title: Sample 337

description: human breast tumor RNA

value: LN+

tag: timesurvival(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER+

tag: conservflag


title: Sample 335

status: Public on Aug 18 2021

type: RNA

city: Syracuse

first: Vladimir

middle: A

last: Kuznetsov

state: NY

address: 750 E Adams St

department: Urology / Biochemistry and Molecular Biology

country: USA

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.

molecule: total RNA

organism: Homo sapiens

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.

tag: tissue

value: breast tumor

source_name: patient sample

tag: lypmph-nodes

tag: metastatis

value: Meta-

tag: death

value: Alive

tag: survival-years

tag: timerecurrence(years)

value: ER-

tag: nih

tag: stgallen


title: genomic DNA from umbilical cord bood 71

type: genomic

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

molecule: genomic DNA

source_name: umbilical cord blood 71

label_protocol: Standard Illumina Protocol

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

tag: gender

value: Male

tag: sample type

value: Umbilical cord blood


title: Sample 336

description: human breast tumor RNA

value: LN-


title: genomic DNA from umbilical cord bood 74

description: umbilical cord blood sample

source_name: umbilical cord blood 74

value: Female


title: genomic DNA from umbilical cord bood 67

description: umbilical cord blood sample

source_name: umbilical cord blood 67


title: 0352; 30 weeks; Male

type: SRA

city: Philadelphia

first: Zhe

last: Zhang

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

description: Male placenta at gestational age 30 weeks

library_source: transcriptomic

data_processing:
Alignemnt to GRCh38 using STAR run in the 2-pass mode
Reads uniquely mapping to the sense strand of known genes were counted
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene-level read counts in tab-delimited text format

source_name: SPTB male

extract_protocol:
Total RNA was extracted from frozen placenta using TRIzol® Reagent (Invitrogen), followed by Qiagen RNeasy® Mini Columns following manufacturer’s instructions.
Multiplexed libraries were created using Agilent SureSelect strand-specific RNA library preparation kit following manufacturer’s instructions

tag: ethnicity

value: African American

tag: experimental group

value: spontaneous preterm birth (SPTB) male

tag: gestation age

value: 30 weeks

tag: placenta sex

value: Placenta


title: 0350; 30 weeks; Male


title: PBMC of control subjects,replicate 1

city: Jinan

first: Xiaoxiao

last: Zhu

address: 18877 Jingshi Road

country: China

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

description: miRNA expression of control subjects

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse miRNA Microarray (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-ColorLow RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/nAM1556 ) following the manufacturer's instructions.

treatment_protocol: Venous blood samples were obtained after overnight fasting at study inclusion. Samples were processed within 4 h of collection.  PBMCs were isolated by Ficoll density-gradient centrifugation.

tag: subject status

value: control

tag: tissue/cell type

value: PBMC


title: HFS-offspring

city: Fukuoka

first: Tomoyo

last: Kawakubo-Yasukochi

address: 3-1-1 Maidashi

country: Japan

institute: Kyushu University

library_source: genomic

data_processing:
The reads are filtered based on quality, and adapter sequences are also trimmed off the raw sequence reads by using Trimmomatic (v0.32).
The trimmed reads are mapped to reference genome with BSMAP which is based on the SOAP (Short Oligo Alignment Program).
The index and PCR duplicates are removed with SAMBAMBA (v0.5.9).
The methylation ratio of every single cytosine location is extracted from the mapping results using 'methylatio.py' script in BSMAP.
Genome_build: mm10
Supplementary_files_format_and_content: methylation profile (CpG site in each chromosome)

organism: Mus musculus

source_name: liver tissue

growth_protocol: Dams were fed normal diet (ND) or high-fat, high-sucrose diet (HFS) during gestational period, and liver was extracted from their pups at postnatal day 24

extract_protocol: The DNA was extracted from tissue using the Qiagen DNeasy kit (Qiagen). DNA samples were quantified by an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality was confirmed with a Tapestation (Agilent).

tag: strain

value: liver

tag: age

value: post natal day 24

tag: diet

value: high-sucrose diet (HFS)


title: 0346; 30 weeks; Male

tag: tissue


title: ND-offspring

value: normal diet (ND)


title: Sample 334

description: human breast tumor RNA

value: breast tumor

tag: lypmph-nodes

value: LN+

tag: metastatis

value: Meta-

tag: death

tag: timesurvival(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER+

tag: conservflag


title: genomic DNA from umbilical cord bood 65

description: umbilical cord blood sample

source_name: umbilical cord blood 65

tag: gender

value: Male

tag: sample type

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 70

description: umbilical cord blood sample

source_name: umbilical cord blood 70

value: Female


title: 0325; 30 weeks; Male

tag: ethnicity

value: African American

tag: experimental group

tag: gestation age

tag: placenta sex


title: mES_m6A-REF_WT_mRNA_rep1

city: Guangzhou

first: Zhang

state: Guangdong

address: Xingangxi Roda 135#

institute: Sun Yat-sen University

data_processing:
RNA-seq analyses for endogenous mRNA and IVT RNA samples: Raw reads were first trimmed to get rid of sequencing adaptors using cutadapt (v1.15) and mapped to reference genome using Hisat2 (v2.1.0) with the parameters ‘--rna-strandness RF’. Integrative Genomics Viewer (IGV) was used for data visualization.
MeRIP-seq data analyses: After removing the adaptor and mapping to reference genome, the sam file was sorted and converted to bam file using samtools (v1.6). Two extensively used software, exomePeak2 (v1.3.7) and Macs2 (v2.1.2), were applied for m6A peak calling. The parameters ‘p_cutoff=0.00001, log2FC_cutoff=1, fragment_length=150’ were set for exomePeak2; and the parameters ‘--keep-dup all -f BAM --nomodel --extsize 150 -q 0.05 --fe-cutoff 2’ were set for Macs2.
m6A-REF-seq data analyses: The raw reads of m6A-REF-seq was firstly removed adaptors using cutadaptor (v1.15) and mapped to reference genome using Hisat2 (v2.1.0). The IVT RNA library reflected the gene signature and expression level of cellular mRNA but was modification-free. Therefore, high confidence m6A sites had undigested reads in endogenous samples but less or none undigested reads in IVT RNA samples. We defined the false positive rate (FPR) and conduct fisher exact test to evaluate each putative m6A site. The false positive rate (FPR) is the ratio of the number of false positive results to the number of total positive results. For each candidate m6A site, the false-positive rate (FPR) was defined as dividing the undigested rate (undigested reads/total reads at each site) in IVT RNA to that in cellular mRNA. Fisher’s exact test was applied to calculate significance. High confidence m6A sites were identified using the following criteria: 1) undigested reads in IVT RNA samples were significantly less than those in cellular mRNA samples (fisher exact test p-value ≤ 0.05); 2) the false positive rate (FPR) ≤ 0.2; 3) reads coverage ≥ 10; 4) reproducible in two replicates.
m5C BS-seq data analyses: To increase the credibility of m5C identification from BS-seq data, a stringent pipeline from published literature (https://github.com/SYSU-zhanglab/RNA-m5C) was adopted.  High confidence m5C sites were determined using IVT RNA as negative control. The false-positive rate (FPR) was defined as the ratio of false-positive results to total positive results, which was calculated by dividing non-conversion rate of IVT RNA sample to that of the endogenous sample. Fisher exact test was applied to calculate significance. In sum, the high confidence m5C sites were identified using the following criteria: 1) the false positive rate (FPR) ≤ 0.2; 2) p-value ≤ 0.05 (fisher exact test); 3) non-conversion rate ≥ 0.05; 4) sequencing coverage ≥ 10; 5) non-conversion read depth ≥ 5; 6) reproducible in two replicates.
Genome_build: GRCh37 (human), mm10 (mouse)
Supplementary_files_format_and_content: RNA-seq processed data was tdf file generated by IGV. RIP-seq processed data was peak file in bed format. Processed data of m6A-REF-seq and m5C BS-seq were detected high confidence sites in text file.

