title: 257.06_D29_V

description: 257.06_D29_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 517 Pixel Size : 10 Laser on time : 167259 Laser Power : 3.12 Scan Date : 2011-12-02 Scan Temperature : 30.08 Scan Time : 16:59:31 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 640, 5350
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.


title: 257.11_D5_V

status: Public on Jun 01 2018

type: RNA

city: Stanford

first: Stephen

last: Popper

state: CA

department: Division of Infectious Diseases, Dept. of Medicine

country: USA

institute: Stanford University

description: 257.11_D5_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

hyb_protocol: reference URL : http://dx.doi.org/10.1371/journal.pntd.0001966 Hybridization method : 8 ug of Cy5-labeled amplified RNA and 5 ug of Cy3-labeled Universal Human Reference aRNA (Stratagene) were hybridized to Human Exonic Evidence Based Oligonucleotide (HEEBO) microarrays at 65C using the HYBEX hybridization system (SciGene) for 14 hours. Following hybridization, microarrays were washed in a series of four solutions containing 2_ SSC with 0.05% SDS, 2x SSC, 1x SSC, and 0.2x SSC, respectively. The first wash was performed for 5 min at 60C; subsequent washes were performed at room temperature for 2 min each.

scan_protocol: Scan Power : 100 PMT Volts : 487 Pixel Size : 10 Laser on time : 186892 Laser Power : 3.12 Scan Date : 2012-07-19 Scan Temperature : 33.29 Scan Time : 11:05:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 970, 5730
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

molecule: total RNA

organism: Homo sapiens

source_name: Strat UHR and v4 MJ doping control aa-aRNA

extract_protocol: Extraction method : Human Universal Reference RNA (Stratagene)

tag: sample name

label_protocol:
Type of label : Cy5
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-1

extract_protocol:
Extraction method : PreAnalytiX PAXgene Blood RNA Kit
Amplification method : Epicentre TargetAmp Aminoallyl aRNA Amp Kit

treatment_protocol:
Treatment : Vaccine
Day : 5

tag: tissue type

value: Whole Bood


title: 257.11_D6_V

description: 257.11_D6_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 483 Pixel Size : 10 Laser on time : 186907 Laser Power : 3.11 Scan Date : 2012-07-19 Scan Temperature : 33.47 Scan Time : 11:21:28 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

value: Human Universal Reference RNA (Stratagene)

treatment_protocol:
Treatment : Vaccine
Day : 6


title: tpa1 ett1 deletion, 60min 100% nitrogen gas (NH_101_5_2)

type: SRA

city: Glassboro

first: Mark

last: Hickman

state: NJ

address: 201 Mullica Hill Road

department: Biological Sciences

institute: Rowan University

library_source: transcriptomic

data_processing:
Each raw file is a de-multiplexed fastq file
FASTQ Quality Trimmer, 5' and 3' ends, window size=1,step size=1,min score=10
Reads aligned to yeast genome using TopHat2
Number of reads per feature was calculated using HTSeq,mode=union
When a sample was sequenced two times (e.g., NH_101_1_1.fastqsanger.gz and NH_101_1_2.fastqsanger.gz), then the FASTQ files were processed separately resulting in two HTSEQ files (e.g., NH_101_1_1.tabular and NH_101_1_2.tabular). The counts were then added to obtain the total counts for that sample.
Genome_build: saccharomyces_cerevisiae_R64-1-1_20110208.fasta
Supplementary_files_format_and_content: tab-delimited text files, first column= feature, second column=number of reads that overlap feature

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: strain yMH1079 (S288C background with repaired HAP1)

growth_protocol: A saturated culture was diluted and grown to mid-log phase (~1-2x10^7 cells/ml). Then the cells were diluted again and placed in 100% nitrogen gas for the indicated time, with the gas flowing through flasks.  Cells were collected in mid-log phase, filtered and frozen in liquid nitrogen.

extract_protocol:
The Qiagen RNeasy kit, using mechanical lysis with beads, to isolate total RNA. PolyA selection was done through oligo-dT capture
TruSeq RNA Sample Preparation Kit (Illumina).
Samples were multiplexed. Some of the libraries were sequenced in two different lanes (e.g., NH_91_8_1 and NH_91_8_2). These were processed separtely but then combined later at the HTSEQ step

tag: time in 100% n2

value: 60 minutes

tag: genotype

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1 tpa1d ett1d


title: tpa1 ett1 deletion, 30min 100% nitrogen gas (NH_101_4_2)

value: 30 minutes


title: tpa1 ett1 deletion, 60min 100% nitrogen gas (NH_101_5_1)


title: 257.06_D42_V

description: 257.06_D42_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 544 Pixel Size : 10 Laser on time : 167275 Laser Power : 3.12 Scan Date : 2011-12-02 Scan Temperature : 30.14 Scan Time : 17:15:33 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 42


title: 257.13_D8_P

description: 257.13_D8_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 510 Pixel Size : 10 Laser on time : 189976 Laser Power : 3.10 Scan Date : 2012-10-17 Scan Temperature : 32.95 Scan Time : 16:02:34 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 520, 3520
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

treatment_protocol:
Treatment : Placebo
Day : 8


title: 257.06_D180_V

description: 257.06_D180_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 533 Pixel Size : 10 Laser on time : 167223 Laser Power : 3.12 Scan Date : 2011-12-02 Scan Temperature : 29.99 Scan Time : 16:23:19 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 180


title: 257.13_D12_P

description: 257.13_D12_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 576 Pixel Size : 10 Laser on time : 190016 Laser Power : 3.11 Scan Date : 2012-10-17 Scan Temperature : 33.25 Scan Time : 16:42:24 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 12


title: 257.06_D14_V

description: 257.06_D14_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 509 Pixel Size : 10 Laser on time : 167105 Laser Power : 3.11 Scan Date : 2011-12-02 Scan Temperature : 29.90 Scan Time : 14:25:48 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 640, 6610
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

treatment_protocol:
Treatment : Vaccine
Day : 14


title: 257.11_D0_Vamp2

description: 257.11_D0_Vamp2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 483 Pixel Size : 10 Laser on time : 186840 Laser Power : 3.09 Scan Date : 2012-07-19 Scan Temperature : 32.34 Scan Time : 10:10:18 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 700, 5540
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

treatment_protocol: Treatment : Vaccine


title: 257.06_D20_V

description: 257.06_D20_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 531 Pixel Size : 10 Laser on time : 167242 Laser Power : 3.12 Scan Date : 2011-12-02 Scan Temperature : 30.05 Scan Time : 16:41:26 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 20


title: 257.13_D9_P

description: 257.13_D9_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 613 Pixel Size : 10 Laser on time : 191550 Laser Power : 3.10 Scan Date : 2012-10-20 Scan Temperature : 32.40 Scan Time : 17:21:09 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 9


title: 257.13_D14_P

description: 257.13_D14_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 557 Pixel Size : 10 Laser on time : 190105 Laser Power : 3.10 Scan Date : 2012-10-17 Scan Temperature : 33.07 Scan Time : 18:11:31 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 14


title: 257.13_D6_P

description: 257.13_D6_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 517 Pixel Size : 10 Laser on time : 189959 Laser Power : 3.10 Scan Date : 2012-10-17 Scan Temperature : 32.83 Scan Time : 15:45:55 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 6


title: tpa1 ett1 deletion, 30min 100% nitrogen gas (NH_101_4_1)


title: 257.13_D5_P

description: 257.13_D5_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 509 Pixel Size : 10 Laser on time : 189942 Laser Power : 3.10 Scan Date : 2012-10-17 Scan Temperature : 32.77 Scan Time : 15:28:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 5


title: tpa1 ett1 deletion, 10min 100% nitrogen gas (NH_101_3_2)

