title: VATTR_rep2a1773


title: VATTR_rep2a1772

status: Public on May 26 2018

type: SRA

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

molecule: total RNA

organism: Mus musculus

source_name: VAT (epididymal)

growth_protocol: Live cells were sorted by flow cytometry from the spleen and visceral adipose tissue (epididymal fat) of mice (carrying a Foxp3 reporter gene).

extract_protocol:
Spleen were mechanically dissociated and visceral adipose tissue were digested with collagenase/dispase to single cell suspensions. Tregs cells were sorted by flow cytometry as DAPI- TCRb+ CD4+ GFP+ cells. Transgenic cells were sorted as TRAV2+ TRBV4+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

tag: library name

tag: sample type

tag: strain

value: B6 Foxp3-Ires-Gfp

tag: Sex

value: male

tag: age (months)

value: notTg

tag: tissue

value: VAT (epididymal)

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: VATTR_rep2a1771


title: VATTR_rep2a1768


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title: VATTR_rep2a591


title: VATTR_rep2a595


title: VATTR_rep2a592


title: VATTR_rep2a628


title: VATTR_rep2a589


title: VATTR_rep2a583


title: VATTR_rep2a588


title: VATTR_rep2a587


title: VATTR_rep2a582


title: VATTR_rep2a586


title: VATTR_rep2a625


title: VATTR_rep2a580


title: VATTR_rep2a581


title: VATTR_rep2a576


title: VATTR_rep2a573


title: VATTR_rep2a579


title: VATTR_rep2a569


title: VATTR_rep2a567


title: VATTR_rep2a566


title: VATTR_rep2a568


title: VATTR_rep2a564


title: VATTR_rep2a562


title: VATTR_rep2a560


title: VATTR_rep2a561


title: VATTR_rep2a557


title: VATTR_rep2a558


title: VATTR_rep2a556


title: VATTR_rep2a554


title: VATTR_rep2a552


title: VATTR_rep2a550


title: VATTR_rep2a549


title: VATTR_rep2a534


title: VATTR_rep2a545


title: VATTR_rep2a533


title: VATTR_rep2a531


title: VATTR_rep2a547


title: VATTR_rep2a529


title: VATTR_rep2a530


title: VATTR_rep2a565


title: VATTR_rep2a570


title: VATTR_rep2a525


title: VATTR_rep2a522


title: VATTR_rep2a520


title: VATTR_rep2a514


title: VATTR_rep2a515


title: VATTR_rep2a563


title: VATTR_rep2a510


title: VATTR_rep2a513


title: VATTR_rep2a509


title: VATTR_rep2a507


title: VATTR_rep2a502


title: VATTR_rep2a506


title: VATTR_rep2a495


title: VATTR_rep2a497


title: VATTR_rep2a493


title: VATTR_rep2a492


title: VATTR_rep2a538


title: VATTR_rep2a535


title: VATTR_rep2a491


title: VATTR_rep2a483


title: VATTR_rep2a484


title: VATTR_rep2a482


title: VATTR_rep2a486


title: VATTR_rep2a481


title: VATTR_rep2a518


title: VATTR_rep2a478


title: VATTR_rep2a720


title: VATTR_rep2a489


title: VATTR_rep2a475


title: VATTR_rep2a472


title: VATTR_rep2a476


title: VATTR_rep2a469


title: VATTR_rep2a477


title: VATTR_rep2a473


title: VATTR_rep2a496


title: VATTR_rep2a463


title: VATTR_rep2a466


title: VATTR_rep2a462


title: VATTR_rep2a448


title: VATTR_rep2a451


title: VATTR_rep2a449


title: VATTR_rep2a454


title: VATTR_rep2a455


title: VATTR_rep2a453


title: VATTR_rep2a447


title: VATTR_rep2a437


title: VATTR_rep2a443


title: VATTR_rep2a439


title: VATTR_rep2a474


title: VATTR_rep2a436


title: VATTR_rep2a460


title: VATTR_rep2a440


title: VATTR_rep2a430


title: VATTR_rep2a433


title: VATTR_rep2a427


title: VATTR_rep2a428


title: VATTR_rep2a464


title: VATTR_rep2a424


title: VATTR_rep2a421


title: VATTR_rep2a425


title: VATTR_rep2a420


title: VATTR_rep2a418


title: VATTR_rep2a458


title: VATTR_rep2a417


title: VATTR_rep2a415


title: VATTR_rep2a413


title: VATTR_rep2a412


title: VATTR_rep2a411


title: VATTR_rep2a410


title: VATTR_rep2a445


title: VATTR_rep2a405


title: VATTR_rep2a399


title: VATTR_rep2a403


title: VATTR_rep2a396


title: VATTR_rep2a385


title: VATTR_rep2a393


title: VATTR_rep2a386


title: VATTR_rep2a394


title: VATTR_rep2a384


title: VATTR_rep2a382


title: VATTR_rep2a369


title: VATTR_rep2a376


title: VATTR_rep2a367


title: VATTR_rep2a366


title: VATTR_rep2a378


title: VATTR_rep2a371


title: VATTR_rep2a365


title: VATTR_rep2a388


title: VATTR_rep2a381


title: VATTR_rep2a370


title: VATTR_rep2a374


title: VATTR_rep2a364


title: VATTR_rep2a359


title: VATTR_rep2a358


title: VATTR_rep2a363


title: VATTR_rep2a395


title: VATTR_rep2a357


title: VATTR_rep2a354


title: VATTR_rep2a355


title: VATTR_rep2a351


title: VATTR_rep2a352


title: VATTR_rep2a349


title: VATTR_rep2a346


title: VATTR_rep2a345


title: VATTR_rep2a350


title: VATTR_rep2a348


title: VATTR_rep2a343


title: VATTR_rep2a339


title: VATTR_rep2a333


title: VATTR_rep2a332


title: VATTR_rep2a330


title: VATTR_rep2a335


title: VATTR_rep2a334


title: VATTR_rep2a328


title: VATTR_rep2a326


title: VATTR_rep2a321


title: VATTR_rep2a331


title: VATTR_rep2a322


title: VATTR_rep2a323


title: VATTR_rep2a360


title: VATTR_rep2a320


title: VATTR_rep2a319


title: VATTR_rep2a314


title: VATTR_rep2a309


title: VATTR_rep2a312


title: VATTR_rep2a311


title: VATTR_rep2a307


title: VATTR_rep2a344


title: VATTR_rep2a301


title: VATTR_rep2a305


title: VATTR_rep2a297


title: VATTR_rep2a341


title: VATTR_rep2a294


title: VATTR_rep2a296


title: VATTR_rep2a325


title: VATTR_rep2a289


title: VATTR_rep2a280


title: VATTR_rep2a277


title: VATTR_rep2a273


title: VATTR_rep2a261


title: VATTR_rep2a274


title: VATTR_rep2a262


title: VATTR_rep2a258


title: VATTR_rep2a256


title: VATTR_rep2a257


title: VATTR_rep2a276


title: VATTR_rep2a253


title: VATTR_rep2a252


title: VATTR_rep2a249


title: VATTR_rep2a248


title: VATTR_rep2a246


title: VATTR_rep2a240


title: VATTR_rep2a241


title: VATTR_rep2a245


title: VATTR_rep2a288


title: VATTR_rep2a236


title: VATTR_rep2a233


title: VATTR_rep2a238


title: VATTR_rep2a232


title: VATTR_rep2a229


title: VATTR_rep2a230


title: VATTR_rep2a227


title: VATTR_rep2a226


title: VATTR_rep2a225


title: VATTR_rep2a218


title: VATTR_rep2a219


title: VATTR_rep2a251


title: VATTR_rep2a215


title: VATTR_rep2a221


title: VATTR_rep2a209


title: VATTR_rep2a286


title: VATTR_rep2a211


title: VATTR_rep2a204


title: VATTR_rep2a206


title: VATTR_rep2a202


title: VATTR_rep2a199


title: VATTR_rep2a207


title: VATTR_rep2a198


title: VATTR_rep2a195


title: VATTR_rep2a192


title: VATTR_rep2a197


title: VATTR_rep2a186


title: VATTR_rep2a191


title: VATTR_rep2a189


title: VATTR_rep2a194


title: VATTR_rep2a183


title: VATTR_rep2a222


title: VATTR_rep2a173


title: VATTR_rep2a176


title: VATTR_rep2a175


title: VATTR_rep2a217


title: VATTR_rep2a214


title: VATTR_rep2a169


title: VATTR_rep2a172


title: VATTR_rep2a168


title: VATTR_rep2a160


title: VATTR_rep2a162


title: VATTR_rep2a158


title: VATTR_rep2a155


title: VATTR_rep2a156


title: VATTR_rep2a150


title: VATTR_rep2a154


title: VATTR_rep2a153


title: VATTR_rep2a144


title: VATTR_rep2a145


title: VATTR_rep2a147


title: VATTR_rep2a141


title: VATTR_rep2a142


title: VATTR_rep2a136


title: VATTR_rep2a135


title: VATTR_rep2a138


title: VATTR_rep2a178


title: VATTR_rep2a133


title: VATTR_rep2a137


title: VATTR_rep2a128


title: VATTR_rep2a132


title: VATTR_rep2a121


title: VATTR_rep2a122


title: VATTR_rep2a126


title: VATTR_rep2a131


title: VATTR_rep2a119


title: VATTR_rep2a123


title: VATTR_rep2a118


title: VATTR_rep2a116


title: VATTR_rep2a115


title: VATTR_rep2a117


title: VATTR_rep2a114


title: VATTR_rep2a143


title: VATTR_rep2a110


title: VATTR_rep2a111


title: VATTR_rep2a107


title: VATTR_rep2a105


title: VATTR_rep2a103


title: VATTR_rep2a139


title: VATTR_rep2a104


title: VATTR_rep2a102