molecule: polyA RNA

source_name: mouse 129 embryonic stem cells

growth_protocol: Human HEK293T cell line was cultured with DMEM (Corning) supplemented with 10% (v/v) FBS (Gibco) at 37℃ in the presence of 5% CO2, and tested to be negative for mycoplasma contamination. Wild type (WT) of mouse 129 embryonic stem cells (mESCs) and Mettl3 knockout (KO) mESCs were provided by Dr. Jiekai Chen (Guangzhou Institutes of Biomedicine and Health, CAS).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, 15596026) and the mRNA was purified using Dynabeads mRNA Purification Kit (Thermo Fisher Scientific,  61006). mRNA was treated by TURBO DNase (Thermo Fisher, AM2238) at 37 ℃ for 30 min and purified by ethanol precipitation or RNA Clean & Concentrator-5 kit (Zymo Research, R1015) to remove genomic DNA.
IVT RNA generation:  The 100 ng (in 3ul volume at most) extracted mRNA was first annealed with 1ul PolyT primer (12 uM) for 3 min at 75 ℃ and 2 min at 42 ℃. Then we prepared the first strand cDNA mix by adding 2ul 5× First-Strand buffer of SMARTScribe Reverse Transcriptase (Takara, 639536), 0.5 ul 100 mM DTT, 0.5 ul RNase inhibitor (Takara, 2313A), 1ul TSO T7 Primer (10uM), 1ul 50× Advantage UltraPure PCR Deoxynucleotide Mix (Takara, 639125) and 1ul SMARTScribe Reverse Transcriptase (Takara, 639536). After adding the first strand cDNA mix to the mRNA/PolyT Primer mixture, the reaction mixture was incubated at 42 ℃ for 1.5 h and stopped by heating at 68 ℃ for 10min for first strand cDNA synthesis. The primer extension was conducted by adding 10 ul 10× Advantage 2 PCR buffer and 1ul Advantage 2 PCR Polymerase mix (Takara, 639207), 2 ul 50× Advantage UltraPure PCR Deoxynucleotide Mix, 2 ul T7 Extension Primer (10 uM), 2ul RNaseH (NEB, M0297) and RNase-free water to 100 ul. The reaction was conducted at 37 ℃ for 15 min, 95 ℃ for 2 min, 60 ℃ for 1 min and 68 ℃ for 10 min. The double-strand cDNA was purified using NucleoSpin PCR cleanup (MACHEREY-NAGEL, 740609.50). The in vitro transcription step was performed using HiScribe™ T7 High Yield RNA Synthesis Kit (NEB, E2040) and NTPs from Takara (cat. 6140). The sample was subjected to TURBO DNase (Thermo Fisher, AM2238) treatment at 37 ℃ for 30 min and purified by RNA Clean & Concentrator-5 kit (Zymo Research, R1015) to remove dsDNA. The concentration of IVT RNA was determined by Qubit RNA HS Assay kit (Thermo Fisher, Q32852).
MeRIP-seq: Cellular mRNA and IVT RNA were fragmented by using Thermo Fisher’s Fragmentation Kit (Thermo Fisher Scientific, AM8740) at 94 °C for 30s and then purified by ethanol precipitation. The commercial antibodies of NEB (EpiMark® N6-Methyladenosine Enrichment Kit, E1610S), SYSY (202003) and Abcam (ab190886) were used in m6A immunoprecipitation. The 25 ul protein G beads (Thermo Fisher Scientific, 1004D) were washed three times with Reaction buffer (150mM NaCl, 10mM pH 7.4 Tris-HCl, 0.1% Igepal CA-630 in nuclease free H2O). Then the protein G beads were resuspended in 250 ul Reaction buffer and 2 ul anti-m6A antibody was added. After incubation with orbital rotation at 4 ℃ for 1 h, the antibody-protein G beads mixture was washed twice with Reaction buffer. A total of 1ul mRNA for each sample was added to the mixture and then incubated with rotation at 4 ℃ for 3 h. After washed with Reaction buffer twice, the mRNA-antibody-protein G mixture was washed low salt buffer (50 mM NaCl, 10 mM pH 7.4 Tris-HCl, 0.1% Igepal CA-630 in nuclease-free H2O) and high salt buffer (500 mM NaCl, 10 mM pH 7.4 Tris-HCl, 0.1% Igepal CA-630 in nuclease-free H2O) twice, respectively. The IP products were eluted with 130 ul Elution buffer (150 mM NaCl, 10 mM pH 7.4 Tris-HCl, 0.1% Igepal CA-630, 6.7 mM m6A in nuclease-free H2O) at 37 °C, 1000 rpm for 1.5 hours. After purified by ethanol precipitation, the IP products and input sample kept before IP were used to constructed the NGS library using NEBNext® Ultra II Directional RNA Library Prep (NEB, E7760S).
m6A-REF-seq: We followed the experimental procedural of m6A-RFE-seq in Zhang et al., (2019) and used IVT RNA as negative control. After heated at 85°C for 5 min and chilled on ice for 2 min, the equivalent endogenous mRNA and IVT RNA were incubated with MazF (Takara, 2415A) in the MazF reaction buffer at 37 °C for 30 min. After purified by RNA Clean & Concentrator-5 kit (Zymo Research, R1015), the fragment mRNA was end-repaired by T4 polynucleotide kinase (T4PNK; Vazyme Biotech). Then the fragment mRNA was purified by RNA Clean & Concentrator-5 kit, and the NGS libraries were constructed by using the VAHTS Small RNA Library Prep Kit (Vazyme Biotech, NR801) with 10 ng of fragmented RNA.
m5C BS-seq: Cellular mRNA and IVT RNA samples were conducted bisulfite treatment following the instruction in Huang et al., (2019) using EZ RNA methylation kit (Zymo Research, R5001). High-stringency conditions: Total among of 1 ug cellular mRNA and IVT RNA were treated with three cycles of 70 °C for 10 min and 64 °C for 45 min in sulfonation step and then 37 °C for 30 min in desulfonation step. The NGS libraries were constructed by using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S).
RNA-seq, MeRIP-seq and m5C BS-seq libraries were constructed by using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S). The m6A-REF-seq libraries were constructed by using the VAHTS Small RNA Library Prep Kit (Vazyme Biotech, NR801) with 10 ng of fragmented mRNA.

tag: cell type

value: mESC

value: WT cellular mRNA

tag: sequence type

tag: treatment

value: MazF (Takara, 2415A), 1ul (20U)


title: Sample 333

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: LN-

tag: metastatis

value: Alive

tag: survival-years

tag: timerecurrence(years)

value: ER-

tag: nih

tag: stgallen


title: 0405; 39 weeks; Female

description: Female placenta at gestational age 39 weeks

source_name: Term female

value: Term female

value: 39 weeks

value: Placenta


title: genomic DNA from umbilical cord bood 62

description: umbilical cord blood sample

source_name: umbilical cord blood 62


title: mES_m6A-REF_WT_IVT_rep2

value: WT in vitro transcribed (IVT) RNA


title: genomic DNA from umbilical cord bood 63

description: umbilical cord blood sample

source_name: umbilical cord blood 63


title: 0397; 39 weeks; Female


title: genomic DNA from umbilical cord bood 69

description: umbilical cord blood sample

source_name: umbilical cord blood 69


title: mES_m6A-REF_WT_IVT_rep1


title: 0376; 39 weeks; Female


title: Sample 330

description: human breast tumor RNA

value: breast tumor

value: LN+

tag: death

tag: timesurvival(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: conservflag


title: Sample 331

description: human breast tumor RNA

value: Meta+

value: Dead

value: ER+


title: Sample 332

description: human breast tumor RNA

value: Meta-


title: genomic DNA from umbilical cord bood 66

description: umbilical cord blood sample

source_name: umbilical cord blood 66

tag: gender

value: Male

tag: sample type

value: Umbilical cord blood


title: Sample 329

description: human breast tumor RNA


title: 0359; 39 weeks; Female

tag: ethnicity

value: African American

tag: experimental group

tag: gestation age

tag: placenta sex

value: Female


title: mES_m6A-REF_KO_mRNA_rep2

tag: cell type

value: mESC

value: Mettl3 KO #1 cellular mRNA

tag: sequence type

tag: treatment

value: MazF (Takara, 2415A), 1ul (20U)


title: 0357; 39 weeks; Female

value: Term female

tag: tissue


title: genomic DNA from umbilical cord bood 59

description: umbilical cord blood sample

source_name: umbilical cord blood 59


title: genomic DNA from umbilical cord bood 58

description: umbilical cord blood sample

source_name: umbilical cord blood 58


title: mES_m6A-REF_KO_mRNA_rep1


title: Sample 327

description: human breast tumor RNA

source_name: pool of individual breast tumors

tag: lypmph-nodes

tag: metastatis

tag: death

value: Alive

tag: survival-years

tag: timerecurrence(years)

tag: nih

tag: stgallen


title: mES_MeRIP_WT_rep2_IP

value: WT cellular mRNA

value: MeRIP-seq

value: m6A-IP, NEB (EpiMark® N6-Methyladenosine Enrichment Kit, E1610S)


title: 0344; 39 weeks; Female

value: 39 weeks

value: Placenta


title: mES_MeRIP_WT_rep2_Input


title: 0337; 39 weeks; Female


title: mES_MeRIP_WT_rep1_IP


title: Sample 326

description: human breast tumor RNA

value: breast tumor

source_name: patient sample

value: LN-

tag: timesurvival(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER-

tag: conservflag


title: 0332; 39 weeks; Female

tag: ethnicity

tag: experimental group

tag: gestation age

tag: placenta sex


title: Sample 325

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: LN+

value: Meta-

value: ER+


title: genomic DNA from umbilical cord bood 57

description: umbilical cord blood sample

source_name: umbilical cord blood 57

tag: gender

value: Female

tag: sample type

value: Umbilical cord blood


title: 0409; 30 weeks; Female

description: Female placenta at gestational age 30 weeks

source_name: SPTB female

value: African American

value: spontaneous preterm birth (SPTB) female

value: 30 weeks


title: mES_MeRIP_WT_rep1_Input

tag: cell type

value: mESC

tag: sequence type

tag: treatment


title: genomic DNA from umbilical cord bood 56

description: umbilical cord blood sample

source_name: umbilical cord blood 56

value: Male


title: Sample 324

description: human breast tumor RNA

tag: metastatis

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: nih

tag: stgallen


title: 0407; 30 weeks; Female

tag: ethnicity

tag: experimental group


title: genomic DNA from umbilical cord bood 64

description: umbilical cord blood sample

source_name: umbilical cord blood 64


title: Sample 328

description: human breast tumor RNA

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: conservflag


title: mES_MeRIP_KO2_IP

tag: cell type

tag: sample type

value: Mettl3 KO #2 cellular mRNA

value: MeRIP-seq

value: m6A-IP, NEB (EpiMark® N6-Methyladenosine Enrichment Kit, E1610S)


title: Sample 322

description: human breast tumor RNA

tag: tissue

value: breast tumor

tag: lypmph-nodes


title: 0400; 30 weeks; Female

tag: gestation age

tag: placenta sex

value: Placenta


title: mES_MeRIP_KO2_Input

tag: sequence type

tag: treatment


title: mES_m6A-REF_WT_mRNA_rep2

value: WT cellular mRNA

value: MazF (Takara, 2415A), 1ul (20U)


