title: P1051815H08 [PBMCs_RNA-seq]

description: P1051815H08_P1_051815_H08_HVMT7CCXX_L6_1

extract_protocol:
RNA extraction was done using Qiagen RNAeasy kit. RNA from ~2 million cells was extracted, with concentration measured on a Qubit (Life Technologies). Additionally, RNA integrity was checked on a Bioanalyzer (Agilent, Santa Clara CA) and only RNA with an RNA integrity number (RIN) of > 7 was used for subsequent library construction.
Two sets of sequencing were carried out. Initially, libraries were constructed using Illumina's TruSeq kits with Ribo-Zero following the manufacturer's protocol. These libraries were sequenced at 125bp paired end reads on an Illumina HiSeq 2500. In the next round of sequencing libraries were constructed by Novogene, with poly-A selection using a Eukaryotic directional  mRNA  library (NEB) and sequenced on a HiSeq4000 at 150bp paired end reads. cDNA was quantitated on a Qubit (Life Technologies) and additionally the library quality was evaluated on a Bioanalyzer (Agilent)

value: blood

value: Peripheral Blood Mononuclear Cell (PBMC)


title: G21_J20_WT_06m

status: Public on Jan 31 2020

type: SRA

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital, Barrack Rd

country: United Kingdom

institute: University of Exeter Medical School

library_source: transcriptomic

data_processing:
Raw files were demultiplexed into FASTQ files (Phred (Q) ≥ 35) and checked for potential contamination
The randomized FASTQ files underwent quality control (QC) assessments using FastQC
Trimming (ribosomal sequences removal, quality threshold 20, minimum sequence length 35) was performed with FastqMcf
Trimmed samples were aligned to the mm10 (GRCm38.p4) reference mouse genome using STAR
Gene expression quantification was achieved using featureCounts
Read counts were analysed for differential expression in R (version 3.4.3) using the R package DESeq2 (version 1.16.1)
Data sets were filtered for non-expressed and lowly expressed genes (minimum of 6 counts across all samples)
Genome_build: mm10 (GRCm38.p4)
Supplementary_files_format_and_content: Format: .csv; Content: output from featureCounts (i.e., DESeq2 input) containing gene expression levels for each gene (rows) in each sample (columns)

molecule: total RNA

organism: Mus musculus

source_name: Entorhinal cortex

growth_protocol: rTg4510 mice, licensed from the Mayo Clinic (Jacksonville, FL, USA), were bred on a mixed 129S6/SvEvTac + FVB/NCrl background (heterozygous tau responder x heterozygous tTA effector). Bi-transgenic (here referred as TG) female mice and littermate controls (here identified as WT), 2, 4, 6 and 8 months-old (n = 9-10 animals per group), were used for this study. J20 mice, licensed from Gladstone Institute (San Francisco, California, United States), with founder mice purchased from MMRRC at The Jackson Laboratory (Bar Harbor, Maine, United States), were bred on a C57BL/6JOlaHsd background (parental generation: hemizygous male x wild type female). Hemizygous (here identified as TG) females and littermate controls (WT), 6, 8, 10 and 12 months of age (n = 9-10 animals per group), were used for this study. Animals were housed under standard conditions (constant temperature and humidity) with a 12h light/dark cycle in individually ventilated cages, with free access to food (Teklad irradiated global rodent diet (Envigo, United Kingdom)) and water.

extract_protocol:
Total RNA from all samples was isolated from the entorhinal cortex using the AllPrep DNA/RNA Mini Kit (Qiagen)
Stranded-specific mRNA sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) using the Bravo Automated Liquid Handling Platform (Agilent). cDNA libraries were prepared from ~450ng of total RNA plus ERCC spike-in synthetic RNA controls (Ambion, dilution 1:100). Final library pools were sequenced on a HiSeq2500 (Illumina) using 125bp paired-end reads at a mean untrimmed read depth of ~20 million reads/sample

treatment_protocol: Mice were terminally anaesthetized with pentobarbital (intraperitoneal injection) and transcardially perfused with phosphate-buffered saline (PBS). The entorhinal cortex was dissected from the left brain hemisphere on wet ice and snap-frozen on dry ice for subsequent RNA-seq analysis

tag: tissue

value: Entorhinal cortex

tag: genotype/variation

value: Wild Type


title: G22_J20_TG_06m


title: P1062715H08 [saliva RNA-seq]

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

country: USA

institute: Michigan State University

description: P1062715H08_S1_062715_H08_HW5J7CCXX_L4_1

data_processing:
Data QC using FastQC, and reads trimmed 15 from the left and 15 from the right
Trimmed paired reads mapped using Tophat 2.0.13 (using --no-coverage-search --library-type fr-firststrand)
Mapped files quantitated using Cufflinks (--no-effective-length-correction, using hg38 annotation)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample corresponding to Cufflinks output.

organism: Homo sapiens

source_name: saliva_post-vaccination respons for pneumococcal vaccine (PPSV23)

growth_protocol: Saliva RNA sequencing: Saliva was collected from the subject in an Oragene RNA sample tube (DNAGenotek). Approximately 2ml were selected and stabilized with the Oragene kit solution. Samples were inclubated in the lab at 60 degrees, aliquoted in 2ml tubes and stored at -80C until processing.

extract_protocol:
For RNA-Seq, total RNA was extracted using the Qiagen RNeasy kit (Qiagen) and treated with RNAse-free DNase (Qiagen). RNA integrity was checked on a Bioanalyzer 2100 (Agilent, Santa Clara CA)
Libraries were constructed by Novogene, using a Eukaryotic directional  mRNA  library (NEB).  cDNA preliminary concentration was quantitated on a Qubit (Life Technologies), an Agilent Bioanalyzer 2100 was used to test the insert size, and Q-PCR was used to quantify the library effective concentration precisely.

treatment_protocol: The subject received vaccination for pneumococcal pneumonia (PPSV23) on  060715, ~10.30 am.

tag: time point (mmddyy_hhh)

value: Saliva


title: P1062615H08 [saliva RNA-seq]

description: P1062615H08_S1_062615_H08_HW5J7CCXX_L4_1


title: P1062515H08 [saliva RNA-seq]

description: P1062515H08_S1_062515_H08_HW5J7CCXX_L2_1


title: A18_KEAP:LKB: KRAS_3

type: RNA

city: South San Francisco

first: Anneleen

last: Daemen

state: CA

address: 1 DNA Way

institute: GENENTECH, INC.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Microarray data were normalized using the R package RMA from Bioconductor. The annotate R package was used for probe-to-gene mapping, and the most variable probeset per gene was selected using the rowIQR function.

label: biotin

source_name: Tumor from BL/6 mouse with mutant Kras allele, knockout of Keap1 and knockout of Stk11

label_protocol: For whole-genome gene expression profiling, 200ng of total RNA was processed and Biotin labeled using the GeneChip WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol. Labeled cRNA was hybridized to Affymetrix Mouse Gene 2.0 ST array.

growth_protocol: All the mice were fed the 2018SX diet (Harlan Teklad) and had access to water ad libitum; they were housed under controlled conditions (23±2°C; 14-h light/ 10-h dark cycles). All experimental protocols conducted on the mice were performed in accordance with National Institutes of Health guidelines and were approved by the Johns Hopkins University Animal Care and Use Committee. Ten-eleven million adenovirus cre-recombinase particles diluted in 50 μl of minimal essential medium were administered by oropharyngeal aspiration (50 μl, twice at an interval of 5 min) according to the standard protocol (DuPage et al., 2009).

extract_protocol: Total RNA was isolated using TRIzol method. RNA was further cleaned up using RNeasy kit. RNA integrity was assessed with an Agilent 2100 Bioanalyzer and the RNA 6000 nano Chip kit.

treatment_protocol: Kras LSL (G12D) (strain number 01XJ6) (Johnson et al., 2001) and Stk11fl/fl (strain number 01XN2) (Bardeesy et al., 2002) were obtained from a mouse repository (NCI, Frederick) and were bred with Keap1fl/fl mice (Blake et al., 2010) to generate compound mutant mice in our facility. All experimental mice were maintained on a mixed genetic background.

tag: strain


title: A19_KEAP:LKB: KRAS_4


title: G20_J20_TG_12m


title: P1062415H08 [saliva RNA-seq]

description: P1062415H08_S1_062415_H08_HW5J7CCXX_L2_1


title: G18_J20_TG_10m


title: A16_KEAP:LKB: KRAS_1


title: P1062315H08 [saliva RNA-seq]

description: P1062315H08_S1_062315_H08_HVMJJCCXX_L5_1


title: A20_KEAP: KRAS_1

source_name: Tumor from BL/6 mouse with mutant Kras allele and knockout of Keap1


title: G19_J20_WT_12m


title: P1062215H08 [saliva RNA-seq]


title: G17_J20_WT_10m


title: F24_J20_TG_06m


title: A17_KEAP:LKB: KRAS_2


title: A14_LKB: KRAS_3

source_name: Tumor from BL/6 mouse with mutant Kras allele and knockout of Stk11


title: P1062115H08 [saliva RNA-seq]

description: P1062115H08_S1_062115_H08_HVMKYCCXX_L3_1


title: F23_J20_WT_06m


title: P1062015H08 [saliva RNA-seq]

description: P1062015H08_S1_062015_H08_HW5J7CCXX_L6_1


title: A15_LKB: KRAS_4


title: F22_J20_TG_12m


title: P1061915H08 [saliva RNA-seq]

description: P1061915H08_S1_061915_H08_HVVH2CCXX_L6_1


title: F21_J20_WT_12m


title: A13_LKB: KRAS_2


title: P1061815H08 [saliva RNA-seq]


title: A12_LKB: KRAS_1


title: P1061715H08 [saliva RNA-seq]


title: A10_N-Tg-KRAS_2

source_name: Tumor from BL/6 mouse with mutant Kras allele and expression of an Nfe2l2 transgene


title: F20_J20_TG_10m


title: P1070715H08 [saliva RNA-seq]

description: P1070715H08_S1_070715_H08_HW5J7CCXX_L4_1


title: F19_J20_WT_10m


title: A11_N-Tg-KRAS_3


title: P1061415H08 [saliva RNA-seq]


title: P1061615H08 [saliva RNA-seq]


title: P1061515H08 [saliva RNA-seq]


title: F18_J20_TG_08m


title: E22_J20_TG_10m


title: A7_KRAS_3

source_name: Tumor from BL/6 mouse with mutant Kras allele


title: P1061315H08 [saliva RNA-seq]


title: E21_J20_WT_10m


title: F17_J20_WT_08m


title: A6_KRAS_2


title: E20_J20_TG_08m


title: A9_N-Tg-KRAS_1


title: A8_KRAS_4


title: P1061115H08 [saliva RNA-seq]


title: A5_KRAS_1


title: P1061215H08 [saliva RNA-seq]


title: P1061015H08 [saliva RNA-seq]


title: P1060915H08 [saliva RNA-seq]


title: E18_J20_TG_06m


title: P1060815H08 [saliva RNA-seq]


title: E19_J20_WT_08m


title: A4_WT-B6_4

source_name: Normal tissue from wild-type BL/6 mouse


title: A3_WT-B6_3


title: D17_J20_WT_12m


title: E17_J20_WT_06m


title: C23_J20_WT_08m


title: P1060815H03 [saliva RNA-seq]

description: P1060815H03_S1_060815_H03_HWFKYCCXX_L6_1


title: P1060815H04 [saliva RNA-seq]

description: P1060815H04_S1_060815_H04_HW5J7CCXX_L6_1


title: A2_WT-B6_2


title: D20_J20_TG_06m


title: C22_J20_TG_06m


title: D19_J20_WT_06m


title: C20_J20_TG_12m


title: P1060815H02 [saliva RNA-seq]


title: P1060815H01 [saliva RNA-seq]

description: P1060815H01_S1_060815_H01_HVVG5CCXX_L8_1


title: A1_WT-B6_1


title: P1060715H22 [saliva RNA-seq]

