title: PostS1 [RRBS]

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Reads were trimmed using  trim_galore v0.4.0 and cutadapt v1.9.1 with the –rrbs flag.
Trimmed reads were mapped to hg38 and methylation levels estimated using Bismark v0.14.4 and Bowtie2 on default settings
Differentially methylated regions were identified using BiSeq 1.10 for positions covered by at least 50% of the samples
Genome_build: hg38
Supplementary_files_format_and_content: Text file in tab separated format with methylation levels

growth_protocol: Not applicable

extract_protocol:
Allprep® DNA/RNA/miRNA Universal Kit (Qiagen)
DNA samples were incubated with MpsI enzyme (NEB #R0106L) to fragment DNA at CCGG position to enrich for CpG regions. Bisulfite conversion was performed using the EZ DNA methylation Kit (Zymo Research) according to the manufacturer’s instructions. The DNA was then PCR amplified and ligated to TruSeq (Illumina) sequencing adapters.

treatment_protocol: High-fat diet (HFD) intervention, sedentary or exercised

tag: subject id

value: Exercise; 9 days of a high-fat diet in combination with resistance exercise (Ex-HFD)

tag: time point

value: Post

value: muscle


title: PostS4 [RRBS]

status: Public on Feb 13 2018

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: group

tag: tissue


title: 13651X12

city: Salt Lake City

first: Jacqueline

last: Paquette

state: UT

address: 15 North Medical Drive #1100

department: Pathology

country: USA

institute: University of Utah

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome from Ensembl release 87 using STAR v 2.5.2b.
Reads mapping uniquely to features in the Ensembl mouse GTF were counted using featureCounts v 1.5.0-p3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2
Genome_build: GRCm38 (mouse)
Supplementary_files_format_and_content: FeatureCount output files

molecule: total RNA

organism: Mus musculus

source_name: ISRCL3_CD45 negative joint cells

extract_protocol:
Total RNA was recovered using TRIzol reagent and purified using the Direct-zol RNA MiniPrep kit
Libraries were prepared using PolyA enrichment and sequenced with Illumina HiSeq 50 Cycle Single-Read Sequencing version 4

tag: strain

tag: mouse status

value: 22 d post infection with B. burgdorferi

tag: cell type

value: CD45 negative joint cells


title: 14089X12


title: 14089X10


title: 14089X11


title: PostS7 [RRBS]


title: PostS14 [RRBS]


title: 13651X9

source_name: ISRCL4_CD45 negative joint cells


title: 13651X11


title: 13651X10


title: PostS12 [RRBS]


title: 1_ATCACG

city: Los Angeles

first: Galyna

last: Bondar

state: CA

address: 10833 Le Conte Ave, CHS 32-164

department: Medicine-Cardiology

institute: UCLA

data_processing:
Single end sequencing runs was performed to align the cDNA sequences to the reference genome.
FASTQ files were generated and transferred to the AdHF Research Data Center.
Avadis NGS 1.5 was used to align raw RNA-Seq FASTQ reads to the reference genome.
RNA extraction, quantification and quality assessment was performed.
Total mRNA was amplified and sequenced on the whole-genome Illumina HiSeq 2500.
Data subjected to DeSeq normalization using NGS Strand/Avadis.
Batch effects were removed using the ‘ComBat’ algorithm in R program.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Excel file of normalized data including gene ID and normalized values.

source_name: RNA from blood, time point, 1 day before MCS surgery

extract_protocol:
Samples were collected on day one before mechanical circulatory support surgery. Eight ml of blood was drawn into a CPT tube (Becton Dickinson, Franklin Lakes, NJ). Peripheral Blood Mononuclear cells (PBMC) from each sample were purified within 2h of phlebotomy. The collected blood was mixed and centrifuged at room temperature (22⁰C) for 20min at 3000 RPM. The cell layer was collected, transferred to 15ml conical tubes and centrifuged for 20min at 1135 RPM at 4°C. The supernatant was aspirated and discharged. The cell pellet was resuspend in cold Phosphate Buffer Saline (Sigma-Aldrich, St. Louis, MO), transferred into an eppendorf tube and centrifuged for 20min at 5.6 RPM at 4°C. The supernatant was discharged. The pellet was resuspended in 0.5 ml RNA Protect Cell Reagent (Qiagen, Valencia, CA) and frozen at -80°C. The RNA was isolated from the PBMC using RNeasy Mini Kit (Qiagen, Valencia, CA).  The quality of the total RNA was assessed using NanoDrop® ND-8000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)  concentration above 50 ng/µl., purity - 260/280 ~ 2.0., integrity - RIN > 9.0 and average > 9.5.
mRNA library was prepared with Illumina TruSeq RNA kit according to the manufacturer’s instructions (Illumina, San Diego, CA). Library construction consists of random fragmentation of the polyA mRNA, followed by cDNA production using random polymers. The cDNA libraries were quantitated using Qubit and size distribution was checked on Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: age

tag: gender

value: Female

tag: underlying disease

value: NICM

tag: mcs type

value: HMII

tag: tp1 intermacs

tag: tp 1 sofa

tag: tp 1 meldxi

tag: tp 5 sofa

tag: tp 5 meld-xi

tag: outcome after 1 year

value: Alive

tag: echo

value: normal/mildly reduced right ventricular function

tag: tp 1 inotropes

value: 2 inotropes

tag: cpb time

value: no major bleeding

tag: blood transfusions

value: major bleeding

tag: Cause of death

value: blood

value: peripheral blood mononuclear cell


title: PostS8 [RRBS]

tag: subject id

tag: group

tag: time point

tag: tissue


title: PostS9 [RRBS]


title: 13651X8

tag: strain

tag: mouse status

tag: cell type


title: LDLRKO Rep 3

city: New Haven

first: Nathan

middle: L

last: Price

state: CT

address: 10 Amistad St Rm 320

department: CMED

institute: Yale University

data_processing:
Base calling was done on Illumina HiSeq 2500 platform.
Reads were trimmed for quality using customs Perl scripts.
Alignment was carried out using TopHat2 with default parameters.
Transcript estimation and differential gene-expression was carried out using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Peritoneal Macrophage

extract_protocol:
Thioglycolate elicited peritoneal macrophages from WT and miR-33-/- mice were harvested by peritoneal lavage.  Cells were then plated for 2hr, then washed to remove non-adherant cells.  Macrophages were then scraped, pelleted and frozen at -80◦C.
Total RNA from WT and miR-33-/- thioglycollate-elicited peritoneal macrophages was extracted and purified using a RNA isolation Kit (Qiagen) followed by DNAse treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen). The purity and integrity of total RNA sample was verified using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina). RNA libraries from WT BMDMs were performed TrueSeq Small RNA Library preparation (Illumina) and were sequenced for 45 cycles on Illumina HiSeq 2000 platformm (1 x 75bp read length). The reads obtained from the sequencer are trimmed for quality using in-house developed scripts.  The trimmed reads are aligned to the reference genome using TopHat2.  The transcript abundances and differences calculated using cuffdiff.  The results were plotted using R and cummeRbund using in-house developed scripts.

value: Peritoneal Macrophage

tag: age

value: 5 month

tag: genotype

value: LDLR-/-


title: 13651X6


title: PostS2 [RRBS]

value: Sedentary; 9 days of a high-fat diet alone (Sed-HFD)

value: Post


title: Hela_CTL_RNA-Seq

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

country: China

institute: Gannan Medical University

data_processing:
For computational analysis of RNA-seq data, sequencing reads were aligned to hg19 human genome using the “Tuxedo suite”: Bowtie2-Tophat
EdgeR (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) was used to compute the differential expressed genes (P<0.001, dispersion 0.001).
The bigwig files were generated by using Homer v4.7, in which the total tags are normalized to 1.00e+07.
The HOMER suite (Hypergeometric Optimization of Motif EnRichment) was used to generate the input of EdgeR and calling EdgeR

source_name: HeLa

growth_protocol: HeLa cells were cultured in MEM alpha medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated from HeLa cells using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L).

treatment_protocol: Cells grown to ~90% confluent were used for RNA-seq.

tag: cell line

value: Hela

tag: tag

value: CTL


title: 13651X5

source_name: B6_CD45 negative joint cells

value: B6 control

value: 22 d post infection with B. burgdorferi

value: CD45 negative joint cells


title: PostS6 [RRBS]

value: muscle


title: 13651X4


title: 13651X3


title: PostS10 [RRBS]


title: 13651X7


title: PostS3 [RRBS]


title: PostS11 [RRBS]


title: 13651X2


title: PostS13 [RRBS]


title: 13651X1


title: PreS12 [RRBS]

value: Exercise; 9 days of a high-fat diet in combination with resistance exercise (Ex-HFD)

value: Pre


title: mucosa_2_spf_8

city: Leipzig

first: Torsten

last: Schöneberg

address: Johannisallee 30

department: Institute of Biochemistry, Medical Faculty

country: Germany

institute: Leipzig University

description: FPKM-matrix.tsv

data_processing:
reads were mapped using Tophat 2.0.8 and Bowtie2
alignment was filtered for maximum mapping quality and all reads mapping to the mitochondrial genome were removed
readcounts were retrieved using BEDtools intersectBED
differential gene expression analysis was performed using the R-package Deseq
Genome_build: mm9
Supplementary_files_format_and_content: FPKMs are provided as matrix for all samples in a tab delimited tsv-file
Supplementary_files_format_and_content: readcounts are provided as matrix for all samples in a tab delimited tsv-file

source_name: mucosa

extract_protocol:
Total RNA from isolated bulb and mucosa was extracted by using the TRI REAGENT™ (Sigma-Aldrich) as described in the manufacturer’s instructions.
Indexed cDNA libraries were generated using TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol, constructing libraries with an average size of 300bp as evaluated on the Agilent 2100 bioanalyzer with DNA 1000 Chips.