title: Sample 321

description: human breast tumor RNA

value: LN+

tag: metastatis

value: Meta+

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: nih


title: 0377; 30 weeks; Female

tag: ethnicity

tag: experimental group

value: Female


title: genomic DNA from umbilical cord bood 54

description: umbilical cord blood sample

source_name: umbilical cord blood 54

tag: gender

value: Umbilical cord blood


title: mES_MeRIP_KO1_IP

tag: cell type

value: Mettl3 KO #1 cellular mRNA


title: mES_MeRIP_KO1_Input

tag: sample type


title: Sample 320

description: human breast tumor RNA

tag: tissue

value: Meta-

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER+

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 53

description: umbilical cord blood sample

source_name: umbilical cord blood 53


title: genomic DNA from umbilical cord bood 52

description: umbilical cord blood sample

source_name: umbilical cord blood 52


title: genomic DNA from umbilical cord bood 55

description: umbilical cord blood sample

source_name: umbilical cord blood 55


title: genomic DNA from umbilical cord bood 49

description: umbilical cord blood sample

source_name: umbilical cord blood 49


title: mES_MeRIP_IVT_rep2_IP

source_name: mouse 129 embryonic stem cells

value: mESC

value: WT in vitro transcribed (IVT) RNA

tag: sequence type

tag: treatment


title: genomic DNA from umbilical cord bood 51

description: umbilical cord blood sample

source_name: umbilical cord blood 51


title: Sample 318

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years


title: Sample 319

description: human breast tumor RNA

value: LN-

value: Dead

tag: timerecurrence(years)

tag: nih


title: Sample 323

description: human breast tumor RNA


title: mES_MeRIP_IVT_rep2_Input

tag: cell type

tag: sample type

value: MeRIP-seq


title: 0348; 30 weeks; Female

tag: ethnicity

value: African American

tag: experimental group

value: spontaneous preterm birth (SPTB) female

tag: gestation age

value: 30 weeks

tag: placenta sex

tag: tissue


title: genomic DNA from umbilical cord bood 46

description: umbilical cord blood sample

source_name: umbilical cord blood 46

tag: gender


title: genomic DNA from umbilical cord bood 50

description: umbilical cord blood sample

source_name: umbilical cord blood 50

value: Male


title: mES_MeRIP_IVT_rep1_IP

tag: sequence type

value: m6A-IP, NEB (EpiMark® N6-Methyladenosine Enrichment Kit, E1610S)


title: genomic DNA from umbilical cord bood 60

description: umbilical cord blood sample

source_name: umbilical cord blood 60


title: mES_MeRIP_IVT_rep1_Input

tag: treatment


title: Sample 315

description: human breast tumor RNA

value: breast tumor

tag: lypmph-nodes

value: LN+

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: stgallen

tag: conservflag


title: 0328; 30 weeks; Female

value: Female

value: Placenta


title: mES_MeRIP_FTO_IP

tag: cell type

value: WT FTO-treated mRNA


title: 0321; 30 weeks; Female


title: hES-MPE7C7TP53-/-

city: New York

first: Fabio

last: Vanoli

address: 1250 1st Avenue

institute: MSKCC

data_processing:
reads were aligned with STAR (ver2.3) and BowTie2 against the reference genome (hg19)
RPKM calculation: mrfQuantifier from RSEQtools<http://info.gersteinlab.org/RSEQtools#mrfQuantifier>
Genome_build: hg19
Supplementary_files_format_and_content: Column A: <composite hg19 transcript>; Column B: <composite transcript names>; Column C:  <strand>(this column should be deleted); Column D:  <composite transcripts description>; Column E:  <RPKM>

source_name: mesenchymal cell line

growth_protocol: cell lines were grow for 7 days and then infected with Cre recombinase for expression of EWSR1-CREB1 oncogenic fusion

extract_protocol:
RNA for tumors and cel lines was extracted using Rneasy Plus Mini
Libraries were prepared following standard Illumina protocol

value: embryonic stem mesenchymal progenitor

tag: fusion type

value: EWSR1-CREB1 TP53-/-

tag: sarcoma type


title: Sample 317

description: human breast tumor RNA

source_name: pool of individual breast tumors

tag: metastatis

value: Meta+

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

value: ER+

tag: nih


title: hES-MPE7C7

tag: tissue


title: mES_MeRIP_FTO_Input

value: mESC

tag: sample type

tag: sequence type

tag: treatment


title: genomic DNA from umbilical cord bood 47

description: umbilical cord blood sample

source_name: umbilical cord blood 47

tag: gender

value: Umbilical cord blood


title: Sample 313

description: human breast tumor RNA

source_name: patient sample

tag: lypmph-nodes

value: LN-

value: Alive

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor


title: genomic DNA from umbilical cord bood 43

description: umbilical cord blood sample

source_name: umbilical cord blood 43


title: Sample 312

description: human breast tumor RNA

value: Meta-

tag: stgallen

tag: conservflag


title: hES-MP

tag: fusion type

value: wild type

tag: sarcoma type


title: mES_RNA-seq_mRNA_rep2

tag: cell type

value: cellular mRNA

value: RNAseq


title: Sample 311

description: human breast tumor RNA

value: breast tumor

tag: metastatis

tag: death

value: Dead

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)


title: GI-CCS75

source_name: tumor

tag: tissue

value: sarcoma

value: GI-CCS tumor


title: mES_RNA-seq_mRNA_rep1

tag: sample type

tag: sequence type

tag: treatment


title: genomic DNA from umbilical cord bood 61

description: umbilical cord blood sample

source_name: umbilical cord blood 61

tag: gender

value: Male


title: genomic DNA from umbilical cord bood 42

description: umbilical cord blood sample

source_name: umbilical cord blood 42

value: Female


title: genomic DNA from umbilical cord bood 44

description: umbilical cord blood sample

source_name: umbilical cord blood 44


title: Sample 310

description: human breast tumor RNA

tag: lypmph-nodes

value: LN+

tag: recurrence-years

tag: timemeta

tag: metastasis-years

value: ER-

tag: nih


title: mES_RNA-seq_IVT_rep2

value: in vitro transcribed (IVT) RNA


title: GI-CCS54

tag: fusion type

tag: sarcoma type


title: Sample 314

description: human breast tumor RNA

tag: metastatis

value: Meta+

tag: estrogen-receptor

value: ER+

tag: stgallen

tag: conservflag


title: 0361; 30 weeks; Female

source_name: SPTB female

tag: ethnicity

value: African American

tag: experimental group

value: spontaneous preterm birth (SPTB) female

tag: gestation age

value: 30 weeks

tag: placenta sex

value: Placenta


title: CCS22

tag: tissue

value: CCS tumor


title: mES_RNA-seq_IVT_rep1

tag: cell type

value: mESC

tag: sample type

tag: sequence type

value: RNAseq

tag: treatment


title: genomic DNA from umbilical cord bood 45

description: umbilical cord blood sample

source_name: umbilical cord blood 45

tag: gender

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 41

description: umbilical cord blood sample

source_name: umbilical cord blood 41


title: Sample 309

description: human breast tumor RNA

value: breast tumor

tag: lypmph-nodes

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: nih


title: genomic DNA from umbilical cord bood 39

description: umbilical cord blood sample

source_name: umbilical cord blood 39

value: Male


title: CCS1

value: sarcoma

tag: fusion type

tag: sarcoma type


title: Sample 308

description: human breast tumor RNA

tag: tissue

value: LN+

tag: metastatis

value: Meta-

tag: estrogen-receptor

tag: stgallen

tag: conservflag


title: Spodoptera frugiperda hemolymph samples [F90]

city: Pomona

first: Peter

last: Arensburger

state: CA

address: 3801 Watkins Avenue

department: Dept. of Biology

institute: California State Polytechnic University Pomona

description:
S1A.xls
S1E.xls
S1J.xls

data_processing:
Low sequencing quality and adapter sequences were removed from the libraries using trimmomatic-0.32
ribosomal contaminants were removed with SortMeRNA version 2.0
Sequencing reads were mapped to one or several of the following reference genome assemblies: 1) viral genome of SfAV , 2) viral genome of TnAV , 3) Spodoptera frugiperda genome, SF_CORN_1 assembly (NCBI accession GCA_900240015.1), and bowtie2 and the splice-aware program hisat2 was used for all other genomes.
Library statistics, read counts and RPKMs calculation were determined using the bedtools intersectBed program in conjunction with custom written Perl scripts (available upon request).
Genome_build: GCA_900240015.1 and ASM360422v1
Supplementary_files_format_and_content: RPKM expression levels, .xlsx files

organism: Spodoptera frugiperda

source_name: hemolymph tissue

extract_protocol:
Hemolymph or combination of other body tissues, which from the standpoint of bulk, consisted primarily of the fat body, epidermis, tracheal matrix and midgutody tissues (referred to as somatic body tissues) were collected and homogenized in Trizol. Samples were DNAse treated and cDNA libraries were constructed.
RNA libraries were prepared for sequencing using NEBNext Utra Directional RNA Library Prep kit.

tag: time point

tag: replicate

value: Replicate 3


title: genomic DNA from umbilical cord bood 40

description: umbilical cord blood sample

source_name: umbilical cord blood 40

tag: gender

tag: sample type


title: Sample 307

description: human breast tumor RNA

tag: lypmph-nodes

value: Meta+

tag: death

value: Dead

tag: timesurvival(years)

tag: survival-years

value: ER-


title: genomic DNA from umbilical cord bood 38

description: umbilical cord blood sample

source_name: umbilical cord blood 38

value: Female


title: Muscle_25 months_biological rep6

city: Saint Genes Champanelle

first: Daniel

last: Bechet

address: Theix

department: UNH

country: France

institute: INRA

hyb_protocol: Following fragmentation and terminal labeling, 5.5 µg of single stranded cDNA were hybridized for 16 h at 45°C and 60 rpm on GeneChip® Mouse Exon 1.0 ST Array in the Affymetrix Oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization Wash and Stain Affymetrix kit.