description: P1060715H22_S1_060715_H22_HWFKYCCXX_L6_1


title: P1060715H21 [saliva RNA-seq]


title: C18_J20_TG_10m


title: C21_J20_WT_06m


title: C17_J20_WT_10m


title: P1060715H18 [saliva RNA-seq]


title: B24_J20_TG_06m


title: P1060715H19 [saliva RNA-seq]


title: P1060715H24 [saliva RNA-seq]

description: P1060715H24_S1_060715_H24_HVVG5CCXX_L8_1


title: B23_J20_WT_06m


title: P1060715H20 [saliva RNA-seq]


title: P1060715H15 [saliva RNA-seq]

description: P1060715H15_S1_060715_H15_HW5NNCCXX_L2_1


title: P1060715H16 [saliva RNA-seq]

description: P1060715H16_S1_060715_H16_HW5NNCCXX_L2_1


title: P1060715H23 [saliva RNA-seq]

description: P1060715H23_S1_060715_H23_HWFKYCCXX_L5_1


title: P1060715H17 [saliva RNA-seq]

description: P1060715H17_S1_060715_H17_HW5J7CCXX_L6_1


title: B18_J20_TG_08m


title: B21_J20_WT_12m


title: P1060715H14 [saliva RNA-seq]

description: P1060715H14_S1_060715_H14_HW5J7CCXX_L4_1


title: B17_J20_WT_08m


title: B22_J20_TG_12m


title: A23_J20_WT_12m


title: P1060715H13 [saliva RNA-seq]

description: P1060715H13_S1_060715_H13_HW5J7CCXX_L6_1


title: A24_J20_TG_12m


title: P1060715H11 [saliva RNA-seq]


title: A22_J20_TG_10m


title: P1060715H10 [saliva RNA-seq]

source_name: saliva_pre-vaccination respons for pneumococcal vaccine (PPSV23)


title: A21_J20_WT_10m


title: P1060715H09 [saliva RNA-seq]


title: A20_J20_TG_08m


title: A19_J20_WT_08m


title: P1060715H07 [saliva RNA-seq]


title: P1060715H08 [saliva RNA-seq]


title: A18_J20_TG_06m


title: A17_J20_WT_06m


title: P1060615H08 [saliva RNA-seq]


title: P1060515H08 [saliva RNA-seq]


title: T22_Tg4510_TG_8m


title: T24_Tg4510_TG_2m


title: T21_Tg4510_WT_8m


title: T23_Tg4510_WT_2m


title: T19_Tg4510_WT_6m


title: P1052615H04 [saliva RNA-seq]

description: P1052615H04_S1_052615_H04_HWFKYCCXX_L5_1


title: P1052615H07 [saliva RNA-seq]

description: P1052615H07_S1_052615_H07_HW5J7CCXX_L5_1


title: P1060215H08 [saliva RNA-seq]


title: P1052615H08 [saliva RNA-seq]

description: P1052615H08_S1_052615_H08_HW5WCCCXX_L5_1


title: P1052615H05 [saliva RNA-seq]

description: P1052615H05_S1_052615_H05_HWFKYCCXX_L5_1


title: T20_Tg4510_TG_6m


title: P1052615H06 [saliva RNA-seq]

description: P1052615H06_S1_052615_H06_HWFKYCCXX_L5_1


title: T18_Tg4510_TG_4m


title: P1052615H03 [saliva RNA-seq]

description: P1052615H03_S1_052615_H03_HVVG5CCXX_L8_1


title: P1052615H02 [saliva RNA-seq]

description: P1052615H02_S1_052615_H02_HWFKYCCXX_L5_1


title: T17_Tg4510_WT_4m


title: RNA-seq DKO2

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

description: rRNA-depleted RNA-seq

data_processing:
The sequences were basecalled by Illumina RTA embedded in HiSeq X Control Software by the standard workflow.
Reads were mapped to the mouse transcriptome (ensembl release 89; cDNA and ncRNA) and quantified by Kallisto with a k-mer index 31 and 60 bootstrapping.
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a tab-delimited file including transcript identifiers, length, expected count, and TPM

source_name: Naïve T cells

growth_protocol: Naive CD4 T cells (TCRb+CD4+CD25-CD62LhiCD44low) from two pairs of WT and DKO mice were isolated by FACS sorting.

extract_protocol:
Total RNAs were isolated by RNeasy Micro Kit (QIAGEN, 74004).
RNA-seq libraries were constructed by Yale Center for Genome Analysis (YCGA) using SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian (Clontech).

tag: cell type

value: naive T cells

tag: surface marker

tag: genotype

value: BTG1/2 double KO, Btg1f/f Btg2f/f-CD4-Cre


title: S23_Tg4510_WT_8m


title: P1052615H01 [saliva RNA-seq]

description: P1052615H01_S1_052615_H01_HWFKYCCXX_L5_1


title: S24_Tg4510_TG_8m


title: RNA-seq DKO1

description: rRNA-depleted RNA-seq


title: P1052515H24 [saliva RNA-seq]

description: P1052515H24_S1_052515_H24_HW5J7CCXX_L4_1


title: RNA-seq WT2

description: rRNA-depleted RNA-seq

value: Wildtype (littermate control), Btg1f/f Btg2f/f


title: P1052515H23 [saliva RNA-seq]

description: P1052515H23_S1_052515_H23_HW5J7CCXX_L5_1


title: RNA-seq WT1

description: rRNA-depleted RNA-seq


title: D23_J20_WT_10m


title: P1052515H22 [saliva RNA-seq]

description: P1052515H22_S1_052515_H22_HW5LCCCXX_L8_1


title: S20_Tg4510_TG_4m


title: S21_Tg4510_WT_6m


title: 65066 R KO +

city: Nijmegen

first: Elja

last: Louer

state: Select State

address: Geert Grootplein 26, M850 route 286

department: Physiology

country: Netherlands

institute: RadboudUMC

description: HLC37DSXX_103606-001-008_TAGGAGCT-GCCTTAAC_L003

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using STAR mapper two-pass mode and the gene-based read counts were quantified at the same time.
Genes with low read number (below 5) were removed
Cufflinks was employed to estimate gene-level abundance in FPKM (Fragments Per Kilobase per Million aligned reads value) values for ENSEMBL genes.
DESeq2 was used for DEG analysis. All time points were compared and. Only genes with a Benjamini-Hochberg-adjusted p-value < 0.05 and fold change > 1.5 were considered significantly deregulated.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample. Ensembl codes are given.

source_name: SUCNR1 KO_right eye + hydroquinone

extract_protocol:
40 week old male WT and SUCNR1 KO mice were randomly distributed over 2 treatments groups(-/+ hydroquinone). Every group contained 4 animals. Anterior segments (cornea, iris and lens) were removed to expose the posterior eyecup. The retina was carefully peeled off, and the eyecup containing the RPE, sclera and choroid were stored in RNAlater solution.   For RNA isolation, the RPE was removed gently from the choroidal layer using fine forceps. The brown clumps of RPE cells were dissolved in RLT Buffer from RNeasy Micro Kit after which RNA was extracted using the RNeasy Micro Kit. Illumina Novaseq 6000 sequencer was used for 1x 150 bp paired-end sequencing, sequencing an average of 20 million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: age

value: 40 weeks

value: SUCNR1 KO

tag: treatment

value: exposed to hydroquinone

value: Retinal pigment epithelium


title: 65069 R KO +

description: HLC37DSXX_103606-001-S02_TTGCGAGA-TATGGCAC_L003


title: P1052515H21 [saliva RNA-seq]

description: P1052515H21_S1_052515_H21_HW5LCCCXX_L7_1


title: S18_Tg4510_TG_2m


title: 65082 R KO +

description: HLC37DSXX_103606-001-004_CAGGTTCA-ATAACGCC_L003


title: P1052515H19 [saliva RNA-seq]

description: P1052515H19_S1_052515_H19_HW5J7CCXX_L4_1


title: S22_Tg4510_TG_6m


title: S17_Tg4510_WT_2m


title: 64986 L KO +

description: HLC37DSXX_103606-001-012R_TCGGATTC-CGCAACTA_L003

source_name: SUCNR1 KO_left eye + hydroquinone


title: P1052515H20 [saliva RNA-seq]

description: P1052515H20_S1_052515_H20_HW5J7CCXX_L5_1


title: 65010 R KO -

description: HLC37DSXX_103606-001-S01_CCAGTATC-AGCGAGAT_L003

source_name: SUCNR1 KO_right eye - hydroquinone

value: untreated (- hydroquinone)


title: P1052515H18 [saliva RNA-seq]

description: P1052515H18_S1_052515_H18_HW5J7CCXX_L5_1


title: 65001 L  KO -

description: HLC37DSXX_103606-001-011R_GGAAGAGA-CGAGAGAA_L003

source_name: SUCNR1 KO_left eye - hydroquinone


title: P1052515H17 [saliva RNA-seq]

description: P1052515H17_S1_052515_H17_HW5J7CCXX_L5_1


title: P1060815H06 [saliva RNA-seq]

description: P1060815H06_S1_060815_H06_HW5WCCCXX_L6_1


title: S19_Tg4510_WT_4m


title: Q24_Tg4510_TG_4m


title: Q23_Tg4510_WT_4m


title: Q22_Tg4510_TG_2m


title: 65079 L KO -

description: HLC37DSXX_103606-001-015_TCATCTCC-CTTGCTAG_L003


title: 65010 L KO -

description: HLC37DSXX_103606-001-003_AAGACCGT-GTCGATTG_L003


title: P1052515H13 [saliva RNA-seq]

description: P1052515H13_S1_052515_H13_HVVG5CCXX_L8_1


title: 65002 R WT +

description: HLC37DSXX_103606-001-006R_CGAATTGC-GTAAGGTG_L003

source_name: wild type_right eye + hydroquinone

value: wild type


title: Q21_Tg4510_WT_2m


title: P1052515H14 [saliva RNA-seq]

description: P1052515H14_S1_052515_H14_HW5J7CCXX_L5_1


title: 65009 L WT +

description: HLC37DSXX_103606-001-014_AGCCTATC-TGCGTAAC_L003

source_name: wild type_left eye + hydroquinone


title: 65021 L WT +

description: HLC37DSXX_103606-001-010_AGTGACCT-TCTAGGAG_L003


title: Q20_Tg4510_TG_8m


title: Q18_Tg4510_TG_6m


title: Q19_Tg4510_WT_8m


title: P1052515H11 [saliva RNA-seq]

description: P1052515H11_S1_052515_H11_HVVG5CCXX_L7_1


title: 65050 R WT +

description: HLC37DSXX_103606-001-002_TACGGTCT-TCCATTGC_L003


title: P1052515H16 [saliva RNA-seq]

description: P1052515H16_S1_052515_H16_HVVG5CCXX_L8_1


title: P1052515H12 [saliva RNA-seq]

description: P1052515H12_S1_052515_H12_HVVG5CCXX_L8_1


title: Q17_Tg4510_WT_6m


title: P1052515H10 [saliva RNA-seq]

description: P1052515H10_S1_052515_H10_HW5WCCCXX_L5_1


title: 65023 L WT -

description: HLC37DSXX_103606-001-R09_CTGTACCA-CACAGACT_L003

source_name: wild type_left eye - hydroquinone


title: P24_Tg4510_TG_2m

source_name: Entorhinal cortex


title: 65023 R WT -

description: HLC37DSXX_103606-001-009_TACTCCAG-GGTATAGG_L003

source_name: wild type_right eye - hydroquinone


title: P1052515H15 [saliva RNA-seq]

description: P1052515H15_S1_052515_H15_HVVG5CCXX_L8_1


title: P1052515H09 [saliva RNA-seq]

description: P1052515H09_S1_052515_H09_HW5J7CCXX_L5_1


title: P1052515H08 [saliva RNA-seq]

description: P1052515H08_S1_052515_H08_HW5WCCCXX_L5_1


title: 65044 L WT -

description: HLC37DSXX_103606-001-001R_GAACGAAG-GAATCACC_L003


title: P1052515H07 [saliva RNA-seq]

description: P1052515H07_S1_052515_H07_HW5WCCCXX_L5_1


title: 65044 R WT -

description: HLC37DSXX_103606-001-001_TTCCAGGT-CAGTGCTT_L003


title: P21_Tg4510_WT_8m


title: P23_Tg4510_WT_2m


title: P1051815H08 [saliva RNA-seq]

description: P1051815H08_S1_051815_H08_HW5WCCCXX_L5_1


title: P20_Tg4510_TG_6m


title: P1051115H08 [saliva RNA-seq]

description: P1051115H08_S1_051115_H08_HW5WCCCXX_L5_1


title: P19_Tg4510_WT_6m


title: LLHC_ZT70_rep2

city: Hanover

first: Kathleen

last: Greenham

state: NH

address: 78 College St.

