title: TT12-9664-AN12-0048 [US-1420893]

description:
US-1420893
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0110 [US-1470969]

status: Public on Feb 24 2020

type: SRA

city: West Point

first: Alexei

middle: A

last: Podtelezhnikov

state: PA

address: 770 Sumneytown Pike

department: Non-clinical Drug Safety

country: USA

institute: Merck & Co., Inc.

description:
US-1470969
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

library_source: transcriptomic

data_processing:
Genome alignment and gene quantitation was performed using OmicSoft Array Studio
Cleaned reads were aligned to the Rnor_6.0 genome reference using the OmicSoft Aligner with a maximum of 2 allowed mismatches
Gene level counts were determined by the RNA-Seq by expectation maximization algorithm as implemented in OmicSoft Array Studio and using Ensembl.R94 gene models
FPKM normalization was applied to RNA-Seq counts followed by log-transformation with smoothing, i.e., log10(FPKM+0.01)
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Count, FPKM

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was purified from frozen liver samples using the MagMAX™ Express Magnetic Particle Processor (Applied Biosystems, # 4400074)
Total RNA samples were converted into cDNA libraries using the TruSeq Stranded mRNA HT Sample Preparation Kit (Illumina, #RS-122-2103)

tag: study

tag: strain

value: Han Wistar

tag: Sex

value: M

tag: agent

value: 0.5percent (w/v) Methylcellulose in Deionized Water

tag: treatment

value: erythromycin

tag: dose(mkd)

tag: days of administration

tag: rin


title: TT12-9646-AN12-0112 [US-1470918]

description:
US-1470918
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0080 [US-1472122]

description:
US-1472122
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: clarithromycin


title: TT12-9646-AN12-0108 [US-1470926]

description:
US-1470926
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9649-AN12-0010 [US-1470698]

description:
US-1470698
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 100percent PEG 400

value: -control-


title: TT12-9646-AN12-0106 [US-1470923]

description:
US-1470923
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0076 [US-1472137]

description:
US-1472137
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0074 [US-1472145]

description:
US-1472145
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0048 [US-1470592]

description:
US-1470592
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: valproate


title: TT12-9646-AN12-0044 [US-1470587]

description:
US-1470587
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0078 [US-1472176]

description:
US-1472176
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0042 [US-1470643]

description:
US-1470643
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0016 [US-1470764]

description:
US-1470764
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0016 [US-1472190]

description:
US-1472190
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0016 [US-1470933]

description:
US-1470933
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2581-AN13-0034 [US-1466386]

description:
US-1466386
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: zolpidem


title: TT12-9649-AN12-0080 [US-1470749]

description:
US-1470749
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9649-AN12-0016 [US-1470742]

description:
US-1470742
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0014 [US-1472153]

description:
US-1472153
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2581-AN13-0006 [US-1466381]

description:
US-1466381
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0010 [US-1470761]

description:
US-1470761
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0010 [US-1472187]

description:
US-1472187
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0012 [US-1472173]

description:
US-1472173
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0010 [US-1470938]

description:
US-1470938
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0078 [US-1470900]

description:
US-1470900
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: ethambutol


title: TT12-9639-AN12-0046 [US-1421055]

description:
US-1421055
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: probenecid


title: TT12-9639-AN12-0044 [US-1421048]

description:
US-1421048
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0048 [US-1421058]

description:
US-1421058
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0042 [US-1421052]

description:
US-1421052
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0046 [US-1470648]

description:
US-1470648
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0016 [US-1421059]

description:
US-1421059
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0074 [US-1470910]

description:
US-1470910
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0076 [US-1470970]

description:
US-1470970
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0014 [US-1470965]

description:
US-1470965
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0012 [US-1421057]

description:
US-1421057
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0014 [US-1421061]

description:
US-1421061
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0012 [US-1470909]

description:
US-1470909
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0014 [US-1470955]

description:
US-1470955
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0014 [US-1470647]

description:
US-1470647
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0016 [US-1470916]

description:
US-1470916
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0012 [US-1470717]

description:
US-1470717
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0010 [US-1421056]

description:
US-1421056
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0108 [US-1470946]

description:
US-1470946
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: methyldopa


title: TT12-9637-AN12-0110 [US-1470913]

description:
US-1470913
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9646-AN12-0012 [US-1470973]

description:
US-1470973
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0106 [US-1470879]

description:
US-1470879
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0112 [US-1470893]

description:
US-1470893
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0080 [US-1421085]

description:
US-1421085
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: sitaxsentan


title: TT12-9637-AN12-0078 [US-1421050]

description:
US-1421050
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0076 [US-1420983]

description:
US-1420983
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0074 [US-1420959]

description:
US-1420959
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0016 [US-1470882]

description:
US-1470882
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0014 [US-1420950]

description:
US-1420950
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0012 [US-1420971]

description:
US-1420971
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0012 [US-1470904]

description:
US-1470904
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0014 [US-1470974]

description:
US-1470974
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0010 [US-1421067]

description:
US-1421067
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9628-AN12-0046 [US-1420987]

description:
US-1420987
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: perhexiline maleate


title: TT12-9628-AN12-0048 [US-1421060]

description:
US-1421060
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9628-AN12-0042 [US-1421091]

description:
US-1421091
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0016 [US-1420943]

description:
US-1420943
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9637-AN12-0010 [US-1470935]

description:
US-1470935
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9628-AN12-0044 [US-1421054]

description:
US-1421054
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9628-AN12-0016 [US-1420976]

description:
US-1420976
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9639-AN12-0010 [US-1470949]

description:
US-1470949
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9628-AN12-0014 [US-1420975]

description:
US-1420975
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0078 [US-1470748]

description:
US-1470748
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: metiamide


title: TT12-9628-AN12-0010 [US-1420965]

description:
US-1420965
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0076 [US-1470895]

description:
US-1470895
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0042 [US-1470877]

description:
US-1470877
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: hydroxyzine


title: TT12-9627-AN12-0074 [US-1470903]

description:
US-1470903
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9628-AN12-0012 [US-1421075]

description:
US-1421075
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0044 [US-1470881]

description:
US-1470881
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0016 [US-1470945]

description:
US-1470945
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0014 [US-1470885]

description:
US-1470885
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0012 [US-1470940]

description:
US-1470940
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0010 [US-1470914]

description:
US-1470914
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0012 [US-1470883]

description:
US-1470883
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9624-AN12-0040 [US-1421074]

description:
US-1421074
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 80percent (w/v) Propylene Glycol/5percent (w/v) Ethanol in Deionized Water

value: ritonavir


title: TT12-9627-AN12-0010 [US-1470911]

description:
US-1470911
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Han Wistar

value: M


title: TT12-9624-AN12-0016 [US-1421089]

description:
US-1421089
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9624-AN12-0030 [US-1421083]

description:
US-1421083
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9624-AN12-0036 [US-1420963]

description:
US-1420963
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9624-AN12-0034 [US-1421077]

description:
US-1421077
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9624-AN12-0014 [US-1420980]

description:
US-1420980
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9607-AN12-0080 [US-1470934]

description:
US-1470934
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: 0.5percent (w/v) Methylcellulose in Deionized Water

value: clofibrate


title: TT12-9627-AN12-0080 [US-1470696]

description:
US-1470696
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9624-AN12-0012 [US-1421070]

description:
US-1421070
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: -control-


title: TT12-9624-AN12-0010 [US-1421062]

description:
US-1421062
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9607-AN12-0076 [US-1470905]

description:
US-1470905
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0016 [US-1470901]

description:
US-1470901
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9607-AN12-0078 [US-1470948]

description:
US-1470948
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9606-AN12-0046 [US-1470640]

description:
US-1470640
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: atorvastatin


title: TT12-9607-AN12-0010 [US-1472130]

description:
US-1472130
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0046 [US-1470972]

description:
US-1470972
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9607-AN12-0014 [US-1472183]

description:
US-1472183
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9607-AN12-0074 [US-1470942]

description:
US-1470942
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9607-AN12-0012 [US-1472128]

description:
US-1472128
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9607-AN12-0016 [US-1472132]

description:
US-1472132
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9627-AN12-0014 [US-1470951]

description:
US-1470951
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9606-AN12-0048 [US-1470594]

description:
US-1470594
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9606-AN12-0044 [US-1470752]

description:
US-1470752
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9606-AN12-0014 [US-1470700]

description:
US-1470700
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9606-AN12-0042 [US-1470646]

description:
US-1470646
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9606-AN12-0012 [US-1470588]

description:
US-1470588
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9606-AN12-0010 [US-1470725]

description:
US-1470725
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9605-AN12-0076 [US-1470896]

description:
US-1470896
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: metformin


title: TT12-9606-AN12-0016 [US-1470585]

description:
US-1470585
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9605-AN12-0078 [US-1470897]

description:
US-1470897
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9605-AN12-0080 [US-1470884]

description:
US-1470884
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9605-AN12-0074 [US-1470917]

description:
US-1470917
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9605-AN12-0016 [US-1470874]

description:
US-1470874
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9605-AN12-0014 [US-1470963]

description:
US-1470963
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9605-AN12-0010 [US-1470919]

description:
US-1470919
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9604-AN12-0076 [US-1472091]

description:
US-1472091
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: cefprozil


title: TT12-9604-AN12-0074 [US-1472167]

description:
US-1472167
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9604-AN12-0078 [US-1472115]

description:
US-1472115
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9604-AN12-0080 [US-1472121]

description:
US-1472121
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9604-AN12-0016 [US-1472175]

description:
US-1472175
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9604-AN12-0010 [US-1472131]

description:
US-1472131
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0078 [US-1470947]

description:
US-1470947
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: megestrol


title: TT12-9604-AN12-0012 [US-1472164]

description:
US-1472164
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0048 [US-1421087]

description:
US-1421087
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: telithromycin


title: TT12-9603-AN12-0080 [US-1470922]

description:
US-1470922
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0046 [US-1420978]

description:
US-1420978
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0074 [US-1470892]

description:
US-1470892
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0076 [US-1470906]

description:
US-1470906
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0042 [US-1421080]

description:
US-1421080
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0044 [US-1421093]

description:
US-1421093
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0016 [US-1421082]

description:
US-1421082
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0016 [US-1470902]