value: 10 minutes


title: 257.13_D0_P

description: 257.13_D0_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 553 Pixel Size : 10 Laser on time : 189836 Laser Power : 3.06 Scan Date : 2012-10-17 Scan Temperature : 31.94 Scan Time : 13:41:48 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol: Treatment : Placebo


title: tpa1 ett1 deletion, 10min 100% nitrogen gas (NH_101_3_1)


title: 257.13_D2_P

description: 257.13_D2_P paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 503 Pixel Size : 10 Laser on time : 189919 Laser Power : 3.10 Scan Date : 2012-10-17 Scan Temperature : 32.74 Scan Time : 15:05:12 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Placebo
Day : 2


title: tpa1 ett1 deletion, 0min 100% nitrogen gas (NH_101_1_2)

value: 0 minutes


title: tpa1 ett1 deletion, 0min 100% nitrogen gas (NH_101_1_1)


title: tpa1 ett1 deletion, 5min 100% nitrogen gas (NH_101_2_1)

value: 5 minutes


title: 257.06_D12_V

description: 257.06_D12_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 520 Pixel Size : 10 Laser on time : 167137 Laser Power : 3.12 Scan Date : 2011-12-02 Scan Temperature : 29.84 Scan Time : 14:57:05 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 12


title: tpa1 ett1 deletion, 5min 100% nitrogen gas (NH_101_2_2)


title: 257.13_D0_Pamp2

description: 257.13_D0_Pamp2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 504 Pixel Size : 10 Laser on time : 189852 Laser Power : 3.08 Scan Date : 2012-10-17 Scan Temperature : 32.22 Scan Time : 13:57:53 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.06_D6_V

description: 257.06_D6_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 512 Pixel Size : 10 Laser on time : 167044 Laser Power : 3.12 Scan Date : 2011-12-02 Scan Temperature : 29.74 Scan Time : 13:24:03 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.05_D180_V

description: 257.05_D180_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 552 Pixel Size : 10 Laser on time : 186628 Laser Power : 3.09 Scan Date : 2012-07-18 Scan Temperature : 30.87 Scan Time : 12:31:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Rap1aa_R_Rsc8_ChEC

city: Geneva

first: Slawomir

last: Kubik

address: quai Ernest-Ansermet 30

department: Molecular Biology Department

country: Switzerland

institute: University of Geneva

description: Chromatin Endogenous Cleavage (ChEC)

library_source: genomic

data_processing:
Library strategy: ChEC-seq
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For nucleosome occupancy tracks each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
For ChEC-seq experiments the mapped reads were extended by 1 bp only to indicate cut sites
For ChIP-seq the reads were shifted by 150 bp and extended by 50 bp
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

molecule: genomic DNA

source_name: whole organism

growth_protocol: cells were grown at 30 degrees in YPD to OD600=0.7

extract_protocol:
DNA was prepared as described in Zentner et al., 2015 (PMID: 26490019)
libraries were prepared as described in Zentner et al., 2015 (PMID: 26490019)

treatment_protocol: 60 minutes rapamycin

tag: strain

tag: genotype/variation

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 RAP1-FRB-RAP1-LEU2 PREB1-3xFLAG-MNase-URA3


title: Rap1aa_V_Rsc8_ChEC

description: Chromatin Endogenous Cleavage (ChEC)

treatment_protocol: No rapamycin


title: Reb1aa_R_Rsc8_ChEC

description: Chromatin Endogenous Cleavage (ChEC)

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 REB1-FRB-KanMX PREB1-3xFLAG-MNase-URA3


title: 257.09_D14_V

description: 257.09_D14_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 538 Pixel Size : 10 Laser on time : 190474 Laser Power : 3.07 Scan Date : 2012-10-18 Scan Temperature : 34.11 Scan Time : 10:26:50 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.09_D180_V

description: 257.09_D180_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 550 Pixel Size : 10 Laser on time : 190534 Laser Power : 3.07 Scan Date : 2012-10-18 Scan Temperature : 34.60 Scan Time : 11:27:43 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.06_D8_V

description: 257.06_D8_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 522 Pixel Size : 10 Laser on time : 167063 Laser Power : 3.11 Scan Date : 2011-12-02 Scan Temperature : 29.84 Scan Time : 13:42:45 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 8


title: 257.05_D29_V

description: 257.05_D29_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 534 Pixel Size : 10 Laser on time : 185913 Laser Power : 3.10 Scan Date : 2012-07-17 Scan Temperature : 32.22 Scan Time : 11:47:18 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 29


title: 257.09_D29_V

description: 257.09_D29_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 541 Pixel Size : 10 Laser on time : 190489 Laser Power : 3.08 Scan Date : 2012-10-18 Scan Temperature : 34.26 Scan Time : 10:42:16 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.09_D42_V

description: 257.09_D42_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 563 Pixel Size : 10 Laser on time : 190512 Laser Power : 3.08 Scan Date : 2012-10-18 Scan Temperature : 34.48 Scan Time : 11:04:45 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 42


title: 257.05_D20_V

description: 257.05_D20_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 523 Pixel Size : 10 Laser on time : 185887 Laser Power : 3.07 Scan Date : 2012-07-17 Scan Temperature : 32.00 Scan Time : 11:20:39 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.06_D9_V

description: 257.06_D9_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 516 Pixel Size : 10 Laser on time : 167086 Laser Power : 3.11 Scan Date : 2011-12-02 Scan Temperature : 29.90 Scan Time : 14:06:32 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 9


title: 257.09_D9_V

description: 257.09_D9_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 624 Pixel Size : 10 Laser on time : 191847 Laser Power : 3.07 Scan Date : 2012-10-22 Scan Temperature : 31.55 Scan Time : 13:09:36 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.06_D5_V

description: 257.06_D5_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 494 Pixel Size : 10 Laser on time : 167027 Laser Power : 3.12 Scan Date : 2011-12-02 Scan Temperature : 29.65 Scan Time : 13:07:11 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 5


title: 257.05_D42_V

description: 257.05_D42_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 504 Pixel Size : 10 Laser on time : 185965 Laser Power : 3.11 Scan Date : 2012-07-17 Scan Temperature : 32.58 Scan Time : 12:38:24 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.05_D9_V

description: 257.05_D9_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 502 Pixel Size : 10 Laser on time : 185597 Laser Power : 3.10 Scan Date : 2012-07-16 Scan Temperature : 33.74 Scan Time : 16:54:05 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Reb1aa_V_Rsc8_ChEC

description: Chromatin Endogenous Cleavage (ChEC)


title: 257.05_D14_V

description: 257.05_D14_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 502 Pixel Size : 10 Laser on time : 185843 Laser Power : 3.09 Scan Date : 2012-07-17 Scan Temperature : 31.33 Scan Time : 10:37:06 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 14


title: 257.05_D12_V

description: 257.05_D12_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 506 Pixel Size : 10 Laser on time : 185822 Laser Power : 3.09 Scan Date : 2012-07-17 Scan Temperature : 30.90 Scan Time : 10:15:44 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.09_D12_V

description: 257.09_D12_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 614 Pixel Size : 10 Laser on time : 191865 Laser Power : 3.07 Scan Date : 2012-10-22 Scan Temperature : 31.82 Scan Time : 13:26:42 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Abf1aa_R_Rsc8_ChEC

description: Chromatin Endogenous Cleavage (ChEC)

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ABF1-FRB-KanMX PREB1-3xFLAG-MNase-URA3


title: Abf1aa_V_Rsc8_ChEC

description: Chromatin Endogenous Cleavage (ChEC)


title: Rap1aa_R_freeMNase_ChEC

description:
Chromatin Endogenous Cleavage (ChEC)
un-fused MNase, used as control for non-specific DNA cutting