department: Biological Sciences

institute: Dartmouth College

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

data_processing:
Illumina Casava was used for base-calling.
Reads were trimmed and filtered using trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic) with default settings and the following parameters: ILLUMINACLIP:../TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 HEADCROP:14 MINLEN:50
Reads were aligned to the B. rapa R500 genome Brapa_R500_V1.2.fasta (available on CoGe) using tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml) with the following options: --library-type fr-firststrand -I 12000 -G R500_v1.7.gff -M --max-segment-inron 12000 --max-coverage-intron 12000. Sample LD_ZT62_rep2 was identified as an outlier and removed, to avoid over-weighting rep1 the rep2 values were imputed by averaging the values of ZT60_rep1 and ZT64_rep1. Raw counts were generated in Subread version 1.6.3 (http://subread.sourceforge.net/)  with the following options: -F SAF -M -T 6 --fraction -s 2 -p -B -C. Count data was normalized using edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) version 3.22.1 using 'calcNormFactors' and log2 FPKM values were calculated using 'rpkm' with log=TRUE, prior.count=0.1.
Genome_build: Brapa_R500_V1.2.fasta genome with R500_v1.7.gff annotation
Supplementary_files_format_and_content: csv files containing the rawCounts generated using subread and log2 transformed FPKM values generated using edgeR for both replicates at each time point.

molecule: polyA RNA

organism: Brassica rapa subsp. trilocularis

source_name: Mature leaf tissue

growth_protocol: Plants were grown in growth chambers under 12h 20°C day/12h 20°C night for LDHH entrainment and 12h 20°C light/12h light at 10°C for the LLHC entrainment. Lights at plant height ~130 µmol photons m-2 s-1. Relative humidity for the LDHH chamber was ~60% and ~50% for the LLHC chamber.

extract_protocol:
Leaf tissue was homogenized and resuspended in LBB buffer (100mM Tris-Cl pH7.5, 500mM LiCl, 10mM EDTA, 1% LiDs, 5mM DTT, 2-BME). mRNA was extracted directly from tissue lysate using Life Technologies Dynabeads oligo (dT)25 (cat. no. 61002), and DNase treated using ThermoFisher TURBO DNase (cat. no. AM2238) in the presence of EDTA. The concentration of mRNA was assessed using a Qubit (Invitrogen, ThermoFisher) and 55ng was used for the cDNA library preparation. The quality of the mRNA was assessed using the Agilent Technologies 2100 Bioanalyzer (Agilent), all RIN values were below 3.
The cDNA libraries were made according to the protocol in Wang et al. 2011 (PLoS One 6(10): e26426, doi:10.1371/journal.pone.0026426). The quality and size of the cDNA libraries were assessed using the Agilent Technologies 2100 Bioanalyzer (Agilent) and run on a gel. All library sizes were ~250bp resulting in insert sizes ~150bp with PE100 sequencing. Libraries were multiplexed 12-samples in a lane - LDHH rep1 ZT24-46, LDHH rep1 ZT48-70, LDHH rep2 ZT24-46, LDHH rep2 ZT48-70, LLHC rep1 ZT24-46, LLHC rep1 ZT48-70, LLHC rep2 ZT24-46, LLHC rep2 ZT48-70..

treatment_protocol: All plants were transferred into constant light (LL) and temperature (HH) of 20°C 24h prior to tissue harvest.

value: leaf

tag: cultivar

tag: entrainment

value: LLHC

tag: time point

value: ZT70 - 70h after dawn

value: 16 DAS


title: P18_Tg4510_TG_4m


title: P17_Tg4510_WT_4m


title: LLHC_ZT70_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: D18_J20_TG_12m


title: P1050415H08 [saliva RNA-seq]

description: P1050415H08_S1_050415_H08_HW5WCCCXX_L4_1


title: P1042715H08 [saliva RNA-seq]

description: P1042715H08_S1_042715_H08_HW5WCCCXX_L4_1


title: P1060815H05 [saliva RNA-seq]

description: P1060815H05_S1_060815_H05_HW5WCCCXX_L4_1

source_name: saliva_post-vaccination respons for pneumococcal vaccine (PPSV23)


title: LLHC_ZT68_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT68 - 68h after dawn


title: P1042015H08 [saliva RNA-seq]

description: P1042015H08_S1_042015_H08_HW5WCCCXX_L6_1


title: P1041315H08 [saliva RNA-seq]


title: O24_Tg4510_TG_8m

value: Entorhinal cortex


title: LLHC_ZT66_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT66 - 66h after dawn


title: LLHC_ZT68_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: LLHC_ZT66_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: O22_Tg4510_TG_6m


title: P1040615H08 [saliva RNA-seq]

description: P1040615H08_S1_040615_H08_HW5LCCCXX_L1_1

value: Saliva


title: LLHC_ZT64_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT64 - 64h after dawn


title: LLHC_ZT64_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: O20_Tg4510_TG_4m


title: P1021516H08 [saliva RNA-seq]

description: P1021516H08_S1_021516_H08_HVLV5CCXX_L7_1


title: P1031416H08 [saliva RNA-seq]

description: P1031416H08_S1_031416_H08_HVVFLCCXX_L5_1


title: LLHC_ZT62_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT62 - 62h after dawn


title: LLHC_ZT62_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: O19_Tg4510_WT_4m

value: Wild Type


title: DNter2L1

city: Paris

first: Odil

last: Porrua Fuerte

address: 15 rue Helene Brion

country: France

institute: Institut Jacques Monod-CNRS

data_processing:
Reads were demultiplexed using the the pyBarcodeFilter script from the pyCRACutility suite
Adaptor trimming  with cutadapt 1.15
Quality-trimming with trimmomatic
Mapping with bowtie2
Normalized coverage obtained with the bamCoverage tool of deepTools2 package. Normalization by the total number of counts to 10^7 counts.
Genome_build: R64
Supplementary_files_format_and_content: bigwig files for each sample and for each strand (plus or minus)

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Cells grown on CSM-TRP to OD600= 0.6, in the presence of 0.5 mM IAA for 2h

extract_protocol:
Powders were defrozen and the resulting extracts were treated for one hour at 25°C with DNase I (165U/g of cells) to solubilize the chromatin and then clarified by centrifugating 20’ at 20000g at 4°C.IgG and nickel purification steps were performed as previously described in the original protocol (granneman et al., 2009) with minor changes: i) IgG purification steps has been realized using M-280 tosylactivated dynabeads (15mg per samples) coupled with rabbit IgG. ii) To increase the stringency, washes following both IgG and nickel purification steps were done at high salt concentration (1 M NaCl). After over-night binding on nickel columns, sequencing adaptors were added on the RNA as described in the original procedure. Because we work on nascent transcripts, some changes were required to fit with our purpose: For instance, since nascent transcripts contain a 3’ hydroxyl group that is protected inside the polymerase, we decided not to do the dephosphorylation step usually required because of the RNAse treatement that leads to 3’ phosphate transcripts. Also, we modified both 5’ and 3’ adaptors in order to sequence RNA molecules from the 3’ end so that we can determine the exact position of the polymerase. The 3’ ligation has been realized with T4 rnl 2 truncated K227Q enzyme (NEB) instead of classical T4 RNA ligase. RNA-protein complexes were eluted in 400 µl of elution buffer (50mM Tris pH 7.8, 50mM NaCl, 150mM Imidazole, 0.1% NP-40, 5mM beta mercaptoethanol).  Sen1 containing fractions were treated with 100 µg of proteinase K in a buffer containing 0.5% SDS. RNA was purified by two phenol chloroform isoamyl and one chloroform steps and precipitated in ethanol.
RNA was reverse transcribed using the Reverse transcriptase IV (Invitrogen). The cDNA solution was used to perform multiple PCR reactions in a final volume of 25 µl using the following conditions: 0.4 µM of each primers, 0.2 mM dNTP, 2.5 U LA Taq DNA polymerase from Takara, 1X LA PCR Buffer II and 2 µl of cDNA per reaction with the programme: 95°C 2’, 95°C 30’’, 58°C 45’’, 72°C 1’, 72°C 5’. PCR were pooled and treated with 200 U of Exonuclease I (NEB) per ml of PCR reaction for 1 hour at 37°C. After Exonuclease I inactivation for 20’ at 80°C, DNA was purified on PCR clean up columns (NucleoSpin® Gel and PCR Clean-up, Macherey-Nagel) and sent to sequence using Illumina technology (NextSeq sequencing).

treatment_protocol: Cells were submitted to UV crosslink in a UV lamp system (Megatron) for 50 seconds. Cells were harvested by centrifugation, washed in cold PBS and resuspended in 2.4 volume / g of cells of TN150 buffer (50 mM Tris pH 7.8, 150 mM NaCl, 0.1% NP-40 and 5 mM beta mercaptoethanol) supplemented with protease inhibitors (cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail). This suspension was flash frozen in droplets and cells were mechanically broken using the Mixer Mill MM 400 by doing 5 cycles of 3 minutes at 20 Hrz. Resulting powder was kept at -80°C

value: W303-derived strain

value: Sen1-AID, supplemented with sen1DNter-HTP in a plasmid


title: LLHC_ZT60_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT60 - 60h after dawn


title: M24_Tg4510_TG_4m


title: LLHC_ZT60_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: LLHC_ZT58_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT58 - 58h after dawn


title: LLHC_ZT56_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT56 - 56h after dawn


title: M23_Tg4510_WT_4m


title: Wtr1L1

value: Sen1-AID,  supplemented with SEN1-HTP in a plasmid


title: O23_Tg4510_WT_8m


title: LLHC_ZT58_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: leaf


title: M22_Tg4510_TG_2m


title: Wtr2L1


title: LLHC_ZT56_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: LLHC


title: DNIMr2L1

value: Sen1-AID, supplemented with sen1DNIM-HTP in a plasmid


title: M20_Tg4510_TG_8m


title: M19_Tg4510_WT_8m


title: LLHC_ZT54_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT54 - 54h after dawn

