title: Pool_980_AD010_indexed


title: Pool_97_AD010_indexed

status: Public on Aug 10 2017

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
genome build: hg19
For multiplexed single nucleus methylome samples, reads were first trimmed to remove sequencing adaptors using Cutadapt 1.11 with the following parameters in paired ends mode: -f fastq -q 20 -m 62 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. For singleplex samples, -m parameter was set to 40. For multiplexed samples, 16bp was further trimmed from both 5’- and 3’- ends of R1 and R2 reads to remove random primer index sequence and C/T tail introduced by Adaptase, with the following parameters: -f fastq -u 16 -u -16 -m 30. For singleplex samples, 10bp was trimmed from both 5’- and 3’- ends of R1 and R2 reads with the following parameters: -f fastq -u 10 -u -10 -m 30. Trimmed reads for mouse and human single nuclei were mapped to mm10 and hg19 reference genome, respectively. R1 and R2 reads were mapped separately as single-ended reads using Bismark v0.15.0 with parameter --bowtie2. --pbat option was activated for mapping R1 reads. Resulted bam files were sorted using samtools 1.3 sort, followed by removal of duplicate reads using Picard 1.141 MarkDuplicates with the option REMOVE_DUPLICATES=true. Non-clonal reads were further filtered for minimal MAPQ = 30 using samtools view with option -q30. To prevent regional mCH level estimation from being skewed by rare reads failed to be bisulfite converted, reads with read-level mCH level greater than 0.7 were excluded. The calling of unmethylated and methylated base calls were performed by call_methylated_sites of Methylpy (https://github.com/yupenghe/methylpy/) (1–3).
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)

molecule: genomic DNA

organism: Homo sapiens

source_name: Human frontal cortex

growth_protocol: For the production of single neuron methylomes from layer dissected mouse frontal cortex tissue, eight week old C57BL/6J male mice were purchased from Jackson Laboratories, Bar Harbor ME, and allowed a week of acclimation in our animal facility with 12 h light/dark cycles and food ad libitum, before dissections. The human brain specimen was obtained from the NICHD Brain and Tissue Bank for Developmental disorders at the University of Maryland, Baltimore, MD. The frozen middle frontal gyrus tissue belonged to a 25-year-old Caucasian male (UMB#4540) with a PMI of 23 h.

