title: GFP_POS_c19_r03

description:
c19_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber miRNA LL-3

status: Public on Jul 31 2018

type: SRA

city: Beijing

first: Xiaohui

last: Zhang

address: Zhong-Guan-Cun South Street 12

country: China

institute: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science

description: miRNA.txt

library_source: transcriptomic

data_processing:
BaseCall V1.6
SOAP
BLAST
Bowtie
RSEM
Genome_build: Cucumis sativus L. var. sativus cv. 9930 _v20; ftp://cucurbitgenomics.org/pub/cucurbit/genome/cucumber/Chinese_long/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Cucumis sativus

source_name: shoot apical tissue

growth_protocol: Seedlings were grown in artificial climate chambers

extract_protocol:
When four true-leaves were unfolded, shoot apical tissues (1 mm) were dissected under a microscope and snap-frozen in liquid nitrogen and kept at −80 °C for further use. In each experiment, more than 500 shoot apices and three biological replicates were used. Total RNA was extracted using the TRIzol reagent (Invitrogen, USA). DNase (Promega, USA) was used to remove potential DNA contamination.
1.  For RNA seq, Total RNAs (10 μg) were subjected to poly-A selection, fragmentation, random priming and cDNA synthesis with the Illumina Gene Expression Sample Prep kit (CA, USA). The cDNA fragments were end repaired, ligated to adapters and then enriched by PCR. The fragments were purified with 6% TBE PAGE gel electrophoresis. After denaturation, the single-chain fragments were fixed onto the Solexa Sequencing Chip (Flowcell) and consequently grown into single-molecule cluster sequencing templates through in situ amplification.
2.  For miRNA seq, A total of 30 μg of RNA was resolved on denatured polyacrylamide gels. Gel fragments with the size range of 18-30 nt were excised and recovered. These small RNAs were ligated with 5’ and 3’RNA adapters using T4 RNA ligase. The adapter-ligated small RNAs were subsequently transcribed into cDNA by Super-Script II Reverse Transcriptase (Invitrogen) and amplified using primers specific for the ends of the adapters.
3.  For degradome seq, Approximately 200 μg of total RNA was polyadenylated using the Oligotex mRNA mini kit (Qiagen). A 5′ RNA adapter was added to the cleavage products (which possessed a free 5′-monophosphate at their 3’ termini) using the T4 RNA ligase (Takara). Then, the ligated products were purified using the Oligotex mRNA mini kit (Qiagen) for reverse transcription to generate the first strand of cDNA using an oligo dT primer via SuperScript II RT (Invitrogen). After the cDNA library was amplified for 6 cycles (94 °C for 30 s, 60 °C for 20 s, and 72 °C for 3 min) using Phusion Taq (NEB), the PCR products were digested with restriction enzymes and further ligated to double-stranded DNA adapters. The ligated products were subjected to PCR amplification and gel purification and finally used for high-throughput sequencing with the Illumina HiSeq 2000.

treatment_protocol: conditions set as follows: 16 h light in 28 °C /8 h dark in 25 °C (high temperature, long day, HL), 8 h light in 28 °C /16 h dark in 25 °C (high temperature, short day, HS), 16 h light in 20 °C /8 h dark in 15 °C (low temperature, long day, LL), and 8 h light in 20 °C /16 h dark in 15 °C (low temperature, short day, LS). A 70% humidity was used for all of these plants.

tag: common name

value: Chinese long 9930

tag: cultivar

tag: tissue

value: shoot apical tissue

tag: developmental stage

value: four-week-seedling

tag: treatment

value: grown in 16 h light at 20°C /8 h dark at 15°C


title: GFP_POS_c19_r02

city: Boston

first: George

last: Murphy

state: MA

address: 670 Albany Street

country: USA

institute: Center for Regenerative Medicine of Boston University and Boston Medical Center

description:
c19_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt

data_processing:
Due to the limited length of R1 reads, they were discarded from the analysis. R2 Reads were aligned to the human genome (hg19) and quantified using the STAR aligner.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: raw_count_matrix.txt: Tab-delimited text file; raw counts matrix.
Supplementary_files_format_and_content: cell_metadata.txt: Tab-delimited text file; metadata containing information for each cell.

organism: Homo sapiens

source_name: Erythroid Cells

extract_protocol:
GFP-positive and -negative cells were sorted and entered into the Fluidigm C1 HT workflow, which was used to capture individual cells, lyse, reverse transcribe, and prepare libraries for sequencing (See: Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing, PN 100-9886).
Sequencing was performed on a Nextseq 500 using a high-output kit, resulting in a total of 475 million, paired-end, 75 bp reads.

treatment_protocol: hiPSC were differentiated towards a hematopoietic stem and progenitor cell (HSPC) fate, followed by commitment to and maturation along the erythroid lineage. To induce erythroid specification, d15 hiPSC-derived HSPCs were embedded in a semi-solid extra-cellular matrix mimetic (MethocultTM), yielding burst-forming unit-erythroid (BFU-E) colonies, which were picked on d28 and cultured in StemSpan™ Serum-Free Expansion Medium II (SFEM II) supplemented with 4U/ml hEPO over night. The following day (d29), floating cells were collected over a strainer, spun and resuspended in sort buffer. Cells were sorted for viability (PI-) and β-globin expression (GFP+ versus GFP-) and resuspended in sort buffer at a concentration of 400 cells/μL for loading onto the C1 platform.

tag: cell type

value: d29 iPSC-derived erythroid cells

tag: sort

value: GFP Positive reporting for beta globin


title: cucumber miRNA LL-1

description: miRNA.txt


title: cucumber miRNA HS-1

description: miRNA.txt

value: grown in 8 h light at 28°C /16 h dark at 25°C


title: GFP_POS_c19_r01

description:
c19_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber miRNA HL-2

description: miRNA.txt

value: grown in 16 h light at 28°C /8 h dark at 25°C


title: cucumber miRNA HS-3

description: miRNA.txt


title: cucumber miRNA LL-2

description: miRNA.txt


title: cucumber miRNA LS-2

description: miRNA.txt

value: grown in 8 h light at 20°C /16 h dark at 15°C


title: differentiated primary non-stem cells_replicate3

type: RNA

city: St. Louis

first: Girdhar

middle: G

last: Sharma

state: MO

address: 4511 Forest Park

department: Radiation Oncology - Cancer Biology

institute: Washington University School of Medicine

description: gene-expression in unirradiated isogenic non-stem cells differentiated from ES cells

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

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

growth_protocol: ES cells were grown on gelatin coated plates in stem cell media containing LIF following standard mouse embryonic stem cell culture procedures of growth without MEF feeder layers. In parallel ES cells were cultured in absence of LIF in normal growth media for 1 week or until expression of stem cell markers (Oct4, Sox2, Nanog, SSEA1 etc.) were lost in these isogenic non-stem differentiated ED cells.

extract_protocol: Total RNA was isolated from cells using RNeasy Kit (QIAGEN Inc. Valencia, CA, USA) following manufacturer's protocol.

treatment_protocol: Isogenic early passage, primary ES cells and non-stem differentiated ED cells were irradiated with 10 Gy in triplicates and RNA isolated at early (15 minutes) and late (4 hours) timepoints post irradiation.

