title: US-1250275_E1_S87

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAGGCATG-CTAAGCCT


title: US-1250275_E1_S89

status: Public on Jul 13 2018

type: SRA

city: Seattle

first: Lucas

middle: T

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

country: USA

institute: Allen Institute for Brain Science

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CAGAGAGG-CTAAGCCT

library_source: transcriptomic

data_processing:
50-base pair paired-end reads were aligned to GRCm38 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 01/18/2016 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/). Sequence alignment was performed using STAR v2.5.3 (Dobin et al., 2013) in twopassMode.
PCR duplicates were masked and removed using STAR option “bamRemoveDuplicates”. Only uniquely aligned reads were used for gene quantification.
Exon and intron counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) sumarizeOverlaps function using “IntersectionNotEmpty”.
We mapped all non-genome-mapped reads to synthetic constructs, including ERCCs and transgene sequences using STAR v2.5.3 and a custom index built using supplementary files synthetic_constructs.gtf and synthetic_constructs.fa.
Genome_build: mm10
Supplementary_files_format_and_content: star_exon_counts.csv: Comma separated values matrix of count values for reads mapping to exons.
Supplementary_files_format_and_content: star_intron_counts.csv: Comma separated values matrix of count values for reads mapping to introns.
Supplementary_files_format_and_content: star_synthetic_counts.csv: Comma separated values matrix of count values for reads mapping to synthetic constructs and transgenes.

molecule: total RNA

organism: Mus musculus

source_name: primary visual cortex (VISp)

growth_protocol: Both male and female transgenic mice ≥ P56 were utilized for all experiments.  All animals were housed 3-5 per cage and maintained on a 12-hour light/dark cycle, in a humidity- and temperature-controlled room with water and food available ad libitum.  All experimental procedures related to the use of mice were conducted with approved protocols in accordance with NIH guidelines, and were approved by the Institutional Animal Care and Use Committee (IACUC) of the Allen Institute for Brain Science.

extract_protocol:
Cells from transgenic mice or transgenic mice injected with AAV-pCAG-FLEX-EGFP-WPRE-pA were collected by microdissection, single-cell suspension, and single-cell FACS. Cells were then frozen at -80ºC.
Frozen cells were later processed for scRNA-seq using the SMART-Seq v4 method, as described in the Allen Institute Transcriptomics Technical Whitepaper (http://help.brain-map.org/download/attachments/8323525/CellTypes_Transcriptomics_Overview.pdf)

treatment_protocol: Induction of DHFR-domain containing dCre, dgCre or dgFlpO driver lines was done by administration via oral gavage (PO) of trimethoprim (TMP) at 0.3 mg/g body weight per day for 3 days. TMP working solution was diluted from a 10x stock in 100% DMSO with a 2% methylcellulose solution. Induction of CreERT2 driver lines was done by administration via oral gavage (PO) of tamoxifen (50 mg/ml in corn oil) at 0.2 mg/g body weight per day for 1-5 days. Mice can be used for experiments starting at 1-2 weeks after TMP or tamoxifen dosing.

tag: donor id

tag: donor genotype

tag: donor driver(s)

tag: donor reporter(s)

tag: donor sex

value: F

tag: dissected layer

tag: facs gating

value: RFP-positive

tag: facs container

tag: rna amplification set

tag: rna amplification date

tag: library preparation set

tag: library preparation date

tag: sequencing batch

tag: total sequenced reads

tag: genes detected

tag: cell class

value: Glutamatergic


title: US-1250275_E1_S86

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GGACTCCT-CTAAGCCT


title: US-1250275_E1_S79

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GCTACGCT-AAGGAGTA


title: LS-14690_S23_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
LS-14690_E1-50_AGGCAGAA-CGTCTAAT

value: M

value: GABAergic


title: US-1250275_E1_S78

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CAGAGAGG-AAGGAGTA


title: US-1250275_E1_S82

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAAGGCGA-CTAAGCCT


title: US-1250275_E1_S76

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAGGCATG-AAGGAGTA


title: US-1250275_E1_S77

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CTCTCTAC-AAGGAGTA


title: US-1250275_E1_S83

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CGTACTAG-CTAAGCCT


title: LS-14690_S21_E1-50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
LS-14690_E1-50_AGGCAGAA-AAGGAGTA


title: US-1250275_E1_S84

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_AGGCAGAA-CTAAGCCT


title: US-1250275_E1_S71

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAAGGCGA-AAGGAGTA


title: US-1250275_E1_S75

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GGACTCCT-AAGGAGTA


title: US-1250275_E1_S72

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CGTACTAG-AAGGAGTA


title: US-1250275_E1_S74

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TCCTGAGC-AAGGAGTA


title: US-1250275_E1_S73

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_AGGCAGAA-AAGGAGTA


title: US-1250275_E1_S68

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GCTACGCT-ACTGCATA


title: US-1250275_E1_S67

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CAGAGAGG-ACTGCATA


title: US-1250275_E1_S66

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CTCTCTAC-ACTGCATA


title: US-1250275_E1_S65

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAGGCATG-ACTGCATA


title: US-1250275_E1_S63

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TCCTGAGC-ACTGCATA


title: US-1250275_E1_S64

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GGACTCCT-ACTGCATA


title: US-1250275_E1_S62

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_AGGCAGAA-ACTGCATA


title: US-1250275_E1_S56

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CAGAGAGG-GTAAGGAG


title: US-1250275_E1_S60

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAAGGCGA-ACTGCATA


title: US-1250275_E1_S61

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CGTACTAG-ACTGCATA


title: US-1250275_E1_S55

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CTCTCTAC-GTAAGGAG


title: US-1250275_E1_S54

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAGGCATG-GTAAGGAG


title: US-1250275_E1_S52

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TCCTGAGC-GTAAGGAG


title: US-1250275_E1_S85

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TCCTGAGC-CTAAGCCT


title: US-1250275_E1_S53

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GGACTCCT-GTAAGGAG


title: US-1250275_E1_S50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CGTACTAG-GTAAGGAG