extract_protocol:
A detailed protocol for MethylC-seq libraries preparation can be found in Urich et al., (2015). MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc 10, 475-483.
Nuclei isolation from mouse and human cortical tissues was performed as described in (Lister et al., 2013) with the following modifications: Proteinase inhibitor (11836153001, Roche) and RNAse Inhibitor (30 U/ml, PRN2611 from Promega) was added to the lysis buffer and sucrose gradients. After centrifugation, nuclei were resupended in 0.5% BSA (AM2616, Ambion) PBS (Ca2+ and Mg2+ free, 14190-144 from Life Technologies,) with protein and RNAse inhibitors. Isolated nuclei from mouse and human tissues were labeled by incubation with 1:1000 dilution of AlexaFluor488 conjugated anti-NeuN antibody (MAB377X, Millipore) at 4°C for 1 hour. Nuclei isolated from CLSun1-G35-Cre line were incubated with AlexaFluor647 conjugated anti-NeuN antibody (anti-NeuN antibody MAB377 labeled using Apex Alexa Fluor 647. A10475, Life Technologies) and AlexaFluor488 conjugated anti-GFP antibody (A21311, Life Technologies). Fluorescence activated sorting of single nuclei was performed using a BD Influx sorter with an 85 µm nozzle at 22.5 PSI sheath pressure. Single nuclei were sorted into each well of a 384-well plate preloaded with 2 µl of Proteinase K digestion buffer (1 µl M-Digestion Buffer, 0.1 µl 20 µg/µl Proteinase K and 0.9 µl H2O). The alignment of receiving 384-well plate was performed by sorting sheath flow into wells of an empty plate and making adjustment based on the liquid drop position. Single cell (1 drop single) mode was selected to ensure the stringency of sorting.
Steps of library preparation prior to SPRI purification were performed in a horizontal laminar flow hood to minimize environmental DNA contamination. Bisulfite conversion of single nuclei was carried out using Zymo EZ-96 DNA Methylation-DirectTM Kit (Deep Well Format, cat. #D5023) following the product’s manual with reduced reaction volume. 384-well plate (ThermoFisher Armadillo PCR Plate cat. # AB2384) containing FACS isolated single nuclei were heated at 50°C for 20 min. 25 µl CT Conversion Reagent was added to each well followed by pipetting up-and-down to mix. Plates were treated with a following program using a thermocycler: 98°C for 8 min, 64°C for 3.5 hours and 4°C. Each well of Zymo-Spin™ I-96 Binding Plates was preloaded with 150 µl M-binding buffer. Bisulfite conversion reactions were transferred from 384-well plates to I-96 Binding Plates followed by pipetting up-and-down to mix. I-96 Binding Plates were centrifuged at 5,000g for 5 min. Wells were washed with 400 µl of M-Wash Buffer followed by centrifugation at 5,000g for 5 min. 200 µl of M-Desulphonation Buffer was added to each well and was incubated for 15 min at room temperature before removed by centrifugation at 5,000g for 5 min. Each well was then washed with 400 µl of M-Wash Buffer for two rounds. 12 µl of M-Elution Buffer was added to each well and was incubated for 5 min at room temperature. I-96 Binding Plate was placed above a 96-well PCR plate (Applied Biosystems MicroAmp® EnduraPlateTM cat. # 4483348) and was centrifuged at 5,000g for 3min. 9 µl of eluted DNA was commonly collected in each well of the PCR plate. 1 µl of 5 µM P5L-AD002-N9, P5L-AD006-N9, P5L-AD008-N9 or P5L-AD010-N9 indexed random primer was added to each well of 96-well plate followed by mixing with vortexing. All DNA oligos were purchased from Integrated DNA Technologies (IDT). Plate was heated at 95°C for 3 min to denature the sample and was immediately chilled on ice for more than 2 min. 10 µl enzyme mix containing 2 µl of Blue Buffer (Enzymatics cat. # B0110), 1 µl of  10mM dNTP (NEB cat. # N0447L), 1 µl of Klenow exo- (50U/µl, Enzymatics cat. # P7010-HC-L) and 6 µl H2O. After mixing with vortexing, plate was treated with a following program: 4°C for 5 min, ramp up to 25°C at 0.1°C/sec, 25°C for 5 min, ramp up to 37°C at 0.1°C/sec, 37°C for 60 min, 4°C. 2 µl of Exonuclease 1 (20U/µl, Enzymatics cat. # X8010L) was added to each well followed by mixing with vortexing. Plate was incubated at 37°C for 30 min and then 4°C. 17.6 µl of home-made SPRI beads was added to each well. Sample/bead mixture from four plates indexed using distinct indexed random primers were combined followed by pipetting up-and-down to mix. Sample/bead mixture was incubated at room temperature for 5 min before placed on a 96-well magnetic separator. Supernatant was removed from each well followed by three rounds of washing with 180 µl of 80% ethanol. After air drying beads at room temperature, 10 µl M-Elution buffer was added to each well to fully resuspend the beads. Eluted sample was transferred to a new 96-well PCR plate. PCR plate was heated at 95°C for 3 min to denature the sample and was immediately chilled on ice for more than 2 min. 10.5 µl Adaptase (Swift Biosciences) mix (2 µl Buffer G1, 2 µl Reagent G2, 1.25 µl Reagent G3, 0.5 µl Enzyme G5, 0.5 µl Enzyme G6 and 4.25 µl M-Elution buffer) was added into each well followed by mixing with vortexing. Plates was incubated at 37°C at 30 min and then 4°C. 30 µl PCR mix (25 µl KAPA HiFi HotStart ReadyMix, KAPA BIOSYSTEMS, cat. # KK2602, 1 µl 30 µM P5 indexing primer and 5 µl 10 µM P7 indexing primer) was added into each well followed by mixing with vortexing. PCR plate was treated with the following program: 95 °C for 2 min, 98°C for 30 sec, 17 cycles of (98°C for 15 sec, 64°C for 30 sec, 72°C for 2min), 72°C for 5 min then 4°C. PCR products were cleaned up using 0.8x SPRI beads and was combined into one tube for each 96–well plate. Pooled PCR product was resolved on 2% agarose gel, smear between 400 bp and 2 Kb were excised and purified using QIAquick Gel Extraction Kit (Qiagen cat. # 28706). Library concentration was determined using Qubit® dsDNA HS (High Sensitivity) Assay Kit (Invitrogen cat. # Q32851).