description:
US-1470902
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0010 [US-1470921]

description:
US-1470921
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0012 [US-1470889]

description:
US-1470889
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9605-AN12-0012 [US-1470894]

description:
US-1470894
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9602-AN12-0078 [US-1470769]

description:
US-1470769
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: trimethobenzamide


title: TT12-9603-AN12-0014 [US-1421084]

description:
US-1421084
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9602-AN12-0080 [US-1470697]

description:
US-1470697
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0010 [US-1421072]

description:
US-1421072
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9602-AN12-0074 [US-1470635]

description:
US-1470635
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9602-AN12-0012 [US-1470599]

description:
US-1470599
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9602-AN12-0014 [US-1470721]

description:
US-1470721
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9602-AN12-0016 [US-1470589]

description:
US-1470589
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9602-AN12-0010 [US-1470718]

description:
US-1470718
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9601-AN12-0044 [US-1472138]

description:
US-1472138
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: azithromycin


title: TT12-9602-AN12-0076 [US-1470601]

description:
US-1470601
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9601-AN12-0048 [US-1472186]

description:
US-1472186
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9601-AN12-0012 [US-1472118]

description:
US-1472118
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9601-AN12-0014 [US-1472155]

description:
US-1472155
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9601-AN12-0010 [US-1472097]

description:
US-1472097
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9601-AN12-0042 [US-1472166]

description:
US-1472166
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6006-AN12-0048 [US-1471940]

description:
US-1471940
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: esomeprazole


title: TT12-9601-AN12-0016 [US-1472149]

description:
US-1472149
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6006-AN12-0046 [US-1471960]

description:
US-1471960
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6006-AN12-0044 [US-1471952]

description:
US-1471952
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0012 [US-1421081]

description:
US-1421081
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6006-AN12-0016 [US-1472070]

description:
US-1472070
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9603-AN12-0014 [US-1470876]

description:
US-1470876
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6006-AN12-0014 [US-1472060]

description:
US-1472060
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6006-AN12-0010 [US-1471927]

description:
US-1471927
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6005-AN12-0044 [US-1472105]

description:
US-1472105
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: tolcapone


title: TT12-6005-AN12-0042 [US-1472102]

description:
US-1472102
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6005-AN12-0012 [US-1472090]

description:
US-1472090
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9601-AN12-0046 [US-1472148]

description:
US-1472148
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6005-AN12-0016 [US-1472094]

description:
US-1472094
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6005-AN12-0010 [US-1472112]

description:
US-1472112
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0080 [US-1471946]

description:
US-1471946
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: labetalol


title: TT12-2558-AN12-0076 [US-1472057]

description:
US-1472057
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0032 [US-1471967]

description:
US-1471967
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: disopyramide


title: TT12-2558-AN12-0078 [US-1472074]

description:
US-1472074
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Han Wistar


title: TT12-6006-AN12-0042 [US-1471918]

description:
US-1471918
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: TT12-2558-AN12-0016 [US-1471963]

description:
US-1471963
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0014 [US-1471971]

description:
US-1471971
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0074 [US-1472051]

description:
US-1472051
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0026 [US-1471914]

description:
US-1471914
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0028 [US-1471942]

description:
US-1471942
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0030 [US-1471958]

description:
US-1471958
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0014 [US-1472068]

description:
US-1472068
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0012 [US-1471964]

description:
US-1471964
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0012 [US-1472059]

description:
US-1472059
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9624-AN12-0032 [US-1420984]

description:
US-1420984
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 80percent (w/v) Propylene Glycol/5percent (w/v) Ethanol in Deionized Water

value: ritonavir


title: TT12-2556-AN12-0080 [US-1471930]

description:
US-1471930
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water

value: amiodarone


title: TT12-6005-AN12-0046 [US-1472114]

description:
US-1472114
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: TT12-6005-AN12-0048 [US-1472101]

description:
US-1472101
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0010 [US-1471953]

description:
US-1471953
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: -control-


title: TT12-2558-AN12-0010 [US-1471915]

description:
US-1471915
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2556-AN12-0078 [US-1471944]

description:
US-1471944
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-6006-AN12-0012 [US-1471928]

description:
US-1471928
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2556-AN12-0074 [US-1471934]

description:
US-1471934
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2556-AN12-0014 [US-1472063]

description:
US-1472063
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2556-AN12-0016 [US-1471970]

description:
US-1471970
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2554-AN12-0030 [US-1472093]

description:
US-1472093
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: paroxetine


title: TT12-2556-AN12-0012 [US-1471936]

description:
US-1471936
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2556-AN12-0010 [US-1471956]

description:
US-1471956
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2554-AN12-0028 [US-1472141]

description:
US-1472141
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2558-AN12-0016 [US-1472080]

description:
US-1472080
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2554-AN12-0026 [US-1472110]

description:
US-1472110
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2554-AN12-0016 [US-1471935]

description:
US-1471935
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2554-AN12-0014 [US-1471965]

description:
US-1471965
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2546-AN12-0108 [US-1472089]

description:
US-1472089
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: fluoxetine


title: TT12-2554-AN12-0010 [US-1471916]

description:
US-1471916
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2546-AN12-0112 [US-1471931]

description:
US-1471931
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2546-AN12-0016 [US-1472061]

description:
US-1472061
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2546-AN12-0014 [US-1472066]

description:
US-1472066
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2546-AN12-0106 [US-1471932]

description:
US-1471932
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2554-AN12-0012 [US-1471966]

description:
US-1471966
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2556-AN12-0076 [US-1471951]

description:
US-1471951
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-1512-AN12-0012 [US-1472098]

description:
US-1472098
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-1512-AN12-0060 [US-1472125]

description:
US-1472125
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: zafirlukast


title: TT12-1512-AN12-0058 [US-1472111]

description:
US-1472111
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-1512-AN12-0064 [US-1472103]

description:
US-1472103
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-1512-AN12-0062 [US-1472095]

description:
US-1472095
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2546-AN12-0010 [US-1472064]

description:
US-1472064
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-2546-AN12-0012 [US-1471917]

description:
US-1471917
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-1512-AN12-0016 [US-1472109]

description:
US-1472109
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-1512-AN12-0014 [US-1472104]

description:
US-1472104
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-1512-AN12-0010 [US-1472099]

description:
US-1472099
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0078 [US-1470756]

description:
US-1470756
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 100percent propylene glycol

value: nefazodone


title: TT11-9789-AN11-0064 [US-1470722]

description:
US-1470722
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Deionized Water

value: ticlopidine


title: TT11-9789-AN11-0032 [US-1470706]

description:
US-1470706
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0060 [US-1470644]

description:
US-1470644
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0062 [US-1470650]

description:
US-1470650
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0058 [US-1470642]

description:
US-1470642
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0028 [US-1470754]

description:
US-1470754
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0026 [US-1470772]

description:
US-1470772
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0016 [US-1470747]

description:
US-1470747
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0030 [US-1470714]

description:
US-1470714
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0014 [US-1470720]

description:
US-1470720
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0010 [US-1470639]

description:
US-1470639
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0012 [US-1470586]

description:
US-1470586
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0056 [US-1470743]

description:
US-1470743
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0052 [US-1470709]

description:
US-1470709
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0050 [US-1470744]

description:
US-1470744
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0036 [US-1470755]

description:
US-1470755
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0038 [US-1470638]

description:
US-1470638
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0040 [US-1470760]

description:
US-1470760
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0076 [US-1470767]

description:
US-1470767
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0080 [US-1470753]

description:
US-1470753
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9789-AN11-0074 [US-1470758]

description:
US-1470758
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0034 [US-1470705]

description:
US-1470705
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0080 [US-1472178]

description:
US-1472178
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: chlorpropamide


title: TT11-9788-AN11-0006 [US-1470699]

description:
US-1470699
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0078 [US-1472189]

description:
US-1472189
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0004 [US-1470710]

description:
US-1470710
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0076 [US-1472182]

description:
US-1472182
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0048 [US-1420974]

description:
US-1420974
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: pentoxifylline


title: TT11-9785-AN11-0074 [US-1472107]

description:
US-1472107
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Han Wistar


title: TT11-9785-AN11-0046 [US-1420992]

description:
US-1420992
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: TT11-9785-AN11-0044 [US-1420928]

description:
US-1420928
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0012 [US-1420845]

description:
US-1420845
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0042 [US-1420935]

description:
US-1420935
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0016 [US-1472180]

description:
US-1472180
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0054 [US-1470766]

description:
US-1470766
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0008 [US-1470746]

description:
US-1470746
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0012 [US-1472158]

description:
US-1472158
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9788-AN11-0002 [US-1470771]

description:
US-1470771
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0010 [US-1420860]

description:
US-1420860
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0014 [US-1420846]

description:
US-1420846
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT12-9624-AN12-0038 [US-1420960]

description:
US-1420960
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 80percent (w/v) Propylene Glycol/5percent (w/v) Ethanol in Deionized Water


title: TT11-9785-AN11-0010 [US-1472136]

description:
US-1472136
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0016 [US-1420848]

description:
US-1420848
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9780-AN11-0012 [US-1470950]

description:
US-1470950
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9779-AN11-0080 [US-1470770]

description:
US-1470770
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: nabumetone


title: TT11-9780-AN11-0010 [US-1470943]

description:
US-1470943
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: TT11-9780-AN11-0046 [US-1470957]

description:
US-1470957
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: dipyridamole


title: TT11-9780-AN11-0048 [US-1470927]

description:
US-1470927
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: TT11-9780-AN11-0044 [US-1470952]

description:
US-1470952
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9779-AN11-0078 [US-1470637]

description:
US-1470637
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9779-AN11-0074 [US-1470582]

description:
US-1470582
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9780-AN11-0014 [US-1470959]

description:
US-1470959
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: -control-


title: TT11-9779-AN11-0016 [US-1470704]

description:
US-1470704
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9780-AN11-0016 [US-1470958]

description:
US-1470958
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9780-AN11-0042 [US-1470908]

description:
US-1470908
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9779-AN11-0076 [US-1470751]

description:
US-1470751
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9779-AN11-0014 [US-1470762]

description:
US-1470762
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9785-AN11-0014 [US-1472147]

