood 322


title: 30111_1729wt-EC-16

city: Pasadena

first: David

middle: Eugene

last: Frankhouser

state: CA

address: 1500 E Duarte Rd

department: Population Sciences

institute: City of Hope

data_processing:
Illumina Casava1.8 software was used for basecalling
Sequenced reads were trimmed for adapter sequence and mapped to the mm10 genome using STAR with options –twopassMode Basic --outSAMstrandField intronMotif
Read counts for each gene were produced using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with raw gene counts for each sample

source_name: Bone marrow

extract_protocol:
RNA was extracted from sorted endothelial cells using miRNeasy micro Kit.
Sequencing libraries were prepared by using SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio, Cat 634888) according to user guide with 2ng of total from each sample

value: Endothelial cells

tag: strain

tag: geneotype/treatment

value: wild type

tag: sorted cells

value: Sca-1- Endothelial cells


title: genomic DNA from umbilical cord bood 318

description: umbilical cord blood sample

source_name: umbilical cord blood 318

value: Umbilical cord blood


title: 30115_CD452-EC-22


title: Sample 198

description: human breast tumor RNA

value: breast tumor

value: LN+

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: 30110_1784wt-EC-8


title: Sample 196

description: human breast tumor RNA

tag: estrogen-receptor

tag: nih

tag: stgallen

tag: conservflag


title: Sample 197

description: human breast tumor RNA

tag: tissue


title: genomic DNA from umbilical cord bood 314

description: umbilical cord blood sample

source_name: umbilical cord blood 314

tag: gender

tag: sample type


title: Sample 195

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

tag: death


title: genomic DNA from umbilical cord bood 316

description: umbilical cord blood sample

source_name: umbilical cord blood 316


title: genomic DNA from umbilical cord bood 319

description: umbilical cord blood sample

source_name: umbilical cord blood 319


title: Sample 194

description: human breast tumor RNA

value: Meta+


title: 30019_86_wt-EC-plus-19

tag: cell type

tag: strain

tag: geneotype/treatment

tag: sorted cells

value: Sca-1+ Endothelial cells


title: genomic DNA from umbilical cord bood 315

description: umbilical cord blood sample

source_name: umbilical cord blood 315


title: genomic DNA from umbilical cord bood 312

description: umbilical cord blood sample

source_name: umbilical cord blood 312


title: Sample 193

description: human breast tumor RNA

value: Meta-

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

value: ER+


title: genomic DNA from umbilical cord bood 310

description: umbilical cord blood sample

source_name: umbilical cord blood 310

value: Female


title: genomic DNA from umbilical cord bood 311

description: umbilical cord blood sample

source_name: umbilical cord blood 311


title: 30108_CD452-EC-14


title: genomic DNA from umbilical cord bood 313

description: umbilical cord blood sample

source_name: umbilical cord blood 313


title: genomic DNA from umbilical cord bood 309

description: umbilical cord blood sample

source_name: umbilical cord blood 309


title: Sample 192

description: human breast tumor RNA

value: Dead

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: nih


title: 30109_452-EC-10


title: 30018_CD452-EC-plus-13


title: genomic DNA from umbilical cord bood 317

description: umbilical cord blood sample

source_name: umbilical cord blood 317

tag: gender


title: 30017_1729_wt-EC-plus-15


title: Sample 191

description: human breast tumor RNA

tag: tissue

value: LN-

value: Alive

tag: stgallen

tag: conservflag


title: 30016_EC-plus-7


title: genomic DNA from umbilical cord bood 307

description: umbilical cord blood sample

source_name: umbilical cord blood 307

tag: sample type


title: genomic DNA from umbilical cord bood 306

description: umbilical cord blood sample

source_name: umbilical cord blood 306


title: genomic DNA from umbilical cord bood 304

description: umbilical cord blood sample

source_name: umbilical cord blood 304


title: Sample 190

description: human breast tumor RNA

source_name: pool of individual breast tumors

source_name: patient sample

tag: lypmph-nodes

tag: metastatis

tag: death


title: genomic DNA from umbilical cord bood 305

description: umbilical cord blood sample

source_name: umbilical cord blood 305


title: Sample 189

description: human breast tumor RNA


title: liver-alcohol-fed and abdominal cavity_MNA3

city: Hangzhou

first: Wenwen

last: Yang

address: No.548 Binwen Road, Binjiang District

institute: Zhejiang Chinese Medical University

description:
4_miRNA_Prediction_expression.txt
AF_1_MNA3

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi).
The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: mmu10
Supplementary_files_format_and_content: tab-delimited text file includes original data and expression of miRNA for each Sample.