value: 16 DAS


title: M21_Tg4510_WT_2m

value: Entorhinal cortex


title: C19_J20_WT_12m


title: O18_Tg4510_TG_2m


title: DNterDNIMr2

extract_protocol:
Powders were defrozen and the resulting extracts were treated for one hour at 25°C with DNase I (165U/g of cells) to solubilize the chromatin and then clarified by centrifugating 20’ at 20000g at 4°C.IgG and nickel purification steps were performed as previously described in the original protocol (granneman et al., 2009) with minor changes: i) IgG purification steps has been realized using M-280 tosylactivated dynabeads (15mg per samples) coupled with rabbit IgG. ii) To increase the stringency, washes following both IgG and nickel purification steps were done at high salt concentration (1 M NaCl). After over-night binding on nickel columns, sequencing adaptors were added on the RNA as described in the original procedure. Because we work on nascent transcripts, some changes were required to fit with our purpose: For instance, since nascent transcripts contain a 3’ hydroxyl group that is protected inside the polymerase, we decided not to do the dephosphorylation step usually required because of the RNAse treatement that leads to 3’ phosphate transcripts. Also, we modified both 5’ and 3’ adaptors in order to sequence RNA molecules from the 3’ end so that we can determine the exact position of the polymerase. The 3’ ligation has been realized with T4 rnl 2 truncated K227Q enzyme (NEB) instead of classical T4 RNA ligase. RNA-protein complexes were eluted in 400 µl of elution buffer (50mM Tris pH 7.8, 50mM NaCl, 150mM Imidazole, 0.1% NP-40, 5mM beta mercaptoethanol). Eluates were concentrated in Vivacon® ultrafiltration spin columns 30 KDa MWCO to a final volume of 120 µl. A protein fractionation step was performed using the Gel Elution Liquid Fraction Entrapment Electrophoresis (Gelfree) system from Expedeon. RNA pol II containing fractions were treated with 100 µg of proteinase K in a buffer containing 0.5% SDS. RNA was purified by two phenol chloroform isoamyl and one chloroform steps and precipitated in ethanol.
RNA was reverse transcribed using the Reverse transcriptase IV (Invitrogen). The cDNA solution was used to perform multiple PCR reactions in a final volume of 25 µl using the following conditions: 0.4 µM of each primers, 0.2 mM dNTP, 2.5 U LA Taq DNA polymerase from Takara, 1X LA PCR Buffer II and 2 µl of cDNA per reaction with the programme: 95°C 2’, 95°C 30’’, 58°C 45’’, 72°C 1’, 72°C 5’. PCR were pooled and treated with 200 U of Exonuclease I (NEB) per ml of PCR reaction for 1 hour at 37°C. After Exonuclease I inactivation for 20’ at 80°C, DNA was purified on PCR clean up columns (NucleoSpin® Gel and PCR Clean-up, Macherey-Nagel) and sent to sequence using Illumina technology (NextSeq sequencing).

value: Sen1-AID, rpb1-HTP, supplemented with sen1DNterDNIM in a plasmid


title: DNterDNIMr1


title: LLHC_ZT54_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: DNterr2

value: Sen1-AID, rpb1-HTP, supplemented with sen1DNter in a plasmid


title: LLHC_ZT52_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT52 - 52h after dawn


title: DNIMr1L1


title: DNter1L1


title: M18_Tg4510_TG_6m


title: M17_Tg4510_WT_6m


title: P1060715H12 [saliva RNA-seq]

value: Saliva


title: LLHC_ZT52_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: L22_Tg4510_TG_8m


title: LLHC_ZT50_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT50 - 50h after dawn


title: LLHC_ZT48_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT48 - 48h after dawn


title: WTr2

value: W303-derived strain

value: Sen1-AID, rpb1-HTP, supplemented with SEN1 in a plasmid


title: L21_Tg4510_WT_8m

value: Wild Type


title: WTr1


title: L17_Tg4510_WT_4m


title: DNterr1


title: DNIMr1

value: Sen1-AID, rpb1-HTP, supplemented with sen1DNIM in a plasmid


title: LLHC_ZT46_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT46 - 46h after dawn


title: Drrp6DNIM_R1

data_processing:
Reads demultiplexing with bcl2fastq2-2.18.12
Adaptor trimming  with cutadapt 1.15
Quality-trimming with trimmomatic
Mapping with bowtie2
Normalized coverage obtained with the bamCoverage tool of deepTools2 package. Normalization by the library size.
Genome_build: R64
Supplementary_files_format_and_content: bigwig files for each sample and for each strand (plus or minus)

growth_protocol: Cells grown on YPD to OD600= 0.3-0.5

extract_protocol:
RNA extraction using standard procedures
Total RNA treated with Ribominus
NextSeq 500/550 High Output Kit

value: Drrp6, sen1DNIM


title: LLHC_ZT48_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: leaf

value: LLHC


title: LLHC_ZT46_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: K23_Tg4510_WT_8m


title: Drrp6_R2


title: L18_Tg4510_TG_4m


title: K24_Tg4510_TG_8m


title: K21_Tg4510_WT_6m


title: LLHC_ZT44_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT44 - 44h after dawn


title: Drrp6_R1


title: L24_Tg4510_TG_2m


title: L23_Tg4510_WT_2m


title: LLHC_ZT50_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: 16 DAS


title: K20_Tg4510_TG_4m

value: Entorhinal cortex


title: DNIMr2


title: LLHC_ZT42_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT42 - 42h after dawn


title: Drrp6DNIM_R2


title: eat-2(ad465); acs-20(tm3232)-3

city: Nanjing

first: Lina

last: Zou

state: Jiangsu

address: 12 Xue-Fu Road, Pukou District , Nanjing, Jiangsu

department: Model Animal Research Center

country: China

institute: Nanjing University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.5.
Reads were aligned to the C.elegans genome (version Wbcel235) using TopHat2 with parameters -r 30 -G  -p 8  --microexon-search --library-type fr-unstranded.
Raw counts of sequencing reads were generated by using the python script HTSeq.
Differential expression and dataset normalization were performed using the Bioconductor package DESeq2.
Genome_build: Wbcel235
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans animals were growing at 20°C until the late L4 stage before collection.

extract_protocol:
Total RNAs were extracted using the RNA MiniPrep (ZYMO RESEARCH#R2052) kit. The concentration and quality of total RNA samples were assessed using a Nanodrop and Agilent’s Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: K19_Tg4510_WT_4m


title: LLHC_ZT44_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: LLHC_ZT40_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT40 - 40h after dawn


title: eat-2(ad465); acs-20(tm3232)-1


title: N2

city: shanghai

first: zhibin

last: zhou

address: 415 Fengyang Road

department: orthopedics

institute: changzheng hospital

data_processing:
The raw reads were cleaned using FASTX (version: 0.0.13).
Cleaned reads were mapped to the mouse reference genome mm10 using Bowtie 2 BWT.Reads that aligned contiguously to the genomes were discarded.
From the remaining reads, we used find_circ pipeline to identify potential circRNAs. Briefly, The unmapped reads were extracted 20-mers from both ends and aligned them independently to find unique anchor positions within spliced exons. Anchors that aligned in the reversed orientation (head-to-tail) indicated circRNA splicing. Then the anchor alignments were extended such that the complete read aligns and the breakpoints were flanked by GU/AG splice sites. Only circRNAs with 2 or more supporting reads within single samples were kept.
The total number of reads supporting a particular head-to-tail junction was used as an absolute measure of circRNA abundance. To estimate its relative expression, we normalized the counts of read mapping across an identified back-splice by the read length and number of read mappings (spliced reads per billion mapping (SRPBM)) . The predicted circRNA of the above method is exactly the same as the location information of circBase, which is expressed as recorded circRNA, and the other is novel circRNAs.
All circRNAs identified from the sequencing data of MACs samples were intersected with known gene models. Depending on the type of intersection with a known transcript, the circRNAs were classified
Genome_build: mm10
Supplementary_files_format_and_content: reads count and SRPBM

source_name: primary mouse articular chondrocyte

growth_protocol: Cells were cultured in DMEM containing 10% fetal bovine serum and 1 % antibiotics at 37 °C in a 5 % CO2 incubator.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
Briefly, total RNA samples were treated using the RiboMinus™ Eukaryote Kit (A10837-08; Qiagen, GmbH, Germany) to remove ribosomal RNA. Next, ribosome-depleted RNA was treated with RNase R (RNR07250; Epicentre, Wisconsin, USA). Strand-specific RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7530L, NEB, Ipswich, MA, USA) following the manufacturer’s instructions.

treatment_protocol: Passage 1-3 cells were thawed, plated in 6-well plates (5×105 cells/cm2) for 24 h, treated with 10 ng/ml recombinant human IL-1β, and incubated for 24 h.

value: primary mouse articular chondrocyte


title: acs-20(tm3232)-3


title: LLHC_ZT42_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: K17_Tg4510_WT_2m


title: acs-20(tm3232)-1


title: OA2

source_name: primary mouse articular chondrocyte treated with interleukin-1β.


title: acs-20(tm3232)-2


title: LLHC_ZT38_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT38 - 38h after dawn


title: K18_Tg4510_TG_2m


title: LLHC_ZT38_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: P1011116H08 [saliva RNA-seq]

source_name: saliva_pre-vaccination respons for pneumococcal vaccine (PPSV23)

value: Saliva


title: N1


title: LLHC_ZT36_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT36 - 36h after dawn


title: eat-2(ad465)-2


title: LLHC_ZT36_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: LLHC_ZT34_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT34 - 34h after dawn


title: eat-2(ad465)-1


title: eat-2(ad465); acs-20(tm3232)-2


title: wild-type N2-3

value: wild-type


title: LLHC_ZT40_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: LLHC_ZT32_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT32 - 32h after dawn


title: OA1


title: eat-2(ad465)-3


title: wild-type N2-2


title: LLHC_ZT32_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: LLHC_ZT28_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT28 - 28h after dawn


title: LLHC_ZT26_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT26 - 26h after dawn


title: LLHC_ZT28_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: LLHC_ZT26_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: LLHC_ZT34_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: LLHC_ZT24_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT24 - 24h after dawn


title: Kidney, Col4a3 KO 7wk 8

city: Toronto

first: Vanessa

middle: R

last: Williams

state: Ontario

address: 1 King's College Circle

department: Institute of Medical Science

country: Canada

institute: University of Toronto

description: RMA expression value derived from Expression Console software; gene-level analysis

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Mouse Gene 2.0 ST Arrays (Thermo Fisher Scientific) for 16 h at 45 °C.

scan_protocol: Arrays were scanned at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Canada) on an Affymetrix GeneChip Scanner 3000 (Thermo Fisher Scientific).

data_processing: Affymetrix Expression Console Software (Thermo Fisher Scientific) was used for microarray processing and normalization by Robust Multi-Array Analysis (RMA); gene-level analysis.

source_name: Mouse kidney

label_protocol: Amplified cDNA was generated and labeled using the Ambion Whole Transcript Expression Kit (Thermo Fisher Scientific) and the Affymetrix GeneChip Whole Transcript Terminal Labeling Kit (Thermo Fisher Scientific), respectively.