description:
US-1472147
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9779-AN11-0010 [US-1470750]

description:
US-1470750
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9778-AN11-0080 [US-1472113]

description:
US-1472113
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: cefuroxime


title: TT11-9778-AN11-0074 [US-1472100]

description:
US-1472100
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9778-AN11-0012 [US-1472106]

description:
US-1472106
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9778-AN11-0016 [US-1472177]

description:
US-1472177
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9778-AN11-0076 [US-1472171]

description:
US-1472171
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9778-AN11-0014 [US-1472146]

description:
US-1472146
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9779-AN11-0012 [US-1470759]

description:
US-1470759
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9758-AN11-0064 [US-1420970]

description:
US-1420970
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: sumatriptan


title: TT11-9758-AN11-0062 [US-1420944]

description:
US-1420944
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9778-AN11-0010 [US-1472142]

description:
US-1472142
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9758-AN11-0016 [US-1420961]

description:
US-1420961
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9758-AN11-0058 [US-1420972]

description:
US-1420972
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9758-AN11-0014 [US-1420956]

description:
US-1420956
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9758-AN11-0012 [US-1420946]

description:
US-1420946
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9741-AN11-0064 [US-1468405]

description:
US-1468405
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: nadolol


title: TT11-9741-AN11-0062 [US-1468409]

description:
US-1468409
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9758-AN11-0060 [US-1420967]

description:
US-1420967
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9741-AN11-0058 [US-1468410]

description:
US-1468410
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9741-AN11-0060 [US-1468428]

description:
US-1468428
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9741-AN11-0016 [US-1468413]

description:
US-1468413
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9741-AN11-0014 [US-1468411]

description:
US-1468411
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9778-AN11-0078 [US-1472116]

description:
US-1472116
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9741-AN11-0012 [US-1468447]

description:
US-1468447
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9655-AN11-0040 [US-1420952]

description:
US-1420952
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: sudoxicam


title: TT11-9741-AN11-0010 [US-1468422]

description:
US-1468422
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9655-AN11-0038 [US-1420942]

description:
US-1420942
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9655-AN11-0034 [US-1421068]

description:
US-1421068
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: myeloid cells, P1FWT_2

city: Dallas

first: Yihong

last: Wan

state: TX

address: 6001 Forest Park Rd.

department: Pharmacology

institute: UT Southwestern Medical Center

data_processing:
Quality control was performed with FastQC (v0.11.2) and FastQ Screen (v0.4.4)
Reads were trimmed to remove adapter sequences using fastq-mcf (ea-utils/1.1.2-806), then mapped to mm10 genome using TopHat (v2.0.12) with duplicated reads marked by Picard tools (v1.127).
RNA counts were generated from Subread/FeatureCounts. After TMM normalization, differentially expressed genes (DEGs) were identified using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each Sample

organism: Mus musculus

source_name: myeloid cells, P1FWT

growth_protocol: Bone marrow cells were filtered with a 40 μm cell strainer, and differentiated with 40 ng/mL of mouse M-CSF in α-MEM containing 10% FBS for 3 days

extract_protocol:
Total RNA was extracted with Trizol and miRNeasy Mini Kit (Qiagen #217004).
RNA library for sequencing was constructed from 4 μg of each DNase-treated RNA sample by using the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina (Illumina #RS-122). RNA was purified and fragmented before strand-specific cDNA synthesis. cDNA was then A-tailed, ligated with indexed adapters, PCR amplified and purified with Ampure XP beads. Library quality was validated on the Agilent 2100 Bioanalyzer.

tag: genotype

value: PARP1 flox/flox

tag: age

value: 2 months

tag: cell type

value: immature myeloid cells


title: myeloid cells, P1FCKO_2

source_name: myeloid cells, P1FCKO

value: PARP1 flox/flox+lysozyme-Cre


title: myeloid cells, P2FCKO_1

source_name: myeloid cells, P2FCKO

value: PARP2 flox/flox+lysozyme-Cre


title: myeloid cells, P2FCKO_2


title: myeloid cells, P2FWT_1

source_name: myeloid cells, P2FWT

value: PARP2 flox/flox


title: myeloid cells, P1FCKO_1


title: myeloid cells, P2FWT_2


title: myeloid cells, P1FWT_1


title: TT11-9758-AN11-0010 [US-1420955]

description:
US-1420955
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: TT11-9655-AN11-0008 [US-1420989]

description:
US-1420989
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9655-AN11-0006 [US-1420962]

description:
US-1420962
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: RANKL with LEA_D1_rep1

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

data_processing:
mRNA-Seq reads were mapped to reference mouse genome (mm10 assembly) using HISAT2 with default parameters.
RNA expression was quantified using analyzeRepeats.pl command in HOMER
DEGs was assessed with DESeq2 using getDiffExpression.pl in HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow-derived macrophage cells

growth_protocol: Bone marrow (BM) cells were collected by flushing femurs and tibias from 6- to 8-week-old C57BL/6 mice. Cells were cultured in α-minimum essential medium (α-MEM) supplemented with 10% FBS and M-CSF (5 ng/ml) for 16 h.  Non-adherent cells were harvested and cultured with M-CSF (30 ng/ml) for 3 days. Floating cells were removed and adherent cells were used as bone marrow-derived macrophage (BMM) cells.

extract_protocol:
Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Osteoclast precursor cells were cultured in 48-well plates with 30 ng/mL of macrophage colony-stimulating factor (M-CSF) and 100 ng/mL of receptor activator of nuclear factor kappaB ligand (RANKL), in the absence or presence of LEA (10 μg/ml).

value: Primary cells

value: 6-8 weeks

value: 100 ng/mL RANKL and 10 μg/ml LEA


title: RANKL_R2_rep2

value: 100 ng/mL RANKL


title: RANKL with LEA_D2_rep2


title: No RANKL_C2_rep2


title: TT11-9655-AN11-0004 [US-1420977]

description:
US-1420977
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: TT11-9655-AN11-0002 [US-1420982]

description:
US-1420982
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: -control-


title: TT11-9652-AN11-0072 [US-1470924]

description:
US-1470924
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 1.0percent (w/v) Methylcellulose in Deionized Water

value: felbamate


title: E: mice using Ellagic acid agaist diarrhea

city: Harbin

first: Jianqing

last: Chen

address: Changjiang Road

country: China

institute: Northeast Agricultral University

library_source: genomic

data_processing: Sequencing was performed on the Illumina Hiseq 2500 (Illumina, USA) and raw data was obtained. Raw data were first processed through in-house Perl scripts. Clean data were obtained by removing reads containing adapter sequences, poly-N sequences, and low quality reads from raw data. The Q20, Q30 and GC content of the clean data were also calculated. Reference genome and gene model annotation files were downloaded from the GenBank directly. An index of the reference genome was built using Bowtie v2.2.3. Paired-end clean reads were aligned using TopHat v2.0.12. Differential expression analysis of the two groups was performed using the DESeq R package (1.18.0). DESeq provided statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. Resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.

molecule: genomic DNA

source_name: diarrhea model

extract_protocol:
Total RNA was extracted with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA). RNA concentration and total quantity were detected by Invitrogen Qubit 3.0 Spectrophotometer (Thermo Fisher Scientific, USA); RNA purity was checked using the Nanodrop 2000 (Thermo Fisher Scientific, USA); and RNA integrity was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA). mRNA was obtained through purifying total RNA, and was broken into fragments of 100–300 bp. Reverse Transcribe was performed to synthetize First Strand cDNA using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific, USA). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Then addition of adenlylate 3’ ends, connection sequencing adapters, selection library size, PCR amplification and checking library quality were performed in turn. Sequencing was performed on the Illumina Hiseq 2500 (Illumina, USA) and raw data was obtained.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: ileums

value: ellagic acid


title: TT11-9652-AN11-0070 [US-1470941]

description:
US-1470941
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: No RANKL_C1_rep1


title: RANKL_R1_rep1


title: TT11-9652-AN11-0066 [US-1470953]

description:
US-1470953
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9652-AN11-0068 [US-1470928]

description:
US-1470928
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: D: mice in Diarrhea models


title: TT11-9652-AN11-0006 [US-1470875]

description:
US-1470875
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2582-AN11-0110 [US-1471922]

description:
US-1471922
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Han Wistar

value: flutamide


title: D6 WT rep1

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: Adoptive transferred p14 T cells form spleen day 6 post immunisation

data_processing:
Primary data analysis was performed with the Illumina RTA v1.18.66.3.
The  sequence assembly and alignment was performed using the ArrayStar software v.13 (DNASTAR, USA).
The level of gene expression was assessed after Reads Per Kilobase Million (RPKM) normalization and log2 transformation.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Tab-delimited text file includes linear total RPKM  normalized values.

source_name: p14 T cells

extract_protocol:
Total RNA was extracted from WT and KO p14 T cells of naïve, D6 and D80 immunized mice using the RNeasy Micro Kit (QIAGEN AG, Switzerland)
Libraries were generated from 10ng total RNA using the SmartSeq2 Kit (Takara Bio, Japan).

treatment_protocol: One day post adoptive transfer of  naïve WT and KO  p14 T cells, mice were immunized with LCMV-WE strain. P14 T cells were purified form spleen at  D6 or D80 post immunisation.