title: VATTR_rep2a101


title: VATTR_rep2a134


title: VATTR_rep2a99


title: VATTR_rep2a97


title: VATTR_rep2a93


title: VATTR_rep2a91


title: VATTR_rep2a94


title: VATTR_rep2a92


title: VATTR_rep2a84


title: VATTR_rep2a87


title: VATTR_rep2a88


title: VATTR_rep2a86


title: VATTR_rep2a79


title: VATTR_rep2a78


title: VATTR_rep2a75


title: VATTR_rep2a73


title: VATTR_rep2a108


title: VATTR_rep2a72


title: VATTR_rep2a71


title: VATTR_rep2a112


title: VATTR_rep2a68


title: VATTR_rep2a67


title: VATTR_rep2a66


title: VATTR_rep2a65


title: VATTR_rep2a64


title: VATTR_rep2a63


title: VATTR_rep2a46


title: VATTR_rep2a60


title: VATTR_rep2a44


title: VATTR_rep2a58


title: VATTR_rep2a52


title: VATTR_rep2a48


title: VATTR_rep2a42


title: VATTR_rep2a38


title: VATTR_rep2a45


title: VATTR_rep2a40


title: VATTR_rep2a80


title: VATTR_rep2a30


title: VATTR_rep2a32


title: VATTR_rep2a33


title: VATTR_rep2a31


title: VATTR_rep2a29


title: VATTR_rep2a19


title: VATTR_rep2a20


title: VATTR_rep2a22


title: VATTR_rep2a11


title: VATTR_rep2a10


title: VATTR_rep2a21


title: VATTR_rep2a7


title: VATTR_rep2a24


title: VATTR_rep2a23


title: VATTR_rep2a5


title: VATTR_rep2a4


title: VATTR_rep2a43


title: VATTR_rep2a3


title: VATTR_rep2a6


title: SpVATCtrlTG_rep1a2408

source_name: spleen

value: B6 Foxp3-Ires-Gfp vTreg53 TCR-tg

value: Tg

value: spleen


title: SpVATCtrlTG_rep1a2398


title: SpVATCtrlTG_rep1a2404


title: SpVATCtrlTG_rep1a2397


title: SpVATCtrlTG_rep1a2394


title: SpVATCtrlTG_rep1a2392


title: SpVATCtrlTG_rep1a2393


title: SpVATCtrlTG_rep1a2391


title: SpVATCtrlTG_rep1a2390


title: VATTR_rep2a26


title: SpVATCtrlTG_rep1a2389


title: SpVATCtrlTG_rep1a2402


title: SpVATCtrlTG_rep1a2386


title: SpVATCtrlTG_rep1a2378


title: SpVATCtrlTG_rep1a2377


title: SpVATCtrlTG_rep1a2385


title: SpVATCtrlTG_rep1a2368


title: SpVATCtrlTG_rep1a2371


title: SpVATCtrlTG_rep1a2374


title: SpVATCtrlTG_rep1a2373


title: SpVATCtrlTG_rep1a2376


title: SpVATCtrlTG_rep1a2355


title: SpVATCtrlTG_rep1a2349


title: SpVATCtrlTG_rep1a2347


title: SpVATCtrlTG_rep1a2370


title: SpVATCtrlTG_rep1a2360


title: SpVATCtrlTG_rep1a2362


title: SpVATCtrlTG_rep1a2344


title: SpVATCtrlTG_rep1a2358


title: SpVATCtrlTG_rep1a2375


title: SpVATCtrlTG_rep1a2361


title: SpVATCtrlTG_rep1a2342


title: SpVATCtrlTG_rep1a2341


title: SpVATCtrlTG_rep1a2340


title: SpVATCtrlTG_rep1a2330


title: SpVATCtrlTG_rep1a2328


title: SpVATCtrlTG_rep1a2325


title: SpVATCtrlTG_rep1a2322


title: SpVATCtrlTG_rep1a2319


title: SpVATCtrlTG_rep1a2318


title: SpVATCtrlTG_rep1a2367


title: SpVATCtrlTG_rep1a2314


title: SpVATCtrlTG_rep1a2315


title: SpVATCtrlTG_rep1a2313


title: SpVATCtrlTG_rep1a2312


title: SpVATCtrlTG_rep1a2309


title: SpVATCtrlTG_rep1a2345


title: SpVATCtrlTG_rep1a2303


title: SpVATCtrlTG_rep1a2308


title: SpVATCtrlTG_rep1a2311


title: SpVATCtrlTG_rep1a2306


title: SpVATCtrlTG_rep1a2304


title: SpVATCtrlTG_rep1a2339


title: SpVATCtrlTG_rep1a2296


title: SpVATCtrlTG_rep1a2294


title: SpVATCtrlTG_rep1a2291


title: SpVATCtrlTG_rep1a2321


title: SpVATCtrlTG_rep1a2343


title: SpVATCtrlTG_rep1a2320


title: SpVATCtrlTG_rep1a2298


title: SpVATCtrlTG_rep1a2286


title: SpVATCtrlTG_rep1a2284


title: SpVATCtrlTG_rep1a2275


title: SpVATCtrlTG_rep1a2290


title: SpVATCtrlTG_rep1a2273


title: SpVATCtrlTG_rep1a2267


title: SpVATCtrlTG_rep1a2283


title: SpVATCtrlTG_rep1a2280


title: SpVATCtrlTG_rep1a2265


title: SpVATCtrlTG_rep1a2263


title: SpVATCtrlTG_rep1a2302


title: SpVATCtrlTG_rep1a2262


title: SpVATCtrlTG_rep1a2261


title: SpVATCtrlTG_rep1a2260


title: SpVATCtrlTG_rep1a2292


title: SpVATCtrlTG_rep1a2256


title: SpVATCtrlTG_rep1a2250


title: SpVATCtrlTG_rep1a2287


title: SpVATCtrlTG_rep1a2255


title: SpVATCtrlTG_rep1a2248


title: SpVATCtrlTG_rep1a2254


title: SpVATCtrlTG_rep1a2238


title: SpVATCtrlTG_rep1a2241


title: SpVATCtrlTG_rep1a2240


title: SpVATCtrlTG_rep1a2247


title: SpVATCtrlTG_rep1a2236


title: SpVATCtrlTG_rep1a2243


title: SpVATCtrlTG_rep1a2229


title: SpVATCtrlTG_rep1a2242


title: SpVATCtrlTG_rep1a2227


title: SpVATCtrlTG_rep1a2226


title: SpVATCtrlTG_rep1a2225


title: SpVATCtrlTG_rep1a2264


title: SpVATCtrlTG_rep1a2224


title: SpVATCtrlTG_rep1a2221


title: SpVATCtrlTG_rep1a2220


title: SpVATCtrlTG_rep1a2222


title: SpVATCtrlTG_rep1a2258


title: SpVATCtrlTG_rep1a2213


title: SpVATCtrlTG_rep1a2218


title: SpVATCtrlTG_rep1a2219


title: SpVATCtrlTG_rep1a2212


title: SpVATCtrlTG_rep1a2214


title: SpVATCtrlTG_rep1a2208


title: SpVATCtrlTG_rep1a2207


title: SpVATCtrlTG_rep1a2206


title: SpVATCtrlTG_rep1a2215


title: SpVATCtrlTG_rep1a2204


title: SpVATCtrlTG_rep1a2244


title: SpVATCtrlTG_rep1a2186


title: SpVATCtrlTG_rep1a2203


title: SpVATCtrlTG_rep1a2205


title: SpVATCtrlTG_rep1a2188


title: SpVATCtrlTG_rep1a2181


title: SpVATCtrlTG_rep1a2202


title: SpVATCtrlTG_rep1a2199


title: SpVATCtrlTG_rep1a2178


title: SpVATCtrlTG_rep1a2187


title: SpVATCtrlTG_rep1a2195


title: SpVATCtrlTG_rep1a2177


title: SpVATCtrlTG_rep1a2166


title: SpVATCtrlTG_rep1a2174


title: SpVATCtrlTG_rep1a2193


title: SpVATCtrlTG_rep1a2175


title: SpVATCtrlTG_rep1a2169


title: SpVATCtrlTG_rep1a2148


title: SpVATCtrlTG_rep1a2159


title: SpVATCtrlTG_rep1a2162


title: SpVATCtrlTG_rep1a2161


title: SpVATCtrlTG_rep1a2146


title: SpVATCtrlTG_rep1a2149


title: SpVATCtrlTG_rep1a2153


title: SpVATCtrlTG_rep1a2142


title: SpVATCtrlTG_rep1a2209


title: SpVATCtrlTG_rep1a2160


title: SpVATCtrlTG_rep1a2163


title: SpVATCtrlTG_rep1a2156


title: SpVATCtrlTG_rep1a2131


title: SpVATCtrlTG_rep1a2128


title: SpVATCtrlTG_rep1a2145


title: SpVATCtrlTG_rep1a2141


title: SpVATCtrlTG_rep1a2138


title: SpVATCtrlTG_rep1a2139


title: SpVATCtrlTG_rep1a2126


title: SpVATCtrlTG_rep1a2132


title: SpVATCtrlTG_rep1a2119


title: SpVATCtrlTG_rep1a2167


title: SpVATCtrlTG_rep1a2125


title: SpVATCtrlTG_rep1a2122


title: SpVATCtrlTG_rep1a2121


title: SpVATCtrlTG_rep1a2120


title: SpVATCtrlTG_rep1a2127


title: SpVATCtrlTG_rep1a2118


title: SpVATCtrlTG_rep1a2117


title: SpVATCtrlTG_rep1a2093


title: SpVATCtrlTG_rep1a2097


title: SpVATCtrlTG_rep1a2104


title: SpVATCtrlTG_rep1a2088


title: SpVATCtrlTG_rep1a2099


title: SpVATCtrlTG_rep1a2114


title: SpVATCtrlTG_rep1a2091


title: SpVATCtrlTG_rep1a2101


title: SpVATCtrlTG_rep1a2113


title: SpVATCtrlTG_rep1a2077


title: SpVATCtrlTG_rep1a2074


title: SpVATCtrlTG_rep1a2110


title: SpVATCtrlTG_rep1a2111


title: SpVATCtrlTG_rep1a2100


title: SpVATCtrlTG_rep1a2115


title: SpVATCtrlTG_rep1a2106


title: SpVATCtrlTG_rep1a2124


title: SpVATCtrlTG_rep1a2087


title: SpVATCtrlTG_rep1a2071


title: SpVATCtrlTG_rep1a2070


title: SpVATCtrlTG_rep1a2137


title: SpVATCtrlTG_rep1a2064


title: SpVATCtrlTG_rep1a2075


title: SpVATCtrlTG_rep1a2073


title: SpVATCtrlTG_rep1a2072


title: SpVATCtrlTG_rep1a2066


title: SpVATCtrlTG_rep1a2082


title: SpVATCtrlTG_rep1a2054


title: SpVATCtrlTG_rep1a2036


title: SpVATCtrlTG_rep1a2080


title: SpVATCtrlTG_rep1a2045


title: SpVATCtrlTG_rep1a2061


title: SpVATCtrlTG_rep1a2035


title: SpVATCtrlTG_rep1a2033


title: SpVATCtrlTG_rep1a2039


title: SpVATCtrlTG_rep1a2024


title: SpVATCtrlTG_rep1a2041


title: SpVATCtrlTG_rep1a2040


title: SpVATCtrlTG_rep1a2060


title: SpVATCtrlTG_rep1a2032


title: SpVATCtrlTG_rep1a2037


title: SpVATCtrlTG_rep1a2031


title: SpVATCtrlTG_rep1a2030


title: SpVATCtrlTG_rep1a2016


title: SpVATCtrlTG_rep1a2056


title: SpVATCtrlTG_rep1a2044


title: SpVATCtrlTG_rep1a2023


title: SpVATCtrlTG_rep1a2013


title: SpVATCtrlTG_rep1a2008