value: mucosa

tag: condition

value: 2 weeks

tag: time under condition

value: spf


title: PreS14 [RRBS]


title: mucosa_2_spf_6

description: FPKM-matrix.tsv


title: PreS8 [RRBS]


title: mucosa_2_spf_7

description: FPKM-matrix.tsv


title: mucosa_2_spf_5

description: FPKM-matrix.tsv


title: PreS9 [RRBS]


title: PreS1 [RRBS]


title: mucosa_2_spf_4

description: FPKM-matrix.tsv


title: PostS5 [RRBS]


title: mucosa_2_spf_3

description: FPKM-matrix.tsv


title: mucosa_2_spf_1

description: FPKM-matrix.tsv


title: PreS4 [RRBS]


title: PreS7 [RRBS]


title: mucosa_2_spf_2

description: FPKM-matrix.tsv


title: PreS10 [RRBS]


title: mucosa_2_nspf_6

description: FPKM-matrix.tsv

value: non-spf


title: mucosa_2_nspf_7

description: FPKM-matrix.tsv


title: mucosa_2_nspf_5

description: FPKM-matrix.tsv


title: PreS11 [RRBS]


title: PreS3 [RRBS]


title: PreS2 [RRBS]


title: mucosa_2_nspf_8

description: FPKM-matrix.tsv


title: mucosa_2_nspf_4

description: FPKM-matrix.tsv


title: mucosa_2_nspf_3

description: FPKM-matrix.tsv


title: PreS6 [RRBS]


title: PreS5 [RRBS]


title: mucosa_2_nspf_2

description: FPKM-matrix.tsv


title: mucosa_2_nspf_1

description: FPKM-matrix.tsv


title: Pre_S8

data_processing:
Reads were trimmed using  trim_galore v0.4.0 and cutadapt v1.9.1 on default settings
Trimmed reads were mapped to hg38 with Rsubread and gene read coverages were computed with featureCounts and the Ensemble v84 gtf file
Differentially expressed genes were determined using edgeR
Genome_build: hg38
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts

extract_protocol:
Allprep® DNA/RNA/miRNA Universal Kit (Qiagen)
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina)


title: Pre_S9


title: mucosa_1_spf_7

description: FPKM-matrix.tsv

value: 1 week


title: PreS13 [RRBS]


title: mucosa_1_spf_6

description: FPKM-matrix.tsv


title: Pre_S6


title: Pre_S2


title: Pre_S4


title: mucosa_1_spf_4

description: FPKM-matrix.tsv


title: mucosa_1_spf_5

description: FPKM-matrix.tsv


title: Pre_S13


title: mucosa_1_spf_3

description: FPKM-matrix.tsv


title: Post_S5


title: Pre_S11


title: mucosa_1_spf_2

description: FPKM-matrix.tsv


title: Post_S3


title: mucosa_1_spf_1

description: FPKM-matrix.tsv


title: mucosa_1_nspf_7

description: FPKM-matrix.tsv


title: Post_S14


title: Post_S1


title: mucosa_1_nspf_4

description: FPKM-matrix.tsv


title: Post_S12


title: Post_S7


title: mucosa_1_nspf_5

description: FPKM-matrix.tsv


title: mucosa_1_nspf_3

description: FPKM-matrix.tsv


title: mucosa_1_nspf_2

description: FPKM-matrix.tsv


title: Post_S10


title: Pre_S7


title: mucosa_1_nspf_1

description: FPKM-matrix.tsv


title: Pre_S5


title: Pre_S3


title: bulbus_2_spf_7

description: FPKM-matrix.tsv

source_name: bulbus

value: bulbus


title: Pre_S14


title: bulbus_2_spf_8

description: FPKM-matrix.tsv


title: mucosa_1_nspf_6

description: FPKM-matrix.tsv


title: bulbus_2_spf_5

description: FPKM-matrix.tsv


title: Pre_S12


title: bulbus_2_spf_4

description: FPKM-matrix.tsv


title: bulbus_2_spf_6

description: FPKM-matrix.tsv


title: bulbus_2_spf_3

description: FPKM-matrix.tsv


title: bulbus_2_spf_1

description: FPKM-matrix.tsv


title: Pre_S10


title: Post_S9


title: Post_S8


title: bulbus_2_spf_2

description: FPKM-matrix.tsv


title: Post_S4


title: Post_S6


title: Post_S13


title: bulbus_2_nspf_7

description: FPKM-matrix.tsv


title: bulbus_2_nspf_6

description: FPKM-matrix.tsv


title: ATAC-adultmSC

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

description: ATAC-seq

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Bowtie with default options then duplicated reads were removed by Samtools
Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated by MACS14

source_name: mouse Schwann cells

extract_protocol:
Dissociated Lats1/2-deficient mouse tumor cells (∼50,000 cells) were spun down at 500 x g for 5 min at 4C, lysed in cold Lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Afterspinning down at 500 x g for 10 min at 4C, nuclei were resuspended in transposition mix containing 25 μl TD (2x reaction buffer)  2.5 μl TDE1 (Nextera Tn5 Transposase), 22.5 μl Nuclease Free H2O, at 37°C for 30 min. Immediately following transposition, DNA were purified using a Qiagen MinElute PCR Purification Kit. Transposed DNA fragments were subsequently amplified and the amplified library was purified using Qiagen MinElute PCR Purification Kit.
Libraries were generated using the Ad1_noMX and Ad2.1–2.4 barcoded primers and were amplified for 7–9 total cycles. Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2000.

value: primary cultured cells

value: Adult

value: Lats1fl/fl;Lats2fl/+ or wildtype


title: Post_S2

value: Sedentary; 9 days of a high-fat diet alone (Sed-HFD)

value: Post


title: bulbus_2_nspf_5

description: FPKM-matrix.tsv


title: H3K4me1-mLats12tumor

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Peak calling was performed using MACS1.4 with a default p value cut off.
genome build: mm10
processed data files format and content: wig files were generated by MACS1.4

source_name: mouse nerve tumor cells

extract_protocol:
Lats1/2-deficient (Lats1fl/fl;Lats2fl/+;CcGFPfl/+;Dhh-Cre) mouse paraspinal tumors were isolated, minced into 1 mm3 pieces and dissociated using collagenase type I (156 U/ml) and dispase protease II (1.25 U/ml) at 37oC. Tumor cells were propagated as an adherent layer on tissue culture dishes in proliferation medium composed of DMEM/10% FBS plus L-glutamine and penicillin/streptomycin.
Dissociated Lats1/2-deficient mouse tumor cells (∼20 million cells) were fixed for 15 min at room temperature with 1% formaldehyde-containing medium. Nuclei were isolated and sonicated in sonication buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA, and protease inhibitor cocktail). Sonicated chromatin (∼300 μg) was used for immunoprecipitation by incubation with rabbit IgG or anti-Tead1, anti-H3K27ac,  anti-H3K4me3,  anti-H3K4me1 antibody (4 μg) overnight at 4°C.
The ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB catalogue number E6240L) and then run on the Illumina sequencer HiSeq 2000.

value: primary cultured nerve tumor  cells

tag: chip antibody

value: H3K4me1 (Rabbit, Abcam, 8895)


title: ATAC-mLats12tumor

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
genome build: mm10
processed data files format and content: wig files were generated by MACS1.4


title: bulbus_2_nspf_4

description: FPKM-matrix.tsv


title: Post_S11


title: 4F 2i RedGreen (Replicate 2)

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St

institute: J David Gladstone Institutes

description:
Cells infected with 4F adenovirus and treated with 2i for 48 hours and were RedGreen for FUCCI
4F 2i RedGreen 2

data_processing:
Alignment: Aligned to human genome build "hg19" using the program STAR_2.5.2b. Gene annotation (GTF file) used was Ensembl version 65. Specific settings: --alignSJDBoverhangMin 3
Reads to gene-level counts: Aligned reads were assigned to genes to arrive at per-gene counts using "featureCounts" (Liao et al., 2014), part of the Subread suite (http://subread.sourceforge.net/).
Any genes where there were not at least two samples with a CPM (counts per million) value between 0.5 and 5000 were filtered out ("NA" values for CPM and FPKM) in preparation for potential future differential expression analysis, which was not performed in these files.
Genome_build: hg19 (human)
Supplementary_files_format_and_content: FPKM and raw count data, tables in plain-text format.

source_name: 4F 2i RedGreen

growth_protocol: hiPS-CM were cultured in RPMI+B27 supplement

extract_protocol:
The RNA was isolated using the miRNeasy Micro Kit (Qiagen, #210874)
Using the Ovation RNA-seq System v2 Kit (NuGEN)

treatment_protocol: hiPS derived cardiomyocytes infected with adenovirus encoding 4 cell cycle genes in the presence or absence of TGFB inhibitor and Wee1 inhibitor (2i) to induce cardiomyocyte proliferation and sorted for the different cell cycle stages according to FUCCI dye. (-ve:G0 phase, Red:G1 phase, RedGreen: S phase, Green: G2/M phase).

value: Heart

value: hiPS derived Cardiomycoytes

tag: infection

value: 4F adenovirus

tag: treatment

tag: cell color

value: RedGreen for FUCCI

tag: replicate number


title: bulbus_2_nspf_3

description: FPKM-matrix.tsv


title: 4F 2i RedGreen (Replicate 1)

description:
Cells infected with 4F adenovirus and treated with 2i for 48 hours and were RedGreen for FUCCI
4F 2i RedGreen 1


title: 4F 2i Green (Replicate 2)

description:
Cells infected with 4F adenovirus and treated with 2ifor 48 hours and were Green for FUCCI
4F 2i Green 2

source_name: 4F 2i Green

value: Green for FUCCI


title: H3K4me3-mLats12tumor


title: bulbus_2_nspf_2

description: FPKM-matrix.tsv

value: 2 weeks


title: bulbus_2_nspf_1

description: FPKM-matrix.tsv


title: Tead1-mLats12tumor

value: TEAD1 (Mouse, Santa Cruz Biotechnology sc-393976)


title: bulbus_2_nspf_8

description: FPKM-matrix.tsv

value: non-spf


title: 4F 2i Green (Replicate 1)

description:
Cells infected with 4F adenovirus and treated with 2i for 48 hours and were Green for FUCCI
4F 2i Green 1


title: RabbitIgG

value: Normal rabbit IgG (Santa Cruz Biotechnology, sc-2027)


title: bulbus_1_spf_7

description: FPKM-matrix.tsv

value: bulbus

value: 1 week

value: spf


title: bulbus_1_spf_6

description: FPKM-matrix.tsv


title: 4F 2i Red (Replicate 2)

description:
Cells infected with 4F adenovirus and treated with 2i for 48 hours and were Red for FUCCI
4F 2i Red 2

source_name: 4F 2i Red

value: Red for FUCCI


title: 4F 2i Red (Replicate 1)

description:
Cells infected with 4F adenovirus and treated with 2i for 48 hours and were Red for FUCCI
4F 2i Red 1


title: Lats12_tumor_GFP6

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
genome build: mm10
processed data files format and content: format:fpkm_traking; Contain the estimated expression values produced by Cufflinks.

source_name: nerve tumor-FACS GFP cells

extract_protocol:
Dhh+ Schwann cell lineage-derived GFP+ cell populations from 3-4-month-old control:ccGFP SNs and Lats1/2-mutant:ccGFP paraspinal tumors were sorted by fluorescence activated cell sorting (FACS). RNA of GFP+ cells were extracted using TRIZOL (Life Technologies) followed by purification using a Direct-zol RNA MicroPrep Kit (Zymo Research).
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.