value: p14 T cells (spleen)

value: post natal week 8

value: wild type;p14


title: TT11-2582-AN11-0112 [US-1472052]

description:
US-1472052
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: TT11-2582-AN11-0108 [US-1472087]

description:
US-1472087
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-9652-AN11-0004 [US-1470967]

description:
US-1470967
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: D80 KO rep1

description: Adoptive transferred p14 T cells form spleen day 80 post immunisation


title: TT11-2582-AN11-0092 [US-1466990]

description:
US-1466990
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 100percent propylene glycol

value: carbamazepine


title: naïve WT rep1

description: Naive p14 T cells form spleen


title: TT11-2582-AN11-0106 [US-1471919]

description:
US-1471919
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: D6 WT rep2


title: naïve WT rep2

description: Naive p14 T cells form spleen


title: D6 KO rep3


title: naïve KO rep2

description: Naive p14 T cells form spleen


title: TT11-9652-AN11-0002 [US-1470932]

description:
US-1470932
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2582-AN11-0090 [US-1466953]

description:
US-1466953
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: D80 KO rep2


title: TT11-2582-AN11-0032 [US-1466959]

description:
US-1466959
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2582-AN11-0094 [US-1470523]

description:
US-1470523
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: cS5Ahi5

city: Vienna

first: Richard

middle: H

last: Moriggl

state: Vienna

address: Veterinaerplatz 1

department: Institute of Animal Breeding and Genetics

country: Austria

institute: University of Veterinary Medicine

description: expression profile of cS5Ahi CD8+ T-cell, replicate 5

data_processing:
Alignment to genome version GRCm37 using transcriptome guided alignment with TopHat version 1.4.1.
Adapter trimming and removing of low quality bases was performed using cutadapt.
Counting of reads was done using htseq-count (HTSeq version 0.6.1p1), mode union.
Genome_build: GRCm37/mm9
Supplementary_files_format_and_content: raw count file (tab delimited)

molecule: polyA RNA

source_name: lymph node, CD8

growth_protocol: not applicable, ex vivo data

extract_protocol: CD8 cells from LN single cell suspension were isolated with MagniSort™ Mouse CD8 Positive Selection Kit. Trizol (Sigma) in combination with RNeasy mini kit (Qiagen)

value: lymph node

tag: cell markers

value: T cells

value: untreated


title: D80 WT rep2


title: TT11-9652-AN11-0008 [US-1470925]

description:
US-1470925
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: naïve KO rep1

description: Naive p14 T cells form spleen


title: D80 WT rep1


title: TT11-2582-AN11-0030 [US-1466977]

description:
US-1466977
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: -control-


title: TT11-2582-AN11-0028 [US-1466964]

description:
US-1466964
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: D6 KO rep2


title: TT11-2582-AN11-0096 [US-1470517]

description:
US-1470517
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: cS5Ahi3

description: expression profile of cS5Ahi CD8+ T-cell, replicate 3


title: D6 KO rep1

description: Adoptive transferred p14 T cells form spleen day 6 post immunisation


title: TT11-2582-AN11-0026 [US-1466966]

description:
US-1466966
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: cS5Ahi2

description: expression profile of cS5Ahi CD8+ T-cell, replicate 2


title: cS5Alo4

description: expression profile of cS5Alo CD8+ T-cell, replicate 4


title: cS5Alo5

description: expression profile of cS5Alo CD8+ T-cell, replicate 5


title: TT11-2582-AN11-0014 [US-1471937]

description:
US-1471937
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: cS5Ahi1

description: expression profile of cS5Alo CD8+ T-cell, replicate 1


title: TT11-2582-AN11-0016 [US-1471923]

description:
US-1471923
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: cS5Alo2

description: expression profile of cS5Alo CD8+ T-cell, replicate 2


title: cS5Alo1


title: TT11-2582-AN11-0010 [US-1471955]

description:
US-1471955
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: cS5Alo3

description: expression profile of cS5Alo CD8+ T-cell, replicate 3


title: TT11-2578-AN11-0016 [US-1471947]

description:
US-1471947
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2578-AN11-0092 [US-1472079]

description:
US-1472079
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: furosemide


title: TT11-2578-AN11-0094 [US-1471941]

description:
US-1471941
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: WT3

description: expression profile of wt CD8+ T-cell, replicate 3

value: WT


title: TT11-2578-AN11-0014 [US-1471925]

description:
US-1471925
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: cS5Ahi4

description: expression profile of cS5Ahi CD8+ T-cell, replicate 4


title: WT5

description: expression profile of wt CD8+ T-cell, replicate 5


title: TT11-2582-AN11-0012 [US-1471943]

description:
US-1471943
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: WT2

description: expression profile of wt CD8+ T-cell, replicate 2


title: TT11-2578-AN11-0012 [US-1471939]

description:
US-1471939
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: WT1

description: expression profile of wt CD8+ T-cell, replicate 1


title: TT11-2578-AN11-0010 [US-1472082]

description:
US-1472082
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2560-AN11-0024 [US-1470532]

description:
US-1470532
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: nevirapine


title: D2A1.2.V

city: Padova

first: Marco

last: Montagner

state: PD

address: viale G. Colombo, 3

country: Italy

institute: University of Padua

data_processing:
The RSEM package (version 1.2.29) and Bowtie2 were used to aling reads to the mouse mm10 transcriptome, taken from Refseq Gene reference table available at UCSC . The “--forward-prob” parameter was set to “0.5” and all other parameters were kept as default.
Differential expression analysis was performed with the DESeq2 package (version 1.12.4) within the R programming (version 3.3.1)
Genome_build: mm10 Refseq
Supplementary_files_format_and_content: Tab delimited text files containing normalised data. Rows represent Refseq mouse genes and columns represent individual samples.

source_name: breast cancer cell line in vivo

extract_protocol:
Lungs and primary tumors were harvested from mice, immersed in PBS, and promptly chopped with scissors to small fragments. Minced lungs were then added to digestion solution (PBS buffer with 75mg/ml TM Liberase, Roche 05401151001, 75mg/ml TH Liberase, Roche 05401127001, 12.5mg/ml DNAse, Sigma-Aldrich DN25) for 1hr at 37°C, rocking. Digested lung pieces were spun down for 5’ at 1300rpm, re-suspended in calcium- and magnesium-free PBS plus 1mM EDTA by vigorous pipetting until the solution was homogeneous and eventually filtered through a 70mm cell strainer to remove undigested fibrous tissue. In the case of stiffer tissues, such as primary tumors, tissue fragments were also mechanically disrupted by passing them through needles of decreasing thickness. Cells were then pelleted and red blood cells lysed with Red Blood Cells Lysis Solution (Miltenyi Biotec, 130-094-183) following manufacturer protocol. After washing, cells were re-suspended in FACS buffer (PBS, 2mM EDTA, 3%BSA) and labelled with CD45-APC antibody for 30min (eBiosciences, 30-F11, 1:400) to avoid contamination from leukocytes during sorting. Samples were then washed repeatedly, filtered through a 70mm cell strainer and kept on ice during fluorescence-activated cell sorting.
Total RNA was extracted with RNeasy Plus Micro kit (Qiagen) following manufacturer protocol. RNA samples were assessed for quantity and integrity using the NanoDrop 8000 spectrophotometer V2.0 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyser (Agilent Technologies), respectively. Samples displayed low levels of degradation with RNA integrity numbers (RIN) between 6.4 and 7.8. Full-length cDNA molecules were generated from 4ng of total RNA per sample using the SMARTer kit for cDNA generation (Clontech). cDNA quantity was measured using the dsDNA High-sensitivity Qubit kit with the Qubit 2.0 Fluorometer (Thermo Fisher Scientific), and were checked for quality using a D1000 ScreenTape with the Agilent 2200 Tapestation (Agilent Technologies). Libraries were prepared using the Illumina Nextera XT Sample Preparation Kit (Illumina Inc.) with an input of 150pg of cDNA per sample. Resulting libraries were checked for average fragment size using the Agilent D1000 ScreenTape, and were quantified using the Qubit dsDNA High-sensitivity reagent kit.

treatment_protocol: BALB/c nude female mice (6- to 8-weeks old) were injected in tail vein with 1x106 D2.A1-eGFP cells or D2.OR-eGFP cells. After 3 weeks, lungs were collected, digested to single cell suspension and stained with CD45-APC antibody. CD45-/eGFP+ cells were FACS sorted and RNA purified. For in vitro samples, breast cancer cells were grown in multiwell plates under standard culture conditions, trypsinised, sorted and processed in parallel with the in vivo samples.

tag: cell line

value: D2.A1-EGFP cells

tag: conditions

value: Isolated from lungs

tag: description


title: TT11-2560-AN11-0022 [US-1470471]

description:
US-1470471
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2560-AN11-0020 [US-1470464]

description:
US-1470464
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: D2A1.1.V

value: BALB/c nude female mice (6- to 8-weeks old) were injected in tail vein with 1x106 D2.A1-eGFP cells


title: TT11-2578-AN11-0090 [US-1472056]

description:
US-1472056
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Han Wistar


title: TT11-2578-AN11-0096 [US-1471912]

description:
US-1471912
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: WT4

description: expression profile of wt CD8+ T-cell, replicate 4


title: TT11-2560-AN11-0016 [US-1470454]

description:
US-1470454
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: D2OR1.4.V

value: D2.OR-EGFP cells

value: BALB/c nude female mice (6- to 8-weeks old) were injected in tail vein with 1x106 D2.OR-eGFP cells.


title: TT11-2560-AN11-0018 [US-1470507]

description:
US-1470507
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: D2OR1.5.V


title: D2OR1.2.V


title: TT11-2560-AN11-0014 [US-1470472]

description:
US-1470472
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2560-AN11-0010 [US-1470446]

description:
US-1470446
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2560-AN11-0012 [US-1470459]

description:
US-1470459
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: D2OR1.2.P

source_name: breast cancer cell line in vitro

value: Grown on plastic


title: D2OR1.1.P


title: D2A1.3.P


title: TT11-2554-AN11-0040 [US-1466967]

description:
US-1466967
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: co-amoxiclav


title: D2OR1.3.P


title: D2A1.1.P


title: TT11-2554-AN11-0038 [US-1467015]

description:
US-1467015
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2554-AN11-0036 [US-1467009]

description:
US-1467009
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2554-AN11-0016 [US-1467008]

description:
US-1467008
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: D2A1.2.P


title: Prox1 pos Rep #3

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
Prox1 positive sorted intestine cells
Prox1_RPMMM_mirs_over_50.csv
Prox1_4_pos_S22_L003_R1_001

data_processing:
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm9 and dm3 for mouse and fruit fly small RNA-seq, mm10 for mouse RNA-seq
Supplementary_files_format_and_content: RPMMM and normalized counts files are comma separated value matrices containing the Reads Per Million miRs Mapped (RPMMM) or DESeq2 normalized counts for each of the samples, respectively.