title: SpVATCtrlTG_rep1a2015


title: SpVATCtrlTG_rep1a2011


title: SpVATCtrlTG_rep1a2007


title: SpVATCtrlTG_rep1a2062


title: SpVATCtrlTG_rep1a2009


title: SpVATCtrlTG_rep1a2025


title: SpVATCtrlTG_rep1a2000


title: SpVATCtrlTG_rep1a2002


title: SpVATCtrlTG_rep1a2003


title: SpVATCtrlTG_rep1a2005


title: SpVATCtrlTG_rep1a1998


title: SpVATCtrlTG_rep1a1993


title: SpVATCtrlTG_rep1a1995


title: SpVATCtrlTG_rep1a2019


title: SpVATCtrlTG_rep1a1997


title: SpVATCtrlTG_rep1a1984


title: SpVATCtrlTG_rep1a1986


title: SpVATCtrlTG_rep1a1980


title: SpVATCtrlTG_rep1a1988


title: SpVATCtrlTG_rep1a1991


title: SpVATCtrlTG_rep1a1987


title: SpVATCtrlTG_rep1a1977


title: SpVATCtrlTG_rep1a1981


title: SpVATCtrlTG_rep1a1979


title: SpVATCtrlTG_rep1a1973


title: SpVATCtrlTG_rep1a1976


title: SpVATCtrlTG_rep1a1983


title: SpVATCtrlTG_rep1a1975


title: SpVATCtrlTG_rep1a1970


title: SpVATCtrlTG_rep1a2012


title: SpVATCtrlTG_rep1a1969


title: SpVATCtrlTG_rep1a1966


title: SpVATCtrlTG_rep1a1968


title: SpVATCtrlTG_rep1a1965


title: SpVATCtrlTG_rep1a1972


title: SpVATCtrlTG_rep1a1967


title: SpVATCtrlTG_rep1a1959


title: SpVATCtrlTG_rep1a1960


title: SpVATCtrlTG_rep1a1958


title: SpVATCtrlTG_rep1a1957


title: SpVATCtrlTG_rep1a1956


title: SpVATCtrlTG_rep1a1952


title: SpVATCtrlTG_rep1a1954


title: SpVATCtrlTG_rep1a1948


title: SpVATCtrlTG_rep1a1944


title: SpVATCtrlTG_rep1a1947


title: SpVATCtrlTG_rep1a1945


title: SpVATCtrlTG_rep1a1943


title: SpVATCtrlTG_rep1a1938


title: SpVATCtrlTG_rep1a1935


title: SpVATCtrlTG_rep1a1933


title: SpVATCtrlTG_rep1a1931


title: SpVATCtrlTG_rep1a1930


title: SpVATCtrlTG_rep1a1936


title: SpVATCtrlTG_rep1a1928


title: SpVATCtrlTG_rep1a1929


title: SpVATCtrlTG_rep1a1926


title: SpVATCtrlTG_rep1a1964


title: SpVATCtrlTG_rep1a1925


title: SpVATCtrlTG_rep1a1924


title: SpVATCtrlTG_rep1a1920


title: SpVATCtrlTG_rep1a1963


title: SpVATCtrlTG_rep1a1921


title: SpVATCtrlTG_rep1a1919


title: SpVATCtrlTG_rep1a1918


title: SpVATCtrlTG_rep1a1909


title: SpVATCtrlTG_rep1a1949


title: SpVATCtrlTG_rep1a1916


title: SpVATCtrlTG_rep1a1908


title: SpVATCtrlTG_rep1a1906


title: SpVATCtrlTG_rep1a1905


title: SpVATCtrlTG_rep1a1939


title: SpVATCtrlTG_rep1a1901


title: SpVATCtrlTG_rep1a1904


title: SpVATCtrlTG_rep1a1900


title: SpVATCtrlTG_rep1a1897


title: SpVATCtrlTG_rep1a1896


title: SpVATCtrlTG_rep1a1894


title: SpVATCtrlTG_rep1a1892


title: SpVATCtrlTG_rep1a1891


title: SpVATCtrlTG_rep1a1890


title: SpVATCtrlTG_rep1a1886


title: SpVATCtrlTG_rep1a1885


title: SpVATCtrlTG_rep1a1887


title: SpVATCtrlTG_rep1a1881


title: SpVATCtrlTG_rep1a1878


title: SpVATCtrlTG_rep1a1877


title: SpVATCtrlTG_rep1a1868


title: SpVATCtrlTG_rep1a1863


title: SpVATCtrlTG_rep1a1876


title: SpVATCtrlTG_rep1a1864


title: SpVATCtrlTG_rep1a1914


title: SpVATCtrlTG_rep1a1866


title: SpVATCtrlTG_rep1a1862


title: SpVATCtrlTG_rep1a1860


title: SpVATCtrlTG_rep1a1848


title: SpVATCtrlTG_rep1a1854


title: SpVATCtrlTG_rep1a1895


title: SpVATCtrlTG_rep1a1846


title: SpVATCtrlTG_rep1a1849


title: SpVATCtrlTG_rep1a1842


title: SpVATCtrlTG_rep1a1847


title: SpVATCtrlTG_rep1a1843


title: SpVATCtrlTG_rep1a1841


title: SpVATCtrlTG_rep1a1833


title: SpVATCtrlTG_rep1a1840


title: SpVATCtrlTG_rep1a1825


title: SpVATCtrlTG_rep1a1827


title: SpVATCtrlTG_rep1a1824


title: SpVATCtrlTG_rep1a1839


title: SpVATCtrlTG_rep1a1828


title: SpVATCtrlTG_rep1a1832


title: SpVATCtrlTG_rep1a1871


title: SpVATCtrlTG_rep1a1823


title: SpVATCtrlTG_rep1a1822


title: SpVATCtrlTG_rep1a1819


title: SpVATCtrlTG_rep1a1820


title: SpVATCtrlTG_rep1a1818


title: SpVATCtrlTG_rep1a1817


title: SpVATCtrlTG_rep1a1816


title: SpVATCtrlTG_rep1a1815


title: SpVATCtrlTG_rep1a1811


title: SpVATCtrlTG_rep1a1855


title: SpVATCtrlTG_rep1a1809


title: SpVATCtrlTG_rep1a1804


title: SpVATCtrlTG_rep1a1800


title: SpVATCtrlTG_rep1a1796


title: SpVATCtrlTG_rep1a1795


title: SpVATCtrlTG_rep1a1799


title: SpVATCtrlTG_rep1a1790


title: SpVATCtrlTG_rep1a1791


title: SpVATCtrlTG_rep1a1792


title: SpVATCtrlTG_rep1a1788


title: SpVATCtrlTG_rep1a1786


title: SpVATCtrlTG_rep1a1787


title: SpVATCtrlTG_rep1a1778


title: SpVATCtrlTG_rep1a1783


title: SpVATCtrlTG_rep1a1776


title: SpVATCtrlTG_rep1a1821


title: SpVATCtrlTG_rep1a1775


title: SpVATCtrlTG_rep1a1774


title: SpVATCtrlTG_rep1a1771


title: SpVATCtrlTG_rep1a1773


title: SpVATCtrlTG_rep1a1770


title: SpVATCtrlTG_rep1a1769


title: SpVATCtrlTG_rep1a1767


title: SpVATCtrlTG_rep1a1761


title: SpVATCtrlTG_rep1a1763


title: SpVATCtrlTG_rep1a1760


title: SpVATCtrlTG_rep1a1756


title: SpVATCtrlTG_rep1a1764


title: SpVATCtrlTG_rep1a1754


title: SpVATCtrlTG_rep1a1753


title: SpVATCtrlTG_rep1a1755


title: SpVATCtrlTG_rep1a1752


title: SpVATCtrlTG_rep1a1750


title: SpVATCtrlTG_rep1a1740


title: SpVATCtrlTG_rep1a1748


title: SpVATCtrlTG_rep1a1751


title: SpVATCtrlTG_rep1a1738


title: SpVATCtrlTG_rep1a1777


title: SpVATCtrlTG_rep1a1734


title: SpVATCtrlTG_rep1a1733


title: SpVATCtrlTG_rep1a1730


title: SpVATCtrlTG_rep1a1729


title: SpVATCtrlTG_rep1a1727


title: SpVATCtrlTG_rep1a1725


title: SpVATCtrlTG_rep1a1718


title: SpVATCtrlTG_rep1a1713


title: SpVATCtrlTG_rep1a1712


title: SpVATCtrlTG_rep1a1717


title: SpVATCtrlTG_rep1a1721


title: SpVATCtrlTG_rep1a1711


title: SpVATCtrlTG_rep1a1710


title: SpVATCtrlTG_rep1a1731


title: SpVATCtrlTG_rep1a1741


title: SpVATCtrlTG_rep1a1702


title: SpVATCtrlTG_rep1a1735


title: SpVATCtrlTG_rep1a1737


title: SpVATCtrlTG_rep1a1703


title: SpVATCtrlTG_rep1a1722


title: SpVATCtrlTG_rep1a1701


title: SpVATCtrlTG_rep1a1697


title: SpVATCtrlTG_rep1a1696


title: SpVATCtrlTG_rep1a1698


title: SpVATCtrlTG_rep1a1728


title: SpVATCtrlTG_rep1a1690


title: SpVATCtrlTG_rep1a1686


title: SpVATCtrlTG_rep1a1683


title: SpVATCtrlTG_rep1a1687


title: SpVATCtrlTG_rep1a1674


title: SpVATCtrlTG_rep1a1705


title: SpVATCtrlTG_rep1a1677


title: SpVATCtrlTG_rep1a1664


title: SpVATCtrlTG_rep1a1671


title: SpVATCtrlTG_rep1a1663


title: SpVATCtrlTG_rep1a1672


title: SpVATCtrlTG_rep1a1667


title: SpVATCtrlTG_rep1a1658


title: SpVATCtrlTG_rep1a1662


title: SpVATCtrlTG_rep1a1700


title: SpVATCtrlTG_rep1a1656


title: SpVATCtrlTG_rep1a1654


title: SpVATCtrlTG_rep1a1655


title: SpVATCtrlTG_rep1a1653


title: SpVATCtrlTG_rep1a1699


title: SpVATCtrlTG_rep1a1651


title: SpVATCtrlTG_rep1a1650


title: SpVATCtrlTG_rep1a1694


title: SpVATCtrlTG_rep1a1652


title: SpVATCtrlTG_rep1a1642


title: SpVATCtrlTG_rep1a1649


title: SpVATCtrlTG_rep1a1647


title: SpVATCtrlTG_rep1a1676


title: SpVATCtrlTG_rep1a1640


title: SpVATCtrlTG_rep1a1638


title: SpVATCtrlTG_rep1a1646


title: SpVATCtrlTG_rep1a1641


title: SpVATCtrlTG_rep1a1673


title: SpVATCtrlTG_rep1a1634


title: SpVATCtrlTG_rep1a1636


title: SpVATCtrlTG_rep1a1632


title: SpVATCtrlTG_rep1a1631


title: SpVATCtrlTG_rep1a1627


title: SpVATCtrlTG_rep1a1626


title: SpVATCtrlTG_rep1a1621


title: SpVATCtrlTG_rep1a1622


title: SpVATCtrlTG_rep1a1619


title: SpVATCtrlTG_rep1a1614


title: SpVATCtrlTG_rep1a1611


title: SpVATCtrlTG_rep1a1604


title: SpVATCtrlTG_rep1a1605


title: SpVATCtrlTG_rep1a1602


title: SpVATCtrlTG_rep1a1608


title: SpVATCtrlTG_rep1a1603


title: SpVATCtrlTG_rep1a1601


title: SpVATCtrlTG_rep1a1613


title: SpVATCtrlTG_rep1a1637


title: SpVATCtrlTG_rep1a1588


title: SpVATCtrlTG_rep1a1586


title: SpVATCtrlTG_rep1a1596


title: SpVATCtrlTG_rep1a1583


title: SpVATCtrlTG_rep1a1580


title: SpVATCtrlTG_rep1a1600


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title: SpVATCtrlTG_rep1a1577