title: US-1250275_E1_S51

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_AGGCAGAA-GTAAGGAG


title: US-1250275_E1_S49

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAAGGCGA-GTAAGGAG


title: US-1250275_E1_S42

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAGGCATG-AGAGTAGA


title: US-1250275_E1_S43

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CTCTCTAC-AGAGTAGA


title: US-1250275_E1_S44

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CAGAGAGG-AGAGTAGA


title: US-1250275_E1_S41

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GGACTCCT-AGAGTAGA


title: US-1250275_E1_S40

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TCCTGAGC-AGAGTAGA


title: US-1250275_E1_S38

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CGTACTAG-AGAGTAGA


title: US-1250275_E1_S31

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CTCTCTAC-TATCCTCT


title: US-1250275_E1_S30

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAGGCATG-TATCCTCT


title: US-1250275_E1_S32

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CAGAGAGG-TATCCTCT


title: US-1250275_E1_S29

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GGACTCCT-TATCCTCT


title: US-1250275_E1_S27

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_AGGCAGAA-TATCCTCT


title: US-1250275_E1_S26

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CGTACTAG-TATCCTCT


title: US-1250275_E1_S25

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAAGGCGA-TATCCTCT


title: US-1250275_E1_S21

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GCTACGCT-CTCTCTAT


title: US-1250275_E1_S20

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CAGAGAGG-CTCTCTAT


title: US-1250275_E1_S57

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GCTACGCT-GTAAGGAG


title: US-1250275_E1_S19

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CTCTCTAC-CTCTCTAT


title: US-1250275_E1_S15

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_AGGCAGAA-CTCTCTAT


title: US-1250275_E1_S14

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CGTACTAG-CTCTCTAT


title: US-1250275_E1_S45

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GCTACGCT-AGAGTAGA


title: US-1250275_E1_S09

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GCTACGCT-GCGTAAGA


title: US-1250275_E1_S08

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CAGAGAGG-GCGTAAGA


title: US-1250275_E1_S13

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAAGGCGA-CTCTCTAT


title: US-1250275_E1_S39

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_AGGCAGAA-AGAGTAGA


title: US-1250275_E1_S07

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CTCTCTAC-GCGTAAGA


title: US-1250275_E1_S37

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAAGGCGA-AGAGTAGA


title: US-1250275_E1_S33

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GCTACGCT-TATCCTCT


title: US-1250275_E1_S18

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAGGCATG-CTCTCTAT


title: US-1250275_E1_S05

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GGACTCCT-GCGTAAGA


title: US-1250275_E1_S28

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TCCTGAGC-TATCCTCT


title: US-1250275_E1_S03

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_AGGCAGAA-GCGTAAGA


title: US-1250275_E1_S02

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_CGTACTAG-GCGTAAGA


title: US-1250275_E1_S06

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAGGCATG-GCGTAAGA


title: US-1250275_E1_S04

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TCCTGAGC-GCGTAAGA


title: US-1250273_E1_S78

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGAGGCTG-ACTGCATA


title: US-1250273_E1_S80

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGAGGCTG-CTAAGCCT


title: US-1250273_E1_S77

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGAGGCTG-GTAAGGAG


title: US-1250273_E1_S76

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGAGGCTG-AGAGTAGA


title: US-1250275_E1_S17

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_GGACTCCT-CTCTCTAT


title: US-1250273_E1_S79

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGAGGCTG-AAGGAGTA


title: US-1250273_E1_S74

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGAGGCTG-CTCTCTAT


title: US-1250275_E1_S16

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TCCTGAGC-CTCTCTAT


title: US-1250273_E1_S72

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GCTACGCT-CTAAGCCT


title: US-1250273_E1_S73

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGAGGCTG-GCGTAAGA


title: US-1250273_E1_S69

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GCTACGCT-GTAAGGAG


title: US-1250273_E1_S70

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GCTACGCT-ACTGCATA


title: US-1250273_E1_S68

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GCTACGCT-AGAGTAGA


title: US-1250273_E1_S66

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GCTACGCT-CTCTCTAT


title: US-1250275_E1_S01

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAAGGCGA-GCGTAAGA


title: US-1250273_E1_S65

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GCTACGCT-GCGTAAGA


title: US-1250273_E1_S64

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CAGAGAGG-CTAAGCCT


title: US-1250273_E1_S61

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CAGAGAGG-GTAAGGAG


title: US-1250273_E1_S63

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CAGAGAGG-AAGGAGTA


title: US-1250273_E1_S62

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CAGAGAGG-ACTGCATA


title: US-1250273_E1_S59

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CAGAGAGG-TATCCTCT


title: US-1250273_E1_S57

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CAGAGAGG-GCGTAAGA


title: US-1250273_E1_S58

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CAGAGAGG-CTCTCTAT


title: US-1250273_E1_S55

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CTCTCTAC-AAGGAGTA


title: US-1250273_E1_S53

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CTCTCTAC-GTAAGGAG


title: US-1250273_E1_S75

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGAGGCTG-TATCCTCT


title: US-1250273_E1_S50

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CTCTCTAC-CTCTCTAT


title: US-1250273_E1_S51

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CTCTCTAC-TATCCTCT


title: US-1250273_E1_S49

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CTCTCTAC-GCGTAAGA


title: US-1250273_E1_S48

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAGGCATG-CTAAGCCT


title: US-1250273_E1_S45

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAGGCATG-GTAAGGAG


title: US-1250273_E1_S47

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAGGCATG-AAGGAGTA


title: US-1250273_E1_S71

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GCTACGCT-AAGGAGTA


title: US-1250273_E1_S44

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAGGCATG-AGAGTAGA


title: US-1250273_E1_S67

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GCTACGCT-TATCCTCT


title: US-1250273_E1_S42

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAGGCATG-CTCTCTAT


title: US-1250273_E1_S43

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAGGCATG-TATCCTCT


title: US-1250273_E1_S41

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAGGCATG-GCGTAAGA


title: US-1250273_E1_S39

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GGACTCCT-AAGGAGTA


title: US-1250273_E1_S37

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GGACTCCT-GTAAGGAG


title: US-1250273_E1_S60

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CAGAGAGG-AGAGTAGA


title: US-1250273_E1_S40

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GGACTCCT-CTAAGCCT


title: US-1250273_E1_S38

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GGACTCCT-ACTGCATA


title: US-1250273_E1_S36

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GGACTCCT-AGAGTAGA


title: US-1250273_E1_S52

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CTCTCTAC-AGAGTAGA


title: US-1250273_E1_S56

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CTCTCTAC-CTAAGCCT


title: US-1250273_E1_S33

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GGACTCCT-GCGTAAGA


title: US-1250273_E1_S35

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GGACTCCT-TATCCTCT


title: US-1250273_E1_S24

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_AGGCAGAA-CTAAGCCT


title: US-1250273_E1_S19

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_AGGCAGAA-TATCCTCT


title: US-1250273_E1_S21

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_AGGCAGAA-GTAAGGAG


title: US-1250273_E1_S20

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_AGGCAGAA-AGAGTAGA


title: US-1250273_E1_S46

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAGGCATG-ACTGCATA


title: US-1250273_E1_S22

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_AGGCAGAA-ACTGCATA


title: US-1250273_E1_S17

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_AGGCAGAA-GCGTAAGA


title: US-1250273_E1_S16

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGTACTAG-CTAAGCCT


title: US-1250273_E1_S18

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_AGGCAGAA-CTCTCTAT


title: US-1250273_E1_S14

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGTACTAG-ACTGCATA


title: US-1250273_E1_S15

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGTACTAG-AAGGAGTA


title: US-1250273_E1_S13

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGTACTAG-GTAAGGAG


title: US-1250273_E1_S11

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGTACTAG-TATCCTCT


title: US-1250273_E1_S07

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAAGGCGA-AAGGAGTA


title: US-1250273_E1_S08

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAAGGCGA-CTAAGCCT


title: US-1250273_E1_S09

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGTACTAG-GCGTAAGA


title: US-1250273_E1_S12

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGTACTAG-AGAGTAGA


title: US-1250273_E1_S23

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_AGGCAGAA-AAGGAGTA


title: US-1250273_E1_S10

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_CGTACTAG-CTCTCTAT


title: US-1250273_E1_S04

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAAGGCGA-AGAGTAGA


title: US-1250273_E1_S03

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAAGGCGA-TATCCTCT


title: US-1250273_E1_S05

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAAGGCGA-GTAAGGAG


title: US-1250273_E1_S02

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAAGGCGA-CTCTCTAT


title: US-1250273_E1_S06

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAAGGCGA-ACTGCATA


title: US-1250273_E1_S01

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_TAAGGCGA-GCGTAAGA


title: HepLPCs scRNA-seq sample 1

status: Public on Jun 22 2018

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

country: China

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Cell Ranger
Read1: Contains the 16bp 10x cell Barcode (bases 1-16) and the 10bp UMI (bases 17-26)
I(ndex): Contains the sample barcode
Read2: Contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

organism: Homo sapiens

source_name: single cells

extract_protocol: Chromium Single Cell 3' Reagent Kit

tag: cell type

value: Hepatocyte-derived liver progenitor-like cells

tag: culture condition

value: in the transition and expansion medium (Passage 5)

tag: race

value: Asian

tag: Sex

value: male


title: true naive CD8 cells timestamped at day 28, rep 1 [ATACseq]

status: Public on Jun 14 2018

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
true naive cells made (Td-Tomato stamped) at 28 days
processed data files:
readCounts.tsv: TgTrueNaive_28dayTimestampA
peaks.bed.gz

library_source: genomic

data_processing:
Illumina pipeline software v1.8 was used for base calling.
Adapter sequences were trimmed and reads were filtered using cutadapt v1.12 (parameters: -a CTGTCTCTTATACACATCT -e 0.06 -m 15).
bowtie2 v.2.2.8 (default parameters) was used to align reads to the mouse mm10 genome (UCSC).
PCR duplicates and low quality alignments (MAPQ < 30) were filtered out using samtools v1.4.1 (commands: rmdup and view).
Peaks were called using macs2 (v2.1.1.20160309) (parameters: -f BAM -g mm -B -q 0.05) on both replicates as well as pooled data for each sample. The peaks from replicate data were used for Irreproducibility Discovery Rate (IDR) analysis to filter for reproducible peaks (IDR < 0.1); and corresponding peaks from pooled data were extracted.
A consolidated peak-set was derived by merging peaks from all samples, followed by filtering out peaks falling in blacklisted regions of mouse genome (https://www.encodeproject.org/annotations/ENCSR636HFF/), and filtering peaks that overlap with high-quality read alignments (MAPQ > 38).
Reads (after removing PCR duplicates and low quality alignments) that mapped to peaks were counted using FeatureCounts v1.5.1 (parameters: -F SAF -s 0 -Q 38).
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: 'peaks.bed': consolidated peak-set (see data processing step), fourth column are peak ids (in this format: 'chr:start-end'), fifth column are genes id (Ensembl) of the nearest promoter; 'readCounts.tsv': read counts for each peak in each sample (FeatureCounts output; see data processing step); '*.bw': bigwig files for each sample were generated from output files (*treat_pileup.bdg) of macs2 using bedGraphToBigWig (UCSC tooklit).

molecule: genomic DNA

source_name: CD4-CD8+CD44lo TdTomato+ sorted cells

growth_protocol: CD4cre-ERT2 mice were crossed to Ai9 mice bearing a floxed-stop TdTomato element such that when F1 offspring are exposed to tamoxifen, all cells bearing CD4 will begin expressing TdTomato for the duration of tamoxifen exposure.

extract_protocol:
CD8+ cells were magnetically enriched with CD8 microbeads and sorted to > 95% purity with a FACS Aria III on CD4- CD8+ TdTomato+ CD44 hi (virtual memory) or lo (true naïve) populations. Cells were permeabilized in lysis buffer (10mM Tris-Cl, 300mM sucrose, 10mM NaCl, 2mM MgAc2, 3mM CaCl2, and 0.1% NP-40(Igepal)) for 10mins, washed, resuspended in storage buffer (50mM Tris-Cl, 40% glycerol, 5mM MgCl2, and 0.1mM EDTA), counted, snap-frozen, and stored at -80°C until further use.
Libraries were prepared from 30,000 permeabilized cells primarily as described in Buenrostro et al, 2015 (Curr Protoc Mol Biol) and Corces et al, 2017 (Nature). Briefly, frozen permeabilized cells were thawed, washed twice in ATAC-RSBbuffer containing 0.1% Tween20, resuspended in Transposition Mix containing 0.1% Tween20 and PBS, and incubated for 30min at 37deg with shaking (1000rpm). After column cleanup, libraries were amplified using Nextera PCR oligos (Illumina) and Ultra II Q5 Master Mix (NEB) for a total of 12-14 PCR cycles based on qPCR quantification after the intial 5 cycles. Post-amplification, libraries were cleaned up twice (in series) with a 2:1 ratio of SPRIselect beads (Beckman Coulter).

treatment_protocol: To mark cell with TdTomato at specific times during development, mice were given tamoxifen at 1 day (through lactation, by administering tamoxifen orally to the Dam) or at 28 days of age (by direct oral administration to the mouse). The mice were then aged to allow for the same amount of post-thymic maturation(4 weeks).

