title: astrocytic-cell_5wk_3D_100ul_7.36mg/ml_Mtrgl_10mpml_rep3

description:
differentiated human astrocytic cells 3D cultured in 100 microliter 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
20C-070517_S62

extract_protocol:
3D culture hydrogel was immersed into a buffer preserving RNA integrity, which was then stored at -80 °C. 3D culture hydrogel was homogenized in lysis buffer. Total RNA isolation was performed using a kit following the manufacturer’s protocol.
RNA-Seq libraries were prepared following the Smart-seq2 protocol. 1 ng of total RNA was used. cDNA was synthesized and then used in each NexteraXT (Illumina) reaction.

value: 3D cultured differentiated human astrocytic cells


title: astrocytic-cell_5wk_3D_100ul_7.36mg/ml_Mtrgl_10mpml_rep1

status: Public on Apr 09 2018

type: SRA

city: Cambridge

first: Halil

last: Tekin

state: MA

address: 75 Ames St.

country: USA

institute: Broad Institute of MIT and Harvard

description:
differentiated human astrocytic cells 3D cultured in 100 microliter 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
20A-070517_S60

library_source: transcriptomic

data_processing:
RSEM v1.3 was run on fastq files using a joint human (hg19 annotation from UCSC) and mouse (mm10 annotation from UCSC) transcriptome and STAR v2.5.2, with the options --star --star-gzipped-read-file --paired-end. The STAR bams output by RSEM were used to filter the original fastq files with seqtk. In particular, all reads that mapped to the mouse transcriptome were removed, as were all unmapped reads. These filtered fastq files were run through RSEM with default parameters using human hg19 UCSC genome to estimate gene expression values, which were then used to create an un-normalized count matrix.
Genome_build: hg19
Supplementary_files_format_and_content: "count_matrix.txt", tab-delimited un-normalized count matrix, contains count reads per gene for each Sample.
Supplementary_files_format_and_content: "singleCell_count1.txt, tab-delimited un-normalized count matrix, with one column for each cell and one row for each gene.
Supplementary_files_format_and_content: "singleCell_count2.txt, tab-delimited un-normalized count matrix, with one column for each cell and one row for each gene.

molecule: total RNA

organism: Homo sapiens

growth_protocol: desribed in H. Tekin et al., Nat Biomed Eng, 2018

tag: strain/cell type

tag: culture condition

tag: age

tag: genotype

value: wild type


title: CS patient cell line (GM1629SV, CS1BE) replicate 4

type: RNA

city: Saito-Asagi, Ibaraki

first: Yooksil

last: SIN

state: Osaka

department: Center for Drug Design

country: Japan

institute: NIBIOHN

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing:
Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1
Data filtered as follows:
1. Cut off Flags of control probe
2. Background correction
3. Cut off Flags of saturated or high background probe
4. Quantile normalization of log2(probes) values using library (preprocessCore) in R

source_name: SV40 virus transformed cell line, GM1629(SV) (CSB-deficient CS patient cell line: CS4BE) derivative

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin mixed solution (product code is 26253-84, Nacalai Tesque, Kyoto, Japan) at 37 °C in an incubator containing 5% CO2.

extract_protocol: Total RNA extracted Rneasy Mini Kit (QIAGEN)

tag: cell line

value: CS patient cell line (GM1629SV, CS1BE)

tag: tissue

value: skin

tag: cell type

value: fibroblast-like

tag: disease state

value: Group B Cockayne syndrome


title: CS patient cell line (GM739SV, CS1AN) replicate 4

source_name: SV40 virus transformed cell line, GM739(SV) (CSB-deficient CS patient cell line: CS4AN) derivative

value: CS patient cell line (GM739SV, CS1AN)


title: CS patient cell line (GM1629SV, CS1BE) replicate 2

source_name: SV40 virus transformed cell line, GM1629(SV) (CSB-deficient CS patient cell line: CS2BE) derivative


title: CS patient cell line (GM1629SV, CS1BE) replicate 3

source_name: SV40 virus transformed cell line, GM1629(SV) (CSB-deficient CS patient cell line: CS3BE) derivative


title: CS patient cell line (GM739SV, CS1AN) replicate 1

source_name: SV40 virus transformed cell line, GM739(SV) (CSB-deficient CS patient cell line: CS1AN) derivative


title: iN_from_5wk_3D_iN_human-primary-astro_100ul_7.36mg/ml_Mtrgl_20mpml_rep3

description:
human neuronal cells sorted from their 3D co-culture with human primary astrocytes in 100 microliter 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
22C-070517_S68

extract_protocol:
3D culture hydrogel was dissociated and human neuronal cells were sorted from dissociated hydrogel-cell suspension into a buffer preserving RNA integrity, which was then centrifuged and then stored at -80 °C. Total RNA isolation was performed using a kit following the manufacturer’s protocol.
RNA-Seq libraries were prepared following the Smart-seq2 protocol. 1 ng of total RNA was used. cDNA was synthesized and then used in each NexteraXT (Illumina) reaction.


title: UVSS patient cell line (UVS1KO) replicate 4

source_name: SV40 virus transformed CSB-deficient UVSS patient cell line (UVS1KO)

value: UVSS patient cell line (UVS1KO)

value: UV sensitive syndrome derived from CSB gene


title: Normal cell line (WI-38 VA13 sub 2 RA) replicate 2

source_name: SV40 virus transformed cell line, WI-38 derivative

value: Normal cell line (WI-38 VA13 sub 2 RA)

value: lung

value: infinite life span

value: normal fetus


title: Normal cell line (WI-38 VA13 sub 2 RA) replicate 1


title: UVSS patient cell line (UVS1KO) replicate 2


title: LCM-HCV-HCC-75-NMH [sample 93]

city: Cagliari

first: Giacomo

last: Diaz

address: Via Porcell 4

department: Dept Biomedical Sciences

country: Italy

institute: University of Cagliari

description: sample 93

hyb_protocol: Following fragmentation, 10 to 18 µg (mean 12.8) of cRNA hybridized for 16 hr at 45°C on Affymetrics Human U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000_7Gplus

data_processing: Affymetrics probeset summaries were computed using RMA algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

label: Biotin

source_name: specimen obtained from laser capture microdissected non-malignant hepatocytes of HCV-HCC

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: patient code

tag: Sex

value: male

value: laser capture microdissected cells

value: HCV-HCC non tumor cells


title: CS patient cell line (GM1629SV, CS1BE) replicate 1

source_name: SV40 virus transformed cell line, GM1629(SV) (CSB-deficient CS patient cell line: CS1BE) derivative


title: UVSS patient cell line (UVS1KO) replicate 1


title: Normal cell line (WI-38 VA13 sub 2 RA) replicate 3


title: CS patient cell line (GM739SV, CS1AN) replicate 3

source_name: SV40 virus transformed cell line, GM739(SV) (CSB-deficient CS patient cell line: CS3AN) derivative


title: astrocytic-cell_5wk_3D_100ul_7.36mg/ml_Mtrgl_10mpml_rep2

description:
differentiated human astrocytic cells 3D cultured in 100 microliter 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
20B-070517_S61


title: iN_from_5wk_3D_iN_human-primary-astro_100ul_7.36mg/ml_Mtrgl_20mpml_rep2

description:
human neuronal cells sorted from their 3D co-culture with human primary astrocytes in 100 microliter 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
22B-070517_S67


title: UVSS patient cell line (UVS1KO) replicate 3


title: Normal cell line (WI-38 VA13 sub 2 RA) replicate 4


title: LCM-HCV-HCC-75-MH [sample 92]

description: sample 92

source_name: specimen obtained from laser capture microdissected malignant hepatocytes of HCV-HCC

value: HCV-HCC tumor cells


title: LCM-HCV-HCC-67-MH [sample 88]

description: sample 88


title: LCM-HCV-HCC-70-MH [sample 90]

description: sample 90

value: female


title: iN_from_5wk_3D_iN_human-primary-astro_100ul_7.36mg/ml_Mtrgl_20mpml_rep1

description:
human neuronal cells sorted from their 3D co-culture with human primary astrocytes in 100 microliter 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
22A-070517_S66

value: wild type


title: LCM-HCV-HCC-70-NMH [sample 91]

description: sample 91


title: iN_from_5wk_3D_iN_astrocytic-cell_100ul_7.36mg/ml_Mtrgl_20mpml_rep2

description:
human neuronal cells sorted from their 3D co-culture with differentiated human astrocytic cells in 100 microliter 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
21B-070517_S64


title: iN_5wk_3D_100ul_7.36mg/ml_Mtrgl_10mpml_rep1

description:
human neuronal cells sorted from their 3D in 100 microliter 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
19A-070517_S57

value: human neuronal cells sorted from 3D only human neuronal cell culture


title: iN_5wk_3D_100ul_7.36mg/ml_Mtrgl_10mpml_rep3

description:
human neuronal cells sorted from their 3D in 100 microliter 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
19C-070517_S59


title: LCM-HCV-HCC-67-NMH [sample 89]

description: sample 89


title: day114_cntf_fbs_astro_diff_passage-6_rep2

description:
cells at passage-6 at day-114 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
15B-070517_S44

extract_protocol:
RNA lysis buffer was used to lyse cells. Each lysate was then transferred to a 1.5 ml centrifuge tube, which was then placed on dry ice for rapid freezing and then stored at -80 °C. Total RNA isolation was performed using a kit following the manufacturer’s protocol.
RNA-Seq libraries were prepared following the Smart-seq2 protocol. 1 ng of total RNA was used. cDNA was synthesized and then used in each NexteraXT (Illumina) reaction.


title: iN_5wk_3D_100ul_7.36mg/ml_Mtrgl_10mpml_rep2

description:
human neuronal cells sorted from their 3D in 100 microliter 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
19B-070517_S58


title: LCM-HCV-HCC-43-NMH [sample 87]

description: sample 87


title: day114_cntf_fbs_astro_diff_passage-6_rep3

description:
cells at passage-6 at day-114 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
15C-070517_S45


title: day114_cntf_fbs_astro_diff_passage-6_rep1

description:
cells at passage-6 at day-114 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
15A-070517_S43


title: day67_cntf_fbs_astro_diff_passage-3_rep2

description:
cells at passage-3 at day-67 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
14B-070517_S41


title: iN_from_5wk_3D_iN_astrocytic-cell_100ul_7.36mg/ml_Mtrgl_20mpml_rep1

description:
human neuronal cells sorted from their 3D co-culture with differentiated human astrocytic cells in 100 microliter 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
21A-070517_S63


title: LCM-HCV-HCC-43-MH [sample 86]

description: sample 86


title: LCM-HCV-HCC-21-MH [sample 82]

description: sample 82


title: day67_cntf_fbs_astro_diff_passage-3_rep1

description:
cells at passage-3 at day-67 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
14A-070517_S40


title: LCM-HCV-HCC-21-NMH [sample 83]

description: sample 83


title: LCM-HCV-HCC-40-MH [sample 84]

description: sample 84


title: LCM-HCV-HCC-14-NMH [sample 79]

description: sample 79


title: LCM-HCV-HCC-173-MH [sample 80]

description: sample 80


title: LCM-HCV-HCC-14-MH [sample 78]

description: sample 78


title: LCM-HCV-HCC-40-NMH [sample 85]

description: sample 85


title: LCM-HCV-HCC-127-NMH [sample 77]

description: sample 77


title: LCM-HCV-HCC-173-NMH [sample 81]

description: sample 81


title: LCM-HCV-HCC-127-MH [sample 76]

description: sample 76


title: WLT-HCV-75-NT [sample 75]

description:
sample 75
re-analysis of  GSM1707790

source_name: tissue specimen obtained from explanted liver of HCV-HCC - non tumor region

value: whole liver tissue

value: HCV-HCC non tumor tissue


title: day30_no-NGN1/2_cntf_astro_diff_control_rep2

description:
cells at day 30 when stem cells exposed to cntf without NGN1/2 expression
count_matrix.txt
2B-070517_S5


title: day30_no-NGN1/2_cntf_astro_diff_control_rep3

description:
cells at day 30 when stem cells exposed to cntf without NGN1/2 expression
count_matrix.txt
2C-070517_S6


title: day30_no-NGN1/2_cntf_astro_diff_control_rep1

description:
cells at day 30 when stem cells exposed to cntf without NGN1/2 expression
count_matrix.txt
2A-070517_S4


title: day67_cntf_fbs_astro_diff_passage-3_rep3

description:
cells at passage-3 at day-67 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
14C-070517_S42


title: day30_cntf_fbs_astro_diff_rep3

description:
cells at day 30 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
12C-070517_S36


title: day30_cntf_fbs_astro_diff_rep2

description:
cells at day 30 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
12B-070517_S35


title: day30_cntf_fbs_astro_diff_rep1

description:
cells at day 30 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
12A-070517_S33


