title: Late stage post-radiation GBM RCAS mouse model cell T3-74

source_name: stage T3,  Cell # 74


title: 1772058147_G12

status: Public on Dec 01 2016

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited file of mRNA molecule counts for each gene and cell. Cells with less than 1500 molecules have been removed from this file.

molecule: polyA RNA

organism: Mus musculus

source_name: hypothalamus

growth_protocol: C57BL/6N mice were housed conventionally (12/12-h light cycle, 55% humidity).

extract_protocol:
Mice were deeply anesthetized (5% isoflurane) and transcardially perfused with 40 ml ice-cold pre-oxygenated (95% O2/5% CO2) cutting solution containing (in mM): 90 NaCl, 26 NaHCO3, 2.5 KCl, 1.2 NaH2PO4, 10 HEPES-NaOH, 5 Na-ascorbate, 5 Na-pyruvate, 0.5 CaCl2, 8 MgSO4 and 20 glucose. A central column of the mouse hypothalamus spanning the preoptic area-Arc (rostrocaudal axis), paraventricular nucleus (dorsal) and the ventrolateral hypothalamic area (lateral) was microdissected from serial 300-micrometer-thick coronal slices under microscopy guidance and dissociated using the Papain Dissociation System (Worthington). Isolated single cells were concentrated by centrifugation to a density of 600-1,000 cells/?microlitre. After mixing C1 suspension reagent (4 microlitre; "C1 reagents", Fluidigm Inc.) to the cell suspension (7 microlitre), this mixture was loaded into a C1-AutoPrep IFC microfluidic chip (Fluidigm Inc.)
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

treatment_protocol: Formalin stress was induced by injection of 4% PFA into the left paw

tag: strain

tag: age (days postnatal)

value: Unknown

tag: Sex

tag: acute stress

value: N

tag: cell diameter

tag: total molecules

tag: level1 class

value: ependymal


title: 1772058147_G11

value: endothelial


title: PU-pre-NEI-br2

city: Wuhan

first: Liu

last: Zheng

country: China

institute: Huazhong Agricultural University

description:
replicate 2 for ovules before nucellar embryo initiation stage
processed data file = "pummelo-grapefruit.rpkm.xlsx"

data_processing:
The transcriptome raw reads were filtered first, by removing the low quality reads, filtering the contaminants and trimming the adaptor sequences.
The retained high quality reads were mapped to the genome of Citrus Sinensis and Clementine by tophat, and then assembled with Cufflinks
The unigenes resulted from mRNA reads assembly were compared with the non-redundant nucleotide and protein database using BLASTN and BLASTX respectively, with the E-vaule cutoffs of 1e-5.
The differentially expressed genes were identified by Cuffdiff, with P-value ≤0.05 and fold change ≥2.0, whereas the differentially expressed miRNAs were identified by edge
Genome_build: Reference genome sequences of Citrus Sinensis were were downloaded from http://citrus.hzau.edu.cn/orange/download/data.php, while Clementine genome sequences were downloaded from http://phytozome.jgi.doe.gov/pz/portal.html.
Supplementary_files_format_and_content: files include raw counts and  RPKM values

molecule: total RNA

organism: Citrus maxima

source_name: Ovules_Huanong red pummelo (Citrus grandis)

extract_protocol:
Total RNA was extracted by Trizol method
Libraries were constructed for sequencing using standard Illumina protocols

tag: cultivar

value: Huanong red pummelo

tag: tissue

value: ovules

tag: age

value: 0 DAF(days after flowering), i.e anthesis


title: 1772058147_G10


title: Late stage post-radiation GBM RCAS mouse model cell T3-73

city: New York

first: Sheng

last: Li

state: New York

address: 525 East 68th Street

department: Neurological Surgery

country: USA

institute: Weill Cornell Medical College

data_processing:
Data analysis was performed through the rmake pipeline, which uses STAR for alignment and TPM measurements for gene expressoin abundance quantification using Gencode mouse V7 protein coding gene model.
Cells were filtered based on number of reads mapped to the mitochondria chromosome (>=20%) and mapping rate (< 50%). In addition, cells were filtered if Pdgfra is not expressed (TPM < 3).
A expression matrix were made by log2 (1+TPM)
Genome_build: mm10
Supplementary_files_format_and_content: gene read count matrix

source_name: stage T3,  Cell # 73

growth_protocol: RCAS-hPDGFb-HA-SV40 containing human PDGFb with partially deleted 59UTR, RCAS-hPDGFb-HA, and RCAS-Cre vectors were transfected into DF-1 chicken cells (ATCC). DF1 cells transfected with RCAS-PSG were cultured in 10% FBS-DMEM media under standard conditions. For tumor induction, transfected DF1 cells were trypsinized, centrifuged and injected into the brain parenchyma of Ntva mice in heterozygous Ink4a/Arf +/-, Ptenfl/fl background at post-natal days 0– 2. The mice transgenically express RCAS binding tv-a receptor after the nestin promoter.

extract_protocol:
The tumor cells were isolated from primary or recurrent tumors from RCAS-tva mice followed by FACS. Tumor masses, which were pre-determined by MRI, were minced and then incubated at 37°C with PAPAIN in PIPES buffer, resuspending after 20 min. After quenching the digestion with fetal calf serum, the suspension was again disrupted with a pipette and passed through 70um cell filters. Samples were collected immediately by centrifugation, and then they were subjected to myelin removal (Miltenyi Biotec.). Wash the remaining cells by PBS with 2% fetal calf serum, centrifuge at 300g for 5 minutes, discard supernatant and re-suspend the pellet in the volume remaining. Follow antibody and live/dead stainings (Invitrogen) procedures. Cells were counted and one million cells in each sample were subjected to flow assisted cells sorting.  The following antibodies were used for staining: FITC-CD45, PE-CD31, APC-CD140a (PDGFRa), (eBiosciece); Pacific Blue/Mouse Lineage Panel (Biolegend). The data were analyzed by Flowjo software. The analysis was done within single cell gate after the exclusion of debris and dead cells.
Tumor cells were isolated from mouse brain tumor tissue samples. Single cells were then captured and mRNA isolated using Clontech's SMARTer chemistry on the Fluidigm C1 Single Cell Auto Prep system. Illumina's Nextera XT kit was used for library preparation.
Single cell sequencing were performed on the HiSeq2500 platform with 100 bp single-end sequencing.

treatment_protocol: Once the mice had developed radiographic high-grade tumors approximately at week 6, they were subjected to head-only fractioned ionizing radiation- 2 Gy a day, every other day for five times. To determine the progression, regression, or recurrence of tumors, high-resolution MRI images were acquired on a 7.0-T animal scanner system (Bruker Biospin). During imaging, animals were under isoflurane anesthesia and monitored for respiration and heart rate; the temperature was kept at 37°C. Images were analyzed by OsiriX DICOM viewer.

tag: tumor stage

value: Late stage post-radiation

value: Brain

tag: time point (weeks)

value: 10 weeks

tag: tumor type

value: Recurrent Tumor

tag: background strain

value: RCAS-TVA

tag: tumor grade

value: High


title: Late stage post-radiation GBM RCAS mouse model cell T3-83

source_name: stage T3,  Cell # 83


title: 1772058147_G09

value: neurons

tag: level2 class (neurons only)

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: Late stage post-radiation GBM RCAS mouse model cell T3-71

source_name: stage T3,  Cell # 71


title: Late stage post-radiation GBM RCAS mouse model cell T3-72

source_name: stage T3,  Cell # 72


title: Late stage post-radiation GBM RCAS mouse model cell T3-70

source_name: stage T3,  Cell # 70


title: Late stage post-radiation GBM RCAS mouse model cell T3-7

source_name: stage T3,  Cell # 7


title: 1772058147_G07

value: microglia


title: Late stage post-radiation GBM RCAS mouse model cell T3-69

source_name: stage T3,  Cell # 69


title: 1772058147_G05


title: 1772058147_H02


title: Late stage post-radiation GBM RCAS mouse model cell T3-68

source_name: stage T3,  Cell # 68


title: Late stage post-radiation GBM RCAS mouse model cell T3-67

source_name: stage T3,  Cell # 67


title: 1772058147_G04


title: Late stage post-radiation GBM RCAS mouse model cell T3-65

source_name: stage T3,  Cell # 65


title: 1772058147_G02


title: 1772058147_G03

value: Galanin


title: 1772058147_G01

value: Unknown

value: Avp-medium


title: 1772058147_F12

value: N

value: ependymal


title: Late stage post-radiation GBM RCAS mouse model cell T3-63

source_name: stage T3,  Cell # 63


title: Late stage post-radiation GBM RCAS mouse model cell T3-60

source_name: stage T3,  Cell # 60


title: Late stage post-radiation GBM RCAS mouse model cell T3-61

source_name: stage T3,  Cell # 61


title: 1772058147_F08


title: Late stage post-radiation GBM RCAS mouse model cell T3-64

source_name: stage T3,  Cell # 64


title: 1772058147_F09


title: 1772058147_F07

value: Oxt;Avp-low


title: 1772058147_F06


title: Late stage post-radiation GBM RCAS mouse model cell T3-59

source_name: stage T3,  Cell # 59


title: Late stage post-radiation GBM RCAS mouse model cell T3-6

source_name: stage T3,  Cell # 6


title: 1772058147_G08

source_name: hypothalamus


title: 1772058147_G06

value: Pomc+/- (ARH)


title: 1772058147_F05


title: 1772058147_F11


title: 1772058147_F04


title: Late stage post-radiation GBM RCAS mouse model cell T3-57

source_name: stage T3,  Cell # 57


title: Late stage post-radiation GBM RCAS mouse model cell T3-58

source_name: stage T3,  Cell # 58


title: 1772058147_F03


title: 1772058147_F02

value: oligos


title: Late stage post-radiation GBM RCAS mouse model cell T3-66

source_name: stage T3,  Cell # 66

value: Late stage post-radiation


title: Late stage post-radiation GBM RCAS mouse model cell T3-56

source_name: stage T3,  Cell # 56

value: Brain


title: Late stage post-radiation GBM RCAS mouse model cell T3-55

source_name: stage T3,  Cell # 55

value: 10 weeks


title: Late stage post-radiation GBM RCAS mouse model cell T3-54

source_name: stage T3,  Cell # 54

value: Recurrent Tumor


title: Late stage post-radiation GBM RCAS mouse model cell T3-62

source_name: stage T3,  Cell # 62

value: RCAS-TVA


title: 1772058147_F01


title: 1772058147_E11


title: Late stage post-radiation GBM RCAS mouse model cell T3-51

source_name: stage T3,  Cell # 51

value: High


title: Late stage post-radiation GBM RCAS mouse model cell T3-53

source_name: stage T3,  Cell # 53


title: 1772058147_E12

value: endothelial


title: Late stage post-radiation GBM RCAS mouse model cell T3-52

source_name: stage T3,  Cell # 52


title: Late stage post-radiation GBM RCAS mouse model cell T3-50

source_name: stage T3,  Cell # 50


title: 1772058147_E10

value: neurons

value: Crh+/-;Gal-low (PVH)