tag: strain background

tag: transgenic insertions

value: gBT-I, Ai9, CD4cre-ERT2

value: CD4-CD8+CD44lo TdTomato+

tag: tissue origin

value: spleen

tag: timestamp age

value: 28 days

tag: age of animal

value: 8 weeks


title: virtual memory CD8 cells timestamped at day 28, rep 2 [ATACseq]

description:
virtual memory cells made (Td-Tomato stamped) at 28 days
processed data files:
readCounts.tsv: TgVirtualMemory_28dayTimestampB
peaks.bed.gz

source_name: CD4-CD8+CD44hi TdTomato+ sorted cells

value: CD4-CD8+CD44hi TdTomato+


title: virtual memory CD8 cells timestamped at day 28, rep 1 [ATACseq]

description:
virtual memory cells made (Td-Tomato stamped) at 28 days
processed data files:
readCounts.tsv: TgVirtualMemory_28dayTimestampA
peaks.bed.gz


title: virtual memory CD8 cells timestamped at day 1, rep 2 [ATACseq]

description:
virtual memory cells made (Td-Tomato stamped) at 1 day
processed data files:
readCounts.tsv: TgVirtualMemory_1dayTimestampB
peaks.bed.gz

value: 1 day

value: 4 weeks


title: US-1250273_E1_S34

description:
processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250273_E1_GGACTCCT-CTCTCTAT

tag: donor id

tag: donor genotype

tag: donor driver(s)

tag: donor reporter(s)

tag: donor sex

value: F

tag: dissected layer

tag: facs gating

tag: facs container

tag: rna amplification set


title: true naive CD8 cells timestamped at day 28, rep 2 [ATACseq]

description:
true naive cells made (Td-Tomato stamped) at 28 days
processed data files:
readCounts.tsv: TgTrueNaive_28dayTimestampB
peaks.bed.gz

tag: cell type


title: CD8m45_D35_3 [ATAC-seq]

status: Public on May 29 2018

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.16-2.19).
ATAC-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on Tn5-shifted, concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated by converting BAM files to size-normalized BEDGRAPH files using bedtools (v2.26.0) and converted to bigWig using UCSC's bedGraphToBigWig (v4).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files normalized by size factors calculated by DESeq2 from peak regions among all samples within each experiment.

source_name: splenic CD8T cells

extract_protocol:
Lymphocytes were harvested as described in manuscript.
Fresh cells were prepared as previously described (Buenrostro et al., 2013). Briefly, cells were washed in cold PBS and lysed. Transposition occurred at 42°C for 45 minutes. DNA was purified using the MinElute PCR purification kit (Qiagen) and amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5x ratio. Libraries were sequenced on a Hiseq 2500 1T in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina). An average of 51 million paired reads were generated per sample.

tag: genotype

value: WT

tag: replicate

tag: condition

value: splenic CD8T cells


title: CD8m45_D35_1 [ATAC-seq]


title: CD8_D0_2 [ATAC-seq]


title: CD8m45_D7_3 [ATAC-seq]


title: CD8_D0_3 [ATAC-seq]


title: CD8m45_D7_1 [ATAC-seq]


title: CD8_D0_1 [ATAC-seq]


title: CD8m45_D35_2 [ATAC-seq]


title: CD8m45_D7_2 [ATAC-seq]


title: NK_D35_3 [ATAC-seq]

source_name: splenic NK cells

value: HPOS

value: splenic NK cells


title: NK_D35_2 [ATAC-seq]


title: NK_D7_2 [ATAC-seq]


title: NK_D14_3 [ATAC-seq]


title: NK_D35_1 [ATAC-seq]


title: NK_D14_2 [ATAC-seq]


title: NK_D7_1 [ATAC-seq]


title: NK_D7_3 [ATAC-seq]


title: NK_D4_3 [ATAC-seq]


title: NK_D4_1 [ATAC-seq]


title: NK_D7_4 [ATAC-seq]


title: NK_D14_1 [ATAC-seq]


title: NK_D4_2 [ATAC-seq]


title: virtual memory CD8 cells timestamped at day 1, rep 1 [ATACseq]

description:
virtual memory cells made (Td-Tomato stamped) at 1 day
processed data files:
readCounts.tsv: TgVirtualMemory_1dayTimestampA
peaks.bed.gz

tag: strain background

tag: transgenic insertions


title: NK_D0_2 [ATAC-seq]


title: NK_D2_2 [ATAC-seq]


title: NK_D2_1 [ATAC-seq]


title: NK_D0_3 [ATAC-seq]


title: STAT1KO_HPOS_D2_003 [ATAC-seq]


title: NK_D2_3 [ATAC-seq]


title: STAT1KO_HPOS_D0_003 [ATAC-seq]


title: STAT1KO_HPOS_D2_001 [ATAC-seq]


title: STAT1KO_HPOS_D0_002 [ATAC-seq]


title: STAT1WT_HPOS_D0_002 [ATAC-seq]


title: STAT1WT_HPOS_D0_003 [ATAC-seq]


title: STAT1WT_HPOS_D2_003 [ATAC-seq]


title: STAT1KO_HPOS_D0_001 [ATAC-seq]


title: STAT1WT_HPOS_D2_001 [ATAC-seq]


title: STAT1WT_HPOS_D2_002 [ATAC-seq]


title: STAT1WT_HPOS_D0_001 [ATAC-seq]


title: STAT4KO_HPOS_D2_002 [ATAC-seq]


title: STAT4KO_HPOS_D2_003 [ATAC-seq]


title: STAT4KO_HPOS_D0_003 [ATAC-seq]


title: STAT4WT_HPOS_D2_002 [ATAC-seq]


title: STAT4KO_HPOS_D2_001 [ATAC-seq]


title: STAT4KO_HPOS_D0_001 [ATAC-seq]


title: STAT4WT_HPOS_D0_003 [ATAC-seq]


title: STAT4KO_HPOS_D0_002 [ATAC-seq]


title: STAT4WT_HPOS_D2_003 [ATAC-seq]


title: NK_D0_1 [ATAC-seq]


title: STAT4WT_HPOS_D0_001 [ATAC-seq]


title: STAT4WT_HPOS_D2_001 [ATAC-seq]


title: STAT4WT_HPOS_D0_002 [ATAC-seq]


title: Domino knockdown replicate 2

status: Public on May 15 2018

city: Cologne

first: Andreas

last: Wodarz

address: Kerpener Str. 62, Building 37

department: Anatomy

country: Germany

institute: Uniklinik Cologne

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control was performed with FastQC (v0.11.2, Babraham Bioinfomatics). Reads were mapped to the Drosophila genome (dm6) with STAR (v2.3.0e). The resulting SAM files were converted to BAM format with samtools (v0.1.19); counts were called using Htseq (v0.6.1).
Genome_build: dm6
Supplementary_files_format_and_content: csv file containing DESeq2 output

organism: Drosophila melanogaster

source_name: Neural cells

growth_protocol: UAS::Dcr-2; insc::Gal4, UAS::CD8-GFP virgins were crossed to either w1118; UAS::dom-RNAi or w1118 males. Offspring was reared at 25C and GFP-positive wandering larval brains were dissected for FAC-sorting.

extract_protocol:
Live (propidium iodide negative), GFP positive cell fractions were sorted in triplicates for each genotype on FACSVantage SE (Becton Dickinson Biosciences). The gate for GFP based sorting was determined using a GFP-negative control sample (w1118; insc::Gal4; UAS::Dcr-2). RNA isolation was performed using TRIzol (ThermoFisher Scientific) by standard phenol-chloroform extraction.
Library preparation was performed using the Illumina TruSeq RNA preparation kit

tag: genotype/variation

value: UAS::Dcr-2; insc::Gal4, UAS::CD8-GFP x w1118; UAS::dom-RNAi

value: GFP-positive FACS-sorted cells from brains of 3rd instar larva


title: Domino knockdown replicate 3


title: Domino knockdown replicate 1


title: Wild type replicate3

value: UAS::Dcr-2; insc::Gal4, UAS::CD8-GFP x w1118


title: DH44 neuron-6#

status: Public on May 04 2018

city: hangzhou

first: Rui

last: Huang

address: Yu-hang-tang road 866

institute: Zhejiang University

data_processing:
Raw reads were removed adapter contaminants (length < 37 bp) and low-quality bases (N > 10%) to get clean reads.
Index of reference genome was built using Drosophila melanogaster genome (r6.14). TopHat was used to align clean reads to the fly transcriptome.
Genome_build: Drosophila melanogaster genome (r6.14)
Supplementary_files_format_and_content: FPKM was used to quantify gene expression for each sample

source_name: DH44 producing neuron

growth_protocol: Flies containing containing cells labeled by mCD8GFP driven from DH44 GAL4 lines were cultured in normal food for 5d.

extract_protocol:
The cDNA were sequenced using a modified SMART-seq2 protocol.
The amplified cDNA were sonicated to ~250 bp fragments by the Covaris S2 system and then subjected to end-repair, dA-tail, adaptor ligation, and 12 cycles of PCR amplification using the library preparation kit (NEBNext Ultra II DNA Library Prep Kit, NEB).

treatment_protocol: After brain dissection, GFP labeled single cells were pooled in situ.

tag: tissue

value: brain

value: DH44 neuron

tag: age


title: DH44 neuron-8#


title: Wild type replicate1


title: Wild type replicate2


title: DH44 neuron-5#


title: DH44 neuron-2#


title: DH44 neuron-1#


title: eworo_RNAseq rep3

status: Public on Apr 18 2018

city: Oxford

first: Sebastian

last: Kittelmann

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description:
eworo_vs_OreR_gene_exp_diff_Cuffdiff.txt
eworo_vs_OreR_genes_fpkm_tracking_Cuffdiff.txt

data_processing:
RNAseq: Reads were aligned to FlyBase D. melanogaster genome version 6.12 using TopHat 2.1.1.
Transcripts were quantified using Cufflinks 2.2.1.
Differential expression analysis was done using Cuffdiff.
ATAC-seq: Reads were end-to-end aligned to D. melanogaster genome version 6.12 (FlyBase) using bowtie2.
Low quality reads were filtered and duplicates were removed using SAMtools.
Reads were re-centered according to Buenrostro et al. (2013) DOI:10.1038/NMETH.2688.
Peaks were called with MACS2.
Genome_build: FlyBase D. melanogaster genome version 6.12
Supplementary_files_format_and_content: Cufflinks files contain output from Cufflinks for each RNAseq replicate
Supplementary_files_format_and_content: narrowPeak files contain peak locations together with peak summit, pvalue and qvalue
Supplementary_files_format_and_content: peaks.txt files are tabular files which contains information about called peaks
Supplementary_files_format_and_content: summits files contain peak summit locations for every peak. Column1: chromosome; Column2: start position of summit; Column3: end position of summit; Colun4: label; Column5: -log10pvalue

source_name: second (T2) pupal legs

growth_protocol: Flies were kept at 25 °C on standard food. Pupae were collected within 1 h after puparium formation and were allowed to develop for another 20-28 h at 25 °C.

extract_protocol:
RNA was isolated using phenol chloroform extraction.
Libraries were prepared by Edinburgh Genomics (TruSeq stranded mRNA-seq library).