title: day30_cntf_astro_diff_rep3

description:
cells at day 30 in human astrocytic cell diffentiation with cntf
count_matrix.txt
11C-070517_S34


title: day30_cntf_astro_diff_rep2

description:
cells at day 30 in human astrocytic cell diffentiation with cntf
count_matrix.txt
11B-070517_S32


title: day30_cntf_astro_diff_rep1

description:
cells at day 30 in human astrocytic cell diffentiation with cntf
count_matrix.txt
11A-070517_S31


title: WLT-HCV-70-T [sample 72]

description:
sample 72
re-analysis of  GSM1707775

source_name: tissue specimen obtained from explanted liver of HCV-HCC - tumor region

value: HCV-HCC tumor tissue


title: WLT-HCV-70-NT [sample 71]

description:
sample 71
re-analysis of  GSM1707782


title: WLT-HCV-70-NT [sample 70]

description:
sample 70
re-analysis of  GSM1707781


title: WLT-HCV-70-T [sample 73]

description:
sample 73
re-analysis of  GSM1707776


title: day30_no-cntf_no-fbs_astro_diff_rep3

description:
cells at day 30 in human astrocytic cell diffentiation without cntf and fbs
count_matrix.txt
13C-070517_S39


title: WLT-HCV-75-NT [sample 74]

description:
sample 74
re-analysis of  GSM1707789


title: WLT-HCV-67-T [sample 69]

description:
sample 69
re-analysis of  GSM1707763


title: RNA-Seq KO TFH LCMV_2

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned using Tophat v2.1.0
Differentially expressed genes were determined by using Cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each genotype in CuffDiff output

organism: Mus musculus

source_name: CXCR5+PD-1+CD4+ T cells

growth_protocol: CD2AP F/F and CD4-Cre CD2AP F/F mice were infected with 2x10^6 PFU LCMV-c13 and CD4+ T cells were isolated via Dynabeads. ~300,000 CXCR5+PD-1+CD4+ T cells were sorted as TFH cells per biological replicate

extract_protocol:
RNA was prepared using Machery-Nagel Nucleospin XS kit according to manufacturers instructions
Libraries were prepared according to manufacturer's instructions using the SMARTER Total RNA Seq Kit-Pico Input

value: CD2AP KO

value: T cells

tag: cell markers

tag: passages

value: Day 22 LCMVc13

tag: strain

tag: infection status

value: infected with LCMV-c13


title: RNA-Seq KO TFH LCMV_1


title: RNA-Seq WT TFH LCMV_2

value: WT


title: WLT-HCV-67-T [sample 68]

description:
sample 68
re-analysis of  GSM1707762


title: RNA-Seq WT TFH LCMV_1


title: WLT-HCV-67-T [sample 67]

description:
sample 67
re-analysis of  GSM1707761


title: day30_no-cntf_no-fbs_astro_diff_rep2

description:
cells at day 30 in human astrocytic cell diffentiation without cntf and fbs
count_matrix.txt
13B-070517_S38


title: WLT-HCV-67-NT [sample 64]

description:
sample 64
re-analysis of  GSM1707774


title: WLT-HCV-67-T [sample 65]

description:
sample 65
re-analysis of  GSM1707760


title: day30_no-cntf_no-fbs_astro_diff_rep1

description:
cells at day 30 in human astrocytic cell diffentiation without cntf and fbs
count_matrix.txt
13A-070517_S37


title: day15_cntf_fbs_astro_diff_rep2

description:
cells at day 15 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
10B-070517_S29


title: day15_cntf_fbs_astro_diff_rep1

description:
cells at day 15 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
10A-070517_S28


title: WLT-HCV-67-NT [sample 63]

description:
sample 63
re-analysis of  GSM1707773


title: WLT-HCV-67-T [sample 66]

description:
sample 66
re-analysis of  GSM1707759


title: day15_cntf_astro_diff_rep3

description:
cells at day 15 in human astrocytic cell diffentiation with cntf
count_matrix.txt
9C-070517_S27


title: day15_cntf_astro_diff_rep2

description:
cells at day 15 in human astrocytic cell diffentiation with cntf
count_matrix.txt
9B-070517_S26


title: day15_cntf_astro_diff_rep1

description:
cells at day 15 in human astrocytic cell diffentiation with cntf
count_matrix.txt
9A-070517_S25


title: WLT-HCV-67-NT [sample 62]

description:
sample 62
re-analysis of  GSM1707772


title: day15_cntf_fbs_astro_diff_rep3

description:
cells at day 15 in human astrocytic cell diffentiation with cntf and fbs
count_matrix.txt
10C-070517_S30


title: day15_no-cntf_no-fbs_astro_diff_rep2

description:
cells at day 15 in human astrocytic cell diffentiation without cntf and fbs
count_matrix.txt
8B-070517_S23


title: day15_no-cntf_no-fbs_astro_diff_rep3

description:
cells at day 15 in human astrocytic cell diffentiation without cntf and fbs
count_matrix.txt
8C-070517_S24


title: WLT-HCV-43-T [sample 60]

description:
sample 60
re-analysis of  GSM1707756


title: WLT-HCV-43-T [sample 59]

description:
sample 59
re-analysis of  GSM1707755


title: day15_no-cntf_no-fbs_astro_diff_rep1

description:
cells at day 15 in human astrocytic cell diffentiation without cntf and fbs
count_matrix.txt
8A-070517_S22


title: C2C

city: Boulder

first: Christopher

last: Link

state: Colorado

address: 1725 Pleasant st

department: Integrative Physiology

institute: University of Colorado Boulder

description:
processed data file:
IPSC_rawCounts.txt
DESeq_IPSC_result.txt

data_processing:
The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina.
Analysis of library complexity and per-base sequence quality (i.e. q > 30) was assessed using FastQC (v0.11.2) software. Low quality bases (q < 10) were trimmed from the 3’ end of reads. Adaptor sequences and reads shorter than 40 nucleotides were removed using Trimmomatic.
Reads were aligned to GRCh37/hg19 using TopHat2 (v2.0.14, --b2-very-sensitive --keep- --nocoverage-search --library-type fr-firststrand). High quality mapped reads (MAPQ > 10) were filtered with SAMtools (v0.1.19).
Gene level counts were obtained using the GRCh37 Ensembl annotation with Rsubread (v 1.18.0, strandSpecific = 2, GTF.featureType = "exon", countMultiMappingReads = FALSE).
Differential expression of genes was determined using DESeq (v1.24.0) software with the options “per-condition”, “maximum”, and “local” for dispersion calculations. Significance was assigned to genes with an FDR less than 10%.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing raw gene counts as well as DESeq results.

molecule: polyA RNA

growth_protocol: IPSC lines were grown on Geltrex (Life Technologies) under feeder-free conditions in mTeSR1 medium according to the protocol of Stem Cell Technologies. iPSC colonies were passaged with dispase, and differentiating colonies were removed manually by scraping. Periodically, live iPSC colonies were stained with anti-Tra-1- 60 or Tra-1-81 conjugated to Dylight fluor 488 to confirm the stem cell character of the colonies. Likewise, fixed cells were shown 117 to express Oct4 by immunostaining. We used ABI/Thermo Fisher TaqMan Copy Number Assays (Hs01180853_cn; Hs02928366_cn; Hs01533676 corresponding to APP, DYRK1A and RCAN1 respectively) to evaluate the number of copies of Chr. 21 in the iPSC lines.

extract_protocol:
RNA for poly(A) RNA sequencing libraries was extracted from IPSC and neuronal cultures via TRIzol extraction. Genomic DNA was removed using TURBO DNase (Invitrogen).
Single-end sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Targeted removal of CHR 21 in IPSC using TKNEO transgene. Li et al., Trisomy correction in Down syndrome induced pluripotent stem cells. Cell Stem Cell 11, 615-619 (2012).

value: human induced pluripotent stem cells (iPSCs)

tag: ploidy

value: trisomic


title: 3D_4.6mg/ml_Mtrgl_20mpml_1wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 4.6 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
4B_S11

organism:
Homo sapiens
Mus musculus

source_name: HUES66 and mouse cortex

extract_protocol:
3D culture hydrogel was transferred to a 1.5 ml centrifuge tube and immersed in RNA lysis buffer, which was placed on dry ice for rapid freezing and then stored at -80 °C. 3D culture hydrogel was homogenized in lysis buffer. Total RNA isolation was performed using a kit following the manufacturer’s protocol.
RNA-Seq libraries were prepared following the Smart-seq2 protocol. 1 ng of total RNA was used. cDNA was synthesized and then used in each NexteraXT (Illumina) reaction.


title: WLT-HCV-43-T [sample 61]

description:
sample 61
re-analysis of  GSM1707757

value: male


title: day5_cntf_astro_diff_rep3

description:
cells at day 5 in human astrocytic cell diffentiation with cntf
count_matrix.txt
7C-070517_S21


title: WLT-HCV-43-NT [sample 56]

description: sample 56


title: WLT-HCV-43-T [sample 58]

description:
sample 58
re-analysis of  GSM1707754


title: WLT-HCV-43-NT [sample 55]

description:
sample 55
re-analysis of  GSM1707758


title: WLT-HCV-40-T [sample 54]

description:
sample 54
re-analysis of  GSM1707739


title: day5_cntf_astro_diff_rep2

description:
cells at day 5 in human astrocytic cell diffentiation with cntf
count_matrix.txt
7B-070517_S20


title: 2012-01-12_unstim_3_(HuGene-1_0-st-v1)

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: mRNA expression profiles from cell culture

hyb_protocol: according to the manufacturers guidelines (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using AGCC (Affymetrix default settings) and normalized using RMA

label: biotin

source_name: T-Rex HeLa unstimulated, shRNA ANRIL silenced

growth_protocol: Cells were cultivated at 37°C and 5% CO2 in appropriate growth medium (EMEM, 10% FCS, 2mM Glutamine, 1% Penicillin-Streptomycin) with Blasticidin (5 µg/ml) and Zeocin (200 µg/ml).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen).

treatment_protocol: Monoclonal cell lines were induced with tetracycline (1 µg/ml) for 48h and for 96h.

tag: sample type

value: Cell culture


title: 2012-01-12_unstim_4_(HuGene-1_0-st-v1)

label_protocol: according to the manufacturers guidelines (Affymetrix)


title: WLT-HCV-40-T [sample 52]

description:
sample 52
re-analysis of  GSM1707737


title: day5_cntf_astro_diff_rep1

description:
cells at day 5 in human astrocytic cell diffentiation with cntf
count_matrix.txt
7A-070517_S19


title: 2012-01-12_unstim_1_(HuGene-1_0-st-v1)


title: 2012-01-12_96hstim_4_(HuGene-1_0-st-v1)

source_name: T-Rex HeLa stimulated with Tetracycline, shRNA ANRIL silenced for 96h


title: day5_no-cntf_astro_diff_rep3

description:
cells at day 5 in human astrocytic cell diffentiation without cntf
count_matrix.txt
6C-070517_S18


title: WLT-HCV-40-T [sample 51]

description:
sample 51
re-analysis of  GSM1707731


title: 2012-01-12_unstim_5_(HuGene-1_0-st-v1)


title: 2012-01-12_96hstim_1_(HuGene-1_0-st-v1)


title: 2012-01-12_unstim_2_(HuGene-1_0-st-v1)


title: iN_from_5wk_3D_iN_astrocytic-cell_100ul_7.36mg/ml_Mtrgl_20mpml_rep3

description:
human neuronal cells sorted from their 3D co-culture with differentiated human astrocytic cells in 100 microliter 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
21C-070517_S65


title: 2012-01-12_96hstim_2_(HuGene-1_0-st-v1)


title: day5_no-cntf_astro_diff_rep2

description:
cells at day 5 in human astrocytic cell diffentiation without cntf
count_matrix.txt
6B-070517_S17


title: WLT-HCV-40-T [sample 50]

description:
sample 50
re-analysis of  GSM1707736


title: 2012-01-12_96hstim_3_(HuGene-1_0-st-v1)


title: 2012-01-12_48hstim_5_(HuGene-1_0-st-v1)

source_name: T-Rex HeLa stimulated with Tetracycline, shRNA ANRIL silenced for 48h


title: 2012-01-12_48hstim_4_(HuGene-1_0-st-v1)


title: 2012-01-12_48hstim_3_(HuGene-1_0-st-v1)


title: day5_no-cntf_astro_diff_rep1

description:
cells at day 5 in human astrocytic cell diffentiation without cntf
count_matrix.txt
6A-070517_S16


title: WLT-HCV-40-T [sample 48]

description:
sample 48
re-analysis of  GSM1707734


title: day2_astro_diff_rep3

description:
cells at day 2 in human astrocytic cell diffentiation
count_matrix.txt
5C-070517_S15


title: day2_astro_diff_rep2

description:
cells at day 2 in human astrocytic cell diffentiation
count_matrix.txt
5B-070517_S14


title: 2012-01-12_48hstim_2_(HuGene-1_0-st-v1)


title: 2012-01-12_48hstim_1_(HuGene-1_0-st-v1)


title: WLT-HCV-40-T [sample 47]

description:
sample 47
re-analysis of  GSM1707733


title: day2_astro_diff_rep1

description:
cells at day 2 in human astrocytic cell diffentiation
count_matrix.txt
5A-070517_S13


title: WLT-HCV-40-T [sample 49]

description:
sample 49
re-analysis of  GSM1707735


title: mCherry tumor 2

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description:
Sample 4
nCherry tumor in mice replicate 2