tag: tissue

value: frontal cortex

tag: Sex

value: Male

tag: age

value: 25 yr


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title: Pool_177_AD008_indexed


title: Pool_175_AD010_indexed


title: Pool_176_AD008_indexed


title: Pool_174_AD010_indexed


title: Pool_176_AD010_indexed


title: Pool_175_AD008_indexed


title: Pool_173_AD010_indexed


title: Pool_173_AD008_indexed


title: Pool_181_AD010_indexed


title: Pool_172_AD010_indexed


title: Pool_172_AD008_indexed


title: Pool_171_AD008_indexed


title: Pool_168_AD010_indexed


title: Pool_169_AD008_indexed


title: Pool_169_AD010_indexed


title: Pool_16_AD010_indexed


title: Pool_168_AD008_indexed


title: Pool_167_AD008_indexed


title: Pool_167_AD010_indexed


title: Pool_166_AD010_indexed


title: Pool_170_AD010_indexed


title: Pool_170_AD008_indexed


title: Pool_16_AD008_indexed


title: Pool_165_AD010_indexed


title: Pool_164_AD008_indexed


title: Pool_164_AD010_indexed


title: Pool_163_AD008_indexed


title: Pool_162_AD008_indexed


title: Pool_161_AD008_indexed


title: Pool_161_AD010_indexed


title: Pool_15_AD010_indexed


title: Pool_160_AD008_indexed


title: Pool_163_AD010_indexed


title: Pool_15_AD008_indexed


title: Pool_160_AD010_indexed


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title: Pool_158_AD010_indexed


title: Pool_159_AD008_indexed


title: Pool_166_AD008_indexed


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title: Pool_165_AD008_indexed


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title: Pool_156_AD008_indexed


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title: Pool_157_AD008_indexed


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title: Pool_154_AD010_indexed


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title: Pool_14_AD008_indexed


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title: Pool_149_AD008_indexed


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title: Pool_1487_AD006_indexed


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title: Pool_1486_AD010_indexed


title: Pool_1486_AD008_indexed


title: Pool_1486_AD002_indexed


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title: Pool_1485_AD010_indexed


title: Pool_1485_AD002_indexed


title: Pool_1485_AD006_indexed


title: Pool_1488_AD008_indexed


title: Pool_1484_AD010_indexed


title: Pool_1488_AD002_indexed


title: Pool_1484_AD008_indexed


title: Pool_1484_AD006_indexed


title: Pool_1483_AD006_indexed


title: Pool_1483_AD010_indexed


title: Pool_1484_AD002_indexed


title: Pool_1482_AD010_indexed


title: Pool_1483_AD008_indexed


title: Pool_1483_AD002_indexed


title: Pool_1482_AD006_indexed


title: Pool_1481_AD006_indexed


title: Pool_1482_AD002_indexed


title: Pool_1481_AD002_indexed


title: Pool_1482_AD008_indexed


title: Pool_1478_AD006_indexed


title: Pool_1477_AD008_indexed


title: Pool_1478_AD010_indexed


title: Pool_1478_AD008_indexed


title: Pool_1480_AD008_indexed


title: Pool_1479_AD010_indexed


title: Pool_1480_AD002_indexed


title: Pool_1480_AD006_indexed


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title: Pool_1479_AD006_indexed


title: Pool_147_AD008_indexed


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title: Pool_1477_AD002_indexed


title: Pool_1479_AD002_indexed


title: Pool_1481_AD010_indexed


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title: Pool_1480_AD010_indexed


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title: Pool_1471_AD008_indexed


title: Pool_1471_AD006_indexed


title: Pool_1470_AD006_indexed


title: Pool_1472_AD010_indexed


title: Pool_1472_AD006_indexed


title: Pool_1471_AD002_indexed


title: Pool_1471_AD010_indexed


title: Pool_1474_AD010_indexed


title: Pool_1475_AD006_indexed


title: Pool_1470_AD002_indexed


title: Pool_1475_AD002_indexed


title: Pool_1469_AD002_indexed


title: Pool_1469_AD006_indexed


title: Pool_1473_AD002_indexed


title: Pool_1468_AD008_indexed


title: Pool_1469_AD008_indexed


title: Pool_1468_AD006_indexed


title: Pool_1468_AD010_indexed


title: Pool_1472_AD008_indexed


title: Pool_1468_AD002_indexed


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title: Pool_1467_AD008_indexed


title: Pool_1466_AD008_indexed


title: Pool_1467_AD006_indexed


title: Pool_1466_AD006_indexed


title: Pool_1466_AD002_indexed


title: Pool_1470_AD008_indexed


title: Pool_1465_AD010_indexed


title: Pool_146_AD008_indexed


title: Pool_1465_AD008_indexed


title: Pool_1465_AD002_indexed


title: Pool_1465_AD006_indexed


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title: Pool_1464_AD006_indexed


title: Pool_1463_AD008_indexed


title: Pool_1463_AD006_indexed


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title: Pool_1463_AD002_indexed


title: Pool_1462_AD002_indexed


title: Pool_1462_AD006_indexed


title: Pool_1462_AD008_indexed


title: Pool_1461_AD008_indexed


title: Pool_1461_AD002_indexed


title: Pool_1461_AD006_indexed


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title: Pool_1460_AD008_indexed