value: paraspinal tumors

tag: developmental stage

value: Adult


title: 4F 2i -ve (Replicate 2)

description:
Cells infected with 4F adenovirus and treated with 2i for 48 hours and were negative for FUCCI
4F 2i -ve 2

source_name: 4F 2i -ve

value: negative for FUCCI


title: bulbus_1_spf_5

description: FPKM-matrix.tsv


title: bulbus_1_spf_4

description: FPKM-matrix.tsv


title: Lats12_tumor_GFP5


title: Lats12_tumor_GFP4


title: bulbus_1_spf_3

description: FPKM-matrix.tsv


title: Lats12_tumor_GFP3


title: 4F RedGreen (Replicate 2)

description:
Cells infected with 4F adenovirus for 48 hours and were RedGreen for FUCCI
4F RedGreen 2

source_name: 4F RedGreen


title: 4F 2i -ve (Replicate 1)

description:
Cells infected with 4F adenovirus and treated with 2i for 48 hours and were negative for FUCCI
4F 2i -ve 1


title: 4F RedGreen (Replicate 1)

description:
Cells infected with 4F adenovirus for 48 hours and were RedGreen for FUCCI
4F RedGreen 1


title: H3K27Ac-mLats12tumor

value: primary cultured nerve tumor  cells

value: H3K27Ac (Rabbit, Abcam, 4729)


title: bulbus_1_spf_2

description: FPKM-matrix.tsv


title: Lats12_tumor_GFP1


title: 4F Green (Replicate 2)

description:
Cells infected with 4F adenovirus for 48 hours and were Green for FUCCI
4F Green 2

source_name: 4F Green

value: Heart

value: hiPS derived Cardiomycoytes


title: Ctr_SN_GFP3

source_name: sciatic nerve-FACS GFP cells

value: sciatic nerve

value: CcGFPfl/+;Dhh-Cre


title: bulbus_1_spf_1

description: FPKM-matrix.tsv


title: 4F Green (Replicate 1)

description:
Cells infected with 4F adenovirus for 48 hours and were Green for FUCCI
4F Green 1

value: 4F adenovirus

value: Green for FUCCI


title: bulbus_1_nspf_6

description: FPKM-matrix.tsv

value: non-spf


title: 4F Red (Replicate 2)

description:
Cells infected with 4F adenovirus for 48 hours and were Red for FUCCI
4F Red 2

source_name: 4F Red


title: bulbus_1_nspf_7

description: FPKM-matrix.tsv


title: Ctr_SN_GFP2


title: bulbus_1_nspf_5

description: FPKM-matrix.tsv


title: 4F Red (Replicate 1)

description:
Cells infected with 4F adenovirus for 48 hours and were Red for FUCCI
4F Red 1


title: bulbus_1_nspf_4

description: FPKM-matrix.tsv


title: 4F -ve (Replicate 2)

description:
Cells infected with 4F adenovirus for 48 hours and were negative for FUCCI
4F -ve 2

source_name: 4F -ve


title: Ctr_SN_GFP1


title: bulbus_1_nspf_3

description: FPKM-matrix.tsv


title: Lats12_tumor_GFP2


title: 4F -ve (Replicate 1)

description:
Cells infected with 4F adenovirus for 48 hours and were negative for FUCCI
4F -ve 1


title: 5_WT1_P4

city: Amsterdam

first: yanling

last: xiao

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
RNA-seq reads were aligned to the GRCm37 build using a mouse gtf file (version 64, downloaded from Ensembl) of the Mus musculus genome using Tophat (version 1.4).
Readcounts were generated using HTSeq-count
Genome_build: GRCm37
Supplementary_files_format_and_content: tab-separated file with number of reads per gene/sample

source_name: bone marrow

extract_protocol:
MODP/MOP progenitor cells were FACS-sorted from the mouse bone marrow. RNA was isolated using TriZol reagent. Libraries were generated using the TruSeq RNA sample preparation kit (Illumina) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD27 high MODP


title: LacZ infected control (Replicate 2)

description:
Cells infected with LacZ virus for 48 hours
Control LACZ 2

source_name: LacZ infected control

value: LacZ virus


title: 3_WT2_P4


title: 4_WT2_P5

value: CD27 low MOP


title: 6_WT1_P5


title: bulbus_1_nspf_2

description: FPKM-matrix.tsv

value: bulbus

value: 1 week


title: Pre_S1

tag: subject id

tag: group

value: Exercise; 9 days of a high-fat diet in combination with resistance exercise (Ex-HFD)

tag: time point

value: Pre

value: muscle


title: Uninfected Control (Replicate 2)

description:
Cells not infected with virus
Control 2

source_name: Uninfected Control

tag: tissue

value: Cells not infected with virus


title: Tet2_MSC_WT_1_5-hmC

city: Tianjin

first: Rong

last: Li

state: Tianjin

address: No.288, Nanjing Road,Heping District

department: Institute of Hematology and Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: Genome-wide 5hmc Profiling (hME-Seal) using isolation with biotin

data_processing:
Library strategy: hME-SEAL
Basecalls performed using Illumina HISeq 2500.
reads were aligned to the mm10 genome assembly using the BWA algorithm with default settings.
Data were filtered using the following specifications:only reads that pass Illumina's purity filter, and map uniquely to the genome were used in the subsequent analysis,than duplicate reads were removed.
peaks were called using MACS version 2.1.1 with default setting.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file

source_name: Mesenchymal stem/progenitor cells

growth_protocol: Bone marrow–derived mesenchymal stem/progenitor cells were cultured with MSC medium (MesenCult basal media plus 20% of MesenCult Supplemental), and replated when the cultures reached 80-90% confluency.

extract_protocol:
MSPCs were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 100 to 500 bp. 5hmC-DNA complexes were isolated with biotin.
Enriched DNA from hME-seal were subjected to library construction using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina according to the manufacturer’s protocol.

value: bone marrow

tag: cell type

value: mesenchymal stem/progenitor cells

tag: strain

tag: passages

value: wild type


title: Tet2_MSC_WT_2_5-hmC

tag: genotype


title: Uninfected Control (Replicate 1)

description:
Cells not infected with virus
Control 1

value: Heart

value: hiPS derived Cardiomycoytes


title: bulbus_1_nspf_1

description: FPKM-matrix.tsv

source_name: bulbus


title: Tet2_MSC_KO_2_5-hmC


title: LacZ infected control (Replicate 1)

description:
Cells infected with LacZ virus for 48 hours
Control LACZ 1


title: Tet2_MSC_KO_1_5-hmC


title: H3p_116

city: Seattle

first: Pritha

last: Chanana

state: WA

address: 1100 Fairview Ave N, PO Box 19024

department: Shared Resources

institute: Fred Hutchinson Cancer Center

data_processing:
Base calling and demultiplexing was performed with the Illumina bcl2fastq 1.8.4 software
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.1.0
Gene counts were generated using Subread featureCounts (http://bioinf.wehi.edu.au/featureCounts/)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: limb rna

extract_protocol:
Limbs were harvested from 1 day-old pups. The bones were cleaned from the adjacent soft tissues, homogenized and lyzed using TRIzol reagent. RNA was isolated using phenol-cholropohrm precepitation and kept in -80oC untill analysis.  The bone were homogenized and lyzed with TRIzol reagent. RNA was extracted using phenol-chlorophorm method.
Standard TruSeq v2 for mRNA (TMRNA)

tag: gentoype

value: Hdac3 CKO

value: limb bone

tag: age

value: 1 day old


title: H3p_120


title: H3p_121


title: SCAT7sh2_A549

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

description: A549_Knockdown_SCAT7sh_samples_hg19_collapse_cpm.txt.gz

data_processing:
[HeLa_S-phase] The samples from AB SOLiD system were aligned using LifeScope
[HeLa_S-phase] All alignments were made using hg19 as reference genome assembly
[HeLa_S-phase] The reads are quantified using ht-seq count
[HeLa_S-phase] Normalization of reads performed as Reads Per Kilobase of transcript per Million (RPKM)
[SCAT7] The samples from ILLUMINA  system were aligned using HISAT
[SCAT7] All alignments were made using hg19 as reference genome assembly
[SCAT7] The reads are quantified using ht-seq count
[SCAT7] Normalization of reads performed as Count Per Million (CPM) from edgeR
Genome_build: hg19
Supplementary_files_format_and_content: CPM, RPKM

source_name: A549 cells

growth_protocol: HeLa cells were routinely cultured using MEM medium supplemented with 10% FBS and 200mM L-glutamin. Caki-2 cells were maintained using RPMI 1640 medium supplemented with 10% FBS. All cells were maintained in humified incubator with continuous 5% CO2 flow.

extract_protocol:
Cells were collected 48 hours post-transfection and RNA extraction was carried out using ReliaPrep RNA Cell Miniprep System
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero from Illumina (Cat #  RS-122-2201)

treatment_protocol:
Stable knockdowntransduction was performed using short hairpin shRNA lentivaral particles targeting the specific transcript. For each knockdown experiment,50000 cells were seeded overnight and transduced with viral particles of 2MOI/cell. Positive cells were selected 24 hours later using 2.5 ug/ml puromycin.
Transient knockdown experiments were performed using 35 µM of siRNA targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded overnight and transfected with lipofectamin RNAi-MAX.

tag: cell line

value: A549 cells

tag: phase

value: Unsynchronized hetergenous population

tag: label status

value: Not labeled

tag: time

value: Collected 48 hours post-transfection

tag: sirna

value: shRNA Sequence:GATATGGACTTGTGCAAATGC


title: Tet2_MSC_WT_1_RNA

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample.

extract_protocol:
Bone marrow–derived mesenchymal stem/progenitor cells were trypsinized and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: SCAT7Csh2_A549

value: Scrambled non-mammalian target control


title: SCAT7sh1_A549

value: shRNA Sequence:GATCTGCCCTGATGATCATGA


title: Tet2_MSC_WT_2_RNA


title: H3p_122

value: WT


title: H3p_119


title: Tet2_MSC_KO_2_RNA


title: 2_WT1_P5

value: CD27 low MOP


title: 1_WT1_P4

value: CD27 high MODP


title: Tet2_MSC_KO_1_RNA

value: bone marrow

value: mesenchymal stem/progenitor cells


title: SCAT7si2_Caki-2

description: Caki-2_Knockdown_SCAT7si_samples_hg19_collapse_cpm.txt.gz

source_name: Caki2 cells

treatment_protocol:
Transient knockdown experiments were performed using 35 µM of siRNA targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded overnight and transfected with lipofectamin RNAi-MAX.
Transient knockdown experiments were performed using 35 µM of siRNA targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded overnight and transfected with lipofectamin RNAi-MAX.

value: Caki2 cells

value: siRNA Sequence:GCAAUGGCUUGGGUUCAGUdTdT


title: H3p_118


title: Osr2RFP/+, E13.5, 3048-4

city: cincinnati

first: HAN

last: LIU

state: oh

address: 3333 burnet avenue

department: DEVELOPMENTAL BIOLOGY

institute: CINCINNATI CHILDREN'S HOSPITAL

data_processing:
Illumina offline basecaller v1.9.0.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.7
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.Implanted in tophat 1.4.1 using parameters:tophat -G mm9.gtf -o tophat -p 4 -r 0 mm9 reads.fastq. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: embryonic palatal mesenchymal cells

extract_protocol:
Palatal shelves were microdissected,digested with trypsin-EDTA solution at 37°C for 4 minutes. After inactivation of trypsin with DMEM containing 10% FBS, cells were dissociated by pipetting. The dissociated palatal cells were resuspended in PBS with 2% FBS and 10 mM EDTA, and filtered through a 40 μm nylon cell strainer, RFP+ cells were isolated using BD FACSAria II. RNA was extracted by Qiagen RNase Micro kit. Sequencing libraries were generated by using Illumina Nextera DNA Sample Prep kit.
150 to 500 ng of total RNA determined by Invitrogen Qbit high sensitivity spectrofluorometric measurement is poly A selected and reverse transcribed using Illumina’s TruSeq stranded mRNA library preparation kit. Each sample can be fitted with one of 24 adapters containing a different 8 base molecular barcode for high level multiplexing. After 15 cycles of PCR amplification, completed libraries are sequenced on an Illumina HiSeq2500 in Rapid Mode, generating 20 million or more high quality 75 base long paired end reads per sample.

value: mixed background

value: embryonic palate

value: embryonic day 13.5

tag: genotype/variation


title: Osr2RFP/+, E13.5, 3048-3


title: Single colored (Replicate 4)

description:
Barcode: TCAGAG
Pos.id_4_bc14

data_processing:
Alignment: Aligned to mouse genome build "mm9" using the program STAR_2.5.2b. Gene annotation (GTF file) used was Ensembl version 65. Specific settings: --alignSJDBoverhangMin 3
Reads to gene-level counts: Aligned reads were assigned to genes to arrive at per-gene counts using "featureCounts" (Liao et al., 2014), part of the Subread suite (http://subread.sourceforge.net/).
Any genes where there were not at least two samples with a CPM (counts per million) value between 0.5 and 5000 were filtered out ("NA" values for CPM and FPKM) in preparation for potential future differential expression analysis, which was not performed in these files.
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: FPKM and raw count data, tables in plain-text format.