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using R/Bioconductor package limma

source_name: mCherry tumor

label_protocol: Standard Illumina hybridization protocolHoxA5 is the experimental group and the mCherry is the control group.

growth_protocol: All of the animal experiments were conducted using protocols approved by the Institutional Animal Care and Use Committees of Fred Hutchinson Cancer Research Center, protocol 50842. Ntva-Ink4a/Arf+/- and Ntva-Ink4a/Arf-/- mice were used to generate mouse gliomas. The genetic backgrounds of tva mice are FVB/N, C57BL6, BALB/C, and 129. To generate mCherry and HoxA5-expressing mouse gliomas, we used the RCAS/tva system. Briefly, DF1 cells were maintained with 10% fetal bovine serum (FBS) in Dulbecco's Modified Eagle Medium (DMEM). Chicken fibroblasts were transfected with each RCAS viral plasmid using Fugene 6 Transfection reagent (Roche) following the manufacturer’s protocol. Then, PDGFb-expressing DF1 cells were mixed with either mCherry- or HoxA5-expressing DF1 cells. This mixture of DF1 cells was injected to Ntva-Ink4a/Arf+/- and Ntva- Ink4a/Arf-/- mice. Adult mice anesthetized with isoflurane were positioned in a stereotactic device (Stoelting, Wood Dale, IL). RCAS transfected DF1 cells were injected using a 30-gauge needle inserted into the right frontal cortex (coordinates: anterior to bregma 1.5 mm, lateral 0.5 mm, and a depth 1.5 mm). Then, mice were monitored daily until they developed signs of illness, such as lethargy, poor grooming, weight loss, dehydration, macrocephaly, seizure, jumping and paralysis.

extract_protocol: Total RNA was extracted from tumor tissues using RNeasy Mini kit (QIAGEN) using the manufacturer’s protocol.

treatment_protocol: No treatment

tag: tumor type

value: mCherry

value: control


title: 3D_7.36mg/ml_Mtrgl_10mpml_5wk_iN_rep3

description:
human neuronal cells cultured in 3D 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
7C_S21

tag: strain/cell type

value: human neuronal cells


title: WLT-HCV-40-T [sample 45]

description:
sample 45
re-analysis of  GSM1707732


title: mCherry tumor 4

description:
Sample 6
nCherry tumor in mice replicate 4

hyb_protocol: Standard Illumina hybridization protocol


title: CS patient cell line (GM739SV, CS1AN) replicate 2

source_name: SV40 virus transformed cell line, GM739(SV) (CSB-deficient CS patient cell line: CS2AN) derivative

value: CS patient cell line (GM739SV, CS1AN)

value: skin

value: fibroblast-like

value: Group B Cockayne syndrome


title: mCherry tumor 1

description:
Sample 3
nCherry tumor in mice replicate 1


title: HoxA5 tumor 2

description:
Sample 2
HoxA5 tumor in mice replicate 2

source_name: HoxA5 tumor

value: experimental


title: HoxA5 tumor 1

description:
Sample 1
HoxA5 tumor in mice replicate 1


title: mCherry tumor 3

description:
Sample 5
nCherry tumor in mice replicate 3


title: 27 CD8M IL7R high

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description:
6071838132_E
SAMPLE 6
normal EM CD8+ T cells

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: RNA from IL-7Ra low EM CD8+ T cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was prepared using the RNeasy mini kit (Qiagen), and assessed RNA integrity using Bioanalyzer 2100 (Agilent). The RNA integrity number (- RINs) was close to 10 for all samples.

tag: sample number

value: normal EM CD8+ T cells

tag: il-7ra level

value: high


title: WLT-HCV-40-NT [sample 44]

description:
sample 44
re-analysis of  GSM1707752

value: whole liver tissue

value: HCV-HCC non tumor tissue


title: WLT-HCV-40-T [sample 46]

description:
sample 46
re-analysis of  GSM1707730

value: HCV-HCC tumor tissue


title: K5 CD8M IL7R high

description:
6071838124_L
SAMPLE 4
normal EM CD8+ T cells


title: WLT-HCV-40-NT [sample 43]

description:
sample 43
re-analysis of  GSM1707751


title: WLT-HCV-40-NT [sample 42]

description:
sample 42
re-analysis of  GSM1707750


title: K5 CD8M IL7R low

description:
6071838124_J
SAMPLE 3
normal EM CD8+ T cells

value: low


title: 3D_7.36mg/ml_Mtrgl_10mpml_1wk_iN_rep3

description:
human neuronal cells cultured in 3D 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
5C_S15

tag: culture condition

tag: age

tag: genotype

value: wild type


title: 3D_7.36mg/ml_Mtrgl_10mpml_5wk_iN_rep2

description:
human neuronal cells cultured in 3D 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
7B_S20


title: 3D_7.36mg/ml_Mtrgl_10mpml_1wk_iN_rep2

description:
human neuronal cells cultured in 3D 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
5B_S14


title: 3D_7.36mg/ml_Mtrgl_10mpml_1wk_iN_rep1

description:
human neuronal cells cultured in 3D 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
5A_S13


title: 3D_7.36mg/ml_Mtrgl_10mpml_5wk_iN_rep1

description:
human neuronal cells cultured in 3D 7.36 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
7A_S19


title: 3D_4.6mg/ml_Mtrgl_10mpml_5wk_iN_rep3

description:
human neuronal cells cultured in 3D 4.6 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
9C_S27


title: 3D_4.6mg/ml_Mtrgl_10mpml_5wk_iN_rep2

description:
human neuronal cells cultured in 3D 4.6 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
9B_S26


title: WLT-HCV-40-NT [sample 40]

description:
sample 40
re-analysis of  GSM1707748

value: male

tag: tissue


title: 3D_4.6mg/ml_Mtrgl_10mpml_5wk_iN_rep1

description:
human neuronal cells cultured in 3D 4.6 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
9A_S25


title: 3D_4.6mg/ml_Mtrgl_10mpml_1wk_iN_rep3

description:
human neuronal cells cultured in 3D 4.6 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
3C_S9


title: WLT-HCV-40-NT [sample 39]

description:
sample 39
re-analysis of  GSM1707747

tag: disease state


title: WLT-HCV-40-NT [sample 41]

description:
sample 41
re-analysis of  GSM1707749

tag: patient code


title: 27 CD8M IL7R low

description:
6071838132_C
SAMPLE 5
normal EM CD8+ T cells

source_name: RNA from IL-7Ra high EM CD8+ T cells

tag: cell type


title: WLT-HCV-40-NT [sample 37]

description:
sample 37
re-analysis of  GSM1707745

tag: Sex


title: 30 CD8M IL7R low

description:
6071838124_D
SAMPLE 1
normal EM CD8+ T cells


title: 2D_5wk_iN_rep3

description:
human neuronal cells cultured on 2D
count_matrix.txt
14C_S42


title: 3D_4.6mg/ml_Mtrgl_10mpml_1wk_iN_rep2

description:
human neuronal cells cultured in 3D 4.6 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
3B_S8


title: WLT-HCV-40-NT [sample 38]

description:
sample 38
re-analysis of  GSM1707746


title: WLT-HCV-233-T [sample 36]

description:
sample 36
re-analysis of  GSM1707820


title: WLT-HCV-233-T [sample 34]

description:
sample 34
re-analysis of  GSM1707818


title: WLT-HCV-233-T [sample 35]

description:
sample 35
re-analysis of  GSM1707819


title: 2D_5wk_iN_rep2

description:
human neuronal cells cultured on 2D
count_matrix.txt
14B_S41


title: 3D_4.6mg/ml_Mtrgl_10mpml_1wk_iN_rep1

description:
human neuronal cells cultured in 3D 4.6 mg/ml Matrigel at 10 million cells per ml.
count_matrix.txt
3A_S7


title: WLT-HCV-233-T [sample 33]

description:
sample 33
re-analysis of  GSM1707817


title: 2D_1wk_iN_rep3

description:
human neuronal cells cultured on 2D
count_matrix.txt
1C_S3


title: WLT-HCV-233-NT [sample 30]

description:
sample 30
re-analysis of  GSM1707831


title: 2D_1wk_iN_rep1

description:
human neuronal cells cultured on 2D
count_matrix.txt
1A_S1


title: WLT-HCV-233-T [sample 32]

description:
sample 32
re-analysis of  GSM1707816


title: 2D_5wk_iN_rep1

description:
human neuronal cells cultured on 2D
count_matrix.txt
14A_S40


title: day3_iN_rep2

description:
induced human neuronal cells at day-3 before 2D or 3D culture
count_matrix.txt
20B061516_S62

value: before 2D or 3D culture


title: WLT-HCV-43-T [sample 57]

description:
sample 57
re-analysis of  GSM1707753


title: day3_iN_rep1

description:
induced human neuronal cells at day-3 before 2D or 3D culture
count_matrix.txt
20A061516_S61


title: WLT-HCV-233-NT [sample 29]

description:
sample 29
re-analysis of  GSM1707830


title: WLT-HCV-233-NT [sample 31]

description:
sample 31
re-analysis of  GSM1707832


title: WLT-HCV-233-NT [sample 28]

description:
sample 28
re-analysis of  GSM1707829


title: CS_BO_FR_12_C

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: Cabernet Sauvignon; Full-ripening; Bolgheri; 2012; Replicate C

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Grapevine berry samples were collected from 7/10-year-old vineyards located in Bolgheri - wine cellar Podere Guado al Melo (Tuscany coast), Montalcino - wine cellar Banfi Srl (Tuscany Apennines) and Riccione - wine cellar Valbruna Soc. Coop. Agricola (Romagna coast) during the 2011-2012 growing seasons at the same time of day (~ 11:00 am). Per each experimental site, berries of two different cultivars, Cabernet Sauvignon and Sangiovese, have been sampled. To avoid major environmental differences, the berry sampling was performed, in each farm, on adjacent vineyards for Cabernet Sauvignon and Sangiovese (Fig. 1a). The most relevant features per each vineyard are reported in Supplementary Table 1.

extract_protocol: Total RNA was isolated from approximately 400 mg of berry pericarps using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich), with modifications as described in Dal Santo et al. (Jove,2016).

value: berry pericarp

tag: cultivar

value: Cabernet Sauvignon

tag: developmental stage

value: Full-ripening, FR, berries ripe for harvest, BBCH 89

tag: area

value: Bolgheri, Tuscany coast, Italy

tag: year


title: WLT-HCV-227-T [sample 26]

description: sample 26


title: CS_RI_FR_12_C

source_name: Cabernet Sauvignon; Full-ripening; Riccione; 2012; Replicate C

value: Riccione, Romagna coast, Italy


title: WLT-HCV-227-T [sample 23]

description: sample 23


title: WLT-HCV-40-T [sample 53]

description:
sample 53
re-analysis of  GSM1707738


title: 2012-01-12_96hstim_5_(HuGene-1_0-st-v1)

description: mRNA expression profiles from cell culture

tag: sample type

value: Cell culture


title: CS_BO_FR_12_A

source_name: Cabernet Sauvignon; Full-ripening; Bolgheri; 2012; Replicate A


title: WLT-HCV-227-T [sample 25]

description: sample 25


title: WLT-HCV-227-NT [sample 20]

description: sample 20


title: WLT-HCV-227-NT [sample 22]

description: sample 22


title: CS_BO_FR_12_B

source_name: Cabernet Sauvignon; Full-ripening; Bolgheri; 2012; Replicate B


title: WLT-HCV-227-T [sample 24]

description: sample 24


title: CS_RI_FR_12_A

source_name: Cabernet Sauvignon; Full-ripening; Riccione; 2012; Replicate A


title: SG_RI_FR_12_C

source_name: Sangiovese; Full-ripening; Riccione; 2012; Replicate C

value: Sangiovese


title: CS_MO_FR_12_C

source_name: Cabernet Sauvignon; Full-ripening; Montalcino; 2012; Replicate C

value: Montalcino, Tuscany Apennines, Italy


title: SG_RI_FR_12_A

source_name: Sangiovese; Full-ripening; Riccione; 2012; Replicate A


title: WLT-HCV-227-NT [sample 21]