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 RAP1-FRB-RAP1-LEU2 RSC8-3xFLAG-MNase-HphMX


title: 257.09_D6_V

description: 257.09_D6_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 541 Pixel Size : 10 Laser on time : 190426 Laser Power : 3.09 Scan Date : 2012-10-18 Scan Temperature : 33.56 Scan Time : 09:39:17 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 6


title: 257.09_D5_V

description: 257.09_D5_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 536 Pixel Size : 10 Laser on time : 190412 Laser Power : 3.11 Scan Date : 2012-10-18 Scan Temperature : 33.38 Scan Time : 09:25:55 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Rap1aa_V_freeMNase_ChEC


title: Reb1aa_R_freeMNase_ChEC

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 REB1-FRB-KanMX RSC8-3xFLAG-MNase-HphMX


title: 257.06_D2_V

description: 257.06_D2_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 562 Pixel Size : 10 Laser on time : 167008 Laser Power : 3.12 Scan Date : 2011-12-02 Scan Temperature : 29.53 Scan Time : 12:48:40 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 2


title: Reb1aa_V_freeMNase_ChEC


title: Abf1aa_R_freeMNase_ChEC

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ABF1-FRB-KanMX RSC8-3xFLAG-MNase-HphMX


title: 257.09_D2_V

description: 257.09_D2_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 526 Pixel Size : 10 Laser on time : 190397 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 33.10 Scan Time : 09:09:35 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.09_D0_Vamp2

description: 257.09_D0_Vamp2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 537 Pixel Size : 10 Laser on time : 190381 Laser Power : 3.09 Scan Date : 2012-10-18 Scan Temperature : 32.83 Scan Time : 08:54:10 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol: Treatment : Vaccine


title: 257.09_D0_V

description: 257.09_D0_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 522 Pixel Size : 10 Laser on time : 190365 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 32.49 Scan Time : 08:37:57 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.05_D2_V

description: 257.05_D2_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 498 Pixel Size : 10 Laser on time : 185529 Laser Power : 3.12 Scan Date : 2012-07-16 Scan Temperature : 33.29 Scan Time : 15:46:01 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.05_D8_V

description: 257.05_D8_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 539 Pixel Size : 10 Laser on time : 185578 Laser Power : 3.09 Scan Date : 2012-07-16 Scan Temperature : 33.62 Scan Time : 16:34:37 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.05_D6_V

description: 257.05_D6_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 499 Pixel Size : 10 Laser on time : 185560 Laser Power : 3.09 Scan Date : 2012-07-16 Scan Temperature : 33.56 Scan Time : 16:17:19 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Abf1aa_V_freeMNase_ChEC


title: 257.08_D9_V

description: 257.08_D9_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 569 Pixel Size : 10 Laser on time : 191815 Laser Power : 3.10 Scan Date : 2012-10-22 Scan Temperature : 31.06 Scan Time : 12:36:27 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D29_V

description: 257.08_D29_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 548 Pixel Size : 10 Laser on time : 191166 Laser Power : 3.08 Scan Date : 2012-10-19 Scan Temperature : 31.45 Scan Time : 08:32:06 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D180_V

description: 257.08_D180_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 519 Pixel Size : 10 Laser on time : 191206 Laser Power : 3.07 Scan Date : 2012-10-19 Scan Temperature : 32.06 Scan Time : 09:12:09 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Treatment : Vaccine
Day : 180


title: 257.05_D0_V

description: 257.05_D0_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 500 Pixel Size : 10 Laser on time : 187081 Laser Power : 3.08 Scan Date : 2012-07-19 Scan Temperature : 34.29 Scan Time : 14:15:34 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D42_V

description: 257.04_D42_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 505 Pixel Size : 10 Laser on time : 185401 Laser Power : 3.11 Scan Date : 2012-07-16 Scan Temperature : 33.10 Scan Time : 13:36:59 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.05_D0_Vamp2hyb2

description: 257.05_D0_Vamp2hyb2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 502 Pixel Size : 10 Laser on time : 187095 Laser Power : 3.09 Scan Date : 2012-07-19 Scan Temperature : 34.26 Scan Time : 14:29:08 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.05_D5_V

description: 257.05_D5_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 185545 Laser Power : 3.12 Scan Date : 2012-07-16 Scan Temperature : 33.41 Scan Time : 16:01:39 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D180_V

description: 257.04_D180_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 614 Pixel Size : 10 Laser on time : 185489 Laser Power : 3.11 Scan Date : 2012-07-16 Scan Temperature : 33.04 Scan Time : 15:05:49 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D14_V

description: 257.08_D14_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 521 Pixel Size : 10 Laser on time : 190953 Laser Power : 3.11 Scan Date : 2012-10-18 Scan Temperature : 34.87 Scan Time : 18:27:04 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D42_V

description: 257.08_D42_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 528 Pixel Size : 10 Laser on time : 191190 Laser Power : 3.06 Scan Date : 2012-10-19 Scan Temperature : 31.88 Scan Time : 08:56:21 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D20_V

description: 257.04_D20_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 530 Pixel Size : 10 Laser on time : 185220 Laser Power : 3.11 Scan Date : 2012-07-16 Scan Temperature : 33.13 Scan Time : 10:35:57 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 840, 6130
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

treatment_protocol:
Treatment : Vaccine
Day : 20


title: 257.04_D29_V

description: 257.04_D29_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 502 Pixel Size : 10 Laser on time : 185259 Laser Power : 3.12 Scan Date : 2012-07-16 Scan Temperature : 33.50 Scan Time : 11:14:52 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D8_V

description: 257.08_D8_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 522 Pixel Size : 10 Laser on time : 190905 Laser Power : 3.11 Scan Date : 2012-10-18 Scan Temperature : 34.96 Scan Time : 17:38:32 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D14_V

description: 257.04_D14_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 512 Pixel Size : 10 Laser on time : 185204 Laser Power : 3.11 Scan Date : 2012-07-16 Scan Temperature : 33.01 Scan Time : 10:20:02 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D5_V

description: 257.08_D5_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 519 Pixel Size : 10 Laser on time : 190875 Laser Power : 3.11 Scan Date : 2012-10-18 Scan Temperature : 34.96 Scan Time : 17:08:57 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D6_V

description: 257.08_D6_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 578 Pixel Size : 10 Laser on time : 191761 Laser Power : 3.07 Scan Date : 2012-10-22 Scan Temperature : 30.29 Scan Time : 11:43:22 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D2_V

description: 257.08_D2_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 510 Pixel Size : 10 Laser on time : 190859 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.02 Scan Time : 16:53:03 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D12_V

description: 257.08_D12_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 520 Pixel Size : 10 Laser on time : 190939 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 34.90 Scan Time : 18:13:02 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D12_V

description: 257.04_D12_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 510 Pixel Size : 10 Laser on time : 185182 Laser Power : 3.10 Scan Date : 2012-07-16 Scan Temperature : 32.77 Scan Time : 09:58:10 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D9_V

description: 257.04_D9_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 517 Pixel Size : 10 Laser on time : 185166 Laser Power : 3.11 Scan Date : 2012-07-16 Scan Temperature : 32.58 Scan Time : 09:41:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D20_V

description: 257.08_D20_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 582 Pixel Size : 10 Laser on time : 191832 Laser Power : 3.08 Scan Date : 2012-10-22 Scan Temperature : 31.30 Scan Time : 12:53:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D6_V

description: 257.04_D6_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 521 Pixel Size : 10 Laser on time : 185134 Laser Power : 3.09 Scan Date : 2012-07-16 Scan Temperature : 32.13 Scan Time : 09:09:22 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D2_V

description: 257.04_D2_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 508 Pixel Size : 10 Laser on time : 185089 Laser Power : 3.08 Scan Date : 2012-07-16 Scan Temperature : 31.42 Scan Time : 08:24:35 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.07_D29_V

description: 257.07_D29_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 562 Pixel Size : 10 Laser on time : 190776 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.06 Scan Time : 15:29:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.03_D20_V

description: 257.03_D20_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 545 Pixel Size : 10 Laser on time : 165292 Laser Power : 3.10 Scan Date : 2011-11-15 Scan Temperature : 27.30 Scan Time : 13:14:08 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 520, 6040
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.