title: 1772058147_E09

value: vsm


title: Late stage post-radiation GBM RCAS mouse model cell T3-5

source_name: stage T3,  Cell # 5


title: 1772058147_E07

value: Unknown


title: 1772058147_E08


title: 1772058147_E06


title: Late stage post-radiation GBM RCAS mouse model cell T3-47

source_name: stage T3,  Cell # 47


title: 1772058147_E03


title: Late stage post-radiation GBM RCAS mouse model cell T3-49

source_name: stage T3,  Cell # 49


title: Late stage post-radiation GBM RCAS mouse model cell T3-48

source_name: stage T3,  Cell # 48


title: 1772058147_E05

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772058147_E04

value: N


title: 1772058147_E01

value: ependymal


title: Late stage post-radiation GBM RCAS mouse model cell T3-45

source_name: stage T3,  Cell # 45


title: S2052 stat C bio3

city: Kgs. Lyngby

first: Sonia

last: Giubergia

address: Matematiktorvet 301

country: Denmark

institute: Technical University of Denmark

data_processing:
Data received from BGI were already sorted according to their respective adaptor sequences, and linker sequences had already been removed. RNA seq data was analyzed using the CLC genomics workbench software (CLC Aarhus, version 8.5). Quality and quantity of RNA sequence data was evaluated by the number of reads, GC%, PHRED-score, nucleotide contribution, quality distribution and enriched 5mers sequences. Reads were trimmed removing the first 15 nucleotides when nucleotide contribution was not normally distributes. Reads were then mapped to the reference genomes and expression values were calculated as RPKM. Gene expression profiles of biological samples were merged and, for each strain at each time point, the profiles deriving from the two media were compared. The quality of the transcriptomic data was evaluated using hierarchical clustering and principal component analysis. Statistically significant gene expression differences were assesses through a Baggerley's test using p-value<0.05 and q-values<0.05
Genome_build: V. coralliilyticus S2052 genome (JXXR01)
Supplementary_files_format_and_content: xslx files including total gene reads, RPKM values etc. for each sample

organism: Vibrio coralliilyticus

source_name: Vibrio coralliilyticus

growth_protocol: Strains were inoculated in 10 ml of ½ YTSS in a 50 ml Erlenmeyer flasks and grown aerated (200 rpm) at 25 degrees for 24 hours. 100 ul of the 24 hours cultures were used to inoculate 10 ml of fresh ½ YTSS, and these cultures were grown for 24 hours, 200 rpm at 25 degrees. 50 ml of the glucose containing medium (SSBG, 2% Sigma Sea Salts, 0.3% casamino acids, 40mM MOPS, 0.2% glucose) and of the chitin containing medium (SSBC, 2% Sigma Sea Salts, 0.3% casamino acids, 0.2% colloidal chitin) were inoculated at a cell density of  approximately 10^3 CFU/ml. Cultures were run in 250 ml Erlenmeyer flasks, 200 rpm, 25 degrees. Samples for gene expression and bacterial counts were taken in the late exponential phase (cell density 10^8 CFU/ml) and in the stationary phase (24 hours old cultures, approx 10^9 CFU/ml)

extract_protocol:
RNA was extracted using the RNeasy kit(Qiagen), following manufacturer's instructions. DNA was removed on column with the Rnase-free Dnase set (Qiagen). Integrity and  quality of total RNA were assesses with a NanoDrop spectrometer and an Agilent 2100 Bioanalyzer. Total RNA samples were sent to the Beijing Genome Institute (BGI, Hong Kong), where rRNA was removed using the Ribo-Zero rRNA removal kit
Library where constructed by BGI with the TruSeq RNA Library Preparation kit (Illumina) and 100 bp paired-enf sequenced on a HiSeq 2000

treatment_protocol: At the harvesting time points, subsamples of the bacterial cultures were taken and mixed with 0.2 volumes of ice-cold STOP solution (95% [v/v] ethanol, 5% [v/v] phenol), incubated for 5 minutes on ice and pelleted by centrifugation. Cell pellets were stored at -80 degrees until RNA extraction.

tag: carbon source

value: Growth on chitin

tag: growth phase

value: Stationary phase


title: Late stage post-radiation GBM RCAS mouse model cell T3-46

source_name: stage T3,  Cell # 46


title: Late stage post-radiation GBM RCAS mouse model cell T3-44

source_name: stage T3,  Cell # 44


title: S2052 stat C bio2

tag: strain


title: Late stage post-radiation GBM RCAS mouse model cell T3-42

source_name: stage T3,  Cell # 42


title: 1772058147_D10

source_name: hypothalamus

tag: age (days postnatal)

tag: Sex


title: S2052 stat C bio1


title: Late stage post-radiation GBM RCAS mouse model cell T3-43

source_name: stage T3,  Cell # 43


title: 1772058147_D11

tag: acute stress

tag: cell diameter


title: 1772058147_D09

tag: total molecules

tag: level1 class


title: Late stage post-radiation GBM RCAS mouse model cell T3-41

source_name: stage T3,  Cell # 41

tag: tissue


title: S2052 stat G bio3

value: Growth on glucose


title: S2052 stat G bio2


title: 1772058147_D08


title: S2052 stat G bio1


title: 1772058147_D06


title: 1772058147_D07


title: 1772058147_D05


title: Late stage post-radiation GBM RCAS mouse model cell T3-4

source_name: stage T3,  Cell # 4

value: Late stage post-radiation


title: Late stage post-radiation GBM RCAS mouse model cell T3-39

source_name: stage T3,  Cell # 39

value: Brain


title: S2052 exp C bio3

value: Exponential phase


title: S2052 exp C bio2


title: 1772058147_D04


title: S2052 exp C bio1


title: Late stage post-radiation GBM RCAS mouse model cell T3-37

source_name: stage T3,  Cell # 37

value: 10 weeks

value: Recurrent Tumor


title: 1772058147_D03


title: S2052 exp G bio3


title: Late stage post-radiation GBM RCAS mouse model cell T3-36

source_name: stage T3,  Cell # 36

value: RCAS-TVA

value: High


title: 1772058147_D01

value: neurons


title: S2052 exp G bio2


title: S2052 exp G bio1


title: Late stage post-radiation GBM RCAS mouse model cell T3-40

source_name: stage T3,  Cell # 40


title: 1772058147_C11


title: 1772058147_C10


title: Late stage post-radiation GBM RCAS mouse model cell T3-33

source_name: stage T3,  Cell # 33


title: Late stage post-radiation GBM RCAS mouse model cell T3-32

source_name: stage T3,  Cell # 32


title: Oak-H-H3

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

data_processing:
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 20 (Q >20).
Quality filtering was done with Scythe v.0.991 with a prior of 0.4
Bowtie2 v.2.1.0  was used to map the processed reads to the combined references with the following options: -q --end-to-end --sensitive --no-unal -p 12
Read counts were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Vitis vinifera cv. PN40024 combined with NCBI accessions: YP_008400117.1, YP_008400116.1, YP_008400118.1, YP_008400114.1, YP_008400113.1, and YP_008400115.1
Supplementary_files_format_and_content: Healdsburg_grape_gene_counts.txt and Oakville_grape_genes_counts.txt: tab delimited text files, raw read counts determined by mapping trimmed sequencing reads

organism: Vitis vinifera

source_name: grape berries

growth_protocol: Individual berries were collected from grapevines that were naturally infected with GRBaV and from healthy grapevines

extract_protocol:
Total RNA was extracted from freeze-ground berry tissues (no seeds) using a CTAB based protocol with a chloroform denaturation step. RNA was cleaned with RNeasy kit (Qiagen, US) including the DNAse treatment on column.
Illumina TruSeq RNA Sample Prep Kit v2 protocol

tag: cultivar

value: Zinfandel

tag: vineyard

value: Oakville

tag: ripening stage

value: Harvest

tag: status

value: Healthy


title: Oak-H-H2


title: 1772058147_C09

value: Unknown

value: N


title: Oak-H-H1


title: 1772058147_C07


title: Late stage post-radiation GBM RCAS mouse model cell T3-31

source_name: stage T3,  Cell # 31

tag: tumor stage

tag: time point (weeks)

tag: tumor type

tag: background strain


title: Late stage post-radiation GBM RCAS mouse model cell T3-38

source_name: stage T3,  Cell # 38

tag: tumor grade


title: Late stage post-radiation GBM RCAS mouse model cell T3-30

source_name: stage T3,  Cell # 30


title: Late stage post-radiation GBM RCAS mouse model cell T3-3

source_name: stage T3,  Cell # 3


title: 1772058147_C05

tag: strain

value: oligos


title: 1772058147_C06

tag: age (days postnatal)

tag: level2 class (neurons only)

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: Oak-H-RB2


title: 1772058147_C04

tag: Sex

tag: acute stress


title: Late stage post-radiation GBM RCAS mouse model cell T3-28

source_name: stage T3,  Cell # 28


title: 1772058147_D02

tag: cell diameter

tag: total molecules


title: Oak-PV-H4

value: Post-veraison


title: Oak-H-RB1


title: Late stage post-radiation GBM RCAS mouse model cell T3-35

source_name: stage T3,  Cell # 35

value: Late stage post-radiation

tag: tissue


title: Late stage post-radiation GBM RCAS mouse model cell T3-27

source_name: stage T3,  Cell # 27

value: Brain


title: Oak-PV-H3

tag: cultivar


title: Late stage post-radiation GBM RCAS mouse model cell T3-34

source_name: stage T3,  Cell # 34


title: 1772058147_C01

source_name: hypothalamus

tag: level1 class

value: microglia


title: 1772058147_C02

value: ependymal


title: Late stage post-radiation GBM RCAS mouse model cell T3-26

source_name: stage T3,  Cell # 26

value: 10 weeks

value: Recurrent Tumor


title: Oak-PV-H1

tag: vineyard

tag: ripening stage


title: Oak-PV-H2

tag: status


title: 1772058147_B12

value: astrocytes


title: Oak-PV-RB3


title: Late stage post-radiation GBM RCAS mouse model cell T3-24

source_name: stage T3,  Cell # 24

tag: tumor stage

tag: time point (weeks)

value: RCAS-TVA

value: High


title: Oak-H-RB3

value: Zinfandel

value: Oakville


title: Oak-PV-RB1


title: Late stage post-radiation GBM RCAS mouse model cell T3-23

source_name: stage T3,  Cell # 23

tag: tumor type

tag: background strain


title: Late stage post-radiation GBM RCAS mouse model cell T3-29

source_name: stage T3,  Cell # 29

tag: tumor grade


title: Late stage post-radiation GBM RCAS mouse model cell T3-21

source_name: stage T3,  Cell # 21


title: Oak-PV-RB2


title: 1772058147_B07

tag: strain

tag: age (days postnatal)


title: 1772058147_B08

tag: Sex

value: neurons

tag: level2 class (neurons only)

value: GABA 1


title: 1772058147_B10

value: Unknown

tag: acute stress

value: N

tag: cell diameter


title: 1772058147_B11

tag: total molecules

value: Oxt;Avp-low


title: Late stage post-radiation GBM RCAS mouse model cell T3-20

source_name: stage T3,  Cell # 20

tag: tissue


title: 1772058147_B05

tag: level1 class


title: Late stage post-radiation GBM RCAS mouse model cell T3-2

source_name: stage T3,  Cell # 2


title: Oak-V-H1

source_name: grape berries

tag: cultivar

tag: vineyard

value: Veraison

value: Healthy


title: 1772058147_B04


title: Late stage post-radiation GBM RCAS mouse model cell T3-19

source_name: stage T3,  Cell # 19

value: Late stage post-radiation

value: Brain


title: Late stage post-radiation GBM RCAS mouse model cell T3-25

source_name: stage T3,  Cell # 25


title: 1772058147_B06

value: ependymal


title: 1772058147_B03


title: Oak-V-RB2

tag: ripening stage

tag: status


title: Late stage post-radiation GBM RCAS mouse model cell T3-22

source_name: stage T3,  Cell # 22

tag: tumor stage

tag: time point (weeks)