title: SpVATCtrlTG_rep1a1575


title: SpVATCtrlTG_rep1a1576


title: SpVATCtrlTG_rep1a1572


title: SpVATCtrlTG_rep1a1571


title: SpVATCtrlTG_rep1a1568


title: SpVATCtrlTG_rep1a1618


title: SpVATCtrlTG_rep1a1570


title: SpVATCtrlTG_rep1a1565


title: SpVATCtrlTG_rep1a1561


title: SpVATCtrlTG_rep1a1564


title: SpVATCtrlTG_rep1a1559


title: SpVATCtrlTG_rep1a1558


title: SpVATCtrlTG_rep1a1557


title: SpVATCtrlTG_rep1a1556


title: SpVATCtrlTG_rep1a1582


title: SpVATCtrlTG_rep1a1554


title: SpVATCtrlTG_rep1a1574


title: SpVATCtrlTG_rep1a1546


title: SpVATCtrlTG_rep1a1544


title: SpVATCtrlTG_rep1a1553


title: SpVATCtrlTG_rep1a1535


title: SpVATCtrlTG_rep1a1551


title: SpVATCtrlTG_rep1a1550


title: SpVATCtrlTG_rep1a1521


title: SpVATCtrlTG_rep1a1524


title: SpVATCtrlTG_rep1a1552


title: SpVATCtrlTG_rep1a1528


title: SpVATCtrlTG_rep1a1539


title: SpVATCtrlTG_rep1a1519


title: SpVATCtrlTG_rep1a1531


title: SpVATCtrlTG_rep1a1530


title: SpVATCtrlTG_rep1a1506


title: SpVATCtrlTG_rep1a1509


title: SpVATCtrlTG_rep1a1512


title: SpVATCtrlTG_rep1a1529


title: SpVATCtrlTG_rep1a1523


title: SpVATCtrlTG_rep1a1510


title: SpVATCtrlTG_rep1a1491


title: SpVATCtrlTG_rep1a1515


title: SpVATCtrlTG_rep1a1504


title: SpVATCtrlTG_rep1a1485


title: SpVATCtrlTG_rep1a1487


title: SpVATCtrlTG_rep1a1492


title: SpVATCtrlTG_rep1a1482


title: SpVATCtrlTG_rep1a1541


title: SpVATCtrlTG_rep1a1484


title: SpVATCtrlTG_rep1a1501


title: SpVATCtrlTG_rep1a1475


title: SpVATCtrlTG_rep1a1488


title: SpVATCtrlTG_rep1a1478


title: SpVATCtrlTG_rep1a1490


title: SpVATCtrlTG_rep1a1503


title: SpVATCtrlTG_rep1a1471


title: SpVATCtrlTG_rep1a1466


title: SpVATCtrlTG_rep1a1483


title: SpVATCtrlTG_rep1a1477


title: SpVATCtrlTG_rep1a1495


title: SpVATCtrlTG_rep1a1474


title: SpVATCtrlTG_rep1a1508


title: SpVATCtrlTG_rep1a1472


title: SpVATCtrlTG_rep1a1480


title: SpVATCtrlTG_rep1a1470


title: SpVATCtrlTG_rep1a1469


title: SpVATCtrlTG_rep1a1468


title: SpVATCtrlTG_rep1a1465


title: SpVATCtrlTG_rep1a1463


title: SpVATCtrlTG_rep1a1459


title: SpVATCtrlTG_rep1a1461


title: SpVATCtrlTG_rep1a1450


title: SpVATCtrlTG_rep1a1449


title: SpVATCtrlTG_rep1a1443


title: SpVATCtrlTG_rep1a1446


title: SpVATCtrlTG_rep1a1431


title: SpVATCtrlTG_rep1a1428


title: SpVATCtrlTG_rep1a1425


title: SpVATCtrlTG_rep1a1430


title: SpVATCtrlTG_rep1a1422


title: SpVATCtrlTG_rep1a1419


title: SpVATCtrlTG_rep1a1414


title: SpVATCtrlTG_rep1a1416


title: SpVATCtrlTG_rep1a1420


title: SpVATCtrlTG_rep1a1415


title: SpVATCtrlTG_rep1a1410


title: SpVATCtrlTG_rep1a1408


title: SpVATCtrlTG_rep1a1413


title: SpVATCtrlTG_rep1a1407


title: SpVATCtrlTG_rep1a1405


title: SpVATCtrlTG_rep1a1462


title: SpVATCtrlTG_rep1a1460


title: SpVATCtrlTG_rep1a1400


title: SpVATCtrlTG_rep1a1398


title: SpVATCtrlTG_rep1a1396


title: SpVATCtrlTG_rep1a1397


title: SpVATCtrlTG_rep1a1394


title: SpVATCtrlTG_rep1a1458


title: SpVATCtrlTG_rep1a1392


title: SpVATCtrlTG_rep1a1393


title: SpVATCtrlTG_rep1a1439


title: SpVATCtrlTG_rep1a1391


title: SpVATCtrlTG_rep1a1389


title: SpVATCtrlTG_rep1a1390


title: SpVATCtrlTG_rep1a1387


title: SpVATCtrlTG_rep1a1386


title: SpVATCtrlTG_rep1a1378


title: SpVATCtrlTG_rep1a1384


title: SpVATCtrlTG_rep1a1379


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title: SpVATCtrlTG_rep1a1367


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title: SpVATCtrlTG_rep1a1380


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title: SpVATCtrlTG_rep1a1341


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title: SpVATCtrlTG_rep1a1335


title: SpVATCtrlTG_rep1a1334


title: SpVATCtrlTG_rep1a1332


title: SpVATCtrlTG_rep1a1333


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title: SpVATCtrlTG_rep1a1359


title: SpVATCtrlTG_rep1a1328


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title: SpVATCtrlTG_rep1a1325


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title: SpVATCtrlTG_rep1a1324


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title: SpVATCtrlTG_rep1a1317


title: SpVATCtrlTG_rep1a1313


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title: SpVATCtrlTG_rep1a1312


title: SpVATCtrlTG_rep1a1311


title: SpVATCtrlTG_rep1a1302


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title: SpVATCtrlTG_rep1a1307


title: SpVATCtrlTG_rep1a1289


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title: SpVATCtrlTG_rep1a1283


title: SpVATCtrlTG_rep1a1281


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title: SpVATCtrlTG_rep1a1305


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title: SpVATCtrlTG_rep1a1254


title: SpVATCtrlTG_rep1a1265


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title: SpVATCtrlTG_rep1a1258


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title: SpVATCtrlTG_rep1a1237


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title: SpVATCtrlTG_rep1a1224


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title: SpVATCtrlTG_rep1a1210


title: SpVATCtrlTG_rep1a1211


title: SpVATCtrlTG_rep1a1209


title: SpVATCtrlTG_rep1a1240


title: SpVATCtrlTG_rep1a1208


title: SpVATCtrlTG_rep1a1216


title: SpVATCtrlTG_rep1a1212


title: SpVATCtrlTG_rep1a1205


title: SpVATCtrlTG_rep1a1203


title: SpVATCtrlTG_rep1a1201


title: SpVATCtrlTG_rep1a1198


title: SpVATCtrlTG_rep1a1200


title: SpVATCtrlTG_rep1a1194


title: SpVATCtrlTG_rep1a1197


title: SpVATCtrlTG_rep1a1199


title: SpVATCtrlTG_rep1a1196


title: SpVATCtrlTG_rep1a1191


title: SpVATCtrlTG_rep1a1189


title: SpVATCtrlTG_rep1a1185


title: SpVATCtrlTG_rep1a1184


title: SpVATCtrlTG_rep1a1186


title: SpVATCtrlTG_rep1a1180


title: SpVATCtrlTG_rep1a1175


title: SpVATCtrlTG_rep1a1183


title: SpVATCtrlTG_rep1a1172


title: SpVATCtrlTG_rep1a1169


title: SpVATCtrlTG_rep1a1167


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title: SpVATCtrlTG_rep1a1153


title: SpVATCtrlTG_rep1a1150


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title: SpVATCtrlTG_rep1a1143


title: SpVATCtrlTG_rep1a1145


title: SpVATCtrlTG_rep1a1146


title: SpVATCtrlTG_rep1a1166


title: SpVATCtrlTG_rep1a1141


title: SpVATCtrlTG_rep1a1142


title: SpVATCtrlTG_rep1a1147


title: SpVATCtrlTG_rep1a1140


title: SpVATCtrlTG_rep1a1190


title: SpVATCtrlTG_rep1a1136


title: SpVATCtrlTG_rep1a1138


title: SpVATCtrlTG_rep1a1160


title: SpVATCtrlTG_rep1a1122


title: SpVATCtrlTG_rep1a1120


title: SpVATCtrlTG_rep1a1118


title: SpVATCtrlTG_rep1a1121


title: SpVATCtrlTG_rep1a1119


title: SpVATCtrlTG_rep1a1103


title: SpVATCtrlTG_rep1a1114


title: SpVATCtrlTG_rep1a1098


title: SpVATCtrlTG_rep1a1099


title: SpVATCtrlTG_rep1a1105


title: SpVATCtrlTG_rep1a1109


title: SpVATCtrlTG_rep1a1090


title: SpVATCtrlTG_rep1a1111


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title: SpVATCtrlTG_rep1a1092


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title: SpVATCtrlTG_rep1a1139


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title: SpVATCtrlTG_rep1a1082


title: SpVATCtrlTG_rep1a1132


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title: SpVATCtrlTG_rep1a1085


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title: SpVATCtrlTG_rep1a1074


title: SpVATCtrlTG_rep1a1075


title: SpVATCtrlTG_rep1a1078


title: SpVATCtrlTG_rep1a1117


title: SpVATCtrlTG_rep1a1076


title: SpVATCtrlTG_rep1a1071


title: SpVATCtrlTG_rep1a1094


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title: SpVATCtrlTG_rep1a1091


title: SpVATCtrlTG_rep1a1068


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title: SpVATCtrlTG_rep1a1058