value: differentiated primary cells


title: GFP_POS_c19_r08

description:
c19_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r40

description:
c18_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r39

description:
c18_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber miRNA LS-3

description: miRNA.txt


title: GFP_POS_c18_r36

description:
c18_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r38

description:
c18_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber transcriptome HL-3

description: Transcriptome.txt


title: cucumber transcriptome HL-2

description: Transcriptome.txt


title: cucumber miRNA HS-2

description: miRNA.txt


title: GFP_POS_c18_r35

description:
c18_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r34

description:
c18_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber transcriptome HS-2

description: Transcriptome.txt


title: cucumber transcriptome HS-3

description: Transcriptome.txt


title: GFP_POS_c18_r33

description:
c18_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r32

description:
c18_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber transcriptome LL-3

description: Transcriptome.txt


title: cucumber miRNA LS-1

description: miRNA.txt


title: GFP_POS_c18_r30

description:
c18_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r31

description:
c18_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r37

description:
c18_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber transcriptome HS-1

description: Transcriptome.txt


title: cucumber transcriptome LL-1

description: Transcriptome.txt


title: GFP_POS_c18_r29

description:
c18_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Human glomeruli DN 24

city: Nanjing

first: Jingsong

last: Shi

state: China

address: No.305, Zhongshan East Road

department: National Clinical Research Center of Kidney Disease

institute: Jinling Hospital, Nanjing University School of Medicine

description: SST RMA expression value derived from Expression Console software

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing: Raw data were processed with Expression Console software (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 3.3.1, http://www.r-project.org/).

label: biotin

source_name: diabetic nephropathy

label_protocol: Total RNA was amplified, labeled and purified by Ovation® Pico WTA System V2(Cat#3302, NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200, NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Kidney tissues were put into RNAlater (Ambion, Austin, TX) and stored at -80°C.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Microdissection of glomeruli was performed manually under a stereomicroscope using two dissection needle holders in RNAlater at 4°C.

value: glomeruli

tag: Sex

value: male


title: GFP_POS_c18_r28

description:
c18_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber transcriptome HL-1

description: Transcriptome.txt


title: GFP_POS_c18_r26

description:
c18_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber transcriptome LS-2

description: Transcriptome.txt


title: cucumber transcriptome LS-1

description: Transcriptome.txt


title: GFP_POS_c18_r24

description:
c18_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r23

description:
c18_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r25

description:
c18_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r21

description:
c18_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r20

description:
c18_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber transcriptome LS-3

description: Transcriptome.txt


title: cucumber transcriptome LL-2

description: Transcriptome.txt


title: GFP_POS_c18_r27

description:
c18_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r19

description:
c18_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r17

description:
c18_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: RNA_Seq_28C_CT78

city: Geneva

first: Guillaume

last: Rey

address: Campus Biotech, Chemin des Mines 9

country: Switzerland

institute: University of Geneva

description:
Sample 39
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt

data_processing:
Tag mapping with TopHat2
Subsampling of aligned reads with Samtools to reach a maximum of 1 million read per sample (Sample 21 to Sample 40)
Quantification with Cufflinks software suite
Genome_build: dm3
Supplementary_files_format_and_content: Cufflinks output files

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

growth_protocol: Drosophila S2 cells were grown Schneider medium using standard cell culture methods.

extract_protocol:
Standard RNA extraction with Zymo Direct-zol™ RNA kits
Illumina TrueSeq platform compatible dual-indexed multiplex library protocol was followed.

treatment_protocol: Cells were entrained by temperature cycles and were transferred to constant temperature (28 degrees Celsius). RNA was extracted at the indicated time points after the end of the entrainment.

value: S2 cells

tag: time

tag: temperature


title: GFP_POS_c18_r16

description:
c18_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r18

description:
c18_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: RNA_Seq_28C_CT81

description:
Sample 40
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT72

description:
Sample 37
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT75

description:
Sample 38
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT66

description:
Sample 35
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT69

description:
Sample 36
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: GFP_POS_c18_r15

description:
c18_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r22

description:
c18_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: RNA_Seq_28C_CT63

description:
Sample 34
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT60

description:
Sample 33
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT57

description:
Sample 32
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT54

description:
Sample 31
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: control-rep2

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

hyb_protocol: Hybridization was carried out for 17 hours at 65°C by rotating at 10 rpm. Microarray slides were washed in GE Wash Buffer-1 for 2 minutes and pre-warmed GE Wash Buffer-2 for 2 minutes at room temperature.

scan_protocol: Microarray slides were scanned in an Agilent Scanner version C (G2505C, Agilent Technologies).

data_processing: Images were analyzed using the Feature Extraction software v10.7. Raw data elaboration was carried out with Bioconductor (www.bioconductor.org), using R statistical language. Background correction was performed with the normexp method with an offset of 50 and quantile was used for between-array normalization. The LIMMA (LInear Models for Microarray Analysis) package was then used to identify differentially expressed genes. The empirical Bayes method was used to compute a moderated t-statistics.

source_name: LNCaP cell lines_control

label_protocol: Labeled cRNA target was prepared starting from100 ng of input RNA by Low Input Quick Amp Labelling Kit and One-Color Spike-In Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendation and protocols. Cyanine3CTP-labelled cRNA was quantified on a NanoDrop ND1000 Spectrophotometer using Microarray/RNA-40 measurement and the specific activity of cyanine 3 was calculated for each reaction. We set the minimum threshold of 2 μg for yield and 7 pmol/μg for the specific activity. Labeled cRNA (600ng) was fragmented by incubation with 5μl of 10× blocking reagent and 1μl of 25× fragmentation buffer in a 25μl reaction volume for 30 minutes at 60°C. Twentyfive microliters of 2× GE Hybridization Buffer Hi-RPM was added to fragmented cRNA;  40 μl of this  “hybridization mix” were placed onto the  SurePrint G3 Human GE V2 8x60K microarrays (50,599 Biological Features/array; Agilent Technologies).

growth_protocol: LNCaP with stable expression of wild type ERG (ERG-WT) or ERG mutant (ERG-K362A) or empty vector (EV) were generated by transfection of the corresponding expression vectors (pCEFL-ha-ERG3, pCEFL-ha-ERG3-K362A, pcDNA3.1) using JetPRIME (Polyplus) and selected with G418. ERG and ERG-K362A expression was determined by RT-PCR and Western blotting. Cells are maintained in RPMI supplemented with serum and G418.

extract_protocol: Qiazol and the miRNeasy Mini Kit together with a DNase I digestion step (Qiagen) were used according to the manufacturer’s recommendations to isolate total RNA from samples. Total RNA quality was checked for integrity using RNA Nano Chips on Agilent Bioanalyzer 2100 (Agilent Technologies).