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title: Pool_1460_AD002_indexed


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title: Pool_1457_AD008_indexed


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title: Pool_1456_AD008_indexed


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title: Pool_1456_AD006_indexed


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title: Pool_1456_AD002_indexed


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title: Pool_1454_AD006_indexed


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title: Pool_1453_AD006_indexed


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title: Pool_1440_AD010_indexed


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title: Pool_1435_AD006_indexed


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title: Pool_1431_AD002_indexed


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title: Pool_1428_AD006_indexed


title: Pool_1429_AD002_indexed


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title: Pool_1426_AD008_indexed


title: Pool_1425_AD006_indexed


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title: Pool_1426_AD002_indexed


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title: Pool_1424_AD008_indexed


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title: Pool_1422_AD006_indexed


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title: Pool_1420_AD008_indexed


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title: Pool_1418_AD002_indexed


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title: Pool_1421_AD008_indexed


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title: Pool_1416_AD010_indexed


title: Pool_1417_AD006_indexed


title: Pool_1415_AD010_indexed


title: Pool_1413_AD006_indexed


title: Pool_1412_AD010_indexed


title: Pool_1412_AD008_indexed


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title: Pool_1414_AD010_indexed


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title: Pool_1419_AD010_indexed


title: Pool_1411_AD010_indexed


title: Pool_1413_AD010_indexed


title: Pool_1412_AD002_indexed


title: Pool_1411_AD008_indexed


title: Pool_1411_AD002_indexed


title: Pool_1410_AD008_indexed


title: Pool_1410_AD010_indexed


title: Pool_1410_AD006_indexed


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title: Pool_1409_AD010_indexed


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title: Pool_1408_AD008_indexed


title: Pool_1408_AD006_indexed


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title: Pool_1408_AD010_indexed


title: Pool_1408_AD002_indexed


title: Pool_1409_AD002_indexed


title: Pool_1407_AD010_indexed


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title: Pool_1406_AD010_indexed


title: Pool_1407_AD002_indexed


title: Pool_1407_AD008_indexed


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title: Pool_1407_AD006_indexed


title: Pool_1405_AD010_indexed


title: Pool_1405_AD008_indexed


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title: Pool_1411_AD006_indexed


title: Pool_1404_AD010_indexed


title: Pool_1405_AD002_indexed


title: Pool_1404_AD006_indexed


title: Pool_1404_AD002_indexed


title: Pool_1403_AD008_indexed


title: Pool_1403_AD010_indexed


title: Pool_1403_AD006_indexed


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title: Pool_1400_AD006_indexed


title: Pool_1401_AD002_indexed


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title: Pool_1402_AD008_indexed


title: Pool_1403_AD002_indexed


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title: Pool_1402_AD006_indexed


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title: Pool_1391_AD006_indexed


title: Pool_1392_AD010_indexed


title: Pool_1391_AD008_indexed


title: Pool_1392_AD006_indexed


title: Pool_1394_AD008_indexed


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title: Pool_1384_AD008_indexed


title: Pool_1384_AD002_indexed


title: Pool_1384_AD006_indexed


title: Pool_1386_AD002_indexed


title: Pool_1385_AD008_indexed


title: Pool_1385_AD002_indexed


title: Pool_1384_AD010_indexed


title: Pool_1383_AD006_indexed


title: Pool_1385_AD006_indexed


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title: Pool_1388_AD010_indexed


title: mut_Rc_2

city: Austin

first: Enamul

last: Huq

state: TX

address: 205 West 24th

department: IB

institute: University of Texas at Austin

description: total RNA (rRNA removed)