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title: SpVATCtrlTG_rep1a1003


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title: SpVATCtrlTG_rep1a979


title: SpVATCtrlTG_rep1a1028


title: SpVATCtrlTG_rep1a971


title: SpVATCtrlTG_rep1a969


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title: SpVATCtrlTG_rep1a1015


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title: SpVATCtrlTG_rep1a927


title: SpVATCtrlTG_rep1a930


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title: SpVATCtrlTG_rep1a926


title: SpVATCtrlTG_rep1a923


title: SpVATCtrlTG_rep1a925


title: SpVATCtrlTG_rep1a920


title: SpVATCtrlTG_rep1a921


title: SpVATCtrlTG_rep1a918


title: SpVATCtrlTG_rep1a919


title: SpVATCtrlTG_rep1a922


title: SpVATCtrlTG_rep1a917


title: SpVATCtrlTG_rep1a914


title: SpVATCtrlTG_rep1a916


title: SpVATCtrlTG_rep1a910


title: SpVATCtrlTG_rep1a911


title: SpVATCtrlTG_rep1a913


title: SpVATCtrlTG_rep1a908


title: SpVATCtrlTG_rep1a907


title: SpVATCtrlTG_rep1a933


title: SpVATCtrlTG_rep1a905


title: SpVATCtrlTG_rep1a932


title: SpVATCtrlTG_rep1a903


title: SpVATCtrlTG_rep1a902


title: SpVATCtrlTG_rep1a900


title: SpVATCtrlTG_rep1a904


title: SpVATCtrlTG_rep1a899


title: SpVATCtrlTG_rep1a898


title: SpVATCtrlTG_rep1a895


title: SpVATCtrlTG_rep1a893


title: SpVATCtrlTG_rep1a889


title: SpVATCtrlTG_rep1a896


title: SpVATCtrlTG_rep1a890


title: SpVATCtrlTG_rep1a888


title: SpVATCtrlTG_rep1a886


title: SpVATCtrlTG_rep1a878


title: SpVATCtrlTG_rep1a874


title: SpVATCtrlTG_rep1a885


title: SpVATCtrlTG_rep1a873


title: SpVATCtrlTG_rep1a870


title: SpVATCtrlTG_rep1a875


title: SpVATCtrlTG_rep1a867


title: SpVATCtrlTG_rep1a880


title: SpVATCtrlTG_rep1a862


title: SpVATCtrlTG_rep1a860


title: SpVATCtrlTG_rep1a855


title: SpVATCtrlTG_rep1a854


title: SpVATCtrlTG_rep1a851


title: SpVATCtrlTG_rep1a852


title: SpVATCtrlTG_rep1a853


title: SpVATCtrlTG_rep1a848


title: SpVATCtrlTG_rep1a849


title: SpVATCtrlTG_rep1a843


title: SpVATCtrlTG_rep1a835


title: SpVATCtrlTG_rep1a831


title: SpVATCtrlTG_rep1a833


title: SpVATCtrlTG_rep1a832


title: SpVATCtrlTG_rep1a828


title: SpVATCtrlTG_rep1a827


title: SpVATCtrlTG_rep1a826


title: SpVATCtrlTG_rep1a830


title: SpVATCtrlTG_rep1a864


title: SpVATCtrlTG_rep1a824


title: SpVATCtrlTG_rep1a861


title: SpVATCtrlTG_rep1a823


title: SpVATCtrlTG_rep1a821


title: SpVATCtrlTG_rep1a822


title: SpVATCtrlTG_rep1a817


title: SpVATCtrlTG_rep1a819


title: SpVATCtrlTG_rep1a818


title: SpVATCtrlTG_rep1a825


title: SpVATCtrlTG_rep1a815


title: SpVATCtrlTG_rep1a850


title: SpVATCtrlTG_rep1a845


title: SpVATCtrlTG_rep1a814


title: SpVATCtrlTG_rep1a811


title: SpVATCtrlTG_rep1a808


title: SpVATCtrlTG_rep1a810


title: SpVATCtrlTG_rep1a807


title: SpVATCtrlTG_rep1a806


title: SpVATCtrlTG_rep1a805


title: SpVATCtrlTG_rep1a799


title: SpVATCtrlTG_rep1a800


title: SpVATCtrlTG_rep1a796


title: SpVATCtrlTG_rep1a791


title: SpVATCtrlTG_rep1a787


title: SpVATCtrlTG_rep1a784


title: SpVATCtrlTG_rep1a786


title: SpVATCtrlTG_rep1a781


title: SpVATCtrlTG_rep1a776


title: SpVATCtrlTG_rep1a775


title: SpVATCtrlTG_rep1a778


title: SpVATCtrlTG_rep1a773


title: SpVATCtrlTG_rep1a767


title: SpVATCtrlTG_rep1a772


title: SpVATCtrlTG_rep1a770


title: SpVATCtrlTG_rep1a765


title: SpVATCtrlTG_rep1a761


title: SpVATCtrlTG_rep1a769


title: SpVATCtrlTG_rep1a760


title: SpVATCtrlTG_rep1a771


title: SpVATCtrlTG_rep1a759


title: SpVATCtrlTG_rep1a753


title: SpVATCtrlTG_rep1a746


title: SpVATCtrlTG_rep1a797


title: SpVATCtrlTG_rep1a755


title: SpVATCtrlTG_rep1a747


title: SpVATCtrlTG_rep1a744


title: SpVATCtrlTG_rep1a737


title: SpVATCtrlTG_rep1a732


title: SpVATCtrlTG_rep1a735


title: SpVATCtrlTG_rep1a730


title: SpVATCtrlTG_rep1a728


title: SpVATCtrlTG_rep1a726


title: SpVATCtrlTG_rep1a727


title: SpVATCtrlTG_rep1a724


title: SpVATCtrlTG_rep1a723


title: SpVATCtrlTG_rep1a722


title: SpVATCtrlTG_rep1a764


title: SpVATCtrlTG_rep1a719


title: SpVATCtrlTG_rep1a717


title: SpVATCtrlTG_rep1a718


title: SpVATCtrlTG_rep1a720


title: SpVATCtrlTG_rep1a714


title: SpVATCtrlTG_rep1a713


title: SpVATCtrlTG_rep1a745


title: SpVATCtrlTG_rep1a707


title: SpVATCtrlTG_rep1a704


title: SpVATCtrlTG_rep1a710


title: SpVATCtrlTG_rep1a711


title: SpVATCtrlTG_rep1a702


title: SpVATCtrlTG_rep1a729


title: SpVATCtrlTG_rep1a700


title: SpVATCtrlTG_rep1a699


title: SpVATCtrlTG_rep1a698


title: SpVATCtrlTG_rep1a695


title: SpVATCtrlTG_rep1a694


title: SpVATCtrlTG_rep1a692


title: SpVATCtrlTG_rep1a689


title: SpVATCtrlTG_rep1a725


title: SpVATCtrlTG_rep1a693


title: SpVATCtrlTG_rep1a703


title: SpVATCtrlTG_rep1a687


title: SpVATCtrlTG_rep1a686


title: SpVATCtrlTG_rep1a683


title: SpVATCtrlTG_rep1a682


title: SpVATCtrlTG_rep1a680


title: SpVATCtrlTG_rep1a715


title: SpVATCtrlTG_rep1a679


title: SpVATCtrlTG_rep1a678


title: SpVATCtrlTG_rep1a681


title: SpVATCtrlTG_rep1a677


title: SpVATCtrlTG_rep1a676


title: SpVATCtrlTG_rep1a672


title: SpVATCtrlTG_rep1a673


title: SpVATCtrlTG_rep1a675


title: SpVATCtrlTG_rep1a669


title: SpVATCtrlTG_rep1a671


title: SpVATCtrlTG_rep1a667


title: SpVATCtrlTG_rep1a662


title: SpVATCtrlTG_rep1a664


title: SpVATCtrlTG_rep1a666


title: SpVATCtrlTG_rep1a663


title: SpVATCtrlTG_rep1a658


title: SpVATCtrlTG_rep1a656


title: SpVATCtrlTG_rep1a655


title: SpVATCtrlTG_rep1a652


title: SpVATCtrlTG_rep1a648


title: SpVATCtrlTG_rep1a650


title: SpVATCtrlTG_rep1a639


title: SpVATCtrlTG_rep1a651


title: SpVATCtrlTG_rep1a645


title: SpVATCtrlTG_rep1a640


title: SpVATCtrlTG_rep1a637


title: SpVATCtrlTG_rep1a636


title: SpVATCtrlTG_rep1a635


title: SpVATCtrlTG_rep1a634


title: SpVATCtrlTG_rep1a630


title: SpVATCtrlTG_rep1a629


title: SpVATCtrlTG_rep1a628


title: SpVATCtrlTG_rep1a668


title: SpVATCtrlTG_rep1a627


title: SpVATCtrlTG_rep1a622


title: SpVATCtrlTG_rep1a624


title: SpVATCtrlTG_rep1a621


title: SpVATCtrlTG_rep1a623


title: SpVATCtrlTG_rep1a620


title: SpVATCtrlTG_rep1a619


title: SpVATCtrlTG_rep1a618


title: SpVATCtrlTG_rep1a614


title: SpVATCtrlTG_rep1a612


title: SpVATCtrlTG_rep1a611


title: SpVATCtrlTG_rep1a608


title: SpVATCtrlTG_rep1a610


title: SpVATCtrlTG_rep1a615


title: SpVATCtrlTG_rep1a605


title: SpVATCtrlTG_rep1a606


title: SpVATCtrlTG_rep1a603


title: SpVATCtrlTG_rep1a604


title: SpVATCtrlTG_rep1a599


title: SpVATCtrlTG_rep1a600


title: SpVATCtrlTG_rep1a601


title: SpVATCtrlTG_rep1a596


title: SpVATCtrlTG_rep1a631


title: SpVATCtrlTG_rep1a595


title: SpVATCtrlTG_rep1a598


title: SpVATCtrlTG_rep1a592


title: SpVATCtrlTG_rep1a594


title: SpVATCtrlTG_rep1a589


title: SpVATCtrlTG_rep1a587


title: SpVATCtrlTG_rep1a584


title: SpVATCtrlTG_rep1a586


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title: SpVATCtrlTG_rep1a534


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title: SpVATCtrlTG_rep1a9


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title: HCT116_PBS_siSETDB1

status: Public on Mar 28 2018

city: Chikusa-ku

first: Hitoshi

last: Ohtani

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

description:
processed data file:
RNA-seq_LTRs_KD.csv
RNA-seq_evolutionary-age.csv

data_processing:
Sequencing reads were aligned against the human hg19 reference genome using TopHat2 v.2.1.0 or HISAT
The number of overlapping mapped reads with ERV elements were obtained using Bedtool
The definitions of ERV elements were based on RepeatMasker
Genome_build: hg19
Supplementary_files_format_and_content: csv file. Expression level of viral defence genes and ERVs in each evolutionary age

organism: Homo sapiens

growth_protocol: HCT116 cells were maintained in McCoy's 5A medium. HepG2 and MCF7 cells were maintained in DMEM. HL60 cells were maintained in RPMI. The cells were cultured according to strandard mammalian tissue culture protocol and sterile technique.