value: Prostate cancer cell line

tag: cell line

value: LNCaP


title: GFP_POS_c18_r12

description:
c18_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: control-rep1


title: wild-type_ERG_overexpression_rep1

source_name: LNCaP cell lines_wildtype_ERG


title: GFP_POS_c18_r14

description:
c18_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: mutant_ERG_overexpression_rep2

source_name: LNCaP cell lines_mutant_ERG


title: mutant_ERG_overexpression_rep1


title: GFP_POS_c18_r11

description:
c18_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: wild-type_ERG_overexpression_rep2


title: RNA_Seq_28C_CT51

description:
Sample 30
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT48

description:
Sample 29
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: GFP_POS_c18_r08

description:
c18_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r09

description:
c18_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: RNA_Seq_28C_CT42

description:
Sample 27
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT45

description:
Sample 28
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT33

description:
Sample 24
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT39

description:
Sample 26
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT36

description:
Sample 25
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: GFP_POS_c18_r04

description:
c18_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r03

description:
c18_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r07

description:
c18_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r06

description:
c18_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r13

description:
c18_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: RNA_Seq_28C_CT27

description:
Sample 22
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: RNA_Seq_28C_CT30

description:
Sample 23
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: GFP_POS_c18_r02

description:
c18_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r01

description:
c18_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: RNA_Seq_28C_CT24

description:
Sample 21
rRNA-depleted RNA
S2_genes_28C.fpkm_table.txt
S2_genes_28C.attr_table.txt


title: GFP_POS_c17_r40

description:
c17_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r39

description:
c17_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r38

description:
c17_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r34

description:
c17_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r35

description:
c17_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r36

description:
c17_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r33

description:
c17_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r37

description:
c17_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r32

description:
c17_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r05

description:
c18_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r31

description:
c17_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r30

description:
c17_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r26

description:
c17_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r23

description:
c17_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c18_r10

description:
c18_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r25

description:
c17_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r24

description:
c17_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r29

description:
c17_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r21

description:
c17_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r19

description:
c17_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r28

description:
c17_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r27

description:
c17_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r18

description:
c17_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r20

description:
c17_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r16

description:
c17_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r12

description:
c17_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r11

description:
c17_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r22

description:
c17_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r10

description:
c17_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r08

description:
c17_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r07

description:
c17_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r06

description:
c17_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r17

description:
c17_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r09

description:
c17_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r05

description:
c17_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r15

description:
c17_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r14

description:
c17_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r04

description:
c17_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r13

description:
c17_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r03

description:
c17_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r02

description:
c17_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c17_r01

description:
c17_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r39

description:
c16_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r40

description:
c16_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r38

description:
c16_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r36

description:
c16_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r35

description:
c16_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r37

description:
c16_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C4P12LJ

type: genomic

city: Montpellier

first: Albertina

last: DE SARIO

address: 641, av du doyen Gaston Giraud

department: PhyMedExp

country: France

institute: INSERM 1046-CNRS 9214-Univ Montpellier

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human Methylation 450 K bead arrays (Illumina Inc., San Diego, CA). Processing was done according to the manufacturer’s protocol using an automated pipeline.  of bisulfite-treated DNA was analyzed using the Infinium  Human Methylation 450 K bead arrays spanning approximately  over 480,000 CpG sites/sample (Illumina Inc., San  Diego, CA). Processing was done according to the manufacturer’s  protocol using an automated pipeline, and the  arrays were scanned on an Illumina iScan platform (Illumina  Inc., San Diego, CA) established at the Life & Brain  Center (Bonn, Germany)

data_processing: Subset quantile normalization, revised version of Touleimat & tost, Epigenomics 2012

label: Cy5 and Cy3

molecule: genomic DNA

source_name: cystic fibrosis patient_severe

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted with the QIAamp DNA Micro Kit (#56304, Qiagen) according to  Bergougnoux et al., Epigenetics. 2014; 9(7):1007-17

tag: diagnosis

value: cystic fibrosis (severe)

tag: gender

value: F

tag: age

value: Nasal epithelium


title: C4P11AJ

scan_protocol: the arrays were scanned on an Illumina iScan platform


title: GFP_POS_c16_r34

description:
c16_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r33

description:
c16_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C1P07CJ

source_name: cystic fibrosis patient_intermediary

value: cystic fibrosis (intermediary)

value: M


title: C1P05MA


title: C1P08MA


title: C4P03PD


title: GFP_POS_c16_r31

description:
c16_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C3P03BE


title: C4P15DG


title: C1P15PA


title: C1P02NN


title: C1P12DA


title: C4P13ML

source_name: cystic fibrosis patient_mild

value: cystic fibrosis (mild)


title: C4P14MY


title: GFP_POS_c16_r29

description:
c16_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt

value: d29 iPSC-derived erythroid cells


title: C3P02OJ


title: GFP_POS_c16_r30

description:
c16_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt

value: GFP Positive reporting for beta globin


title: C3P06VQ


title: C1P04SD


title: GFP_POS_c16_r27

description:
c16_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r28

description:
c16_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r26

description:
c16_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C1P21TA


title: C1P19PF


title: C4P10LF


title: GFP_POS_c16_r23

description:
c16_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r25

description:
c16_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r24

description:
c16_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C1P18CS


title: C1P20PJ


title: GFP_POS_c16_r22

description:
c16_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C4P09PA


title: C3P04PB


title: C4P04VF


title: C1P16AB


title: C4P08JS


title: C1P17CG


title: C1P14HS


title: C4P02TR


title: GFP_POS_c16_r18

description:
c16_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r17

description:
c16_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r20

description:
c16_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r19

description:
c16_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r16

description:
c16_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C1P03MX


title: C1P11BL


title: GFP_POS_c16_r15

description:
c16_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r14

description:
c16_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r13

description:
c16_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r12

description:
c16_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r32

description:
c16_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r21

description:
c16_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C1T10LA

source_name: healthy controls

value: healthy


title: GFP_POS_c16_r10

description:
c16_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r11

description:
c16_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C1T07GV


title: C1P01RD


title: GFP_POS_c16_r09

description:
c16_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r08

description:
c16_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: m19-musBBz CAR T cells, biological rep2

city: Tampa

first: Gongbo

last: Li

state: Florida

address: 3011 W Holly Dr. MRC 2068

institute: Moffitt Cancer Center

hyb_protocol: Amplification and hybridization on to Affymetrix murine 430A2.0 microarrays were performed by the Core Facility

scan_protocol: Probe intensities were deteced with a Genepix 400B Scanner

data_processing: Gene expression analyses and graphic representations were performed with the Partek Genomics Suite Software.  RMA normalization was performed and values generated for each probeset for all samples.  Differentially expressed genes were detected by ANOVA and probesets of statistical significance were defined by a-fold change > 2 and a FDR 0.05.

label: Biotin

source_name: m19-musBBz CAR T cells_Ag stimulated_overnight

label_protocol: RNA from samples that met QC/QA checks on a bioanalyzer were amplified and labeled with a MessageAmp Premier RNA Kit according to manufacturer protocols

growth_protocol: Mouse T cells were isolated from mouse spleens using a negative T cell enrichment kit at day 0. Isolated T cells were activated with anti-mouse dynabeads and 30 IU/ml IL2 for 4 days. At day 1 and day 2 T cells were spin-transduced with retroviral supernatant at 2000×g for 1 hr at 32 °C. Complete medium with fresh IL2 were added at day 3. At day 4 CAR T cells were collected, beads removed, and ready for treatment.

extract_protocol: After stimulation, live CAR T cells were sorted into Trizol and extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: CAR T cells were incubated with 3T3-mCD19 cells at 10:1 ratio overnight.