title: 257.03_D29_V

description: 257.03_D29_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 531 Pixel Size : 10 Laser on time : 163982 Laser Power : 3.13 Scan Date : 2011-11-03 Scan Temperature : 29.26 Scan Time : 12:16:51 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.07_D8_V

description: 257.07_D8_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 559 Pixel Size : 10 Laser on time : 190679 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.06 Scan Time : 13:53:04 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D8_V

description: 257.04_D8_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 507 Pixel Size : 10 Laser on time : 185151 Laser Power : 3.11 Scan Date : 2012-07-16 Scan Temperature : 32.37 Scan Time : 09:26:43 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.07_D20_V

description: 257.07_D20_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 577 Pixel Size : 10 Laser on time : 190756 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.15 Scan Time : 15:09:42 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.07_D42_V

description: 257.07_D42_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 577 Pixel Size : 10 Laser on time : 190792 Laser Power : 3.11 Scan Date : 2012-10-18 Scan Temperature : 35.02 Scan Time : 15:45:20 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D0_Vamp2

description: 257.08_D0_Vamp2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 524 Pixel Size : 10 Laser on time : 190838 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.06 Scan Time : 16:31:24 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D0_Vamp2

description: 257.04_D0_Vamp2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 500 Pixel Size : 10 Laser on time : 185074 Laser Power : 3.10 Scan Date : 2012-07-16 Scan Temperature : 31.15 Scan Time : 08:09:37 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.07_D14_V

description: 257.07_D14_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 536 Pixel Size : 10 Laser on time : 190727 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.21 Scan Time : 14:40:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.03_D42_V

description: 257.03_D42_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 528 Pixel Size : 10 Laser on time : 164001 Laser Power : 3.13 Scan Date : 2011-11-03 Scan Temperature : 29.26 Scan Time : 12:35:55 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.07_D180_V

description: 257.07_D180_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 596 Pixel Size : 10 Laser on time : 190808 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.02 Scan Time : 16:01:07 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D0_V

description: 257.04_D0_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 501 Pixel Size : 10 Laser on time : 185056 Laser Power : 3.08 Scan Date : 2012-07-16 Scan Temperature : 30.87 Scan Time : 07:51:07 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.07_D5_V

description: 257.07_D5_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 564 Pixel Size : 10 Laser on time : 190641 Laser Power : 3.11 Scan Date : 2012-10-18 Scan Temperature : 34.96 Scan Time : 13:14:37 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.08_D0_V

description: 257.08_D0_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 527 Pixel Size : 10 Laser on time : 190823 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.06 Scan Time : 16:17:19 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.03_D180_V

description: 257.03_D180_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 500 Pixel Size : 10 Laser on time : 164022 Laser Power : 3.13 Scan Date : 2011-11-03 Scan Temperature : 29.35 Scan Time : 12:56:26 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.07_D9_V

description: 257.07_D9_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 564 Pixel Size : 10 Laser on time : 190696 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.12 Scan Time : 14:09:01 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.07_D12_V

description: 257.07_D12_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 566 Pixel Size : 10 Laser on time : 190712 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.18 Scan Time : 14:25:35 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.04_D5_V

description: 257.04_D5_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 512 Pixel Size : 10 Laser on time : 185110 Laser Power : 3.07 Scan Date : 2012-07-16 Scan Temperature : 31.76 Scan Time : 08:46:40 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.07_D0_V

description: 257.07_D0_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 550 Pixel Size : 10 Laser on time : 190587 Laser Power : 3.07 Scan Date : 2012-10-18 Scan Temperature : 34.72 Scan Time : 12:19:56 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: D4_WT_2

city: San Francisco

first: Walter

last: Eckalbar

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

data_processing:
Sequence alignment and splice junction estimation was performed using STAR (doi:10.1093/bioinformatics/bts635).
Mappings were restricted to those that were uniquely assigned to the mouse genome, as provided by Ensembl (GRCm38.78) and aggregated on a per-gene basis.
Genome_build: GRCm38.78
Supplementary_files_format_and_content: counts file

organism: Mus musculus

source_name: D4_WT, sorted CD62L-high Tregs activated in vitro

growth_protocol: CD62L-high Tregs were sorted, activated in vitro with anti-CD3/anti-CD28 microbeads and cultured in standard T cell media with 2000 U/ml IL-2.

extract_protocol:
Treg cells were harvested from cultures by centrifugation and total RNA was harvested using Trizol reagent.
RNA sequencing libraries were generated using the Illumina TruSeq stranded mRNA kit, according to the manufacturer’s protocol (Illumina).
Library fragment size distributions were assessed using the Bioanalyzer 2100 and the DNA high-sensitivity chip.  Sequencing libraries were tested for sequencing efficiency on a MiSeq, and subsequently pooled for sequencing on a HiSeq 4000 (Illumina).

treatment_protocol: No treatments

tag: cell type

value: Treg T cells


title: 257.03_D14_V

description: 257.03_D14_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 517 Pixel Size : 10 Laser on time : 163940 Laser Power : 3.15 Scan Date : 2011-11-03 Scan Temperature : 29.07 Scan Time : 11:33:56 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: D4_WT_5


title: 257.07_D6_V

description: 257.07_D6_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 569 Pixel Size : 10 Laser on time : 190664 Laser Power : 3.10 Scan Date : 2012-10-18 Scan Temperature : 35.06 Scan Time : 13:36:43 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.03_D12_V

description: 257.03_D12_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 535 Pixel Size : 10 Laser on time : 163918 Laser Power : 3.14 Scan Date : 2011-11-03 Scan Temperature : 28.95 Scan Time : 11:12:59 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.03_D9_V

description: 257.03_D9_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 544 Pixel Size : 10 Laser on time : 163877 Laser Power : 3.09 Scan Date : 2011-11-03 Scan Temperature : 28.46 Scan Time : 10:31:22 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: D4_WT_3


title: D4_Ez_3

source_name: D4_Ez, sorted CD62L-high Tregs activated in vitro


title: D4_WT_4


title: D4_Ez_4


title: D4_WT_1


title: 257.03_D2_V

description: 257.03_D2_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 538 Pixel Size : 10 Laser on time : 165278 Laser Power : 3.09 Scan Date : 2011-11-15 Scan Temperature : 27.00 Scan Time : 13:00:17 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.03_D6_V

description: 257.03_D6_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 515 Pixel Size : 10 Laser on time : 163839 Laser Power : 3.10 Scan Date : 2011-11-03 Scan Temperature : 27.82 Scan Time : 09:53:03 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: D4_Ez_2


title: 257.07_D0_Vamp2hyb2

description: 257.07_D0_Vamp2hyb2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 595 Pixel Size : 10 Laser on time : 191463 Laser Power : 3.08 Scan Date : 2012-10-20 Scan Temperature : 31.21 Scan Time : 15:53:04 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: D4_Ez_1


title: 257.07_D2_V

description: 257.07_D2_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 597 Pixel Size : 10 Laser on time : 190623 Laser Power : 3.11 Scan Date : 2012-10-18 Scan Temperature : 34.87 Scan Time : 12:57:14 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.03_D5_V

description: 257.03_D5_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 561 Pixel Size : 10 Laser on time : 163821 Laser Power : 3.11 Scan Date : 2011-11-03 Scan Temperature : 27.52 Scan Time : 09:35:01 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.03_D0_V

description: 257.03_D0_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 556 Pixel Size : 10 Laser on time : 163782 Laser Power : 3.05 Scan Date : 2011-11-03 Scan Temperature : 26.72 Scan Time : 08:55:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.02_D42_V

description: 257.02_D42_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 528 Pixel Size : 10 Laser on time : 166604 Laser Power : 3.11 Scan Date : 2011-11-30 Scan Temperature : 27.58 Scan Time : 09:08:57 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 640, 5400
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.