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0.
Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing (50bp) on an Illumina Hiseq 2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.

tag: strain

value: liver

tag: age

value: post natal day 8 weeks

tag: treatment

value: Mice were fed for 5 weeks, alcohol-fed (AF); MNA was intraperitoneally injected daily at 50mg/kg mouse weight


title: genomic DNA from umbilical cord bood 302

description: umbilical cord blood sample

source_name: umbilical cord blood 302

value: Male


title: genomic DNA from umbilical cord bood 303

description: umbilical cord blood sample

source_name: umbilical cord blood 303


title: Sample 188

description: human breast tumor RNA

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)


title: genomic DNA from umbilical cord bood 299

description: umbilical cord blood sample

source_name: umbilical cord blood 299


title: liver-alcohol-fed and abdominal cavity_MNA1

description:
4_miRNA_Prediction_expression.txt
AF_1_MNA1


title: genomic DNA from umbilical cord bood 300

description: umbilical cord blood sample

source_name: umbilical cord blood 300


title: Sample 187

description: human breast tumor RNA

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: genomic DNA from umbilical cord bood 301

description: umbilical cord blood sample

source_name: umbilical cord blood 301

tag: gender


title: genomic DNA from umbilical cord bood 298

description: umbilical cord blood sample

source_name: umbilical cord blood 298


title: genomic DNA from umbilical cord bood 295

description: umbilical cord blood sample

source_name: umbilical cord blood 295


title: genomic DNA from umbilical cord bood 308

description: umbilical cord blood sample

source_name: umbilical cord blood 308


title: Sample 185

description: human breast tumor RNA

tag: tissue

tag: estrogen-receptor

tag: nih


title: liver-alcohol-fed2

description:
4_miRNA_Prediction_expression.txt
AF2

value: Mice were fed for 5 weeks, alcohol-fed (AF)


title: genomic DNA from umbilical cord bood 291

description: umbilical cord blood sample

source_name: umbilical cord blood 291

tag: sample type


title: genomic DNA from umbilical cord bood 297

description: umbilical cord blood sample

source_name: umbilical cord blood 297


title: liver-alcohol-fed and abdominal cavity_MNA2

description:
4_miRNA_Prediction_expression.txt
AF_1_MNA2


title: Sample 184

description: human breast tumor RNA

tag: lypmph-nodes

value: ER-

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 296

description: umbilical cord blood sample

source_name: umbilical cord blood 296

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 294

description: umbilical cord blood sample

source_name: umbilical cord blood 294


title: genomic DNA from umbilical cord bood 293

description: umbilical cord blood sample

source_name: umbilical cord blood 293


title: genomic DNA from umbilical cord bood 290

description: umbilical cord blood sample

source_name: umbilical cord blood 290


title: liver-pair-fed3

description:
4_miRNA_Prediction_expression.txt
PF3

tag: strain

value: Mice were fed for 5 weeks, pair-fed (PF)


title: liver-alcohol-fed3

description:
4_miRNA_Prediction_expression.txt
AF3

tag: age


title: liver-alcohol-fed1

description:
4_miRNA_Prediction_expression.txt
AF1

tag: treatment


title: liver-pair-fed2

description:
4_miRNA_Prediction_expression.txt
PF2


title: genomic DNA from umbilical cord bood 292

description: umbilical cord blood sample

source_name: umbilical cord blood 292


title: genomic DNA from umbilical cord bood 289

description: umbilical cord blood sample

source_name: umbilical cord blood 289


title: liver-pair-fed1

description:
4_miRNA_Prediction_expression.txt
PF1

source_name: liver


title: genomic DNA from umbilical cord bood 288

description: umbilical cord blood sample

source_name: umbilical cord blood 288


title: genomic DNA from umbilical cord bood 287

description: umbilical cord blood sample

source_name: umbilical cord blood 287


title: genomic DNA from umbilical cord bood 280

description: umbilical cord blood sample

source_name: umbilical cord blood 280


title: genomic DNA from umbilical cord bood 286

description: umbilical cord blood sample

source_name: umbilical cord blood 286


title: genomic DNA from umbilical cord bood 281

description: umbilical cord blood sample

source_name: umbilical cord blood 281


title: genomic DNA from umbilical cord bood 283

description: umbilical cord blood sample

source_name: umbilical cord blood 283


title: Sample 178

description: human breast tumor RNA

source_name: pool of individual breast tumors

value: breast tumor

source_name: patient sample

value: LN+

tag: metastatis

tag: death

tag: timesurvival(years)