value: 10 weeks


title: 1772058147_B02


title: 1772058147_B01


title: Late stage post-radiation GBM RCAS mouse model cell T3-16

source_name: stage T3,  Cell # 16

tag: tumor type

value: Recurrent Tumor

tag: background strain


title: Oak-V-H4


title: Oak-V-RB1


title: Late stage post-radiation GBM RCAS mouse model cell T3-17

source_name: stage T3,  Cell # 17

tag: tumor grade


title: 1772058147_A11

tag: strain

tag: age (days postnatal)


title: 1772058147_A10

tag: Sex

tag: level2 class (neurons only)


title: Oak-PRV-H2

value: Pre-veraison


title: Oak-V-H3


title: Late stage post-radiation GBM RCAS mouse model cell T3-15

source_name: stage T3,  Cell # 15

value: RCAS-TVA


title: Oak-PRV-H3


title: Oak-V-H2


title: 1772058147_A09

tag: acute stress

tag: cell diameter


title: Late stage post-radiation GBM RCAS mouse model cell T3-14

source_name: stage T3,  Cell # 14

tag: tissue

value: High


title: 1772058147_A08

tag: total molecules

tag: level1 class


title: Oak-PRV-RB3

tag: cultivar

value: Zinfandel

tag: vineyard


title: 1772058147_A07


title: Oak-PRV-RB2

value: Oakville

tag: ripening stage

tag: status


title: Oak-V-RB3


title: Late stage post-radiation GBM RCAS mouse model cell T3-18

source_name: stage T3,  Cell # 18

tag: tumor stage

tag: time point (weeks)


title: Late stage post-radiation GBM RCAS mouse model cell T3-13

source_name: stage T3,  Cell # 13

tag: tumor type

tag: background strain


title: Oak-PRV-RB1


title: Late stage post-radiation GBM RCAS mouse model cell T3-12

source_name: stage T3,  Cell # 12

tag: tumor grade


title: 1772058147_A06

source_name: hypothalamus

tag: strain

tag: age (days postnatal)

value: oligos


title: Late stage post-radiation GBM RCAS mouse model cell T3-11

source_name: stage T3,  Cell # 11


title: Late stage post-radiation GBM RCAS mouse model cell T3-10

source_name: stage T3,  Cell # 10


title: Oak-PRV-H1


title: He-H-H3

value: Healdsburg

value: Harvest


title: 1772058147_A05

value: Unknown

tag: Sex

value: N

value: neurons

tag: level2 class (neurons only)

value: Crh+/-;Gal-low (PVH)


title: Late stage post-radiation GBM RCAS mouse model cell T3-1

source_name: stage T3,  Cell # 1

value: Late stage post-radiation


title: He-H-H2

value: Healthy


title: Early stage post-radiation GBM RCAS mouse model cell T2-96

source_name: stage T2,  Cell # 96

value: Early stage post-radiation

value: Brain

value: 7 weeks

value: Post-radiation Residual Tumor


title: 1772058147_A02

tag: acute stress

tag: cell diameter

value: endothelial


title: He-H-RB6


title: Early stage post-radiation GBM RCAS mouse model cell T2-94

source_name: stage T2,  Cell # 94

tag: tissue

value: RCAS-TVA

value: High


title: Early stage post-radiation GBM RCAS mouse model cell T2-95

source_name: stage T2,  Cell # 95


title: Early stage post-radiation GBM RCAS mouse model cell T2-93

source_name: stage T2,  Cell # 93


title: Early stage post-radiation GBM RCAS mouse model cell T2-92

source_name: stage T2,  Cell # 92


title: He-H-RB1

source_name: grape berries

value: Zinfandel


title: He-H-RB2


title: He-PostV-H3

value: Post-veraison


title: Early stage post-radiation GBM RCAS mouse model cell T2-91

source_name: stage T2,  Cell # 91


title: Early stage post-radiation GBM RCAS mouse model cell T2-90

source_name: stage T2,  Cell # 90


title: VC-1

city: Lanzhou

first: Y

last: Gao

address: Xujiaping 1

institute: LVRI

data_processing:
Basecalls performed using Perl package developed by BGI
We will get rid of some contaminant reads from the fq file and get the final clean reads. And then summarize the length distribution of these clean reads. Normally, length of small RNA is between 18nt and 30nt. The length distribution analysis is helpful to see the compositions of small RNA sample. For example, miRNA is normally 21nt or 22nt, siRNA is 24nt, and piRNA is 30nt.
Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table).
Getting rid of reads with 5' primer contaminants or without 3' primer.
Getting rid of reads without the insert tag or poly A.
Getting rid of reads shorter than 18nt.
Summarize the length distribution of the clean reads.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

growth_protocol: The J1 mESC was gelatin adapted and plated on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF at condition of 37℃ and 5% CO2.

extract_protocol:
Total cellular RNA was isolated from J1 mESC using TRIzol RNA Isolation Reagent (Invitrogen, USA) following the manufacturer's recommendations.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The J1 mESCs were treated with a final concentration of BIO (1μM), CHIR99021 (3μM), RA (1μM), DMSO (1μL), VC (50μg/ml), ddH2O (1μL)

tag: treatment

tag: cell type

value: J1 mESC


title: CHIR


title: J1_U

value: DMSO


title: VC-36

value: vitamin C


title: J1_D

value: Retinoic acid


title: He-PostV-H1

tag: cultivar

tag: vineyard

value: Healdsburg


title: Early stage post-radiation GBM RCAS mouse model cell T2-89

source_name: stage T2,  Cell # 89


title: Early stage post-radiation GBM RCAS mouse model cell T2-9

source_name: stage T2,  Cell # 9


title: He-PostV-H2

tag: ripening stage

tag: status


title: He-H-H1

value: Harvest


title: 1772058147_A01

value: Unknown

value: N

tag: total molecules

tag: level1 class

value: vsm


title: RBP-J KO rep2

first: Baohong

last: Zhao

address: 535 E70th ST

institute: Hospital for Special Surgery

data_processing:
Sequenced reads were passed Quality Control, and mapped to the mouse genome (mm9, NCBI Build 37) using TopHat.
Cufflinks was subsequently used to assemble the aligned reads into transcripts.
Cufflinks was then used to estimate the transcript abundances as RPKM (reads per kilo base per million) values.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow cells were harvested from 8 week old mice, and cultured with CMG14-12 supernatant, which contained the equivalent of 20 ng/ml of recombinant M-CSF for 3 days to induce bone marrow derived macrophages.

extract_protocol:
Bone marrow were harvested from 8 week old mice.
Illumina TrueSeq RNA sample preparation protocol

value: Bone marrow derived macrophages

tag: genotype

value: RBP-J KO; Rbpj f/f;LysM cre


title: Early stage post-radiation GBM RCAS mouse model cell T2-88

source_name: stage T2,  Cell # 88

tag: tumor stage

value: Early stage post-radiation

value: Brain

tag: time point (weeks)

value: 7 weeks

tag: tumor type

value: Post-radiation Residual Tumor

tag: background strain

tag: tumor grade


title: Early stage post-radiation GBM RCAS mouse model cell T2-87

source_name: stage T2,  Cell # 87

value: RCAS-TVA

value: High


title: WT rep1

tag: strain

value: wildtype control


title: WT rep2


title: He-PostV-RB4

value: Zinfandel

value: Post-veraison


title: He-PostV-RB6


title: RBP-J KO rep1


title: He-PostV-RB2


title: He-PostV-RB1


title: He-H-RB4


title: He-V-H3

value: Veraison

value: Healthy


title: Early stage post-radiation GBM RCAS mouse model cell T2-85

source_name: stage T2,  Cell # 85


title: Early stage post-radiation GBM RCAS mouse model cell T2-86

source_name: stage T2,  Cell # 86


title: He-V-H1

value: Healdsburg


title: Early stage post-radiation GBM RCAS mouse model cell T2-84

source_name: stage T2,  Cell # 84


title: Early stage post-radiation GBM RCAS mouse model cell T2-83

source_name: stage T2,  Cell # 83


title: He-V-RB6


title: He-V-RB4


title: He-PreV-H2

value: Pre-veraison


title: He-PreV-H3


title: He-V-RB2


title: Early stage post-radiation GBM RCAS mouse model cell T2-82

source_name: stage T2,  Cell # 82


title: Early stage post-radiation GBM RCAS mouse model cell T2-81

source_name: stage T2,  Cell # 81


title: Early stage post-radiation GBM RCAS mouse model cell T2-8

source_name: stage T2,  Cell # 8


title: Early stage post-radiation GBM RCAS mouse model cell T2-78

source_name: stage T2,  Cell # 78


title: Early stage post-radiation GBM RCAS mouse model cell T2-79

source_name: stage T2,  Cell # 79


title: He-PreV-H1

source_name: grape berries


title: Early stage post-radiation GBM RCAS mouse model cell T2-76

source_name: stage T2,  Cell # 76


title: He-PreV-RB1


title: He-PreV-RB2


title: Early stage post-radiation GBM RCAS mouse model cell T2-80

source_name: stage T2,  Cell # 80


title: Early stage post-radiation GBM RCAS mouse model cell T2-74

source_name: stage T2,  Cell # 74


title: Early stage post-radiation GBM RCAS mouse model cell T2-77

source_name: stage T2,  Cell # 77


title: Early stage post-radiation GBM RCAS mouse model cell T2-75

source_name: stage T2,  Cell # 75


title: He-PreV-RB6


title: Early stage post-radiation GBM RCAS mouse model cell T2-72

source_name: stage T2,  Cell # 72


title: Early stage post-radiation GBM RCAS mouse model cell T2-71

source_name: stage T2,  Cell # 71


title: Early stage post-radiation GBM RCAS mouse model cell T2-70

source_name: stage T2,  Cell # 70


title: PmTbr MASO rep3

city: Pittsburgh

first: Gregory

last: Cary

state: PA

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

description: Pm-Tbr knockdown

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Pmin_1.0 draft genome assembly using tophat v2.0.12 with parameters: --no-coverage-search --library-type fr-unstranded --b2-very-sensitive --transcriptome-index <bwtidx> -G <pm.genes.gff3>. Alignments were filtered to include only uniquely mapped reads using samtools 0.1.19-44428cd. Transcripts were assembled using cufflinks v2.2.1 with parameters: -u -b <pmin.scaff.fa> -g <pm.genes.gff3> and all cufflinks assemblies were merged using cuffmerge.
Transcript abundance was calculated against the merged transcriptome assemblies using HTSeq-count v0.6.1p1 using the parameters: --format=bam --minaqual=2 --stranded=no -i gene_id. Genes with at least 2 tag counts per 1x10^6 reads in at least three separate samples were retained for further analysis. Normalization, dispersion estimation and differential expression testing were all done using functions contained in the edgeR_3.10.5 Bioconductor package. The sample batch (rep#) and treatment were included in the design model matrix (~0+treatment+batch) and significance was assessed using the quasi-liklihood F test (glmQLFit) and controlled for errors based on multiple hypothesis testing.
Genome_build: Pmin_1.0
Supplementary_files_format_and_content: Tab-delimited text files include sequence tag counts for each sample to the assembled genes as well as the output of the edgeR differential expression analysis for expressed genes which includes the genomic loci of each assembled gene.

organism: Patiria miniata

source_name: Pooled Embryos

growth_protocol: Embryos were cultured in artificial seawater at 15°C until hatching, approximately 30 hpf for standard control injected and typically 36 hpf for Tbr MASO injected.

extract_protocol:
RNA was extracted using the GenElute Mammalian Total RNA Kit (Sigma-Aldrich).
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq)

treatment_protocol: Patiria miniata zygotes were injected with 600 µM Tbr MASO or standard control MASO (Gene Tools) as described previously. Embryos were sorted on the basis of rhodamine tracer and morphology to ensure that only healthy injected embryos were processed for RNA.  Embryos that arrested in early development or that exhibited aberrant development were discarded.