title: 257.02_D20_V

description: 257.02_D20_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 529 Pixel Size : 10 Laser on time : 166901 Laser Power : 3.10 Scan Date : 2011-12-02 Scan Temperature : 28.25 Scan Time : 11:01:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.02_D12_V

description: 257.02_D12_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 535 Pixel Size : 10 Laser on time : 166537 Laser Power : 3.10 Scan Date : 2011-11-30 Scan Temperature : 26.20 Scan Time : 08:00:37 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.03_D0_Vamp2

description: 257.03_D0_Vamp2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 163765 Laser Power : 3.09 Scan Date : 2011-11-03 Scan Temperature : 26.33 Scan Time : 08:38:58 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.02_D8_V

description: 257.02_D8_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 538 Pixel Size : 10 Laser on time : 166320 Laser Power : 3.11 Scan Date : 2011-11-29 Scan Temperature : 29.74 Scan Time : 18:07:56 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.02_D29_V

description: 257.02_D29_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 544 Pixel Size : 10 Laser on time : 166588 Laser Power : 3.10 Scan Date : 2011-11-30 Scan Temperature : 27.30 Scan Time : 08:52:28 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.02_D9_V

description: 257.02_D9_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 547 Pixel Size : 10 Laser on time : 166336 Laser Power : 3.11 Scan Date : 2011-11-29 Scan Temperature : 29.78 Scan Time : 18:23:45 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.02_D2_V

description: 257.02_D2_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 546 Pixel Size : 10 Laser on time : 166270 Laser Power : 3.12 Scan Date : 2011-11-29 Scan Temperature : 29.53 Scan Time : 17:18:03 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.01_D29_V

description: 257.01_D29_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 540 Pixel Size : 10 Laser on time : 166189 Laser Power : 3.12 Scan Date : 2011-11-29 Scan Temperature : 28.95 Scan Time : 15:56:31 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.02_D5_V

description: 257.02_D5_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 529 Pixel Size : 10 Laser on time : 166288 Laser Power : 3.12 Scan Date : 2011-11-29 Scan Temperature : 29.62 Scan Time : 17:35:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.01_D42_V

description: 257.01_D42_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 554 Pixel Size : 10 Laser on time : 166206 Laser Power : 3.13 Scan Date : 2011-11-29 Scan Temperature : 29.10 Scan Time : 16:13:34 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.02_D14_V

description: 257.02_D14_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 540 Pixel Size : 10 Laser on time : 166554 Laser Power : 3.04 Scan Date : 2011-11-30 Scan Temperature : 26.54 Scan Time : 08:16:34 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: KO2_TGF_rep1

city: Osaka

first: Tsuyoshi

last: Morita

address: Yamadaoka 2-2, Suita

department: Graduate School of Medicine

country: Japan

institute: Osaka University

description: Gene expression after TGF-ß1 treatment in KO2 cells

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Tmsb4x KO clone 2, TGF-ß1, 2 days, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cells were cultured with a Dulbecco Modified Eagle medium and 10% foetal bovine serum.

extract_protocol: Total RNAs were extracted using  RNAiso plus, and purified using NucleoSpin RNA Plus.

treatment_protocol: Cells were treated with 10 ng/ml of TGF-ß1 and 10 µM CCG1423 for 2 days.

value: Tmsb4x KO

tag: treatment

value: 10 ng/ml of TGF-ß1 for 2 days


title: 257.01_D20_V

description: 257.01_D20_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 565 Pixel Size : 10 Laser on time : 166171 Laser Power : 3.10 Scan Date : 2011-11-29 Scan Temperature : 28.80 Scan Time : 15:38:33 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

value: Whole Bood


title: 257.02_D0_V

description: 257.02_D0_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 546 Pixel Size : 10 Laser on time : 166252 Laser Power : 3.12 Scan Date : 2011-11-29 Scan Temperature : 29.47 Scan Time : 17:00:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

value: Human Universal Reference RNA (Stratagene)


title: B16F1_TGF/CCG_rep1

description: Gene expression after TGF-ß1/CCG1423 treatment in B16F1 cells

source_name: B16F1, TGF-ß1&CCG14123, 2 days, replicate 1

value: 10 µM MRTF inhibitor CCG1423


title: 257.01_D9_V

description: 257.01_D9_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 543 Pixel Size : 10 Laser on time : 166079 Laser Power : 3.08 Scan Date : 2011-11-29 Scan Temperature : 28.46 Scan Time : 14:06:17 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.01_D12_V

description: 257.01_D12_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 546 Pixel Size : 10 Laser on time : 166142 Laser Power : 3.09 Scan Date : 2011-11-29 Scan Temperature : 28.59 Scan Time : 15:08:42 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.01_D8_V

description: 257.01_D8_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 543 Pixel Size : 10 Laser on time : 166066 Laser Power : 3.08 Scan Date : 2011-11-29 Scan Temperature : 28.28 Scan Time : 13:53:19 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: B16F1_TGF_rep1

description: Gene expression after TGF-ß1 treatment in B16F1 cells

source_name: B16F1, TGF-ß1, 2 days, replicate 1


title: 257.01_D180_V

description: 257.01_D180_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 537 Pixel Size : 10 Laser on time : 166240 Laser Power : 3.13 Scan Date : 2011-11-29 Scan Temperature : 29.35 Scan Time : 16:47:35 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.02_D6_V

description: 257.02_D6_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 531 Pixel Size : 10 Laser on time : 166304 Laser Power : 3.11 Scan Date : 2011-11-29 Scan Temperature : 29.68 Scan Time : 17:51:20 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.01_D5_V

description: 257.01_D5_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 552 Pixel Size : 10 Laser on time : 166048 Laser Power : 3.12 Scan Date : 2011-11-29 Scan Temperature : 28.07 Scan Time : 13:35:01 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.01_D14_V

description: 257.01_D14_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 545 Pixel Size : 10 Laser on time : 166158 Laser Power : 3.10 Scan Date : 2011-11-29 Scan Temperature : 28.68 Scan Time : 15:25:44 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: 257.01_D2_V

description: 257.01_D2_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 541 Pixel Size : 10 Laser on time : 166032 Laser Power : 3.11 Scan Date : 2011-11-29 Scan Temperature : 27.73 Scan Time : 13:19:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: Forsythia_viridissima_var_koreana_Flower

city: Chiba

first: Mami

last: Yamazaki

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

department: Graduate School of Pharmaceutical Sciences

institute: Chiba University

data_processing:
For de novo transcriptome assembly, we pre-processed raw reads, and removed adapter sequences, empty reads, reads with ambiguous ‘N’ bases > 5%, raw reads of low quality (Q<20), and raw reads with an average length less than 30 bases. Filtering of raw reads was performed using Trimmomatic program (Bolger et al., 2014), resulting into paired end raw reads, and unpaired reads which lost its corresponding sequence partner due to quality control.
The Trinity program ver 2.0.6 was used for the de novo transcriptome assembly using clean reads from all the samples. De novo assembly was further processed through CD-HIT-EST program (Li and Godzik 2006) to remove transcripts redundancies, resulting in our final assembly of 69,458 unigenes with N50 value as 1,198 bps.
We then processed these contigs for read alignment and abundance estimation using Bowtie2.0 and RSEM respectively. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method.
Supplementary_files_format_and_content: .fasta file was generated using CD-HIT-EST program. De novo transcriptome assembly of F. viridissima var. Koreana was constructed using the Trinity program ver 2.0.6, and processed through CD-HIT-EST program to remove transcripts redundancies. These unigene sequences generated were used for further analysis.
Supplementary_files_format_and_content: .results files were generated using RSEM program. Clean reads for each tissues were aligned on F. viridissima var. Koreana de novo transcriptome assembly (.fasta file), and abundace were measured using RSEM. Content of each file contains transcript_id (which is contig), gene_id (which is unigene), length, effective_length, expected_count, TPM, FPKM and IsoPct for each tissues. FPKM values were calculated using RSEM program. FPKM values for each tissues were used for further analysis.
Supplementary_files_format_and_content: Tab-delimited text file includes transcript_id, gene_id, seq_length, and FPKM values for each tissues. .results files for both tissues were used to extract FPKM values for each tissues, and were combined/aligned against transcript_id and gene_id.