tag: strain

value: female

tag: cell origin

value: Spleen T cell

value: m19-musBBz CAR T cells


title: GFP_POS_c16_r07

description:
c16_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: m19-musBBz CAR T cells, biological rep1


title: m1928z CAR T cells, biological rep2

source_name: m1928z CAR T cells_Ag stimulated_overnight

value: m1928z CAR T cells


title: C4T03FP


title: GFP_POS_c16_r05

description:
c16_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: m1928z CAR T cells, biological rep1


title: m19z CAR T cells, biological rep3

source_name: m19z CAR T cells_Ag stimulated_overnight

value: m19z CAR T cells


title: GFP_POS_c16_r04

description:
c16_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c16_r03

description:
c16_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: m19-musBBz CAR T cells, biological rep3


title: C3T04PM


title: GFP_POS_c16_r02

description:
c16_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: m19z CAR T cells, biological rep1


title: GFP_POS_c16_r01

description:
c16_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Elongation_H2O2 at 6h, rep2

city: Nagoya

first: Hironaka

last: Tsukagoshi

state: Aichi

address: 1-501 Shiogamaguchi, Tempaku-ku

department: Faculty of Agriculture

country: Japan

institute: Meijo University

description: Gene expression data from root elongation zone of Col-0 under 1 mM H2O2 condition, 6hr treatment

hyb_protocol: Samples were submitted to Duke Microarray Facility (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. For background correction, normalization and expression estimate computation were conducted by the gcRMA implementation

organism: Arabidopsis thaliana

source_name: Elongation zone_1mM H2O2 treatment for 6hr

label_protocol: Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.

growth_protocol: Seeds were sterilized by treating with 1 % bleach and 0.05% Triton X-100 for 5 min, washed 3 times with sterilized water. Seeds were germinated on the MS medium supplemented 1 % sucrose and 1 % agarose after two days at 4 ˚C. Plants were grown vertically in a growth chamber at 22 ˚C with a 16h light/8h dark condition.

extract_protocol: 30 roots were collected per replicate. Samples were briefly sonicated to disrupt the tissue. RNA was extracted using the Rneasy Micro Kit (Qiagen).

treatment_protocol: 5 day after imbibition (dai) seedlings were transferred onto MS media containing 1 mM H2O2 for 1,3, and 6 hour.Then roots were cut into the meristematic and elongation zone with a razor blade under microscope and collected into RNA extraction buffer.  30 roots wer collected per replicate, with two biological replicates being performed per sample. Samples were briefly sonicated to disrupt the tissue.

tag: ecotype

value: Seedling root elongation zone

value: 5 days after germination

tag: time point

tag: agent

value: H2O2 treatment (MS_cotaining 1mM H2O2)


title: C1T05TY

tag: tissue


title: m19z CAR T cells, biological rep2


title: GFP_POS_c15_r40

description:
c15_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C1T06RT


title: Elongation_H2O2 at 6h, rep1

scan_protocol: Samples were submitted to Duke Microarray Facility (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.


title: m1928z CAR T cells, biological rep3


title: GFP_POS_c15_r38

description:
c15_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C1T11LT


title: Meristem_H2O2 at 6h, rep2

description: Gene expression data from root meristematic zone of Col-0 under 1 mM H2O2 condition, 6hr treatment

source_name: Meristematic zone_1mM H2O2 treatment for 6hr

value: Seedling root meristematic zone


title: GFP_POS_c15_r37

description:
c15_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C1T03BE

value: F


title: C3T01CL

value: Nasal epithelium


title: Meristem_H2O2 at 6h, rep1


title: GFP_POS_c15_r36

description:
c15_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C3T02BG


title: GFP_POS_c15_r35

description:
c15_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Elongation_MS at 6h, rep2

description: Gene expression data from root elongation zone of Col-0 under standard condition, 6hr control

source_name: Elongation zone_no treatment for 6hr

value: No treatment (MS_control media)


title: C1T02CC


title: Meristem_MS at 6h, rep2

description: Gene expression data from root meristematic zone of Col-0 under standard condition, 6hr control

source_name: Meristematic zone_no treatment for 6hr


title: Elongation_MS at 6h, rep1


title: GFP_POS_c15_r34

description:
c15_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt

source_name: Erythroid Cells


title: C1T04HM

value: M


title: GFP_POS_c15_r32

description:
c15_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Meristem_MS at 6h, rep1


title: GFP_POS_c15_r31

description:
c15_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C4T01SC


title: C1T01ZR


title: C3T05PJ


title: GFP_POS_c15_r29

description:
c15_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r33

description:
c15_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r27

description:
c15_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r26

description:
c15_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r25

description:
c15_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r30

description:
c15_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Meristem_H2O2 at 3h, rep2

description: Gene expression data from root meristematic zone of Col-0 under 1 mM H2O2 condition, 3hr treatment

source_name: Meristematic zone_1mM H2O2 treatment for 3hr


title: Elongation_MS at 3h, rep2

description: Gene expression data from root elongation zone of Col-0 under standard condition, 3hr control

source_name: Elongation zone_no treatment for 3hr


title: Elongation_H2O2 at 3h, rep1

description: Gene expression data from root elongation zone of Col-0 under 1 mM H2O2 condition, 3hr treatment

source_name: Elongation zone_1mM H2O2 treatment for 3hr


title: GFP_POS_c15_r24

description:
c15_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r28

description:
c15_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Meristem_H2O2 at 3h, rep1


title: GFP_POS_c15_r23

description:
c15_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: C4T02AA


title: GFP_POS_c16_r06

description:
c16_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Elongation_H2O2 at 3h, rep2


title: Elongation_MS at 3h, rep1


title: Meristem_MS at 3h, rep1

description: Gene expression data from root meristematic zone of Col-0 under standard condition, 3hr control

source_name: Meristematic zone_no treatment for 3hr


title: GFP_POS_c15_r21

description:
c15_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Meristem_MS at 3h, rep2


title: GFP_POS_c15_r22

description:
c15_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r19

description:
c15_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Elongation_H2O2 at 1h, rep2

description: Gene expression data from root elongation zone of Col-0 under 1 mM H2O2 condition, 1hr treatment

source_name: Elongation zone_1mM H2O2 treatment for 1hr


title: Elongation_H2O2 at 1h, rep1


title: GFP_POS_c15_r20

description:
c15_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r18

description:
c15_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Meristem_H2O2 at 1h, rep2

description: Gene expression data from root meristematic zone of Col-0 under 1 mM H2O2 condition, 1hr treatment

source_name: Meristematic zone_1mM H2O2 treatment for 1hr


title: GFP_POS_c15_r17

description:
c15_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r14

description:
c15_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r16

description:
c15_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r13

description:
c15_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Elongation_MS at 1h, rep2

description: Gene expression data from root elongation zone of Col-0 under standard condition, 1hr control

source_name: Elongation zone_no treatment for 1hr


title: GFP_POS_c15_r15

description:
c15_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r10

description:
c15_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r11

description:
c15_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r12

description:
c15_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r39

description:
c15_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Meristem_H2O2 at 1h, rep1


title: GFP_POS_c15_r09

description:
c15_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r08

description:
c15_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r06

description:
c15_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r07

description:
c15_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Meristem_MS at 1h, rep2

description: Gene expression data from root meristematic zone of Col-0 under standard condition, 1hr control

source_name: Meristematic zone_no treatment for 1hr


title: Elongation_MS at 1h, rep1


title: Meristem at 0h, rep2

description: Gene expression data from root meristematic zone of Col-0 under standard condition, no treatment control

source_name: Meristematic zone_no treatment for 0hr


title: GFP_POS_c15_r03

description:
c15_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r01

description:
c15_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r05

description:
c15_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r40

description:
c14_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Meristem_MS at 1h, rep1