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

data_processing:
Data were generated with Affymetrix Expression Console v 1.2.1 software using robust multiarray average (RMA) algorithm. Affymetrix data files were processed using GeneSpring GX 14.9 13 (Agilent ).
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

label: biotin

source_name: gastrocnemius, 25 months

label_protocol: Biotinylated single stranded cDNA were prepared from 400 ng of depleted total RNA according to the Affymetrix WT protocol (Ambion WT Expression kit).

growth_protocol: Gastrocnemius muscle dissected from C57BL/6 male mice

extract_protocol: Gastrocnemius muscles of both legs were snap-frozen in liquid N2. RNA was isolated using a TissueRuptor and RNeasy Fibrous Tissue Mini Kit (Qiagen). Integrity of RNA  was verified using an Agilent Bioanalyser with the RNA 6000 Nano labchip® kit (Agilent). Concentration and purity was determined with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies). The depletion of the ribosomal fractions was processed using 2 µg of total RNA and magnetic beads from Ribominus Kit (Invitrogen).

treatment_protocol: not applicable

tag: strain

value: male

tag: age

value: 25 months

value: Gastrocnemius muscle


title: Muscle_25 months_biological rep5


title: Sample 306

description: human breast tumor RNA

value: LN-

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

value: ER+

tag: nih


title: genomic DNA from umbilical cord bood 48

description: umbilical cord blood sample

source_name: umbilical cord blood 48

value: Umbilical cord blood


title: Spodoptera frugiperda hemolymph samples [F88]

description:
S1A.xls
S1E.xls
S1J.xls

value: Replicate 1


title: Muscle_25 months_biological rep4

tag: tissue


title: Sample 305

description: human breast tumor RNA

source_name: pool of individual breast tumors

value: breast tumor

tag: metastatis

value: Alive

tag: estrogen-receptor

tag: stgallen

tag: conservflag


title: Spodoptera frugiperda hemolymph samples [F89]

description:
S1A.xls
S1E.xls
S1J.xls

tag: time point

tag: replicate

value: Replicate 2


title: Muscle_25 months_biological rep3

tag: gender


title: Spodoptera frugiperda hemolymph samples [F87]

description:
S1A.xls
S1E.xls
S1J.xls


title: Sample 304

description: human breast tumor RNA

tag: lypmph-nodes

tag: death

tag: timesurvival(years)


title: Spodoptera frugiperda hemolymph samples [F86]

description:
S1A.xls
S1E.xls
S1J.xls


title: Sample 303

description: human breast tumor RNA

value: LN+

tag: survival-years


title: Muscle_25 months_biological rep1

tag: strain

tag: age


title: genomic DNA from umbilical cord bood 36

description: umbilical cord blood sample

source_name: umbilical cord blood 36

value: Male

tag: sample type


title: Sample 302

description: human breast tumor RNA

source_name: patient sample

value: Meta-

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years


title: Spodoptera frugiperda hemolymph samples [F85]

description:
S1A.xls
S1E.xls
S1J.xls


title: AFH31.2

tag: tissue

value: sarcoma

tag: fusion type

tag: sarcoma type

value: AFH tumor


title: Muscle_25 months_biological rep2


title: Sample 301

description: human breast tumor RNA

tag: metastatis

tag: estrogen-receptor

tag: nih

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 37

description: umbilical cord blood sample

source_name: umbilical cord blood 37

tag: gender


title: Muscle_11 months_biological rep6

source_name: gastrocnemius, 11 months

value: 11 months


title: Sample 300

description: human breast tumor RNA

tag: lypmph-nodes

value: Meta+

tag: death

value: Dead

tag: timesurvival(years)

tag: survival-years


title: Sample 298

description: human breast tumor RNA

tag: timerecurrence(years)


title: genomic DNA from umbilical cord bood 32

description: umbilical cord blood sample

source_name: umbilical cord blood 32

value: Female

tag: sample type


title: Spodoptera frugiperda hemolymph samples [F82]

description:
S1A.xls
S1E.xls
S1J.xls

tag: time point

tag: replicate


title: genomic DNA from umbilical cord bood 33

description: umbilical cord blood sample

source_name: umbilical cord blood 33


title: Muscle_11 months_biological rep4

tag: strain

value: male

tag: age

tag: tissue

value: Gastrocnemius muscle


title: genomic DNA from umbilical cord bood 31

description: umbilical cord blood sample

source_name: umbilical cord blood 31


title: Muscle_11 months_biological rep3


title: Spodoptera frugiperda hemolymph samples [F83]

description:
S1A.xls
S1E.xls
S1J.xls


title: genomic DNA from umbilical cord bood 30

description: umbilical cord blood sample

source_name: umbilical cord blood 30


title: Sample 297

description: human breast tumor RNA

tag: metastatis

tag: recurrence-years

tag: timemeta

tag: metastasis-years

value: ER+


title: Sample 296

description: human breast tumor RNA

value: LN-

tag: estrogen-receptor

tag: nih

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 29

description: umbilical cord blood sample

source_name: umbilical cord blood 29

tag: gender

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 35

description: umbilical cord blood sample

source_name: umbilical cord blood 35


title: Spodoptera frugiperda hemolymph samples [F84]

description:
S1A.xls
S1E.xls
S1J.xls

value: Replicate 3


title: Spodoptera frugiperda hemolymph samples [F81]

description:
S1A.xls
S1E.xls
S1J.xls

value: Control


title: Spodoptera frugiperda hemolymph samples [F80]

description:
S1A.xls
S1E.xls
S1J.xls

value: Replicate 2


title: Muscle_11 months_biological rep2


title: Spodoptera frugiperda hemolymph samples [F79]

description:
S1A.xls
S1E.xls
S1J.xls

value: Replicate 1


title: Sample 295

description: human breast tumor RNA

value: breast tumor

tag: lypmph-nodes

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years


title: Muscle_11 months_biological rep1


title: genomic DNA from umbilical cord bood 26

description: umbilical cord blood sample

source_name: umbilical cord blood 26

tag: sample type


title: genomic DNA from umbilical cord bood 34

description: umbilical cord blood sample

source_name: umbilical cord blood 34


title: genomic DNA from umbilical cord bood 27

description: umbilical cord blood sample

source_name: umbilical cord blood 27

value: Male


title: Spodoptera frugiperda somatic samples [F114]

description:
S1A.xls
S1C.xls
S1I.xls

source_name: somatic body tissues

tag: time point

tag: replicate


title: Muscle_2 months_biological rep6

source_name: gastrocnemius, 2 months

tag: strain

tag: age

value: 2 months

tag: tissue


title: Sample 294

description: human breast tumor RNA

value: LN+

tag: metastatis

value: Meta-

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta


title: genomic DNA from umbilical cord bood 25

description: umbilical cord blood sample

source_name: umbilical cord blood 25


title: Spodoptera frugiperda somatic samples [F113]

description:
S1A.xls
S1C.xls
S1I.xls


title: Muscle_2 months_biological rep5


title: Sample 292

description: human breast tumor RNA

source_name: pool of individual breast tumors

tag: metastasis-years

tag: estrogen-receptor

tag: nih

tag: stgallen


title: Sample 293

description: human breast tumor RNA

tag: lypmph-nodes

tag: death

tag: conservflag


title: Spodoptera frugiperda somatic samples [F112]

description:
S1A.xls
S1C.xls
S1I.xls


title: Sample 291

description: human breast tumor RNA

tag: timesurvival(years)

tag: survival-years


title: Muscle_2 months_biological rep4

tag: gender


title: Spodoptera frugiperda somatic samples [F99]

description:
S1A.xls
S1C.xls
S1I.xls

tag: time point

tag: replicate


title: Muscle_2 months_biological rep2

tag: strain

tag: age

tag: tissue


title: genomic DNA from umbilical cord bood 22

description: umbilical cord blood sample

source_name: umbilical cord blood 22

tag: sample type


title: Muscle_2 months_biological rep3


title: Sample 290

description: human breast tumor RNA

source_name: patient sample

tag: metastatis

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta


title: Spodoptera frugiperda somatic samples [F98]

description:
S1A.xls
S1C.xls
S1I.xls


title: genomic DNA from umbilical cord bood 21

description: umbilical cord blood sample

source_name: umbilical cord blood 21


title: Muscle_11 months_biological rep5

source_name: gastrocnemius, 11 months

value: 11 months


title: R47H_MK2206_Tau_3

first: Li

last: Gan

address: 413 E 69th Street

institute: Weill Cornell Medicine

description:
mRNA expression of primary mouse microglia
LG18

data_processing:
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software
FeatureCounts was used to count the read numbers mapped of each gene
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: counts

source_name: Bulk RNA-Seq

growth_protocol: harvested microglia from post-natal day 0-3 mouse pups; grew in mixed culture for 10 days before isolating microglia and plating for experiment

extract_protocol:
did RNA extraction using Zymo micro kit
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
bulk RNA-seq; sequencing strategy PE150

treatment_protocol: pre-treated +/- 1 uM MK2206 or 0.01% DMSO control for 6 hours, followed by +/- 1 ug/ml 0N4R tau fibril stimulation

tag: cell type

value: Primary microglia

tag: genotype

value: hTrem2 R47H/+

tag: tau treatment

value: 1 ug/ml 0N4R tau

tag: inhibitor treatment


title: Spodoptera frugiperda somatic samples [F97]

description:
S1A.xls
S1C.xls
S1I.xls


title: Muscle_2 months_biological rep1

value: male

value: Gastrocnemius muscle


title: R47H_MK2206_Tau_2

description:
mRNA expression of primary mouse microglia
LG17


title: Spodoptera frugiperda somatic samples [F96]

description:
S1A.xls
S1C.xls
S1I.xls


title: genomic DNA from umbilical cord bood 28

description: umbilical cord blood sample

source_name: umbilical cord blood 28

value: Female

value: Umbilical cord blood


title: Sample 288

description: human breast tumor RNA

tag: lypmph-nodes

value: Meta+

tag: death

value: Dead

tag: timesurvival(years)

tag: metastasis-years

tag: estrogen-receptor

value: ER+

tag: nih

tag: stgallen

tag: conservflag


title: Sample 287

description: human breast tumor RNA

tag: tissue

value: breast tumor

tag: survival-years


title: R47H_MK2206_Tau_1

description:
mRNA expression of primary mouse microglia
LG16


title: genomic DNA from umbilical cord bood 20

description: umbilical cord blood sample

source_name: umbilical cord blood 20

tag: gender

tag: sample type


title: Sample 285

description: human breast tumor RNA

value: LN-

tag: metastatis

value: Alive

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta


title: Sample 286

description: human breast tumor RNA


title: Spodoptera frugiperda somatic samples [F95]