source_name: Intestine

extract_protocol: Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

value: small intestine


title: Prox1 neg Rep #3

description:
Prox1 negative sorted intestine cells
Prox1_RPMMM_mirs_over_50.csv
Prox1_4_neg_S19_L003_R1_001


title: TT11-2554-AN11-0034 [US-1466951]

description:
US-1466951
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2554-AN11-0014 [US-1466956]

description:
US-1466956
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: Prox1 pos Rep #2

description:
Prox1 positive sorted intestine cells
Prox1_RPMMM_mirs_over_50.csv
Prox1_3_pos_S21_L003_R1_001


title: D2OR1.3.V


title: Prox1 neg Rep #2

description:
Prox1 negative sorted intestine cells
Prox1_RPMMM_mirs_over_50.csv
Prox1_3_neg_S18_L003_R1_001


title: TT11-2554-AN11-0010 [US-1466976]

description:
US-1466976
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2554-AN11-0012 [US-1466965]

description:
US-1466965
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: Prox1 pos Rep #1

description:
Prox1 positive sorted intestine cells
Prox1_RPMMM_mirs_over_50.csv
Prox1_2_pos_S20_L003_R1_001


title: Lgr5 Rep #2

description:
Lgr5 sorted intestine cells
Lgr5_RPMMM_mirs_over_50.csv
LH_2_S53_L008_R1_001


title: Lgr5 Rep #1

description:
Lgr5 sorted intestine cells
Lgr5_RPMMM_mirs_over_50.csv
LH_1_S52_L008_R1_001


title: TT11-2552-AN11-0076 [US-1472191]

description:
US-1472191
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: carisoprodol


title: Prox1 neg Rep #1

description:
Prox1 negative sorted intestine cells
Prox1_RPMMM_mirs_over_50.csv
Prox1_2_neg_S17_L003_R1_001


title: TT11-2552-AN11-0080 [US-1471954]

description:
US-1471954
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: TT11-2552-AN11-0078 [US-1472185]

description:
US-1472185
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: Sox9eGFP Sublow Male Rep #3

description:
Sox9eGFP Sublow sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC340_Sublow_S33_L005_R1_001

tag: gender

value: male


title: Sox9eGFP Negative Male Rep #3

description:
Sox9eGFP Negative sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC340_Neg_S34_L005_R1_001


title: TT11-2552-AN11-0074 [US-1472184]

description:
US-1472184
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: study

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: TT11-2552-AN11-0044 [US-1471921]

description:
US-1471921
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: strain

value: levofloxacin


title: TT11-2552-AN11-0048 [US-1471913]

description:
US-1471913
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: Sex


title: Sox9eGFP Sublow Male Rep #2

description:
Sox9eGFP Sublow sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC339_Sublow_S44_L006_R1_001


title: Sox9eGFP Non-sorted Male Rep #2

description:
Sox9eGFP Non-sorted sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC339_NS_S46_L006_R1_001


title: Sox9eGFP Low Male Rep #3

description:
Sox9eGFP Low sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC340_Low_Combo_L000_R1_001


title: TT11-2552-AN11-0046 [US-1471938]

description:
US-1471938
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: agent


title: TT11-2552-AN11-0016 [US-1472055]

description:
US-1472055
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: treatment

value: -control-


title: Sox9eGFP Negative Male Rep #2

description:
Sox9eGFP Negative sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC339_Neg_S45_L006_R1_001


title: TT11-2552-AN11-0016 [US-1472165]

description:
US-1472165
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: dose(mkd)


title: TT11-2552-AN11-0014 [US-1471926]

description:
US-1471926
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: days of administration


title: Sox9eGFP Low Male Rep #2

description:
Sox9eGFP Low sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC339_Low_Combo_L000_R1_001


title: TT11-2552-AN11-0042 [US-1471961]

description:
US-1471961
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: rin


title: TT11-2552-AN11-0014 [US-1472135]

description:
US-1472135
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2552-AN11-0012 [US-1471959]

description:
US-1471959
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: Sox9eGFP Non-sorted Male Rep #1

description:
Sox9eGFP Non-sorted sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC338_NS_S41_L006_R1_001


title: TT11-2552-AN11-0012 [US-1472159]

description:
US-1472159
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: Sox9eGFP Sublow Male Rep #1

description:
Sox9eGFP Sublow sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC338_Sublow_S37_L005_R1_001


title: TT11-2552-AN11-0010 [US-1472054]

description:
US-1472054
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: Sox9eGFP High Male Rep #2

description:
Sox9eGFP High sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC339_High_Combo_L000_R1_001


title: Sox9eGFP Negative Male Rep #1

description:
Sox9eGFP Negative sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC338_Neg_S40_L006_R1_001


title: Sox9eGFP Low Male Rep #1

description:
Sox9eGFP Low sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC338_Low_S36_L005_R1_001


title: TT11-2552-AN11-0010 [US-1472123]

description:
US-1472123
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2551-AN11-0038 [US-1468432]

description:
US-1468432
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Imwitor 742/Polysorbate 80 (1:1)

value: telcagepant


title: Sox9eGFP High Male Rep #3

description:
Sox9eGFP High sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC340_High_S76_L008_R1_001


title: Sox9eGFP High Male Rep #1

description:
Sox9eGFP High sorted intestine crypt cells
Sox9_sorted_males_RPMMM_over_50.csv
BC338_High_Combo_L000_R1_001


title: TT11-2551-AN11-0040 [US-1468467]

description:
US-1468467
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2551-AN11-0036 [US-1468415]

description:
US-1468415
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2551-AN11-0016 [US-1468408]

description:
US-1468408
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: Sox9eGFP Low  Female HFD Rep #3

description:
Sox9-EGFP Low sorted intestine crypt cells from high fat diet sample
Sox9_HFD_RPMMM_mirs_over_50.csv
BC242_chow_Low_AGTCAA_L002_R1

value: female

tag: diet

value: HFD


title: TT11-2551-AN11-0034 [US-1468423]

description:
US-1468423
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: Sox9eGFP Low Female HFD Rep #4

description:
Sox9-EGFP Low sorted intestine crypt cells from high fat diet sample
Sox9_HFD_RPMMM_mirs_over_50.csv
BC244_HFD_Low_GGCTAC_L003_R1


title: Sox9eGFP Low  Female Chow Rep #3

description:
Sox9-EGFP Low sorted intestine crypt cells from chow diet sample
Sox9_HFD_RPMMM_mirs_over_50.csv
BC241_HFD_Low_GGTAGC_L001_R1

value: chow


title: Sox9eGFP Low  Female Chow Rep #4

description:
Sox9-EGFP Low sorted intestine crypt cells from chow diet sample
Sox9_HFD_RPMMM_mirs_over_50.csv
BC243_chow_Low_GTTTCG_L001_R1


title: TT11-2551-AN11-0012 [US-1468401]

description:
US-1468401
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2551-AN11-0014 [US-1468395]

description:
US-1468395
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: Sox9eGFP Low  Female HFD Rep #2

description:
Sox9-EGFP Low sorted intestine crypt cells from high fat diet sample
Sox9_HFD_RPMMM_mirs_over_50.csv
BC182_HFD_Low_GAGTGG_L002_R1


title: Sox9eGFP Low Female HFD Rep #1

description:
Sox9-EGFP Low sorted intestine crypt cells from high fat diet sample
Sox9_HFD_RPMMM_mirs_over_50.csv
BC181_HFD_Low_TGACCA_L004_R1


title: Sox9eGFP Low  Female Chow Rep #2

description:
Sox9-EGFP Low sorted intestine crypt cells from chow diet sample
Sox9_HFD_RPMMM_mirs_over_50.csv
BC183_chow_Low_CAGATC_L001_R1


title: TT11-2547-AN11-0048 [US-1471924]

description:
US-1471924
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: omeprazole


title: TT11-2547-AN11-0044 [US-1472058]

description:
US-1472058
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2551-AN11-0010 [US-1468441]

description:
US-1468441
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: Sox9eGFP Low Female Chow Rep #1

description:
Sox9-EGFP Low sorted intestine crypt cells from chow diet sample
Sox9_HFD_RPMMM_mirs_over_50.csv
BC180_chow_Low_GCCAAT_L001_R1


title: TT11-2547-AN11-0046 [US-1471948]

description:
US-1471948
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2547-AN11-0042 [US-1471933]

description:
US-1471933
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: STAT5BN642H, replicate 4

city: Wien

first: Ha T T

last: Pham

address: SCHWARZSPANIERSTR 17

institute: Ludwig Boltzmann Institute for Cancer Research

description: expression profile of hSTAT5BN642H CD8+ T-cell, replicate 4

source_name: CD8+ T-cells

extract_protocol:
Lymph nodes were isolated and kept on ice, single-cell suspensions were inclubated with CD8 antibody and magnetic bead, isolated CD8 T-cells were flash-frozen in Trizol reagent, RNA was harvested
1µg of total RNA per sample was taken for cDNA library synthesis using SENSE mRNA-Seq Library preparation kit according to the manufacturers recommendations.
50 bp single-end RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD8+ T-cells were sorted using magnisort kit (eBioscience)

value: Lymph node

tag: genotype

value: hSTAT5B N642H +/T


title: STAT5BN642H, replicate 2

description: expression profile of hSTAT5BN642H CD8+ T-cell, replicate 2


title: TT11-2547-AN11-0016 [US-1471929]

description:
US-1471929
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: STAT5BN642H, replicate 1

description: expression profile of hSTAT5BN642H CD8+ T-cell, replicate 1


title: TT11-2547-AN11-0014 [US-1471920]

description:
US-1471920
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: STAT5BN642H, replicate 3

description: expression profile of hSTAT5BN642H CD8+ T-cell, replicate 3


title: TT11-2547-AN11-0012 [US-1472069]

description:
US-1472069
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: hSTAT5B, replicate 4

description: expression profile of hSTAT5B CD8+ T-cell, replicate 4

value: hSTAT5B +/T


title: TT11-2547-AN11-0010 [US-1472053]

description:
US-1472053
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: hSTAT5B, replicate 3

description: expression profile of hSTAT5B CD8+ T-cell, replicate 3


title: TT11-2543-AN11-0070 [US-1468488]

description:
US-1468488
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: clopidogrel


title: wild-type, replicate 5

description: expression profile of wt CD8+ T-cell, replicate 5

value: wt


title: hSTAT5B, replicate 1

description: expression profile of hSTAT5B CD8+ T-cell, replicate 1


title: TT11-2543-AN11-0072 [US-1468452]