description: sample 21

source_name: tissue specimen obtained from explanted liver of HCV-HCC - non tumor region


title: SG_RI_FR_12_B

source_name: Sangiovese; Full-ripening; Riccione; 2012; Replicate B


title: CS_MO_FR_12_A

source_name: Sangiovese; Full-ripening; Montalcino; 2012; Replicate A


title: CS_RI_FR_12_B

source_name: Cabernet Sauvignon; Full-ripening; Riccione; 2012; Replicate B


title: SG_MO_FR_12_C

source_name: Sangiovese; Full-ripening; Montalcino; 2012; Replicate C


title: 2D_1wk_iN_rep2

description:
human neuronal cells cultured on 2D
count_matrix.txt
1B_S2

value: human neuronal cells


title: CS_MO_FR_12_B

source_name: Cabernet Sauvignon; Full-ripening; Montalcino; 2012; Replicate B


title: WLT-HCV-227-NT [sample 19]

description: sample 19


title: WLT-HCV-227-NT [sample 18]

description: sample 18


title: SG_MO_FR_12_B

source_name: Sangiovese; Full-ripening; Montalcino; 2012; Replicate B


title: SG_BO_FR_12_C

source_name: Sangiovese; Full-ripening; Bolgheri; 2012; Replicate C


title: WLT-HCV-227-T [sample 27]

description: sample 27

source_name: tissue specimen obtained from explanted liver of HCV-HCC - tumor region


title: SG_MO_FR_12_A


title: SG_BO_FR_12_A

source_name: Sangiovese; Full-ripening; Bolgheri; 2012; Replicate A


title: WLT-HCV-21-T [sample 17]

description: sample 17


title: NPC1-KO_PBS_3

city: bethesda

first: antony

middle: cyril

last: cougnoux

state: md

address: BG 10-CRC RM 1-3288 10 CENTER DR

department: nichd

institute: nih

data_processing:
RNA-STAR 2.5.1 to
Quantitation by subread featureCounts against RefSeq genes
Genome_build: mm10
Supplementary_files_format_and_content: gzipped fastqs

source_name: microglia

extract_protocol:
FACS sorted cells were spun and stored in Trizol (ThermoScientific) prior isolation using RNAesasy Micro kit (Quiagen)
Clontech RNA-Seq Pico kit

value: FACS isolated microglia Cx3cr1+CD45+

tag: strain

value: BalbC

tag: genotype/variation

value: KO

tag: treatment

value: PBS


title: SG_BO_FR_12_B

source_name: Sangiovese; Full-ripening; Bolgheri; 2012; Replicate B


title: WLT-HCV-21-NT [sample 16]

description: sample 16

value: whole liver tissue

value: HCV-HCC non tumor tissue


title: CS_RI_MR_12_C

source_name: Cabernet Sauvignon; Mid-ripening; Riccione; 2012; Replicate C

value: Mid-ripening, MR, berries developing color, BBCH 83


title: NPC1-KO_PBS_1


title: WLT-HCV-173-T [sample 12]

description:
sample 12
re-analysis of  GSM1707807

value: male

value: HCV-HCC tumor tissue


title: WLT-HCV-173-T [sample 11]

description:
sample 11
re-analysis of  GSM1707806


title: CS_BO_MR_12_A

source_name: Cabernet Sauvignon; Mid-ripening; Bolgheri; 2012; Replicate A

value: berry pericarp

value: Cabernet Sauvignon


title: WLT-HCV-173-T [sample 13]

description:
sample 13
re-analysis of  GSM1707808


title: SG_RI_MR_12_A

source_name: Sangiovese; Mid-ripening; Riccione; 2012; Replicate A


title: CS_BO_MR_12_B

source_name: Cabernet Sauvignon; Mid-ripening; Bolgheri; 2012; Replicate B

value: Bolgheri, Tuscany coast, Italy


title: CS_BO_MR_12_C

source_name: Cabernet Sauvignon; Mid-ripening; Bolgheri; 2012; Replicate C


title: CS_RI_MR_12_A

source_name: Cabernet Sauvignon; Mid-ripening; Riccione; 2012; Replicate A

value: Riccione, Romagna coast, Italy


title: WLT-HCV-173-T [sample 15]

description:
sample 15
re-analysis of  GSM1707805


title: CS_RI_MR_12_B

source_name: Cabernet Sauvignon; Mid-ripening; Riccione; 2012; Replicate B


title: SG_MO_MR_12_C

source_name: Sangiovese; Mid-ripening; Montalcino; 2012; Replicate C


title: NPC1-WT_PBS_3

value: wild type


title: CS_MO_MR_12_C

source_name: Cabernet Sauvignon; Mid-ripening; Montalcino; 2012; Replicate C


title: WLT-HCV-173-T [sample 14]

description:
sample 14
re-analysis of  GSM1707809


title: CS_MO_MR_12_B

source_name: Cabernet Sauvignon; Mid-ripening; Montalcino; 2012; Replicate B


title: CS_MO_MR_12_A

source_name: Sangiovese; Mid-ripening; Montalcino; 2012; Replicate A

value: Sangiovese


title: SG_RI_MR_12_C

source_name: Sangiovese; Mid-ripening; Riccione; 2012; Replicate C


title: NPC1-WT_PBS_2


title: WLT-HCV-14-T [sample 10]

description: sample 10


title: SG_MO_MR_12_A

value: Montalcino, Tuscany Apennines, Italy


title: SG_RI_MR_12_B

source_name: Sangiovese; Mid-ripening; Riccione; 2012; Replicate B


title: NPC1-WT_PBS_1


title: NPC1-WT_HPBCD_2

value: HPBCD


title: NPC1-WT_HPBCD_3

value: FACS isolated microglia Cx3cr1+CD45+


title: SG_BO_MR_12_B

source_name: Sangiovese; Mid-ripening; Bolgheri; 2012; Replicate B


title: WLT-HCV-14-NT [sample 9]

description: sample 9

source_name: tissue specimen obtained from explanted liver of HCV-HCC - non tumor region


title: NPC1-WT_HPBCD_1

source_name: microglia

value: BalbC


title: NPC1-KO_HPBCD_3

value: KO


title: SG_BO_MR_12_C

source_name: Sangiovese; Mid-ripening; Bolgheri; 2012; Replicate C


title: CS_BO_PV_12_C

source_name: Cabernet Sauvignon; Pre-veraison; Bolgheri; 2012; Replicate C

value: Pre-veraison, PV, majority of berries touching, BBCH 79


title: SG_BO_MR_12_A

source_name: Sangiovese; Mid-ripening; Bolgheri; 2012; Replicate A


title: NPC1-KO_HPBCD_2


title: CS_BO_PV_12_A

source_name: Cabernet Sauvignon; Pre-veraison; Bolgheri; 2012; Replicate A


title: WLT-HCV-127-T [sample 8]

description:
sample 8
re-analysis of  GSM1707795

source_name: tissue specimen obtained from explanted liver of HCV-HCC - tumor region

value: whole liver tissue


title: WLT-HCV-127-T [sample 5]

description:
sample 5
re-analysis of  GSM1707792


title: WLT-HCV-127-T [sample 4]

description:
sample 4
re-analysis of  GSM1707791


title: CS_RI_PV_12_A

source_name: Cabernet Sauvignon; Pre-veraison; Riccione; 2012; Replicate A


title: WLT-HCV-127-T [sample 6]

description:
sample 6
re-analysis of  GSM1707793


title: CS_RI_PV_12_C

source_name: Cabernet Sauvignon; Pre-veraison; Riccione; 2012; Replicate C


title: WLT-HCV-127-NT [sample 3]

description:
sample 3
re-analysis of  GSM1707804

value: HCV-HCC non tumor tissue


title: CS_RI_PV_12_B

source_name: Cabernet Sauvignon; Pre-veraison; Riccione; 2012; Replicate B


title: SG_RI_PV_12_B

source_name: Sangiovese; Pre-veraison; Riccione; 2012; Replicate B


title: 30 CD8M IL7R high

description:
6071838124_F
SAMPLE 2
normal EM CD8+ T cells

source_name: RNA from IL-7Ra high EM CD8+ T cells

tag: sample number

value: normal EM CD8+ T cells

tag: il-7ra level

value: high


title: NPC1-KO_5


title: WLT-HCV-127-T [sample 7]

description:
sample 7
re-analysis of  GSM1707794

value: male

value: HCV-HCC tumor tissue


title: CS_BO_PV_12_B

source_name: Cabernet Sauvignon; Pre-veraison; Bolgheri; 2012; Replicate B

value: berry pericarp

value: Cabernet Sauvignon


title: SG_RI_PV_12_C

source_name: Sangiovese; Pre-veraison; Riccione; 2012; Replicate C

value: Riccione, Romagna coast, Italy


title: CS_MO_PV_12_B

source_name: Cabernet Sauvignon; Pre-veraison; Montalcino; 2012; Replicate B


title: CS_MO_PV_12_A

source_name: Sangiovese; Pre-veraison; Montalcino; 2012; Replicate A


title: CS_MO_PV_12_C

source_name: Cabernet Sauvignon; Pre-veraison; Montalcino; 2012; Replicate C


title: SG_RI_PV_12_A

source_name: Sangiovese; Pre-veraison; Riccione; 2012; Replicate A


title: NPC1-KO_4

source_name: microglia


title: NPC1-KO_HPBCD_1


title: NPC1-KO_3


title: NPC1-KO_2


title: NPC1-KO_1


title: SG_MO_PV_12_B

source_name: Sangiovese; Pre-veraison; Montalcino; 2012; Replicate B


title: SG_MO_PV_12_C

source_name: Sangiovese; Pre-veraison; Montalcino; 2012; Replicate C


title: NPC1-WT_5

value: wild type


title: SG_BO_PV_12_C

source_name: Sangiovese; Pre-veraison; Bolgheri; 2012; Replicate C

value: Sangiovese

value: Bolgheri, Tuscany coast, Italy


title: CS_BO_PS_12_C

source_name: Cabernet Sauvignon; Pea Size; Bolgheri; 2012; Replicate C

value: Pea Size, PS, 5 mm of diameter berries, BBCH 75


title: SG_BO_PV_12_B

source_name: Sangiovese; Pre-veraison; Bolgheri; 2012; Replicate B


title: LCM-HDV-HCC-5-NMH, sample 74

source_name: specimen obtained from laser capture microdissected non-malignant hepatocytes of HDV-HCC

value: laser capture microdissected cells - non-malignant hepatocytes of HDV-HCC

value: HDV-HCC non tumor cells


title: WLT-HCV-127-NT [sample 2]

description:
sample 2
re-analysis of  GSM1707803

source_name: tissue specimen obtained from explanted liver of HCV-HCC - non tumor region


title: LCM-HDV-HCC-27-NMH, sample 73


title: SG_MO_PV_12_A

value: Montalcino, Tuscany Apennines, Italy


title: CS_BO_PS_12_B

source_name: Cabernet Sauvignon; Pea Size; Bolgheri; 2012; Replicate B


title: CS_RI_PS_12_C

source_name: Cabernet Sauvignon; Pea Size; Riccione; 2012; Replicate C


title: NPC1-WT_4

value: FACS isolated microglia Cx3cr1+CD45+

value: BalbC


title: SG_BO_PV_12_A

source_name: Sangiovese; Pre-veraison; Bolgheri; 2012; Replicate A

value: Pre-veraison, PV, majority of berries touching, BBCH 79


title: LCM-HDV-HCC-129-NMH, sample 71


title: CS_BO_PS_12_A

source_name: Cabernet Sauvignon; Pea Size; Bolgheri; 2012; Replicate A


title: CS_MO_PS_12_C

source_name: Cabernet Sauvignon; Pea Size; Montalcino; 2012; Replicate C


title: CS_MO_PS_12_B

source_name: Cabernet Sauvignon; Pea Size; Montalcino; 2012; Replicate B


title: LCM-HDV-HCC-19-NMH, sample 72


title: CS_RI_PS_12_B

source_name: Cabernet Sauvignon; Pea Size; Riccione; 2012; Replicate B


title: LCM-HDV-HCC-104-NMH, sample 70


title: CS_MO_PS_12_A

source_name: Cabernet Sauvignon; Pea Size; Montalcino; 2012; Replicate A


title: LCM-HDV-HCC-5-MH, sample 69

source_name: specimen obtained from laser capture microdissected malignant hepatocytes of HDV-HCC