extract_protocol:
All cells were harvested at 5 days post-treatments. RNA was purified using phenol chloroform extraction.
cDNA linraries were prepared using KAPA RNA HyperPrep Kits and pooled using standard illumina protocols.

treatment_protocol: HCT116 and HL60 cells were treated with PBS or 300 nM 5-aza-CdR for 24 h. For MCF7 and HepG2 cells, the dose and exposure time were 100 nM and 72 h respectively.

tag: cell line

tag: cell type

value: colorectal carcinoma

tag: treatment

value: Dual inhibition


title: HCT116_5-aza-CdR_siG9a

description:
processed data file:
RNA-seq_5-aza-CdR+KD.csv
RNA-seq_evolutionary-age.csv


title: HCT116_PBS_siSUV39H1


title: HCT116_5-aza-CdR_siTRIM28


title: HCT116_5-aza-CdR_siNon-target


title: HCT116_5-aza-CdR_siSUV39H1


title: Uninfected

status: Public on May 10 2018

city: San Francisco

first: Jason

last: Cyster

state: California

address: HSE 1001/Cyster Lab/Box 0414, 513 Parnassus Ave.

department: Microbiology and Immunology

institute: University of California, San Francisco

description:
Samples combined and treated as replicates during computational analysis and thus are combined in processed data files.
uninf_lcmv_genesVcells.txt
uninf_lcmv_metadata.xlsx
Table S1 Mean Expression.xlsx
Table S2 Ccl19hi TRC_Ccl19lo TRC_Cxcl9 TRC.xlsx
Table S3 MRC.xlsx
Table S4 PvC.xlsx
Table S5 CD34+ SC.xlsx
Table S6 Inmt+ SC.xlsx
Table S7 Nr4a1+ SC.xlsx
Table S8 FDC.xlsx

data_processing:
Demultiplexing base calls into fastq, alignment, filtering, UMI counting, barcode counting and filtering and gene-barcode matrix generation performed with 10X Cell Ranger (v1.2.0, 10X Genomics).
Briefly, Illumina BCLs were demultiplexed into fastqs using cell ranger mkfastq with indentifier lines with machine name, run number, flowcell name, tile numbers and the barcode.
Quality control (cells with 200 genes, genes in 3 cells), library-size normalization, linear regression of number of UMIs, mitochondrial gene expression and ribosomal gene expression, scaling and centering performed with Seurat (v2.2).
Quality control to retain only non-endothelial stromal cells by unsupervised clustering of samples separately with Seurat (v2.2)
Merging sample data and adjustment for batch with Canonical Correlation Analysis, alignment and clustering (10 CCs, resolution 0.5) with Seurat (v2.2)
Pseudobulk raw UMIs within sample and cluster (this paper).
Differential expression analysis of clusters with samples as replicates using DESeq2 (v1.16.1). Tables S1 includes averaged log-transformed gene expression across cells in each cluster for each gene detected (cluster_mean), proportion of cells within the cluster expressing the gene (pct_in) and standard deviation of expression among cells with detectable expression (std_dev_in). Tables S2-S8 report DEGs for each cluster as determined by the difference between the average expression of pseudobulk samples in the cluster and the average expression of pseudobulk samples not in the cluster (log2FoldChange). Also reported are the average pseudobulk counts across the dataset (baseMean), the log fold change standard error (lfcSE), Wald statistic (stat), p-value (pvalue), Benjamini and Hochberg adjusted p-value (FDR) and proportion of cells in the cluster expressing the gene (pct_in). DEGs (log2FoldChange >0.5, FDR < 0.05 and pct_in > 0.10) are highlighted.
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene expression matrix reporting log normalized UMIs after CCA merging of both samples; Metadata includes cell sample source and cluster assignment; Table S1 reports log-normalized UMI counts averaged for each sample within each cluster;  Tables S2-8 report differential expression of detected genes for each cluster

source_name: Peripheral lymph node non-endothelial stromal cells

extract_protocol:
Peripheral lymph nodes were harvested into DMEM (Fisher Scientific) with 2% FCS (HyClone), 10mM HEPES (Fisher Scientific) and Pen/Strep (P/S)(Fisher Scientific) on ice and minced with 25G needles (Fisher Scientific). Tissue was transferred to room temperature digestion buffer (DMEM + 2%FCS + HEPES + P/S + 3mg/ml Collagenase IV (Worthington Biochemical) and 40μg/ml DNase I (Sigma-Aldrich) and incubated at 37oC in a beaker with water and a stirbar gently spinning for 15 min. Tissue was pipetted 50x with a Pasteur pipet and incubated another 15min before being pipetted 100x and filtered through a 100μm filter into MACS Buffer (PBS with 2% FCS and 2mM EDTA) on ice. The cell suspension was spun down and resuspended to 1x107 cells/ml in MACS buffer with 10μl/4x107cells anti-CD45 MACS microbeads (Miltenyi) to rotate for 40min at 4oC. After MACS depletion of CD45+ cells, the remaining suspension was stained with anti-CD45 PerCpCy5.5 (30-F11, Biolegend), anti-CD31 PE (MEC 13.3, BD Biosciences), anti-gp38 APC (8.1.1, Biolegend) and DAPI (Invitrogen) for flow cytometry assisted cell sorting for viable CD45- CD31- cells on a FACSAria Fusion into PBS + 0.04% BSA. Cells with the lowest DAPI staining were excluded as SSC-Alo CD45- CD31- PDPN- insufficiently stained CD45+ cells. Data was analyzed using FlowJo (Treestar).
Samples were immediately run on the 10X Chromium (10X Genomics) and then processed through library preparation following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit (v2 Chemistry, 10X Genomics). Libraries were run on the HiSeq4000 for Illumina sequencing.

value: Peripheral lymph node CD45- CD31- stromal cells

value: inguinal, brachial and axillary lymph nodes, pooled from 12 mice

value: female

tag: age

value: 9 weeks old

tag: infection


title: HCT116_5-aza-CdR_siSETDB2


title: SpVATCtrlTG_rep1a8


title: PBMCs_indigenous_21dpv

city: Bareilly

first: AMIT

last: KUMAR

state: Uttar Pradesh

address: Izatnagar

department: Animal Genetics

country: India

institute: Indian Veterinary Research Institute

description: mRNA expression in PBMCs of indigenous pigs  at 21 days post CSF vaccination

data_processing:
The fastq files containing mRNA sequencing reads, the adapters were trimmed  from the reads. The low quality reads (phred score < 25 and read length <50) were trimmed using (PRINSEQLITET). Hereafter, known mRNAs were identified by annotating the clean reads to reference genome of pig. The counts obtained were analyzed using DESeq2, edgeR and EBSeq  for identifying differentially expressed mRNAs under CSF infection. The common differentially expressed genes were further selected for downstrem analysis.
Supplementary_files_format_and_content: tab-delimited text files include mRNA gene name,  expression values (log2 fold change) and significant p-value using edgeR softwares

organism: Sus scrofa

source_name: PBMCs collected at 21 days post CSF vaccination from indigenous pigs

extract_protocol:
Total RNA from each of the collected samples was isolated using the RNeasy Mini kit (Qiagen GmbH, Germany) according to the manufacturer’s protocol. The integrity and quantity of isolated RNA were assessed on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples was found greater than 7, which is considered suitable for further processing.
Library was prepared using mRNA Library Prep Kit following the manufacturer’s protocol. The quality of the libraries was assessed on Bioanalyzer and quantification was done using a Qubit 2.0 Fluorometer (Life Technologies) and by quantitative real-time PCR. Libraries wee sequenced on Illumina – HiSeq2000  following manufacturer’s protocol.

treatment_protocol: Three indigenous and crossbred pigs were vaccinated and PBMCs were collected at 7 and 21 days post vaccination. Also MDMs of indigenous and crossbred pigs were harvested 60 hours post infection with CSF virulant virus. The crossbred were taken as control and the gene expression were compared in indigenous pigs.  The isolated PBMCs of both groups were collected in RNase free 1.5 ml centrifuge tube in RNA later.

tag: breed

value: Indigenous

tag: infection status

value: 21 days post CSF vaccination


title: PBMCs Control_crossbred_7dpv

description: mRNA expression in PBMCs of crossbred (control) pigs at 7 days post CSF vaccination

source_name: PBMCs collected at 7 days post CSF vaccination from crossbred pigs

value: Crossbred

value: 7 days post CSF vaccination


title: HCT116_5-aza-CdR_siSETDB1


title: Macrophage_indigenous_60hpi

description: mRNA expression in MDMs of indigenous pigs at 60 hpi post CSF infection

source_name: Monocyte derived Macrophages  of indigenous pigs at 60 hours post infection with CSF virulent virus

value: 60 hours post infection with CSF virulant virus.


title: HCT116_PBS_siG9a


title: PBMCs Control_crossbred_21dpv

description: mRNA expression in PBMCs of crossbred (control) pigs  at 21 days post CSF vaccination

source_name: PBMCs collected at 21 days post CSF vaccination from crossbred pigs


title: Post-infection

value: inguinal, brachial and axillary lymph nodes, pooled from 9 mice

value: LCMV-Armstrong (infection intravenously (iv) at 2.5x10^5 pfu and analyzed on day 15)


title: Macrophage_control_Crossbred_60hpi

description: mRNA expression in MDMs of crossbred (control) pigs at 60 hpi post CSF infection

source_name: Monocyte derived Macrophages  of crossbred pigs at 60 hours post infection with CSF virulent virus


title: SpVATCtrlTG_rep1a4

value: male


title: PBMCs_indigenous_7dpv

description: mRNA expression in PBMCs of indigenous pigs  at 7 days post CSF vaccination

source_name: PBMCs collected at 7 days post CSF vaccination from indigenous pigs


title: HCT116_PBS_siTRIM28


title: HCT116_5-aza-CdR_siEZH2


title: HCT116_5-aza-CdR_siSUV39H2


title: HCT116_PBS_siNon-target


title: HCT116_PBS_siSETDB2


title: HepG2_PBS_rep2

description:
processed data file:
RNA-seq_LTRs_Cell-lines.csv
RNA-seq_viral-defense-genes.csv

value: hepatocellular carcinoma

value: PBS


title: HCT116_PBS_siEZH2


title: HepG2_5-aza-CdR_rep2


title: NLRP3 KO PBS

status: Public on May 18 2018

type: RNA

city: Los Angeles

first: Shuang

last: Chen

state: CA

address: 8700 Beverly blvd

department: Pediatrics

institute: Cedars Sinai Medical Center

description: Gene expression data from NLRP3 KO peritoneal macrophage

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: NLRP3 KO Peritoneal  macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Resident peritoneal macrophages were collected and the pooled cells were incubated overnight in RPMI 1640 medium (Cellgro) with 10% FBS at 37°C in 5% CO2 and non-adherent cells were rinsed away.