treatment_protocol:
Tissue was kept in RNAlater until RNA extraction.
Pupae were dissected under PBS.

tag: strain

value: ebony[4],white ocelli[1], rough[1]

value: 20-28 h after puparium formation

value: second (T2) pupal legs


title: eworo_RNAseq rep2


title: OreR_RNAseq rep2

value: Oregon R


title: OreR_RNAseq rep1


title: eworo_RNAseq rep1


title: OreR_RNAseq rep3


title: Homoz FB+ovaries Replicate3

status: Public on Apr 16 2018

city: Rochester

first: Benoit

middle: of

last: Biteau

state: NEW YORK

address: 601 Elmwood Avenue, Box 633

department: Biomedical Genetics

institute: University of Rochester Medical Center

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.36 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
REFERENCE - dm6
READ COUNTING - subread-1.5.0p3,featurecounts,Unique"-s 0 -t exon -g gene_name"Multi-Mapping "-s 0 -M -t exon -g gene_name"
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include Normalized Counts for each Sample and each Gene

source_name: larval fatbody + ovaries

growth_protocol: A balanced dLmx1a knock-out fly stock was cultivated under standard conditions at 25oC. Animals were selected at LL3/P0 transition. Heterozygous and homozygous females were distinguished by the presence or absence of the TM3-GFP balancer respectively.

extract_protocol:
Qiagen RNAeasy
RNA libraries were prepared for sequencing using standard Illumina protocols

value: larval fatbody + ovaries

value: dLmx1a delta1 / dLmx1a delta7


title: Homoz FB+ovaries Replicate2

value: dLmx1a delta1 / dLmx1a delta6


title: Homoz FB+ovaries Replicate4

value: dLmx1a delta1 / dLmx1a delta8


title: Homoz FB Replicate4

source_name: larval fatbody

value: larval fatbody

value: dLmx1a delta1 / dLmx1a delta4


title: Homoz FB+ovaries Replicate1

value: dLmx1a delta1 / dLmx1a delta5


title: Homoz FB Replicate2

value: dLmx1a delta1 / dLmx1a delta2


title: CG7358 mutant  sample3

city: Shanghai

first: Guo

last: Jian

address: Fenglin Road

department: Chinese Academy of Science

institute: Shanghai Institutes for Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie2 and Tophat were used to align reads to genome.
Culfflicks were used to do differential expressing analysis.
Genome_build: GCA_000001215.4 Release 6 plus ISO1 MT
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: whole organism

growth_protocol: Normal conditions for the maintenace of fly in lab

extract_protocol:
Total RNA were estracted according to Qiagen RNeasy mini kit
Library were constructed according to NEXTflexTM Rapid Directional RNA-Seq Kit (BIOO SCIENTIFIC)

value: whole organism

tag: developmental stage

value: pupae 4 days postWPP

value: y1 w* CG7358A P{neoFRT}19A/FM7c, P{GAL4-Kr.C}DC1, P{UAS-GFP.S65T}DC5, sn+


title: Wild type  sample2

value: w*


title: CG7358 mutant  sample2


title: CG7358 mutant  sample1


title: Homoz FB Replicate3

value: dLmx1a delta1 / dLmx1a delta3


title: Wild type  sample3


title: Het FB+ovaries Replicate4

value: dLmx1a delta1 / TM3-GFP


title: PIWI1: Piwi RNAi 7 days 1

status: Public on Apr 06 2018

city: Novato

first: Pedro

last: Sousa-Victor

state: CALIFORNIA

address: 8001 Redwood Blvd.

institute: Buck Institute for Research on Aging

data_processing:
TopHat was used to align RNA-seq reads to the reference genome
Cufflinks was used for final transcriptome reconstruction and expression quantification
Genome_build: Drosophila genome release 5.2

source_name: sorted ISCs - PiwiRNAi (7d 29ºC)

growth_protocol: Flies were kept at 29C to express RNAi against Piwi or mCherry for 7 days.

extract_protocol:
RNA was extracted from sorted ISCs using Trizol (Invitrogen)
RNA libraries were prepared for sequencing using standard protocol of TruSeq RNA Library Prep Kit

value: Intestinal Stem Cells


title: Het FB Replicate4


title: Het FB+ovaries Replicate1


title: Homoz FB Replicate1

value: dLmx1a delta1 / dLmx1a delta1


title: Het FB Replicate2


title: Het FB Replicate3


title: Het FB+ovaries Replicate3


title: Het FB+ovaries Replicate2


title: T2_ASH1ko_5

status: Public on Mar 28 2018

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

data_processing:
Primary data analysis was done using Illumina’s real-time analysis software (RTA)
Sequenced reads containing adaptor sequences were discarded, remaining reads were trimmed, then mapped to the dm3 genome assembly and Ensembl gene-annotation version 78 using STAR aligner (using ENCODE settings)
Gene-level exon read counts were quantified using featurecounts (using ensembl78) and differential expression calculated using the limma voom pipeline
Replicate expression levels were quantified using rsem (using ensembl version 78)
Genome_build: dm3
Supplementary_files_format_and_content: Table (as tab separated values) with replicate expression levels [TPM], fold changes and p-values (Ash1-/- over wild type) for all quantifiable genes as output by the limma voom pipeline for T3 and T2 disks

molecule: polyA RNA

source_name: T3 discs ash1[22] homozygous larvae replicate 5

growth_protocol: Drosophila were grown on standard medium at 25˚C

extract_protocol:
RNA was isolated from independently prepared batches of hand-dissected haltere and third-leg imaginal discs (T3 discs) or wing discs (T2 discs) from wild-type or ash122 homozygous larvae, using the Direct-zol RNA mini Prep Kit (Zymo Research). After additional Agencourt AMPure XP purification (Beckman Coulter) isolated RNA was analyzed on a Bioanalyzer (Agilent) using an RNA 6000 Nano Chip (Agilent).
Non-degraded RNA from independent biological replicates of each type of sample was used to construct sequencing libraries with the sense mRNA-Seq Library Prep Kit (Lexogen).
Quality-controlled and quantified libraries were sequenced on an HiSeq1500 system (Illumina) in the single-end mode (100 nt reading length).

value: wing imaginal discs (T2 discs)

value: ash1[22] null mutation


title: WT1: mCherry RNAi 7 days 1

source_name: sorted ISCs - yw (7d 29º)


title: Het FB Replicate1


title: Wild type  sample1


title: T2_ASH1ko_4

source_name: T3 discs ash1[22] homozygous larvae replicate 4


title: T2_ASH1ko_3

source_name: T3 discs ash1[22] homozygous larvae replicate 3


title: T2_ASH1ko_2

source_name: T3 discs ash1[22] homozygous larvae replicate 2


title: T2_ASH1ko_1

source_name: T3 discs ash1[22] homozygous larvae replicate 1


title: T2_wt_5

source_name: T2 discs wt larvae replicate 5

value: wild type


title: T2_wt_4

source_name: T2 discs wt larvae replicate 4


title: T2_wt_3

source_name: T2 discs wt larvae replicate 3


title: T2_wt_2

source_name: T2 discs wt larvae replicate 2


title: T2_wt_1

source_name: T2 discs wt larvae replicate 1


title: T3_ASH1ko_4

value: haltere imaginal discs (T3 discs)


title: T3_wt_1

source_name: T3 discs wt larvae replicate 1


title: T3_ASH1ko_1


title: T3_wt_4

source_name: T3 discs wt larvae replicate 4


title: T3_ASH1ko_3


title: T3_ASH1ko_2


title: EXR-DERLE1UCSF063

status: Public on Mar 27 2018

city: San Francisco

first: David

last: Erle

state: CA

address: 1550 4th Street, Bldg 19B

institute: University of California, San Francisco

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of TGGAATTCTCGGGTGCCAAGG and random barcode length 4 (on 5' and 3' ends). Information about exceRpt is available at https://rkitchen.github.io/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Bile

extract_protocol:
Low speed centrifugation (5 minutes in 4 C room at 2,000 x g) was performed to pellet cells and cryoprecipitate. Extracellular vesicles were not pre-purified. RNA was isolated using miRNeasy (Qiagen).
Modified TruSeq Small RNA with randomized 4N adapters.

value: Liver transplant recipient

tag: anatomical location

value: Entire gallbladder

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: miRNeasy (Qiagen)


title: EXR-DERLE1UCSF065


title: EXR-DERLE1UCSF062


title: EXR-DERLE1UCSF064


title: EXR-DERLE1UCSF059


title: EXR-DERLE1UCSF067


title: EXR-DERLE1UCSF058


title: EXR-DERLE1UCSF068


title: EXR-DERLE1UCSF060


title: EXR-DERLE1UCSF066


title: EXR-DERLE1UCSF061


title: CAGE control rep 4

status: Public on Mar 22 2018

city: Copenhagen N

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

description: The first 9 positions of the reads contain the barcore (3 nt) and the EcoP15I restriction enzyme recognition site (CAGCAG). At the 5' end, two extra nt in position 10-11 of the reads, right after the barcode, need to be trimmed. This is due to an artifact in the reverse transcription of the capped G. The last 15 nt also need to be trimmed due to 3' end adaptors.

data_processing:
The first 11 nt and the last 15 nt of reads were trimmed off. All the reads were then filtered by fastq_quality_filter (fastx_toolkit) using -q 30 -p 50 and mapped to dm3 (r5.33) by bowtie version 1.1.1 using --strata --best -k 10. Only 5'ends of uniquely mapped reads were used in the analysis.
Genome_build: dm3 (r5.33)
Supplementary_files_format_and_content: CAGE bed files contain positions of 5' ends of unique locations of CAGE tags and the number of CAGE tags at that position (score column).

growth_protocol: S2 cells were cultured at 27 degrees C in Schneider’s medium (Sigma, S0146) supplemented with 10% FBS (Sigma, F7524) and 1% penicilin/streptomycin (Sigma, P0781).

extract_protocol:
Total RNA was purified from S2 cells with TRIzol (Ambion, 15596018) according to the manufacturer’s protocol.
CAGE libraries were prepared as described elsewhere (PMID: 21938627, PMID: 25387874), barcoded and pooled in libraries of four (one pool per sequencing lane). Sequencing of samples was performed twice to generate deeper sequening depth.