description:
US-1468452
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: STAT5BN642H, replicate 5

description: expression profile of hSTAT5BN642H CD8+ T-cell, replicate 5


title: wild-type, replicate 4

description: expression profile of wt CD8+ T-cell, replicate 4


title: wild-type, replicate 3

description: expression profile of wt CD8+ T-cell, replicate 3


title: wild-type, replicate 1

description: expression profile of wt CD8+ T-cell, replicate 1


title: TT11-2543-AN11-0036 [US-1468495]

description:
US-1468495
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: nitrofurantoin


title: TT11-2543-AN11-0008 [US-1468469]

description:
US-1468469
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: wild-type, replicate 2

description: expression profile of wt CD8+ T-cell, replicate 2


title: circRNAs_High_Metastasis_S18

city: Guangzhou

first: Yingqin

last: Li

state: Guangdong

address: Room 927, Building 2, No. 651 Road Dong Feng East

institute: Sun Yat-sen University Cancer Center

data_processing:
Low quality which have more than 20% low base quality bases or adapter sequence contamination reads were discarded. Then high quality reads were aligned to the human reference genome (hg19) using BWA mem alignment module.
CircRNA identify and characterize was used the CIRI software based on the following process. First, reads aligning contiguously to the genome without any trimming were discarded. The remaining reads were used for circRNA candidate detection. Next, terminal sequences (anchors) were extracted and re-aligned independently to find unique anchor positions. Anchors that aligned in the reverse orientation (head-to-tail) indicated circRNA splicing (back-splicing).
Counts of reads mapping across an identified back-splice are normalized by number of reads mapping (spliced tags reads per million mapping, TPM), which allows expression comparisons between two circRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

organism: Homo sapiens

source_name: NPC Cell Line, High Metastasis Potential

growth_protocol: Human nasopharyngeal carcinoma cell lines (S18 and S26) were cultured in DMEM (Invitrogen, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, Grand Island, NY, USA). These cell lines were incubated in a humidified chamber with 5% CO2 at 37°C.

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNA from NPC cell lines. RNA was isolated with RNAeasy system, including oncolumn DNase digestion (Qiagen, GmbH, Hilden, Germany). After that,  total RNA was depleted for ribosomal RNAs using the RiboMinus kit, followed by RNase R treatment to enrich circRNAs.
1) Total RNA was treated with the RiboMinus kit (Life Technologies, Thermo Fisher Scientific, Rockford, IL, USA) to remove the ribosomal RNAs; 2) RNAs were incubation with 16 units RNase R (Sigma–Aldrich, St. Louis, MO, USA) for 15 min at 37℃ to deplete linear and enrich circRNAs; 3) The remaining RNAs were fragmented and reverse-transcribed using random primers and reverse transcriptase. Second strand cDNA synthesis was completed using DNA polymerase I and RNase H; 4) The Illumina series KAPA Library Preparation Kit (Kapa Biosystems) was used to perform end repair, dA-tailing, and adapter ligation; 5) The cDNA was enriched by PCR amplification to create the final cDNA libraries.
After RNase R digestion and fragmentation, libraries were prepared and subjected to deep sequencing using the TruSeq library.

tag: cell type

value: nasopharyngeal carcinoma cell line

tag: genotype/variation

value: high metastasis potiential


title: circRNAs_Low_Metastasis_S26

source_name: NPC Cell Line, Low Metastasis Potential

value: low metastasis potiential


title: TT11-2543-AN11-0002 [US-1468474]

description:
US-1468474
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: -control-


title: TT11-2536-AN11-0056 [US-1468430]

description:
US-1468430
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: tacrine


title: TT11-2536-AN11-0054 [US-1468416]

description:
US-1468416
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2543-AN11-0068 [US-1468473]

description:
US-1468473
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: DENV-K135A-IFNARKO

city: Wuhan

first: xi

last: zhou

state: Hubei

address: Luojia Hill

department: State Key Laboratory of Virology, College of Life Sciences

institute: Wuhan University

description: small RNA

data_processing:
Libraries of small RNAs from cell culture were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s instructions. The libraries were sequenced by Illumina HiSeq 2000 at RiboBio. The sequencing reads were mapped to the human genome (release hg19) or mosquito genome (AaeGL5.0) by using Bowite 2.2.5 and the cellular miRNA expression level was determined on the basis of the number of reads that was identical to the annotated miRNA sequences in miRBase version 18, only allowing −2 or +2 nt to be templated by the corresponding genomic sequence at the 3′ end. Viral small RNA (vsRNA) reads which cannot be mapped to human genome were then mapped to DENV2 genome with 100% identity. The subsequent analysis of length and location of these vsRNAs were calculated using in-house Perl scripts. Pairs of complementary 22-nt vsRNAs in each library in different distance categories were computed using principles as previously described (Li et al., 2016; Li et al., 2013).
Genome_build: hg19, AaeGL5.0
Supplementary_files_format_and_content: *_reads.txt: Tab-delimited text files include read sequences and counts.

source_name: Human HEK293T cells

extract_protocol: TruSeq Small RNA Library Preparation Kits (Illumina).

tag: infection

value: Dengue virus serotype 2


title: DENV-K135A-293T

description: small RNA

tag: cell line


title: hSTAT5B, replicate 2

description: expression profile of hSTAT5B CD8+ T-cell, replicate 2

tag: tissue


title: DENV-K135A-NoDice

description: small RNA


title: TT11-2536-AN11-0052 [US-1468396]

description:
US-1468396
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MT4_Rosu

city: Berlin

first: Stefanie

last: Grunwald

address: Lindenberger Weg 80

department: Muscle Research Unit

country: Germany

institute: Charité Medical Faculty - Experimental and Clinical Research Center

description:
Readcounts_alleSamples.txt
Data-file-S2_Transcriptome_DEG_Rosuvastatin.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Pre-processed raw RNA-Seq data were imported into CLC Genomics Workbench (v. 7.5.1) and processed using a standardized workflow. The workflow defines the following steps: (1) trimming sequences (Sequenced reads were trimmed for adaptor sequence and low-quality sequence. ) (2) creating sequence quality check report (3) RNA-Seq analysis with reporting of read tracks, gene expression tracks, transcript expression tracks, fusion tracks, and un-mapped reads. Trimmed reads were aligned to human reference genome (GRCh37) and mapped back to the human transcriptome (v. 19).
Mapped read counts were statistically analyzed using the R packages EdgeR and DESeq for matched sample data. (Lohse et al., 2012) Samples without any and with DMSO treatment were considered as reference group. Gene expression data from simvastatin and rosuvastatin treated samples with FDR <0.05 (Bonferroni) were considered as statistically significantly different from control groups.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include DESeq-analyzed data.

source_name: M vast lat

growth_protocol: Muscle biopsy specimens for myoblast isolation were obtained from M. vast. lat. after IRB approval (EA1/203/08 and EA2/051/10). Experiments were conducted from a total of 25 different primary myoblast cultures (Supplemental Table S1). Isolation was performed as described. (Marg et al., 2012) Contamination of myoblast cultures with fibroblasts was always below 5%. Myoblasts were seeded and grown in skeletal muscle growth medium (ProVitro, Germany) until they reached 70-80% confluence.  Differentiation into myotubes was induced using Opti-MEM (Invitrogen, Germany).

extract_protocol:
RNA was isolated using the NucleoSpin® RNA/Protein Kit (Marcherey-Nagel, Germany). Treated myotubes were washed and either frozen at -80°C or scraped into the NucleoSpin® RNA lysis buffer. RNA quantity and purity were determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, USA) and RNA integrity using Agilent 2100 bioanalyzer (Agilent Technologies, USA). The RIN factor was >8 for all samples.
cDNA libraries for paired-end sequencing were prepared using the TruSeq Stranded mRNA library preparation kit (Illumina, USA). RNA sequencing was performed at Illumina HiSeq platform (Illumina, USA).

treatment_protocol: myoblasts were cultured in 100 mm cell culture plates until 70-80 % confluence was reached. After a washing step with PBS, cell culture medium was switched to Opti-MEM (Invitrogen, Germany) to initiate differentiation of human primary myoblasts into myotubes. All reagents were applied in Opti-MEM for each sample set per myoblast cell line. One sample set consists of untreated, 7 mM DMSO, 5 µM Sim, and 5 µM Rosu samples. Medium was changed every 24 h to refresh medium including substances.

value: Human primary myotubes

tag: source

value: Human Muscle Biopsie Specimen

tag: passage

value: 5 uM Rosu


title: TT11-2543-AN11-0066 [US-1468478]

description:
US-1468478
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

source_name: Liver

tag: study


title: TT11-2543-AN11-0034 [US-1468479]

description:
US-1468479
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: strain


title: MT4_Sim

description:
Readcounts_alleSamples.txt
Data-file-S1_Transcriptome_DEG_Simvastatin.txt

value: 5 uM Sim


title: TT11-2536-AN11-0050 [US-1468482]

description:
US-1468482
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: Sex

value: M


title: TT11-2543-AN11-0040 [US-1468427]

description:
US-1468427
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: agent


title: TT11-2536-AN11-0030 [US-1468453]

description:
US-1468453
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: treatment

value: quinidine


title: MT4_DMSO

value: 7 mM DMSO


title: TT11-2536-AN11-0032 [US-1468461]

description:
US-1468461
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: dose(mkd)


title: TT11-2543-AN11-0006 [US-1468437]

description:
US-1468437
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: days of administration


title: TT11-2536-AN11-0026 [US-1468485]

description:
US-1468485
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: rin


title: MT4_UT

value: untreated


title: TT11-2536-AN11-0028 [US-1468454]

description:
US-1468454
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley


title: TT11-2536-AN11-0008 [US-1468462]

description:
US-1468462
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MT3_Rosu


title: TT11-2536-AN11-0004 [US-1468477]

description:
US-1468477
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MT3_DMSO


title: MT3_Sim


title: TT11-2536-AN11-0006 [US-1468440]

description:
US-1468440
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2543-AN11-0004 [US-1468465]

description:
US-1468465
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2535-AN11-0072 [US-1468459]

description:
US-1468459
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: valsartan


title: MT3_UT


title: DENV-WT-293T

description: small RNA

value: DENV-WT


title: MT2_DMSO


title: MT2_UT


title: TT11-2535-AN11-0068 [US-1468468]

description:
US-1468468
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: TT11-2536-AN11-0002 [US-1468487]

description:
US-1468487
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MT2_Sim


title: MT1_Rosu

description:
Readcounts_alleSamples.txt
Data-file-S2_Transcriptome_DEG_Rosuvastatin.txt


title: TT11-2535-AN11-0006 [US-1468472]

description:
US-1468472
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2535-AN11-0004 [US-1468480]

description:
US-1468480
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2535-AN11-0066 [US-1468476]

description:
US-1468476
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MT1_Sim

description:
Readcounts_alleSamples.txt
Data-file-S1_Transcriptome_DEG_Simvastatin.txt


title: TT11-2535-AN11-0070 [US-1468475]

description:
US-1468475
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MT1_UT


title: dcl4 sRNA

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: total small RNA

data_processing:
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
ShortStack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.