extract_protocol: Kidney samples were stabilized in RNAlater (Thermo Fisher Scientific) and then stored at -80 °C until time of extraction. RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: Sex

value: male

value: 7 weeks

value: kidney


title: LLHC_ZT24_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: leaf

value: LLHC

value: 16 DAS


title: O21_Tg4510_WT_6m

value: Entorhinal cortex

value: Wild Type


title: Kidney, Col4a3 KO 7wk 7


title: LDHH_ZT70_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: LDHH

value: ZT70 - 70h after dawn


title: Kidney, Col4a3 KO 7wk 3


title: Kidney, Col4a3 KO 7wk 6


title: wild-type N2-1


title: LLHC_ZT30_rep2

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt

value: ZT30 - 30h after dawn


title: LLHC_ZT30_rep1

description:
LLHC_rawCounts.txt
LLHC_FPKM.txt


title: LDHH_ZT68_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT68 - 68h after dawn


title: LDHH_ZT70_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT68_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT66_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT66 - 66h after dawn


title: Kidney, Col4a3 KO 7wk 4


title: LDHH_ZT66_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT64_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT64 - 64h after dawn


title: LDHH_ZT64_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT62_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT62 - 62h after dawn


title: LDHH_ZT62_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: Kidney, Col4a3 KO 4wk 8

value: 4 weeks


title: LDHH_ZT60_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT60 - 60h after dawn


title: LDHH_ZT60_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT58_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT58 - 58h after dawn


title: LDHH_ZT58_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT56_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT56 - 56h after dawn


title: LDHH_ZT56_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT54_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT54 - 54h after dawn


title: Kidney, Col4a3 KO 4wk 7

value: male

value: kidney


title: LDHH_ZT54_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: leaf

value: 16 DAS


title: LDHH_ZT52_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT52 - 52h after dawn


title: Kidney, Col4a3 KO 7wk 1

value: 7 weeks


title: Kidney, Col4a3 KO 7wk 2


title: LDHH_ZT52_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: LDHH


title: Kidney, 129 WT 4wk 8


title: Kidney, 129 WT 7wk 5


title: Kidney, Col4a3 KO 4wk 5


title: Kidney, 129 WT 7wk 1


title: Kidney, Col4a3 KO 4wk 3


title: Kidney, 129 WT 4wk 6


title: Kidney, Col4a3 KO 4wk 2


title: Kidney, 129 WT 4wk 5


title: Kidney, 129 WT 7wk 7


title: Kidney, Col4a3 KO 4wk 6


title: Kidney, Col4a3 KO 7wk 5


title: Kidney, 129 WT 4wk 7


title: Kidney, 129 WT 7wk 6


title: Kidney, 129 WT 7wk 2


title: Kidney, Col4a3 KO 4wk 1


title: Kidney, 129 WT 4wk 2


title: Kidney, Col4a3 KO 4wk 4


title: Kidney, 129 WT 4wk 4


title: Kidney, 129 WT 7wk 8


title: Kidney, 129 WT 7wk 3


title: LDHH_ZT48_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT48 - 48h after dawn


title: Kidney, 129 WT 4wk 3


title: LDHH_ZT48_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: Kidney, 129 WT 7wk 4


title: LDHH_ZT46_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT46 - 46h after dawn


title: LDHH_ZT50_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT50 - 50h after dawn


title: Kidney, 129 WT 4wk 1


title: LDHH_ZT24_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT24 - 24h after dawn


title: 72hpa_ATAC-seq rep1

city: Stanford

first: Jessica

middle: Kay

last: Chang

address: 300 Pasteur Drive, Alway Building M311

department: Genetics

institute: Stanford University

library_source: genomic

data_processing:
Adapter sequences and low quality bases were trimmed using Trim Galore (trim_galore v0.3.3).  Reads were subsequently mapped to the Xentr9.0 genome assembly via BowTie v2.0.13 with very-sensitive parameters.
Multimapped or unmapped reads were filtered using samtools v1.1 and Picard tools v1.92.
Peaks were called using MACS2 with paramaters “--nomodel --shift -100 --extsize 200”.
Genome_build: Xentr9.0
Supplementary_files_format_and_content: Wig files for each ATAC-Seq library and for the composite of repilcates were generated with MACS2.

molecule: genomic DNA

organism: Xenopus tropicalis

source_name: 72hpa_tadpole tail

extract_protocol:
ATAC-Seq libraries were prepared from 20 tadpole tail tips in biological duplicate using independent clutches. Tissue was homogenized by incubating in liberase (0.35mg/mL) for 10 minutes at room temperature.  Cells were gently spun at 2100 rpm for 2min, and the resulting cell pellet was then incubated in a transposition mix
DNA was fractionated via transposition with a modified Tn5 transposase (Nextera DNA Sample Prep, Illumina), where sequencing adapters are also integrated to the fragment ends.  Libraries were PCR amplified with cycle numbers determined by a side qPCR reaction.  Following purification, libraries were quality checked for expected banding patterns on a 5% Bio-Rad Mini-Protean TBE Precast gel.  ATAC-Seq libraries were paired end sequenced on HiSeq and NextSeq platforms.

tag: developmental stage

value: Tail


title: 2hpa_ATAC-seq rep1

source_name: 2hpa_tadpole tail


title: 1hpa_ATAC-seq rep2

source_name: 1hpa_tadpole tail


title: 1hpa_ATAC-seq rep1


title: LDHH_ZT50_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: 3hpa_ATAC-seq rep2

source_name: 3hpa_tadpole tail


title: Uncut_ATAC-seq rep1

source_name: Uncut_tadpole tail

value: Uncut


title: Uncut_ATAC-seq rep2


title: LDHH_ZT28_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT28 - 28h after dawn


title: LDHH_ZT36_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT36 - 36h after dawn


title: LDHH_ZT28_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT44_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT44 - 44h after dawn


title: LDHH_ZT46_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT40_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT40 - 40h after dawn


title: LDHH_ZT42_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT42 - 42h after dawn


title: LDHH_ZT38_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT38 - 38h after dawn


title: LDHH_ZT36_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: leaf


title: LDHH_ZT34_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT34 - 34h after dawn

value: 16 DAS


title: LDHH_ZT26_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT26 - 26h after dawn


title: LDHH_ZT42_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: LDHH


title: LDHH_ZT38_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT44_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT34_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT24_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT32_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT32 - 32h after dawn


title: LDHH_ZT30_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt

value: ZT30 - 30h after dawn


title: input LP day 28

city: Edinburgh

first: Matthew

middle: M

last: Hindle

state: Midlothian

address: Easter Bush

department: Functional Genetics and Development

institute: The Roslin Institute

description: LP 4 Weeks ZT4 pooled biological rep1 + rep2

data_processing:
Basecalls performed using bcl2fastq 2.17.1.14
ChIP-seq reads were trimmed using trimmomatic ver. 0.36 with the following parameters, ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Trimmed reads were aligned to Oar_rambouillet_v1.0 genome assembly using BWA MEM ver. 0.7.17 with the default parameters and sorted by samtools ver. 0.1.19
Peaks were called using MACS ver. 2.1.0 with the following parameters, --format BAMPE –gsize 2.81e9 --keep-dup 1 --broad --broad-cutoff 0.1 --bdg --SPMR --qvalue 0.05
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: Bedgraph files of MACS2 outputs were converted to BigWig format using BedGraphToBigWig

organism: Ovis aries

source_name: pars tuberalis

growth_protocol: 6 month castrate males were used for the study

extract_protocol:
Samples were frozen on dry ice. Then nuclei were extracted using modified version of this protocol: http://www.nature.com/protocolexchange/protocols/3501
Libraries were constructed by the Manchester sequencing facility according to illumina standard protocols

treatment_protocol: Animals were (SP, 8L:16D) for 84 days, then transfered to long photoperiod (16L:8D) for 112 days and transfered back to SP for 28 days.

value: blackface

value: pars tuberalis

value: post natal month 10

tag: chip antibody


title: input LP day 7

description: LP Day 7 ZT4 pooled biological rep1 + rep2

value: post natal month 9


title: input SP day 28

description: SP 4 Weeks ZT4 pooled biological rep1 + rep2

value: post natal month 14


title: input LP day 112

description: LP 16 Weeks ZT4 pooled biological rep1 + rep2

value: post natal month 13


title: input LP day 1

description: LP Day 1 ZT4 pooled biological rep1 + rep2


title: LDHH_ZT40_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT32_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: input SP day 1

description: SP Day 1  ZT4 pooled biological rep1 + rep2


title: LDHH_ZT26_rep1

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: LDHH_ZT30_rep2

description:
LDHH_rawCounts.txt
LDHH_FPKM.txt


title: H3K4me3 SP day 28 rep 2

value: H3K4me3 (ActiveMotif, 39915)


title: input SP day 7

description: SP Day 7 ZT4 pooled biological rep1 + rep2


title: H3K4me3 SP day 7 rep 2


title: H3K4me3 SP day 1 rep 1


title: H3K4me3 SP day 1 rep 2


title: SEQ819

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

description:
F33
cfDNA
processed data file: 5hmC_Count_Matrix.csv

data_processing:
Library strategy: 5hmC-Seal
Raw sequencing reads were trimmed for adaptor sequences using Trimmomatic.
Low quality bases were also trimmed to a minimum length of 30 bp, followed by alignment to the current human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode. Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project (release 19), using featureCounts without strand information.
Peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
The 5hmC-Seal libraries were sequenced to produce a median number of ~25 million reads in cfDNA samples, and a median number of ~13.5 million unique reads (~55% of total reads) were mapped to the ~22,000 gene body regions.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: 5hmC_Count_Matrix.csv: Comma-separated text file

source_name: Plasma

extract_protocol:
CfDNA samples from T2D patients were prepared from peripheral blood with EDTA anticoagulation. Briefly, 4 mL of peripheral blood was collected from each subject, and plasma was separated within 4 h by centrifuging twice, one at 1 350× g for 12 min, and another at 13 500× g for 5 min. The processed plasma samples were stored at –80 °C immediately. CfDNA was extracted using the Circulating Nucleic Acid Kit (Qiagen, Germany) according to the manufacturer’s instructions. On average, 1-2 ng of cfDNA was obtained from each cfDNA sample. The quality of cfDNA was checked using the standard molecular biology approach.
Each cfDNA sample was first repaired and ligated with adaptors. Next, the T4 bacteriophage enzyme β-glucosyltransferase (β-GT) was used to transfer an engineered glucose moiety containing an azide-group to 5hmC in duplex DNA. A biotin tag was then installed onto the azide group using Huisgen cycloaddition (click) chemistry, followed by capturing of 5hmC-containing DNA fragments using avidin beads. The 5hmC-Seal library for each cfDNA sample was then constructed through PCR amplification, followed by paired-end sequencing (PE38) at Shanghai Epican Genetech, Co. Ltd. (Shanghai, China), using the Illumina NextSeq500 platform according to Illumina’s protocol. We randomized cfDNA samples when constructing the 5hmC-Seal libraries and sequencing.

value: Plasma

tag: disease diagnosis

value: Type 2 Diabetes

tag: population

value: Chinese

tag: sample

tag: batch

tag: binary for gender

tag: athero

value: Yes

value: Single


title: H3K4me3 LP day 112 rep 2

tag: strain

tag: tissue


title: H3K4me3 SP day 28 rep 1


title: H3K4me3 LP day 112 rep 1


title: H3K4me3 SP day 7 rep 1


title: input SP day 84

description: SP 12 weeks ZT4 pooled biological rep1 + rep2


title: SEQ817

description:
F31
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: H3K4me3 LP day 28 rep 1


title: SEQ815

description:
F29
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: No


title: SEQ818

description:
F32
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: H3K4me3 LP day 28 rep 2


title: SEQ814

description:
F28
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: H3K4me3 LP day 7 rep 1


title: SEQ810

description:
F24
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: H3K4me3 LP day 1 rep 2


title: AFF4_ChIPSeq

city: Houston

first: Qin

last: Feng

state: TX

address: 3517 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings.
ChIP-seq samples yielded 31-40million single-ended reads. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis.
Peak calling was performed using MACS with the following settings: mfold 10-30, p value 10e-13
Compared to the default MASC setting for peak calling (which is mfold 10-30, p value 10e-5, we used a much more stringent criterion and therefore resulted in very robust peaks, with 90% of the peaks with higher than 5 fold enrichment over background.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: breast cancer MCF7 cells

growth_protocol: MCF7 cells were maintained in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 mins, followed by incubation with a stop solution containing 0.125M of Glycine. Lysates were clarified from sonicated nuclei and chromatin fragemnts were isolated with antibody.
The library construction was performed by Active Motif according to the company's protocol

tag: antibody

value: AFF4 (Bethyl Labs, A302-538A)

tag: cell line


title: H3K27ac_ChIPSeq

value: H3K27ac (Active Motif, 39133)


title: Input DNA


title: SEQ809

description:
F23
cfDNA
processed data file: 5hmC_Count_Matrix.csv

tag: age


title: H3K4me3 SP day 84 rep2


title: H3K4me3 LP day 1 rep 1


title: SEQ813

description:
F27
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ811

description:
F25
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Multiple


title: SEQ816

description:
F30
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: H3K4me3 LP day 7 rep 2

description: LP Day 7 ZT4 pooled biological rep1 + rep2


title: H3K4me3 SP day 84 rep1


title: SEQ806

description:
F20
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ807

description:
F21
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ808

description:
F22
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ803

description:
F17
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ805

description:
F19
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ804

description:
F18
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ801

description:
F15
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: PTU + TH Treated mice 3