source_name: Single colored

treatment_protocol: Hearts were injected with adenovirus encoding 4 cell cycle gene and the cells were isolated 2 weeks after.

value: Heart

tag: genetic background

value: alpha-MHC MERCREMER MADM

tag: replicate number

tag: treatment

value: Cells treated with 4F to induce cell cycle and performed cell cycle

value: Isolated Adult Cardiomyocytes

tag: cell color

value: Single colored


title: Single colored (Replicate 3)

description:
Barcode: CACAGT
Pos.id_3_bc12

tag: tissue


title: SCAT7Csi2_Caki-2

value: Unsynchronized hetergenous population

value: Not labeled

value: Collected 48 hours post-transfection

value: Scrambled non-mammalian target control


title: SCAT7Csi1_Caki-2


title: Osr2RFP/-, E13.5, 3047-2


title: SCAT7Csh3_A549

value: A549 cells


title: SCAT7si3_HeLa

description: HeLa_Knockdown_SCAT7si_samples_hg19_collapse_cpm.txt.gz

source_name: HeLa cells

value: HeLa cells


title: Osr2RFP/+, E12.5, 2962-6

value: embryonic day 12.5


title: SCAT7si2_HeLa

value: siRNA Sequence:GCCAGAGAAUUGGCUACAAdTdT


title: SCAT7Csh1_A549


title: Osr2RFP/-, E12.5, 2962-3


title: Double colored (Replicate 3)

description:
Barcode: AGCATG
Neg.id_3_bc13

source_name: Double colored

value: Cells treated with 4F to induce cell cycle but not performed cell cycle

tag: cell type

value: Double colored


title: Double colored (Replicate 2)

description:
Barcode: GTCGTA
Neg.id_2_bc11


title: SCAT7si1_Caki-2

value: Caki2 cells

value: siRNA Sequence:CACAGACUGGACAGAACUCdTdT


title: shSmyd5_Input_CC (GA3445)

city: Detroit

first: Benjamin

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description: Direct sequencing following sonication of x-linked chromatin

data_processing:
Basecalls performed using GAPipeline or CASAVA
Sequence reads were obtained and mapped to the mouse (mm8) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm8
Supplementary_files_format_and_content: bedGraph

growth_protocol: shLuc and shSmyd5 ES cells were cultured on low binding dishes in the absence of LIF to form embryoid bodies (EB) at 37oC with 5% CO2. ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

value: Smyd5 depletion

value: cancer cells (CC)

tag: chip antibody


title: Double colored (Replicate 1)

description:
Barcode: AAGAGG
Neg.id_1_bc09

value: Heart

value: alpha-MHC MERCREMER MADM


title: shSmyd5_Input_mESC (GA3471)

value: embryoid body (EB)


title: SCAT7Csi1_HeLa

value: Unsynchronized hetergenous population


title: p16/p21-DKO Mo-MDSCs_rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description:
Mo-MDSCs purified from the spleen of pindle cell tumor (SCT) cells-bearing p16/p23 DKO mice
#9_CHIP0331

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10

source_name: Mo-MDSCs derived from the spleen of SCT-bearing p16/p21 DKO mice

extract_protocol:
RNA isolation was performed by the mirVana RNA Isolation kit.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: PMN- and Mo-MDSCs were purified from the spleen of SCT-bearing WT and p16/p21 DKO mice.

tag: strain

value: 3 weeks

value: spleen

value: monocytic myeloid-derived suppressor cells

tag: trans-gene

value: p16/p21 double knockout


title: SCAT7Csi2_HeLa

value: HeLa cells

value: Not labeled

value: Collected 48 hours post-transfection

value: Scrambled non-mammalian target control


title: shLuc_Input_mESC (GA3475)

value: control


title: shSmyd5_Input_CC (GA6724)

description:
Direct sequencing following sonication of x-linked chromatin
Barcode: CAGATC


title: K599_I

city: Beijing

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No.2

department: State Key Lab of Plant Genomics

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: replicate 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to soybean whole genome using Tophat software (http://ccb.jhu.edu/software/tophat/).
Reads per kilo bases per million reads (RPKM) were calculated.
Genome_build: Glycine max (https://phytozome.jgi.doe.gov/pz/portal.html)
Supplementary_files_format_and_content: Excel files containing RPKM value of each sample

organism: Glycine max

source_name: hairy roots

growth_protocol: The seedlings were grown at 28℃ under artificial light with a photoperiod of 16-h light and 8-h dark.

extract_protocol:
Total RNA was extracted using TRNzol Reagent (TIANGEN company).
Library were prepared according to the protocol of RNA-Seq RNA sample Prep Kit (Illumina)

treatment_protocol: One-week-old soybean seedlings (KF1) were injected with A. rhizogenes strain K599 harboring the over-expression or the RNAi construct, 2 cm above the soil. The injected seedlings were kept in high humidity level for about 2 weeks, until the hairy roots came out of the injected sites. The seedlings were moved to water for further growth. Hairy roots of 2-10 cm long were harvested for RNA extraction.

value: hairy roots

tag: genotype

value: wild type


title: K599_II

description: replicate 2


title: shSmyd5_H3K9me3_CC (GA6717)

description:
Chromatin IP against H3K9me3
Barcode: ACTTGA

value: Smyd5 depletion

value: Anti-H3K9me3 (Abcam; ab8898)


title: Single colored (Replicate 2)

description:
Barcode: GAGTCA
Pos.id_2_bc10

value: Heart

value: Cells treated with 4F to induce cell cycle and performed cell cycle

value: Isolated Adult Cardiomyocytes

value: Single colored


title: Osr2RFP/-, E13.5, 3048-5

value: mixed background

value: embryonic palate

tag: age

value: embryonic day 13.5


title: p16/p21-DKO Mo-MDSCs_rep1

description:
Mo-MDSCs purified from the spleen of pindle cell tumor (SCT) cells-bearing p16/p21 DKO mice
#3_CHIP0239

value: 3 weeks

value: spleen

value: monocytic myeloid-derived suppressor cells

value: p16/p21 double knockout


title: Single colored (Replicate 1)

description:
Barcode: CGTAGA
Pos.id_1_bc08

value: alpha-MHC MERCREMER MADM


title: RNAi_II

description: replicate 2

value: RNAi


title: RNAi_I

description: replicate 1

value: hairy roots


title: shSmyd5_H4K20me3_CC (GA6716)

description:
Chromatin IP against H4K20me3
Barcode: CAGATC

value: cancer cells (CC)

value: Anti-H4K20me3 (Abcam; ab9053)


title: Double colored (Replicate 4)

description:
Barcode: GGAGAA
Neg.id_4_bc15

value: Cells treated with 4F to induce cell cycle but not performed cell cycle

value: Double colored


title: shSmyd5_Input_mESC (GA6722)

description:
Direct sequencing following sonication of x-linked chromatin
Barcode: TGACCA

value: Smyd5 depletion

value: embryoid body (EB)


title: WT Mo-MDSCs_rep3

description:
Mo--MDSCs purified from the spleen of pindle cell tumor (SCT) cells-bearing WT mice
#8_CHIP0330

source_name: Mo-MDSCs derived from the spleen of SCT-bearing WT mice

value: p16/p21 wild-type


title: WT Mo-MDSCs_rep1

description:
Mo-MDSCs purified from the spleen of pindle cell tumor (SCT) cells-bearing WT mice
#2_CHIP0238


title: SCAT7si1_HeLa

tag: cell line

value: HeLa cells

value: Unsynchronized hetergenous population

value: Not labeled

value: Collected 48 hours post-transfection

value: siRNA Sequence:CACAGACUGGACAGAACUCdTdT


title: shLuc_Input_mESC (GA6720)

description:
Direct sequencing following sonication of x-linked chromatin
Barcode: CGATGT

value: control


title: PMN-MDSCs_rep3

description:
PMN-MDSCs purified from the spleen of pindle cell tumor (SCT) cells-bearing WT mice
#7_CHIP0329

source_name: PMN-MDSCs derived from the spleen of SCT-bearing WT mice

value: 3 weeks

value: spleen

value: polymorphonuclear myeloid-derived suppressor cells


title: shSmyd5_H3K9me3_EB (GA6714)

description:
Chromatin IP against H3K9me3
Barcode: ACAGTG

value: Anti-H3K9me3 (Abcam; ab8898)


title: shLuc_H3K9me3_EB (GA6711)

description:
Chromatin IP against H3K9me3
Barcode: CGATGT


title: GmPHD6-OE_I

description: replicate 1

value: hairy roots

value: over-expression


title: E-HA35-D2_S17_L002_R1_001

city: Cleveland

first: Laura

middle: E

last: Nagy

address: 9500 Euclid Avenue

department: Pathobiology

institute: Cleveland Clinic

description: Kupffer cells isolated from Ethanol fed HA35 Day 2

data_processing:
Small RNA alignment
Sequenced reads were trimmed for adaptor sequence, and then align  to RefSeq Transcript 2012.12.15 of rn4 build using Strand NGS 2.5.1
Reads were quantified using HTSeq
Filter genes by geneic regions
Differential gene expression analysis using DESeq
Genome_build: rat rn4 UCSC
Supplementary_files_format_and_content: Excel files include fold change and p values for the comparison

organism: Rattus norvegicus

growth_protocol: Primary Kupffer cells were grown in CMRL medium containg 10%FBS at 5%CO2

extract_protocol:
Small RNA was isolated using QIAGEN miRNeasy kit.
RNA libraries were prepared for sequencing using The illumina TruSeq Small RNA library prep protocol

treatment_protocol: Primary  cells were treated with or without HA35 for 5hrs.

value: Wistar

tag: gender

value: male

value: adult

value: liver-derived primary Kupffer cells

tag: isolated from

value: Ethanol fed HA35 Day 2


title: PMN-MDSCs_rep2

description:
PMN-MDSCs purified from the spleen of pindle cell tumor (SCT) cells-bearing WT mice
#4_CHIP0326

value: p16/p21 wild-type


title: sSmyd5_H4K20me3_EB (GA6713)

description:
Chromatin IP against H4K20me3
Barcode: TGACCA

value: Smyd5 depletion

value: embryoid body (EB)

value: Anti-H4K20me3 (Abcam; ab9053)


title: E-HA35-D3_S25_L002_R1_001.

description: Kupffer cells isolated from Ethanol fed HA35 Day 3

value: Ethanol fed HA35 Day 3


title: PMN-MDSCs_rep1

description:
PMN-MDSCs purified from the spleen of pindle cell tumor (SCT) cells-bearing WT mice
#1_CHIP0237


title: E-HA35-D1_S9_L002_R1_001

description: Kupffer cells isolated from Ethanol fed HA35 Day 1

value: Ethanol fed HA35 Day 1


title: p16/p21-DKO Mo-MDSCs_rep2

description:
Mo-MDSCs purified from the spleen of pindle cell tumor (SCT) cells-bearing p16/p22 DKO mice
#6_CHIP0328

value: 3 weeks

value: monocytic myeloid-derived suppressor cells

value: p16/p21 double knockout


title: E-Basal-D3_S23_L002_R1_001

description: Kupffer cells isolated from Ethanol fed Basal Day 3

value: Ethanol fed Basal Day 3


title: E-Basal-D2_S15_L002_R1_001.