description:
S1A.xls
S1C.xls
S1I.xls

tag: time point

tag: replicate

value: Replicate 2


title: R47H_MK2206_3

description:
mRNA expression of primary mouse microglia
LG15

tag: cell type

tag: genotype

tag: inhibitor treatment


title: Spodoptera frugiperda somatic samples [F94]

description:
S1A.xls
S1C.xls
S1I.xls

value: Replicate 1


title: Spodoptera frugiperda somatic samples [F93]

description:
S1A.xls
S1C.xls
S1I.xls

value: Control

value: Replicate 3


title: R47H_MK2206_2

description:
mRNA expression of primary mouse microglia
LG14

value: Primary microglia


title: genomic DNA from umbilical cord bood 24

description: umbilical cord blood sample

source_name: umbilical cord blood 24


title: R47H_MK2206_1

description:
mRNA expression of primary mouse microglia
LG13

value: hTrem2 R47H/+


title: Sample 284

description: human breast tumor RNA

tag: lypmph-nodes

value: LN+

tag: death

tag: timesurvival(years)

tag: metastasis-years

tag: estrogen-receptor


title: Spodoptera frugiperda somatic samples [F92]

description:
S1A.xls
S1C.xls
S1I.xls


title: R47H_Tau_3

description:
mRNA expression of primary mouse microglia
LG12

tag: tau treatment

value: 1 ug/ml 0N4R tau


title: Sample 283

description: human breast tumor RNA

tag: tissue

value: Meta-

tag: survival-years

tag: nih

tag: stgallen

tag: conservflag


title: Spodoptera frugiperda somatic samples [F91]

description:
S1A.xls
S1C.xls
S1I.xls


title: Sample 282

description: human breast tumor RNA

tag: metastatis

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta


title: genomic DNA from umbilical cord bood 17

description: umbilical cord blood sample

source_name: umbilical cord blood 17

tag: gender

value: Male

tag: sample type


title: Sample 281

description: human breast tumor RNA

tag: lypmph-nodes


title: CD206+ Mfs of A20meyl WT mice on SD, replicate 4

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description:
SD_WT_M2_4
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl WT mice on Standard Diet, replicate 4.

data_processing:
FastQC v0.11.4 is used to check the quality of the samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.35 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort.
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files including raw counts (output HTSeqCount) for each sample.

source_name: Epididymal adipose tissue

extract_protocol: All Methods listed in Catrysse and Maes et al. A20 deficiency in myeloid cells protects mice from diet-induced obesity and insulin resistance due to increased fatty acid metabolism. Cell Reports. 2021.

tag: strain

tag: genotype

value: wild-type

value: Epididymal adipose tissue

tag: cell type

tag: condition

value: 12 weeks of standard diet


title: R47H_Tau_2

description:
mRNA expression of primary mouse microglia
LG11

tag: tau treatment


title: CD206+ Mfs of A20meyl WT mice on SD, replicate 3

description:
SD_WT_M2_3
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl WT mice on Standard Diet, replicate 3.

tag: tissue


title: genomic DNA from umbilical cord bood 16

description: umbilical cord blood sample

source_name: umbilical cord blood 16

value: Female

value: Umbilical cord blood


title: R47H_3

description:
mRNA expression of primary mouse microglia
LG9


title: Sample 278

description: human breast tumor RNA

value: breast tumor

value: LN-

tag: death

tag: timesurvival(years)

tag: survival-years

tag: metastasis-years

tag: estrogen-receptor

value: ER+


title: Sample 280

description: human breast tumor RNA

tag: metastatis

value: Alive

tag: timerecurrence(years)

tag: nih

tag: stgallen

tag: conservflag


title: genomic DNA from umbilical cord bood 18

description: umbilical cord blood sample

source_name: umbilical cord blood 18

tag: gender

tag: sample type


title: CD206+ Mfs of A20meyl WT mice on SD, replicate 2

description:
SD_WT_M2_2
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl WT mice on Standard Diet, replicate 2.

tag: strain

tag: genotype


title: R47H_Tau_1

description:
mRNA expression of primary mouse microglia
LG10

tag: cell type


title: genomic DNA from umbilical cord bood 19

description: umbilical cord blood sample

source_name: umbilical cord blood 19


title: R47H_2

description:
mRNA expression of primary mouse microglia
LG8


title: CD4_DN_BC5

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

hyb_protocol: Hybridization was performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

scan_protocol: Scanning was performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the RMA procedure using R with oligo package (v.1.42.00) and hugene21sttranscriptcluster (v.8.7.0) and pd.hugene.2.1.st (V.3.14.1) libraries.

source_name: KLRG1-CD57- (DN) T cells from breast cancer

label_protocol: 100 ng of RNA was used to synthesize cDNA using reverse-transcription reactions according to the standard Affymetrix protocol.

extract_protocol: Cells were lysed with TCL buffer (Qiagen) and Total RNA was isolated with RNA purification kit (Norgen), and its integrity evaluated with Agilent RNA 6000 pico kit.

treatment_protocol: DP and DN CD4+ T cells were sorted from blood from 3 luminal (ER+PR+HER2-) BC patients and 3 age-matched healthy HD

tag: cell markers

value: KLRG1-CD57- (DN) T cells

tag: disease state

value: breast cancer

value: CD4+ T cells from breast


title: CD206+ Mfs of A20meyl WT mice on SD, replicate 1

description:
SD_WT_M2_1
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl WT mice on Standard Diet, replicate 1.

tag: tissue

tag: condition


title: Sample 276

description: human breast tumor RNA

tag: lypmph-nodes

value: Meta+

tag: death

value: Dead

tag: timesurvival(years)

tag: survival-years

tag: recurrence-years

tag: timemeta

value: ER-


title: WT_Tau_3

description:
mRNA expression of primary mouse microglia
LG6

value: Primary microglia

value: mTrem2 +/+

tag: tau treatment

value: 1 ug/ml 0N4R tau


title: CD4_DP_BC5

source_name: KLRG1+CD57+ (DP) T cells from breast cancer

value: KLRG1+CD57+ (DP) T cells


title: R47H_1

description:
mRNA expression of primary mouse microglia
LG7

value: hTrem2 R47H/+


title: CD11c+ Mfs of A20meyl WT mice on SD, replicate 2

description:
SD_WT_M1_2
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl WT mice on Standard Diet, replicate 2.

value: wild-type

value: Epididymal adipose tissue

value: 12 weeks of standard diet


title: genomic DNA from umbilical cord bood 15

description: umbilical cord blood sample

source_name: umbilical cord blood 15

value: Female

value: Umbilical cord blood


title: Sample 273

description: human breast tumor RNA

source_name: pool of individual breast tumors

value: breast tumor

value: LN+

tag: metastatis

value: Meta-

value: Alive

tag: timerecurrence(years)

tag: metastasis-years

tag: estrogen-receptor

value: ER+

tag: nih

tag: stgallen

tag: conservflag


title: Sample 275

description: human breast tumor RNA


title: CD11c+ Mfs of A20meyl WT mice on SD, replicate 4

description:
SD_WT_M1_4
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl WT mice on Standard Diet, replicate 4.

tag: strain

tag: genotype

tag: cell type


title: CD4_DP_BC1

tag: cell markers

tag: disease state

value: breast cancer

value: CD4+ T cells from breast


title: CD4_DP_BC4


title: WT_Tau_1

description:
mRNA expression of primary mouse microglia
LG4

value: Primary microglia


title: CD11c+ Mfs of A20meyl WT mice on SD, replicate 3

description:
SD_WT_M1_3
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl WT mice on Standard Diet, replicate 3.

tag: tissue

tag: condition


title: WT_Tau_2

description:
mRNA expression of primary mouse microglia
LG5

value: mTrem2 +/+


title: CD11c+ Mfs of A20meyl WT mice on SD, replicate 1

description:
SD_WT_M1_1
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl WT mice on Standard Diet, replicate 1.


title: genomic DNA from umbilical cord bood 8

description: umbilical cord blood sample

source_name: umbilical cord blood 8

tag: gender

value: Male

tag: sample type


title: genomic DNA from umbilical cord bood 10

description: umbilical cord blood sample

source_name: umbilical cord blood 10


title: genomic DNA from umbilical cord bood 11

description: umbilical cord blood sample

source_name: umbilical cord blood 11


title: Sample 272

description: human breast tumor RNA

source_name: patient sample

tag: lypmph-nodes

tag: death

tag: timesurvival(years)

tag: survival-years

tag: recurrence-years

tag: timemeta


title: genomic DNA from umbilical cord bood 12

description: umbilical cord blood sample

source_name: umbilical cord blood 12


title: genomic DNA from umbilical cord bood 7

description: umbilical cord blood sample

source_name: umbilical cord blood 7


title: WT_3

description:
mRNA expression of primary mouse microglia
LG3

source_name: Bulk RNA-Seq


title: Sample 277

description: human breast tumor RNA

tag: metastatis

tag: timerecurrence(years)

tag: metastasis-years

tag: estrogen-receptor

tag: nih

tag: stgallen


title: CD4_DN_BC4

tag: cell markers

value: KLRG1-CD57- (DN) T cells

tag: disease state

tag: cell type


title: CD206+ Mfs of A20meyl KO mice on SD, replicate 4

description:
SD_KO_M2_4
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl KO mice on Standard Diet, replicate 4.

tag: strain

tag: genotype

value: myeloid-specific knockout of A20

tag: tissue

tag: condition


title: genomic DNA from umbilical cord bood 14

description: umbilical cord blood sample

source_name: umbilical cord blood 14

tag: gender

tag: sample type


title: WT_2

description:
mRNA expression of primary mouse microglia
LG2


title: Sample 274

description: human breast tumor RNA

tag: lypmph-nodes

value: LN-

tag: death

tag: timesurvival(years)

tag: survival-years

tag: recurrence-years

tag: conservflag


title: genomic DNA from umbilical cord bood 4

description: umbilical cord blood sample

source_name: umbilical cord blood 4


title: CD4_DN_BC1


title: CD206+ Mfs of A20meyl KO mice on SD, replicate 3

description:
SD_KO_M2_3
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl KO mice on Standard Diet, replicate 3.