treatment_protocol: Double-stranded RNAs (dsRNA) to deplete Rrp6 and Dis3 were prepared by in vitro transcription from a PCR template with T7 promoters on both ends using the Megascript RNAi kit (Ambion, AM1626) according to the manufacturer’s instructions. DsRNA against GFP was used as a control. For each condition, 3x10^6 cells were seeded in a well of a 6-well plate. The following day, cells were washed twice with Schneider’s media with no FBS and no antibiotica, a mixture of 40 microgram of dsRNA (20 microgram Rrp6 dsRNA and 20 microgram Dis3 dsRNA or 40 microgram GFP dsRNA) in 500 microlitre media was added dropwise to the cells, the plates were agitated for 30 sec and incubated for 6h at 27 degrees C. Finally, 2.5 millilitre of media with FBS and penicilin/streptomycin were added. The treatment was repeated 2 days later and the cells were harvested 4 days after the first dsRNA treatment.

tag: sample note

value: GFP knockdown (control)

tag: barcode

value: ATCCAGCAG


title: CAGE control rep 3

value: ACGCAGCAG


title: CAGE control rep 2

value: GATCAGCAG


title: CAGE control rep 1

value: CTTCAGCAG


title: CAGE KD rep 4

value: Dis3 and Rrp6 double knockdown (exosome)


title: CAGE KD rep 2


title: CAGE KD rep 3


title: T3_wt_5

source_name: T3 discs wt larvae replicate 5


title: CAGE KD rep 1


title: p53_0.7mSucrose_4_96

status: Public on Mar 13 2018

city: Binghamton

first: Laura

middle: Palanker

last: Musselman

address: 4400 Vestal Parkway East

department: Biological Sciences

institute: Binghamton University

data_processing:
To produce bed alignments, sequenced reads were aligned to the D. melanogaster UCSC dm3 assembly using Tophat (v1.3.2) and Bowtie (v0.12.7). Default Tophat settings were used.
Gene expression was quantified by processing the Tophat produced bam alignments with Cufflinks (v1.1.0) and the modENCODE MB8 annotation.
Expression was normalized by applying upper-quartile normalization as defined in "Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments", Bullard et al. BMC Bioinformatics. 2010; 11: 94
Genome_build: MB8
Supplementary_files_format_and_content: Excel worksheet "4KD+ processed data" containing normalized RPKM for each raw dataset, indexed by gene Accession (CG number)

source_name: fat body

growth_protocol: Wild-type males (VDRC's w1118 or 60100 control stocks) were crossed to fat body GAL4 driver line virgin females to produce so-called wild-type offspring that served as controls for the following RNAi line crosses: VDRC lines targeting dFOXO (CG3143), Stat92E (CG4257), p53 (CG33336), or Tfb1 (CG8151) as described in Musselman et al, GENETICS, 2018. Larval offspring were collected at the end of larval development (also known as the wandering third instar stage).

extract_protocol:
Fat bodies were homogenized in Trizol and total RNA isolated after DNAse digestion.
RiboZero subtraction was used to remove rRNA and then reverse transcription, size exclusion, amplification, and bar coding produced the final library.
Reads using bar-coded cDNA were generated by Illumina Hi-Seq analyzer.

treatment_protocol: Larvae were reared on control (0.15M) or high-sugar (0.7M or 1 M sucrose) diets using a modified Bloomington semi-defined food as previously described (J Biol Chem 288(12):8028-42). Fat bodies were isolated by fine dissection or by shearing and separation by centrifugation.

value: fat body

value: wandering third instar larva

tag: Sex

value: Female

tag: treatment

value: 0.7m Sucrose

value: VDRC's 103001 stock crossed with a UAS-Dcr2 (X); r4-GAL4) stock

tag: extraction method

value: Floated


title: Stat92E_0.7mSucrose_3_97

tag: genotype

value: VDRC's 106980 stock crossed with a UAS-Dcr2 (X); r4-GAL4) stock


title: EXR-DERLE1UCSF057

tag: condition

value: Liver transplant recipient


title: FOXO_0.7mSucrose_4_94

value: VDRC's 106097 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock


title: FOXO_0.7mSucrose_3_93


title: ctrl_0.7mSucrose_4_92

value: VDRC's 60100 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock


title: ctrl_0.7mSucrose_3_91


title: Stat92E_0.15mSucrose_4_90

value: 0.15m Sucrose


title: Stat92E_0.15mSucrose_3_89


title: p53_0.15mSucrose_3_87


title: ctrl_0.15mSucrose_4_84


title: FOXO_0.15mSucrose_3_85


title: Stat92E_0.7mSucrose_1_81


title: FOXO_0.15mSucrose_4_86


title: p53_0.15mSucrose_4_88


title: p53_0.7mSucrose_2_80


title: ctrl_0.7mSucrose_2_76


title: ctrl_0.7mSucrose_1_75


title: FOXO_0.7mSucrose_1_77


title: Stat92E_0.15mSucrose_2_74


title: p53_0.7mSucrose_3_95


title: p53_0.15mSucrose_2_72


title: FOXO_0.15mSucrose_1_69


title: FOXO_0.15mSucrose_2_70


title: ctrl_0.15mSucrose_1_67


title: ctrl_0.15mSucrose_2_68


title: ctrl_1.0mSucrose_1_64

value: 1.0m Sucrose

value: VDRC's w1118 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock


title: ctrl_1.0mSucrose_3_66


title: ctrl_0.7mSucrose_3_63


title: ctrl_1.0mSucrose_2_65


title: p53_0.7mSucrose_1_79


title: ctrl_0.7mSucrose_1_61


title: ctrl_0.3mSucrose_2_59

value: 0.3m Sucrose


title: FOXO_0.7mSucrose_2_78


title: ctrl_0.7mSucrose_2_62


title: Stat92E_0.15mSucrose_1_73


title: ctrl_0.7mSucrose_1_52

value: VDRC's w1118 stock crossed with a UAS-Dcr2 (X); cg-GAL4 stock


title: ctrl_0.7mSucrose_3_54


title: ctrl_0.15mSucrose_3_51


title: ctrl_0.3mSucrose_1_58


title: ctrl_0.15mSucrose_2_56


title: ctrl_0.15mSucrose_1_55


title: ctrl_0.15mSucrose_3_57


title: Tfb1_1.0mSucrose_2_47

value: Male

value: VDRC's 12580 stock crossed with a UAS-Dcr2 (X); cg-GAL4 stock

value: Dissected


title: Tfb1_1.0mSucrose_1_46

value: fat body

value: wandering third instar larva


title: p53_0.15mSucrose_1_71

value: Female


title: ctrl_1.0mSucrose_3_45


title: ctrl_0.15mSucrose_1_49


title: Tfb1_0.15mSucrose_2_41


title: Tfb1_0.15mSucrose_1_40


title: ctrl_0.15mSucrose_3_39


title: ctrl_0.15mSucrose_2_38


title: ctrl_0.7mSucrose_2_53

value: 0.7m Sucrose


title: ctrl_1.0mSucrose_1_43


title: ctrl_0.15mSucrose_1_37


title: ctrl_0.3mSucrose_3_60

value: Floated


title: OrgR1-2

status: Public on Mar 02 2018

city: Brisbane

first: Stefan

last: Thor

state: QLD

address: Skerman Bldg (65) room 506  Faculty of Medicine

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

description:
pool 200+ st14+15 whole embryos
OrgR-esc-linearRPKM-nofilter.csv

data_processing:
LaserGene suite v14-v15, DNASTAR SeqMan Ngen Qseq alignment (unpacked FASTQ)
Reference dmel genome, focus on CDS/mRNA/ncRNA
RPKM normalization
Data exported from Dnastar to .csv, linear RPKM values, no filtering
Genome_build: dm6 plus iso1 mt
Supplementary_files_format_and_content: .csv (genesymbol annotation with linear RPKM per sample, column 1: genesymbol, column 2-9 samples, row 1: headers, each subsequent row is a gene, values rounded to three decimal places).

source_name: pooled st14+15 whole embryo OrgR wt

growth_protocol: Flies were maintained under standard conditions

extract_protocol:
200+ whole embryos from stage 14 and 15 were pooled, then RNA extraction with Qiagen Rneasy kit
NEBNext Ultra RNA Library Prep Kit; RNA-seq Illumina HiSeq2500 ~40M reads PE 150bp unstranded

treatment_protocol: esc mutants were maternal zygotic mutants

value: whole embryos

value: stage 14 and 15

value: wt


title: esc2-2

source_name: pooled st14+15 whole embryo esc maternal zygotic mutant

value: esc


title: OrgR2-2


title: esc2-1


title: MBE-CE-00162_72hrE1

status: Public on Feb 23 2018

city: Cambridge

first: Carolyn

last: Elya

state: MA

address: 52 Oxford Street

department: Organismic and Evolutionary Biology

institute: Harvard University

data_processing:
Fastq files were aligned as single reads to the D. melanogaster reference (r6.21), a de novo E. muscae 'Berkeley' transcriptome or a de novo E. muscae 'Berkeley' genome (NCBI PRJNA479887) using bowtie2 as described in Elya et al., 2018 (bioRxiv). Transcript abundance was estimated from the resultant .bam files using Salmon.
Genome_build: 6.21
Supplementary_files_format_and_content: dmel_expression.txt (D. melanogaster alignments), emus_transcriptome_expression.txt (E. muscae 'Berkeley' transcriptome alignments) and emus_genome_expression.txt (E. muscae 'Berkeley' genome alignments): Tables of estimated transcript abundance (transcripts per million, TPM) for each sample. Sample key for table (including accession number, original index name and sample identity) are provided as sample_key.txt.

source_name: Exposed_72 hours_Dissected brain

growth_protocol: Young, CantonS Wolbachia-free flies were exposed to Entomophthora muscae 'Berkeley' as described in Elya et al, bioRxiv 2017

extract_protocol:
Total RNA was isolated from individual whole flies or dissected brains using Trizol (Invitrogen) per manufacturer's protocol.
mRNA libraries were prepared using Illumina's RNA TruSeq v2 kit per manufacturer's protocol.
Libraries were sequenced multiplexed 18-21 samples a lane at approximately equal concentrations  and sequenced 100 PE on the Illumina HiSeq4000.