tag: developmental stage

value: hatched blastula

tag: age

value: 36 hpf

tag: morpholino

value: Pm-Tbr


title: He-V-RB1


title: Early stage post-radiation GBM RCAS mouse model cell T2-7

source_name: stage T2,  Cell # 7

tag: tissue


title: PmTbr MASO rep1

description: Pm-Tbr knockdown


title: Control MASO rep2

description: Control

value: 30 hpf

value: Control


title: Control MASO rep3

description: Control


title: Control MASO rep1

description: Control


title: Early stage post-radiation GBM RCAS mouse model cell T2-69

source_name: stage T2,  Cell # 69

value: Early stage post-radiation

value: Brain


title: Pmin input DNA

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to either the Spur_3.1 or Pmin_1.0 draft genome assembly using bowtie v2.2.2 and the following paramters: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.
Alignments were filtered with samtools v0.1.19 to only include alignments with MAPQ >1. Furthermore, for Patiria miniata, any alignments that overlap predicted RTE2 retroelements were masked from downstream peak calling analyses.
Peaks were called using MACS2 v2.1.0 with the following parameters, for sea urchin -g 8e+8 -m 5 50 -q 0.05 , and for sea star -g 8e+8 --bw 250 -m 10 50 -p 1e-5.
Genome_build: Spur_3.1 and Pmin_1.0
Supplementary_files_format_and_content: For each species, a bed file is supplied reporting the position and statistics associated with each macs2 called peak. In addition, bedgraph files showing sequence tag pileups in treatment and control samples are provided for each.

molecule: genomic DNA

source_name: Pooled embryos

growth_protocol: Approximately 100,000 embryos (1 x 10^8 cells) were cultured in artificial seawater at 15 °C until mesenchyme blastula stage (S. purpuratus, approximately 24 hpf) or hatched blastula stage (P. miniata, approximately 30 hpf.

extract_protocol:
Embryo samples were fixed in 1% formaldehyde in PBS for 10 minutes at room temperature, and fixation was stopped by addition of 0.125 M glycine.  Samples were pelleted and flash-frozen.  Chromatin was extracted using standard protocols, except that shearing was achieved by enzymatic digestion rather than sonication.  Micrococcal nuclease (Cell Signaling Technology) and digestion was performed according to the manufacturer’s SimpleChIP® instructions.  Chromatin immunoprecipitation was performed using standard protocols with 50 µg of fragmented chromatin and 10 µg of custom antibody for each Tbr ortholog.
Sequencing libraries were prepared from total (input) and immunoprecipitated chromatin using standard Illumina TruSeq ChIP library preparation protocols (Yale Center for Genome Analysis).

tag: chip antibody


title: Early stage post-radiation GBM RCAS mouse model cell T2-68

source_name: stage T2,  Cell # 68

value: 7 weeks

value: Post-radiation Residual Tumor


title: Early stage post-radiation GBM RCAS mouse model cell T2-67

source_name: stage T2,  Cell # 67

value: RCAS-TVA

value: High


title: Early stage post-radiation GBM RCAS mouse model cell T2-73

source_name: stage T2,  Cell # 73


title: Early stage post-radiation GBM RCAS mouse model cell T2-66

source_name: stage T2,  Cell # 66


title: Early stage post-radiation GBM RCAS mouse model cell T2-64

source_name: stage T2,  Cell # 64


title: Early stage post-radiation GBM RCAS mouse model cell T2-63

source_name: stage T2,  Cell # 63


title: Early stage post-radiation GBM RCAS mouse model cell T2-65

source_name: stage T2,  Cell # 65


title: PmTbr MASO rep2

description: Pm-Tbr knockdown


title: Early stage post-radiation GBM RCAS mouse model cell T2-62

source_name: stage T2,  Cell # 62


title: Early stage post-radiation GBM RCAS mouse model cell T2-59

source_name: stage T2,  Cell # 59


title: Early stage post-radiation GBM RCAS mouse model cell T2-60

source_name: stage T2,  Cell # 60


title: Early stage post-radiation GBM RCAS mouse model cell T2-57

source_name: stage T2,  Cell # 57


title: Early stage post-radiation GBM RCAS mouse model cell T2-55

source_name: stage T2,  Cell # 55


title: Early stage post-radiation GBM RCAS mouse model cell T2-61

source_name: stage T2,  Cell # 61


title: Early stage post-radiation GBM RCAS mouse model cell T2-54

source_name: stage T2,  Cell # 54


title: Early stage post-radiation GBM RCAS mouse model cell T2-58

source_name: stage T2,  Cell # 58


title: Early stage post-radiation GBM RCAS mouse model cell T2-53

source_name: stage T2,  Cell # 53


title: Early stage post-radiation GBM RCAS mouse model cell T2-52

source_name: stage T2,  Cell # 52


title: Early stage post-radiation GBM RCAS mouse model cell T2-51

source_name: stage T2,  Cell # 51


title: Early stage post-radiation GBM RCAS mouse model cell T2-50

source_name: stage T2,  Cell # 50


title: Early stage post-radiation GBM RCAS mouse model cell T2-5

source_name: stage T2,  Cell # 5


title: Early stage post-radiation GBM RCAS mouse model cell T2-49

source_name: stage T2,  Cell # 49


title: Early stage post-radiation GBM RCAS mouse model cell T2-46

source_name: stage T2,  Cell # 46


title: Early stage post-radiation GBM RCAS mouse model cell T2-47

source_name: stage T2,  Cell # 47


title: Early stage post-radiation GBM RCAS mouse model cell T2-45

source_name: stage T2,  Cell # 45


title: PmTbr ChIP DNA

source_name: Pooled embryos

value: anti-PmTbr (custom)


title: Early stage post-radiation GBM RCAS mouse model cell T2-48

source_name: stage T2,  Cell # 48


title: Early stage post-radiation GBM RCAS mouse model cell T2-44

source_name: stage T2,  Cell # 44


title: Early stage post-radiation GBM RCAS mouse model cell T2-43

source_name: stage T2,  Cell # 43


title: Early stage post-radiation GBM RCAS mouse model cell T2-56

source_name: stage T2,  Cell # 56


title: Early stage post-radiation GBM RCAS mouse model cell T2-6

source_name: stage T2,  Cell # 6


title: Early stage post-radiation GBM RCAS mouse model cell T2-42

source_name: stage T2,  Cell # 42


title: Early stage post-radiation GBM RCAS mouse model cell T2-38

source_name: stage T2,  Cell # 38


title: Early stage post-radiation GBM RCAS mouse model cell T2-40

source_name: stage T2,  Cell # 40


title: Early stage post-radiation GBM RCAS mouse model cell T2-34

source_name: stage T2,  Cell # 34


title: Early stage post-radiation GBM RCAS mouse model cell T2-37

source_name: stage T2,  Cell # 37


title: Early stage post-radiation GBM RCAS mouse model cell T2-41

source_name: stage T2,  Cell # 41


title: Early stage post-radiation GBM RCAS mouse model cell T2-4

source_name: stage T2,  Cell # 4


title: Early stage post-radiation GBM RCAS mouse model cell T2-33

source_name: stage T2,  Cell # 33


title: Early stage post-radiation GBM RCAS mouse model cell T2-30

source_name: stage T2,  Cell # 30


title: Early stage post-radiation GBM RCAS mouse model cell T2-29

source_name: stage T2,  Cell # 29


title: Early stage post-radiation GBM RCAS mouse model cell T2-3

source_name: stage T2,  Cell # 3


title: Early stage post-radiation GBM RCAS mouse model cell T2-31

source_name: stage T2,  Cell # 31


title: Early stage post-radiation GBM RCAS mouse model cell T2-39

source_name: stage T2,  Cell # 39


title: Early stage post-radiation GBM RCAS mouse model cell T2-36

source_name: stage T2,  Cell # 36


title: Early stage post-radiation GBM RCAS mouse model cell T2-28

source_name: stage T2,  Cell # 28


title: Early stage post-radiation GBM RCAS mouse model cell T2-25

source_name: stage T2,  Cell # 25


title: Early stage post-radiation GBM RCAS mouse model cell T2-27

source_name: stage T2,  Cell # 27


title: Early stage post-radiation GBM RCAS mouse model cell T2-26

source_name: stage T2,  Cell # 26


title: Early stage post-radiation GBM RCAS mouse model cell T2-23

source_name: stage T2,  Cell # 23


title: Early stage post-radiation GBM RCAS mouse model cell T2-32

source_name: stage T2,  Cell # 32


title: Early stage post-radiation GBM RCAS mouse model cell T2-24

source_name: stage T2,  Cell # 24


title: CD-6

city: Indianapolis

first: Jingmei

last: Lin

state: IN

address: 350 West 11th Street, Room 4048

department: Department of Pathology and Laboratory Medicine

institute: Indiana University School of Medicine

data_processing:
adaptor removed from raw reads, and QC to remove low quality reads
align reads to miRNA gene sequences using novoalign
aligned reads statistics: percentage of alignment, read length distribution
miRNA gene differential expression analysis using MR_DRSS which is based on DESeq;Benjamani Hochberg False Discovery Rate FDR > 10%;  > 20 reads in one sample; fold change > 2
build classifier which can distinguish UC_P, UC_NP, and CD; PCA analysis
Genome_build: hg19
Supplementary_files_format_and_content: microRNA gene expression value in log2 fold-change with FDR

organism: Homo sapiens

source_name: colon epithelial cells

growth_protocol: Fresh frozen colonic mucosa was sampled from colectomies of the patients.

extract_protocol:
The total small RNA was extracted using miRNeasy mini isolation kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Briefly, the frozen tissues were dissolved in Qiazol reagent for digestion, followed by separation, then nucleic acid was bound in the Mini-column, and washed using the buffer.
Illumina next generation sequencing of small RNA cDNA libraries from each patient’s tissue sample was performed at the Genomic Sequencing Core of the Cleveland Clinic

treatment_protocol: snap frozen in liquid nitrogen, and held at –80 ºC.