organism: Arabidopsis thaliana

growth_protocol: Plants were grown under 16-hour day conditions at 22ºC in a growth chamber. All tissue is inflorescence (stage 1-12) immature flower buds.

extract_protocol:
Inflorescence small RNA was isolated with TRIzol reagent (Invitrogen) and concentrated using the mirVana microRNA Isolation Kit (Ambion).
For AGO1-IP samples, AGO1 was immunoprecipitated from inflorescence tissue using Agrisera anti-AGO1 primary antibody. RNA was isolated from AGO1-IP or mock-IP samples using TRIzol reagent.
Size-enriched small RNAs were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina).
Multiplexed libraries were sequenced on HiSeq2500 or HiSeq4000.

tag: ecotype background

value: Columbia

tag: molecule subtype

value: small RNA


title: TT11-2531-AN11-0016 [US-1470531]

description:
US-1470531
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: -control-


title: TT11-2531-AN11-0056 [US-1470539]

description:
US-1470539
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: clozapine


title: MT2_Rosu

tag: cell type


title: TT11-2531-AN11-0054 [US-1470449]

description:
US-1470449
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2531-AN11-0010 [US-1470522]

description:
US-1470522
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: WT Nutlin H3K4me2 ChIPseq

city: Albany

first: Morgan

last: Sammons

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

data_processing:
PolyA+ RNAseq raw data were aligned to the human hg19 genome using STAR. Transcript counts were generated using STAR in quant-mode using the UCSC RefSeq transcriptome assembly for hg19. Raw read counts across treatments and biological replicates were processed for differential gene expression using DESeq2.
MPRA RNAseq data were analyzed using fastx-toolkit (hannonlab.cshl.edu) modules fastx-splitter and fastx-collapser.
CCNG1 amplicon ChIP data were analyzed using the fastx-toolkit (hannonlab.cshl.edu) modules fastx-collapser in order to extract count values per unique sequencing read.
Genome_build: hg19 Homo sapiens
Supplementary_files_format_and_content: PolyA+ RNAseq processed data contain raw read counts per RefSeq/UCSC gene in the hg19 assembly. MPRA RNAseq processed files contain raw MPRA expression counts for each barcode found in the original MPRA library across all 6 conditions (HCT116 WT or p53-/- cells treated with either DMSO or Nutlin, plus Genomic DNA barcode counts). CCNG1 amplicon ChIP processed data contains read counts for each sequence found over 2000 times in the genomic DNA input experiment for the Nutlin ChIP and Input conditions.

source_name: Colon carcinoma cells

growth_protocol: HCT116 WT, p53-/-, and ATF3-/- colon carcinoma cells were grown at 37˚C in a humidified, water-jacketed incubator with 5% carbon dioxide. Cells were grown in McCoy's 5A medium supplemented with 10% fetal bovine serum.

extract_protocol: Nuclei were crosslinked with 1% formaldehyde, sonicated to an average DNA fragment size of 500, and chromatin immunoprecipitation experiments were performed using 5ug of the specified antibody. Eluted DNA was used in an Illumina-compatible library prep process using the NEBNext Ultra II DNA Library Kit.

treatment_protocol: Either DMSO or 5 micromolar Nutlin-3A were added to fresh, pre-warmed complete McCoy's 5A medium at t=0 and cells were incubated for 6 hours before harvest.

tag: genotype

value: WT

tag: drug treatment

value: 5 micromolar Nutlin-3A

value: colon carcinoma

tag: antibody

value: Anti H3K4me2 (millipore 07-030)


title: dcl2/dcl4 sRNA

description: total small RNA

source_name: inflorescence (stage 1-12) immature flower buds

tag: genotype/variation

tag: tissue

tag: ecotype


title: rdr1 sRNA

description: total small RNA

value: inflorescence (stage 1-12) immature flower buds


title: TT11-2531-AN11-0050 [US-1470516]

description:
US-1470516
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: study

value: M


title: TT11-2530-AN11-0036 [US-1470483]

description:
US-1470483
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: strain

value: ticrynafen


title: wt Col sRNA - replicate D

description:
total small RNA
Replicate A,B, & C (1,2, & 3) in GSE118705.

value: wt Col


title: p53-null DMSO Replicate 3 RNAseq

extract_protocol:
For HCT116 WT, p53-/-, and ATF3-/- colon carcinoma RNA-seq experiments, total RNA was isolated using standard methods (Omega Biotek). PolyA+ RNA was isolated from 2 micrograms of total RNA using polydT beads supplied with the BioO Stranded RNAseq kit.
Illlumina-compatible RNA-seq libraries were created from fragmented polyA+ RNA using the BioO NextFlex Stranded RNAseq Kit as per manufacturer's instructions. Illumina-compatible, dual barcodes; 75bp single-end reads

value: DMSO

tag: cell line


title: TT11-2530-AN11-0034 [US-1470457]

description:
US-1470457
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

tag: Sex

tag: agent


title: p53-null DMSO Replicate 1 RNAseq


title: WT Nutlin H3K27ac ChIPseq

value: Anti H3K27ac (active motif 39133)


title: TT11-2530-AN11-0008 [US-1470431]

description:
US-1470431
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: treatment

tag: dose(mkd)


title: TT11-2531-AN11-0012 [US-1470513]

description:
US-1470513
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: days of administration

tag: rin


title: WT Nutlin Replicate 3 RNAseq


title: TT11-2531-AN11-0014 [US-1470514]

description:
US-1470514
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: p53-null Nutlin Replicate 3 RNAseq


title: TT11-2535-AN11-0008 [US-1468438]

description:
US-1468438
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2530-AN11-0040 [US-1470477]

description:
US-1470477
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: p53-null Nutlin Replicate 2 RNAseq


title: TT11-2530-AN11-0006 [US-1470448]

description:
US-1470448
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2530-AN11-0038 [US-1470486]

description:
US-1470486
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2530-AN11-0004 [US-1470468]

description:
US-1470468
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: p53-null DMSO Replicate 2 RNAseq


title: TT11-2530-AN11-0002 [US-1470529]

description:
US-1470529
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: p53-null Nutlin Replicate 1 RNAseq


title: WT Nutlin Replicate 2 RNAseq


title: WT Nutlin Replicate 1 RNAseq


title: TT11-2527-AN11-0138 [US-1468486]

description:
US-1468486
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: acetaminophen


title: WT DMSO Replicate 2 RNAseq


title: MPRA Rep3 WT Nutlin reads

data_processing:
Library strategy: massively parallel reporter assay (MPRA)
PolyA+ RNAseq raw data were aligned to the human hg19 genome using STAR. Transcript counts were generated using STAR in quant-mode using the UCSC RefSeq transcriptome assembly for hg19. Raw read counts across treatments and biological replicates were processed for differential gene expression using DESeq2.
MPRA RNAseq data were analyzed using fastx-toolkit (hannonlab.cshl.edu) modules fastx-splitter and fastx-collapser.
CCNG1 amplicon ChIP data were analyzed using the fastx-toolkit (hannonlab.cshl.edu) modules fastx-collapser in order to extract count values per unique sequencing read.
Genome_build: hg19 Homo sapiens
Supplementary_files_format_and_content: PolyA+ RNAseq processed data contain raw read counts per RefSeq/UCSC gene in the hg19 assembly. MPRA RNAseq processed files contain raw MPRA expression counts for each barcode found in the original MPRA library across all 6 conditions (HCT116 WT or p53-/- cells treated with either DMSO or Nutlin, plus Genomic DNA barcode counts). CCNG1 amplicon ChIP processed data contains read counts for each sequence found over 2000 times in the genomic DNA input experiment for the Nutlin ChIP and Input conditions.

extract_protocol: Total RNA was extracted using standard column-based methods with on-column DNAse treatment (Omega BioTek). Total RNA was then treated with an additional round of Dnase (Promega TurboDNAse) before reverse-transcription using primers specific for the 3'UTR of the eGFP construct. 1st strand cDNA product was then used for PCR with barcoded primers for creation of an amplicon covering the MRPA unique molecular identifier sequence. The resulting dsDNA amplicon was then used for DNA library prep using the NEBNext Ultra II DNA Library prep kit.


title: MT1_DMSO

value: Human primary myotubes

tag: source

value: Human Muscle Biopsie Specimen

tag: passage

value: 7 mM DMSO


title: TT11-2527-AN11-0028 [US-1468471]

description:
US-1468471
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water

value: -control-


title: TT11-2527-AN11-0134 [US-1468446]

description:
US-1468446
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2527-AN11-0030 [US-1468490]

description:
US-1468490
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MPRA Rep3 Null Nutlin reads

tag: genotype

tag: cell type


title: TT11-2523-AN11-0072 [US-1472108]

description:
US-1472108
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: caffeine


title: TT11-2523-AN11-0068 [US-1472129]

description:
US-1472129
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MPRA Rep3 WT DMSO reads

value: WT

tag: drug treatment

tag: antibody


title: TT11-2527-AN11-0026 [US-1468456]

description:
US-1468456
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TBT 10 month 8 9M10T

city: Houston

first: Cheryl

middle: L

last: Walker

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

institute: Baylor College of Medicine

description: TBT 10 month 8

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
After trimming samples were aligned to mm10 using HISAT2
Features were quantified using featureCounts and the Gencode gene model
Differential gene expression was inferred after TMM and RUVSeq normalization using edgeR; significance was achieved for fold change exceeding 2x and FDR-adjusted q-value<0.05
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression as read counts for all samples.