value: CantonS

value: 1-2 days old

value: Exposed

value: 72 hours

value: Dissected brain


title: Tfb1_1.0mSucrose_3_48

value: Male

value: 1.0m Sucrose


title: MBE-CE-00162_48hrE3

source_name: Exposed_48 hours_Dissected brain

value: 48 hours


title: MBE-CE-00162_48hrE2


title: MBE-CE-00162_72hrC3

source_name: Unexposed_72 hours_Dissected brain

value: Unexposed


title: MBE-CE-00162_24hrC3

source_name: Unexposed_24 hours_Dissected brain

value: 24 hours


title: MBE_CE_00156_9

source_name: Unexposed_120 hours_Whole fly

value: 0-1 day old

value: 120 hours

value: Whole fly


title: MBE-CE-00162_24hrE1

source_name: Exposed_24 hours_Dissected brain


title: MBE-CE-00162_48hrC1

source_name: Unexposed_48 hours_Dissected brain


title: MBE-CE-00162_24hrE2


title: MBE_CE_00156_7

source_name: Infected cadaver_120 hours_Whole fly

value: Infected cadaver


title: MBE_CE_00156_3

source_name: Exposed_72 hours_Whole fly


title: MBE_CE_00156_6

source_name: Unexposed_96 hours_Whole fly

value: 96 hours


title: MBE_CE_00156_5


title: MBE_CE_00156_4


title: MBE_CE_00156_21

source_name: Unexposed_24 hours_Whole fly


title: MBE_CE_00156_20

source_name: Exposed_24 hours_Whole fly


title: MBE_CE_00156_19


title: MBE_CE_00156_18


title: OrgR1-1

value: whole embryos

value: stage 14 and 15

value: wt


title: MBE_CE_00156_17

source_name: Unexposed_48 hours_Whole fly

value: CantonS


title: MBE_CE_00156_16


title: MBE_CE_00156_14

source_name: Exposed_48 hours_Whole fly

value: Exposed


title: MBE_CE_00156_15


title: MBE_CE_00156_12

source_name: Exposed_96 hours_Whole fly


title: MBE_CE_00156_2

value: 72 hours


title: MBE_CE_00156_10


title: MBE_CE_00155_Index8


title: MBE_CE_00156_1

source_name: Unexposed_72 hours_Whole fly


title: MBE_CE_00156_13


title: MBE_CE_00155_Index22


title: MBE_CE_00155_Index7


title: MBE_CE_00155_Index19

source_name: Infected cadaver_96 hours_Whole fly


title: MBE_CE_00155_Index5


title: MBE_CE_00155_Index21


title: MBE_CE_00155_Index3


title: MBE_CE_00155_Index15


title: MBE_CE_00155_Index18


title: MBE_CE_00155_Index16


title: MBE_CE_00155_Index13


title: MBE_CE_00155_Index11


title: MBE_CE_00155_Index12


title: MBE_CE_00155_Index1


title: MBE_CE_00155_Index2


title: MBE_CE_00155_Index4


title: MBE_CE_00155_Index20


title: r4gal4_ecri_0_5m_2

status: Public on Feb 10 2018

description: VDRC's 37058 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock

data_processing:
To produce bed alignments, sequenced reads were aligned to the D. melanogaster reference build Ensembl_R72  using Tophat (v1.3.2) and Bowtie (v0.12.7). Default Tophat settings were used.
Gene expression was quantified by processing the Tophat produced bam alignments with Cufflinks (v1.1.0) and the modENCODE MB8 annotation.
Genome_build: MB8
Supplementary_files_format_and_content: Excel worksheet "GEO upload processed data" containing normalized abundance for each raw dataset using EdgeR, indexed by FlyBase Gene Name

source_name: fat body

growth_protocol: Wild-type males (VDRC's 60000 control stock or 37058 UAS-EcR RNAi stock) were crossed to r4-GAL4 driver line virgin females to produce offspring whose fat bodies were to be isolated and profiled. Larval offspring were collected at the end of larval development (also known as the wandering third instar stage)

treatment_protocol: Larvae were reared on control (0.15M) or high-sugar (0.5M) diets using a modified Bloomington semi-defined food as previously described (J Biol Chem 288(12):8028-42). Fat bodies were isolated by fine dissection, shearing and separation by centrifugation.

value: wandering third instar larva

value: fat body

value: female


title: r4gal4_ecri_0_5m_1


title: r4gal4_ecri_0_5m_3


title: MBE_CE_00155_Index14


title: r4gal4_vw1118_0_5m_2

description: VDRC's 60000 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock


title: MBE_CE_00155_Index10


title: r4gal4_ecri_0_15m_1


title: r4gal4_vw1118_0_15m_2


title: r4gal4_ecri_0_15m_3


title: r4gal4_vvw1118_0_15m_1


title: Mock Replicate 6_RNA-seq

status: Public on Feb 04 2018

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
Alignment to Drosophila melanogaster genome sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics 11:e1005655.
Expression values in RNAi-treated BG3 replicates were averaged and compared to the average of six mock treated BG3 replicates published in Pherson et al. 2017 Sci Adv 3:e1700944 [GSE100548 (GSM2686307, GSM2686308, GSM2686309, GSM2686310, GSM2686311, GSM2686312)]. Expression values in wing discs with mutant brca2 alleles (brca2[56e/ko], brca2[ko]) were averaged and compared to the averaged expression values from wing discs with wild type brca2 alleles (Canton S, y w).
Genome_build: Drosophila melanogaster release 5 (April 2006) with chrU and U_extra sequences removed
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in RNAi treated cells to mock RNAi control cells and between wing discs with wild type brca2  to wing discs with mutant brca2 (brca2[56e/ko], brca2[ko]).

source_name: ML-DmBG3-c2 cultured cells

growth_protocol: BG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin. Drosophila were grown at 25 degrees on cornmeal-molasses-yeast based food.

extract_protocol:
Total RNA was extracted using the Zymo Research Quick-RNA MicroPrep Kits with DNaseI treatment following the manufacturer's directions.
Ion Xpress IonXpressRNA barcoded sequencing libraries were constructed using the Eukaryotic Ribominus and Ion Total v2 kits (Life Technologies) according to the manufacturer's directions.

treatment_protocol: For RNAi treatment of BG3 cells, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 3 hours. For RNAi of all factors, from 0.7 to 40 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS with Schneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against each target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools.

tag: RNAi treatment

value: Mock

tag: cell line

value: CNS-derived cell-line


title: r4gal4_ecri_0_15m_2


title: r4gal4_vw1118_0_15m_3


title: Mock Replicate 5_RNA-seq


title: r4gal4_vw1118_0_5m_3


title: Mock Replicate 1_RNA-seq


title: Canton S wing disc replicate 2

source_name: third instar larval wing discs

value: wild type

value: wing disc


title: Mock Replicate 4_RNA-seq


title: r4gal4_vw1118_0_5m_1


title: Canton S wing disc replicate 1


title: iWapl BG3 replicate 3

value: Wapl


title: brca2[ko] wing disc replicate 1

value: brca2 mutant


title: brca2[56e/ko] wing disc replicate 3


title: brca2[56e/ko] wing disc replicate 1


title: brca2[56e/ko] wing disc replicate 2


title: iWapl BG3 replicate 1


title: iRad21 BG3 replicate 3


title: iWapl BG3 replicate 2


title: iRad21 BG3 replicate 2


title: iRad21 BG3 replicate 1


title: iPds5 BG3 replicate 2


title: iNipped-B BG3 replicate 3

value: Nipped-B


title: iNipped-B BG3 replicate 2


title: iBrca2 iPds5 BG3 replicate 3

value: Brca2 Pds5


title: yw wing disc replicate 1


title: iBrca2 iPds5 BG3 replicate 2


title: iBrca2 iPds5 BG3 replicate 1


title: iBrca2 BG3 replicate 2


title: iBrca2 BG3 replicate 3


title: brca2[ko] wing disc replicate 2


title: soma_l(3)mbt_mut3

status: Public on Feb 01 2018

city: Paris

first: Remi-Xavier

last: Coux

address: 25 rue du docteur Roux

department: Developmental and Stem Cell Biology dpt

country: France

institute: Pasteur Institute

description:
PolyA RNA
processed data file: Soma_RNAseq.xlsx

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina Bcl2FastQ software (Illumina).
Reads were aligned to the fly genome (build dm3/BDGP5) using the splice-aware STAR aligner (Dobin et al., 2013)
PCR duplicates were removed using the Picard toolkit (https://broadinstitute.github.io/picard/)
HTSeq package was used to generate counts for each gene based on how many aligned reads overlap its exons (Anders et al., 2015).
These counts were then used to test for differential expression using negative binomial generalized linear models implemented by the DESeq2 R package.
Genome_build: dm3/BDGP5
Supplementary_files_format_and_content: Soma_RNAseq.xlsx: Excel spreadsheet contains differential expression per experiment, as well as normalized counts.
Supplementary_files_format_and_content: *.bw: Normalized bigwig files.

source_name: somatic ovaries (ovaries devoid of germ cells)

growth_protocol: Flies were maintained at 25˚C following standard procedures.

extract_protocol:
Somatic ovaries: 60-70 ovaries from females of maternal tud[1]/tud[B42] and zygotic l(3)mbt[GM76]/+ (control) or l(3)mbt[GM76]/Df genotypes were dissected in cold PBS and RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s protocol.
Libraries were generated from 1µg of total RNA using the NEBNext Poly(A) magnetic Isolation Module (NEB #7490) and the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB # E7420). Libraries from 3 biological replicates were sequenced on an Illumina Hi-Seq2000, paired-end 50 run.