value: colon

tag: cell type

value: epithelial cells

tag: diagnosis

value: Crohns disease


title: CD-7


title: CD-5


title: Early stage post-radiation GBM RCAS mouse model cell T2-22

source_name: stage T2,  Cell # 22


title: Early stage post-radiation GBM RCAS mouse model cell T2-35

source_name: stage T2,  Cell # 35


title: Early stage post-radiation GBM RCAS mouse model cell T2-20

source_name: stage T2,  Cell # 20


title: Early stage post-radiation GBM RCAS mouse model cell T2-2

source_name: stage T2,  Cell # 2


title: Early stage post-radiation GBM RCAS mouse model cell T2-19

source_name: stage T2,  Cell # 19


title: CD-19


title: CD-15


title: CD-20


title: Early stage post-radiation GBM RCAS mouse model cell T2-18

source_name: stage T2,  Cell # 18


title: CD-13


title: Early stage post-radiation GBM RCAS mouse model cell T2-17

source_name: stage T2,  Cell # 17


title: CD-11


title: JM65

value: diverticular disease (used here as control)


title: CD-12


title: Early stage post-radiation GBM RCAS mouse model cell T2-15

source_name: stage T2,  Cell # 15


title: JM64


title: Early stage post-radiation GBM RCAS mouse model cell T2-16

source_name: stage T2,  Cell # 16


title: Early stage post-radiation GBM RCAS mouse model cell T2-14

source_name: stage T2,  Cell # 14


title: JM62


title: JM60


title: JM58


title: Early stage post-radiation GBM RCAS mouse model cell T2-10

source_name: stage T2,  Cell # 10


title: Early stage post-radiation GBM RCAS mouse model cell T2-21

source_name: stage T2,  Cell # 21


title: JM56


title: Early stage post-radiation GBM RCAS mouse model cell T2-11

source_name: stage T2,  Cell # 11


title: Primary GBM RCAS mouse model cell T1-96

source_name: stage T1,  Cell # 96

value: Primary

value: 5 weeks

value: Primary Tumor


title: JM54


title: Primary GBM RCAS mouse model cell T1-95

source_name: stage T1,  Cell # 95


title: JM47


title: Primary GBM RCAS mouse model cell T1-94

source_name: stage T1,  Cell # 94


title: JM51

source_name: colon epithelial cells


title: Primary GBM RCAS mouse model cell T1-93

source_name: stage T1,  Cell # 93


title: Primary GBM RCAS mouse model cell T1-92

source_name: stage T1,  Cell # 92


title: JM43


title: Primary GBM RCAS mouse model cell T1-91

source_name: stage T1,  Cell # 91


title: Primary GBM RCAS mouse model cell T1-90

source_name: stage T1,  Cell # 90


title: Early stage post-radiation GBM RCAS mouse model cell T2-12

source_name: stage T2,  Cell # 12


title: JM36


title: Early stage post-radiation GBM RCAS mouse model cell T2-13

source_name: stage T2,  Cell # 13


title: Primary GBM RCAS mouse model cell T1-9

source_name: stage T1,  Cell # 9


title: Early stage post-radiation GBM RCAS mouse model cell T2-1

source_name: stage T2,  Cell # 1


title: Primary GBM RCAS mouse model cell T1-89

source_name: stage T1,  Cell # 89


title: JM27


title: JM52


title: JM53


title: JM15


title: Primary GBM RCAS mouse model cell T1-85

source_name: stage T1,  Cell # 85


title: JM8


title: Primary GBM RCAS mouse model cell T1-82

source_name: stage T1,  Cell # 82


title: JM61

value: ulcerative colitis


title: JM71


title: JM81


title: JM45


title: JM75


title: JM82


title: Primary GBM RCAS mouse model cell T1-88

source_name: stage T1,  Cell # 88


title: Primary GBM RCAS mouse model cell T1-87

source_name: stage T1,  Cell # 87


title: Primary GBM RCAS mouse model cell T1-84

source_name: stage T1,  Cell # 84


title: Primary GBM RCAS mouse model cell T1-86

source_name: stage T1,  Cell # 86


title: JM29


title: Primary GBM RCAS mouse model cell T1-83

source_name: stage T1,  Cell # 83


title: Primary GBM RCAS mouse model cell T1-81

source_name: stage T1,  Cell # 81


title: JM44

source_name: colon epithelial cells


title: Primary GBM RCAS mouse model cell T1-8

source_name: stage T1,  Cell # 8


title: Primary GBM RCAS mouse model cell T1-80

source_name: stage T1,  Cell # 80


title: Primary GBM RCAS mouse model cell T1-78

source_name: stage T1,  Cell # 78


title: Primary GBM RCAS mouse model cell T1-77

source_name: stage T1,  Cell # 77


title: Primary GBM RCAS mouse model cell T1-79

source_name: stage T1,  Cell # 79


title: JM11


title: JM4c


title: JM22


title: CellSample_12_smallRNA

city: Reykjavik

first: Benjamin

last: Sigurgeirsson

address: Sturlugata 7

country: Iceland

institute: Reykjavik University

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C12_smallRNA

data_processing:
Quality filterin and adapter removal. TrimGalore!
Mapping to reference genome. STAR v2.4.1
Ribosomal removal. RseQC v.2.6.1
Expression quantification. HTSeq-Count
Differential expression. DESeq2
Genome_build: Reference: Ensembl GRCh38. Annotation: GRCh38.82
Supplementary_files_format_and_content: Gene expression. Text file with raw counts.

source_name: Endometrial stromal cells

extract_protocol:
miRNeasy Mini Kit (Qiagen)
TruSeq Small RNA Sample Preparation Kit (Illumina) (small RNA samples); TruSeq Stranded Total RNA kit (Illumina) (totalRNA samples)

tag: time point

value: TP2 (decidualized)

value: Endometrial stromal cells


title: CellSample_11_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C11_smallRNA

value: TP1 (naïve)


title: CellSample_10_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C10_smallRNA


title: CellSample_09_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C09_smallRNA


title: Primary GBM RCAS mouse model cell T1-76

source_name: stage T1,  Cell # 76

value: Brain


title: CellSample_07_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C07_smallRNA


title: Primary GBM RCAS mouse model cell T1-73

source_name: stage T1,  Cell # 73


title: Primary GBM RCAS mouse model cell T1-75

source_name: stage T1,  Cell # 75


title: CellSample_08_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C08_smallRNA


title: Primary GBM RCAS mouse model cell T1-74

source_name: stage T1,  Cell # 74


title: Primary GBM RCAS mouse model cell T1-71

source_name: stage T1,  Cell # 71


title: CellSample_04_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C04_smallRNA


title: CellSample_03_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C03_smallRNA


title: Primary GBM RCAS mouse model cell T1-69

source_name: stage T1,  Cell # 69


title: CellSample_06_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C06_smallRNA


title: Primary GBM RCAS mouse model cell T1-72

source_name: stage T1,  Cell # 72


title: Primary GBM RCAS mouse model cell T1-7

source_name: stage T1,  Cell # 7


title: CellSample_02_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C02_smallRNA


title: CellSample_05_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C05_smallRNA


title: JM41


title: Primary GBM RCAS mouse model cell T1-68

source_name: stage T1,  Cell # 68


title: Primary GBM RCAS mouse model cell T1-70

source_name: stage T1,  Cell # 70


title: CellSample_01_smallRNA

description:
small RNA
single end
processed data file: smallRNA_cells.counts.txt
Sample name: C01_smallRNA


title: Primary GBM RCAS mouse model cell T1-64

source_name: stage T1,  Cell # 64


title: TissueSample_14_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T14_smallRNA

source_name: Endometrium

value: TP2 (7-9 days after ovulation)

value: Endometrium


title: Primary GBM RCAS mouse model cell T1-67

source_name: stage T1,  Cell # 67

value: RCAS-TVA


title: TissueSample_13_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T13_smallRNA

value: TP1 (proliferative phase)


title: Primary GBM RCAS mouse model cell T1-65

source_name: stage T1,  Cell # 65

value: High


title: TissueSample_11_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T11_smallRNA


title: Primary GBM RCAS mouse model cell T1-66

source_name: stage T1,  Cell # 66


title: TissueSample_12_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T12_smallRNA


title: Primary GBM RCAS mouse model cell T1-63

source_name: stage T1,  Cell # 63


title: TissueSample_09_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T09_smallRNA


title: Primary GBM RCAS mouse model cell T1-62

source_name: stage T1,  Cell # 62


title: TissueSample_08_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T08_smallRNA


title: TissueSample_10_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T10_smallRNA


title: Primary GBM RCAS mouse model cell T1-60

source_name: stage T1,  Cell # 60


title: Primary GBM RCAS mouse model cell T1-6

source_name: stage T1,  Cell # 6


title: Primary GBM RCAS mouse model cell T1-59

source_name: stage T1,  Cell # 59


title: Primary GBM RCAS mouse model cell T1-58

source_name: stage T1,  Cell # 58


title: TissueSample_03_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T03_smallRNA


title: TissueSample_02_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T02_smallRNA


title: Primary GBM RCAS mouse model cell T1-56

source_name: stage T1,  Cell # 56


title: TissueSample_04_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T04_smallRNA


title: TissueSample_01_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T01_smallRNA


title: Primary GBM RCAS mouse model cell T1-55

source_name: stage T1,  Cell # 55


title: TissueSample_14_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T14_totalRNA


title: Primary GBM RCAS mouse model cell T1-54

source_name: stage T1,  Cell # 54


title: Primary GBM RCAS mouse model cell T1-53

source_name: stage T1,  Cell # 53


title: TissueSample_13_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T13_totalRNA


title: Primary GBM RCAS mouse model cell T1-52

source_name: stage T1,  Cell # 52


title: Primary GBM RCAS mouse model cell T1-51

source_name: stage T1,  Cell # 51


title: TissueSample_12_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T12_totalRNA


title: Primary GBM RCAS mouse model cell T1-50

source_name: stage T1,  Cell # 50


title: Primary GBM RCAS mouse model cell T1-61

source_name: stage T1,  Cell # 61


title: TissueSample_11_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T11_totalRNA

source_name: Endometrium


title: TissueSample_10_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T10_totalRNA


title: TissueSample_05_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T05_smallRNA


title: Primary GBM RCAS mouse model cell T1-5

source_name: stage T1,  Cell # 5


title: TissueSample_07_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T07_smallRNA


title: Primary GBM RCAS mouse model cell T1-49

source_name: stage T1,  Cell # 49


title: TissueSample_08_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T08_totalRNA


title: TissueSample_06_smallRNA

description:
small RNA
paired end
processed data file: smallRNA_tissue.counts.txt
Sample name: T06_smallRNA


title: Primary GBM RCAS mouse model cell T1-57

source_name: stage T1,  Cell # 57


title: TissueSample_09_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T09_totalRNA


title: Primary GBM RCAS mouse model cell T1-47

source_name: stage T1,  Cell # 47


title: TissueSample_05_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T05_totalRNA


title: TissueSample_07_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T07_totalRNA


title: TissueSample_04_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T04_totalRNA


title: Primary GBM RCAS mouse model cell T1-46

source_name: stage T1,  Cell # 46


title: Primary GBM RCAS mouse model cell T1-45

source_name: stage T1,  Cell # 45


title: TissueSample_03_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T03_totalRNA


title: Primary GBM RCAS mouse model cell T1-44

source_name: stage T1,  Cell # 44


title: Primary GBM RCAS mouse model cell T1-43

source_name: stage T1,  Cell # 43


title: Primary GBM RCAS mouse model cell T1-42

source_name: stage T1,  Cell # 42


title: TissueSample_02_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T02_totalRNA


title: TissueSample_01_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T01_totalRNA


title: Primary GBM RCAS mouse model cell T1-41

source_name: stage T1,  Cell # 41


title: GF-NEI-br1

description:
replicate 1 for ovules at nucellar embryo initiation stage
processed data file = "pummelo-grapefruit.rpkm.xlsx"

organism: Citrus x paradisi

source_name: Ovules_Cocktail grapefruit (Citrus x paradisi)

tag: cultivar

value: Cocktail

value: ovules

value: 3 DAF(days after flowering)


title: GF-pre-NEI-br2

description:
replicate 2 for ovules before nucellar embryo initiation stage
processed data file = "pummelo-grapefruit.rpkm.xlsx"

value: 0 DAF(days after flowering), i.e anthesis


title: GF-pre-NEI-br1

description:
replicate 1 for ovules before nucellar embryo initiation stage
processed data file = "pummelo-grapefruit.rpkm.xlsx"


title: Primary GBM RCAS mouse model cell T1-39

source_name: stage T1,  Cell # 39

value: Primary


title: Primary GBM RCAS mouse model cell T1-38

source_name: stage T1,  Cell # 38

value: 5 weeks


title: MT-EC_3D_D8-rep2

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to hg19 genome using Tophat2.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
Genome_build: hg19
Supplementary_files_format_and_content: testl files of gene names and FPKM values for each sample.

source_name: cultured cells

growth_protocol: Undifferentiated hESCs was cultured in homemade E8 medium without feeders.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and treated with RNase free DNase.
RNA library was prepared following the instruction of SMARTer® Ultra™ Low RNA Kit for Illumina® Sequencing（Clontech）

treatment_protocol: For monolayer based cardiomyocyte differentiation, we employed a protocol published by Lian et al (Yan et al., 2013).  On day 3 and day 5 of differentiation, MESP1-mTomato positive and negative cells were sorted.