library_source: transcriptomic

data_processing:
FastQC analyze the sequencing quality.
TopHat2 is used to map the reads to the TAIR10 genome.
Cufflinks are used to analyze the differential gene expression.
ASpli is used to analyze the differential spliced events.
The website agriGO is used to analyze the enriched GO categories.
Genome_build: TAIR10
Excel or tab-delimited text files include differential expressed genes, differential spliced genes, or GO terms. C = WT, M = mutant, D = dark, L = red light.
Supplementary_files_format_and_content: C_DL_expression.diff.xlsx: The abundance measurement of differential expressed genes.
Supplementary_files_format_and_content: M_DL_expression.diff.xlsx: The abundance measurement of differential expressed genes.
Supplementary_files_format_and_content: CM_D_expression.diff.xlsx: The abundance measurement of differential expressed genes.
Supplementary_files_format_and_content: CM_L_expression.diff.xlsx: The abundance measurement of differential expressed genes.
Supplementary_files_format_and_content: C_DL_AS.diff.xlsx: The splicing efficiency measurement of differential spliced bins.
Supplementary_files_format_and_content: M_DL_AS.diff.xlsx: The splicing efficiency measurement of differential spliced bins.
Supplementary_files_format_and_content: CM_D_AS.diff.xlsx: The splicing efficiency measurement of differential spliced bins.
Supplementary_files_format_and_content: CM_L_AS.diff.xlsx: The splicing efficiency measurement of differential spliced bins.
Supplementary_files_format_and_content: CM_D_expression.GO.txt: GO categories analysis for the differential expressed genes.
Supplementary_files_format_and_content: CM_L_expression.GO.txt: GO categories analysis for the differential expressed genes.
Supplementary_files_format_and_content: CM_D_AS.GO.txt: GO categories analysis for the differential spliced genes.
Supplementary_files_format_and_content: CM_L_AS.GO.txt: GO categories analysis for the differential spliced genes.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 4-day-old dark grown sfps-2 seedlings with 3hrs red light irradiation

growth_protocol: Wild type Col-0 and SFPS mutant seeds in the Col-0 background were used. Wild type and mutant seeds were surface-sterilized and plated on Murashige and Skoog (MS) growth medium containing 0.9% agar without sucrose. After 4 d of chilling at 4°C in the dark for stratification, seeds were exposed to 3 h of white light at room temperature to induce germination before placing them in the dark for four days.

extract_protocol:
0.1g seedling materials are harvested. RNA were extracted using the Sigma plant RNA isolation kit (Catalog # STRN50-1KT). 5 µg total RNA was used to generate the RNA library for sequencing.
The RNA library generation process followed the manufacturer’s protocol from the Illumina kit TruSeq Stranded Total RNA with Ribo-Zero Plant (Catalog # RS-122-2401).

treatment_protocol: 4-day-old dark grown seedlings transfer to dark for 3hrs or continous red light (7μmolm-2s-1) condition for 3hrs.

tag: cultivar/background

tag: genotype/variation

value: sfps-2 (SFPS -/-)

value: 4 days

value: seedlings

tag: growth conditions

value: dark

tag: treatment

value: 3hrs red light irradiation (7μmolm-2s-1)


title: mut_D_3

description: total RNA (rRNA removed)

source_name: 4-day-old dark grown sfps-2 seedlings


title: mut_Rc_1

description: total RNA (rRNA removed)


title: Pool_1383_AD002_indexed


title: mut_D_2

description: total RNA (rRNA removed)


title: Pool_1382_AD010_indexed


title: Pool_1386_AD008_indexed


title: mut_D_1

description: total RNA (rRNA removed)


title: Pool_1382_AD008_indexed


title: Pool_1382_AD006_indexed


title: Col_Rc_2

description: total RNA (rRNA removed)

source_name: 4-day-old dark grown WT seedlings with 3hrs red light irradiation

value: wild type


title: Col_Rc_1

description: total RNA (rRNA removed)


title: Pool_1381_AD010_indexed


title: Pool_1382_AD002_indexed


title: Col_Rc_3

description: total RNA (rRNA removed)


title: Pool_1383_AD008_indexed


title: Pool_1381_AD002_indexed


title: Pool_1381_AD006_indexed


title: mut_Rc_3

description: total RNA (rRNA removed)


title: Pool_1380_AD006_indexed


title: T-1082_st2_rep3

city: Seoul

first: Koeun

last: Han

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

data_processing:
Illumina Hiseq 2500 for base calling
Digital expressions with 98% identity threshold using CLC Genomics Workbenchi 6.0
Normalization and transformation of digital expression data using CLC Genomics Workbench 6.0 internal algorithms
Genome_build: ITAG2.3_CDS (http://solgenomics.net)

organism: Solanum lycopersicum

source_name: Fertile tomato

extract_protocol:
Trizol extraction method
RNA-seq library (Zhong et al, Cold Spring Harbor Protocols, 940-949, 2011)

value: floral bud

tag: developmental stage

value: stage 2

tag: phenotype

value: male fertile


title: Col_D_2

description: total RNA (rRNA removed)

source_name: 4-day-old dark grown WT seedlings


title: Col_D_1

description: total RNA (rRNA removed)


title: T-1082_st3_rep3

value: stage 3


title: Pool_1380_AD002_indexed


title: Col_D_3

description: total RNA (rRNA removed)