title: Elongation at 0h, rep1

description: Gene expression data from root elongation zone of Col-0 under standard condition, no treatment control

source_name: Elongation zone_no treatment for 0hr


title: Meristem at 0h, rep1


title: GFP_POS_c14_r37

description:
c14_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Elongation at 0h, rep2


title: GFP_POS_c14_r36

description:
c14_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r38

description:
c14_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r33

description:
c14_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r34

description:
c14_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r35

description:
c14_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r32

description:
c14_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r30

description:
c14_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r29

description:
c14_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r28

description:
c14_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r26

description:
c14_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r27

description:
c14_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r31

description:
c14_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r04

description:
c15_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c15_r02

description:
c15_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r24

description:
c14_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r22

description:
c14_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r23

description:
c14_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r20

description:
c14_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r39

description:
c14_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r19

description:
c14_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r15

description:
c14_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r16

description:
c14_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r14

description:
c14_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r18

description:
c14_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r17

description:
c14_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r12

description:
c14_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r10

description:
c14_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r13

description:
c14_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r09

description:
c14_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r08

description:
c14_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r04

description:
c14_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r25

description:
c14_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r05

description:
c14_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r07

description:
c14_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r38

description:
c13_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r02

description:
c14_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r37

description:
c13_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r21

description:
c14_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r01

description:
c14_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r36

description:
c13_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r35

description:
c13_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r03

description:
c14_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r11

description:
c14_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r33

description:
c13_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r31

description:
c13_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r32

description:
c13_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r28

description:
c13_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r29

description:
c13_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r30

description:
c13_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r27

description:
c13_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c14_r06

description:
c14_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r26

description:
c13_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r25

description:
c13_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r22

description:
c13_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r24

description:
c13_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r40

description:
c13_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r39

description:
c13_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r19

description:
c13_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r16

description:
c13_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r17

description:
c13_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r15

description:
c13_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r20

description:
c13_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r34

description:
c13_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r11

description:
c13_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r10

description:
c13_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r14

description:
c13_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r13

description:
c13_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r12

description:
c13_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r23

description:
c13_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r08

description:
c13_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r09

description:
c13_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r06

description:
c13_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r07

description:
c13_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r21

description:
c13_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r05

description:
c13_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r02

description:
c13_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r03

description:
c13_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r01

description:
c13_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r04

description:
c13_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r40

description:
c12_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c13_r18

description:
c13_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r34

description:
c12_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r37

description:
c12_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r36

description:
c12_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r35

description:
c12_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r39

description:
c12_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r22

description:
c12_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r26

description:
c12_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r31

description:
c12_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r32

description:
c12_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r19

description:
c12_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r21

description:
c12_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r17

description:
c12_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r20

description:
c12_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r13

description:
c12_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r11

description:
c12_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r10

description:
c12_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r05

description:
c12_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r36

description:
c11_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r37

description:
c11_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r38

description:
c11_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r40

description:
c11_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r39

description:
c11_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r35

description:
c11_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r08

description:
c12_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r01

description:
c12_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r25

description:
c12_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r34

description:
c11_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r18

description:
c12_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r02

description:
c12_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r30

description:
c11_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r31

description:
c11_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r33

description:
c11_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r29

description:
c11_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r28

description:
c11_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r23

description:
c11_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r26

description:
c11_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r27

description:
c11_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r24

description:
c11_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r22

description:
c11_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r25

description:
c11_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r07

description:
c12_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r21

description:
c11_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r20

description:
c11_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c12_r03

description:
c12_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r15

description:
c11_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r19

description:
c11_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r14

description:
c11_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r32

description:
c11_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r17

description:
c11_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r16

description:
c11_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r09

description:
c11_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r13

description:
c11_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r11

description:
c11_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r10

description:
c11_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r12

description:
c11_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r03

description:
c11_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r04

description:
c11_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r08

description:
c11_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r07

description:
c11_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r06

description:
c11_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r05

description:
c11_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r02

description:
c11_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r01

description:
c11_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c11_r18

description:
c11_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: RKO_P4_NCD38_day30_H3K4me2

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

library_source: genomic

data_processing:
Read were aligned with Hisat v2.2.1.0 for RNA-Seq and BWA (version 0.5.9) for ChIP-Seq.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1for RNA-seq and Aligned reads were converted to BedGraph format with bedtools v2.20.1 for ChIP-seq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Bedgraph files are generated from bedtools and converted to bigwig file.

source_name: RKO

growth_protocol: RKO cells were cultured in MEM containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
ChIP samples were purified by QIAquick PCR purification kit (Qiagen, Hilden, Germany) and total RNAs were collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) for ChIP-seq. TruSeq Stranded mRNA Sample Prep Kit (Illumina) were used for RNA-seq following the manufacturer’s protocol.

treatment_protocol: RKO cells were treated with 2 µM P4, PPIP, NCD38, P4-NCD38, or PPIP-NCD38 with 0.1% DMSO for 4days or 30 days. The medium containing the compound was refreshed every 5 days.

value: RKO

value: colorectal cancer cells

value: conjugated NCD38 with Py-Im polyamide P4_NCD38

tag: antibody

value: Anti-H3K4me2 (#05-1334, Merck Millipore, Lot#2768425)


title: RKO_PIPP_NCD38_day30_RNAseq

tag: treatment

value: conjugated NCD38 with Py-Im polyamide PPIP_NCD38


title: RKO_NCD38_day30_RNAseq

tag: cell type


title: RKO_DMSO_day30_RNAseq

value: DMSO


title: RKO_DMSO_day30_H3K4me2


title: RKO_P4_NCD38_day30_RNAseq


title: E2075-Y-F-APOE4-S

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

data_processing:
fastq to bam using subread v1.5.0
featurecounts usinge Rsubread v1.24.2
edgeR analysis using v3.16.5
Genome_build: mm10
Supplementary_files_format_and_content: raw expresison counts form featurecounts

source_name: brain

growth_protocol: All animal experiments were approved through the University of Pittsburgh Institutional Animal Care and Use Committee and carried out in accordance with PHS policies on the use of animals in research. All mice were on the C57BL/6 genetic background and experimental groups consisted of both genders. Experimental mice were kept on a 12 h light-dark cycle with ad libitum access to food and water.

extract_protocol:
Fourteen days post-injury, mice were anesthetized using Avertin (250 mg/kg of body weight, i.p.) and perfused transcardially with 20mL of cold 0.1M PBS pH 7.4. Brains were rapidly removed and a 1.5 mm coronal section of the brain, including the injury site, taken by slicing the brain at -2.5 mm and -4.0 mm from bregma. Within the coronal slice, the hemispheres were separated, and the subcortical tissue was dissected out; hippocampal and cortical tissue were snap-frozen together for RNA isolation and RNA-seq. RNA was isolated from frozen cortices and hippocampi at the injury site and purified using RNeasy kit (Qiagen) according to the manufacturer recommendations. Quality control of all RNA samples was performed on a 2100 Bioanalyzer instrument (Agilent Technologies) and samples with RIN > 8 were further used for library construction.
Quality control of all RNA samples was performed on a 2100 Bioanalyzer instrument (Agilent Technologies) and samples with RIN > 8 were further used for library construction using RNA Library Prep Reagent Set (Illumina). Libraries for Next Generation Sequencing were generated by PCR enrichment including incorporation of barcodes to enable multiplexing. Sequencing was performed by the Next Generation Sequencing Center (University of Pennsylvania, http://fgc.genomics.upenn.edu/) on HiSeq 2500 machine.