value: Embryonic stem cells

value: endothelial differentiating MESP1+ cells in 3D


title: Primary GBM RCAS mouse model cell T1-37

source_name: stage T1,  Cell # 37

value: Primary Tumor


title: MT-EC_3D_D8-rep1


title: MT-EC_2D_D8-rep2

value: endothelial differentiating MESP1+ cells in 2D


title: TissueSample_06_totalRNA

description:
total RNA
paired end
processed data file: totalRNA_tissue.counts.txt
Sample name: T06_totalRNA


title: MESP1-mTomato-_D3-rep2

value: MESP- cells


title: MESP1-mTomato+_D3-rep2

value: mesoderm differentiating MESP1+


title: MESP1-mTomato-_D3-rep1


title: Primary GBM RCAS mouse model cell T1-34

source_name: stage T1,  Cell # 34

value: Brain


title: MESP1-mTomato+_D3-rep1


title: Undiff-MESP1-mTomato-rep2

tag: cell line


title: GF-NEI-br2

description:
replicate 2 for ovules at nucellar embryo initiation stage
processed data file = "pummelo-grapefruit.rpkm.xlsx"


title: Undiff-MESP1-mTomato-rep1


title: Primary GBM RCAS mouse model cell T1-32

source_name: stage T1,  Cell # 32


title: Primary GBM RCAS mouse model cell T1-33

source_name: stage T1,  Cell # 33


title: Primary GBM RCAS mouse model cell T1-31

source_name: stage T1,  Cell # 31


title: Primary GBM RCAS mouse model cell T1-40

source_name: stage T1,  Cell # 40


title: Primary GBM RCAS mouse model cell T1-4

source_name: stage T1,  Cell # 4


title: MT-EC_2D_D8-rep1


title: Primary GBM RCAS mouse model cell T1-30

source_name: stage T1,  Cell # 30


title: sh_#7

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.4.0j with default parameters.
Raw reads number of genes was calculated by HTSeq. cufflinks v2.2.1 was run for relative quantitation of genes expression and differential expression analysis.
bigwig files were generated by STAR with --outWigType wiggle --outWigStrand Unstranded --outWigNorm RPM parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: hepatocellular carcinoma_FTO_sh#7

growth_protocol: All cell lines use in sequencing were cultured in DMEM medium supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin,  5% CO2, 37°C.

extract_protocol:
Total RNA were isolated by Trizol reagent , digested with DNase  and purified with RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human hepatoma derived cell line

tag: shRNA

tag: passage


title: Primary GBM RCAS mouse model cell T1-3

source_name: stage T1,  Cell # 3

tag: tumor stage

tag: time point (weeks)

value: RCAS-TVA


title: sh_Neg

source_name: hepatocellular carcinoma_control_sh


title: sh_#2

source_name: hepatocellular carcinoma_FTO_sh#2


title: Primary GBM RCAS mouse model cell T1-36

source_name: stage T1,  Cell # 36

tag: tumor type

tag: background strain


title: Primary GBM RCAS mouse model cell T1-29

source_name: stage T1,  Cell # 29

tag: tumor grade


title: ARPE19-2a_D32_7dA83

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

description:
Technical sequencing replicate of GSM2075289
processed data file: ARPE19-2_D32_7dA83.txt

data_processing:
Base-calling was carried out using Torrent Suite and default parameters
Read alignment was accomplished using a 2-stage pipeline. The ten 5-prime bases from each sequence were trimmed using FASTX Trimmer 0.0.14. Sequences with a remaining length of  50 bases or greater were then aligned to the human genome (hg38 + 45S-RNA and 5S-RNA bait sequences) using TopHat 2.0.12 (Bowtie2 2.2.3) and settings optimized for variable read-length Ion Torrent sequences: read-mismatches = 4; read-gap-length = 4; read-edit-dist = 8; max-multihits =1; b2-i = S,1,1.15; b2-mp=6,2; b2-rdg = 5,2; and b2-rfg=5,2. Any unmapped sequences were passed to TMAP 3.4.1 and aligned using 5-prime and 3-prime soft-clipping (g = 0). The resulting TopHat and TMAP alignments were merged into a single alignment file.
Gene-level RNA quantification was determined using Partek Genomics Suite 6.6 and the hg38 RefSeq Transcript annotation (10/17/14). Only reads aligned to exons were considered in the determination of the number of reads per gene. In the case where there were two sequencing runs for the same condition (RPEC_P0_D32 and ARPE19-2) the alignments results were combined prior to quantification. Any fractional read count values were rounded to the nearest integer.
Protein coding RNA gene level results were normalized using the trimmed mean of the M-values (TMM) method of Robinson and Oshlack [Genome Biology 2010, 11:R25] as implemented by “edgeR”. Using the raw integer read counts for protein coding genes (HUGO Gene Nomenclature Database, 4/13/2015) as input and selection of genes with at least one count per million reads in 3 or more samples, the normalization factor (norm.factor) and  total number of mRNAs reads for each sample (lib.size) were determined.  The final processed normalized data for each gene is expressed as reads per million aligned reads (RPM) where RPM = (raw read count * 1 x 106) /(norm.factor * lib.size) .
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text; Annotations, mRNA  gene-level raw read counts (Reads) and TMM-normalized read counts per million mRNA alignments (RPM) for all protein coding genes

source_name: Adult RPE cell line, ARPE-19, Experimental Replicate 2

growth_protocol: RPE cells were isolated from fetal donor eyes (Advanced Biosciences Resources, Alameda, CA USA) according to the methods of Hu and Bok [Mol. Vis. 2001, 7:14-19; Methods Mol. Biol. 2010, 652:55-73]. Beyond the initial isolation, all cell culture was carried out using a base medium described by Maminiskis [Invest. Ophthalmol. Vis. Sci.2006, 47:3612-3624]. For 2-3 days post-plating the medium included 15% heat inactivated fetal calf serum. Thereafter, it was reduced to 5%. To generate a working cell bank, primary fetal RPE stocks were expanded approximately 10-fold and these working stocks were designated Passage 0. For routine serial passage, cells were harvested using trypsin digestion and plated at 4,000 cells/cm2. At approximately 80% confluence (every 3-5 days depending on passage number) the cells were enzymatically harvested and re-seeded at 4,000 cells/cm2.  For the purpose of transcriptome analysis cells were plated at 80,000 cells/cm2 and harvested after 32 days. Cultures were carried out on laminin-coated porous supports (mouse laminin, Life Technologies, Grand Island, NY USA; Millicell-HA Culture Inserts, EMD Millipore Inc., Billerica, MA USA) or laminin-coated tissue culture plastic as indicated. All cultures were fed every 2-4 days by complete exchange of the medium.

extract_protocol:
Total RNA was purified using miRNeasy mini-preps (Qiagen Inc., Valencia, CA USA)
PolyA RNA was purified from 1 microgram of total RNA using the Magnetic mRNA Isolation Kit (New England Biolabs, Inc ., Ipswitch MA USA) and mRNA-Seq libraries were constructed using the  Ion Total RNA-Seq Kit v2 (Life Technologies, Inc., Grand Island NY USA).

value: Adult RPE cell line

tag: plating density

tag: passage number

value: Unknown

tag: culture time

value: 32 Days

tag: treatment

tag: substrate

value: TC Plastic


title: Primary GBM RCAS mouse model cell T1-28

source_name: stage T1,  Cell # 28

tag: tissue

value: High


title: Primary GBM RCAS mouse model cell T1-27

source_name: stage T1,  Cell # 27


title: Primary GBM RCAS mouse model cell T1-48

source_name: stage T1,  Cell # 48


title: RPEC_P0_D32_1 [re-analysis]

description:
Reanalysis of GSM1657679
processed data file: RPEC_P0_D32.txt

source_name: Fetal RPE-Donor "C"

tag: donor id

value: Microporous support


title: 03_KARPAS422_8dEZH2i_H3K27me3_hg19

city: Cambridge

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

data_processing:
50-nucleotide sequence reads were aligned to the hg19 genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches and mapped uniquely to the genome, were used in subsequent analyses.
The aligned read files were sorted and duplicates removed using sort and rmdup functions from samtools version 0.1.18 (Li et al., 2009).
Peak calling was done with the SICER-rb script (SICER v1.1; without Input file; using gap=600).
Genome_build: hg19
Supplementary_files_format_and_content: TDF files for viewing with Broad IGV platform

source_name: Diffuse large B cell lymphoma

growth_protocol: KARPAS-422 cell line was grown in Roswell Park Memorial Institute (RPMI) GlutaMAX medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reactions were set up using precleared chromatin and antibodies and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500 (50 nt reads, single end).

tag: treated with

tag: timepoint

value: 8 days

tag: chip antibody

tag: antibody vendor

value: Cell Signaling Technology

tag: antibody catalog number

tag: antibody batch number

value: Lot 10


title: Primary GBM RCAS mouse model cell T1-26

source_name: stage T1,  Cell # 26

tag: tumor stage

value: Primary

tag: time point (weeks)

value: 5 weeks


title: 01_KARPAS422_8dDMSO_H3K27me3_hg19

tag: cell line

value: DMSO


title: Primary GBM RCAS mouse model cell T1-35

source_name: stage T1,  Cell # 35

tag: tumor type

value: Primary Tumor

tag: background strain

tag: tumor grade


title: Primary GBM RCAS mouse model cell T1-25

source_name: stage T1,  Cell # 25


title: 02_KARPAS422_4dEZH2i_H3K27me3_hg19

value: 4 days


title: Primary GBM RCAS mouse model cell T1-24

source_name: stage T1,  Cell # 24

value: Brain


title: RPEA_P0_D32 [re-analysis]

description: Reanalysis of GSM1657677

source_name: Fetal RPE-Donor "A"

tag: plating density

tag: passage number

tag: culture time


title: Primary GBM RCAS mouse model cell T1-22

source_name: stage T1,  Cell # 22

tag: tissue


title: KARPAS-422_EZH2i_8d_H3K9me3

data_processing:
50-nucleotide sequence reads were aligned to the hg19 genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches and mapped uniquely to the genome, were used in subsequent analyses.
The aligned read files were sorted and duplicates removed using sort and rmdup functions from samtools version 0.1.18 (Li et al., 2009).
Peak calling was done with the SICER-rb script (SICER v1.1; without Input file; using gap=600).
Genome_build: hg19
Supplementary_files_format_and_content: SICER scoreisland interval data for each sample in BED format.

tag: cell type

value: Diffuse large B cell lymphoma

value: EZH2i for 8 days

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #

tag: chip antibody lot #

value: Lot 2


title: KARPAS-422_DMSO_8d_H3K9me3

tag: treated with

value: DMSO for 8 days

tag: chip antibody


title: KARPAS-422_DMSO_8d_H3K27me3


title: KARPAS-422_EZH2i_4d_H3K27me3

value: EZH2i for 4 days


title: Primary GBM RCAS mouse model cell T1-21

source_name: stage T1,  Cell # 21

value: RCAS-TVA

value: High


title: KARPAS-422_EZH2i_8d_H3K27me3


title: KARPAS-422_EZH2i_4d_H3K9me3


title: Primary GBM RCAS mouse model cell T1-18

source_name: stage T1,  Cell # 18


title: Primary GBM RCAS mouse model cell T1-17

source_name: stage T1,  Cell # 17


title: Primary GBM RCAS mouse model cell T1-20

source_name: stage T1,  Cell # 20


title: Primary GBM RCAS mouse model cell T1-16

source_name: stage T1,  Cell # 16


title: Dp3a-seedling

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

description: processed data file: seedling_gene_exp.diff.txt

data_processing:
Basecalls performed using Illumina CASAVA.
Raw reads from RNA-seq data were mapped to the B73 RefGen_v3 genome using TopHat (v2.0.12) with the default parameters.
The following procedures and steps were combined with cufflinks and cuffdiff for differential expression analysis on different sanples.
The raw bisulfite sequencing reads were aligned by BS-Seeker2 with parameters “-m 3 --aligner=bowtie2 --bt2”, and then methylation was called.
Cytosine sites covered by more than five reads were used for subsequent analyses. The mean DNA methylation level of selected regions was calculated separately for “CG”, “CHG” and “CHH”.
Genome_build: Maize B73 RefGen_v3
Supplementary_files_format_and_content: TXT files from RNA-seq data contain the differentially genes expression level. BED files contains the mapped reads of the ChIP-bisulfite-seq. TXT files from ChIP-BS contain results for the DNA methylation level in each C site.