value: laser capture microdissected cells - malignant hepatocytes of HDV-HCC

value: HDV-HCC tumor cells


title: CS_RI_PS_12_A

source_name: Cabernet Sauvignon; Pea Size; Riccione; 2012; Replicate A


title: LCM-HDV-HCC-27-MH, sample 68


title: SG_RI_PS_12_C

source_name: Sangiovese; Pea Size; Riccione; 2012; Replicate C


title: NPC1-WT_2

source_name: microglia


title: SG_RI_PS_12_B

source_name: Sangiovese; Pea Size; Riccione; 2012; Replicate B


title: NPC1-WT_1


title: NPC1-KO_PBS_2

value: KO

value: PBS


title: NPC1-WT_3


title: SG_RI_PS_12_A

source_name: Sangiovese; Pea Size; Riccione; 2012; Replicate A

value: berry pericarp


title: SG_MO_PS_12_B

source_name: Sangiovese; Pea Size; Montalcino; 2012; Replicate B


title: LCM-HDV-HCC-19-MH, sample 67


title: LCM-HDV-HCC-129-MH, sample 66


title: SG_BO_PS_12_B

source_name: Sangiovese; Pea Size; Bolgheri; 2012; Replicate B


title: WLT-HDV-177-CIRRHOSISwithoutHCC, sample 64

source_name: tissue specimen obtained from explanted liver of HDV-cirrhosis

value: whole liver

value: HDV-cirrhosis without HCC tissue


title: SG_MO_PS_12_C

source_name: Sangiovese; Pea Size; Montalcino; 2012; Replicate C


title: SG_RI_FR_11_C

source_name: Sangiovese; Full-ripening; Riccione; 2011; Replicate C

value: Full-ripening, FR, berries ripe for harvest, BBCH 89

value: Riccione, Romagna coast, Italy


title: WLT-HDV-177-CIRRHOSISwithoutHCC, sample 63


title: SG_BO_PS_12_C

source_name: Sangiovese; Pea Size; Bolgheri; 2012; Replicate C

value: Sangiovese

value: Bolgheri, Tuscany coast, Italy


title: SG_BO_PS_12_A

source_name: Sangiovese; Pea Size; Bolgheri; 2012; Replicate A

value: Pea Size, PS, 5 mm of diameter berries, BBCH 75


title: SG_MO_PS_12_A

source_name: Sangiovese; Pea Size; Montalcino; 2012; Replicate A


title: SG_RI_MR_11_C

source_name: Sangiovese; Mid-ripening; Riccione; 2011; Replicate C

value: Mid-ripening, MR, berries developing color, BBCH 83


title: SG_RI_FR_11_B

source_name: Sangiovese; Full-ripening; Riccione; 2011; Replicate B


title: SG_RI_FR_11_A

source_name: Sangiovese; Full-ripening; Riccione; 2011; Replicate A


title: SG_RI_MR_11_A

source_name: Sangiovese; Mid-ripening; Riccione; 2011; Replicate A


title: SG_RI_MR_11_B

source_name: Sangiovese; Mid-ripening; Riccione; 2011; Replicate B


title: LCM-HDV-HCC-104-MH, sample 65

source_name: specimen obtained from laser capture microdissected malignant hepatocytes of HDV-HCC


title: SG_RI_PV_11_C

source_name: Sangiovese; Pre-veraison; Riccione; 2011; Replicate C


title: WLT-HDV-177-CIRRHOSISwithoutHCC, sample 62


title: SG_RI_PS_11_B

source_name: Sangiovese; Pea Size; Riccione; 2011; Replicate B


title: WLT-HDV-152-CIRRHOSISwithoutHCC, sample 60


title: SG_RI_PV_11_B

source_name: Sangiovese; Pre-veraison; Riccione; 2011; Replicate B


title: SG_RI_PS_11_C

source_name: Sangiovese; Pea Size; Riccione; 2011; Replicate C


title: SG_RI_PV_11_A

source_name: Sangiovese; Pre-veraison; Riccione; 2011; Replicate A


title: WLT-HDV-177-CIRRHOSISwithoutHCC, sample 61

source_name: tissue specimen obtained from explanted liver of HDV-cirrhosis


title: WLT-HDV-152-CIRRHOSISwithoutHCC, sample 59


title: SG_RI_PS_11_A

source_name: Sangiovese; Pea Size; Riccione; 2011; Replicate A


title: CS_RI_FR_11_C

source_name: Cabernet Sauvignon; Full-ripening; Riccione; 2011; Replicate C

value: Cabernet Sauvignon


title: SG_MO_MR_12_B

source_name: Sangiovese; Mid-ripening; Montalcino; 2012; Replicate B

value: Montalcino, Tuscany Apennines, Italy


title: WLT-HDV-152-CIRRHOSISwithoutHCC, sample 58


title: WLT-HDV-152-CIRRHOSISwithoutHCC, sample 57


title: CS_RI_MR_11_C

source_name: Cabernet Sauvignon; Mid-ripening; Riccione; 2011; Replicate C


title: WLT-HDV-152-CIRRHOSISwithoutHCC, sample 55


title: CS_RI_MR_11_B

source_name: Cabernet Sauvignon; Mid-ripening; Riccione; 2011; Replicate B


title: CS_RI_PV_11_B

source_name: Cabernet Sauvignon; Pre-veraison; Riccione; 2011; Replicate B


title: CS_RI_FR_11_A

source_name: Cabernet Sauvignon; Full-ripening; Riccione; 2011; Replicate A


title: CS_RI_FR_11_B

source_name: Cabernet Sauvignon; Full-ripening; Riccione; 2011; Replicate B


title: WLT-HDV-152-CIRRHOSISwithoutHCC, sample 56


title: CS_RI_PV_11_C

source_name: Cabernet Sauvignon; Pre-veraison; Riccione; 2011; Replicate C


title: WLT-HDV-152-CIRRHOSISwithoutHCC, sample 54


title: WLT-HDV-134-CIRRHOSISwithoutHCC, sample 52


title: CS_RI_PS_11_C

source_name: Cabernet Sauvignon; Pea Size; Riccione; 2011; Replicate C


title: SG_BO_FR_11_B

source_name: Sangiovese; Full-ripening; Bolgheri; 2011; Replicate B


title: CS_RI_PS_11_A

source_name: Cabernet Sauvignon; Pea Size; Riccione; 2011; Replicate A


title: CS_RI_PV_11_A

source_name: Cabernet Sauvignon; Pre-veraison; Riccione; 2011; Replicate A


title: WLT-HDV-152-CIRRHOSISwithoutHCC, sample 53


title: SG_BO_FR_11_C

source_name: Sangiovese; Full-ripening; Bolgheri; 2011; Replicate C


title: CS_RI_MR_11_A

source_name: Cabernet Sauvignon; Mid-ripening; Riccione; 2011; Replicate A


title: SG_BO_MR_11_C

source_name: Sangiovese; Mid-ripening; Bolgheri; 2011; Replicate C


title: SG_BO_FR_11_A

source_name: Sangiovese; Full-ripening; Bolgheri; 2011; Replicate A


title: WLT-HDV-134-CIRRHOSISwithoutHCC, sample 50

source_name: tissue specimen obtained from explanted liver of HDV-cirrhosis


title: SG_BO_MR_11_B

source_name: Sangiovese; Mid-ripening; Bolgheri; 2011; Replicate B


title: CS_RI_PS_11_B

source_name: Cabernet Sauvignon; Pea Size; Riccione; 2011; Replicate B


title: WLT-HCV-127-NT [sample 1]

description:
sample 1
re-analysis of  GSM1707802

source_name: tissue specimen obtained from explanted liver of HCV-HCC - non tumor region

value: male

value: whole liver tissue

value: HCV-HCC non tumor tissue


title: WLT-HDV-113-CIRRHOSISwithoutHCC, sample 48


title: WLT-HDV-134-CIRRHOSISwithoutHCC, sample 49


title: SG_BO_PV_11_B

source_name: Sangiovese; Pre-veraison; Bolgheri; 2011; Replicate B

value: Pre-veraison, PV, majority of berries touching, BBCH 79


title: SG_BO_MR_11_A

source_name: Sangiovese; Mid-ripening; Bolgheri; 2011; Replicate A


title: SG_BO_PV_11_A

source_name: Sangiovese; Pre-veraison; Bolgheri; 2011; Replicate A


title: WLT-HDV-134-CIRRHOSISwithoutHCC, sample 51


title: SG_BO_PS_11_A

source_name: Sangiovese; Pea Size; Bolgheri; 2011; Replicate A


title: WLT-HDV-113-CIRRHOSISwithoutHCC, sample 47


title: SG_BO_PV_11_C

source_name: Sangiovese; Pre-veraison; Bolgheri; 2011; Replicate C


title: WLT-HDV-90-CIRRHOSISwithoutHCC, sample 42


title: CS_BO_MR_11_A

source_name: Cabernet Sauvignon; Mid-ripening; Bolgheri; 2011; Replicate A


title: WLT-HDV-113-CIRRHOSISwithoutHCC, sample 45


title: CS_BO_PV_11_B

source_name: Cabernet Sauvignon; Pre-veraison; Bolgheri; 2011; Replicate B


title: CS_BO_PV_11_A

source_name: Cabernet Sauvignon; Pre-veraison; Bolgheri; 2011; Replicate A


title: CS_BO_PV_11_C

source_name: Cabernet Sauvignon; Pre-veraison; Bolgheri; 2011; Replicate C


title: CS_BO_FR_11_C

source_name: Cabernet Sauvignon; Full-ripening; Bolgheri; 2011; Replicate C


title: CS_BO_MR_11_C

source_name: Cabernet Sauvignon; Mid-ripening; Bolgheri; 2011; Replicate C


title: CS_BO_PS_11_A

source_name: Cabernet Sauvignon; Pea Size; Bolgheri; 2011; Replicate A


title: SG_BO_PS_11_B

source_name: Sangiovese; Pea Size; Bolgheri; 2011; Replicate B


title: CS_BO_FR_11_B

source_name: Cabernet Sauvignon; Full-ripening; Bolgheri; 2011; Replicate B


title: CS_BO_FR_11_A

source_name: Cabernet Sauvignon; Full-ripening; Bolgheri; 2011; Replicate A


title: CS_BO_PS_11_B

source_name: Cabernet Sauvignon; Pea Size; Bolgheri; 2011; Replicate B


title: WLT-HDV-90-CIRRHOSISwithoutHCC, sample 43

source_name: tissue specimen obtained from explanted liver of HDV-cirrhosis


title: WLT-HDV-90-CIRRHOSISwithoutHCC, sample 44


title: WLT-HDV-90-CIRRHOSISwithoutHCC, sample 41


title: SG_BO_PS_11_C

source_name: Sangiovese; Pea Size; Bolgheri; 2011; Replicate C


title: CS_BO_PS_11_C

source_name: Cabernet Sauvignon; Pea Size; Bolgheri; 2011; Replicate C


title: CS_BO_MR_11_B

source_name: Cabernet Sauvignon; Mid-ripening; Bolgheri; 2011; Replicate B


title: SG_MO_FR_11_C

source_name: Sangiovese; Full-ripening; Montalcino; 2011; Replicate C


title: WLT-HDV-113-CIRRHOSISwithoutHCC, sample 46


title: WLT-HDV-73-CIRRHOSISwithoutHCC, sample 39


title: SG_MO_FR_11_A

source_name: Sangiovese; Full-ripening; Montalcino; 2011; Replicate A


title: SG_MO_MR_11_A

source_name: Sangiovese; Mid-ripening; Montalcino; 2011; Replicate A


title: WLT-HDV-73-CIRRHOSISwithoutHCC, sample 38


title: WLT-HDV-73-CIRRHOSISwithoutHCC, sample 40


title: SG_MO_FR_11_B

source_name: Sangiovese; Full-ripening; Montalcino; 2011; Replicate B


title: SG_MO_MR_11_C

source_name: Sangiovese; Mid-ripening; Montalcino; 2011; Replicate C


title: SG_MO_PV_11_C

source_name: Sangiovese; Pre-veraison; Montalcino; 2011; Replicate C


title: SG_MO_PS_11_B

source_name: Sangiovese; Pea Size; Montalcino; 2011; Replicate B


title: SG_MO_PS_11_C

source_name: Sangiovese; Pea Size; Montalcino; 2011; Replicate C


title: SG_MO_PV_11_B

source_name: Sangiovese; Pre-veraison; Montalcino; 2011; Replicate B


title: SG_MO_PS_11_A

source_name: Sangiovese; Pea Size; Montalcino; 2011; Replicate A


title: SG_MO_PV_11_A

source_name: Sangiovese; Pre-veraison; Montalcino; 2011; Replicate A


title: WLT-HDV-6-CIRRHOSISwithoutHCC, sample 36


title: CS_MO_FR_11_C

source_name: Cabernet Sauvignon; Full-ripening; Montalcino; 2011; Replicate C


title: WLT-HDV-HCC-129-NT, sample 35

source_name: tissue specimen obtained from explanted liver of HDV-HCC - non tumor region