description: Kupffer cells isolated from Ethanol fed Basal Day 2

value: Ethanol fed Basal Day 2


title: LRCs

city: Montréal

first: Maude

last: Dumont-Lagacé

state: Quebec

address: 2950 chemin de la polytechnique

country: Canada

institute: IRIC - Université de Montréal

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were masked for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

molecule: polyA RNA

source_name: UEA1 - thymic epithelial cells (TECs)

growth_protocol: Extracted frin 11 mice (pooled)

extract_protocol:
RNA was extracted using Trizol as recommended by the manufacturer and purified using Rneasy micro columns from Qiagen.
Transcriptome libraries were made using the TruSeq RNA Sample Prep Kit (v2) (Illumina) following the manufacturer’s protocols.
Poly-A enriched RNA seq

treatment_protocol: Enzymatic digestion of thymic stroma using liberase TM and DNase-1 and sorted by flow cytometry

value: TetO-H2BGFP; ROSA26-rtTA

value: Thymic epithelium

value: UEA1- quiescent (label-retaining cells, called LRCs) cells

tag: h2bgfp expression

value: GFPhi


title: DBP+chemopreventive agent BR extract Sample 3

city: Cambridge

first: Anna

last: Salzberg

state: MA

address: 399 Binney St UNIT 300

institute: Rubius Therapeutics

data_processing:
sequencing reads with phred quality scores < 20 were trimmed and the adaptors were cut using trim_galore v0.3.3 (Babraham Bioinformatcis, UK)
resulting reads were mapped to the mm9 mouse assembly and methylation calls were performed using Bismark v0.10.1 (Babraham Bioinformatcis, UK)
Genome_build: mm9
Supplementary_files_format_and_content: Bismark methylation calls in tab delimited text format

source_name: oral tissue

growth_protocol: Eight week-old female B6C3F1/J mice (Jackson Laboratories, Bar Harbor, ME) were used in this study.  Mice were quarantined for about 1 week before treatment.  All mice were kept on a 12-hr light:12-hr dark cycle, maintained at 50% relative humidity and 21± 2°C, and were fed with AIN-93M diet (5% corn oil), and water ad libitum. The bioassay was carried out in accordance with the NIH Guide for the Care and Use of Laboratory Animals and was approved by Institutional Animal Care and Use Committee.

extract_protocol: Genomic DNA from oral tissues of mice treated with DBP or DMSO were extracted and purified according to the DNeasy Blood and Tissue kit (Qiagen).  DNA was subjected to Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) to examine the DNA methylation status in CpG sites and the surrounding regions with single nucleotide resolution.  Briefly, 50 ng of genomic DNA was digested by MspI (Thermo Scientific), which recognizes and cleaves C^CGG sites, followed by end repair, adenylation and adapter ligation using NEXTflex Bisulfite-Seq Library Prep Kit and NEXTflex Bisulfite-Seq Barcodes (Bioo Scientific) with a modification of bead size selection to capture MspI fragments of 70-320 bp size. The resulting libraries were bisulfite-converted by using EZ DNA Methylation Kit (Zymo Research), followed by 18 cycles of PCR amplification using the NEXTflex Bisulfite-Seq U+PCR Master Mix and NEXTflex Primer Mix (BioO Scientific). Purified and quantified libraries were pooled at 6 samples per sequencing lane and read by 1X50 bp on HiSeq 2500 (Illumina). CASAVA-demultiplexed .fastq files were subjected to downstream analyses.

treatment_protocol:
DBP+chemopreventive agent BR extract
Mice received topical treatment of DBP (24 nmol, 3 times per week for 5 weeks) in the oral cavity and were sacrificed 48 h after the last dose.  Animals treated with vehicle (DMSO) were used as control.  At termination, mice were sacrificed by CO2 asphyxiation; soft tissues of the oral cavity, including the buccal mucosa and floor of the mouth as well as soft tissues attached to the hard palate, were collected and pooled together for DNA extraction.

value: female

value: oral tissue


title: DBP+chemopreventive agent BR extract Sample 2


title: DBP+chemopreventive agent BR extract Sample 1


title: GmPHD6-OE_II

description: replicate 2

value: hairy roots

value: over-expression


title: WT Mo-MDSCs_rep2

description:
Mo-MDSCs purified from the spleen of pindle cell tumor (SCT) cells-bearing WT mice
#5_CHIP0327

value: spleen

value: p16/p21 wild-type


title: P-HA35-D3_S29_L002_R1_001

description: Kupffer cells isolated from Pair fed HA35 Day 3

value: Wistar

value: male

value: adult

value: liver-derived primary Kupffer cells

value: Pair fed HA35 Day 3


title: wild type non-RGC 2

city: Boston

first: Dong Feng

last: Chen

state: Massachusetts

address: 20 Staniford St

institute: Schepens Eye Research Institute

description: wt_other_vs_single_ko_other.sort.primary.dedup.deseq

data_processing:
RNA-Seq was performed by The Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA.
data was aligned against the mm10 genome (ftp://ftp.ensembl.org/pub/release-75/fasta/  mus_musculus/dna/  1)
alignments were performed with STAR aligner (version 2.3.1z4)
RNA-seq quality metrics are produced by the Broad Institute's RNA-SeQC tool
Read quantification was carried out with featureCounts software
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files from desseq

source_name: Retina

growth_protocol: not applied

extract_protocol:
Retinas were removed, dissociated with papain digestion system (worthington Biochem. Corporation. #LK003150) according to protocol. For separation of RGCs from non-RGCs, we continue with cell separation using magnetic microbeads labelled with anti-CD90-antibody (MACS Miltenyi Biotec, #130-094-523; 130-041-305). After centrifugation, cell pellet was used for RNA-Extraction using Qiagen RNEasy Mini Kit (Qiagen, #74104). 1ug of total RNA was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: not applied

value: retina


title: wild type non-RGC 3


title: P-HA35-D2_S21_L002_R1_001

description: Kupffer cells isolated from Pair fed HA35 Day 2

value: Pair fed HA35 Day 2


title: wild type non-RGC 1


title: P-HA35-D1_S13_L002_R1_001

description: Kupffer cells isolated from Pair fed HA35 Day 1

value: Pair fed HA35 Day 1


title: DBP+chemopreventive agent Sample 1

treatment_protocol:
DBP+chemopreventive agent
Mice received topical treatment of DBP (24 nmol, 3 times per week for 5 weeks) in the oral cavity and were sacrificed 48 h after the last dose.  Animals treated with vehicle (DMSO) were used as control.  At termination, mice were sacrificed by CO2 asphyxiation; soft tissues of the oral cavity, including the buccal mucosa and floor of the mouth as well as soft tissues attached to the hard palate, were collected and pooled together for DNA extraction.


title: DBP Sample 3

treatment_protocol:
carcinogen dibenzo[a,l]pyrene(DBP}
Mice received topical treatment of DBP (24 nmol, 3 times per week for 5 weeks) in the oral cavity and were sacrificed 48 h after the last dose.  Animals treated with vehicle (DMSO) were used as control.  At termination, mice were sacrificed by CO2 asphyxiation; soft tissues of the oral cavity, including the buccal mucosa and floor of the mouth as well as soft tissues attached to the hard palate, were collected and pooled together for DNA extraction.


title: wild type RGC 2

description: wt_rgc_vs_single_ko_rgc.sort.primary.dedup.deseq


title: wild type RGC 3


title: NonLRCs

value: TetO-H2BGFP; ROSA26-rtTA

value: Thymic epithelium

value: UEA1- GFP- (nonquiescent, NonLRCs) TECs.

value: GFP-


title: P-Basal-D3_S27_L002_R1_001

description: Kupffer cells isolated from Pair fed Basal Day 3

value: Pair fed Basal Day 3


title: P-Basal-D2_S19_L002_R1_001

description: Kupffer cells isolated from Pair fed Basal Day 2

value: Pair fed Basal Day 2


title: shLuc_H4K20me3_EB (GA6710)

description:
Chromatin IP against H4K20me3
Barcode: ATCACG

value: control

value: embryoid body (EB)

value: Anti-H4K20me3 (Abcam; ab9053)


title: P-Basal-D1_S11_L002_R1_001

description: Kupffer cells isolated from Pair fed Basal Day 1

value: Wistar

value: Pair fed Basal Day 1


title: DBP Sample 1

value: female

value: oral tissue


title: Ezh2 Knockout non RGC 3


title: Control Sample 3

treatment_protocol:
vehicle
Mice received topical treatment of DBP (24 nmol, 3 times per week for 5 weeks) in the oral cavity and were sacrificed 48 h after the last dose.  Animals treated with vehicle (DMSO) were used as control.  At termination, mice were sacrificed by CO2 asphyxiation; soft tissues of the oral cavity, including the buccal mucosa and floor of the mouth as well as soft tissues attached to the hard palate, were collected and pooled together for DNA extraction.


title: Mutant 04

city: Salt Lake City

first: Carl

last: Thummel

department: Human Genetics

institute: University of Utah

data_processing:
Base-calling by Illumina HiSeq 50 Cycle Single Read Sequencing v3
Standard replicate RNAseq analysis was performed using USeq and DESeq analysis packages with alignment to the Drosophila melanogaster dm3 genome assembly
Converted splice coordinates to genome coordinates with SamTranscriptomeParser
Generated ReadCoverage USeq file and ran DefinedRegionDifferentialSeq using Ensembl transcripts and default settings
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

organism: Drosophila melanogaster

source_name: Whole animal lysate

growth_protocol: One week old female DHR78 rescued mutants and controls (btl>DHR78) were raised on a 8% yeast, 9% sugar diet

extract_protocol:
Eight biological replicates per genotype (n=12 females per sample) were collected. RNA was extracted using Trizol and pairs of biological replicates were pooled to obtain four biological replicates for further purification using an RNeasy Mini kit (Qiagen 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: 1 week old

value: Whole animal lysate


title: E-Basal-D1_S7_L002_R1_001

description: Kupffer cells isolated from Ethanol fed Basal Day 1

value: male

value: adult

value: liver-derived primary Kupffer cells

value: Ethanol fed Basal Day 1


title: DBP+chemopreventive agent Sample 3


title: Ezh2 Knockout non RGC 2

value: retina


title: Ezh2 Knockout non-RGC 1


title: Mutant 03


title: Control Sample 2


title: Ezh2 Knockout RGC 3


title: Mutant 02


title: wild type RGC 1


title: Ezh2 Knockout RGC 1


title: Mutant 01


title: Control Sample 1


title: Control 04


title: DBP+chemopreventive agent Sample 2


title: Control 03


title: Control 02


title: Ezh2 Knockout RGC 2


title: HJV_1

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

data_processing:
The raw sequencing data was processed to remove any adaptor, PCR primers and low quality transcripts using FASTQC and Trimomatic software.
Alignment to Mouse genome MM9 using Tophat and Cufflinks
FPKM
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

extract_protocol:
Liver RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions.  One microgram of RNA from each sample was sequenced with a HiSeq 2000 (Illumina, Inc., San Diego, CA).
Illumina TruSeq RNA Sample Prep Kit

treatment_protocol: Ethical approval was obtained from the institutional animal care and use committee of Beth Israel Deaconess Medical Center (Animal Welfare Assurance #A3153-01; Boston, MA) in accord with national and international guidelines.  All wild type mice were C57BL/6 males (Jackson Laboratories).  Prof. Nancy Andrews provided hemojuvelin knockout mice (Niederkofler et al. J Clin Invest (2005.115(8):p.2180-6) on a C57BL/6 background.  At 5 weeks of age, the mice were transitioned to a soy-free diet (AIN-93G) containing different amounts of iron per kilogram of food: iron-deficient (2.5 mg/kg, n=3), iron-sufficient (37.5 mg/kg, n=3), or iron-excess (1000 mg/kg, n=3). 5-week old male C57BL/6 mice that were either wild type or HJV knockout mice homozygous for the disruption of the murine hemojuvelin (HJV) gene (n=2-3 per group) were maintained on the iron-deficient (2.5 mg/kg iron). After 50 days, the mice were sacrificed, and liver RNA was extracted.