value: somatic ovaries

tag: maternal genotype

tag: zygotic genotype

tag: Stage

value: 2-3 day old females


title: soma_l(3)mbt_mut2

tag: tissue


title: iBrca2 BG3 replicate 1


title: soma_l(3)mbt_mut1


title: soma_wt2


title: germline_l(3)mbt_mut2

description:
PolyA RNA
processed data file: Germline_RNAseq.xlsx

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina Bcl2FastQ software (Illumina).
Reads were aligned to the fly genome (build dm3/BDGP5) using the splice-aware STAR aligner (Dobin et al., 2013).
PCR duplicates were removed using the Picard toolkit (https://broadinstitute.github.io/picard/).
HTSeq package was used to generate counts for each gene based on how many aligned reads overlap its exons (Anders et al., 2015).
These counts were then used to test for differential expression using negative binomial generalized linear models implemented by the DESeq2 R package.
Genome_build: dm3/BDGP5
Supplementary_files_format_and_content: Germline_RNAseq.xlsx: Excel spreadsheet contains differential expression per experiment, as well as normalized counts.
Supplementary_files_format_and_content: *.bw: Normalized bigwig files.

source_name: embryos

extract_protocol:
Early embryos, TJ>UAS-l(3)mbt::myc;l(3)mbt[GM76]/+ and TJ>UAS-l(3)mbt::myc;l(3)mbtGM76/Df females were allowed to lay for 30 minutes to 1 hour on agar plates. Embryos were dechorionated in 50% bleach for 5 minutes, rinsed with PBS, and then lysed in TRIzol following manufacturer's guidelines.
Libraries were generated from 1µg of total RNA using the NEBNext Poly(A) magnetic Isolation Module (NEB #7490) and the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB # E7420). Libraries from 2 biological replicates were sequenced on an Illumina Hi-Seq2500, paired-end 50 run.

value: embryos

value: 30 mins to 1 hour


title: soma_wt3


title: iPds5 BG3 replicate 3


title: iBrca2 iWapl BG3 replicate 1

value: Brca2 Wapl


title: iNipped-B BG3 replicate 1


title: S2_WT_mRNA

status: Public on Dec 29 2017

city: Waltham

first: Weijin

last: Xu

address: 415 South st.

institute: Brandeis University

data_processing:
RNA sequencing data were analyzed as described in (Rodriguez et al., 2012; McMahon et al., 2016), with minor modifications.
Scripts available on GitHub (https://github.com/rosbashlab/TRIBE).
Alignment to dm3 genome was done with Tophat v2.1.1 with referenence annotation in gtf format. Multimapped reads are removed.
PCR duplicate is removed with Picard v2.8.2
Genome_build: Release 5/dm3

source_name: S2 Cell

extract_protocol:
RNA extracted by TRIzol
s2 cell mRNA libraries were prepared using Illumina Truseq kits according to manufacturers protocol.  Neuronal cell sorting libraries were prepared according to Abruzzi et al, 2015.

tag: genotype/variation

value: Wild Type


title: germline_wt1


title: Aspergillus niger wild type grown on D-glucose 2 hours, replicate 2

status: Public on Jan 29 2018

type: RNA

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

description:
Glc-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-glucose.

hyb_protocol: Following fragmentation, 10 µg of cRNA was hybridized to Affymetrix A. niger Genome GeneChips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned.

data_processing: Microarray data was analyzed using the Bioconductor tool package version 2.8 (http://www.bioconductor.org/) together with house-made Perl (version .5.0) and Python (version 3.0) scripts. Probe intensities were normalized for background by the robust multi-array average (RMA) method using the R statistical language and environment. This method makes use of only perfect match (PM) probes. Normalization was processed by the quantiles algorithm. The median polish summary method was used to calculate the gene expression values.

label: biotin

organism: Aspergillus niger

source_name: A. niger wild type growing on D-glucose

label_protocol: Biotin-labeled antisense cRNA was produced from 2 µg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).

growth_protocol: A. niger N402 wild type was pre-cultured in 1 L Erlenmeyer flasks in 250 mL complete medium (CM) supplemented with 2% D-fructose. The pre-cultures were inoculated with 10e6 spores/mL and incubated at 250 rpm for 16 h at 30°C.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer.

treatment_protocol: Mycelium was washed with MM and transferred for 2 h to 250 ml Erlenmeyer flasks containing 50 ml MM supplemented with 25 mM D-glucose, D-fructose, D-galactose, L-arabinose, D-xylose, D-mannose, D-galacturonic acid, L-rhamnose, Maltose, Sucrose, Ferulic acid or ferulic acid, or mixture of 25 mM L-rhamnose and 25 mM D-galacturonic acid, or 1% Inulin from chicory, Cellulose, Guar gum, Xyloglucan, Xylan (from beechwood), Polygalacturonic acid (from apples), Apple pectin, Galactan (from potato), Debranched 1,5-α-L-arabinan (from sugar beet), Rhamnogalacturonan I (from potato), Mannan (ivory nut), Citrus pulp, Sugar beet pulp or Soy bean hulls. The only exceptions were D-maltose cultures of N402 and ∆amyR strains that were incubated for 4 h. Mycelium was harvested by vacuum filtration, dried between towels and frozen in liquid nitrogen. While N402 liquid cultures were performed on all carbon sources listed before as well as on the mixture of L-rhamnose and D-galacturonic acid, the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX were grown on D-xylose, L-arabinose, maltose, L-rhamnose and D-galactose, respectively, and L-rhamnose and D-galacturonic acid. All cultures were performed as biological duplicates.

tag: strain

value: cspA1 (wild type)

value: mycelium

tag: age

value: 2 hours

tag: substrate

value: 25 mM D-glucose


title: Aspergillus niger wild type grown on D-mannose 2 hours, replicate 2

description:
Man-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-mannose.

source_name: A. niger wild type growing on D-mannose

value: 25 mM D-mannose


title: Aspergillus niger wild type grown on guar-gum 2 hours, replicate 1

description:
GG-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on guar-gum.

source_name: A. niger wild type growing on guar-gum

value: 1% guar-gum


title: Aspergillus niger wild type grown on D-galactose 2 hours, replicate 1

description:
Gal-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-galactose.

value: 25 mM D-galactose


title: Aspergillus niger wild type grown on D-galactose 2 hours, replicate 2

description:
Gal-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-galactose.


title: Aspergillus niger wild type grown on mannan 2 hours, replicate 1

description:
Mnn-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on mannan.

source_name: A. niger wild type growing on mannan

value: 1% mannan


title: Copper 48h treatment replicate 1

status: Public on Dec 27 2017

city: Aachen

last: Sonnack

address: Forckenbeckstr. 6

institute: Fraunhofer IME

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized overnight for 17 h at 65°C

scan_protocol: Slides were scanned immediately after washing on Agilent Microarray Scanner (Agilent Technologies) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and QC Metric Set GE_QCMT_Jan09) During this step the background was subtracted and outliers detected and flagged.

organism: Danio rerio

source_name: Copper 48h treatment replicate 1

label_protocol: The samples were processed following the Agilent´s One-Color Microarray-Based Gene Expression Analysis Protocol (Low Input Quick Amp Labeling, Version 6.6, September 2012). The starting amount of all samples was 100 ng of total RNA.

growth_protocol: Zebrafish embryo toxicity test followig DIN EN ISO 15088; After harvest of the eggs, the embryos were quickly transferred to the wells (one embryo/well) of the plates and incubated for 48 h and 96 h at 26 ± 1°C with a 14-h photoperiod

extract_protocol: Total RNA was extracted from the frozen, pooled embryos by the Trizol-Method and homogenization with motor-driven plastic micro pistils. Subsequently, RNA was cleaned-up using RNeasy Mini Spin Columns (QIAGEN, Hilden, Germany) according to the manufacturers' protocols. For all RNA samples, the absorbance ratio 260/280 was above 2.0 and 260/230 above 1.8 while the RNA integrity number was above 8.7

treatment_protocol: All metal test solutions were prepared in ISO-standard water (prepared according to OECD guideline 203, Annex 2) diluted 1:5

tag: developmental stage

value: 48hpf embryos


title: Aspergillus niger wild type grown on D-mannose 2 hours, replicate 1

description:
Man-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-mannose.


title: Aspergillus niger wild type grown on mannan 2 hours, replicate 2

description:
Mnn-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on mannan.


title: Copper 96h treatment replicate 3

source_name: Copper 96h treatment replicate 3

value: 96hpf embryos


title: Aspergillus niger wild type grown on D-glucose 2 hours, replicate 1

description:
Glc-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on D-glucose.


title: Copper 96h treatment replicate 1

source_name: Copper 96h treatment replicate 1


title: Cobalt 96h treatment replicate 3

source_name: Cobalt 96h treatment replicate 3


title: Copper 48h treatment replicate 3

source_name: Copper 48h treatment replicate 3


title: Aspergillus niger wild type grown on guar-gum 2 hours, replicate 2

description:
GG-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on guar-gum.


title: Cobalt 48h treatment replicate 2

source_name: Cobalt 48h treatment replicate 2


title: Cobalt 96h treatment replicate 4

source_name: Cobalt 96h treatment replicate 4


title: Copper 48h treatment replicate 2

source_name: Copper 48h treatment replicate 2


title: Copper 96h treatment replicate 4

source_name: Copper 96h treatment replicate 4


title: Cobalt 48h treatment replicate 1

source_name: Cobalt 48h treatment replicate 1


title: Copper 96h treatment replicate 2

source_name: Copper 96h treatment replicate 2


title: Cadmium 48h treatment replicate 3

source_name: Cadmium 48h treatment replicate 3


title: Cobalt 96h treatment replicate 2

source_name: Cobalt 96h treatment replicate 2


title: Cadmium 96h treatment replicate 2

source_name: Cadmium 96h treatment replicate 2


title: Cadmium 96h treatment replicate 4

source_name: Cadmium 96h treatment replicate 4


title: Cobalt 48h treatment replicate 3

source_name: Cobalt 48h treatment replicate 3


title: Cadmium 96h treatment replicate 3

source_name: Cadmium 96h treatment replicate 3


title: Cadmium 96h treatment replicate 1

source_name: Cadmium 96h treatment replicate 1


title: Cobalt 96h treatment replicate 1

source_name: Cobalt 96h treatment replicate 1


title: Cadmium 48h treatment replicate 2

source_name: Cadmium 48h treatment replicate 2


title: Cadmium 48h treatment replicate 1

source_name: Cadmium 48h treatment replicate 1


title: H2O2_20_30R

status: Public on Nov 15 2017

type: genomic

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

description: JSC24 and JSC25 have similar genotypes. Both of these two strains were constructed by crossing PSL2 (isogenic with W303-1A) and PSL5 (isogenic with YJM789). The MATα gene was replaced by NAT marker in JSC24, while was replaced by HYG marker in JSC25. JSC25 is heterozygous for all SNPs that distinguish W303-1A and YJM789 except for a small region (SGD coordinates 369892-373127) on chromosome XV that is homozygous for YJM789-derived SNPs. JSC24 has no homologous regions on its genome.