source_name: Epididymal adipose tissue

value: Epididymal adipose tissue


title: Sample 271

description: human breast tumor RNA

tag: metastatis

tag: timerecurrence(years)

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: nih


title: Sample 270

description: human breast tumor RNA

value: Dead

value: ER-

tag: stgallen


title: CD206+ Mfs of A20meyl KO mice on SD, replicate 2

description:
SD_KO_M2_2
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl KO mice on Standard Diet, replicate 2.

tag: strain

tag: genotype

tag: tissue

tag: cell type

value: 12 weeks of standard diet


title: CD4_DP_HD3

source_name: KLRG1+CD57+ (DP) T cells from healthy donor

tag: cell markers

value: KLRG1+CD57+ (DP) T cells

tag: disease state

value: healthy donor


title: MPP3_rep3

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

source_name: Multipotent progenitor 3

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

tag: treatment

value: untreated

tag: sequencing method

value: bulk RNA-seq (Illumina Nova Seq 6000)


title: CD11c+ Mfs of A20meyl KO mice on SD, replicate 4

description:
SD_KO_M1_4
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl KO mice on Standard Diet, replicate 4.

tag: condition


title: genomic DNA from umbilical cord bood 9

description: umbilical cord blood sample

source_name: umbilical cord blood 9

tag: gender

tag: sample type

value: Umbilical cord blood


title: genomic DNA from umbilical cord bood 23

description: umbilical cord blood sample

source_name: umbilical cord blood 23

value: Female


title: CD206+ Mfs of A20meyl KO mice on SD, replicate 1

description:
SD_KO_M2_1
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl KO mice on Standard Diet, replicate 1.


title: genomic DNA from umbilical cord bood 3

description: umbilical cord blood sample

source_name: umbilical cord blood 3


title: genomic DNA from umbilical cord bood 2

description: umbilical cord blood sample

source_name: umbilical cord blood 2


title: genomic DNA from umbilical cord bood 6

description: umbilical cord blood sample

source_name: umbilical cord blood 6


title: Sample 267

description: human breast tumor RNA

source_name: pool of individual breast tumors

value: breast tumor

tag: lypmph-nodes

value: LN+

tag: metastatis

value: Meta-

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

value: ER+

tag: conservflag


title: Sample 266

description: human breast tumor RNA

tag: tissue

value: LN-

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: nih

tag: stgallen


title: CD11c+ Mfs of A20meyl KO mice on SD, replicate 3

description:
SD_KO_M1_3
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl KO mice on Standard Diet, replicate 3.

tag: strain

tag: genotype

value: myeloid-specific knockout of A20

value: Epididymal adipose tissue

tag: cell type

tag: condition


title: MPP3_rep1

tag: treatment

tag: sequencing method


title: genomic DNA from umbilical cord bood 5

description: umbilical cord blood sample

source_name: umbilical cord blood 5

tag: gender

tag: sample type


title: CD4_DP_HD1

tag: cell markers

tag: disease state

value: CD4+ T cells from breast


title: Sample 269

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

value: Meta+

tag: death

value: Dead

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

value: ER-

tag: conservflag


title: CD11c+ Mfs of A20meyl KO mice on SD, replicate 2

description:
SD_KO_M1_2
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl KO mice on Standard Diet, replicate 2.

tag: strain

tag: genotype

tag: tissue

value: 12 weeks of standard diet


title: Sample 268

description: human breast tumor RNA

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

tag: nih

tag: stgallen


title: GMP_rep3

source_name: Granulocyte/macrophage progenitor

value: Bone marrow

tag: treatment

value: untreated

tag: sequencing method


title: CD4_DP_HD2

tag: cell markers

value: KLRG1+CD57+ (DP) T cells

tag: disease state

value: healthy donor

tag: cell type


title: GMP_rep1

value: bulk RNA-seq (Illumina Nova Seq 6000)


title: GMP_rep2


title: HumanSalivaryGlandCells.exposedMeHgl.rep5

city: Belém

first: Lygia

middle: Sega

last: Nogueira

address: R. Augusto Correa 01

country: Brazil

institute: Federal University of Pará

description: Gene expression after MeHg exposure to salivary gland human cells line

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software  12.0.3.1 (Agilent) using default parameters (protocol GE1_QCMT_Jun14 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Human salivary gland cells line, exposed to MeHg, replicate 5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: We isolated RNA from the human salivary gland cells line using the RNA extract kit (Promega, catalog#Z3101). We evaluated the samples for RNA integrity using the Tapestation (TapeStation Analysis Software A.02.02 (SR1) and samples with RINs >9.0 were used for further analysis.

treatment_protocol: Human salivary gland cells line were mantained in control condicitions (control groups) and exposed to 2.5 uM MeHg (exposed group) for 24h (n=5)

tag: cell culture

value: salivary gland cells line

value: 2.5 uM MeHg


title: HumanSalivaryGlandCells.exposedMeHgl.rep4

source_name: Human salivary gland cells line, exposed to MeHg, replicate 4


title: Sample 265

description: human breast tumor RNA

value: breast tumor

source_name: patient sample

tag: lypmph-nodes

value: LN+

tag: metastatis

value: Meta-

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)


title: CD206+ Mfs of A20meyl WT mice on HFD, replicate 4

description:
HFD_WT_M2_4
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl WT mice on High Fat Diet, replicate 4.

tag: strain

tag: genotype

value: wild-type

tag: tissue

value: Epididymal adipose tissue

tag: condition

value: 12 weeks of high fat diet


title: HumanSalivaryGlandCells.control.rep5

source_name: Human salivary gland cells line, non-exposed, replicate 5

value: control


title: CD11c+ Mfs of A20meyl KO mice on SD, replicate 1

description:
SD_KO_M1_1
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl KO mice on Standard Diet, replicate 1.

value: myeloid-specific knockout of A20


title: WT_1

description:
mRNA expression of primary mouse microglia
LG1

source_name: Bulk RNA-Seq

value: Primary microglia

value: mTrem2 +/+


title: Sample 264

description: human breast tumor RNA

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER+

tag: nih

tag: stgallen

tag: conservflag


title: HumanSalivaryGlandCells.exposedMeHgl.rep3

source_name: Human salivary gland cells line, exposed to MeHg, replicate 3

tag: cell culture

tag: treatment


title: CD206+ Mfs of A20meyl WT mice on HFD, replicate 3

description:
HFD_WT_M2_3
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl WT mice on High Fat Diet, replicate 3.

source_name: Epididymal adipose tissue

tag: cell type


title: CD206+ Mfs of A20meyl WT mice on HFD, replicate 2

description:
HFD_WT_M2_2
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl WT mice on High Fat Diet, replicate 2.


title: MPP3_ERlow_rep3

source_name: Multipotent progenitor 3 ER volume low cells

value: Bone marrow

value: untreated

tag: sequencing method


title: HumanSalivaryGlandCells.control.rep4

source_name: Human salivary gland cells line, non-exposed, replicate 4


title: Sample 263

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

value: Meta+

tag: death

value: Dead

tag: timesurvival(years)

tag: survival-years


title: MPP3_ERlow_rep1

tag: tissue

tag: strain

value: bulk RNA-seq (Illumina Nova Seq 6000)


title: MPP3_ERlow_rep2


title: HumanSalivaryGlandCells.control.rep3

source_name: Human salivary gland cells line, non-exposed, replicate 3

value: salivary gland cells line


title: CD206+ Mfs of A20meyl WT mice on HFD, replicate 1

description:
HFD_WT_M2_1
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl WT mice on High Fat Diet, replicate 1.

tag: genotype

tag: condition


title: CD11c+ Mfs of A20meyl WT mice on HFD, replicate 4

description:
HFD_WT_M1_4
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl WT mice on High Fat Diet, replicate 4.


title: Sample 261

description: human breast tumor RNA

value: breast tumor

value: LN+

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor


title: HumanSalivaryGlandCells.exposedMeHgl.rep2

source_name: Human salivary gland cells line, exposed to MeHg, replicate 2

tag: cell culture

tag: treatment

value: 2.5 uM MeHg


title: MPP3_ERhigh_rep2

source_name: Multipotent progenitor 3 ER volume high cells

tag: sequencing method


title: CD11c+ Mfs of A20meyl WT mice on HFD, replicate 3

description:
HFD_WT_M1_3
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl WT mice on High Fat Diet, replicate 3.

value: wild-type

tag: cell type


title: HumanSalivaryGlandCells.control.rep2

source_name: Human salivary gland cells line, non-exposed, replicate 2


title: HumanSalivaryGlandCells.exposedMeHgl.rep1

source_name: Human salivary gland cells line, exposed to MeHg, replicate 1


title: MPP3_ERhigh_rep1


title: Sample 258

description: human breast tumor RNA

source_name: pool of individual breast tumors

tag: lypmph-nodes

tag: metastatis

tag: nih

tag: stgallen

tag: conservflag


title: HumanSalivaryGlandCells.control.rep1

source_name: Human salivary gland cells line, non-exposed, replicate 1


title: HSC_rep3

source_name: Hematopoietic stem cells

tag: tissue

tag: strain


title: CD11c+ Mfs of A20meyl WT mice on HFD, replicate 1

description:
HFD_WT_M1_1
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl WT mice on High Fat Diet, replicate 1.

tag: genotype

value: Epididymal adipose tissue

tag: condition


title: CD11c+ Mfs of A20meyl WT mice on HFD, replicate 2

description:
HFD_WT_M1_2
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl WT mice on High Fat Diet, replicate 2.