source_name: mouse liver

extract_protocol:
RNA was exptracted from frozen liver or adenoma tissue using the Rneasy kit from Qiagen with the Dnase treatment kit amendment.
Sequencing libraries were prepared using the Illumina Truseq stranded total RNA kit using 1000 ng of RNA per sample.

treatment_protocol: Dams were exposed to tributyltin during gestation on lactation in drinking water

value: TBT

tag: age

value: 10 month

tag: tissue

value: liver


title: VEH 10 month 7 7M10V

description: VEH 10 month 7

value: VEH


title: MPRA Rep2 WT Nutlin reads

value: 5 micromolar Nutlin-3A

value: colon carcinoma


title: MPRA Rep3 Null Genomic reads


title: TT11-2523-AN11-0070 [US-1472139]

description:
US-1472139
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

extract_protocol:
Total RNA was purified from frozen liver samples using the MagMAX™ Express Magnetic Particle Processor (Applied Biosystems, # 4400074)
Total RNA samples were converted into cDNA libraries using the TruSeq Stranded mRNA HT Sample Preparation Kit (Illumina, #RS-122-2103)

tag: study

value: M


title: TBT 10 month 8 8M10T

description: TBT 10 month 8


title: TBT 10 month 7 7M10T

description: TBT 10 month 7

source_name: mouse liver adenoma

value: adenoma


title: WT DMSO Replicate 1 RNAseq

value: DMSO


title: MPRA Rep3 Null DMSO reads


title: TT11-2527-AN11-0136 [US-1468436]

description:
US-1468436
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: strain

value: Sprague Dawley

value: acetaminophen


title: TT11-2523-AN11-0066 [US-1472152]

description:
US-1472152
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MPRA Rep2 WT Genomic reads

tag: cell line


title: MPRA Rep3 WT Genomic reads


title: WT DMSO Replicate 3 RNAseq


title: VEH 10 month 6 6M10V

description: VEH 10 month 6


title: VEH 5 month 6 6M5V

description: VEH 5 month 6

value: 5 month


title: TT11-2523-AN11-0006 [US-1472144]

description:
US-1472144
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: Sex


title: TBT 5 month 6 6M5T

description: TBT 5 month 6


title: TBT 5 month 5 5M5T

description: TBT 5 month 5


title: VEH 5 month 5 5M5V

description: VEH 5 month 5


title: MPRA Rep2 WT DMSO reads


title: MPRA Rep2 Null Nutlin reads


title: TT11-2523-AN11-0004 [US-1472124]

description:
US-1472124
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: agent


title: TBT 10 month 5 5M10T

description: TBT 10 month 5

tag: treatment


title: TBT 10 month 6 6M10T

description: TBT 10 month 6


title: TT11-2523-AN11-0002 [US-1472162]

description:
US-1472162
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

tag: dose(mkd)


title: MPRA Rep2 Null Genomic reads


title: VEH 5 month 4 4M5V

description: VEH 5 month 4


title: TBT 5 month 4 4M5T

description: TBT 5 month 4


title: TT11-2515-AN11-0070 [US-1470470]

description:
US-1470470
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: diclofenac

tag: days of administration


title: MPRA Rep2 Null DMSO reads


title: TBT 10 month 4 4M10T

description: TBT 10 month 4


title: VEH 5 month 3 3M5V

description: VEH 5 month 3


title: VEH 10 month 4 4M10V

description: VEH 10 month 4


title: TBT 5 month 3 3M5T

description: TBT 5 month 3


title: TBT 10 month 3 3M10T

description: TBT 10 month 3


title: TT11-2523-AN11-0008 [US-1472092]

description:
US-1472092
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water

tag: rin


title: MPRA Rep1 WT Nutlin reads


title: TT11-2515-AN11-0068 [US-1470527]

description:
US-1470527
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: MPRA Rep1 WT Genomic reads


title: VEH 5 month 2 2M5V

description: VEH 5 month 2


title: VEH 10 month 5 5M10V

description: VEH 10 month 5


title: MPRA Rep1 WT DMSO reads


title: TBT 5 month 2 2M5T

description: TBT 5 month 2


title: MPRA Rep1 Null Nutlin reads


title: VEH 10 month 2 2M10V

description: VEH 10 month 2


title: TT11-2515-AN11-0016 [US-1470441]

description:
US-1470441
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: -control-


title: VEH 5 month 1 1M5V

description: VEH 5 month 1


title: MPRA Rep1 Null Genomic reads


title: TT11-2515-AN11-0012 [US-1470515]

description:
US-1470515
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TBT 10 month 2 2M10T

description: TBT 10 month 2


title: TBT 10 month 1 1M10T

description: TBT 10 month 1


title: MPRA Rep1 Null DMSO reads


title: TT11-2515-AN11-0014 [US-1470535]

description:
US-1470535
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: p53RE CCNG1 ChIP

extract_protocol: Treated cells were crosslinked using 1% methanol-free formaldehyde for 10minutes at room temperature. Isolated nuclei were then sonicated to create sheared DNA of an average size of 600-800bp. DNA:protein complexes were then used for immunoprecipitation with anti-p53 (DO1) antibodies. Immunoprecipitated DNA was then used for multiple PCR reactions using specific barcoded primers to amplify a 150bp region of the CCNG1 enhancer. The resulting DNA product was used to construct an Illumina-compatible DNA sequencing library using the NEBNext Ultra II DNA Library Kit.

value: Anti-p53 (clone DO1)


title: VEH 10 month 1 1M10V

description: VEH 10 month 1


title: TT11-2512-AN11-0070 [US-1468448]

description:
US-1468448
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: propranolol


title: TT11-2515-AN11-0010 [US-1470526]

description:
US-1470526
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: wild-type, replicate 1

description:
DNA methylation profile of wt CD8+ T cells, replicate 1
wt_2

data_processing:
Sequences were trimmed for adapters using Trimmomatic with ILLUMINACLIP settings “:2:40:7 SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18”
Reads were aligned to the GRCm38 (mm10) assembly of the mouse genome, using BSMAP in its RRBS mapping mode
DNA methylation levels for individual CpGs were calculated using custom Python scripts
Genome_build: mm10
Supplementary_files_format_and_content: DNA methylation calls (text file, BED format: chrom, start, end, methylated/total-reads, score, strand)

source_name: Lymph node

extract_protocol:
Genomic DNA from purified CD8+ T-cells was isolated using AllPrep DNA/RNA mini kit (Qiagen) and subsequently subjected to RRBS and analysis.
RRBS was carried out as described earlier (Tomazou et al. Cell Rep, 2015).

value: CD8+ T-cells

value: wt


title: TT11-2512-AN11-0072 [US-1468442]

description:
US-1468442
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: hSTAT5BN642H, replicate 2

description:
DNA methylation profile of hSTAT5B-N642 mutant CD8+ T cells, replicate 2
STAT5B_N_H_50_2

value: hSTAT5B N642H +/T


title: TBT 10 month 10 10M10T

description: TBT 10 month 10

value: TBT

value: 10 month

value: liver


title: TBT 10 month 11 11M10T

description: TBT 10 month 11


title: TT11-2515-AN11-0066 [US-1470511]

description:
US-1470511
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: hSTAT5BN642H, replicate 1

description:
DNA methylation profile of hSTAT5B-N642 mutant CD8+ T cells, replicate 1
STAT5B_N_H_50_1


title: wild-type, replicate 2

description:
DNA methylation profile of wt CD8+ T cells, replicate 2
wt_95


title: TT11-2512-AN11-0068 [US-1468444]

description:
US-1468444
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: R2 CCNG1 ChIP-seq

value: WT

value: colon carcinoma


title: hSTAT5B, replicate 2

description:
DNA methylation profile of hSTAT5B CD8+ T cells, replicate 2
STAT5B_263

value: hSTAT5B +/T


title: TT11-2512-AN11-0040 [US-1420958]

description:
US-1420958
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Sprague Dawley

value: cimetidine


title: hSTAT5B, replicate 1

description:
DNA methylation profile of hSTAT5B CD8+ T cells, replicate 1
STAT5B_262


title: TBT 10 month 12 12M10T

description: TBT 10 month 12

value: adenoma


title: Control CCNG1 ChIP-seq


title: L2 CCNG1 ChIP-seq


title: TT16-9022-AN16-8998 [US-10017349]

description:
US-10017349
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: Han Wistar

value: 99percent Corn Oil, 1percent Acetone

value: TCDD


title: TT11-2512-AN11-0036 [US-1420973]

description:
US-1420973
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.5percent (w/v) Methylcellulose in Deionized Water


title: TT16-9022-AN16-8995 [US-10017346]

description:
US-10017346
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: ATF3-null Nutlin Replicate 2 RNAseq

value: 5 micromolar Nutlin-3A


title: TT11-2512-AN11-0034 [US-1420947]

description:
US-1420947
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT16-9022-AN16-8996 [US-10017347]

description:
US-10017347
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT16-9022-AN16-8997 [US-10017348]

description:
US-10017348
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT16-9022-AN16-8941 [US-10017344]

description:
US-10017344
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: -control-


title: ATF3-null Nutlin Replicate 1 RNAseq


title: ATF3-null DMSO Replicate 3 RNAseq

value: DMSO


title: TT16-9022-AN16-8940 [US-10017343]

description:
US-10017343
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2572-AN13-0014 [US-10017314]

description:
US-10017314
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: 0.9percent (w/v) Sodium Chloride for Injection

value: pyrazole


title: ATF3-null DMSO Replicate 2 RNAseq


title: TT11-2512-AN11-0006 [US-1468464]

description:
US-1468464
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT11-2512-AN11-0008 [US-1468434]

description:
US-1468434
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz


title: TT13-2572-AN13-0013 [US-10017313]

description:
US-10017313
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: F


title: TT13-2572-AN13-0012 [US-10017312]

description:
US-10017312
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz

value: M


title: TT11-2512-AN11-0038 [US-1421086]

description:
US-1421086
Rx-TGx.Count.txt.gz
Rx-TGx.FPKM.txt.gz