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

organism: Saccharomyces cerevisiae

source_name: cell culture of JSC25-derived strain HO-20-30R

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: JSC25 cells were grown in 7 mL YPD overnight to reach an OD600 of 0.2. Yeast cells (5×107) were collected by centrifugation and arrested in G1 in 1 mL YPD containing 2.5 μg α-factor at 300. After two hours, H2O2 was added into the cell culture. Cell culture was incubated at 300 for another hour. Yeast cells were then washed twice to remove α-factor and H2O2 before plating. Yeast  cells were cultured at 300  for 3 days and sectored colonies were selected for whole genome SNP microarray analysis.

source_name: cell culture of control strain JSC24


title: H2O2_20_29R

source_name: cell culture of JSC25-derived strain HO-20-29R


title: H2O2_20_25W

source_name: cell culture of JSC25-derived strain HO-20-25W


title: H2O2_20_28R

source_name: cell culture of JSC25-derived strain HO-20-28R


title: H2O2_20_27W

source_name: cell culture of JSC25-derived strain HO-20-27W


title: H2O2_20_32W

source_name: cell culture of JSC25-derived strain HO-20-32W


title: H2O2_20_22W

source_name: cell culture of JSC25-derived strain HO-20-22W


title: H2O2_20_21W

source_name: cell culture of JSC25-derived strain HO-20-21W


title: H2O2_20_27R

source_name: cell culture of JSC25-derived strain HO-20-27R


title: H2O2_20_26W

source_name: cell culture of JSC25-derived strain HO-20-26W


title: H2O2_20_26R

source_name: cell culture of JSC25-derived strain HO-20-26R


title: H2O2_20_21R

source_name: cell culture of JSC25-derived strain HO-20-21R


title: H2O2_20_31R

source_name: cell culture of JSC25-derived strain HO-20-31R


title: H2O2_20_32R

source_name: cell culture of JSC25-derived strain HO-20-32R


title: H2O2_20_29W

source_name: cell culture of JSC25-derived strain HO-20-29W


title: H2O2_20_18R

source_name: cell culture of JSC25-derived strain HO-20-18R


title: H2O2_20_28W

source_name: cell culture of JSC25-derived strain HO-20-28W


title: H2O2_20_22R

source_name: cell culture of JSC25-derived strain HO-20-22R

source_name: cell culture of control strain JSC24


title: H2O2_20_30W

source_name: cell culture of JSC25-derived strain HO-20-30W


title: H2O2_20_25R

source_name: cell culture of JSC25-derived strain HO-20-25R


title: H2O2_20_18W

source_name: cell culture of JSC25-derived strain HO-20-18W


title: H2O2_20_15W

source_name: cell culture of JSC25-derived strain HO-20-15W


title: H2O2_20_13W

source_name: cell culture of JSC25-derived strain HO-20-13W


title: H2O2_20_13R

source_name: cell culture of JSC25-derived strain HO-20-13R


title: H2O2_20_12W

source_name: cell culture of JSC25-derived strain HO-20-12W


title: H2O2_20_14R

source_name: cell culture of JSC25-derived strain HO-20-14R


title: H2O2_20_15R

source_name: cell culture of JSC25-derived strain HO-20-15R


title: H2O2_20_12R

source_name: cell culture of JSC25-derived strain HO-20-12R


title: H2O2_20_14W

source_name: cell culture of JSC25-derived strain HO-20-14W


title: Copper 96h treatment 3 replicate 4

status: Public on Aug 31 2017

source_name: Copper 96h treatment 3 replicate 4


title: Copper 96h treatment 3 replicate 3

source_name: Copper 96h treatment 3 replicate 3


title: Copper 48h treatment 3 replicate 3

source_name: Copper 48h treatment 3 replicate 3


title: Cobalt 96h treatment 3 replicate 4

source_name: Cobalt 96h treatment 3 replicate 4


title: Copper 48h treatment 3 replicate 2

source_name: Copper 48h treatment 3 replicate 2


title: Copper 96h treatment 3 replicate 2

source_name: Copper 96h treatment 3 replicate 2


title: Cobalt 48h treatment 3 replicate 1

source_name: Cobalt 48h treatment 3 replicate 1


title: Cadmium 48h treatment 3 replicate 2

source_name: Cadmium 48h treatment 3 replicate 2


title: Cobalt 96h treatment 3 replicate 2

source_name: Cobalt 96h treatment 3 replicate 2


title: Cadmium 96h treatment 3 replicate 1

source_name: Cadmium 96h treatment 3 replicate 1


title: Copper 96h treatment 3 replicate 1

source_name: Copper 96h treatment 3 replicate 1


title: Cadmium 96h treatment 3 replicate 3

source_name: Cadmium 96h treatment 3 replicate 3


title: Cobalt 96h treatment 3 replicate 3

source_name: Cobalt 96h treatment 3 replicate 3


title: Copper 48h treatment 3 replicate 1

source_name: Copper 48h treatment 3 replicate 1


title: Cadmium 96h treatment 3 replicate 2

source_name: Cadmium 96h treatment 3 replicate 2


title: Cobalt 48h treatment 3 replicate 3

source_name: Cobalt 48h treatment 3 replicate 3


title: Cadmium 48h treatment 3 replicate 1

source_name: Cadmium 48h treatment 3 replicate 1


title: Cobalt 48h treatment 3 replicate 2

source_name: Cobalt 48h treatment 3 replicate 2


title: Cobalt 96h treatment 3 replicate 1

source_name: Cobalt 96h treatment 3 replicate 1


title: Cadmium 96h treatment 3 replicate 4

source_name: Cadmium 96h treatment 3 replicate 4


title: SR21_H018

status: Public on Jun 30 2016

city: Taipei

first: Men-Chi

last: Chang

address: No. 1, Section 4, Roosevelt Road

department: Agronomy

country: Taiwan

institute: National Taiwan University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by GenePix 4200A 01 Autoloader (635nm power 100 PMT 520 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We filtered out spots that the flag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method. Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

organism: Oryza sativa

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Seeds were immersed in water for germination and then hydroponically cultivated in Kimura B solution at pH 5.0. These seedlings were grown in phytotron under 30oC day/25oC night and 70~80% relative humidity condition.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: Until growing to three-leaf stage, these plants were transferred into 4oC growth chamber for cold treatment. After 3-hr or 24-hr of cold treatment or recovery to normal growth condition for 24 hrs, rice roots and shoots were harvested and immediately freezed in liquid nitrogen for RNA extraction.

tag: cultivar

value: Root

value: 3-leaf seedlings

value: Cold treatment for 24hrs

tag: biological replicate

tag: technical replicate


title: SR22_H020

tag: treatment

value: Recovery for 24hrs after cold treatment for 24hrs


title: SR23_H022


title: SR24_H023


title: SR20_H016


title: SR22_H019


title: Cadmium 48h treatment 3 replicate 3

source_name: Cadmium 48h treatment 3 replicate 3


title: SR23_H021


title: SR20_H015


title: SR24_H024


title: SR21_H017


title: SR18_H012

value: Cold treatment for 3hrs


title: SR17_H010


title: SR19_H013


title: SR17_H009


title: SR15_H005

value: Control


title: SR18_H011


title: SR16_H008


title: SR14_H004


title: SS22_H020

value: Shoot


title: SR13_H002


title: SS23_H021


title: SR14_H003


title: SR15_H006


title: SR19_H014


title: SS24_H024


title: SS23_H022


title: SS24_H023


title: SR16_H007


title: SR13_H001


title: SS21_H018


title: SS22_H019


title: SS21_H017


title: SS20_H016


title: SS19_H013


title: SS18_H012


title: SS19_H014


title: SS17_H010


title: SS18_H011


title: SS15_H006


title: SS16_H007


title: SS20_H015


title: SS14_H004


title: SS15_H005


title: SS17_H009


title: SS16_H008


title: SR12_H024


title: SR11_H021


title: SR8_H015


title: SR11_H022


title: SS13_H001


title: SS14_H003


title: SR10_H020


title: SR12_H023


title: SR6_H012


title: SR5_H009


title: SR9_H017


title: SR8_H016


title: SR7_H013


title: SR9_H018


title: SS13_H002


title: SR5_H010


title: SR4_H008


title: SR7_H014


title: SR4_H007


title: SR10_H019


title: SR3_H006


title: SR6_H011


title: SR2_H003


title: SS11_H022


title: SR1_H002


title: SS12_H024


title: SS12_H023


title: SR1_H001


title: SS9_H017


title: SS10_H019


title: SS9_H018


title: SR2_H004


title: SS8_H015


title: SR3_H005


title: SS8_H016


title: SS11_H021


title: SS10_H020


title: SS7_H014


title: SS6_H011


title: SS6_H012


title: SS5_H010


title: SS3_H005


title: SS7_H013


title: SS5_H009


title: SS4_H008


title: SS2_H004


title: SS2_H003


title: SS3_H006


title: SS1_H002


title: SS4_H007


title: CR21_H018

status: Public on Oct 15 2014

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method. Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

organism: Oryza sativa Indica Group

source_name: Cold treatment for 24hrs(biological repeat 3-technical repeat 2)

tag: sample name


title: CR23_H021

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 2-technical repeat 1)


title: CR24_H024

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 3-technical repeat 2)


title: CR24_H023

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 3-technical repeat 1)


title: CR22_H020

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 1-technical repeat 2)


title: CR23_H022

source_name: Recovery for 24hrs after cold treatment for 24hrs(biological repeat 2-technical repeat 2)


title: SS1_H001


title: CR21_H017

source_name: Cold treatment for 24hrs(biological repeat 3-technical repeat 1)


title: CR19_H014

source_name: Cold treatment for 24hrs(biological repeat 1-technical repeat 2)