organism: Forsythia koreana

source_name: Plant Material in NIBIOHN

growth_protocol: Flower and leaf tissues were collected from F. viridissima var. Koreana growing in the natural conditions at the Tsukuba Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN, Tsukuba, Japan) in April, 2014.

extract_protocol:
Frozen samples of F. viridissima var. Koreana were powdered for RNA extraction. Total RNA for each of the two tissues was extracted using RNeasy Plant Mini Kit (Qiagen, USA), according to the manufacturer’s instruction.
cDNA library was then prepared using SureSelect Strand Specific RNA Library kit (Agilent 150 Technologies, USA) according to the manufacturer’s specifications. mRNA was isolated from total RNA of each tissue using beads containing oligo(dt), which was then added with fragmentation buffer to shear mRNA into short fragments and used as a template for the synthesis of first strand cDNA synthesis using random hexamer primers. The cDNA library for Illumina sequencing was prepared using SureSelect Strand Specific RNA Library kit (Agilent, USA) according to the manufacturer’s instruction.

treatment_protocol: Not applicable

tag: tissue

value: Flower

tag: age


title: KO1_TGF_rep1

description: Gene expression after TGF-ß1 treatment in KO1 cells

source_name: Tmsb4x KO clone 1, TGF-ß1, 2 days, replicate 1


title: Forsythia_viridissima_var_koreana_Leaf

value: Leaf


title: HD-6

city: Guangzhou

first: Liang

last: Zhang

state: Guangdong

address: Xingnan Road 521

department: Translational Medicine Research Center

country: China

institute: Guangdong Women and Children Hospital

hyb_protocol: Labeled cDNAs were combined and hybridized to the microarray (Custom Human GE 8×60K, Agilent-071342).

scan_protocol: slides washing, scanning were performed and image data were extracted using Agilent Feature Extraction software

data_processing: Signals were normalized by using loess normalization.

source_name: pooled normal full-thickness bowel

label_protocol: The dual-color approach was employed in this experiment. Individual diseased samples and their paired adjacent normal tissues were all labeled with Cy3 and hybridized with a common reference consisted of 8 normal controls labeled with Cy5.

extract_protocol: Total RNA was extracted from tissue samples with Trizol reagent (Invirtrogen) following the manufacturer’s instruction. The yield and quality of RNA was checked using the NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific) and formaldehyde agarose gel electrophoresis. cDNA synthesis and cRNA amplification were conducted using the Low-Input Quick AmpWT Labeling Kit (Agilent).

tag: sample type

value: common reference comprising 8 normal controls

value: bowel

source_name: diseased full-thickness bowel

tag: gender

value: male

value: diseased full-thickness bowel


title: 257.01_D0_V

description: 257.01_D0_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 569 Pixel Size : 10 Laser on time : 166013 Laser Power : 3.10 Scan Date : 2011-11-29 Scan Temperature : 27.33 Scan Time : 13:00:51 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: CK-5

source_name: normal full-thickness bowel

value: female

value: normal full-thickness bowel


title: CK-4


title: HD-8


title: HD-7


title: HD-5


title: K562 cells transduced with pCDH-RUNX1-WT

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description:
RUNX1-WT
Experimental

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2.

label: biotin

source_name: K562 cells transduced with RUNX1-WT

label_protocol: Standard Affymetrix protocol.

growth_protocol: K562 cells were cultured in RPMI (GibCo, Invitrogen) and contained 10% FBS and 100 mg/mL streptomycin-penicillin.

extract_protocol: Total RNA was extracted with Trizol total RNA isolation reagent (Invitrogen) by following manufacturer's instructions.

treatment_protocol: K562 cells were transduced with EV, RUNX1-WT and RUNX1-R135T plasmid. Cells were selected with 2 μg/ml puromycin for 2 weeks.

tag: cell line

value: Chronic myelocytic leukemia cell line

tag: transduction


title: B16F1_vehicle_rep1

description: Gene expression in B16F1 cells

source_name: B16F1, control, replicate 1

value: vehicle


title: HD-4


title: CK-7


title: HD-3


title: CK-8


title: CK-6


title: 257.01_D0_Vhyb2

description: 257.01_D0_Vhyb2 paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 531 Pixel Size : 10 Laser on time : 166845 Laser Power : 3.10 Scan Date : 2011-12-02 Scan Temperature : 27.06 Scan Time : 10:04:57 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: CK-3


title: K562 cells transduced with pCDH-EV

description:
EV
Control

source_name: K562 cells transduced with empty vector

value: pCDH-EV


title: K562 cells transduced with pCDH-RUNX1-R135T

description:
RUNX1-R135T
Experimental

source_name: K562 cells transduced with RUNX1-R135T


title: CK-2


title: HD-2


title: Forsythia_viridissima_Flower

data_processing:
For de novo transcriptome assembly, we pre-processed raw reads, and removed adapter sequences, empty reads, reads with ambiguous ‘N’ bases > 5%, raw reads of low quality (Q<20), and raw reads with an average length less than 30 bases. Filtering of raw reads was performed using Trimmomatic program (Bolger et al., 2014), resulting into paired end raw reads, and unpaired reads which lost its corresponding sequence partner due to quality control.
The Trinity program ver 2.0.6 was used for the de novo transcriptome assembly using clean reads from all the samples. De novo assembly was further processed through CD-HIT-EST program (Li and Godzik 2006) to remove transcripts redundancies, resulting in our final assembly of 88,491 unigenes with N50 value as 1,423 bps.
We then processed these contigs for read alignment and abundance estimation using Bowtie2.0 and RSEM respectively. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method.
Supplementary_files_format_and_content: .fasta file was generated using CD-HIT-EST program. De novo transcriptome assembly of F. viridissima was constructed using the Trinity program ver 2.0.6, and processed through CD-HIT-EST program to remove transcripts redundancies. These unigene sequences generated were used for further analysis.
Supplementary_files_format_and_content: .results files were generated using RSEM program. Clean reads for each tissues were aligned on F. viridissima de novo transcriptome assembly (.fasta file), and abundace were measured using RSEM. Content of each file contains transcript_id (which is contig), gene_id (which is unigene), length, effective_length, expected_count, TPM, FPKM and IsoPct for each tissues. FPKM values were calculated using RSEM program. FPKM values for each tissues were used for further analysis.
Supplementary_files_format_and_content: Tab-delimited text file includes transcript_id, gene_id, seq_length, and FPKM values for each tissues. .results files for both tissues were used to extract FPKM values for each tissues, and were combined/aligned against transcript_id and gene_id.

organism: Forsythia viridissima

growth_protocol: Flower and leaf tissues were collected from F. viridissima growing in the natural conditions at the Tsukuba Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN, Tsukuba, Japan) in April, 2014.