title: Pool_1380_AD008_indexed


title: Pool_137_AD008_indexed


title: Pool_137_AD010_indexed


title: T-1082_st1_rep3

value: stage 1


title: Pool_1381_AD008_indexed


title: T-1082_st2_rep2


title: T-1082_st3_rep2


title: Pool_1379_AD010_indexed


title: T-1082_st3_rep1


title: T-1082_st2_rep1


title: Pool_1379_AD008_indexed


title: ms1035_st3_rep3

source_name: Sterile tomato

value: male sterile


title: ms1035_st2_rep3


title: Pool_1378_AD008_indexed


title: ms1035_st1_rep3


title: Pool_1380_AD010_indexed


title: ms1035_st1_rep2


title: ms1035_st2_rep2


title: Pool_1378_AD006_indexed


title: ms1035_st3_rep2


title: Pool_1377_AD006_indexed


title: Pool_1377_AD002_indexed


title: Pool_1377_AD008_indexed


title: ms1035_st1_rep1


title: Pool_1379_AD002_indexed


title: Pool_1376_AD010_indexed


title: Pool_1375_AD008_indexed


title: Pool_1376_AD002_indexed


title: ms1035_st2_rep1


title: Pool_1375_AD010_indexed


title: Pool_1375_AD002_indexed


title: Pool_1376_AD008_indexed


title: Pool_1374_AD008_indexed


title: Pool_1374_AD010_indexed


title: Pool_1378_AD010_indexed


title: Pool_1374_AD006_indexed


title: Pool_1374_AD002_indexed


title: Pool_1373_AD010_indexed


title: Pool_1373_AD008_indexed


title: Pool_1373_AD002_indexed


title: T-1082_st1_rep2


title: ms1035_st3_rep1


title: Pool_1372_AD010_indexed


title: Pool_1376_AD006_indexed


title: Pool_1372_AD006_indexed


title: Pool_1372_AD008_indexed


title: Pool_1372_AD002_indexed


title: Pool_1371_AD002_indexed


title: Pool_1371_AD006_indexed


title: Pool_1371_AD008_indexed


title: Pool_1371_AD010_indexed


title: Pool_1370_AD010_indexed


title: Pool_1377_AD010_indexed


title: Pool_1370_AD006_indexed


title: Pool_1373_AD006_indexed


title: Pool_1370_AD002_indexed


title: Pool_1368_AD010_indexed


title: Pool_136_AD008_indexed


title: Pool_1369_AD006_indexed


title: Pool_136_AD010_indexed


title: Pool_1369_AD002_indexed


title: Pool_1370_AD008_indexed


title: Pool_1368_AD002_indexed


title: Pool_1367_AD008_indexed


title: Pool_1368_AD008_indexed


title: Pool_1367_AD006_indexed


title: Pool_1366_AD010_indexed


title: Pool_1367_AD010_indexed


title: Pool_1366_AD008_indexed


title: Pool_1366_AD006_indexed


title: Pool_1366_AD002_indexed


title: Pool_1369_AD008_indexed


title: Pool_1365_AD006_indexed


title: Pool_1365_AD008_indexed


title: Pool_1369_AD010_indexed


title: Pool_1367_AD002_indexed


title: Pool_1364_AD002_indexed


title: Pool_1363_AD010_indexed


title: Pool_1364_AD010_indexed


title: Pool_1368_AD006_indexed


title: Pool_1365_AD002_indexed


title: Pool_1361_AD008_indexed


title: Pool_1362_AD002_indexed


title: Pool_1362_AD008_indexed


title: Pool_1361_AD006_indexed


title: Pool_1362_AD006_indexed


title: Pool_1363_AD008_indexed


title: Pool_1361_AD010_indexed


title: Pool_1364_AD006_indexed


title: Pool_1360_AD008_indexed


title: Pool_1365_AD010_indexed


title: Pool_1360_AD002_indexed


title: Pool_1360_AD006_indexed


title: Pool_1360_AD010_indexed


title: Pool_135_AD010_indexed


title: Pool_1362_AD010_indexed


title: Pool_135_AD008_indexed


title: Pool_1359_AD008_indexed


title: Pool_1375_AD006_indexed


title: Pool_1359_AD006_indexed


title: Pool_1359_AD002_indexed


title: Pool_1358_AD010_indexed


title: Pool_1358_AD008_indexed


title: Pool_1361_AD002_indexed


title: Pool_1357_AD010_indexed


title: Pool_1357_AD008_indexed


title: Pool_1358_AD002_indexed


title: Pool_1357_AD006_indexed


title: Pool_1356_AD010_indexed


title: Pool_1358_AD006_indexed


title: Pool_1355_AD006_indexed