extract_protocol: RNA was puriﬁed using the RNeasy kit (QIAGEN, Valencia, CA), including treatment with DNase.

treatment_protocol: Peritoneal macrophages, pooled from three mice, were stimulated C.pn with  oxLDL for 8h

tag: genotype/variation

value: NLRP3 KO

value: PBS treament

value: Peritoneal  macrophages


title: MCF7_5-aza-CdR_rep2

value: breast carcinoma


title: HL60_PBS_rep2

value: acute myeloid leukemia


title: HepG2_5-aza-CdR_rep1


title: HepG2_PBS_rep1


title: HL60_PBS_rep1


title: MCF7_PBS_rep2


title: HCT116_PBS_rep1

value: colorectal carcinoma


title: MCF7_5-aza-CdR_rep1


title: HL60_5-aza-CdR_rep1


title: HL60_5-aza-CdR_rep2


title: HCT116_5-aza-CdR_rep1


title: Nrd1-AA MNase-seq +Rap rep1

status: Public on Feb 24 2018

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

library_source: genomic

data_processing:
fastq files were processed through the mapping function of HTS EPFL station.PCR duplicates were discarded from the analysis.
bigwig were generated using HTS EPFL station. Strands were merged by 125bp for BrdU-seq.
Genome_build: saccer3
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Nrd1-AA MNase-seq +Rap

growth_protocol: Nrd1AA strain is pre-cultured and grown to the log phase, half of the culture is fixed by adding 37% formaldehyde (final concentration of 1%) followed by quenching with Glycine (final concentration 125mM) and the other half was treated with rapamycin for 60 minutes before fixation. The cells were harvested using centrifugation and washed twice with H2O.

extract_protocol:
MNase treatment was performed as described in (Weiner et al., 2015).The chromatin was extracted by breaking cells with bead beating in magnalyser (Roche). The chromatin was then collected by centrifugation and then re-suspended in NP-buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2). MNase (Thermo-Scientific) treatment is performed at a previously optimised concentration to have comparable intensity of both mono and di nucleosomes within and between the samples.  MNase treatment was followed by de-crosslinking, protease treatment and DNA was extracted using NucleoSpin gel and PCR extraction columns (Macherey-Nagel).
MNase treatment was performed as described in (Weiner et al., 2015).The chromatin was extracted by breaking cells with bead beating in magnalyser (Roche). The chromatin was then collected by centrifugation and then re-suspended in NP-buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2). MNase (Thermo-Scientific) treatment is performed at a previously optimised concentration to have comparable intensity of both mono and di nucleosomes within and between the samples.  MNase treatment was followed by de-crosslinking, protease treatment and DNA was extracted using NucleoSpin gel and PCR extraction columns (Macherey-Nagel).

value: +Rap


title: HCT116_PBS_siSUV39H2

value: Dual inhibition


title: Nrd1-AA MNase-seq -Rap rep1

source_name: Nrd1-AA MNase-seq -Rap

value: -Rap


title: MCF7_PBS_rep1


title: Day 75 rep1

status: Public on Feb 22 2018

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi package in R

label: Biotin

source_name: hiPSCs differentiation at day 75

label_protocol: Standard Illumina labelling protocol

growth_protocol: Three oriP/EBNA—based episomal vectors (obtained from Addgene), pEP4EO2SEN2K, pEP4EO2SET2K, and pCEP4-M2L were co-transfected into 2X10^6 human newborn fibroblasts (ATCC CRL-2703) via nucleofection using Amaxa 4D-nucleofector system. The transfected fibroblasts were placed on Matrigel-coated dishes in human fibroblast medium (DMEM, 10% FBS, 2mM L-glutamine, 50U/ml penicillin + 50 mg/ml streptomycin). On day one post-transfection, the fibroblast medium was replaced with human embryonic stem cell (hESC) medium (GlobalStem, Molecular Transfer, Inc.), supplemented with 20% KnockOut™ serum (Invitrogen) and 0.5mM sodium butyrate (Invitrogen). Culture medium was refreshed every other day. Around 18 days, the visible ESC-like morphology colonies were picked and transferred to MEF feeder layers in hESC medium supplemented with 20ng/ml of basic fibroblast growth factor

extract_protocol: Total RNA was extracted using Trizol (Life Technologies) according to the manufacturer’s instructions

value: hiPSCs derived neuronal cultures

tag: days of differentiation


title: Day 115 rep2

description: replicate 2

source_name: hiPSCs differentiation at day 115


title: Day 25 rep2

description: replicate 2

source_name: hiPSCs differentiation at day 25


title: Day 10 rep1

description: replicate 1

source_name: hiPSCs differentiation at day 10


title: Day 75 rep2

description: replicate 2


title: Day 0 rep1

description: replicate 1

source_name: hiPSCs differentiation at day 0


title: siERBB2 transfected KPL-4 cell lines, rep 2

status: Public on Dec 21 2017

city: Oslo

first: Evita

last: Lindholm

address: Ullernchausseen 70

department: Genetics

country: Norway

institute: Oslo University Hospital, Radiumhospitalet

description: Gene expression 24h after siERBB2 transfection of KPL-4 cell lines

hyb_protocol: Agilent Protocol

scan_protocol: Arrays were read with Agilent Scanner G2565A, using AgilentG3_GX_1Color as profile.

data_processing: Signals were extracted using FEv.10.7.3.1 and protocol GE1_107_Sep09 (Agilent Technologies)

label_protocol: mRNA expression was measured using SurePrint G3 Human GE 8x60K one-color microarrays (Agilent Technologies) according to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, v.6.5, May 2010). For each sample, 100 ng of RNA was amplified and hybridized on the array

extract_protocol: total RNA was extracted directly from each well using MiRVana™ Total RNAIsolation kit (Ambion Inc.) according to the manufacturer`s protocol.

treatment_protocol: The cells were transiently transfected with 20 nM precursor for miR-342-5p or scrambled miRNA negative control (Ambion Inc., Austin, TX, USA) using SilentFect (Bio-Rad Laboratories, Hercules, CA, USA). Transfected cells were incubated for 24 hours

tag: transfection

tag: tumor type

value: HER2+ breast cancer


title: Day 0 rep2

description: replicate 2


title: Day 95 rep2

description: replicate 2

source_name: hiPSCs differentiation at day 95


title: Day 45 rep1

description: replicate 1

source_name: hiPSCs differentiation at day 45


title: Day 10 rep2

description: replicate 2


title: Day 25 rep1

description: replicate 1


title: siERBB2 transfected JIMT-1 cell lines, rep 2

description: Gene expression 24h after siERBB2 transfection of JIMT-1 cell lines


title: Day 55 rep2

description: replicate 2

source_name: hiPSCs differentiation at day 55


title: not transfected KPL-4 cell lines, rep 3

description: Gene expression of KPL-4 cell lines, without transfection

source_name: not transfected KPL-4 cell lines, rep 3


title: Day 45 rep2

description: replicate 2


title: not transfected KPL-4 cell lines, rep 1

source_name: not transfected KPL-4 cell lines, rep 1


title: Day 55 rep1

description: replicate 1


title: siERBB2 transfected KPL-4 cell lines, rep 1


title: JCMS 24hours rep4

status: Public on Feb 01 2018

city: Manhattan

first: Michael

middle: A

last: Herman

state: KS

address: 266 Chalmers Hall

department: Division of Biology

institute: Kansas State University, Ecological Genomics Institute

description: RMA Call summary of mean expression

hyb_protocol: Performed by NimbleGen Gene Expression Services (Roche NimbleGen Inc.)

organism: Caenorhabditis elegans

source_name: nematode,  JCMS, 24hrs

label_protocol: cDNA was synthesized using the SMARTer PCR cDNA synthesis kit (Clontech), amplified and optimized using the Advantage 2 PCR Kit (Clontech). Double-stranded cDNA was purified using the PureLinkTM Quick PCR Purification Kit (Invitrogen) and ethanol precipitation. Purified cDNA was sent to NimbleGen Gene Expression Services (Roche NimbleGen Inc.) for labeling.

growth_protocol: Synchronized wild-type nematodes were reared at 20˚C on E. coli OP50 from egg to larval stage 4 (L4).

extract_protocol: After 24 hours of feeding on the treatment bacteria at 25˚C, young adult nematodes were collected in M9 buffer and lysed in TRIzol® reagent (Life Technologies). This bulk extraction was considered one biological replicate and was repeated four times for each bacterial treatment. RNA extraction and DNAse treatment were performed using the PureLink RNA Mini Kit (Invitrogen) and on-column PureLink® DNase Treatment (Invitrogen).

treatment_protocol: L4s were then washed off the rearing plates with M9 buffer and placed onto lawns of S. maltophilia JCMS, K279a or E. coli OP50.

tag: bacterial strain

value: JCMS virulent S. maltophilia

tag: developmental stage

value: Young adult

tag: strain


title: siERBB2 transfected JIMT-1 cell lines, rep 3


title: Day 115 rep1

description: replicate 1


title: Day 35 rep1

description: replicate 1

source_name: hiPSCs differentiation at day 35


title: siERBB2 transfected KPL-4 cell lines, rep 3


title: Day 35 rep2

description: replicate 2


title: Day 95 rep1

description: replicate 1


title: siERBB2 transfected JIMT-1 cell lines, rep 1


title: not transfected JIMT-1 cell lines, rep 3

description: Gene expression of JIMT-1 cell lines, without transfection


title: not transfected JIMT-1 cell lines, rep 2


title: not transfected KPL-4 cell lines, rep 2

source_name: not transfected KPL-4 cell lines, rep 2


title: RNAseq_SCer_12_Async_37C_rep2

status: Public on Oct 25 2017

city: New York City

first: Matthew

middle: R

last: Paul

address: 1230 York Ave

department: Bioinformatics Resource Center

institute: Rockefeller University

data_processing:
RNA-seq mapping: Mapping was conducted using tophat version 2.1.0 to the SacCer3 genome and S. pombe ASM294v2. Mapping paraeters used are: --no-novel-juncs --library-type fr-firststrand. Reads with unique mapping to a organism were kept for further analysis,
RNA-seq counts and correction: Read counts per gene was calculated using featureCounts of the subread package version 1.4.6-p3. Parameters used are -s 2 -t CDS. Linear correction was used to corerect for differeces in spike-in data. To this end a linear curve was plotted between CPM for each gene between each spike-in S. pombe data set and the baseline (i.e. untreated wild-type cells). The slope of the curve was compared to the expected 1:1 ratio. The transformation required to move the spike-in data set on to the 1:1 line was then applied to the expeirmental S . cerevisiae dataset for the same comparison.
processed data files format and content: RNA counts per million reads per gene
Genome_build: SacCer3 (S. cerevisiae), SK1 (S. cerevisiae - Chip only: https://yjx1217.github.io/Yeast_PacBio_2016/welcome/),  WS220 (C. elegans) and  ASM294v2 (S. pombe)