value: 12 weeks of high fat diet


title: Sample 260

description: human breast tumor RNA

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years


title: genomic DNA from umbilical cord bood 13

description: umbilical cord blood sample

source_name: umbilical cord blood 13

tag: gender

value: Male

tag: sample type

value: Umbilical cord blood


title: CD206+ Mfs of A20meyl KO mice on HFD, replicate 4

description:
HFD_KO_M2_4
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl KO mice on High Fat Diet, replicate 4.

value: myeloid-specific knockout of A20

tag: cell type


title: Sample 257

description: human breast tumor RNA

tag: lypmph-nodes

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER-


title: CD206+ Mfs of A20meyl KO mice on HFD, replicate 3

description:
HFD_KO_M2_3
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl KO mice on High Fat Diet, replicate 3.


title: HSC_rep1

value: Bone marrow

tag: treatment

tag: sequencing method


title: U937-M2-1_rep3

city: Nanning

first: Lequn

last: Li

state: Guangxi

address: Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, He Di Rd #71

institute: Guangxi Medical University

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).Scanned images (TIFF format) were then imported into Agilent software (version 11.0.1.1)for grid alignment and expression data analysis.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent). After quantile normalization of the raw data, lncRNAs and coding RNAs were chosen for further data analysis. Differentially expressed lncRNAs and coding RNAs statistically different between the 2 groups were identified through volcano plot filtering

source_name: U937-M2 macrophages

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, 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, Arraystar).

growth_protocol: U937 cells were plated in 24-well plates at a density 2 x 10e5 cells per well and cultured with fresh RPMI-1640 medium supplemented with 5% FBS at 37˚C in humidified air with 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol® reagent according to the manufacturer’s instructions and the mRNA was further purified using a mRNA-ONLY™ Eukaryotic mRNA Isolation kit (Epicentre, Madison, WI, USA) according to the manufacturer’s instructions. RNA quantity and integrity were examined using a NanoDrop® ND-1000 (Thermo scientific, Scotts Valley, CA, USA) and standard denaturing agarose gel electrophoresis, respectively

treatment_protocol: To acquire the M2 phenotype, the cells were stimulated with phorbol 12-myristate 13-acetate (PMA, 100 ng/mL) for 24 h, followed by the addition of interleukin (IL)-4 (20 ng/mL) and IL-13 (20 ng/mL) for 12 h. The M1 phenotype was obtained by pretreating with PMA (100 ng/mL) for 24 h, followed by incubating with lipopolysaccharide (LPS; 100 ng/mL) and interferon (IFN)-gamma (20 ng/mL).

tag: cell line

value: macrophage

tag: phenotype

value: M2 (M2 macrophages induced from M0 U937 cells)


title: CD206+ Mfs of A20meyl KO mice on HFD, replicate 2

description:
HFD_KO_M2_2
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl KO mice on High Fat Diet, replicate 2.

tag: strain

tag: genotype

tag: tissue

tag: condition


title: WT liver rep2

city: milano

first: Saverio

last: Minucci

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

description: combined.rds

data_processing:
demultiplexing was performed with bcl2fastq software v2
Data from two different replicates were processed with CellRanger version 2.1.1 and align to mm10 genome reference
filtering count matrix were used to create two different object subsequently merged into one combined sample
data normalization and clustering analysis were performed with Seurat v 3.2.0
Genome_build: mm10
Supplementary_files_format_and_content: Seurat object with metadata table and Cell Ranger output

source_name: foetal liver

extract_protocol:
a single cell suspension from one E12.5 liver, obtained by enzymatic digestion and mechanical dissociation was purified from debris, dead cells and doublets through fluorescence activated cell sorting (FACS). To maximise the yield in droplet encapsulation of single cells, two separate technical replicates of the sample were independently processed
the library was prepared using the Chromium Single-Cell Controller (10X Genomics, Pleasanton, CA) and sequenced at a depth of 50k reads/cell on a NovaSeq 6000 (Illumina)

tag: age

value: liver


title: HSC_rep2

value: untreated

value: bulk RNA-seq (Illumina Nova Seq 6000)


title: genomic DNA from umbilical cord bood 1

description: umbilical cord blood sample

source_name: umbilical cord blood 1


title: CD206+ Mfs of A20meyl KO mice on HFD, replicate 1

description:
HFD_KO_M2_1
CD206+ (CD206highCD11clow) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD206+ Mfs of A20meyl KO mice on High Fat Diet, replicate 1.


title: WT liver rep1

description: combined.rds


title: MPP3_rep2

source_name: Multipotent progenitor 3


title: Sample 252

description: human breast tumor RNA

value: breast tumor

source_name: patient sample

value: LN-

tag: metastatis

value: Meta+

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

value: ER+

tag: nih

tag: stgallen

tag: conservflag


title: CD11c+ Mfs of A20meyl KO mice on HFD, replicate 4

description:
HFD_KO_M1_4
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl KO mice on High Fat Diet, replicate 4.

source_name: Epididymal adipose tissue

value: Epididymal adipose tissue

tag: cell type


title: Sample 24_MPA_24

city: Atlanta

first: Danielle

last: Clarkson-Townsend

state: Georgia

address: 1518 Clifton Road

department: Environmental Health

institute: Emory University

description:
column header in processed data file:
1024

data_processing:
FastQC performed
Fastq files aligned using STAR v2.7 to the C57 mouse genome (Ensemble assembly GRCm38.p6)
Read counts derived with STAR v2.7 with "quantmode" command and default commands.
Count data were analyzed using DESeq2 for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: count data were generated using STAR 2.7 with the "quantmode" command

source_name: E15.5 Placenta

extract_protocol:
RNA isolated using Qiagen Allprep DNA/RNA Mini Kit and concentration and RIN score measured with Thermo Scientific NanoDrop and Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female C57BL/6J mice were randomized into 2 different light treatments: standard control lighting (CL, 12:12 light:dark) schedule, or circadian disruption (inversions of the photoperiod every 3-4 days)). Females remained in this light treatment for 4 weeks of pre-dosing before timed breeding with male mice. Females remained in their light treatments until placental tissue collection at E15.5. Samples were collected from 6 pregnant mice in the CL group and 6 pregnant mice in the CD group. 2 placenta from each dam were selected for representation of a male and female sample (where possible) from each dam, for a total of 24 placenta samples. Isolated RNA were sequenced with PolyA RNA sequencing (paired-end) at a 30M read depth.

tag: developmental stage

value: Embryonic day 15.5 (E15.5)

tag: Sex

value: Female

tag: treatment

value: Circadian Disruption

value: placenta


title: Sample 254

first: Vladimir

address: 750 E Adams St

institute: SUNY Upstate Medical University

description: human breast tumor RNA

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.

tag: lypmph-nodes

value: Dead

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor


title: U937-M2-1_rep2

tag: cell line

tag: phenotype


title: U937-M2-1_rep1


title: Sample 251

description: human breast tumor RNA

tag: tissue

tag: metastatis

value: Meta-

tag: death

value: Alive

tag: timesurvival(years)


title: U937-M1-3_rep3

source_name: U937-M1 macrophages

value: macrophage

value: M1 (M1 macrophages produced from M2 macrophages)


title: Sample 250

description: human breast tumor RNA

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: nih


title: shNIK no.2_1

city: Shinjuku-ku

first: Yusuke

last: Hayashi

state: Tokyo

address: 2-2 Wakamatsu-cho

department: Dept. of Life Sci. & Med.Biosci.

institute: Waseda Univ.

description:
NIK knockdown lines were established by retroviral infection of pSUPER- shNIK knockdown vector and puromycin selection.
shNIK-C1-1

data_processing:
Raw sequence reads were trimmed and clipped for quality control by Trim-Galore (v0.6.4).
Read quality was checked by FastQC (v0.11.9).
Mapping was performed using HISAT2 (v2.2.0).
SAM files were converted Bam files using SAMtool (v1.10).
Gene expression matrix was constructed by prepDE.py and StringTie (v2.1.2).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: CSV file with un-normalized estimated read counts

source_name: Human breast cancer cells

growth_protocol: These cell lines were seeded in culture dishes in RPMI1640 medium (gibco) with 10% fetal bovine serum (gibco) and 1% Antibiotic-Antimycotic solution (gibco) at 37 °C in 5% CO2.

extract_protocol:
Total RNA was extracted using QIAzol (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
cDNA libraries for RNA sequencing were established from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) for selecting poly-A mRNA followed by strand-specific library preparation using MGIEasy RNA Directional Library Prep Set V2.0 (MGI tech). The resulting double-stranded library fragments were further processed into single-stranded circular DNA (sscDNA), which is the final form of MGI library. The sscDNA libraries were quantified by Qubit ssDNA Assay Kit and used for generating DNA nanoballs (DNBs) by rolling circle replication reaction. DNBs were then loaded into a flow cell for sequencing on DNBSEQ-G400 platform (MGI tech), according to the manufacturer’s instructions.

tag: genotype/variation

value: NIK knockdown


title: Sample 249

city: Syracuse

last: Kuznetsov

description: human breast tumor RNA

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.

value: LN+

tag: stgallen

tag: conservflag


title: Sample 23_MPA_23

description:
column header in processed data file:
1023

tag: strain

tag: developmental stage

tag: Sex

tag: treatment

value: Control Light


title: U937-M1-2_rep2

tag: cell line

tag: cell type


title: CD11c+ Mfs of A20meyl KO mice on HFD, replicate 3

description:
HFD_KO_M1_3
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl KO mice on High Fat Diet, replicate 3.