value: HDV-HCC non tumor tissue


title: WLT-HDV-HCC-129-NT, sample 34


title: WLT-HDV-HCC-129-NT, sample 33


title: CS_MO_PV_11_C

source_name: Cabernet Sauvignon; Pre-veraison; Montalcino; 2011; Replicate C


title: CS_MO_MR_11_C

source_name: Cabernet Sauvignon; Mid-ripening; Montalcino; 2011; Replicate C


title: CS_MO_MR_11_A

source_name: Cabernet Sauvignon; Mid-ripening; Montalcino; 2011; Replicate A


title: CS_MO_MR_11_B

source_name: Cabernet Sauvignon; Mid-ripening; Montalcino; 2011; Replicate B


title: CS_MO_PV_11_B

source_name: Cabernet Sauvignon; Pre-veraison; Montalcino; 2011; Replicate B


title: WLT-HDV-73-CIRRHOSISwithoutHCC, sample 37

source_name: tissue specimen obtained from explanted liver of HDV-cirrhosis


title: CS_MO_FR_11_B

source_name: Cabernet Sauvignon; Full-ripening; Montalcino; 2011; Replicate B


title: CS_MO_PS_11_A

source_name: Cabernet Sauvignon; Pea Size; Montalcino; 2011; Replicate A


title: CS_MO_PV_11_A

source_name: Cabernet Sauvignon; Pre-veraison; Montalcino; 2011; Replicate A


title: WLT-HDV-HCC-129-NT, sample 31


title: WLT-HDV-HCC-129-NT, sample 30


title: WLT-HDV-HCC-129-NT, sample 32


title: SG_MO_MR_11_B

source_name: Sangiovese; Mid-ripening; Montalcino; 2011; Replicate B


title: CS_MO_PS_11_B

source_name: Cabernet Sauvignon; Pea Size; Montalcino; 2011; Replicate B


title: WLT-HDV-HCC-129-NT, sample 28


title: WLT-HDV-HCC-129-NT, sample 29


title: WLT-HDV-HCC-129-NT, sample 26


title: WLT-HDV-HCC-104-NT, sample 21


title: WLT-HDV-HCC-104-NT, sample 23


title: WLT-HDV-HCC-104-NT, sample 22


title: WLT-HDV-HCC-104-NT, sample 17


title: CS_MO_PS_11_C

source_name: Cabernet Sauvignon; Pea Size; Montalcino; 2011; Replicate C


title: WLT-HDV-HCC-104-NT, sample 19


title: WLT-HDV-HCC-104-NT, sample 25


title: WLT-HDV-HCC-104-NT, sample 24


title: WLT-HDV-HCC-104-NT, sample 20


title: WLT-HDV-HCC-104-NT, sample 18


title: WLT-HDV-HCC-129-NT, sample 27


title: CS_MO_FR_11_A

source_name: Cabernet Sauvignon; Full-ripening; Montalcino; 2011; Replicate A


title: WLT-HDV-HCC-104-NT, sample 15


title: WLT-HDV-HCC-129-T, sample 10

source_name: tissue specimen obtained from explanted liver of HDV-HCC - tumor region

value: HDV-HCC tumor tissue


title: WLT-HDV-HCC-19-NT, sample 13


title: WLT-HDV-HCC-129-T, sample 9


title: WLT-HDV-HCC-27-NT, sample 14


title: WLT-HDV-HCC-129-T, sample 8


title: WLT-HDV-HCC-104-NT, sample 16


title: WLT-HDV-HCC-104-T, sample 7


title: WLT-HDV-HCC-104-T, sample 6


title: WLT-HDV-HCC-104-T, sample 4


title: WLT-HDV-HCC-104-T, sample 5


title: WLT-HDV-HCC-129-T, sample 11


title: WLT-HDV-HCC-104-T, sample 3


title: WLT-HDV-HCC-5-NT, sample 12


title: WLT-HDV-HCC-27-T, sample 2


title: rep2 o11 ChIP

city: Shanghai

first: Liming

last: Xu

address: 333 Nanchen Road

country: China

institute: Shanghai University

description:
rep2 ChIP control
rep2_peaks.txt
rep2_summits.bed

library_source: genomic

data_processing:
CASAVA1.8.2 (Illumina) were used for image analysis and base calling.
Raw fastq data were trimmed using SolexaQA v2.5 program with Q20 (Phred score) and L40 (Length).
Cleaned data were then mapped to the maize reference genome (AGPv3.26, http://plants.ensembl.org/) using Bowtie2 (v2.3.2) with default parameters and allowing unique reads only.
Peak calling was performed separately for each biological replicate using MACS2 (v2.1.0) (band width = 300；model fold = [10, 30]; qvalue cutoff = 0.01)
UCSC bedGraph files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: Ensembl plants release-26 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include information about called peaks.  bed files include the peak summits locations for every peak.

molecule: genomic DNA

organism: Zea mays

source_name: kernal

extract_protocol:
Dissected 15 DAP kernels was immediately cross-linked in buffer containing 1% formaldehyde on ice under vacuum for 15 min, released the vacuum and reapplied for another 14 min. Fixation was stopped by adding 1.25M glycine. The cross-linked kernels were dried and ground into powder in liquid nitrogen, followed by nuclear isolation and sonication. Protein A-agarose beads (Millipore) and Antibody against O11 were used to precipitate the DNA. The precipitated DNA was digest by proteinase K and recovered using a QIAquick PCR purification kit (Qiagen) and analyzed by qPCR
[ChIP antibody anti-O11 preparation] Prepared by Abclonal of China company. The full-length O11 cDNA was cloned into the EcoR I and Xho I sites of the pET-32a vector (Novagen) and transformed into BL21. The 6xHis fusion recombinant O11 protein was purfied with the ÄKTA purfication system using a 1 mL HisTrap FF crude column (GE Healthcare). Then the antibody was prepared in rabbits by Abclonal of China company.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Catalog# IP-202-1012). ChIP DNA samples were subjected to end repair and A-base addition, followed by ligation with adapters. Then libraries werebarcoded to allow multiplexed sequencing.

value: kernel

value: 15 DAP

value: mutant (o11/o11)

tag: chip antibody


title: rep2 WT ChIP

description:
rep2 ChIP sample
rep2_peaks.txt
rep2_summits.bed

tag: genotype

value: wildtype


title: rep1 o11 ChIP

description:
rep1 ChIP control
rep1_peaks.txt
rep1_summits.bed

tag: tissue


title: rep1 WT ChIP

description:
rep1 ChIP sample
rep1_peaks.txt
rep1_summits.bed


title: C1-2

city: Wuhan P.R. China

first: Bin

last: Zhu

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province · 430070 · P.R.China

department: College of Plant Science and Technology

institute: Huazhong Agricultural University

data_processing:
150bp paired-end reads were generated via Illumina HiSeqTM 3000
The clean reads were directly aligned to the reference genome of Brassica napus using Hisat software (version 0.1.6), with a strict mismatch tolerance according to the follow criterion: specifying -L, 0, -0.15.
The genes were assembled with Cufflinks according to a reference-guided method.
The differentially expressed genes between three different samples were computed on RNA-seq data by using CuffDiff2.
Genome_build: Brassica_napus.annotation_v5.gff3 available at http://www.genoscope.cns.fr/brassicanapus/data/

organism: Brassica rapa

source_name: C1_young leaf

growth_protocol: All of the samples were established in green house for transcriptomic analyses.

extract_protocol:
Using TRIzol reagent (Invitrogen, Life Technologies) according the manufacturer’s protocol, total RNA was extracted from two biological replicates (three plants per replicate) for each genotype.
NanoDrop ND 1000 (NanoDrop technologies) was used to initially calculate the quality and quantity of the extracted RNA, and then the RNA Integrity Number (RIN) value was assessed by Agilent Technologies 2100 Bioanalyzer (Agilent). Only when the value of RIN was higher than 8, the RNA was used to prepare the c-DNA library according to the TruSeq RNA Sample Prep v2 protocol

value: monosomic addition line

value: Leaf

tag: development

value: The newly expanded third leaves without petioles

tag: phenotype

value: Lost one pair of  C2 chromosome


title: Cs1-3

source_name: Cs1_young leaf

value: substitution line


title: C_R2

city: Changchun

first: yonghong

last: zhang

state: Jilin Province

address: No.2699 Qianjin Street

institute: Jilin University

data_processing:
The sequenced data was filtered with the Sickle (https://github.com/najoshi/sickle) and SeqPrep (https://github.com/jstjohn/SeqPrep) software to remove the noise and low-quality sequences.
The clean reads were mapped on the reference genome of  Gallus_gallus_5.0.
The expression abundance of the unigenes was calculated according to fragments per kilobase of exon per million (FPKM) fragments mapped.
Differentially expressed genes (DEGs), with a false discovery rate (FDR) < 0.05, were selected as the criteria for significant differences.
Genome_build: GCA_000002315.3
Supplementary_files_format_and_content: FPKM

organism: Gallus gallus

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: control

tag: liver phenotype

value: non-fatty liver

tag: age

value: 36 week


title: Cs1-1


title: RBR-3

source_name: RBR_young leaf

value: restituted Brassica rapa

value: normal


title: RBR-2


title: Cs1-2


title: C_R1

tag: Sex

value: male


title: FL_R1

value: paternal inheritance

value: fatty liver


title: C_R3


title: RBR-1


title: FL_R3


title: FL_R2


title: A-549

status: Public on Apr 08 2018

type: genomic

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a HiScanSQ Reader (Illumina).

data_processing:
Data matrix was generated using GenomeStudio software (V2011.2)
Genotype: AA,AB,BB,or NC (no call)

label: Cy3, Cy5

label_protocol: 400ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and random primer mix (WG-RPM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Total DNA was isolated by standard procedures

tag: tumor type

value: Non-Small Cell Lung Cancer

tag: cell line


title: HBEC-3KT

value: Human bronchial epithelial cells


title: C1-3


title: NCI-H1395


title: NCI-H1437


title: NCI-H1993


title: DEF1

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

country: France

institute: U1208, INSERM

description:
28
processed data file: Duck_repro.xlsx

data_processing:
The raw files were converted into Fastq files (fastq.gz) and demultiplexed using Bcl2fastq 2.0 software (Illumina).
Quality control was performed on Fastq files using the FastQC v0.11.5 software.
Reads were quantified on BGI_duck_1.0 using Salmon v0.9.1.
Normalized counts and DE genes were calculated using DESeq2.
Genome_build: BGI_duck_1.0
Supplementary_files_format_and_content: Duck_repro.xlsx: Excel file includes normalized counts and DE genes using DEF as reference.

organism: Anas platyrhynchos

source_name: in vitro culture

growth_protocol: Cells were isolated and maintained as described in Fuet et al., (2018).

extract_protocol:
Total RNAs were prepared by Trizol extraction using standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: embryonic fibroblasts


title: BC1

description:
22
processed data file: Duck_repro.xlsx

source_name: Stages EGK-X - EGKXII embryos

value: blastodermal cells


title: BC2

description:
23
processed data file: Duck_repro.xlsx

source_name: Stages > EGKXV embryos


title: R71-2

description:
3082
processed data file: Duck_repro.xlsx

value: somatic reprogrammed cells


title: R71-5

description:
3076
processed data file: Duck_repro.xlsx


title: C1-1

value: monosomic addition line

value: Leaf

value: Lost one C2 chromosome


title: DEF2

description:
Pekin
processed data file: Duck_repro.xlsx


title: mES untreated r2

status: Public on Apr 07 2018

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Sequencing reads were aligned to the mm9 revision of the mouse reference genome using Tophat with –no-novel-juncs and -G set to a list of known RefSeq transcripts downloaded 2/1/17.
Per-transcript expression was quantified as RPKMs using RPKM_count from the RSeQC package.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown on 0.2% gelatinized tissue culture plates in 2i media, DMEM-F12, 0.5X B27 supplement, 0.5X N2 supplement , an extra 0.5mM L-glutamine , 0.1mM b-mercaptoethanol,  1% Penicillin Streptomycin , 0.5X nonessential amino acids , 1000 U/ml LIF , 1μM PD0325901 , and 3μM CHIR99021

extract_protocol:
RNA was extracted with RNeasy mini kit (Qiagen 74104).
TruSeq Stranded RNA library prep kit (Illumina) was used for preparation of libraries, followed by single-end sequencing


title: input_Hexanediol

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 1 -m 1 --sam -l 40
mm9
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

growth_protocol: V6.5 (C57BL/6-129) murine ES cells  were grown on 0.2% gelatinized tissue culture plates in 2i media, DMEM-F12, 0.5X B27 supplement, 0.5X N2 supplement , an extra 0.5mM L-glutamine , 0.1mM b-mercaptoethanol,  1% Penicillin Streptomycin , 0.5X nonessential amino acids , 1000 U/ml LIF , 1μM PD0325901 , and 3μM CHIR99021

extract_protocol:
Purified immunoprecipitated DNA was prepared for sequencing using the Swift Biosciences ChIP kit by the Whitehead Institute Genome Technology Core.
Whole cell extracts were sonicated using a Covaris S220 under manufacturer's recommended settings for 12 minutes to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using indicated antibodies.