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: RNAseq  12 aynchronous 37C rep2

growth_protocol: Overnight cultures were prepared for cells. They were reseeded in the morning and grown to OD1.

extract_protocol:
RNA-seq: Cells were counted and 10% S. pombe cells were added. Total RNA was extracated with Qiagen Rneasy columns. mRNA was selected with oligo-dT bead. cDNA was prepared based on the incorporation of dUTPs using reverse transcription.
DNA was ligated to Illumina or home-made multiplexed adapters and amplified by PCR. For 3C-seq library DNA between 400-1Kb was gel purified. For ChIP Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Anchor-away samples were treated with 1ug/ml of rapamycin. Temperature-senstive strains were either shifted to 37C or maintained at 23C for 2 hrs.

value: 12 - wild type strain

value: Growth at restrictive 37C

tag: tissue

value: 90% S. cerevisiae cells, 10% S.pombe cells


title: RNAseq_SCer_4662_Async_37C_rep3

source_name: RNAseq  4662 aynchronous 37C rep3

value: 4662 - ycs4-2 strain


title: RNAseq_SCer_12_Async_23C_rep2

source_name: RNAseq 12 aynchronous 23C rep2

value: Growth at permissive 23C


title: RNAseq_SCer_4662_Async_23C_rep2

source_name: RNAseq  4662 aynchronous 23C rep2


title: RNAseq_SCer_4662_Async_37C_rep2

source_name: RNAseq  4662 aynchronous 37C rep2


title: 3Cseq_HindIII_SCer_7637_Async_rep1

data_processing:
Library strategy: 3C-seq
3C-seq: Iterative mapping : Iterative mapping was done using the hiclib and mirnylib packages produced by the Mirny Lab. This utilised bowtie2 version 2.2.9 to map reads to the SacCer3 Genome build
3C-seq: iterative correction: Iterative correction was done using the hiclib and mirnylib packages produced by the Mirny Lab. Input parameters include: maximumMoleculeLength=1000, cutH=0.005, cutL=0, resolution=10000,high=0.0005,cutoff=1.
processed data files format and content: Genome-wide interaction matrix (10kb bins)
Genome_build: SacCer3 (S. cerevisiae), SK1 (S. cerevisiae - Chip only: https://yjx1217.github.io/Yeast_PacBio_2016/welcome/),  WS220 (C. elegans) and  ASM294v2 (S. pombe)

source_name: 3Cseq HindIII 7637 aynchronous rep1

extract_protocol:
3C-seq: Cells were fixed in 3% FA. Cells were then spheroblasted with zymolase and Nuclei were extracted with douncing. Nuclei were counted after staining with Crystal Violet. At this point if a spike-in was used (ycs4-2 experiments), 10% of N2 embryonis C.elegans nuclei were added. Nuclei were permeabilised and then the restriction enzyme HindIII was used to digest the genome. Digested genomic DNA was subjected to proximity ligation using a T4 DNA Ligase in dilute condtions. DNA was then purifed using Qiagen PCR purifaction columns and DNA sonicated down to 200bp-1kb size with a Diagenode Bioruptor.
DNA was ligated to Illumina or home-made multiplexed adapters and amplified by PCR. For 3C-seq library DNA between 400-1Kb was gel purified. For ChIP Library DNA between 250-500 bp in size was gel purified.

value: 7637 - Brn1-FRB tagged in anchor-away background

value: S. cerevisiae nuclei


title: 3Cseq_HindIII_SCer_6840_Async_rep1

source_name: 3Cseq HindIII 6840 aynchronous rep1

value: 6840 - Anchor away parental strain


title: 3Cseq_HindIII_SCer_7637_Async_+rap_rep1

source_name: 3Cseq HindIII 7637 aynchronous plus rapamycin rep1

value: Rapamycin (1ug/ml)


title: RNAseq_SCer_4662_Async_37C_rep1

source_name: RNAseq  4662 aynchronous 37C rep1


title: 3Cseq_HindIII_SCer_6840_Async_+rap_rep1

source_name: 3Cseq HindIII 6840 aynchronous plus rapamycin rep1


title: RNAseq_SCer_12_Async_37C_rep3

source_name: RNAseq  12 aynchronous 37C rep3


title: RNAseq_SCer_12_Async_37C_rep1

source_name: RNAseq  12 aynchronous 37C rep1


title: RNAseq_SCer_4662_Async_23C_rep1

source_name: RNAseq  4662 aynchronous 23C rep1


title: RNAseq_SCer_7637_Async_+rap_rep3

source_name: RNAseq  7637 aynchronous plus rapamycin rep3


title: RNAseq_SCer_12_Async_23C_rep1

source_name: RNAseq 12 aynchronous 23C rep1


title: RNAseq_SCer_6840_Async_+rap_rep3

source_name: RNAseq  6840 aynchronous plus rapamycin rep3


title: negative control miRNA transfected KPL-4 cell lines, rep 2

description: Gene expression 24h after scrambled miRNA transfection of KPL-4 cell lines

source_name: scrambled miRNA transfected KPL-4 cell lines, rep 2

value: negative control miRNA


title: miR-342-5p transfected JKPL-4 cell lines, rep 2

description: Gene expression 24h after miR-342-5p transfection of KPL-4 cell lines


title: RNAseq_SCer_4662_Async_23C_rep3

source_name: RNAseq  4662 aynchronous 23C rep3


title: negative control miRNA transfected KPL-4 cell lines, rep 3

source_name: scrambled miRNA transfected KPL-4 cell lines, rep 3


title: miR-342-5p transfected KPL-4 cell lines, rep 3


title: negative control miRNA transfected JIMT-1 cell lines, rep 3

description: Gene expression 24h after scrambled miRNA transfection of JIMT-1 cell lines

source_name: scrambled miRNA transfected JIMT-1 cell lines, rep 3


title: not transfected JIMT-1 cell lines, rep 1


title: miR-342-5p transfected JIMT-1 cell lines, rep 2

description: Gene expression 24h after miR-342-5p transfection of JIMT-1 cell lines


title: negative control miRNA transfected KPL-4 cell lines, rep 1

source_name: scrambled miRNA transfected KPL-4 cell lines, rep 1


title: miR-342-5p transfected KPL-4 cell lines, rep 1


title: miR-342-5p transfected JIMT-1 cell lines, rep 3


title: RNAseq_SCer_7637_Async_+rap_rep2

source_name: RNAseq  7637 aynchronous plus rapamycin rep2


title: miR-342-5p transfected JIMT-1 cell lines, rep 1


title: RNAseq_SCer_6840_Async_+rap_rep1

source_name: RNAseq  6840 aynchronous plus rapamycin rep1


title: RNAseq_SCer_6840_Async_rep1

source_name: RNAseq  6840 aynchronous rep1


title: negative control miRNA transfected JIMT-1 cell lines, rep 1

source_name: scrambled miRNA transfected JIMT-1 cell lines, rep 1


title: insitu3Cseq_HindIII_Scer_Async_12 _2hr_37C_pombespike_rep2

source_name: insitu3Cseq HindIII asynchronous 12 37C pombespike rep2

value: 90% S. cerevisiae nuclei, 10% S.pombe nuclei


title: RNAseq_SCer_6840_Async_+rap_rep2

source_name: RNAseq  6840 aynchronous plus rapamycin rep2


title: insitu3Cseq_HindIII_Scer_Async_12 _2hr_37C_elegansspike_rep1

organism:
Saccharomyces cerevisiae
Caenorhabditis elegans

source_name: insitu3Cseq HindIII asynchronous 12 37C elegansspike rep1

value: 90% S. cerevisiae nuclei, 10% C. elegans nuclei


title: insitu3Cseq_HindIII_Scer_Async_4662 _2hr_37C_pombespike_rep2


title: insitu3Cseq_HindIII_Scer_Async_4662 _2hr_23C_elegansspike_rep1

source_name: insitu3Cseq HindIII asynchronous 12 23C elegansspike rep1


title: insitu3Cseq_HindIII_Scer_Async_4662 _2hr_37C_elegansspike_rep1


title: negative control miRNA transfected JIMT-1 cell lines, rep 2

source_name: scrambled miRNA transfected JIMT-1 cell lines, rep 2


title: insitu3Cseq_HindIII_Scer_Async_4662 _2hr_23C_pombespike_rep2

source_name: insitu3Cseq HindIII asynchronous 12 23C pombespike rep2


title: insitu3Cseq_HindIII_Scer_Async_12 _2hr_23C_elegansspike_rep1


title: insitu3Cseq_HindIII_Scer_Async_12 _2hr_23C_pombespike_rep2


title: RNAseq_SCer_7637_Async_+rap_rep1

source_name: RNAseq  7637 aynchronous plus rapamycin rep1


title: RNAseq_SCer_7637_Async_rep1

source_name: RNAseq  7637 aynchronous rep1


title: Sample_144_Severe_Spm

status: Public on Oct 02 2017

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

hyb_protocol: hybridized to Affymetrix HG U133+ PM GeneChips following standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw microarray gene expression data was normalized using RMA in R and subjected to several quality control procedures. Differentially expressed genes were identified using a linear modelling approach in the limma package in R and only genes with FDR corrected p-values < 0.05 for multiple testing (using the Benjamini-Hochberg method) were considered significant.

source_name: Induced sputum gene expression data from severe asthmatic

label_protocol: standard Affymetrix protocol; RNA was isolated and reverse transcribed into cDNA using a High Capacity cDNA Reverse Transcription Kit with random hexamers. RT-qPCR was performed for each gene target in duplicate using Taqman Universal PCR Master Mix, No AmpErase UNG on 7900HT Fast Real-Time PCR System. GAPDH was used as a normalizer to obtain fold changes and t-tests were performed to determine significance. Thermal cycling conditions were 95˚C for 10 minutes followed by 40 cycles of 95˚C for 15 seconds and 60˚C for 1 minute.

growth_protocol: sample collection: Lung samples were obtained by hypertonic-saline sputum induction, bronchoscopy, bronchoalveolar lavage and endobronchial epithelial brushing as previously described (Hinks et al., 2015).

extract_protocol: RNA was isolated from the samples using the Absolutely RNA Nanoprep Kit. RNA quality was assessed using a Bioanalyzer 2100 and samples were hybridized to Affymetrix HG U133+ PM GeneChips

tag: Sex

value: F

tag: age (yrs)

tag: acq

tag: smoking

value: Never

tag: allergic rhinitis

value: Yes

tag: nasal polyps

value: No

tag: ics dose

tag: ocs dose

tag: fvc

tag: reversibility

tag: gina control


title: Sample_142_Severe_Spm

value: M

value: Former


title: Sample_145_Severe_Spm


title: Sample_140_Severe_Spm


title: Sample_141_Severe_Spm


title: Sample_138_Severe_Spm