tag: genotype

value: myeloid-specific knockout of A20

tag: tissue

tag: condition

value: 12 weeks of high fat diet


title: U937-M1-1_rep1

tag: phenotype


title: shNIK no.1_2

description:
NIK knockdown lines were established by retroviral infection of pSUPER- shNIK knockdown vector and puromycin selection.
shNIK-Y1-2


title: Sample 248

description: human breast tumor RNA

value: breast tumor

tag: lypmph-nodes

value: LN-

tag: metastatis

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER-


title: shNIK no.1_1

description:
NIK knockdown lines were established by retroviral infection of pSUPER- shNIK knockdown vector and puromycin selection.
shNIK-Y1-1

tag: genotype/variation


title: Sample 22_MPA_22

description:
column header in processed data file:
1022

tag: strain

tag: developmental stage

value: Embryonic day 15.5 (E15.5)

tag: Sex

value: Male


title: Sample 256

description: human breast tumor RNA

value: Meta+

tag: timerecurrence(years)

tag: recurrence-years

value: ER+

tag: nih

tag: stgallen

tag: conservflag


title: shNIK no.2_2

description:
NIK knockdown lines were established by retroviral infection of pSUPER- shNIK knockdown vector and puromycin selection.
shNIK-C1-2


title: CD11c+ Mfs of A20meyl KO mice on HFD, replicate 2

description:
HFD_KO_M1_2
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl KO mice on High Fat Diet, replicate 2.

tag: genotype

tag: tissue

value: Epididymal adipose tissue

tag: cell type

tag: condition


title: shGFP_2

description:
Control cell line was established by retroviral infection of pSUPER- shGFP knockdown vector and puromycin selection.
shGFP-2

value: Control


title: Sample 21_MPA_21

description:
column header in processed data file:
1021

tag: treatment

value: Circadian Disruption

value: placenta


title: CD11c+ Mfs of A20meyl KO mice on HFD, replicate 1

description:
HFD_KO_M1_1
CD11c+ (CD206lowCD11chigh) adipose tissue macrophages (ATMs) FACS-sorted from eWAT.
CD11c+ Mfs of A20meyl KO mice on High Fat Diet, replicate 1.


title: Sample 247

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

value: Meta-

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years

tag: timemeta


title: Sample 20_MPA_20

description:
column header in processed data file:
1020

tag: strain

tag: developmental stage

tag: Sex

value: Female


title: shGFP_1

description:
Control cell line was established by retroviral infection of pSUPER- shGFP knockdown vector and puromycin selection.
shGFP-1

tag: genotype/variation


title: Sample 246

description: human breast tumor RNA

tag: timerecurrence(years)

tag: recurrence-years

tag: metastasis-years

tag: estrogen-receptor

tag: nih

tag: stgallen


title: Sample 245

description: human breast tumor RNA

tag: tissue

value: LN+

tag: conservflag


title: Hippocampus-GVHD3

city: Brisbane

first: Dylan

middle: Patrick

last: Carter-Cusack

state: Queensland

address: 300 Herston Rd

department: Department of Immunology

country: Australia

institute: QIMR Berghofer Medical Research Institute

description:
S3_FRAS202334364
stranded RNA

data_processing:
base calling performed with Illumina basecaller
Sequence reads were trimmed for adapter sequences using Cutadapt (version 1.9) and aligned using STAR (version 2.5.2a) to the Mus musculus GRCm38 assembly with the gene, transcript, and exon features of Ensembl (release 70) gene model. Quality control metrics were computed using RNA-SeQC (version 1.1.8)
Expression was estimated using RSEM (version 1.2.30)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited tsv files include raw counts for each sample as well as differential expression analysis of each treatment vs the vehicle (DMSO).

growth_protocol: NA - didn't use any cultured cells

extract_protocol:
RNA was isolated using either the Qiagen Rneasy Mini Kit (74104) or the Quick-RNA Microprep Kit (Zymo)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Recipient mice received 1100-cGy split-dose total-body irradiation, followed by 5x10^6 T-cell depleted BM with or without 0.5x10^6 splenic T cells

tag: cell type

value: whole hippocampus

value: hippocampus

tag: disease state

value: GVHD


title: Sample 19_MPA_19

description:
column header in processed data file:
1019

tag: treatment


title: Hippocampus-TCD3

description:
S12_FRAS202334373
stranded RNA

value: TCD (non GVHD control)


title: Sample 18_MPA_18

description:
column header in processed data file:
1018


title: Hippocampus-TCD2

description:
S11_FRAS202334372
stranded RNA


title: Hippocampus-GVHD2

description:
S2_FRAS202334363
stranded RNA


title: 93142

city: Copenhagen N

first: Rabiah

last: Fardoos

address: Blegdamsvej 3B

department: Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

data_processing:
Illumina Novaseq 6000 reads were trimmed ans clipped for quality control in Trimmomatic v0.39. Read quality was checked for each smole using factQC v0.11.9.
high-quality reads were then aligned to hg19 genome assembly and aligned using Dopseq-tools pipline on Terra (app-terra.bio).
Data was normalized and scaled using Seurat R package v.3.1.0 (http://satijalab.org/seurat/)
Cells with fewer than 750 UMIs or greater than 2500 UMIs were excluded.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Duodenum

extract_protocol:
mRNA was captured from single cell using Seq-well protocol. Illumina Nextera XT DNA Sample Prep Kit (Cat#FC-122-1001) was used with 900 pg of cDNA library was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

tag: age

tag: hiv

value: Negative


title: 93141

value: Positive


title: Sample 16_MPA_16

description:
column header in processed data file:
1016

tag: strain

tag: developmental stage

value: Embryonic day 15.5 (E15.5)


title: 93140


title: Sample 15_MPA_15

description:
column header in processed data file:
1015

tag: Sex

value: Male

value: Control Light


title: Hippocampus-GVHD1

description:
S1_FRAS202334362
stranded RNA


title: 92194


title: 92195


title: Sample 239

description: human breast tumor RNA

value: breast tumor

tag: lypmph-nodes

value: LN-

tag: metastatis

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: timemeta

value: ER+


title: Hippocampus-TCD1

description:
S10_FRAS202334371
stranded RNA

tag: tissue


title: Sample 241

description: human breast tumor RNA

value: Meta+

value: Dead

tag: recurrence-years

tag: metastasis-years

tag: estrogen-receptor

value: ER-

tag: nih

tag: stgallen

tag: conservflag


title: Sample 243

description: human breast tumor RNA

value: Meta-

value: Alive


title: Sample 14_MPA_14

description:
column header in processed data file:
1014

tag: strain

tag: treatment

value: Circadian Disruption

value: placenta


title: 92190

tag: gender

value: Female

tag: age

tag: hiv


title: Sample 237

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

tag: death


title: Sample 17_MPA_17

description:
column header in processed data file:
1017

tag: developmental stage

tag: Sex


title: Sample 13_MPA_13

description:
column header in processed data file:
1013

tag: tissue


title: Sample 12_MPA_12

description:
column header in processed data file:
1012


title: Sample 236

description: human breast tumor RNA

value: LN+

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta


title: 92142

value: Negative


title: TCD_Host3_(API_197)

description:
API197TCDHost4
stranded RNA

source_name: Group 2 - Non-GVHD Host

tag: cell type

value: microglia

value: Isolated microglia

tag: disease state

value: TCD (non GVHD control)


title: 92141

value: Positive


title: Sample 240

description: human breast tumor RNA

value: breast tumor

tag: metastasis-years

tag: estrogen-receptor

tag: nih

tag: stgallen

tag: conservflag


title: 92127

tag: gender

tag: age

tag: hiv


title: TCD_Host2_(API_197)

description:
API197TCDHost3
stranded RNA


title: GVHD_Host2_(API_197)

description:
API197GVHDHost2
stranded RNA

source_name: Group 1 - GVHD Host

value: GVHD


title: Sample 10_MPA_10

description:
column header in processed data file:
1010

tag: strain

tag: developmental stage

value: Embryonic day 15.5 (E15.5)

tag: Sex

tag: treatment


title: Sample 233

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: LN-

tag: metastatis

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

value: ER+


title: Sample 11_MPA_11

description:
column header in processed data file:
1011


title: GVHD_Donor6_(API197)

description:
API197GVHDDonor5
stranded RNA

source_name: Group 2 - GVHD Donor

tag: cell type

value: bone marrow derived macrophage

value: Isolated macrophages

tag: disease state


title: Sample 9_MPA_09

description:
column header in processed data file:
1009

value: Control Light


title: GVHD_Host4_(API_197)

description:
API197GVHDHost5
stranded RNA


title: GVHD_Host3_(API_197)

description:
API197GVHDHost4
stranded RNA


title: 92107


title: Sample 238

description: human breast tumor RNA

source_name: pool of individual breast tumors

value: Meta+

value: Dead

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER-

tag: nih

tag: stgallen

tag: conservflag


title: Sample 8_MPA_08

description:
column header in processed data file:
1008

tag: strain

tag: developmental stage

tag: Sex

value: Male

tag: treatment

value: Circadian Disruption

value: placenta


title: Sample 235

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

tag: metastatis

value: Meta-

tag: death

value: Alive


title: 92105

tag: gender

value: Female

tag: age

tag: hiv

value: Negative


title: GVHD_Donor5_(API_197)

description:
API197GVHDDonor4
stranded RNA

tag: cell type

tag: disease state

value: GVHD


title: Sample 229

description: human breast tumor RNA

value: breast tumor

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor


title: 92192

value: Positive


title: Sample 259

description: human breast tumor RNA

value: LN-

value: ER+

tag: nih

tag: stgallen

tag: conservflag


title: 92104


title: Sample 230

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

tag: metastatis


title: GVHD_Donor4_(API_197)

description:
API197GVHDDonor3
stranded RNA

value: bone marrow derived macrophage

value: Isolated macrophages


title: Sample 6_MPA_06

description:
column header in processed data file:
1006

tag: strain

tag: developmental stage

value: Embryonic day 15.5 (E15.5)

tag: Sex

tag: treatment

value: Control Light


title: Sample 5_MPA_05

description:
column header in processed data file:
1005


title: MPP3_ERhigh_rep3

source_name: Multipotent progenitor 3 ER volume high cells

value: Bone marrow

value: untreated

tag: sequencing method

value: bulk RNA-seq (Illumina Nova Seq 6000)


title: GVHD_Donor2_(API_197)

description:
API197GVHDDonor1
stranded RNA

tag: cell type

tag: disease state


title: GVHD_Donor3_(API_197)

description:
API197GVHDDonor2
stranded RNA