tag: strain background

tag: genotype/variation

tag: diet

value: AIN-93G low iron diet (2.5 ppm)

tag: duration of special diet

value: 50 days

tag: age at tissue harvest

value: 12 weeks

value: liver


title: WT_1

value: wild type

tag: tissue


title: Fe_High_12L

description: AIN-93G high iron diet (1000 ppm)

data_processing:
The raw sequencing data was processed to remove any adaptor, PCR primers and low quality transcripts using FASTQC and Trimomatic software.
Alignment to Mouse genome MM10
Unique Read Counting
Genome_build: mm9
Supplementary_files_format_and_content: Read Counts Files

source_name: liver

value: AIN-93G high iron diet (1000 ppm)


title: WT_2


title: P5

city: Urbana

first: Karen

state: IL

address: 1201 W Gregory St

department: Division of Nutritional Sciences

institute: University of Illinois at Urbana-Champaign

data_processing:
Reads from the HiSeq 2000 were processed and analyzed through a series of steps. Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2. FASTQ files were trimmed using FASTQ Trimmer (version 1.0.0).  TopHat2 (version 0.5) was employed to map paired end RNA-Seq reads to version mm10 of the Homo sapiens reference genome in the UCSC genome browser, in conjunction with the RefSeq genome reference annotation hg19. Gene expression values (raw read counts) from BAM files were calculated using StrandNGS (version 2.1) Quantification tool.  Partial reads were considered and option of detecting novel genes and exons were selected.  Default paramteres for finding novel exons and genes were specified.  DESeq normalization algorithm using default values was selected.  Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene for each treatment relative to the vehicle control. We considered genes with fold-change >2 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: bam files were generated using TopHat2

source_name: Liver

extract_protocol:
For gene expression analysis, total RNA was extracted from 3 biological replicates for each ligand treatment using Trizol reagent and further cleaned using the RNAeasy kit from QIAGEN.
Once the sample quality and replicate reproducibility was verified 2 samples from each group were subjected to sequencing. RNA at a concentration of 100 ng/µL in nuclease-free water was used for library construction.The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNAseq Sample Prep kit.  The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000  using a TruSeq SBS sequencing kit version 3. Fastq files were generated with the software Casava 1.8.2 (Illumina).. Briefly, the poly-A containing mRNA was purified from total RNA, RNA was fragmented, double-stranded cDNA was generated from fragmented RNA, and adapters were ligated to the ends.

value: Jackson Laboratory

value: Female

tag: treatment

value: Liver


title: P8

value: Bazedoxifene


title: Control 01

value: female

value: 1 week old


title: P40

value: Vehicle


title: DBP Sample 2

value: oral tissue


title: HJV_2

value: homozygous for the disruption of the murine hemojuvelin (HJV) gene


title: P4


title: Fe_Low_9L

description: AIN-93G low iron diet (2.5 ppm)


title: Fe_High_8L

description: AIN-93G high iron diet (1000 ppm)


title: HS16

city: tyuo-ku

first: noriko

last: nishi

state: Tokyo

address: 5-11 hakozaki 5F Yunibasaru Bldg

institute: Axiohelix Co. Ltd.

data_processing:
Sequenced reads were mapped to hg19 whole genome using Bowtie version 2.0.5 with default.
Read per million (RPM) were calculated using an in-house developed script.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using bedtools version 2.13.2; tab-delimited text files include RPM values for each gene;

source_name: Esophagus

extract_protocol: SAGE-seq libraries were prepared for sequencing using SOLiD SAGE Kit with Barcoding Adaptor Module and multiplexed by using SOLiD RNA Barcoding Kit Module 1-16 according to the manufacturer’s instructions.

value: esophagus

tag: tumor stage

value: ESCC-adjacent noncancerous, normal mucosa


title: HS17

value: ESCC


title: HM08

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 2.1.0 with default.
peaks were called using an in-house developed script, defining a region where depth is more than 10 RP100M (Reads per 100 Millions mapped reads) as a peak.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using https://github.com/daler/rdbio-scripts/blob/master/sequenceFiles/bed2wig.py;

extract_protocol: MeDIP-seq libraries were prepared for sequencing using the SOLiD Fragment Library Construction Kit and multiplexed by using SOLiD™ Fragment Library Barcoding Kit Module 1-16 according to the manufacturer’s instructions.

tag: mediip antibody

value: MBD2 protein


title: P39

tag: strain


title: HM07


title: P38


title: Fe_Medium_6L

description: AIN-93G sufficient iron diet (37.5 ppm)

value: AIN-93G sufficient iron diet (37.5 ppm)

value: 50 days

value: 12 weeks


title: P36

value: Conjugated estrogen+Bazedoxifene


title: col_ZT16-27c

first: Patrick

middle: James

last: Dickinson

address: The Sainsbury Laboratory , Bateman Street

department: Sainsbury Laboratory University of Cambridge

country: United Kingdom

institute: University of Cambridge

description: Processed data file: Col_22_27_timecourse_TPM.txt

data_processing:
The raw reads obtained from the sequencing facilities were analysed in house. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 transcriptome using Tophat (Trapnell et al., 2009). The potential optical duplicates resulted from library preparation were removed using the Picard tools (http://sourceforge.net/p/picard/wiki/Main_Page/#q-how-should-i-cite-picard-in-my-manuscript). For each gene, raw reads, FPKM and TPM (Transcripts Per Million) (Wagner et al., 2012) were computed.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: Col0 WT seedlings

extract_protocol:
Total RNA was isolated from a pool og 25 seedlings using the MagMAX-96 Total RNA Isolation kit (Ambion, AM1830), following the manufacturer’s instructions. RNA quality and integrity was assessed on the Agilent 2200 TapeStation.
Library preparation was performed using 1 ug of total RNA using the TruSeq Stranded mRNA library preparation kit and TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2101 and RS-122-2001), following manufacturer’s instruction. The libraries were sequenced on a HiSeq2000 using paired-end sequencing of 100 bp in length at Max Planck Institute (MPI) Tubingen and the Beijing Genomics Institute (BGI) sequencing centres.

value: seedlings

tag: ecotype

tag: genotype

value: wild type

tag: growth conditions

value: 27°C, short days (8 h light, 16 h dark), 170 umol light.

tag: timepoint sampled

tag: replicate

value: Only


title: Fe_Low_5L

description: AIN-93G low iron diet (2.5 ppm)

value: AIN-93G low iron diet (2.5 ppm)


title: P3

value: Jackson Laboratory

value: Female

value: Bazedoxifene

value: Liver


title: col_ZT12-27c


title: Fe_High_4L

description: AIN-93G high iron diet (1000 ppm)

value: AIN-93G high iron diet (1000 ppm)


title: col_ZT8-27c


title: Fe_Medium_2L

description: AIN-93G sufficient iron diet (37.5 ppm)


title: col_ZT4-27c


title: Fe_Low_1L

description: AIN-93G low iron diet (2.5 ppm)


title: Fe_Medium_10L

description: AIN-93G sufficient iron diet (37.5 ppm)


title: col_ZT2-27c


title: HeLa_S-phase_Unsynchronized_EtU_labeled

description: S-phase_EtU-labeled_samples_lncRNAs_hg19_collapse_rpkm.txt.gz

data_processing:
[HeLa_S-phase] The samples from AB SOLiD system were aligned using LifeScope
[HeLa_S-phase] All alignments were made using hg19 as reference genome assembly
[HeLa_S-phase] The reads are quantified using ht-seq count
[HeLa_S-phase] Normalization of reads performed as Reads Per Kilobase of transcript per Million (RPKM)
[SCAT7] The samples from ILLUMINA  system were aligned using HISAT
[SCAT7] All alignments were made using hg19 as reference genome assembly
[SCAT7] The reads are quantified using ht-seq count
[SCAT7] Normalization of reads performed as Count Per Million (CPM) from edgeR
Genome_build: hg19
Supplementary_files_format_and_content: CPM, RPKM

treatment_protocol:
Unsynchronized cells were exposed to ethynyl uridine label and cells were harvested and nascent RNA was captured using Click-iT chemistry from. The captured RNA pool was depleted of rRNA using Ribo-Minus kit from Invitrogen.
Transient knockdown experiments were performed using 35 µM of siRNA targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded overnight and transfected with lipofectamin RNAi-MAX.

tag: cell line

value: HeLa cells

tag: phase

value: Unsynchronized hetergenous population

tag: label status

value: Ethynyl Uridine (EtU label)

tag: time

value: collected after overnight incubation

tag: sirna

value: Not applicable


title: P24

tag: Sex

value: Conjugated estrogen


title: col_ZT1-27c


title: P21

value: Conjugated estrogen+Bazedoxifene


title: P2


title: col_ZT0-27c

value: seedlings


title: HeLa_S-phase-T3_Unlabeled

description: S-phase_Unlabeled_samples_lncRNAs_hg19_collapse_rpkm.txt.gz

treatment_protocol:
Cells were synchronized at G1/S phase usind double-block method
Transient knockdown experiments were performed using 35 µM of siRNA targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded overnight and transfected with lipofectamin RNAi-MAX.

value: S-phase (T3)

value: Not labeled

value: Collected after 5 hours


title: P18


title: HeLa_S-phase-T2_Unlabeled

value: S-phase (T2)

value: Collected after 3.5 hours


title: col_ZT-4-27c

value: wild type

value: 27°C, short days (8 h light, 16 h dark), 170 umol light.

value: Only


title: col_ZT16-22c

value: 22°C, short days (8 h light, 16 h dark), 170 umol light.


title: P11

value: Jackson Laboratory

value: Female

value: Vehicle

value: Liver


title: col_ZT12-22c


title: HeLa_S-phase-T1_Unlabeled

value: HeLa cells

value: S-phase (T1)

value: Collected after 2 hours

value: Not applicable


title: col_ZT8-22c

value: seedlings


title: col_ZT4-22c


title: P25


title: P23

value: Conjugated estrogen+Bazedoxifene


title: HeLa_S-phase-T1_EtU_labeled

treatment_protocol:
Nascent RNA capture assay was perfomed using synchronized HeLa cells at G1/S phase. The culturing media were exposed to pulses of ethynyl uridine (2 h, 3.5 h and 5h for T1, T2 and T3 samples). T1, T2 and T3 Cells were harvested and nascent RNA was captured using Click-iT chemistry from. The captured RNA pool was depleted of rRNA using Ribo-Minus kit from Invitrogen.
Transient knockdown experiments were performed using 35 µM of siRNA targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded overnight and transfected with lipofectamin RNAi-MAX.