treatment_protocol: At 3 months of age, these mice were randomly assigned to either sham or controlled cortical impact (CCI) experimental group. Anesthesia was induced using 5% isoflurane, after which it was maintained at 1.5% isoflurane. The head was secured using a stereotaxic frame, and core body temperature was held at 37°C using a heating pad. After shaving the heads, two separate iodine - alcohol washes were performed to sterilize the surgical site. A 50% mixture of bupivacaine and lidocaine was applied to the area and ophthalmic ointment was applied to the eyes. The scalp was opened with a midline incision exposing the dorsal aspect of the skull and the skull leveled. A 4.5 mm diameter craniotomy was performed over the left parietal cortex using a dental drill. Once the bone flap was removed, mice in the CCI group received a single impact at 1.0 mm depth with a 3.0 mm diameter metal tip onto the cortex (3 m/s, 100 ms dwell time; Impact One, Leica). Sham mice received identical anesthesia and craniotomy, but did not receive impact and are considered negative controls.

value: Female

tag: genotype/variation

value: Sham


title: E2101-Y-APOE4het-F-T

tag: Sex

value: TBI


title: E2118-Y-F-APOE4-T


title: E2243-Y-APOE4het-F-S


title: E2109-Y-APOE4het-M-S

value: Male


title: E2225-Y-APOE4het-M-S


title: E2106-Y-F-APOE4-S


title: E2117-Y-F-APOE4-S


title: E2223-Y-APOE4het-M-T


title: E2232-Y-APOE4het-F-S


title: E2147-Y-APOE4het-F-T


title: E2250-Y-APOE4het-F-T


title: E2074-Y-F-APOE4-T


title: F1372-Y-M-APOE3-S


title: E2245-Y-APOE4het-F-T


title: E2124-Y-APOE4het-F-S


title: E2215-Y-APOE4het-F-S


title: hEKs, biological rep2

city: Lausanne

first: Melissa

last: Maggioni

address: Station 15

department: IBI

institute: EPFL

description:
miRNA expression in hEKs
YF29 2

hyb_protocol: The labeled RNA was hybridized to Agilent human miRNA microarrays for 20 hours at 55°C with rotation.

scan_protocol: After hybridization and washing the arrays were scanned with an Agilent microarray scanner G2505B using high dynamic range settings as specified by the manufacturer.

data_processing: Agilent Feature Extraction Software v 10.7.3.1 was used to extract the data. Quantile normalization was applied to the Total Gene Signal intensity values, using the function normalize.quantiles from the R Bioconductor package preprocessCore.

source_name: Cultivated hEKs

label_protocol: Each sample was prepared according to the Agilent’s miRNA Microarray System protocol. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase, denatured with dimethyl sulfoxide and labeled with pCp-Cy3 using T4 RNA ligase

growth_protocol: hTECs and hEKs were cultivated at low density (5000 cells / 100mm dish) for 10 days on a feeder layer of lethally irradiated mouse embryonic fibroblasts (3T3-J2)  in medium (cFAD) consisting of a 3:1 mixture of DMEM and Ham's F12 medium supplemented with 10% FBS, 0.4 μg/ml hydrocortisone, 10-6M cholera toxin, 5 μg/ml insulin, 2 x 10-9 M 3,3',5-Triiodo-L-Thyronin (T3)

extract_protocol: Total RNA was extracted from 50'000 cells aliquots using the Phenol-Free Total RNA Purification Kit (Amresco), according to the manufacturer's instructions.

treatment_protocol: hEKs, EpCAM positive and EpCAM negative hTECs pure cell populations were isolated by FACS.

tag: source gender

value: Epidermis

value: cultivated Human Epidermal derived Keratinocytes (hEKs)


title: hEKs, biological rep3

description:
miRNA expression in hEKs
YF29 3


title: hEKs, biological rep1

description:
miRNA expression in hEKs
YF29 1


title: E2240-Y-APOE4het-M-T


title: hTECs expressing the surface molecule EpCAM, biological rep2

description:
miRNA expression in hTECs expressing the surface molecule EpCAM
Thy14 EpCAM pos 2

source_name: Cultivated hTECs expressing the surface molecule EpCAM

value: Thymus

value: cultivated Human Thymic Epithelial Cells (hTECs)


title: hTECs expressing the surface molecule EpCAM, biological rep1

description:
miRNA expression in hTECs expressing the surface molecule EpCAM
Thy14 EpCAM pos 1


title: E2119-Y-F-APOE4-T


title: E2030-Y-APOE4het-M-S


title: E2023-Y-APOE4het-M-T


title: hTECs expressing the surface molecule EpCAM, biological rep3

description:
miRNA expression in hTECs expressing the surface molecule EpCAM
Thy14 EpCAM pos 3


title: E2016-Y-APOE4het-M-T


title: hTECs not expressing the surface molecule EpCAM, biological rep2

description:
miRNA expression in hTECs not expressing the surface molecule EpCAM
Thy14 EpCAM neg 2

source_name: Cultivated hTECs not expressing the surface molecule EpCAM


title: hTECs not expressing the surface molecule EpCAM, biological rep1

description:
miRNA expression in hTECs not expressing the surface molecule EpCAM
Thy14 EpCAM neg 1


title: Stage 4 rep1 [ncRNA]

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

institute: University of Zurich

description:
S4_R1
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt

data_processing:
Clip adapter (Version 1.0.1 FASTX-toolkit by Assaf Gordon), removal of adapter sequences (3' adapter sequence (TGGAATTCTCGGGTGCCAAGG)).
PCR duplicates were removed using the four random nucleotides on each side of the RNA fragment introduced with the adapters as molecular codes by running the tool “Collapse”. Then, the four random bases were removed from each side and “Collapse” was again used to obtain the unique sequences and the corresponding read counts corrected for PCR duplicates. Subsequently, a count table for all obtained unique sequences corresponding to a small ncRNA was generated using a series of further standard Galaxy tools as well as converting tools from the ToolShed (https://toolshed.g2.bx.psu.edu/). The resulting table contained the unique sequences and the number of reads per sample.
CPM per sample filtering tool (Chen et al. 2014), removal of sequences with negligible read counts, comprising sequencing errors or sequences with very low evidence for potential expression, CPM cut-off: 8.41 cpm (corresponding to an average of 20 reads per library) for at least 3 out of 20 libraries.
Small RNA sequences were annotated based on BLAST (Basic Local Alignment Search Tool) searches against a number of sequence databases. The collection of BLAST databases contained sequences from miRBase (bovine, human, and porcine precursor and canonical mature miRNAs, release 21), transcript sequences from NCBI and Ensembl, including non-coding RNAs, as well as tRNA and piRNA cluster sequences retrieved from the NCBI Bos taurus UMD 3.1.1 GFF3 file and http://www.smallrnagroup.uni-mainz.de/piRNAclusterDB.html , Rosenkranz D. piRNA cluster database: a web resource for piRNA producing loci. Nucleic Acids Research 2016 44(D1):D223-D230, respectively.
Genome_build: bosTau8, UMD_3.1.1
Supplementary_files_format_and_content: *.txt: Tab-delimited text files:
Supplementary_files_format_and_content: Filtered_sequence_counttable_smallRNA_exo.txt: Unique sequences and read counts per sample after filtering low abundance sequences.
Supplementary_files_format_and_content: Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt: Unique sequences with annotation and read counts per sample, excluding some outlier samples.
Supplementary_files_format_and_content: miRNA_isoforms_counts.txt: isomiR sequences and read counts per sample.
Supplementary_files_format_and_content: miRNA_isoforms_summarized_counts.txt: isomiRs summarized read counts.