title: Pool_1355_AD010_indexed


title: Pool_1356_AD006_indexed


title: Pool_1353_AD002_indexed


title: Pool_1352_AD010_indexed


title: Pool_1352_AD008_indexed


title: Pool_1353_AD006_indexed


title: Pool_1354_AD008_indexed


title: Pool_1354_AD006_indexed


title: Pool_1354_AD010_indexed


title: Pool_1355_AD002_indexed


title: Pool_1353_AD008_indexed


title: Pool_1354_AD002_indexed


title: Pool_1352_AD006_indexed


title: Pool_1351_AD008_indexed


title: Pool_1351_AD006_indexed


title: Pool_1351_AD002_indexed


title: Pool_1357_AD002_indexed


title: Pool_1359_AD010_indexed


title: Pool_1351_AD010_indexed


title: Pool_1355_AD008_indexed


title: Pool_134_AD010_indexed


title: Pool_1350_AD010_indexed


title: Pool_134_AD008_indexed


title: Pool_1349_AD010_indexed


title: Pool_1349_AD008_indexed


title: Pool_1352_AD002_indexed


title: Pool_1349_AD002_indexed


title: Pool_1348_AD010_indexed


title: Pool_1350_AD008_indexed


title: Pool_1356_AD008_indexed


title: Pool_1348_AD006_indexed


title: Pool_1348_AD002_indexed


title: Pool_1346_AD010_indexed


title: Pool_1347_AD010_indexed


title: Pool_1347_AD006_indexed


title: Pool_1347_AD002_indexed


title: Pool_1348_AD008_indexed


title: Pool_1350_AD006_indexed


title: Pool_1345_AD008_indexed


title: Pool_1345_AD010_indexed


title: Pool_1344_AD010_indexed


title: Pool_1346_AD002_indexed


title: Pool_1345_AD002_indexed


title: Pool_1347_AD008_indexed


title: Pool_1343_AD006_indexed


title: Pool_1343_AD010_indexed


title: Pool_1343_AD002_indexed


title: Pool_1346_AD008_indexed


title: Pool_1349_AD006_indexed


title: Pool_1344_AD002_indexed


title: Pool_1344_AD006_indexed


title: Pool_1342_AD008_indexed


title: Pool_1342_AD010_indexed


title: Pool_1342_AD002_indexed


title: Pool_1346_AD006_indexed


title: Pool_1341_AD008_indexed


title: Pool_1341_AD006_indexed


title: Pool_1341_AD002_indexed


title: Pool_1340_AD010_indexed


title: Pool_133_AD010_indexed


title: Pool_1340_AD006_indexed


title: Pool_1339_AD008_indexed


title: Pool_1343_AD008_indexed


title: Pool_1344_AD008_indexed


title: Pool_1340_AD002_indexed


title: Pool_1339_AD006_indexed


title: Pool_1340_AD008_indexed


title: Pool_1338_AD010_indexed


title: Pool_133_AD008_indexed


title: Pool_1338_AD006_indexed


title: Pool_1338_AD008_indexed


title: Pool_1339_AD002_indexed


title: Pool_1337_AD008_indexed


title: Pool_1337_AD010_indexed


title: Pool_1337_AD002_indexed


title: Pool_1342_AD006_indexed


title: Pool_1336_AD008_indexed


title: Pool_1341_AD010_indexed


title: HEK 293T

city: Oxford

first: Simon

last: Davis

address: MRC Weatherall Institute of Molecular Medicine

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Used TopHat version 1.1.1b for read mapping with parameters -p 4 -r 183.
Used Cufflinks version 0.9.1b for gene expression quantification with parameter -p 4.
Obtained all the proteins whose UniProt pages contained the keyword 'G-protein coupled receptor' (KW-0297).
Mapped the UniProt accession numbers to Ensembl gene IDs.
Obtained the expression of these genes.
Genome_build: Homo_sapiens.GRCh37.58.gtf
Supplementary_files_format_and_content: Tab-delimited file containing FPKM values for each gene.

molecule: polyA RNA

source_name: Embryonic kidney

extract_protocol:
HEK 293T cells were grown. RNA was extracted, tested, flash frozen on dry ice, and polyA-selected. Illumina mRNA-Seq Sample Prep Kit was used with 1 ug of RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina Genome Analyzer II + TruSeq PE Cluster Generation Kit v2 + TruSeq SBS v5 Kit).