treatment_protocol: Cells were treated with 1.5% 1,6-hexanediol for 30 minutes

tag: antibody manu.

tag: antibody catalog


title: RNAPII_Hexanediol

value: RNA Pol II (8WG16)

value: Abcam


title: MED1_Control

value: Bethyl


title: BRD4_Hexanediol


title: MED1_Hexanediol


title: RNAPII_Control


title: input_Control


title: BRD4_Control


title: wbi_minus_1

city: Charlottesville

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

data_processing:
Base calling an quality scoring performed by real-Time Analysis (RTA) v2.
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC.
Reads were splice-aware aligned to the UCSC mm9 genome using STAR.
Reads overlapping Gencode mm9 gene regions were counted using HTSeq.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with the raw counts.

source_name: Total RNA from MACS sorted microglia

growth_protocol: Adult C57BL/6J mice were purchased from Jackson Labs and house in our vivarium prior to use.

extract_protocol:
RNA was extracted using the RNAqueous Micro Kit (Ambion)
All RNA sample processing (including linear RNA amplification and cDNA library generation) and RNA-seq was performed by HudsonAlpha Genomic Services Laboratory

treatment_protocol: Mice were given BMT with or without head shield. After recovery, mice were given PLX5622 in food for 2 weeks then placed on standard chow. After 6 weeks, mice were injected with 50ug of LPS or saline (ip). Microglia were sorted 6 hours post injection.

tag: strain

value: brain

value: 6 months

value: Wild type

tag: treatment

value: BMT, PLX5622, then saline


title: wbi_plus_1

value: BMT, PLX5622, then LPS


title: wbi_plus_2


title: wbi_minus_3


title: hc_minus_3

value: BMT with head shield, PLX5622, then LPS


title: hc_plus_2


title: hc_plus_1


title: hc_minus_1

value: BMT with head shield, PLX5622, then Saline


title: hc_plus_3


title: mES untreated r1


title: hc_minus_2


title: gfp_minus_1

growth_protocol: Mice were bred and housed in our vivarium prior to use.

value: 10 months

value: GFP negative


title: gfp_plus_3

value: GFP positive


title: gfp_minus_2


title: gfp_plus_1


title: wbi_minus_2


title: wbi_plus_3


title: gfp_minus_3


title: gfp_plus_2


title: Sinorhizobium meliloti EC176, biological rep1

city: Stanford

first: Melanie

middle: J

last: Barnett

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G

data_processing: The data were analyzed using Affymetrix software GCOS v1.4 with Affymetrix default analysis setting and global scaling as the normalization method. The mean target intensity of each array was arbitrarily set to 500. Affymetrix Data Mining Tool v3.1 was used for data mining as previously described by Barnett et al. 2004.

organism: Sinorhizobium meliloti

source_name: Rm1021 wild type with hygromycin resistance marker (control strain)

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol: Bacteria were cultured in LB medium supplemented with 500 ug/ml streptomycin. Cells were harvested at OD-600 = 0.5 - 0.7

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.


title: fetal fibroblasts_control clone_1-15

city: Würzburg

first: Anna

last: Maierhofer

address: Biozentrum, Am Hubland

department: Institute of Human Genetics

institute: University of Würzburg

description:
SAMPLE 46
control clone

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: arrays were imaged using Illumina iScan using standard recommended Illumina scanner settings

data_processing:
Chip Analysis Methylation Pipeline (ChAMP) (Morris et al., 2014)
supplementary files contain normalized (BMIQ normalization method) average Beta for different sample groups.

label: Cy5 and Cy3

source_name: fetal fibroblast strain 1

label_protocol: Standard Illumina Protocol

growth_protocol: cells were cultured in T25 flasks in Chang Medium with L-glutamine (Irvine Scientific) at 37°C in an incubator with 5% CO2 atmosphere

extract_protocol: genomic DNA was extracted from fetal fibrobalsts using Quick-gDNA MiniPrep Kit (Zymo Research) according to standard instructions

treatment_protocol: cultures were exposed at room temperature to a single X-ray dose of 2 Gray (8 Gy/min) using a Siemens Primus L linear accelerator

value: fetal fibroblast

value: non-irradiated

tag: stability


title: Sinorhizobium meliloti EC69, biological rep3

source_name: Rm1021 with ChvI K214T mutation and hygromycin resistance marker


title: Sinorhizobium meliloti EC176, biological rep2


title: Sinorhizobium meliloti EC220, biological rep3

source_name: Rm1021, merodiploid with ChvI D52E mutation/wild type ChvI and hygromycin resistance marker


title: Sinorhizobium meliloti EC220, biological rep2


title: fetal fibroblasts_irradiated clone_1-300E6

description:
SAMPLE 47
irradiated clone

value: irradiated

value: unstable


title: Sinorhizobium meliloti EC220, biological rep1


title: Sinorhizobium meliloti EC176, biological rep3


title: fetal fibroblasts_irradiated clone_1-300A4

description:
SAMPLE 48
irradiated clone


title: fetal fibroblasts_irradiated clone_1-200F6

description:
SAMPLE 45
irradiated clone

value: stable


title: Sinorhizobium meliloti EC69, biological rep2


title: fetal fibroblasts_irradiated clone_1-100A1

description:
SAMPLE 44
irradiated clone


title: fetal fibroblasts_irradiated clone_1-100B1

description:
SAMPLE 43
irradiated clone


title: Sinorhizobium meliloti EC69, biological rep1


title: fetal fibroblasts_irradiated clone_1-200G4

description:
SAMPLE 42
irradiated clone


title: fetal fibroblasts_control clone_1-39

description:
SAMPLE 41
irradiated clone


title: fetal fibroblasts_irradiated clone_1-300B4

description:
SAMPLE 40
irradiated clone


title: fetal fibroblasts_irradiated clone_1-300D1

description:
SAMPLE 39
irradiated clone


title: fetal fibroblasts_irradiated clone_1-300B7

description:
SAMPLE 36
irradiated clone


title: WLT-HDV-HCC-5-T, sample 1

last: Diaz

address: Via Porcell 4

institute: University of Cagliari

data_processing: Affymetrics probeset summaries were computed using RMA algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: patient code

value: whole liver

tag: disease state

value: HDV-HCC tumor tissue


title: gDNA-1Q_381_1-vs-PreMA

city: College Station

first: Vaishali

last: Katju

state: Texas

address: Veterinary Integrative Bioscience, MS 4458

department: Veterinary Integrative Bioscience

institute: Texas A&M University

description: Genome variation profiling by genome tiling array

hyb_protocol: The sample was rehydrated in 40 μl of NimbleGen Hybridization Buffer (NimbleGen Systems, Inc.), denatured at 95 °C for 5 min, and then cooled to 42 °C. Hybridizations were carried out for 18 hr at 42 °C in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) and immediately dried down by centrifugation. See Selzer,R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44:305-319 (PMID 16075461).

scan_protocol: The scanner used was an Axon Scanner (Model # 40008). See Selzer,R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44:305-319 (PMID 16075461).

data_processing: The raw log2 intensity ratios were normalized with the LOESS regression.

organism: Caenorhabditis elegans

source_name: PreMA gDNA from ancestral population

label_protocol: Cy3/Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 μl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 μl/ml β-Mercaptoethanol. 1 μg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 °C and then chilled on ice in 0.2 ml PCR tubes. 10 μl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP, and dTTP), 8 μl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixede well with a pipet. Samples were centrifuged and incubated at 37 °C for 2 hours. 10 μl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precpitated by adding 11.5 μl 0.5 M NaCl and 110 μl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrfuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 μl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 μl DI water. DNA concentration was measured using a spectrophotometer. See Maydan JS, Lorch A, Edgley ML, Flibotte S, and Moerman DG. 2010. Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. BMC Genomics Jan 25;11:62 (PMID: 20100350)

growth_protocol: The population was grown on NGM plates (Nematode Growth Medium) at 20˚C and maintained on 60x15 mm petri dishes seeded with 250μl of Escherichia coli (OP50) in YT medium.

extract_protocol: DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using solid tissue protocol.

treatment_protocol: This is the ancestral control line. It was cryogenically frozen at −86°C throughout the MA period of the other lines.

tag: population

value: Ancestral

tag: generations

tag: individual

tag: sample

value: final

source_name: 1Q_381_1 gDNA from populations

treatment_protocol: Spontaneous mutation accumulation via population bottlenecks of N = 1 every generation.


title: gDNA-1O_397_1-vs-PreMA

source_name: 1O_397_1 gDNA from populations


title: gDNA-1T_305_1_2-vs-PreMA

source_name: 1T_305_1_2 gDNA from populations


title: gDNA-1G_346_1-vs-PreMA

source_name: 1G_346_1 gDNA from populations


title: gDNA-1T_305_1-vs-PreMA

value: pre

source_name: 1T_305_1 gDNA from populations


title: gDNA-1I_368_1-vs-PreMA

source_name: 1I_368_1 gDNA from populations


title: gDNA-1E_368_1-vs-PreMA

source_name: 1E_368_1 gDNA from populations


title: fetal fibroblasts_control clone_1-34

description:
SAMPLE 38
control clone

tag: group


title: PBMC_T56_207

city: Brisbane

first: Andreas

last: Suhrbier

state: Queensland

address: 300 Herston Road, Herston

country: Australia

institute: QIMR Berghofer Medical Research Institute

description:
207 t 56
Gene expression from RA patient after 56 days of CPN10 treatment.

hyb_protocol: Labeled RNA was hybridized to GeneChip® HumanGenome U133 Plus 2.0 Arrays (Affymetrix) according to standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 according to standard Affymetrix protocol.

data_processing: Fluorescence intensity data from CEL files were normalized by robust multiarray analysis (RMA) with Bioconductor software.

source_name: PBMC after 56 days of CPN10 treatment

label_protocol: According to GeneChip IVT labelling kit Affymetrix protocol.

extract_protocol: Extraction performed with PAXgene Blood RNA Kit following manufacturer's instructions.

treatment_protocol: 10 mg rCpn10 i.v. twice weekly for 56 days. Whole blood collected in PAXgene tubes at baseline and after 56 days.

tag: patient id

tag: disease status

value: Rheumatoid arthritis

tag: gender

value: Female

tag: ethnicity

value: Caucasian

value: PBMC

value: 10mg rCpn, twice/week, intravenous infusion


title: fetal fibroblasts_irradiated clone_1-100B4

description:
SAMPLE 34
irradiated clone

tag: cell type


title: fetal fibroblasts_irradiated clone_1-200G7

description:
SAMPLE 32
irradiated clone


title: fetal fibroblasts_control clone_1-33

description:
SAMPLE 33
control clone


title: fetal fibroblasts_irradiated clone_1-200A5

description:
SAMPLE 35
irradiated clone


title: gDNA-1M_395_1-vs-PreMA

source_name: 1M_395_1 gDNA from populations


title: gDNA-1R_386_1-vs-PreMA

source_name: 1R_386_1 gDNA from populations


title: gDNA-1S_291_1-vs-PreMA

source_name: 1S_291_1 gDNA from populations


title: gDNA-1K_349_1-vs-PreMA

source_name: 1K_349_1 gDNA from populations


title: fetal fibroblasts_irradiated clone_1-200A4

description:
SAMPLE 31
irradiated clone


title: gDNA-1J_396_1-vs-PreMA

source_name: 1J_396_1 gDNA from populations


title: gDNA-1F_386_1-vs-PreMA

source_name: 1F_386_1 gDNA from populations


title: gDNA-1P_393_1-vs-PreMA

source_name: 1P_393_1 gDNA from populations


title: PBMC_T56_205

description:
205 t 56
Gene expression from RA patient after 56 days of CPN10 treatment.

value: Male


title: gDNA-1L_342_1-vs-PreMA

source_name: 1L_342_1 gDNA from populations


title: fetal fibroblasts_irradiated clone_1-200E2

description:
SAMPLE 29
irradiated clone

source_name: fetal fibroblast strain 1


title: fetal fibroblasts_control clone_1-7

description:
SAMPLE 28
control clone


title: PBMC_T0_207

description:
207 t 0
Gene expression from RA patient before CPN10 treatment.

source_name: PBMC at baseline

value: T0 (baseline)


title: fetal fibroblasts_irradiated clone_1-200D5

description:
SAMPLE 30
irradiated clone

value: fetal fibroblast


title: fetal fibroblasts_starting culture_1-rep2

description:
SAMPLE 27
mass culture

value: starting culture


title: PBMC_T0_205

description:
205 t 0
Gene expression from RA patient before CPN10 treatment.