organism: Bos taurus

source_name: oviduct luminal fluid

growth_protocol: EVs were isolated by ultracentrifugation (Théry et al., 2006; Almiñana et al., 2017). First, flushing samples were centrifuged at 300 g for 15 min, followed by 2,000 g for 15 min, and then at 12,000 g for 15 min to remove cells, blood, and cell debris and ultracentrifuged twice at 100,000 g for 90 min (BECKMAN L8-M; SW41T1 rotor) to pellet EVs. The pellets were resuspended in 50 µL of PBS and stored at -80ºC for further analysis. Oviductal flushings from 3 animals were pooled for each replicate.

extract_protocol:
RNA was isolated from a total of 20 EVs samples (4-5 replicates, 4 stages) using miRNeasy Mini kit (QIAGEN) according to the manufacturer's instructions. RNA quality and concentration were evaluated by Agilent 2100 Bioanalyzer Nano and small RNA assay (Agilent Technologies, Santa Clara, CA.) and NanoDrop (ThermoFisher).
A total of 444 ng RNA was used for the preparation of each small RNA library using NEXTflex™ Small RNA-Seq Kit v3 (Bioo Scientific). Library preparation followed the manufacturer's instructions.

value: oviduct luminal fluid

tag: estrous cycle stage

value: pre-ovulatory stage, days 18-20


title: Stage 4 rep2 [ncRNA]

description:
S4_R2
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: Stage 4 rep4 [ncRNA]

description:
S4_R4
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: E1818-Y-M-APOE4-S


title: E1800-Y-M-APOE4-T


title: Stage 3 rep2 [ncRNA]

description:
S3_R2
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt

value: late luteal phase, days 11-17


title: Stage 3 rep1 [ncRNA]

description:
S3_R1
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: Stage 3 rep4 [ncRNA]

description:
S3_R4
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt


title: Stage 3 rep3 [ncRNA]

description:
S3_R3
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: Stage 4 rep5 [ncRNA]

description:
S4_R5
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: E1770-Y-M-APOE4-S


title: D2562-Y-APOE3het-F-T


title: E1727-Y-M-APOE4-T


title: Stage 3 rep5 [ncRNA]

description:
S3_R5
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: E1794-Y-M-APOE4-S


title: E1751-Y-M-APOE4-T


title: E1731-Y-M-APOE4-S


title: D2560-Y-APOE3het-F-S


title: D2487-Y-APOE3het-F-T


title: Stage 2 rep4 [ncRNA]

description:
S2_R4
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt

value: early luteal phase, days 5-11


title: D2464-Y-APOE3het-F-T


title: Stage 4 rep3 [ncRNA]

description:
S4_R3
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt


title: Stage 2 rep3 [ncRNA]

description:
S2_R3
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: D2460-Y-APOE3het-M-T


title: Stage 2 rep2 [ncRNA]

description:
S2_R2
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: E1829-Y-M-APOE4-T


title: D2454-Y-APOE3het-F-S


title: D2439-Y-F-APOE3-T


title: Stage 1 rep3 [ncRNA]

description:
S1_R3
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt

value: postovulatory-stage, days 1-4 of estrous cycle


title: Stage 1 rep1 [ncRNA]

description:
S1_R1
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: Stage 1 rep5 [ncRNA]

description:
S1_R5
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: D2420-Y-APOE3het-M-T


title: D2438-Y-F-APOE3-S


title: D2411-Y-APOE3het-M-S


title: Stage 1 rep2 [ncRNA]

description:
S1_R2
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt


title: Stage 1 rep4 [ncRNA]

description:
S1_R4
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt


title: D2406-Y-APOE3het-F-S


title: D2392-Y-F-APOE3-T


title: Stage 4 rep5 [mRNA]

data_processing:
Trim Galore!, remove low quality from the 3′ end, adapter sequences, and sequences below a minimal length of 50 nt after the trimming steps
FastUniq, removal of PCR duplicates
Trimmomatic, cut 9 bases from the start of the read (HEADCROP), these bases are derived from the molecular code contained in the adapter sequence
HISAT2 (v1.4.0), mapping to the bovine genome sequence assembly
QuasR Qcount, generation of read count table for all annotated bovine genes based on the NCBI GFF3 annotation file
Counts per million (CPM) per sample filtering tool (Chen et al. 2014), remove sequences with negligible read counts, CPM cutoff: 4.21 (corresponding to an average of 20 reads per library) for at least 3 out of 20 libraries
Genome_build: bosTau8, UMD_3.1.1
Supplementary_files_format_and_content: tab-delimited text files, mRNA-Seq_count_table.txt contains mapped read counts, mRNA-Seq_filtered_counts.txt contains mapped read counts of the genes that passed the CPM filter, mRNA-Seq_CPM.txt contains counts per million (cpm) values of the genes that passed the CPM filter

extract_protocol:
RNA was isolated from a total of 20 EVs samples (5 replicates, 4 stages) using RNeasy Micro kit (QIAGEN) according to the manufacturer's instructions. RNA quality and concentration was evaluated by Agilent 2100 Bionalyzer (Agilent Technologies, Santa Clara, CA.) and NanoDrop (ThermoFisher).
Poly(A) RNA was isolated starting from of 450 ng of total RNA by the use of NEXTflex™ Poly(A) beads. Poly(A) RNA was used for the preparation of mRNA libraries with the NEXTflex™ Rapid Directional qRNA-Seq Kit (Bioo Scientific). Library preparation followed the manufacturer's instructions.


title: D2391-Y-APOE3het-M-T


title: IRT3-I [TH4_t1]

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

institute: CNR

description:
Pool1_Index8_ACTTGA_L004
smallRNAseq from dissected hearts

data_processing:
Data extraction was performed using bcl2fastq-1.8.3, Read data were extracted in FastQ format
Sequenced reads were trimmed for 3' adaptor sequences.
Reads were aligned to mirBase v20.0 using mirExpress
Low counting miRNAs were filtered out and expression values were normalized for library size using estimateSizeFactors function of DESeq.
Genome_build: rattus pre-mirna mirBase v20
Supplementary_files_format_and_content: tab-delimited text file includes normalized read count per sample

organism: Rattus norvegicus

source_name: myocardial ischemia reperfusion with an early short-term T3-replacement (IRT3)

growth_protocol: Rats were  housed in authorized Experimental Biomedical Centre of the CNR Research Area according to the national current regulations

extract_protocol:
Total RNA from heart specimens was extracted with the miRneasy mini kit (QIAGEN, Italy) as directed by the manufacturers’ instructions.
cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis (Invitrogen) and eluted into 300 µl elution buffer (Illumina) for at least 2 hours at room temperature, to enrich for molecules containing inserts in the range of 18–33 nt.