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

institute: ENSL

data_processing:
Bowtie2 (Galaxy Version 2.3.4.2)
htseq-count Galaxy Version 0.6.1galaxy3
Deseq2 differential gene expression(Galaxy Version 2.1.8.3)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Count table .txt

source_name: Striatum

growth_protocol: Post-natal day 25

extract_protocol:
Machery Nagel total RNA extraction.
Lexogen SENSE mRNA-Seq

tag: treatment

value: PTU + TH

value: Rescued


title: PTU Treated mice 4

value: PTU

value: Hypothyroid


title: PTU + TH Treated mice 2


title: PTU + TH Treated mice 4


title: PTU Treated mice 2


title: PTU Treated mice 3


title: PTU Treated mice 1


title: SEQ802

description:
F16
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: PTU + TH Treated mice 1


title: SEQ798

description:
F12
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: Euthyroid control 4

value: control

value: Euthyroid


title: SEQ796

description:
F10
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: Euthyroid control 3


title: Sample 35

city: Shanghai

first: Yanqing

last: Wang

address: NO. 160 Pujian Road

department: Urology

institute: Shanghai Renji Hospital

description: serum  extracellular vesicle delivered miRNAs of patients with bone -metastatic prostate cancer

hyb_protocol: According to Agilent micrornas chip Hybridization standard process and accessory Kit, Gene Expression Hybridization Kit (Cat. # 5188-5242, Agilent technologies, Santa Clara, CA, US), the hybrid furnace in scroll Hybridization Oven (Cat. # G2545A, Agilent technologies, Santa Clara, CA, US) in 65 ℃, 10 RPM, scroll hybrid 17 hours, hybrid cRNA 1.65 mu g / 600 ng, on sample amount and staining in washing cylinder dishes (Cat. # 121, Thermo Shandon, Waltham, MA, US) in the Wash, Wash the slice of the reagents used for Gene Expression for Wash Buffer Kit (Cat. # 5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Place the chip right in slide holder, place the sample point and face down, and then put it in the scanner. Open the Agilent Scan Control software for 8 x 60 k chips, select AgilentG3_miRNA mode (resolution 3 microns). Set to automatically file access, confirm the scanner status to ready, click Scan Slot m - n, confirm the placement of the chip position. The above steps, when confirmed start scanning chip

data_processing: Scanning image Feature Extraction are analyzed with Agilent Feature Extraction (AFE) software version 10.7.1.1 or higher outliers were excluded. Get background subtract and space to trend signal strength for processing. Uneven function markers in the feature extraction function of outliers are excluded.

source_name: serum

label_protocol: Sample tag and reagents are included in the hybrid need Agilent ` s micrornas Complete Labeling and Hyb Kit (p/n 5190-0456), Agilent ` s mirnas Spike - In Kit (p/n 5190-1934) contains two kinds of mirnas Spike - solution In Labeling Spike In solution and Hyb Spike - In solution, used for marking and hybridization reaction In the experimental process quality control

extract_protocol: Venous blood samples (5ml) were collected in non-anticoagulant acquisition tubes one day before prostate biopsy for serum harvest (1ml) after coagulation.The blood was centrifuged at 2000 g for 10 min at 4 °C to extract the serum. The serum was stored at -80°C till processed.One milliliter serum was used to isolate EV for each sample. After unfrozen in a 25 °C water bath, the serum was centrifuged at 2000 g for 30 min at room temperature to eliminate residual cell fragments. The serum EV was extracted using Total Exosome Isolation Kit (from serum, Thermo fisher scientific) according to the manufacturer's protocol. After extraction, Exosome Purification and RNA Isolation Kit (Norgen Biotek) was employed to purify EV and extract total RNA in EV consequentially. Agilent-070156 Human_miRNA_V21.0_Microarray  platform was used for miRNA-chip assay.

value: extracellular vesicle

tag: diagnosis

value: bone -metastatic prostate cancer


title: Sample 38


title: Sample 37


title: SEQ800

description:
F14
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Plasma


title: Sample 34


title: Euthyroid control 2


title: SEQ571

description:
F5
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Type 2 Diabetes


title: SEQ795

description:
F9
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Chinese


title: Sample 36


title: Sample 33


title: SEQ792

description:
F3
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Yes


title: Euthyroid control 1


title: Sample 32


title: SEQ790

description:
F1
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ791

description:
F2
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Single


title: Sample 29

description: serum  extracellular vesicle delivered miRNAs of patients with non-bone -metastatic prostate cancer

value: non-bone -metastatic prostate cancer


title: Sample 30


title: Sample 31


title: SEQ569

description:
E38
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ570

description:
E39
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: Sample 28


title: Striatum IP fraction 2

data_processing:
Pool of data from sample 2,3,4
Bowtie2 (Galaxy Version 2.3.4.2) mapping
MACS2 (Galaxy Version 2.1.1.20160309.0) peak calling using smaple 1 as background signal.
Blacklist filtering (https://www.encodeproject.org/annotations/ENCSR636HFF/).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Bigwig Bed

source_name: striatum

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to the ChIP-Seq Library Preparation on the Ion Proton™ System

value: striatum

value: IgG-coated magnetic beads


title: Striatum IP fraction 1


title: Striatum Input


title: Striatum IP fraction 3


title: SEQ789

description:
E37
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Multiple


title: SEQ788

description:
E36
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: Sample 27


title: Squamous_SCC_Tyr

city: Baltimore

first: Theresa

middle: K

last: Hodges

state: MD

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

description: pTyrosine IP SCC

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Human (hg19) whole genome reference using Bowtie v0.12.9
Raw read count were calculated for each sample.
Differential expression of piRNA were computed for Immortalized vs Normal Samples and Squamous Cell Carcinoma (SCC) vs Normal
Genome_build: H. sapiens (hg19)
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: piRNA Library Lung

growth_protocol: SCC cells were cultured in RPMI 1640 with 10% FBS; HBE cells were cultured in Keratinocyte-SFM with L-Glutamine, prequalified human recombinant Epidermal Growth Factor 1-53 (EGF 1-53) and Bovine Pituitary Extract (BPE)

extract_protocol:
small RNAs were extracted using mirVanaTM miRNA isolation kit (Ambion)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were lysed using cells using lysis buffer (20mM Tris-cl, pH7.6, 150mM NaCl, 20mM KCl, 1.5mM MgCl2, 0.5% NP-40, 0.5mM PMSF); phosphorylated small RNAs were immunoprecipitated using specific antibodies targeting p-Ser, p-Thr and P-Tyr.

value: Lung

tag: cell type

value: Squamous Cell Carcinoma (SCC) cells

value: phosphor-Tyrosine antibody (catalog No. 9411, Cell Signaling)

tag: molecule subtype

value: small RNA


title: Sample 26


title: Sample 23


title: Sample 25


title: Sample 24


title: Squamous_SCC_Thr

description: pThreonine IP SCC

value: phosphor-Threonine antibody (catalog No. 9381, Cell Signaling)


title: Squamous_SCC_Ser

description: pSerine IP SCC

value: phosphor-Serine antibody (catalog No. 4911M, Invitrogen)


title: SEQ787

description:
E35
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: No


title: Normal_NHBE_Tyr

description: pTyrosine IP NHBE

value: normal human lung bronchial epithelial (HBE) cells


title: Normal_NHBE_Thr

description: pThreonine IP NHBE


title: Sample 22

value: extracellular vesicle


title: Sample 20


title: Sample 19


title: SEQ568

description:
E33
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Plasma

value: Type 2 Diabetes


title: Sample 21


title: SEQ566

description:
E31
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Chinese

value: Yes


title: SEQ565

description:
E30
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Single


title: Immortalized_HBE_Thr

description: pThreonine IP HBE

value: Immortalized human lung bronchial epithelial (HBE) cells


title: Sample 18

value: non-bone -metastatic prostate cancer


title: Immortalized_HBE_Tyr

description: pTyrosine IP HBE


title: Immortalized_HBE_Ser

description: pSerine IP HBE


title: Normal_NHBE_Ser

description: pSerine IP NHBE


title: Sample 17


title: Sample 16


title: Sample 15


title: SEQ786

description:
E34
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ564

description:
E29
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ567

description:
E32
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ563

description:
E28
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Multiple


title: SEQ561

description:
E26
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ562

description:
E27
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ560

description:
E23
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: ATRT_VAL_66

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description: DNA methylation data from an ATRT tumor sample

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Normalization was performed by applying the function preprocessIllumina available in Bioconductor package minfi

label: biotin/DNP

source_name: Primary ATRT tumor tissue

label_protocol: standard Illumina protocol

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: molecular subgroup

value: MYC

tag: gender

tag: age (yr)

tag: tumor location


title: Sample 14

description: serum  extracellular vesicle delivered miRNAs of patients with non-bone -metastatic prostate cancer


title: Sample 13


title: Sample 11


title: Sample 10


title: SEQ785

description:
E22
cfDNA
processed data file: 5hmC_Count_Matrix.csv

tag: disease diagnosis

tag: population

tag: sample


title: ATRT_VAL_43

value: TYR

value: female

value: infratentorial


title: ATRT_VAL_61

value: SHH


title: SEQ784

description:
E21
cfDNA
processed data file: 5hmC_Count_Matrix.csv

tag: batch

tag: binary for gender

tag: athero


title: ATRT_VAL_42

value: male


title: Sample 12

tag: tissue


title: Sample 8

description: serum  extracellular vesicle delivered miRNAs of patients with benign prostatic hyperplasia

value: benign prostatic hyperplasia


title: Sample 6


title: ATRT_VAL_41


title: Sample 7


title: Sample 5


title: SEQ559

description:
E19
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ558

description:
E18
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: No


title: SEQ781

description:
E16
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ782

description:
E17
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: ATRT_VAL_40

value: supratentorial


title: Sample 9

value: extracellular vesicle


title: Sample 3


title: Sample 4


title: SEQ783

description:
E20
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Plasma

value: Type 2 Diabetes


title: ATRT_VAL_20


title: SEQ780

description:
E15
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Chinese

value: Yes


title: ATRT_EURHAB_84


title: SEQ779

description:
E14
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: ATRT_EURHAB_83


title: 24hpa_ATAC-seq rep2

source_name: 24hpa_tadpole tail

tag: developmental stage

tag: time point

value: Tail


title: ATRT_EURHAB_81


title: ATRT_EURHAB_80


title: 15hpa_ATAC-seq rep2

source_name: 15hpa_tadpole tail


title: 24hpa_ATAC-seq rep1


title: Sample 1

tag: age


title: ATRT_EURHAB_79


title: 15hpa_ATAC-seq rep1


title: Sample 2

tag: diagnosis


title: ATRT_EURHAB_78


title: SEQ557

description:
E10
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: 6hpa_ATAC-seq rep2

source_name: 6hpa_tadpole tail


title: SEQ776

description:
E11
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: 72hpa_ATAC-seq rep2


title: 6hpa_ATAC-seq rep1


title: SEQ556

description:
E8
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Single


title: ATRT_EURHAB_77


title: SEQ775

description:
E9
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: 3hpa_ATAC-seq rep1


title: 2hpa_ATAC-seq rep2


title: ATRT_EURHAB_75


title: SEQ554

description:
E5
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: ATRT_EURHAB_72