title: gDNA-1N_363_1-vs-PreMA

source_name: PreMA gDNA from ancestral population

source_name: 1N_363_1 gDNA from populations


title: gDNA-1D_326_1-vs-PreMA

source_name: 1D_326_1 gDNA from populations


title: gDNA-1H_281_1-vs-PreMA

source_name: 1H_281_1 gDNA from populations


title: myelolipoma18_S6-READs

city: Budapest

first: Abel

last: Decmann

address: Korányi str. 2a

department: Department of Internal Medicine and Oncology

country: Hungary

institute: Semmelweis University

data_processing:
trimming of adapters using cutadapt (http://cutadapt.readthedocs.io/en/stable/guide.html).
Reads with less than 16 bp insert sequences or with less than 10 bp Unique Molecular Index (UMI) were discarded.
Alignment of reads was performed using bowtie (http://bowtie-bio.sourceforge.net/index.shtml),
miRbase V21 was used for miRNAs.
Genome_build: miRbase V21
Supplementary_files_format_and_content: .xls file was generated by Qiagen online primary data analysing tool: (http://ngsdataanalysis.sabiosciences.com/QIAseqmiRNA).
Supplementary_files_format_and_content: counts

source_name: adrenal myelolipoma

extract_protocol:
FFPE samples were siolated by Ambion RecoverAll Total Nucleic Acid Isolatoin Kit for FFPE
Library was made by QIAseq microRNA Library Kit (by Qiagen)

tag: tissue

value: tumor tissue

tag: method

value: formalin-fixes paraffin-embedded

tag: tumor type

value: adrenal myelolipoma


title: fetal fibroblasts_irradiated clone_1-200D7

description:
SAMPLE 26
irradiated clone

value: irradiated

value: stable


title: fetal fibroblasts_control clone_1-6

description:
SAMPLE 25
control clone

value: non-irradiated


title: PBMC_T0_110

description:
110 t 0
Gene expression from RA patient before CPN10 treatment.

tag: treatment


title: myelolipoma15_S8-READs


title: myelolipoma16_S5-READs


title: fetal fibroblasts_irradiated clone_1-200C1

description:
SAMPLE 24
irradiated clone

tag: stability


title: myelolipoma14_S7-READs


title: fetal fibroblasts_control clone_1-32

description:
SAMPLE 23
control clone


title: gDNA-1B_397_1-vs-PreMA

value: Ancestral

value: final

source_name: 1B_397_1 gDNA from populations


title: PBMC_T0_108

description:
108 t 0
Gene expression from RA patient before CPN10 treatment.

value: Rheumatoid arthritis


title: PBMC_T56_108

description:
108 t 56
Gene expression from RA patient after 56 days of CPN10 treatment.

source_name: PBMC after 56 days of CPN10 treatment

value: Female


title: gDNA-10H_408_2-vs-PreMA

source_name: 10H_408_2 gDNA from populations

treatment_protocol: Spontaneous mutation accumulation via population bottlenecks of N = 10 every generation.


title: gDNA-10J_408_2-vs-PreMA

source_name: 10J_408_2 gDNA from populations


title: fetal fibroblasts_irradiated clone_1-100A3

description:
SAMPLE 22
irradiated clone

value: unstable


title: gDNA-10I_409_1-vs-PreMA

source_name: 10I_409_1 gDNA from populations


title: gDNA-1A_389_1-vs-PreMA

source_name: 1A_389_1 gDNA from populations


title: fetal fibroblasts_irradiated clone_1-100B7

description:
SAMPLE 21
irradiated clone


title: myelolipoma13_S6-READs


title: gDNA-10G_408_2-vs-PreMA

source_name: 10G_408_2 gDNA from populations


title: BJ 4-2: ovarian cancer

city: Atlanta

first: Cai

last: Huang

state: Georgia

address: North Ave NW

institute: Georgia Institute of Technology

description: ovarian cancer patients were snap frozen in liquid nitrogen within one minute of surgical removal and transferred to the lab for laser capture microdissection of cancer cells

hyb_protocol: Chips were hybridized to platform GPL570 platform (Gene Chip Human Transcriptome Array 2.0 (Affymetrix) and GeneChip® miRNA 3.0 Array (Affymetrix)) using Affymetrix HWS KIT and FS450_0004 Protocol.

scan_protocol: Scan on 7G Affymetrix GeneChip scanner.

data_processing: The data were analyzed with Robust Multi-Array Average (RMA) using Affymetrix default analysis.

source_name: primary tumors collected from ovarian cancer patients

label_protocol: Total RNA was amplified with Applause 3'-Amplification KIT (NuGen) and labeled with Encor Biotin Module (NuGen). Labeling of miRNAs was performed with the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, ThermoFisher).

extract_protocol: Cells were collected from frozen sections using LCM. RNA was isolated with PicoPure RNA KIT (LifeTechnologies). miRNAs were isolated from the cells using the miRNeasy Micro KIT (Qiagen, Germantown, MD). The quality and quantity of mRNA and miRNAs were assessed on the Bioanalyzer RNA PicoChip (Agilent Technologies, Santa Clara, CA).

value: primary ovarian cancer tumor

value: female

tag: diagnosis

value: ovarian cancer


title: myelolipoma6_S8-READs


title: fetal fibroblasts_control clone_1-3

description:
SAMPLE 20
control clone


title: BJ 4-3: ovarian cancer


title: fetal fibroblasts_irradiated clone_1-300F1

description:
SAMPLE 19
irradiated clone


title: myelolipoma4_S7-READs


title: BJ 1-3: ovarian cancer


title: myelolipoma3_S6-READs


title: fetal fibroblasts_irradiated clone_1-200F3

description:
SAMPLE 18
irradiated clone


title: fetal fibroblasts_irradiated clone_1-200E5

description:
SAMPLE 37
irradiated clone


title: gDNA-10G_408_1-vs-PreMA

source_name: 10G_408_1 gDNA from populations


title: BJ 4-1: ovarian cancer


title: PBMC_T56_110

description:
110 t 56
Gene expression from RA patient after 56 days of CPN10 treatment.

value: Male

value: Caucasian

value: PBMC

value: 10mg rCpn, twice/week, intravenous infusion


title: gDNA-1C_392_1-vs-PreMA

source_name: 1C_392_1 gDNA from populations


title: myelolipoma1_S5-READs

value: tumor tissue

value: formalin-fixes paraffin-embedded


title: fetal fibroblasts_irradiated clone_1-300D4

description:
SAMPLE 17
irradiated clone

source_name: fetal fibroblast strain 1

value: fetal fibroblast

value: irradiated


title: BJ 1-1: ovarian cancer


title: fetal fibroblasts_irradiated clone_1-200A2

description:
SAMPLE 16
irradiated clone


title: gDNA-10J_408_1-vs-PreMA

source_name: 10J_408_1 gDNA from populations


title: gDNA-10H_408_1-vs-PreMA

source_name: PreMA gDNA from ancestral population

source_name: 10H_408_1 gDNA from populations


title: BJ 1-2: ovarian cancer


title: 1145-3: ovarian cancer


title: carcinoma14_S4-READs

source_name: adrenocortical carcinoma

value: adrenocortical carcinoma


title: carcinoma12_S4-READs


title: fetal fibroblasts_irradiated clone_1-200B2

description:
SAMPLE 15
irradiated clone


title: fetal fibroblasts_irradiated clone_1-100B8

description:
SAMPLE 14
irradiated clone


title: gDNA-10F_409_2-vs-PreMA

value: Ancestral

source_name: 10F_409_2 gDNA from populations


title: 1145-2: ovarian cancer


title: carcinoma7_S2-READs


title: fetal fibroblasts_control clone_1-30

description:
SAMPLE 13
control clone

value: non-irradiated


title: gDNA-10C_408_2-vs-PreMA

value: final

source_name: 10C_408_2 gDNA from populations


title: 1129L-3: ovarian cancer


title: 1129L-2: ovarian cancer


title: 1129L-1: ovarian cancer


title: fetal fibroblasts_irradiated clone_1-300D5

description:
SAMPLE 12
irradiated clone


title: gDNA-10D_408_2-vs-PreMA

source_name: 10D_408_2 gDNA from populations


title: carcinoma6_S1-READs


title: gDNA-10D_408_1-vs-PreMA

source_name: 10D_408_1 gDNA from populations


title: gDNA-10E_409_1-vs-PreMA

source_name: 10E_409_1 gDNA from populations


title: fetal fibroblasts_control clone_1-2

description:
SAMPLE 11
control clone


title: carcinoma4_S3-READs


title: carcinoma5_S4-READs


title: 1122R-3: ovarian cancer


title: myelolipooma10_S5-READs

source_name: adrenal myelolipoma

value: adrenal myelolipoma


title: carcinoma3_S3-READs


title: 1145-1: ovarian cancer


title: gDNA-10E_409_2-vs-PreMA

source_name: 10E_409_2 gDNA from populations


title: fetal fibroblasts_starting culture_1-rep1

description:
SAMPLE 10
mass culture

value: starting culture


title: fetal fibroblasts_irradiated clone_1-300C2

description:
SAMPLE 8
irradiated clone

value: unstable


title: fetal fibroblasts_irradiated clone_1-200G6

description:
SAMPLE 9
irradiated clone


title: carcinoma2_S2-READs


title: gDNA-10C_408_1-vs-PreMA

source_name: 10C_408_1 gDNA from populations


title: carcinoma1_S1-READs


title: gDNA-10B_409_2_2-vs-PreMA

source_name: 10B_409_2_2 gDNA from populations


title: adenoma10_S2-READs

source_name: adrenocortical adenoma

value: adrenocortical adenoma


title: fetal fibroblasts_control clone_1-1

description:
SAMPLE 7
control clone


title: fetal fibroblasts_irradiated clone_1-100B62

description:
SAMPLE 6
irradiated clone

value: stable


title: 1012R-2: ovarian cancer

source_name: primary tumors collected from ovarian cancer patients

value: primary ovarian cancer tumor

value: female

value: ovarian cancer


title: gDNA-10B_409_2-vs-PreMA

value: pre

source_name: 10B_409_2 gDNA from populations


title: gDNA-10F_409_1-vs-PreMA

source_name: 10F_409_1 gDNA from populations


title: 1122R-1: ovarian cancer


title: fetal fibroblasts_irradiated clone_1-200C5

description:
SAMPLE 5
irradiated clone

source_name: fetal fibroblast strain 1


title: 1012R-3: ovarian cancer


title: adenoma8_S8-READs

value: tumor tissue


title: 1012R-1: ovarian cancer


title: adenoma9_S1-READs

value: formalin-fixes paraffin-embedded


title: carcinoma11_S3-READs


title: gDNA-10B_409_1-vs-PreMA

source_name: PreMA gDNA from ancestral population

source_name: 10B_409_1 gDNA from populations


title: fetal fibroblasts_control clone_1-25

description:
SAMPLE 4
control clone

value: fetal fibroblast


title: 992om-2: ovarian cancer


title: gDNA-10A_409_2-vs-PreMA

source_name: 10A_409_2 gDNA from populations


title: fetal fibroblasts_irradiated clone_1-100B6

description:
SAMPLE 3
irradiated clone

value: irradiated


title: gDNA-10B_409_1_2-vs-PreMA

source_name: 10B_409_1_2 gDNA from populations


title: adenoma7_S7-READs


title: adenoma6_S6-READs


title: fetal fibroblasts_irradiated clone_1-200C3

description:
SAMPLE 2
irradiated clone


title: 992om-1: ovarian cancer


title: adenoma5_S5-READs


title: fetal fibroblasts_irradiated clone_1-100A4

description:
SAMPLE 1
irradiated clone


title: 813L-2: ovarian cancer


title: 813L-3: ovarian cancer


title: gDNA-10A_409_1-vs-PreMA

source_name: 10A_409_1 gDNA from populations


title: gDNA-100E_409_4-vs-PreMA

growth_protocol: The population was grown on NGM plates (Nematode Growth Medium) at 20˚C and maintained on 90x15 mm petri dishes seeded with 750μl of Escherichia coli (OP50) in YT medium.

source_name: 100E_409_4 gDNA from populations

treatment_protocol: Spontaneous mutation accumulation via population bottlenecks of N = 100 every generation.


title: gDNA-10A_409_2_2-vs-PreMA

source_name: 10A_409_2_2 gDNA from populations


title: 813L-1: ovarian cancer


title: 1122R-2: ovarian cancer


title: adenoma4_S4-READs


title: adenoma3_S3-READs


title: adenoma2_S2-READs


title: gDNA-10A_409_1_2-vs-PreMA

source_name: 10A_409_1_2 gDNA from populations


title: 545R-2: ovarian cancer


title: adenoma1_S1-READs