extract_protocol:
Frozen samples of F. viridissima were powdered for RNA extraction. Total RNA for each of the two tissues was extracted using RNeasy Plant Mini Kit (Qiagen, USA), according to the manufacturer’s instruction.
cDNA library was then prepared using SureSelect Strand Specific RNA Library kit (Agilent 150 Technologies, USA) according to the manufacturer’s specifications. mRNA was isolated from total RNA of each tissue using beads containing oligo(dt), which was then added with fragmentation buffer to shear mRNA into short fragments and used as a template for the synthesis of first strand cDNA synthesis using random hexamer primers. The cDNA library for Illumina sequencing was prepared using SureSelect Strand Specific RNA Library kit (Agilent, USA) according to the manufacturer’s instruction.


title: Forsythia_viridissima_Leaf


title: dgriZA27Z3_m_wb_R4.leftover

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: mixed-species RNA preparation

data_processing:
We performed single-end 76 bp sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego, CA) according to the manufacturer. De-multiplexed reads (Chastity > 0.6) FASTQ output was from Illumina CASAVA v.1.8.2. For each mixed sample, the RNA-seq reads were first mapped to a merged genome and annotation including D. grimshawi (dgri_caf1 assembly; Drosophila_grimshawi.GCA_000005155.1.29.dna_sm.genome.fa), D. melanogaster (FlyBase release 6 version 04 ; FlyBase file: dmel-all-chromosome-r6.04.fasta), and A. stephensi (Anopheles-stephensi-Indian_SCAFFOLDS_AsteI2.fa), appended with updated ERCC sequences (Jiang et al., Genome Research, 2011, PMID21816910; Lee et al., J Genomics, 2016, PMID27512518) using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID23104886) with default parameters or HiSAT2 (v2.0.5; --dta and -max-intronlen = 300,000) (Kim et al., 2015, Nature Methods, PMID25751142). All processed data for Hawaiian species was based on alignment to D. grimshawi (FlyBase version 2016_05). For each chromosome or scaffold in the merged annotation, we add a four letter prefix to identify the species (e.g., scaffold_15110 => dgri_ scaffold_15110) for bam file parsing using SAMtools (v0.1.19) (Li et al., 2009, PMID19505943). We used a demultiplexer (http://github.com/haiwangyang/demultiplexer) to fetch the prefix of read names in the bam alignments and obtained all uniquely-mapped and multi-hit (with < 10 hits, >10 hits are excluded) reads (in bam format) that mapped exclusively to a single species or exclusively to ERCC. We reconverted bam files for each species to raw read fastq files using BEDTools (2.25.0; bamtofastq) (Quinlan and Hall, 2010, Bioinformatics, PMID20110278).
After this step, reads of each multi-species sample were split into three categories based on the mapped genome– D. grimshawi, ERCC, and leftover, which includes unmapped reads, reads mapped to multiple species (or multiple species plus ERCC), and reads mapped to either D. melanogaster or A. stephensi. For multi-species samples, the original fastq file can be restored by merging the reads of D. grimshawi as well as the ERCC and leftover reads. We provide both STAR (SRR3355*) and HiSAT2 (SRR724* & SRR725*) fastq files in this GEO entry. We provided associated gene-level read count files based on HiSAT2 alignments, and the read count files have both FlyBase version (*htseq_reverse.HiSAT2.FB.txt) and YO version (*htseq_reverse.HiSAT2.YO.txt) in Supplementary files of this GEO. For the latter one, we also provide two extra columns in the expression matrix, showing the maximum exon-level overlap (Jaccard index) between YO gene ID and FlyBase gene ID. In addition, we provided bigWig tracks for all samples (replicated merged), YO annotation files (in both gtf and gff3 format), ortholog look up table (among YO gene ID, FlyBase gene ID, and dmel gene), gene-level normalized read counts based on either YO or FlyBase annotation, and transcript-level transcripts per million (TPM) based on YO or FlyBase annotation.

organism: Drosophila grimshawi

source_name: leftover of unmapped reads plus reads mapped to Drosophila melanogaster and Anopheles stephensi

growth_protocol: All lines were originated from a single wild-caught female (iso-female line) and were reared at the Hawaiian Drosophila Research Stock Center. For D. grimishawi, the G1 strain was isolated from the Auwahi dry forest of East Maui in July 1965, the ZA27Z2 and ZA27Z3 strains were isolated from the Makawao Forest Reserve of East Maui in March 2010, and Mo010 strain was isolated from the southeast of Kawela Gulch of Molokai Island in December 2010, and Wm1041 strain was isolated from the Iao Valley of West Maui in July 2014. For D. silvestris, Y11R6 strain was isolated from the Olaa Forest Reserve of Hawaii in December 1986, and U26B9 strain was isolated from the Kahuku Ranch of Hawaii in January 1997. The D. hemipeza strain W40B14 was isolated from the Palikea Ridge of Oahu in July 1983. The D. heteroneura W48B6 strain was isolated from the base of Hinakapoula of Hawaii in August 1983. The D. hawaiiensis Y17P5 strain was isolated from Kipuka Ki, Hawaii Volcano National Park in March 1987. 70-100 Flies were grown in gallon glass jars with a 5 cm bed of dry sterile sand. Flies were fed once a week with five vials containing ~3ml of Yeastless Wheeler Clayton medium (placed horizontally in each jar). A single batch of this media was prepared with: 16g each of agar, rice cereal, Kellogg’s Special K, and wheat germ powder, plus 400g Gerber’s banana baby food and 1400ml water. These ingredients were mixed, cooked to boil and cooled. After cooling (but still liquid), 6ml each of 95% ethanol and propionic acid was added and mixed and then used to fill glass dram vials, which were stored 4oC until needed. 1/5 sheet of folded non-bleached facial tissue paper saturated with a water extract of fermenting Clermontia sp. leaves was added to each vial. Females of each strain laid eggs onto the tissue. Vials with eggs were collected weekly. Eggs hatched in about one week. Larvae were fed weekly for 2 weeks (as needed based on density of larvae). The recipe for cornmeal paste larval food was: 800g cornmeal, 100g brewers yeast, 90g soybean meal, 90g agar, 133ml karo syrup, 45g molasses and 4L water. This mixture was boiled, cooled, and 45ml each of 95% ethanol and propionic acid was added. The cornmeal paste is mixed with the water extract of fermenting Clermontia sp. leaves. After 3 weeks the larval tubes were transferred to moist sterile sand jars. Larvae burrow into the sand for pupation. Adults eclosed after 6 weeks and were aged for dissection. Females of all sequenced species began laying eggs around 4 weeks. Males of some species tend to die much earlier than females, making it problematic to collect sexually mature flies of both sexes at the same age for dissection. All flies were grown at 18oC with a 12h/12h Day/Night cycle.

extract_protocol:
Flies were anesthetized by briefly chilling on a 0oC glass plate. All samples were dissected in Phosphate Buffered Saline solution pH7.4 and transferred to 112ul of RNA later (Life Technologies, Carlsbad, CA) in 96-well plates at room temperature after being macerated with forceps. After transport, plates were stored at -80oC. For D. grimshawi samples, we added 20-30 1.0mm glass beads (BioSpec Products, Bartlesville, OK) to each sample and added 600ul RLT buffer from the RNeasy 96 kit (Qiagen, Valencia, CA) to each well. We homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville, OK). Extraction of total RNA was performed using the RNeasy 96 kit according to manufacturer's guide (spin version), except that we used 712μl of 70% ethanol in each well to dilute the RNAlater and RLT buffer. D. grimshawi RNA was added to D. melanogaster RNA and A. stephensi embryos for homogenization and a second round of RNA extraction using the RNeasy kit. D. melanogaster and A. stephensi RNAseq will be reported elsewhere. Four head and gonad samples of Wm1041 were split into mixed-species and single-species RNA preparations. All other samples were prepared without mixing with other species using the same RNeasy protocol. RNA was quantified using the Quant-iT RiboGreen quantification kit Life Technologies, Carlsbad, CA).
We used the Truseq PolyA+ and stranded mRNA kit with half volumes (Illumina, San Diego, CA). 100ng total RNA was input for all samples. We also added 20pg Pool 78A or 78B ERCC spike-ins (Jiang et al., Genome Research, 2011, PMID 21816910) added to the Fragment-Prime-Finish Mix during mRNA fragmentation step. Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad, CA), and pooled for multiplexed sequencing.