title: genomic DNA from umbilical cord bood 279

description: umbilical cord blood sample

source_name: umbilical cord blood 279


title: genomic DNA from umbilical cord bood 284

description: umbilical cord blood sample

source_name: umbilical cord blood 284


title: genomic DNA from umbilical cord bood 282

description: umbilical cord blood sample

source_name: umbilical cord blood 282


title: Sample 182

description: human breast tumor RNA

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years


title: Sample 183

description: human breast tumor RNA

tag: timemeta

tag: metastasis-years


title: Sample 186

description: human breast tumor RNA

tag: tissue

tag: estrogen-receptor


title: Sample 179

description: human breast tumor RNA

tag: nih


title: genomic DNA from umbilical cord bood 278

description: umbilical cord blood sample

source_name: umbilical cord blood 278

tag: gender

tag: sample type


title: Sample 180

description: human breast tumor RNA

tag: lypmph-nodes

value: Meta+

tag: stgallen

tag: conservflag


title: Sample 176

description: human breast tumor RNA

value: Meta-


title: Sample 181

description: human breast tumor RNA


title: genomic DNA from umbilical cord bood 275

description: umbilical cord blood sample

source_name: umbilical cord blood 275


title: Sample 177

description: human breast tumor RNA


title: Sample 174

description: human breast tumor RNA

value: ER+


title: Sample 175

description: human breast tumor RNA


title: genomic DNA from umbilical cord bood 277

description: umbilical cord blood sample

source_name: umbilical cord blood 277

value: Female


title: db Vehicle rep3

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: run0347_lane9_read*_indexN703-S502=db-Veh-48h-3.fastq.gz

data_processing:
RNA-Seq data were pseudoaligned and quantified (transcript per million estimates) using a call to the software Kallisto within AltAnalyze version 2.1.4 and an Ensembl version 72 reference database.
Genome_build: mm10
Supplementary_files_format_and_content: exp.db-BSO.txt

source_name: Obese SLAM HSC cultured for 48 hours

growth_protocol: 1,000 HSC-SLAMs were isolated from db and littermate control mice and cultured for 48h in StemSpan media (StemCell Technologies) with cytokines (SCF 20 ng/mL; TPO 20 ng/mL).

extract_protocol:
After culture, cells were washed with phosphate-buffered saline (PBS), and collected for RNA isolation.
The cDNA synthesis and amplification were done as recommended by Clontech. cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents. Fragmented and tagged libraries were quantified using an agilent bio-analyzer, pooled and sequenced on a HiSeq 2500 platform (Illumina) using the pair-end 75-bp sequencing strategy.

treatment_protocol: Cells were cultured in the presence or absence of BSO (100 µM). After culture, cells were washed with phosphate-buffered saline (PBS), and collected for RNA isolation.

tag: cell type

value: SLAM HSC

tag: age

value: 4 months old

tag: treatement

value: Vehicle


title: Sample 172

description: human breast tumor RNA

tag: metastatis

tag: death

value: Dead

tag: timesurvival(years)