treatment_protocol: 24h after induction of cardiac IR, rats were subjected to 48h infusion with T3 at 3mg/Kg day (IR-T3 group) or its vehicle (IR-group), Sham operated rats were used as control

value: Wistar

tag: developmental stage

value: Adult

value: male

value: cardiac

tag: tissue subtype

value: left ventricle myocardial peri-infarct zone


title: IRT3-II [TH6_t2]

description:
Pool1_Index9_GATCAG_L004
smallRNAseq from dissected hearts


title: Fruit-set-grape_Seeded_rep2

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

country: Spain

institute: CSIC

description:
660-50_seeded
This sample is of developing seeded fruitlets from the 660-50 table grape Red Globe × Crimson Seedless F1 hybrid with sdi- genotype collected on 3 June 2010 at 2 weeks after anthesis developmental stage

hyb_protocol: If the quality control was correct according to Bioanalyzer results, 4 µg of labelled cDNA were hybridized. Hybridization solution (NimbleGen Hybridization kit) was added to each labelled cDNA and hybridization was performed for 16 h at 42ºC in a HS 4 Hybridization station (NimbleGen-Roche).

scan_protocol: Hybridized microarrays were washed with Wash buffer kit (NimbleGen-Roche) and scanned at 532 nm and 2 µm resolution in a DNA Microarray Scanner with Surescan High-Resolution Technology (Agilent technologies).

data_processing: After evaluation of hybridization quality by Experimental metrics report implemented in NimbleScan Software version 2.6 (NimbleGen-Roche), probeset signal values from all the microarray hybridizations were background corrected and normalized together using Robust Microarray Average (RMA) (Irizarry et al., 2003) in NimbleScan Software, which produces a calls file for each sample with normalized expression data for each gene.

organism: Vitis vinifera

source_name: Vitis vinifera Red Globe × Crimson Seedless F1 sdi- hybrid seeded fruitlets collected 2 weeks after anthesis

label_protocol: cDNA was synthesized from 10 µg of total RNA using cDNA Synthesis System Kit (NimbleGen-Roche). The cDNA preparation (1 µg) was amplified and labelled with Cy3-random nonamers using One color labeling kit (NimbleGen-Roche).

growth_protocol: A Red Globe×Crimson Seedless F1 table grape cross populations was generated from controlled crosses carried out in 2003. Progeny plants were grown in the same experimental field belonging to Sociedad Murciana de Investigación y Tecnología de Uva de Mesa (ITUM) located in Blanca, Murcia, Spain. Plants were grafted onto 1103 Paulsen rootstock conducted under parral trellis, ferti-irrigated and cultivated under the same management practices.

extract_protocol: Total RNA was extracted from frozen fruitlets of Red Globe × Crimson Seedless F1 hybrids using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich) with the manufacturer’s protocol. An in column DNase digestion step with the RNase-Free DNase Set (QIAGEN) was added.

treatment_protocol: Five sdi+ seedless (660-40, 660-41, 660-57, 669-19, 671-34) and four sdi- seeded (660-43, 660-50, 669-45, 671-19) Red Globe × Crimson Seedless F1 hybrids were compared using NimbleGen microarrays. RNA was obtained form fruit set green fruits collected simultaneously for every progeny individual around midday on 3 June 2010.

tag: variety background

value: Red Globe × Crimson Seedless F1

tag: planto id

tag: genotype in sdi qtl

value: sdi-

value: 2 weeks after anthesis

value: Fruit-set green fruit

tag: fruit type

value: seeded


title: Fruit-set-grape_Seeded_rep3

description:
669-45_seeded
This sample is of developing seeded fruitlets from the 669-45 table grape Red Globe × Crimson Seedless F1 hybrid with sdi- genotype collected on 3 June 2010 at 2 weeks after anthesis developmental stage


title: Fruit-set-grape_Seeded_rep4

description:
671-19_seeded
This sample is of developing seeded fruitlets from the 671-19 table grape Red Globe × Crimson Seedless F1 hybrid with sdi- genotype collected on 3 June 2010 at 2 weeks after anthesis developmental stage


title: Fruit-set-grape_Seeded_rep1

description:
660-43_seeded
This sample is of developing seeded fruitlets from the 660-43 table grape Red Globe × Crimson Seedless F1 hybrid with sdi- genotype collected on 3 June 2010 at 2 weeks after anthesis developmental stage


title: Fruit-set-grape_Seedless_rep4

description:
669-19_seedless
This sample is of developing stenospermocarpic fruitlets from the 669-19 table grape Red Globe × Crimson Seedless F1 hybrid with sdi+ genotype collected on 3 June 2010 at 2 weeks after anthesis developmental stage

source_name: Vitis vinifera Red Globe × Crimson Seedless F1 sdi+ hybrid stenospermocarpic fruitlets collected 2 weeks after anthesis

value: sdi+

value: stenospermocarpic


title: Fruit-set-grape_Seedless_rep2

description:
660-41_seedless
This sample is of developing stenospermocarpic fruitlets from the 660-41 table grape Red Globe × Crimson Seedless F1 hybrid with sdi+ genotype collected on 3 June 2010 at 2 weeks after anthesis developmental stage


title: Fruit-set-grape_Seedless_rep1

description:
660-40_seedless
This sample is of developing stenospermocarpic fruitlets from the 660-40 table grape Red Globe × Crimson Seedless F1 hybrid with sdi+ genotype collected on 3 June 2010 at 2 weeks after anthesis developmental stage


title: IR-II [TH35_c2]

description:
Pool1_Index7_CAGATC_L004
smallRNAseq from dissected hearts

source_name: myocardial ischemia reperfusion (IR)

tag: strain


title: Stage 2 rep5 [ncRNA]

description:
S2_R5
Total RNA enriched for shorter molecules.
miRNA_isoforms_counts.txt
miRNA_isoforms_summarized_counts.txt
Filtered_sequence_counttable_smallRNA_exo.txt
Filtered_sequence_counttable_smallRNA_exo_annotation_outliers_removed.txt

value: oviduct luminal fluid


title: D2383-Y-F-APOE3-T

value: Female

value: TBI


title: IR-I [TH9_c1]

description:
Pool1_Index6_GCCAAT_L004
smallRNAseq from dissected hearts


title: D2353-Y-F-APOE3-S

value: Sham


title: Stage 4 rep3 [mRNA]

value: pre-ovulatory stage, days 18-20


title: Stage 4 rep2 [mRNA]


title: Sham [TH14]

description:
Pool1_Index5_ACAGTG_L004
smallRNAseq from dissected hearts

source_name: Sham

value: Wistar

value: left ventricle myocardium


title: Fruit-set-grape_Seedless_rep3

description:
660-57_seedless
This sample is of developing stenospermocarpic fruitlets from the 660-57 table grape Red Globe × Crimson Seedless F1 hybrid with sdi+ genotype collected on 3 June 2010 at 2 weeks after anthesis developmental stage


title: D2322-Y-F-APOE3-T


title: Stage 3 rep5 [mRNA]

value: late luteal phase, days 11-17


title: D2300-Y-APOE3het-M-S

value: Male


title: D2319-Y-F-APOE3-S


title: Stage 4 rep4 [mRNA]


title: Stage 3 rep3 [mRNA]


title: D2291-Y-APOE3het-M-S


title: D2389-Y-F-APOE3-S