description: DNA methylation data from an ATRT tumor sample


title: 0hpa_ATAC-seq rep1

source_name: 0hpa_tadpole tail


title: SEQ772

description:
E1
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: SEQ773

description:
E3
cfDNA
processed data file: 5hmC_Count_Matrix.csv

value: Multiple


title: pOsNAR2.1-OsNAR2.1 WGBS replicate 3

city: Nanjing, Jiangshu Province

first: Xiaorong

last: Fan

state: Jiangshu

address: Tongwei Road 1

institute: Nanjing Agricultural University

description:
WTvspOsNAR2.1-OsNAR2.1_DMR.xls
pOsNAR2.1-OsNAR2.1 3

data_processing:
Whole-genome bisulfite sequencing
After downloading raw data from sequencing machine, in order to avoid alignment error, the raw reads will be filtered and trimmed to obtain clean reads. First, remove polluted adapter reads (remove the reads with the number of contaminants in the base more than 5bp) . Second, remove the reads with base calling quality Qemo), and third, remove reads with the percentage of N >5% (For pair-end sequencing, if one end is removed, both ends will be removed). After filtering, the available data were compared with the reference genome Oryza_sativa.IRGSP-1.0.32 to obtain the alignment results using Bismark (v0.9.0) (K Felix, et al. 2011).  The uniquely mapped reads will be used to call the methylated cytosines(C) in highly enriched regions.Valid coverage of methylated cytosine, i.e. the percentage of methylated C among all C on genome, is associated with methylation level. C sites with read depths less than 5 are eliminated firstly. Then for each C site, valid coverage is calculated by for all C or C within each pattern (CpG, CGH, and CHH). Coverage is the count of C sites with more than 5 depth divided by total number of C site by its pattern. For each C site, the methylation level (%) is calculated by: 100* (reads supportted methylation)/ (total reads depth of this site). For methylated region, methylation level (%) is calculated by: 100*methylation level of all C sites in this region/Total number of C sites in this region. The conversion ratio of  Lambda DNA is around 99.5% to 99.6% in all samples.
MeDIP sequecing
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). After passing Solexa CHASTITY quality filter, the clean reads were aligned to rice genome (Ensembl Plants Oryza sativa Japonica, IRGSP-1.0) using BOWTIE software (V2.1.0, B Langmead, et al. 2012). MeDIP peaks were identified by MACS2(Zhang et al 2008), and statistically significant MeDIP-enriched regions (peaks) were identified by comparison to a Poisson background model (Cut-off q-value=10-2). Differentially Methylated Regions (DMRs) in MeDIP dataset was identified by diffReps(Shen et al 2013) (p < 0.0001), and promoter-associated DMRs were annotated with IRGSP-1.0 database.
Genome_build: IRGSP1
Supplementary_files_format_and_content: Processed data were stored in excel files, which included differentially methylated regions from WGBS and enriched peaks from MeDIP.

organism: Oryza sativa

source_name: DNA methylation of pOsNAR2.1-OsNAR2.1

growth_protocol: We grew plants water for 10 days after germination. The Nipponbare WT (NP), OsNAR2.1 RNAi and  pUbi-OsNAR2.1 lines for MEDIP-seq were  grown in plots at Nanjing Agricultural University in Nanjing, Jiangsu, 2014. Nanjing, Jiangsu is in a subtropical monsoon climate zone. Chemical properties of the soils in the plots included organic matter, 11.56 g/kg; total N content, 0.91 g/kg; available P content, 18.91 mg/kg; exchangeable K, 185.67 mg/kg; and pH 6.5. Basal applications of 30 kg P/ha (Ca(H2PO4)2) and 60 kg K/ha (KCl) were made to all plots 3 days before transplanting. N fertilizer as urea accounted for 40%, 30% and 40% of the total N fertilizer was applied prior to transplanting, at tillering, just before the heading stage, respectively.

extract_protocol:
Genomic DNA were extracted from 10-day-old seedlings, and shipped to the Anoroad Genome company(Beijing) for whole-genome bisulfite sequencing(WGBS). WGBS librarie preparation, sequencing and data analysis was described as before. WGBS libraries are prepared for subsequent cluster generation starting from sample DNA through adaptor ligation, library purification, and quantification. Input gDNA (5 μg) is fragmented by sonication. The fragments are blunt-ended and phosphorylated, and a single ʹAʹ nucleotide is added to the 3ʹ ends of the fragments in preparation for ligation to a methylated adapter that has a single-base ʹTʹ overhang. The ligation products are purified and size-selected by agarose gel electrophoresis. Size-selected DNA is bisulfite-treated and purified. The treated DNA is PCR-amplified to enrich the fragment that have adapters on both ends. The final purified product is then quantitated prior to cluster generation. The WGBS libraries will be sequenced using Illumina HiSeq2500 /4000 Analyzer according to the manufacturer’s instructions.
MeDIP sequecing in this study done by KangChen Bio-tech, Shanghai, China. Sequencing library preparation and data analysis was described as before (Ding et al 2015 ). Genomic DNA was sonicated to ~200 - 600bp with a Bioruptor sonicator (Diagenode). 800 ng of sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina genomic DNA protocol. After agarose size-selection to remove unligated adapters, the adaptor-ligated DNA was used for immunoprecipitation using a Rat monoclonal anti-5-methylcytosine antibody (Diagenode). For this, DNA was heat-denatured at 94°C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μL primary antibody overnight at 4°C with rocking agitation in 400 μL immunoprecipitation buffer (0.5% BSA in PBS). To recover the immunoprecipitated DNA fragments, 100 μL of protein G magnetic beads (Life Technologies) were added and incubated for an additional 2 hours at 4°C with agitation. After immunoprecipitation, a total of five immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. A nonspecific Rat IgG immunoprecipitation was performed in parallel to methyl DNA immunoprecipitation as a negative control. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/mL proteinase K for 2 hours at 65°C and then allowed to cool down to room temperature. MeDIP and supernatant DNA were purified using Qiagen MinElute columns and eluted in 16 μL EB (Qiagen). 14 cycles of PCR were performed on 5 μL of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (300-700 bp) was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Agilent 2100 Bioanalyzer. An aliquot of each library was diluted in EB to 5 ng/μL and 1 μL was used in real-time PCR reactions to confirm the enrichment for methylated region.

value: shoot


title: SEQ552

description:
E2
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: pOsNAR2.1-OsNAR2.1 WGBS replicate 2

description:
WTvspOsNAR2.1-OsNAR2.1_DMR.xls
pOsNAR2.1-OsNAR2.1 2


title: SEQ774

description:
E6
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: ATRT_EURHAB_76

value: TYR


title: 0hpa_ATAC-seq rep2


title: ATRT_EURHAB_74


title: ATRT_EURHAB_68

value: female


title: pOsNAR2.1-OsNAR2.1 WGBS replicate 1

description:
WTvspOsNAR2.1-OsNAR2.1_DMR.xls
pOsNAR2.1-OsNAR2.1 1


title: SEQ553

description:
E4
cfDNA
processed data file: 5hmC_Count_Matrix.csv


title: ATRT_EURHAB_63


title: ATRT_EURHAB_62


title: ATRT_EURHAB_61

value: MYC


title: FP WGBS replicate 1

description:
WTvsFP_DMR.xls
FP1

source_name: DNA methylation of FP


title: ATRT_EURHAB_59

value: SHH

value: infratentorial


title: P1_3

city: Hangzhou

first: Xu

last: Ping

state: Zhejiang

address: 866 Yuhangtang Road

department: Tea Research Institute

institute: Zhejiang University

description: Tea samples (one bud and two leaves) planted at the Tea Research Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, China (N30°11′7.21″, E120°03′52.45″), on 15th September, 2019

data_processing:
The quality of raw sequence data were assessed using FASTQC (version 0.10.1) (www.bioinformatics.bbsrc.ac.uk/projects/fastqc.) and high-quality reads were filtered using Trimmomatic
The previously published genome database CSS (cv.Shuchazao) was used as a reference genome for mapping filtered high-quality reads using HISAT (v 2.0.5) with default parameters
StringTie (v 1.3.1) was used to assemble the aligned reads from samples into transcripts. StringTie assembly results from each sample were combined by StringTie-Merge
Gene expression (FPKM) was calculated using StringTie's own script prepDE.py
Ballgown was used for the analysis of differently expressed genes (DEGs)
Genome_build: Teaplant_CSS_version2 from TPIA (http://tpia.teaplant.org/download.html)
Supplementary_files_format_and_content: Genes_rcounts.xls

organism: Camellia sinensis

source_name: the leaves samples after harvested for 1 hour

extract_protocol:
A Thermo GeneJET Plant RNA Purification Mini Kit (Thermo Fisher Scientific Inc, USA) was used to isolate total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The rate of tea leaf harvesting was 1 h per basket by practicing. After 3 min picking, the leaves in basket reached around 1.5 cm thick (Sample P2), and then a layer of tulle was used to separate samples. Tea leaves were then picked for 57 minutes and another layer of tulle was added on top, followed by 3 minutes further picking (Sample P1). The basket filled with tea leaves was then incubated in a cool and ventilated area for 1 h to simulate the transportation process. After 57 minutes of incubation, tea was picked again for a further 3 min (Sample P0)

tag: cultivar

value: Camellia sinensis cv. Longjing43

value: leaf


title: FP WGBS replicate 3

description:
WTvsFP_DMR.xls
FP3


title: P2_2

source_name: the leaves samples after harvested for 2 hours

growth_protocol: Tea samples (one bud and two leaves) planted at the Tea Research Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, China (N30°11′7.21″, E120°03′52.45″), on 15th September, 2019


title: ATRT_EURHAB_58


title: P1_1


title: FP WGBS replicate 2

description:
WTvsFP_DMR.xls
FP2


title: CK WGBS replicate 1

description:
WTvsCK_DMR.xls
CK1

source_name: DNA methylation of CK


title: P0_3

source_name: the leaves samples after harvested for 0 hour


title: P0_2


title: ATRT_EURHAB_57


title: P1_2


title: CK WGBS replicate 3

description:
WTvsCK_DMR.xls
CK3


title: P2_1


title: P0_1


title: CK WGBS replicate 2

description:
WTvsCK_DMR.xls
CK2


title: wuyujing 7 (the wild type) WGBS replicate 3

description:
WTvspOsNAR2.1-OsNAR2.1_DMR.xls
WT3

source_name: DNA methylation of wuyujing 7


title: P2_3


title: wuyujing 7 (the wild type) WGBS replicate 2

description:
WTvspOsNAR2.1-OsNAR2.1_DMR.xls
WT2


title: ATRT_EURHAB_60

value: male

value: supratentorial


title: ATRT_EURHAB_55


title: ATRT_EURHAB_42


title: NMB959_850k

description:
200819570005_R06C01
DNA methylation data from an ATRT tumor sample

hyb_protocol: standard Illumina Protocol

scan_protocol: standard Illumina Protocol

data_processing: Data processing of the microarry methylation data included standard quality controls as recommended by Ilumina. Further downstream analysis was performed as detailed in Capper et al., 2018, Nature.

label: cy3, cy5

label_protocol: standard Illumina Protocol

extract_protocol: DNA was extracted using the DNAeasy blood and tissue kit (Qiagen)

value: Primary ATRT (Atypical Teratoid Rhabdoid Tumor)


title: ATRT_EURHAB_44


title: ATRT_EURHAB_54


title: AnoSag_st7_HL_Rep5

city: Athens

first: Douglas

last: Menke

state: GA

address: 500 DW Brooks Drive

institute: University of Georgia

data_processing:
Sequencing read quality was assessed with FastQC
Illumina adapters were trimmed with STAR
Trimmed reads were aligned to the Green anole (Anolis carolinensis) AnoCar2.0 genome assembly with STAR
Mapped reads were assigned to genes using FeatureCounts
Principal component and differential expression analyses were performed using DESeq2
Genome_build: AnoCar2.0
Supplementary_files_format_and_content: Tab-delimited text files which include feature count for each sample,  Differential_Gene_Expression file.

organism: Anolis sagrei

source_name: Hindlimb

extract_protocol:
Pairs of forelimb and hindlimb buds were collected and total RNA was isolated using the mirVana RNA Isolation Kit (Ambion).
Libraries were constructed with TruSeq Stranded mRNA Sample Prep Kit (Illumina) and sequenced on the Illumina NextSeq 500 platform.