organism: Zea mays

source_name: maize

growth_protocol: Suitable materials were planted in the greenhouse or in the field for RNA-seq and ChIP-bisulfite experiments.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) and was subjected to the Illumina RNA-seq protocol, followed by sequencing using the HiSeq2000 platform. Seedling and young leaf tissues harvested from plant materials with and without Dp3a were used for RNA-seq analysis. Extracted nuclei were digested with micrococcal nuclease (Sigma-Al drich) for ChIP experiments using the maize CENH3 and ph-H2A-T133 antibody.The ChIP-enriched DNA of Dp3a was treated with sodium bisulfite and then performed Illumina sequence. The maize CENH3 is a rabbit polyclonal antiserum and was raised against the peptides: C-RPGTVALREIRKYQKS; STSATPERAAGTGGR-C. The ph-H2A-T133 antibody was generated with a single phosphorylated Thr at maize H2A (AAB04687.1) position 133 (LPKK(pT)AEKA). Keyhole limpet hemocyanin (KLH)-conjugated peptide was used to immunize rabbits.

tag: genotype/variation

value: seedling


title: Dp3a-bisulfite-ph-H2A-T133

description: ChIP-bisulfite-seq

value: young leaves


title: Dp3a-bisulfite-CENH3

description: ChIP-bisulfite-seq


title: Control-seedling

value: control


title: Primary GBM RCAS mouse model cell T1-15

source_name: stage T1,  Cell # 15

tag: tumor stage

value: Primary


title: Control-leaf

description: processed data file: leaf_gene_exp.diff.txt


title: Primary GBM RCAS mouse model cell T1-19

source_name: stage T1,  Cell # 19

tag: time point (weeks)

value: 5 weeks


title: Primary GBM RCAS mouse model cell T1-12

source_name: stage T1,  Cell # 12


title: Dp3a-leaf


title: Primary GBM RCAS mouse model cell T1-10

source_name: stage T1,  Cell # 10


title: Primary GBM RCAS mouse model cell T1-11

source_name: stage T1,  Cell # 11


title: Primary GBM RCAS mouse model cell T1-23

source_name: stage T1,  Cell # 23


title: Primary GBM RCAS mouse model cell T1-13

source_name: stage T1,  Cell # 13


title: Primary GBM RCAS mouse model cell T1-1

source_name: stage T1,  Cell # 1


title: High-cholesterol Diet Rep 4

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

data_processing:
Reads were aligned to the GRCm38/Ensembl V54 transcriptome using Tophat v2.0.8 with default parameters
Counts and differential gene expression were determined using CuffLinks v2.2.1 using default parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: Fastq files for raw data and FPKM values in tab-delimted txt format

source_name: Splenic marginal zone B cells_High-cholesterol diet for 8 weeks

extract_protocol:
RNA were extracted from FACS isolated marginal zone B cells using Ambion mirVAna isolation kit
RNA was subjected to whole-transcriptome amplification using NuGEN RNAseq v2 System followed by fragmentation to 200bp with a Diagenode Bioruptor Pico sonicator, The resulting fragments were then used to make bar-coded libraries using NuGEN Ovation Rapid DR Multiplex System

value: Primary Splenic marginal zone B cells

tag: strain

value: C57BL/6 LDLr -/-

tag: diet

value: High-cholesterol diet for 8 weeks

value: spleen


title: High-cholesterol Diet Rep 5


title: High-cholesterol Diet Rep 3


title: High-cholesterol Diet Rep 2


title: Primary GBM RCAS mouse model cell T1-2

source_name: stage T1,  Cell # 2

value: Brain

tag: tumor type

value: Primary Tumor

tag: background strain


title: Control Rep 4

source_name: Splenic marginal zone B cells_standard_chow

value: standard chow


title: High-cholesterol Diet Rep 1


title: Control Rep 3


title: Control Rep 1


title: Primary GBM RCAS mouse model cell T1-14

source_name: stage T1,  Cell # 14

tag: tumor grade


title: MeCP2IP_MeCP2_ChIP_CTL3

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

data_processing:
Base calling was performed using CASAVA software.
Illumina raw reads in .fastq files were aligned to mouse mm9 reference genome with bwa 0.6.2. Uniquely mapped reads  were extended in silico to reflect average fragment size  of the input DNA(~250bp).
Aligned reads from each sample were downsampled to an equivalent number of reads to maintain equal representation across all samples. These mapped files were then pooled by genotype and immunoprecipitation to generate bed files of mapped read positions.
Genome_build: mm9
Supplementary_files_format_and_content: Pooled bed files of mapped read positions of in silico extended reads
Supplementary_files_format_and_content: Tab-separated table (with header) of genes, methylation, and MeCP2 content. Reads from pooled bed formats were mapped to genes using in-house software, and read counts from MeCP2 chip and input were divided to calculate MeCP2 ChIP/Input. These values, from the control and Dnmt3a knockout, respectively, form columns "PooledControlsMECP2_GeneBody" and "PooledDnmt3a_CKOsMECP2_GeneBody".

source_name: Cortex

growth_protocol: Brain tissue was taken from Dnmt3a knockout and wild-type mice maintained under standard housing conditions.

extract_protocol:
total MeCP2 ChIP was performed as described in Cohen et al. Neuron 2012, Ebert et al Nature 2013
Single-end short read sequencing libraires were prepared using standard protocols, following the manufacturers instructions. Libraries were sequenced on the Illumina NextSeq
ChIP-Seq was performed according to Gabel et.al., Nature 2015.

tag: genotype

value: wild type

value: Brain Cortex

value: Total MeCP2 antibody (Zhou et al. 2006)

tag: age

value: 6 weeks


title: INPUT_MeCP2_ChIP_CTL2

tag: tissue

value: Input


title: INPUT_MeCP2_ChIP_CTL3


title: MeCP2IP_MeCP2_ChIP_CTL2


title: MeCP2IP_MeCP2_ChIP_DKO3

value: Dnmt3a knockout


title: MeCP2IP_MeCP2_ChIP_CTL1


title: INPUT_MeCP2_ChIP_DKO3


title: INPUT_MeCP2_ChIP_CTL1


title: MeCP2IP_MeCP2_ChIP_DKO2


title: INPUT_MeCP2_ChIP_DKO1


title: INPUT_MeCP2_ChIP_DKO2


title: MeCP2IP_MeCP2_ChIP_DKO1


title: 2.4h_AnO2_2

city: Seattle

first: Caroline

middle: S

last: Harwood

state: WA

address: 1705 NE Pacific St.

department: Microbiology

institute: University of Washington

description: continuous cultures on synthetic cystic fibrosis medium

data_processing:
Differentially expressed genes were identified from the raw count data using statistical package DESeq (Anders & Huber, 2010) available for Bioconductor (http://www.bioconductor.org).
Supplementary_files_format_and_content: DESeq_slow_slowestMicro_analysis.txt: estimates of abundance from raw count data for detection of fold-change due to one conditional change
Supplementary_files_format_and_content: DESeq_slow_slowestAnaer_analysis.txt: estimates of abundance from raw count data for detection of fold-change due to one conditional change

organism: Pseudomonas aeruginosa PAO1

source_name: AnO2_anaerobic cultures_doubling time of 2.4 h_rep2

growth_protocol: Bacteria were continuously grown at 37C in 150 ml synthetic cystic fibrosis mediumin in duplicate per growth rate tested (2.4 h and 9.8 h doubling times) per conditions tested (anaerobic and microaerobic)

extract_protocol:
Cells were spun-down, then resuspended in 1 ml QIAzol lysis reagent (Qiagen) and disrupted by bead beating at maximum rpm for 3 - 1 min intervals with rests on ice with a Mini-Beadbeater-24 (BioSpec). RNA was then isolated using a miRNeasy Mini Kit (Qiagen), then DNA-digested with TURBO DNase (Life Technologies) followed by another purification step using a RNeasy MinElute Cleanup Kit (Qiagen).
Ovation Complete Prokaryotic RNA-Seq DR Multiplex System (NuGEN)

treatment_protocol: 5 ml culture treated with RNAprotect Bacteria reagent (Qiagen)

value: derviative of P. aeruginosa MPAO1-contains pel and psl unmarked deletions


title: 9.8h_AnO2_1

source_name: AnO2_anaerobic cultures_doubling time of 9.8 h_rep1


title: 9.8h_mO2_2

source_name: mO2_microaerobic cultures_doubling time of 9.8 h_rep2


title: 2.4h_AnO2_1

source_name: AnO2_anaerobic cultures_doubling time of 2.4 h_rep 1


title: 9.8h_AnO2_2

source_name: AnO2_anaerobic cultures_doubling time of 9.8 h_rep2


title: Control Rep 5

tag: cell type


title: 9.8h_mO2_1

source_name: mO2_microaerobic cultures_doubling time of 9.8 h_rep1


title: 2.4h_mO2_1

source_name: mO2_microaerobic cultures_doubling time of 2.4 h_rep 1


title: 2.4h_mO2_2

source_name: mO2_microaerobic cultures_doubling time of 2.4 h_rep2


title: Smed_Sexual_Virgin_3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Single intact virgin, sexually mature adult hermaphrodite

data_processing:
Base calls were performed using CASAVA-1.8.2
Reads were aligned using bowtie with the following parameters: --best --strata -v 2 -m 5 against transcriptome smed_20140614 defined in GEO submission: GSE72389
Read counts to genes were tallied from the SAM files with a custom script. RPKM values were generated using the rpkm function from the edgeR library from Bioconductor in R.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: rpkm.txt contains tab-delimited RPKM vales for each sample.

organism: Schmidtea mediterranea

source_name: virgin, sexuallly mature adult

growth_protocol: Animals were maintained in 1x Montjuic water at 20˚C in the dark and fed homogenized beef liver once or twice per week. Cultures subjected to intensive feeding regimens were supplemented with 100 µg/mL gentamicin sulfate Gemini Bioproducts, #400-100P).  The asexual clonal strain CIW-4 (Newmark and Sanchez Alvarado 2002) was propagated via successive rounds of amputation and regeneration. Sexually reproducing S. mediterranea stocks were descendants of animals collected in Corsica by Dr. Maria Pala in 1999.  Egg capsules were collected daily from outbred cohorts of sexually mature adults cultured at low density (6-8 animals per 400 mL culture), and were stored in dated petri dishes at 20˚C in constant darkness until use.  The collection date was considered to be 1 day post-egg capsule deposition. To maintain optimal fertility levels, sexually mature animals used for egg capsule collections were replaced every 3-4 months with either juveniles (6-8 weeks post hatching) or adult regenerates (6-8 weeks post cut).