value: Ethynyl Uridine (EtU label)


title: col_ZT2-22c


title: HeLa_S-phase-T2_EtU_labeled

value: S-phase (T2)


title: HeLa_S-phase-T3_EtU_labeled

value: S-phase (T3)

value: Collected after 5 hours


title: Tumor Kidney (Dox ON)_whole transcriptome_RNA-seq

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

description: Dox+/ exons (Total: 33169818.0) RPKM

data_processing:
Illumina bcl2fastq Conversion Software v2.17.1.14 was used for conversion into FASTQ files.
Trimmotatic was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads were mapped to mouse genome mm10 with STAR (2.5.0c) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools (Li et al. 2009).
The bigWig files were normalized to display uniquely mapped reads per 10 million uniquely mapped reads with duplicates. There are separate bigWig files for + and - genomic strands.
Raw reads and Reads Per Kilobase per Million mapped reads (RPKM) were calculated using HOMER (Heinz et al. 2010)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig and tab-delimited text files include raw reads and RPKM values for each Sample.

source_name: Tumor Kidney (Dox ON)

growth_protocol: Chimeric embryos were generated from Rosa26-M2rtTA TetO-OSKM mPer2-luc ESCs by injection into C57BL/6 x DBA/2 F1 hybrid blastocysts.

extract_protocol:
Tissue samples were homogenized in Invitrogen TRIzol reagent. RNA was extracted by using QIAGEN RNeasy columns as per manufacturer’s protocol.
Total RNA (0.25 μg) was depleted of ribosomal RNAs using Ribo-Zero Gold (Illumina). Sequencing libraries were constructed using a TruSeq Stranded Total RNA LT Sample Prep Kit according to the manufacturer’s instruction (Illumina).

treatment_protocol: Doxycycline (Dox) treatment was performed as previously described (Ohnishi et al. 2014).

tag: strain background

value: C57BL/6 x DBA/2 F1

tag: genotype/variation

tag: dox treatment

value: yes

value: Kidney


title: col_ZT1-22c

tag: tissue

value: wild type

value: 22°C, short days (8 h light, 16 h dark), 170 umol light.

value: Only


title: HeLa_S-phase_Unsynchronized_Unlabeled

extract_protocol:
Cells were collected 48 hours post-transfection and RNA extraction was carried out using ReliaPrep RNA Cell Miniprep System
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero from Illumina (Cat #  RS-122-2201)

treatment_protocol:
No treatment
Transient knockdown experiments were performed using 35 µM of siRNA targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded overnight and transfected with lipofectamin RNAi-MAX.

value: Unsynchronized hetergenous population

value: Not labeled

value: collected after overnight incubation


title: col_ZT0-22c


title: Rep_3_OxA_8h

city: Jupiter

first: Thomas

last: Kodadek

state: FL

address: 130 Scripps Way

institute: The Scripps Research Institute

data_processing:
Demultiplexed and quality filtered raw reads (fastq) generated from the NextSeq 500 were trimmed (adaptor sequences) using Trimmomatic, version 0.3, and aligned to the reference genome (UCSC-mm10) using STAR, version 2.5.2a
HTSeq-count (version 0.6.0) was used to generate gene counts and differential gene expression analysis was performed using DESeq2 (version 1.10.1, R version: 3.2.3), comparing the OxA-treated samples to those treated with vehicle.
For statistical analyses, raw counts for the two conditions of interest were imported into DESeq2 and transformed using the negative binomial Wald test.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with the regularized log transformations of the raw counts (DESeq2)

source_name: Immortalized neuronal cell line

growth_protocol: Cells were cultured in DMEM, high-glucose plus 10% heat-inactivated FBS and kept at 37C, 5.0% CO2.

extract_protocol:
RNA was isolated with TRIzol Reagent (Life Technologies) according to manufacturer’s protocol, including the addition of 10µg RNase-free glycogen (ThermoFisher). The RNA samples were then treated with DNase (New England Biolabs) to remove any genomic DNA contamination and then cleaned up with the Purelink RNA Micro Kit (Invitrogen).
The DNase-treated Total RNA (250ng) was depleted of ribosomal RNA (rRNA) using the TruSeq Stranded Total RNA kit (Illumina) and quality assessed on an Agilent 2100 Bioanalyzer to confirm that 18S and 28S rRNA peaks were depleted. The rRNA-depleted RNA was converted to dsDNA libraries by following the TruSeq Stranded Total RNA sample prep kit user guide. Briefly, the RNA was fragmented, converted to cDNA, and ligated with adaptors. The adaptor-ligated DNA was then PCR amplified using 11 cycles to generate the final libraries. The final libraries were size selected and purified using 1.0 x Ampure XP beads (Beckman Coulter) then validated by the Bioanalyzer and qPCR quantified using primers that recognize the Illumina adaptors. The libraries were then pooled at equimolar ratios, quantified using qPCR (quantification of only the adaptor-ligated libraries) and loaded onto the NextSeq 500 flow cell (Illumina) at 1.8pM final concentration.

treatment_protocol: Culture media was replaced with fresh, warm media containing vehicle (H2O) for 8 hours, or 200nM OxA for 3 or 8 hours.

value: Stable incorporation of human orexin receptor 1


title: Normal Kidney_whole transcriptome_RNA-seq

description: WT/ exons (Total: 40408775.0) RPKM

source_name: Normal Kidney

value: WT

value: no


title: col_ZT-4-22c

value: seedlings


title: Streptozotocin treated Rep3

city: Bloomington

first: Ram

last: Podicheti

state: IN

institute: Indiana University

data_processing:
Bases were called using bcl2fasta v2.16.0.10
Using Trimmomatic ver. 0.33 (Bolger et al., 2014), reads were adaptor trimmed and quality filtered setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 15 bases post-trimming were excluded.
Cleaned reads were mapped to the complete genome of Staphylococcus_aureus_USA300_FPR3757, complete genome (CP000255.1) and the three plasmid sequences (CP000256.1, CP000257.1 and CP000258.1) using bowtie2 ver. 2.2.6.
For each library, number of uniquely mapped reads overlapping with annotated genes are counted using htseq-counts ver. 0.5.4p1.
Genome_build: Staphylococcus_aureus_USA300_FPR3757, complete genome (CP000255.1) and the three plasmid sequences (CP000256.1, CP000257.1 and CP000258.1)
Supplementary_files_format_and_content: The counts files contain counts of uniqulely mapped reads overlapping with annotated genes. Each table has two columns - Gene ID, Count of uniquely mapped reads overlapping with that gene.

organism: Staphylococcus aureus

source_name: exponentially grown cells

growth_protocol: Cultures of strains USA300_P23, USA300_P23_streptozotocin treated, and USA300_P23_floxuridine treated in TSB media at 37ºC. Starter cultures were used to inoculate 3 mL cultures of TSB broth in 15 mL test tubes.

extract_protocol:
To isolate RNA for RNA-sequencing, overnight culture in TSB was diluted 100 times in a fresh TSB and incubated in a shaking incubator at 37°C for 2 h, followed by treatment of streptozotocin and floxuridine for 3 h.  After immediate stabilization of RNA in all samples by RNAprotect Bacteria Reagent (Qiagen), cells were collected by centrifugation, suspended in 50 mM of Tris HCl (pH 8) and treated with lysostaphin (50 µg/mL final concentration) at 37°C for 10 min. The resulting protoplasts were collected by centrifugation and RNA isolation was done using RNeasy Mini Kit (Qiagen), including on-column treatment with DNase I (Qiagen), according to the manufacturer’s recommendations. The amount and purity of all RNA samples isolated were assessed by NanoDrop spectroscopy (Thermo Fisher) and sent to the Center for Genomics and Bioinformatics at Indiana University. Sequencing libraries were constructed using the ScriptSeq Complete Kit for Bacteria (Epicentre).
cDNA libraries were prepared from total RNA by the Center for Genomics and Bioinformatics at Indiana University. mRNA was enriched from two micrograms total RNA using RiboZeroTM rRNA Removal (Gram-positive bacteria) Kit (EpiCentre Inc., Madison, WI, USA). rRNA-depleted mRNA samples were purified by ethanol precipitation and quantified by fluorometry with the Qubit® RNA assay kit (Invitrogen, Carlsbad, CA, USA).Double stranded cDNA synthesis was performed following  ScriptSeqTM v2 RNA-Seq Library Preparation guide (EpiCentre Inc., Madison, WI, USA) in accordance with the manufacturer’s standard protocol. Thirty nanograms of enriched mRNA was fragmented using divalent cations via incubation for 5 min at 85oC. The first strand of cDNA was synthesized by reverse transcription using random-sequence primers containing a tagging sequence at their 5’ ends. Di-tagged cDNA was synthesized by random annealing of a terminal-Tagging Oligo (TTO) to the 3’ end of the cDNA for extension of the cDNA by DNA polymerase. Di-tagged cDNA was purified using Agencourt AMPure® XP beads (Beckman Coulter, Indianapolis IN, USA) followed by PCR amplification for 15 cycles using FailsafeTM PCR enzyme and ScriptSeq Index DNA primer set (EpiCentre Inc., Madison, WI). This step generated the second strand of cDNA and completed the addition of Illumina adapter sequences incorporating a user-defined barcode. The amplified libraries were purified using Agencourt AMPure® XP beads. Quality and quantity were assessed using an Agilent DNA 1000 chip (Agilent Technologies, Inc., Santa Clara, CA, USA) and Qubit® dsDNA HS assay kit (Invitrogen, Carlsbad, California, USA), respectively. Libraries were standardized to 2 μM. Cluster generation was performed using standard Cluster kits (v3) and Illumina Cluster Station.

treatment_protocol: 1 ug/ml of streptozotocin and floxuridine was treated for 3 hr

tag: treatment

value: streptozotocin


title: Rep_3_Negative


title: Rep_3_OxA_3h


title: Rep_2_OxA_3h


title: Streptozotocin treated Rep1

tag: strain


title: Streptozotocin treated Rep2


title: Rep_1_OxA_8h


title: Rep_1_OxA_3h


title: Rep_2_Negative


title: Rep_1_Negative


title: Floxuridine treated Rep1

value: floxuridine


title: WT Rep3


title: Floxuridine treated Rep3


title: Floxuridine treated Rep2


title: FLT_72_3

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

description: Exposed

data_processing:
The FASTQ sequence reads were generated using the Illumina Casava pipeline version 1.8.2, initial quality assessment was based on data passing the Illumina Chastity filtering.
Reads containing adapters and/or PhiX control signal were removed
The sequence reads were trimmed using Trimmomatic v0.32
The trimmed reads were aligned against the C. elegans genome using TopHat (v2.0.8) and Bowtie (v2.1.0)
Genome_build: Ensembl, WBcel235.75
Supplementary_files_format_and_content: text file with raw counts

organism: Caenorhabditis elegans

source_name: Whole Worm Culture

growth_protocol: Nematodes were cultured on NGM plates and fed OP50 Escherichia coli lawn at 20oC

extract_protocol:
RNA was extracted from worm pellets using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) as described by the manufacturer. RNA integrity and quality were analyzed using the Agilent 2100 Bioanalyser (G2938A) before Illumina Sequencing (BaseClear B.V., Leiden, The Netherlands).
Sequencing was carried out using the Illumina TruSeq library preparation kit, sequencing with a minimum of 20 million reads per sample.

treatment_protocol: Synchronized L1 larvae were placed on NGM plates with an OP50 bacterial lawn until L4, and transferred to plates containing the drug of interest for 24 or 72 hours. A final concentration of 100µM was added to the NGM media before pouring. Besides unexposed nematodes, a representative DMSO concentration (0,033%) was used as a control. Bacteria and eggs were removed from the culture using a SEFAR NITEX® 31µM pore mesh (03-31/24) before immediately freezing the samples at -80oC until RNA extraction. 72 hour cultures were moved to fresh plates every day after meshing.