value: Stage 7

tag: genotype

value: wild type

value: Hindlimb


title: NMB1040_850k

description:
200819570005_R04C01
DNA methylation data from an ATRT tumor sample

value: M

value: INF

tag: molecular subgroup


title: ATRT_EURHAB_26

tag: gender


title: ATRT_EURHAB_40

tag: age (yr)


title: AnoSag_st7_HL_Rep4


title: wuyujing 7 (the wild type) WGBS replicate 1

description:
WTvspOsNAR2.1-OsNAR2.1_DMR.xls
WT1


title: AnoSag_st7_HL_Rep2


title: AnoSag_st7_HL_Rep3


title: ATRT_EURHAB_56

tag: tumor location


title: ATRT_EURHAB_16


title: AnoSag_st7_HL_Rep1


title: AnoSag_st7_FL_Rep5

source_name: Forelimb

value: Forelimb


title: ATRT_EURHAB_73


title: ATRT_EURHAB_15


title: INSTINCT_1_850k

description:
200790260058_R06C01
DNA methylation data from an ATRT tumor sample

value: SUP


title: ATRT_EURHAB_82


title: NMB960_850k

description:
200819570005_R07C01
DNA methylation data from an ATRT tumor sample


title: AnoSag_st7_FL_Rep4


title: NMB1039_850k

description:
200819570005_R03C01
DNA methylation data from an ATRT tumor sample

value: TYR


title: AnoSag_st7_FL_Rep3


title: ATRT_EURHAB_12

value: female


title: AnoSag_st7_FL_Rep2


title: AnoSag_st7_FL_Rep1


title: SEQ778

description:
E13
cfDNA
processed data file: 5hmC_Count_Matrix.csv

source_name: Plasma

value: Plasma

tag: disease diagnosis

value: Type 2 Diabetes

value: Chinese

value: Yes

value: Multiple


title: ATRT_EURHAB_14

value: MYC


title: Liver_PXDDE_rep4

city: Cordoba

first: Nieves

last: Abril

state: Not Applicable

address: Campus Rabanales, edificio C6, 2ª planta

country: Spain

institute: University of Córdoba

description:
K4
Gene expression after 60 days of 450mg/kg feed DDE and Pedro Ximenez must supplemented diet.
Replicate 4

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µL containing 1x Fragmentation Buffer (Agilent) and 2x Gene Expression Blocking Agent (Agilent) following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 µL of 2x Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression v2 8 x 60K Microarray (G4858A-074809) for 17 hours at 65°C in a rotating Agilent G2545A hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash Buffer 2 (Agilent), then dried in an ozone-free atmosphere.

scan_protocol: Microarray slides were scanned with an Agilent Microarray Scanner (Agilent G2565C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
Image analysis and quantification of fluorescence data were carried out with Agilent Feature Extraction Software 11.5.1.1 using the Agilent protocol GE1_1105_Oct12, grid template 074809_D_F_20150624 and the QC Metric Set GE1_QCMT_Oct12, default parameters.
After background subtraction by RMA, quantile normalization was performed on pre-processed data with limma.

organism: Mus spretus

source_name: Liver, PXDDE

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2000 ng RNA using the Agilent Low-Input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. Total RNA was quantified in a NanoDrop ND-1000 Spectrophotometer and quality was confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies, Palo Alto, California USA) assay.

tag: strain/background

value: SPRET/EiJ

value: Male

value: Liver

tag: treatment

value: 22 months


title: PyruvatelowCO2_2

city: Wageningen

first: Nico

middle: J

last: Claassens

address: Stippeneng 4

department: Laboratory of Microbiology

institute: Wageningen University

data_processing:
Sequence data of all samples were mapped with STAR v2.5.4b using default parameters. Ensembl version 38 genome reference in FASTA format and Ensembl version 38 cDNA Annotation in GTF format were used for genome indexing with adapted parameters for genome size (--genomeSAindexNbases 10) and read length (--sjdbOverhang 150).
Anti-strand read counts from the ReadsPerGene files of all 6 samples were merged in order to perform a differential expression analysis with DESeq2 as guided by the rnaseqGene Bioconductor workflow. Briefly, samples were grouped by their single parameter condition, read count data were then loaded with DESeqDataSetFromMatrix to create a DeSeqDataSet ct to subsequently run the standard analysis consisting of the functions DESeq and Results. Transcript abundance data were expressed as log2-transformed fold changes (log2fc).
Genome_build: Bacteria ensembl version 38 of Ralstonia eutropha H16 (synonymous species name)
Supplementary_files_format_and_content: Default STAR output files (ASCII format, tab delimited): Gene identifier, Read count (unstranded RNA-seq), Read count (counts for the 1st read strand aligned with RNA), Read count (counts for the 2nd read strand aligned with RNA)

organism: Cupriavidus necator

source_name: Bacterial cells

growth_protocol: Pre-cultures of Cupriavidus necator were inoculated at a starting OD600 of 0.05 on 10 mL minimal medium (JMM medium, Li et al., Science, 2012 doi: 10.1126/science.1217643) in 50 mL erlenmeyer flasks. For the heterotrophic growth 40 mM sodium pyruvate. Autotrophic were incubated inside a dessicator filled with 4% H2 and either ambient or 10% CO2. Cultures were incubated at 30C while shaking at 180 rpm.

extract_protocol:
RNA was extracted after stabilization of 2 mL samples using RNA Protect Bacteria Kit (Qiagen). Total RNA was isolated using RNeasy mini-kit QIAGEN, including enzymatic (15 mg/mL lysozyme) and phsyical lysis (Retschmill, 5 min, 30Hz). An on-column DNAase step was performed to digest all DNA (RNase-Free DNAse Set Qiagen).
cDNA libraties were made at after rRNA depletion using the Ribozero Bacteria kit (Illumina ) at the Max Planck-Genome-centre Cologne, Germany , sequencing was performed using 150 bp single read sequencing in Illuminqa HiSeq3000

tag: strain

tag: condition

value: Pyruvate, low CO2

tag: replicate


title: PyruvatelowCO2_1


title: ATRT_EURHAB_01

description: DNA methylation data from an ATRT tumor sample

source_name: Primary ATRT tumor tissue

value: male

value: infratentorial


title: SEQ555

description:
E7
cfDNA
processed data file: 5hmC_Count_Matrix.csv

tag: tissue

tag: population

tag: sample

tag: batch

tag: binary for gender

tag: athero


title: H2highCO2_2

value: H2, high CO2


title: H2highCO2_1


title: ATRT_EURHAB_02

value: supratentorial


title: H2lowCO2_1

value: H2, low CO2


title: ATRT_EURHAB_03

value: SHH

value: female


title: Liver_PXDDE_rep2

description:
K2
Gene expression after 60 days of 450mg/kg feed DDE and Pedro Ximenez must supplemented diet.
Replicate 2

tag: age


title: Liver_PXDDE_rep1

description:
K1
Gene expression after 60 days of 450mg/kg feed DDE and Pedro Ximenez must supplemented diet.
Replicate 1


title: Liver_DDE_rep3

description:
J3
Gene expression after 60 days of 450mg/kg feed DDE supplemented diet.
Replicate 3

source_name: Liver, DDE

value: DDE supplemented diet


title: Liver_control_rep4

description:
H4
Gene expression after 60 days of normal diet.
Replicate 4

source_name: Liver, control

value: normal (Teklad) diet


title: Liver_PXDDE_rep3

description:
K3
Gene expression after 60 days of 450mg/kg feed DDE and Pedro Ximenez must supplemented diet.
Replicate 3


title: Liver_DDE_rep4

description:
J4
Gene expression after 60 days of 450mg/kg feed DDE supplemented diet.
Replicate 4


title: CIN3_37 cervical intraepithelial neoplasia grade 3

status: Public on Jan 30 2020

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

institute: McGill

hyb_protocol: The Illumina hybridization oven was used for incubating amplified DNA (37°C) and for BeadChips hybridization (48°C). A Hybex incubator was used for fragmentation (37°C) and denaturation (95°C) steps.

scan_protocol: Arrays were scanned in Illumina HiScan Reader

data_processing: Raw data were analyzed using the ChAMP package (for HumanMethylationEPIC array) in R.

label: Cy5 and Cy3

source_name: Exfoliated cervical cell specimen

label_protocol: Illumina Infinium protocol

growth_protocol: Exfoliated cervical cell specimens were suspended in a preservative solution (PreservCyt, Hologic Inc., Mississauga) and stored at 4C.

extract_protocol: Exfoliated cervical cell specimens were suspended in a preservative solution (PreservCyt, Hologic Inc., Mississauga) and stored at 4oC. For specimens in the discovery set, total genomic DNA was extracted using QIAamp DNA Mini Kit (QIAGEN GmbH, Germany).32 Genomic DNA was quantified using Picogreen protocol (Quant-iTTM PicoGreen_ dsDNA Products, Invitrogen, P-7589) and read on a Spectra-MAX GeminiXS Spectrophotometer.

value: Female

tag: grade

value: Grade 3


title: CIN3_32 cervical intraepithelial neoplasia grade 3

tag: gender


title: CIN3_35 cervical intraepithelial neoplasia grade 3


title: CIN3_36 cervical intraepithelial neoplasia grade 3


title: CIN3_42 cervical intraepithelial neoplasia grade 3


title: CIN3_40 cervical intraepithelial neoplasia grade 3


title: CIN3_33 cervical intraepithelial neoplasia grade 3


title: CIN3_39 cervical intraepithelial neoplasia grade 3


title: H2lowCO2_2


title: CIN3_30 cervical intraepithelial neoplasia grade 3


title: CIN3_41 cervical intraepithelial neoplasia grade 3


title: CIN3_34 cervical intraepithelial neoplasia grade 3


title: CIN3_31 cervical intraepithelial neoplasia grade 3


title: CIN3_29 cervical intraepithelial neoplasia grade 3


title: Liver_control_rep2

description:
H2
Gene expression after 60 days of normal diet.
Replicate 2


title: Liver_DDE_rep1

description:
J1
Gene expression after 60 days of 450mg/kg feed DDE supplemented diet.
Replicate 1


title: CIN3_27 cervical intraepithelial neoplasia grade 3


title: CIN3_38 cervical intraepithelial neoplasia grade 3


title: CIN3_25 cervical intraepithelial neoplasia grade 3


title: CIN3_28 cervical intraepithelial neoplasia grade 3


title: CIN3_26 cervical intraepithelial neoplasia grade 3


title: CIN3_14 cervical intraepithelial neoplasia grade 3


title: CIN3_18 cervical intraepithelial neoplasia grade 3


title: CIN3_15 cervical intraepithelial neoplasia grade 3


title: CIN3_22 cervical intraepithelial neoplasia grade 3


title: Liver_control_rep1

description:
H1
Gene expression after 60 days of normal diet.
Replicate 1


title: Liver_control_rep3

description:
H3
Gene expression after 60 days of normal diet.
Replicate 3


title: CIN3_23 cervical intraepithelial neoplasia grade 3


title: CIN3_16 cervical intraepithelial neoplasia grade 3


title: CIN3_19 cervical intraepithelial neoplasia grade 3


title: CIN3_13 cervical intraepithelial neoplasia grade 3


title: CIN3_12 cervical intraepithelial neoplasia grade 3


title: CIN3_20 cervical intraepithelial neoplasia grade 3


title: CIN3_21 cervical intraepithelial neoplasia grade 3


title: CIN3_11 cervical intraepithelial neoplasia grade 3


title: CIN3_9 cervical intraepithelial neoplasia grade 3


title: CIN3_24 cervical intraepithelial neoplasia grade 3


title: CIN3_10 cervical intraepithelial neoplasia grade 3


title: CIN3_8 cervical intraepithelial neoplasia grade 3


title: CIN3_7 cervical intraepithelial neoplasia grade 3


title: CIN3_4 cervical intraepithelial neoplasia grade 3


title: CIN3_3 cervical intraepithelial neoplasia grade 3


title: CIN3_6 cervical intraepithelial neoplasia grade 3


title: CIN3_5 cervical intraepithelial neoplasia grade 3