extract_protocol:
Live embryos were dissected out of egg capsules in 1x Holfreter’s buffer (3.5 g/L NaCl; 0.2 g/L NaHCO3; 0.05 g/L KCl; 0.2 g/L MgSO4; 0.1 g/L CaCl2; 1.0 g/L dextrose, pH 7.0-7.5) for Stage (S) S2-S7 egg capsules, or 1x Montjuic water for S8 hatchlings.  Yolk samples were obtained from 8 d egg capsules that contained neither spherical nor elongating embryos.  Single embryos were  transferred into microfuge tubes containing 200 µl TRIzol reagent (Thermo Fisher, item #15596-018), homogenized by pipetting, and stored at -80˚C. Single animal samples of intact C4 adults and virgin, sexually mature adults were homogenized in 1.0 mL TRIzol using an IKA Ultra Turrax T 25 Basic tissue disruptor prior to storage at -80˚C.  Total RNA extraction was performed in 1.0 mL TRIzol per sample according to the manufacturer’s protocol, following the recommendations for working with small amounts of tissue.
PolyA-selected, single stranded RNA-Sequencing libraries were prepared for four biological replicates per stage using the Illumina TruSeq RNA Sample V2 kit (item # RS-122-2001 and RS-122-2002), starting with 500 ng total RNA per sample (C4, virgin sexual adult (SX), Y, S4, S5, S6, S7, S8), or 100 ng total RNA per sample (S2, S3).

tag: biotype

value: sexual

tag: day

value: not applicable

tag: replicate


title: Smed_Sexual_Virgin_4


title: Smed_Sexual_Virgin_2


title: Smed_Sexual_Virgin_1


title: C4_4

description: Single intact, CIW4 asexual adult

source_name: asexual CIW4 adult

value: asexual


title: Control Rep 2

value: Primary Splenic marginal zone B cells


title: C4_3

description: Single intact, CIW4 asexual adult


title: C4_2

description: Single intact, CIW4 asexual adult


title: e14_3

description: Single Stage 8 embryo

source_name: Stage 8 embryo


title: Spur input DNA

organism: Strongylocentrotus purpuratus

source_name: Pooled embryos

tag: developmental stage

value: mesenchyme blastula

value: 24 hpf


title: e14_2

description: Single Stage 8 embryo


title: SpTbr ChIP DNA

tag: chip antibody

value: anti-SpTbr (custom)


title: e10_4

description: Single Stage 7 embryo

source_name: Stage 7 embryo


title: Gifu

city: Vienna

first: Manu

last: Dubin

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute, Austrian Academy of Sciences

data_processing:
Casava version 1.7 was used for base-calling
Reads were aligned to the reference genome Lj3.0 using using NexGenMap version 0.4.3 with the following settings -p -i 0.90 -R 45 --bs-mapping --silent-clip
Genome_build: Lotus japonicus v3.0 (Lj3.0)
Supplementary_files_format_and_content: A TSV (tab separated values) detailing the methylation levels at each cytosine was generated using the methratio.py script from the BSMAP (version 2.73) using the -z  and -u flags

organism: Lotus japonicus

source_name: Lotus japonicus 'Gifu'_aerial_tissue

growth_protocol: Seeds were sown on soil moist filter paper and allowed to germinate. Seedlings were transfered to single pots transferred to a greenhouse set at 20C under long day conditions (04:00-20:00) and individual seedlings were transplanted to single pots after one week. After 6 weeks growth the arial tissues of the plant were harvested and flash frozen in liquid nitrogen.

extract_protocol:
Total DNA was extracted using the Macherey-Nagel Nucleomag96 Plant kit according to the manufacturer's instructions
Libraries were prepared according to Lister et al., 2008 (Cell) with the following modifications: Bisulfite conversion was performed using Qiagen epitech kit. PCR amplification was done using KAPA HIFI Uracil plus polymerase together with bar-coded primers (Illumina Tru-seq barcodes 1-48) to allow muiltiplexing

tag: cultivar

value: Gifu

value: aerial tissue


title: e10_3

description: Single Stage 7 embryo


title: e14_1

description: Single Stage 8 embryo


title: e10_1

description: Single Stage 7 embryo


title: e9_4

description: Single Stage 6 embryo

source_name: Stage 6 embryo


title: e9_3

description: Single Stage 6 embryo


title: e6_4

description: Single Stage 5 embryo

source_name: Stage 5 embryo


title: e6_2

description: Single Stage 5 embryo


title: e9_1

description: Single Stage 6 embryo


title: e6_3

description: Single Stage 5 embryo


title: e9_2

description: Single Stage 6 embryo


title: e6_1

description: Single Stage 5 embryo


title: e4_3

description: Single Stage 4 embryo

source_name: Stage 4 embryo


title: e4_2

description: Single Stage 4 embryo


title: e3_4

description: Single Stage 3 embryo

source_name: Stage 3 embryo


title: e3_3

description: Single Stage 3 embryo


title: C4_1

description: Single intact, CIW4 asexual adult


title: e3_1

description: Single Stage 3 embryo


title: e14_4

description: Single Stage 8 embryo


title: e3_2

description: Single Stage 3 embryo


title: p2_3

description: Single Stage 2 embryo

source_name: Stage 2 embryo


title: p2_4

description: Single Stage 2 embryo


title: e10_2

description: Single Stage 7 embryo


title: y_2

description: Yolk was harvested from a single egg capsule that did not contain visible embryos at 8 days post-egg capsule deposition

source_name: Yolk


title: p2_1

description: Single Stage 2 embryo


title: p2_2

description: Single Stage 2 embryo


title: y_1


title: y_4


title: y_3


title: O_pumila_HR_ERF2i-2

city: Chiba

first: Mami

last: Yamazaki

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

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Chiba University

data_processing:
Raw read pre-processing, alignment of clean reads to a reference O. pumila de novo assembly (Rohani et al., 2016), transcript abundant estimation and expression level in Fragment per Kilobase exon per Million mapped fragment (FPKM) were performed as described by (Rai et al., 2016a).
Briefly, For transcriptome expression analysis, clean pair reads for each samples were used for alignment over O. pumila transcriptome assembly (published by Rohani et al., 2016) using Bowtie 2.0 program , and RSEM program was used for abundance estimation. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method. Unsupervised principal component analysis for all samples were performed by DESeq 2 program using count data for unigenes obtained from RSEM program.
Supplementary_files_format_and_content: .results.txt files were generated using RSEM program. Clean reads for each tissues were aligned on O. pumila de novo transcriptome assembly (Trinity_MYBox-Emelda-san.fasta is linked as a supplementary file on the Series record), and abundance were measured using RSEM  program. Content of each file contains transcript_id (which is contig), gene_id (which is unigene), length, effective_length, expected_count, TPM, FPKM, and IsoPct for each tissues. FPKM values for each tissues were used for further analysis.
Supplementary_files_format_and_content: .xlsx file includes transcript_id, gene_id, FPKM values for transcripts from all six transgenic hairy root lines of O. pumila, and blastx based annotation and top hits associated with each transcript. This  processed dataset combines top-hit blastx annotaion of transcripts and their abundance across different samples.

organism: Ophiorrhiza pumila

source_name: RNA interference (RNAi) transgenic HR with suppressed OpERF2 (ERF2i), clone number 2

growth_protocol: O. pumila transgenic HRs were maintained in the condition as described by Saito et al. (2001).  Collected HRs were immediately frozen in liquid nitrogen and homogenized using multibeads shocker (Yasui Kikai, Japan).

extract_protocol:
Total RNA was extracted from homogenized 3-week-old HR using RNeasy Plant Mini Kit (Qiagen, Germany) and treated with RNase-free DNase (Qiagen, Germany). First strand cDNA synthesis was carried out using Superscript® VILO™ Reverse Transcriptase (Invitrogen, USA) according to the manufacturer’s instructions.
mRNA for each samples were isolated from the total RNA by using beads with oligo (dT), and were added with fragmentation buffer to shear mRNA into short fragments, which were then used as template for the synthesis of first strand of cDNA using random hexamer primers. cDNA library for Illumina sequencing was prepared using SureSelect Strand specific RNA library kit (Agilent Technology, USA) according to manufacturer’s instructions.

treatment_protocol: Not applicable

value: Hairy root

tag: genotype/variation

value: suppressed OpERF2

tag: clone number


title: e4_4

description: Single Stage 4 embryo


title: ZH2 rep2

city: Hangzhou

first: Xiong-wei

last: Li

state: Zhejiang

address: Yuhangtang Road866

department: Department of Horticulture

institute: Zhejiang University

data_processing:
Raw data of fastq format were processed through in-house Perl scripts to obtain clean data by removing reads containing adapter or ploy-N and low quality reads.
Reference genome and gene model annotation files were downloaded from the genome website (http://www.rosaceae.org/species/prunus_persica/genome_v1.0) directly. The index of the reference genome was built using Bowtie v0.12.8, and paired-end clean reads were aligned to the reference genome using TopHat v1.4.0. We selected TopHat as the mapping tool as it can generate a database of splice junctions based on the gene model annotation file, so giving better mapping results than other non-splice mapping tools (Trapnell et al. 2009).
HTSeq v0.5.3 was used to count the reads mapped to each gene, and the RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two biological replicates per sample was performed using the DESeq R package (1.10.1) (Wang et al. 2010; Robinson et al. 2010). The P values were adjusted using the Benjamini & Hochberg method (Robinson et al. 2010; Benjamini et al. 1995)
Genome_build: Prunus persica Whole Genome v1.0 Assembly & Annotation
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Prunus persica

source_name: fruit mesocarp

extract_protocol:
Total RNA for each sample was isolated from 1g frozen fruit tissue, according to Zhang (2010). Contaminating genome DNA was removed by RNase-free DNase I (Fermentas, Vilnius, Lithuania). RNA integration and quantification was by agarose electrophoresis at an absorbance of 260nm (A260) using the NanoDrop® ND-3300 Fluorospectrometer with Quant-iT™ RiboGreen® RNA Reagent (Invitrogen, USA). First-strand cDNA was synthesized using 2.0 μl DNA-free RNA with the PrimeScript RT reagent Kit with gDNA Eraser, following the manufacturer’s instructions (Takara), and was diluted for RT-qPCR using a CFX 96 real-time PCR detection system (Bio-Rad, Hercules, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fruit mesocarp

tag: aromatic strength

value: slight

tag: flesh texture

value: hard melting

tag: brix

value: Zhong Hua Shou Tao


title: ZH2 rep1


title: JX2 rep2

value: strong

value: soft melting

value: Jin Xiu Huang Tao


title: O_pumila_HR_ERF2i-3

source_name: RNA interference (RNAi) transgenic HR with suppressed OpERF2 (ERF2i), clone number 3


title: e4_1

description: Single Stage 4 embryo

value: sexual


title: O_pumila_HR_Gusi-10

source_name: RNA interference (RNAi) transgenic HR with suppressed GUS (Gusi), clone number 10. Full ORF of Escherichia coli β-glucuronidase (GUS) was used as target sequence in the negative control construct

value: control


title: JX2 rep1


title: O_pumila_HR_ERF1i-19

source_name: RNA interference (RNAi) transgenic HR with suppressed OpERF1 (ERF1i), clone number 19

value: suppressed OpERF1


title: O_pumila_HR_ERF1i-7

source_name: RNA interference (RNAi) transgenic HR with suppressed OpERF1 (ERF1i), clone number 7


title: YL2 rep2

value: Yu Lu


title: HJ3 rep2

value: Hu Jing Mi Lu


title: YL2 rep1


title: HJ3 rep1


title: O_pumila_HR_Gusi-9

source_name: RNA interference (RNAi) transgenic HR with suppressed GUS (Gusi), clone number 9. Full ORF of Escherichia coli β-glucuronidase (GUS) was used as target sequence in the negative control construct