value: whole worm

tag: exposure

value: 100µM 3'-deoxy-3'-fluorothymidine (alovudine or FLT)

tag: exposure time


title: WT Rep1


title: FLT_72_1

description: Exposed


title: FLT_72_2

description: Exposed


title: Rep_2_OxA_8h


title: PolII_KO_ChIPSeq

city: Miami

first: Feng-Chun

last: Yang

address: 1011 NW 15th Street

institute: University of Miami Miller School of Medicine

data_processing:
Basecalls performed using Illumina NextSeq 500
ChIP-Seq reads were aligned to the mm10 genome assembly using the BWA algorithm with default settings
Data were filtered using the following specifications:only reads that pass Illumina's purity filter,aligned with no more than 2 mismatches,and map uniquely to the genome were used in the subsequent analysis,than duplicate reads were removed.
peaks were called using MACS version 2.1.1 with default setting
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file

source_name: Mesenchymal stem/progenitor cells

extract_protocol:
MSPCs were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 300 to 500 bp. Histone-DNA complexes were isolated with specific histone modification antibodies.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced.

tag: cell type

value: BM-derived MSPCs

tag: passages

tag: chip antibody

value: PolII (Abcam ab5095)


title: INPUT_ChIPSeq


title: FLT_24_2

description: Exposed

tag: replicate


title: FLT_24_3

description: Exposed


title: ASXL1_WT_ChIPSeq

value: ASXL1 (Santa Cruz sc-85283)


title: d4T_72_3

description: Exposed

value: 100µM 2',3'-didehydro-2',3'-deoxythymidine (stavudine or d4T)


title: WT Rep2


title: FLT_24_1

description: Exposed


title: PolII_WT_ChIPSeq


title: Nsk2

city: Guangzhou

first: yazhou

last: hu

state: Guangdong

address: xingang west road no. 135

institute: Sun Yat-sen University

data_processing:
The raw data (raw reads) generated from Illumina sequencing experiment was first quality-fultered to eliminate adaptor sequences, low-quality bases (Q < 20) and unpaired reads based on the FastX toolkit program
The quality-filtered reads were mapped back to C. irritans and Tetrahymena thermophila database to remove protozoa contamination using soft bowtie2
The trimmed final clean reads were de novo assembled into contigs using Trinity package with k-mer length of 25
The assembled contigs of all the samples were cleaned by removing redundancies and were further assembled as primary unigenes with CD-HIT software. The final clean reads were aligned to the primary unigenes using FNASe2. The primary unigenes with at least 10 mapped reads were considered reliable unigenes.
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Epinephelus coioides

source_name: non-infected skin

growth_protocol: Infected and control E. coioides were bred in flow-through water system

extract_protocol:
Total RNA from all samples was extracted using the RNAiso Plus Total RNA extraction reagent (TAKARA)
RNA-Seq library was constructed using the TruSeq™ RNA Sample Prep Kit (Illumina)

treatment_protocol: E. coioides was local infected with C. irritans

value: skin


title: Nsk3


title: Isk1

source_name: infected skin


title: Isk2


title: Nsk1


title: Isk3


title: d4T_72_2

description: Exposed


title: d4T_72_1

description: Exposed


title: C3

source_name: normal skin


title: C2


title: d4T_24_3

description: Exposed


title: d4T_24_1

description: Exposed


title: C1


title: d4T_24_2

description: Exposed


title: AZT_72_3

description: Exposed

value: 100µM 3'-azido-3'-deoxythymidine (zidovudine or AZT)


title: AZT_72_1

description: Exposed


title: AZT_72_2

description: Exposed


title: Control_1367

city: Chapel Hill

first: Brian

middle: Colwell

last: Jensen

state: NC

address: 6012 Burnett-Womack Building, CB 7075

department: Cardiology

institute: UNC School of Medicine

data_processing:
QC-passed reads were aligned to the mouse reference genome (mm9) using MapSplice v2.1.4.
The alignment profile was determined by Picard Tools v1.88.
Aligned reads were sorted and indexed using SAMtools v1.2 and translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UNC Bioinformatics Utilities (UBU) v1.2.
Transcript abundance estimates for each sample were performed using RSEM expectation-maximization algorithm.
RSEM abundance estimates were upper-quartiled normalized.
Genome_build: mm9
Supplementary_files_format_and_content: *.genes.xlsx files contain expected and upper quartile normalized RSEM values, normalizedRSEM_summary.xlsx contains normalized RSEM values for all samples

source_name: murine heart tissue

extract_protocol:
total RNA was extracted using Qiagen RNeasy kit
4 ug total RNA was used to create libraries with KAPA stranded mRNA-Seq kit using 10 cycles of amplification following the manufacturer's recommended protocol with the exception of using 0.5X the recommended PCR template amount

treatment_protocol: control (water)

value: heart

value: female

value: FVB


title: Erlotinib_1375

treatment_protocol: erlotinib (50 mg/kg/day) 14 day treatment


title: Control_1366


title: Control_1365


title: Sunitinib_1370

treatment_protocol: sunitinib (40 mg/kg/day) 14 day treatment


title: Sorafenib_1372

treatment_protocol: sorafenib (30 mg/kg/day) 14 day treatment


title: Sunitinib_1369


title: Sorafenib_1373


title: Sunitinib_1368


title: Erlotinib_1374


title: Sorafenib_1371


title: Erlotinib_1376


title: AZT_24_1

description: Exposed


title: AZT_24_3

description: Exposed


title: XZH_F07_2

city: Fuzhou

first: Xuanyang

address: 15,Shangxiadian road,cangshan district

institute: Fujian Agriculture and Forestry University

data_processing:
Basecalls performed using CASAVA version 1.7
The clean reads with high quality were obtained by removing reads containing adapter, reads that containing N (indefinite base) higher than 10% and reads with low quality from raw reads
Transcriptome assembly was accomplished  using Trinity (version:r20140413p1).
The level of gene expression was determined by normalizing the number of unambiguous tags in each library to expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM). For the samples with biological replicates, differential expression analysis of two groups was performed using the DESeq R package (1.10.1)(qvalue< 0.005 &|log2(foldchange)| > 1)
Genome_build: Trinity.fasta
Supplementary_files_format_and_content: Fastq files of clean data were generated including error rate and Q20, Q30

organism: Ipomoea batatas

source_name: sweet potato_XZH_F07

growth_protocol: The sweet potato seedlings were field grown for at least 28 d until they were cut and used as experimental material. After treatment the seedlings were grown in growth chambers at 28°C for 24 hours,

extract_protocol:
Total RNA was isolated from each sample respectively using RNAprep pure plant kit (polysaccharides and polyphenolics-rich, Tianen biotech,Beijing,China), according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. mRNA was purified and cDNA synthesis was subsequently performed. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structurewere ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system. Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and paired-end reads were generated

treatment_protocol: Seedling stems were cut freshly with 20 cm long, grew in a glass bottle containing conidial solutions of 1 × 10^7 conidia/mL of Fob-07 (strong pathogenic),or of Fob-04 (nonpathogenic), respectively. Control was set in which the seedling grew in the water.

tag: cultivar

value: XinZhongHua(XZH)

tag: resistance phenotype

value: highly susceptible to Fusarium wilt

tag: inoculated with

value: pathogenic F. oxyspurum f.sp.batatas Fo-07

tag: timepoint

value: 24 hours after inoculation

value: stem


title: XZHCK_3

source_name: sweet potato_XZHCK

value: water (control)


title: XZHCK_1


title: XZHCK_2


title: XZH_F07_1


title: MIX_assembly

description: Mix RNA equally from all five sample groups

source_name: sweet potato_MIX_assembly

value: JinShan 57(JS57) and XinZhongHua(XZH)


title: XZH_F07_3


title: DMSO_72_3

description: Control

value: whole worm


title: bisulfite sequencing by TEPBAT tail

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

description: bisulfite-treated genomic DNA

data_processing:
The sequencing reads were mapped to the appropriately converted mouse genomic sequences (mm10) by bismark.
Using these mapping results, methylation at individual CpG sites were determined by bismark-methylation-extractor.
Genomic positions of IAP LTRs were downloaded from UCSC genome browser, and their methylation levels were calculated using the bismak-generated files.
Genome_build: mm10
Supplementary_files_format_and_content: The cov files contain methylation levels of individual CpG sites: chromosome name, position of cytosine, methylation level (%), the number of methylated calls, and the number of unmethylated calls.

source_name: tail DNA

extract_protocol:
High molecular weight genomic DNA was prepared from tail and sperm samples of the same adult mouse by a standard procedure.
The DNAs were treated with 10M bisulfite, and their comprelemtary strands were synthesized by Klenow fragment with tagged-random primer (5'-GCAGTGAACTGACTACAGGNNNN-3'). IAP-containing genomic regions were amplified by PCR using KOD-plus neo, tag primer (5'-CAGTGAAC- TGACTACAGG-3'), and either of IAP-BS1 (5'-GGGGAAGGTAGAGTATAWG-3') or IAP-BS2 (5'-GGTTTTTGAAGATGTAAGTAATAAAGTTTT-3') primer. The PCR products of 350 to 450 bp were purified from a 2% agarose gel, and the Illumina sequencing adaptors were added to their ends using TruSeq DNA Sample Prep kit (Illumina).
BS-seq (target enrichment after PBAT)

tag: stain

tag: Sex

value: male

tag: age

value: adult


title: DMSO_72_2

description: Control


title: JSCK_3

source_name: sweet potato_JSCK

value: JinShan 57(JS57)

value: highly resistance to Fusarium wilt

value: nonpathogenic F. oxyspurum f.sp.batatas Fo-04


title: AZT_24_2

description: Exposed

value: 100µM 3'-azido-3'-deoxythymidine (zidovudine or AZT)


title: DMSO_72_1

description: Control


title: JSCK_1


title: bisulfite sequencing by TEPBAT sperm

description: bisulfite-treated genomic DNA

source_name: sperm DNA


title: JSCK_2


title: 08_P47_CTX_cKO_DJ5

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Single-end reads (quality checked, filtered and adapter trimmed) were aligned to reference sequences (mm10 from UCSC) using STAR allowing three mismatches.
RNA-seq counts were quantified using HTSeq python suite. Reference gene model (mm10 GTF from Gencode vM11) were provided to assist the counting.
RNA-seq CPM values were then quantified using EdgeR (R package).
Gene-level CPM quantifications were used for all downstream processing.
Genome_build: UCSC Mouse GRCm38 / mm10
Supplementary_files_format_and_content: tab-delimited text file with CPM values for genes (rows) across samples (columns).

source_name: Cortex

extract_protocol:
Brain regions were dissected out and immediately flash frozen in liquid nitrogen. Total RNA was then purified from these samples, using an mRNeasy kit (Qiagen), following the manufacturer's instructions.
mRNA was purified via poly(A) selection from 2ug of total RNA. Purified mRNA was then utilized to generated cDNA libraries using previously published protocols (Takahashi et al., 2015).
Pooled libraries (at a final concentration of 2nM) were sequenced on a NextSeq 500 sequencer (Illumina) by the McDermott Sequencing Core at the UT Southwestern Medical Center.

value: postnatal day 47

tag: genotype

value: conditional knock-out

tag: hemisphere

value: left


title: 11_P47_HIP_CTL_DJ21

source_name: Hippocampus

value: control


title: 16_P47_HIP_cKO_DJ19


title: 12_P47_HIP_CTL_DJ22


title: 13_P47_HIP_cKO_DJ15


title: 14_P47_HIP_cKO_DJ16


title: 15_P47_HIP_cKO_DJ18


title: 09_P47_HIP_CTL_DJ17