value: Embryonic kidney

value: Fetus


title: Pool_1336_AD010_indexed

value: frontal cortex


title: Pool_1336_AD006_indexed

value: Male


title: Pool_1336_AD002_indexed

value: 25 yr


title: Pool_1335_AD010_indexed


title: Pool_1339_AD010_indexed


title: Pool_1335_AD008_indexed


title: Pool_1335_AD002_indexed


title: Pool_1334_AD010_indexed


title: Pool_1335_AD006_indexed


title: Pool_1334_AD006_indexed


title: Pool_1338_AD002_indexed


title: Pool_1333_AD010_indexed


title: Pool_1333_AD006_indexed


title: Pool_1332_AD010_indexed


title: Pool_1333_AD002_indexed


title: Pool_1332_AD008_indexed


title: Pool_1333_AD008_indexed


title: Pool_1331_AD010_indexed


title: mPC_1.3h

city: Frankfurt am Main

first: Christoph

middle: Michael

last: Zehendner

address: Theodor Stern Kai 7

country: Germany

institute: Goethe University

description:
total RNA ribosomal depleted
Hypoxic conditions
mouse PC hypox vs normox_FPKM.txt
mPC_3h

data_processing:
(RNA-SEQ) Reads were mapped with Tophat default parameters to MM10 (mouse brain primary pericytes), or GRCH38 (human primary pericytes).  Afterwards Cufflinks was utilized with the default attributes for gene quantification.
Genome_build: MM10 (mouse brain primary pericytes), or GRCH38 (human primary pericytes)
Supplementary_files_format_and_content: Tab delimited text file which includes FPKM values for each sample

organism: Mus musculus

source_name: mouse brain primary pericytes

growth_protocol: Human pericytes (passages 2-9; from ScienCell, Carlsbad, CA, USA) were cultured as recommended by the manufacturer. Cells were kept at 5% CO2, 20% O2, 37°C and humidified atmosphere. Pericyte medium consisted of DMEM Glutamax (Gibco, Life Technologies, Carlsbad, CA, USA) supplemented with Penicillin/Streptomycin (Roche Diagnostics) and 10% fetal calf serum. Primary mouse brain pericytes were isolated and cultured as documented in detail (Tigges et al. Microvascular Research 84 (2012) 74–80).

extract_protocol:
RNA deep sequencing was performed by analyzing ribosomal depleted total RNA from human pericytes. RNA was isolated using a RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions including DNA digestion.
RNA was fragmented and primed for cDNA synthesis. Human samples: Libraries were created using a NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer. Mouse sample libraries were created using a Scriptseq v2 Kit from Illumina SSV21124 as recommended by the manufacturer.

treatment_protocol: Hypoxia was induced using a hypoxic incubator (Labotect, Göttingen, Germany). Cell culture medium was pre-equilibrated overnight at 1% O2, 5% CO2 in a humidified atmosphere. Normoxic cell culture medium was carefully switched to hypoxic medium and hypoxic pO2 levels were verified by measuring VEGFA induction by qPCR and pO2 levels with a hypoxia sensing probe from Oxford Optronix (Oxford, UK) as described in detail before (Zehendner et al. Plos One 2013). Cells were transfected after reaching a confluency of 60-80% using Opti-MEM Medium, Lipofectamine RNAiMAX (both from Life technologies, Carlsbad, CA, USA) and 50 nmol/l of LNA GapmeR (Exiqon, Vedbaek, Denmark). After 4h transfection medium was exchanged to the appropriate cell culture medium. 48h upon transfection RNA was isolated and processed for RNA Sequencing.

tag: cell type

value: mouse brain primary pericytes

tag: passage

value: passage 8

value: Hypoxia 1% O2, 5% CO2 humidified atmosphere


title: mPC_0.3n

description:
total RNA ribosomal depleted
Normoxic conditions
mouse PC hypox vs normox_FPKM.txt
mPC_3n

value: Normoxia 20% O2, 5% CO2 humidified atmosphere


title: Pool_1331_AD006_indexed


title: mPC_1.1h

description:
total RNA ribosomal depleted
Hypoxic conditions
mouse PC hypox vs normox_FPKM.txt
mPC_1h


title: mPC_0.2n

description:
total RNA ribosomal depleted
Normoxic conditions
mouse PC hypox vs normox_FPKM.txt
mPC_2n


title: mPC_0.1n

description:
total RNA ribosomal depleted
Normoxic conditions
mouse PC hypox vs normox_FPKM.txt
mPC_1n


title: Pool_1331_AD002_indexed


title: Pool_1330_AD010_indexed


title: Pool_1332_AD006_indexed


title: Pool_1332_AD002_indexed


title: Pool_1330_AD008_indexed


title: Pool_1331_AD008_indexed


title: Pool_1334_AD002_indexed


title: Pool_1334_AD008_indexed


title: Pool_1330_AD006_indexed


title: Pool_132_AD008_indexed


title: Pool_1330_AD002_indexed


title: Pool_1329_AD010_indexed


title: Pool_1329_AD006_indexed