title: Sample 170

description: human breast tumor RNA

value: Alive

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years


title: genomic DNA from umbilical cord bood 285

description: umbilical cord blood sample

source_name: umbilical cord blood 285


title: genomic DNA from umbilical cord bood 274

description: umbilical cord blood sample

source_name: umbilical cord blood 274


title: db Vehicle rep2

description: run0347_lane9_read*_indexN702-S502=db-Veh-48h-2.fastq.gz


title: genomic DNA from umbilical cord bood 273

description: umbilical cord blood sample

source_name: umbilical cord blood 273


title: genomic DNA from umbilical cord bood 272

description: umbilical cord blood sample

source_name: umbilical cord blood 272


title: genomic DNA from umbilical cord bood 276

description: umbilical cord blood sample

source_name: umbilical cord blood 276


title: genomic DNA from umbilical cord bood 270

description: umbilical cord blood sample

source_name: umbilical cord blood 270


title: genomic DNA from umbilical cord bood 271

description: umbilical cord blood sample

source_name: umbilical cord blood 271


title: Sample 167

description: human breast tumor RNA

tag: tissue

value: LN-

tag: timemeta

tag: metastasis-years


title: Sample 169

description: human breast tumor RNA

tag: estrogen-receptor

tag: nih


title: genomic DNA from umbilical cord bood 269

description: umbilical cord blood sample

source_name: umbilical cord blood 269

tag: gender

value: Male

tag: sample type


title: genomic DNA from umbilical cord bood 259

description: umbilical cord blood sample

source_name: umbilical cord blood 259


title: genomic DNA from umbilical cord bood 267

description: umbilical cord blood sample

source_name: umbilical cord blood 267


title: db Vehicle rep1

description: run0347_lane9_read*_indexN701-S502=db-Veh-48h


title: db BSO rep3

description: run0347_lane9_read*_indexN707-S502=db-BSO-48h-3.fastq.gz

source_name: Obese SLAM HSC cultured with BSOfor 48hrs

value: buthionine sulfoximine


title: genomic DNA from umbilical cord bood 261

description: umbilical cord blood sample

source_name: umbilical cord blood 261


title: genomic DNA from umbilical cord bood 263

description: umbilical cord blood sample

source_name: umbilical cord blood 263


title: Sample 166

description: human breast tumor RNA

source_name: pool of individual breast tumors

source_name: patient sample

tag: lypmph-nodes

tag: stgallen

tag: conservflag


title: Sample 165

description: human breast tumor RNA


title: genomic DNA from umbilical cord bood 256

description: umbilical cord blood sample

source_name: umbilical cord blood 256


title: genomic DNA from umbilical cord bood 258

description: umbilical cord blood sample

source_name: umbilical cord blood 258


title: genomic DNA from umbilical cord bood 253

description: umbilical cord blood sample

source_name: umbilical cord blood 253


title: db BSO rep2

description: run0347_lane9_read*_indexN706-S502=db-BSO-48h-2.fastq.gz

tag: cell type

tag: age

tag: treatement


title: genomic DNA from umbilical cord bood 262

description: umbilical cord blood sample

source_name: umbilical cord blood 262


title: genomic DNA from umbilical cord bood 264

description: umbilical cord blood sample

source_name: umbilical cord blood 264


title: Sample 164

description: human breast tumor RNA

tag: metastatis

tag: death

tag: timesurvival(years)

value: ER-


title: genomic DNA from umbilical cord bood 268

description: umbilical cord blood sample

source_name: umbilical cord blood 268

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 260

description: umbilical cord blood sample

source_name: umbilical cord blood 260


title: genomic DNA from umbilical cord bood 266

description: umbilical cord blood sample

source_name: umbilical cord blood 266


title: Control Vehicle rep3

description: run0347_lane9_read*_indexN703-S517=Ctrl-Veh-48h-3.fastq.gz

source_name: SLAM HSC cultured for 48 hours


title: Sample 163

description: human breast tumor RNA

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years


title: genomic DNA from umbilical cord bood 254

description: umbilical cord blood sample

source_name: umbilical cord blood 254


title: Control Vehicle rep2

description: run0347_lane9_read*_indexN702-S517=Ctrl-Veh-48h-2.fastq.gz


title: genomic DNA from umbilical cord bood 251

description: umbilical cord blood sample

source_name: umbilical cord blood 251


title: genomic DNA from umbilical cord bood 255

description: umbilical cord blood sample

source_name: umbilical cord blood 255


title: Sample 162

description: human breast tumor RNA

tag: tissue

tag: timemeta

tag: metastasis-years


title: genomic DNA from umbilical cord bood 250

description: umbilical cord blood sample

source_name: umbilical cord blood 250

tag: gender


title: db BSO rep1

description: run0347_lane9_read*_indexN705-S502=db-BSO-48h

source_name: Obese SLAM HSC cultured with BSOfor 48hrs


title: Control Vehicle rep1

description: run0347_lane9_read*_indexN701-S517=Ctrl-Veh-48h


title: genomic DNA from umbilical cord bood 257

description: umbilical cord blood sample

source_name: umbilical cord blood 257

tag: sample type


title: genomic DNA from umbilical cord bood 248

description: umbilical cord blood sample

source_name: umbilical cord blood 248


title: genomic DNA from umbilical cord bood 265

description: umbilical cord blood sample

source_name: umbilical cord blood 265


title: Sample 160

description: human breast tumor RNA

source_name: pool of individual breast tumors

source_name: patient sample

tag: lypmph-nodes

tag: estrogen-receptor

tag: nih


title: Sample 161

description: human breast tumor RNA

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 247

description: umbilical cord blood sample

source_name: umbilical cord blood 247


title: Control BSO rep1

description: run0347_lane9_read*_indexN705-S517=Ctrl-BSO-48h

source_name: SLAM HSC cultured with BSOfor 48hrs

tag: cell type

tag: age

tag: treatement


title: genomic DNA from umbilical cord bood 252

description: umbilical cord blood sample

source_name: umbilical cord blood 252


title: Control BSO rep3

description: run0347_lane9_read*_indexN707-S517=Ctrl-BSO-48h-3.fastq.gz


title: Sample 159

description: human breast tumor RNA

tag: metastatis

tag: death

tag: timesurvival(years)