value: not applicable

tag: Sex

tag: replicate


title: dgriZA27Z3_m_wb_R3.leftover

description: mixed-species RNA preparation


title: dgriZA27Z3_m_wb_R2.leftover

description: mixed-species RNA preparation


title: 257.03_D8_V

description: 257.03_D8_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 496 Pixel Size : 10 Laser on time : 165254 Laser Power : 3.07 Scan Date : 2011-11-15 Scan Temperature : 26.51 Scan Time : 12:35:44 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : SpotReader
Extraction Software Version : 1.0
Datafile type : GenePix Results 3
Image Origin : 960, 6040
Note: The order of lines in the supplemental raw files matches the order of lines in the Platform table and Sample table.

source_name: Strat UHR and v4 MJ doping control aa-aRNA


title: HD-1


title: dgriZA27Z3_m_wb_R1.leftover

description: mixed-species RNA preparation


title: dgriZA27Z3_f_wb_R3.leftover

description: mixed-species RNA preparation


title: ATAC_MT_SMC3KD_rep2

city: Bethsda

first: Vittorio

last: Sartorelli

address: 50 South Dr.

department: NIAMS

institute: NIH

data_processing:
Basecalls performed using CASAVA version 1.8.2 and bcl2fastq/2.17.1
ATAC-seq reads were processed with CASAVA 1.8.2 to generate FastQ files. The raw reads were trimmed with cutadapt/1.12 and redundant reads were removed using FastUniq at pair end  FastQ level.  Reads of 50 bases were aligned to mouse genome build mm9 with Bowtie 1.1.1, allowing two mismatches. Only uniquely mapped, non-redundant reads were used for peak calling after removing highly repetitive reads.
ChIP-seq reads were were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were aligned to mouse genome build mm9 with Bowtie 1.1.1, allowing two mismatches. Only uniquely mapped, non-redundant reads were used for peak calling.
ChIRP-seq reads were mapped to the mm9 genome assembly using Bowtie2 version 2.2.4 with the default configurations.
ChIP-seq reads were mapped to the mm9 genome assembly using Bowtie 1.1.1 with the default configurations.
peaks of ATAC-seq were called using MACS 1.4.2 ( Zhang et al., 2008) with the following setting: p-value cutoff of 1.0 E-03 .
peaks of ChIRP were called using MACS2 ( Zhang et al., 2008) with the following setting: p-value cutoff of 1.0E-05 .
peaks of ChIP were called using MACS 1.4.2 ( Zhang et al., 2008) with the following setting: p-value cutoff of 1.0E-05 .
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include peak values for each Sample

source_name: muscle

growth_protocol: C2C12 cells were cultured  in DMEM medium with 20% HyClone FBS. For differentiation, cells were cultured in differentiation medium (DMEM with 2% horse serum and 1x insulin-transferrin-selenium)

extract_protocol:
For ChIPSeq,cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments.  Lysates were cleared from sonicated nuclei and used for immunoprecipitation  For ChIRPseq, cells were cross-linked in 1% glutaraldehyde. Nuclei were sonicated and used for probe hybridization. For ATACseq, nucli were isolated and   treated with Tn5 transpoase.
For ChIPSeq,  10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with NEBNext Ultra DNA library prep kit for Illumina (New England BioLabs) following the manufacturer’s protocol.  NEBNext Ultra II RNA library prep kit (New England BioLabs) was used to process RNA-Seq libraries following the manufacturer’s protocol.

treatment_protocol: Cells were transfected with control and DRR or SMC3 siRNA with RNAiMAX according to manufacturer's protocol.

tag: differentiation stage

value: myotube (MT)

tag: transfection


title: dgriZA27Z3_f_wb_R4.leftover

description: mixed-species RNA preparation


title: dgriZA27Z3_f_wb_R1.leftover

description: mixed-species RNA preparation


title: dgriZA27Z2_m_wb_R2.leftover

description: mixed-species RNA preparation


title: ATAC_MT_DRRKD_rep2

value: siDRR


title: ATAC_MT_control_rep2

value: Control


title: dgriZA27Z3_f_wb_R2.leftover

description: mixed-species RNA preparation


title: dgriZA27Z2_m_wb_R4.leftover

description: mixed-species RNA preparation


title: CK-1


title: ATAC_MT_SMC3KD_rep1


title: ATAC_MT_DRRKD_rep1


title: ChIP_MT_DRRKD_SMC3_rep2

tag: chip antibody


title: ATAC_MT_control_rep1


title: dgriZA27Z2_f_wb_R4.leftover

description: mixed-species RNA preparation


title: dgriZA27Z2_m_wb_R1.leftover

description: mixed-species RNA preparation


title: dgriZA27Z2_f_wb_R2.leftover

description: mixed-species RNA preparation


title: ChIP_MT_DRRKD_Input_rep2


title: dgriZA27Z2_f_wb_R3.leftover

description: mixed-species RNA preparation


title: ChIP_MT_SMC3_rep2


title: ChIP_MT_Input_rep2


title: dgriWm1041_m_rg_R2.leftover

description: mixed-species RNA preparation


title: dgriZA27Z2_f_wb_R1.leftover

description: mixed-species RNA preparation


title: ChIP_MB_Input_rep2

value: myoblast (MB)


title: ChIP_MB_SMC3_rep2


title: dgriWm1041_f_rg_R2.leftover

description: mixed-species RNA preparation


title: ChIP_MT_DRRKD_SMC3_rep1


title: dgriWm1041_f_rg_R1.leftover

description: mixed-species RNA preparation


title: dgriZA27Z2_m_wb_R3.leftover

description: mixed-species RNA preparation


title: ChIP_MT_DRRKD_Input_rep1


title: ChIP_MT_SMC3_rep1


title: ChIP_MT_Input_rep1


title: dgriWm1041_f_go_R2a.leftover

description: mixed-species RNA preparation


title: ChIP_MB_SMC3_rep1


title: dgriWm1041_f_ca_R2.leftover

description: mixed-species RNA preparation


title: dgriWm1041_f_ca_R1.leftover

description: mixed-species RNA preparation


title: dgriWm1041_f_go_R1a.leftover

description: mixed-species RNA preparation


title: dgriMo010_m_wb_R4.leftover

description: mixed-species RNA preparation


title: 257.02_D180_V

description: 257.02_D180_V paxgene total RNA amplified with targetamp, vs amplified Stratagene UHR, with 10ng v4 MJ doping control aRNA

scan_protocol: Scan Power : 100 PMT Volts : 529 Pixel Size : 10 Laser on time : 166623 Laser Power : 3.13 Scan Date : 2011-11-30 Scan Temperature : 27.82 Scan Time : 09:27:35 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

tag: sample name

value: Human Universal Reference RNA (Stratagene)

tag: tissue type

value: Whole Bood


title: ChIP_MB_Input_rep1

tag: strain


title: dgriMo010_f_wb_R3.leftover

description: mixed-species RNA preparation


title: dgriMo010_f_wb_R4.leftover

description: mixed-species RNA preparation


title: dgriWm1041_f_hd_R2a.leftover

description: mixed-species RNA preparation


title: dgriMo010_m_wb_R1.leftover

description: mixed-species RNA preparation


title: dgriG1_m_wb_R4.leftover

description: mixed-species RNA preparation


title: dgriMo010_f_wb_R1.leftover

description: mixed-species RNA preparation