title: Mono_nonclassical_S114


title: Mono_nonclassical_S121

status: Public on Apr 21 2017

type: SRA

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute

description:
paired-end RNA-seq data
processed data file:
raw.expMatrix_DCnMono.discovery.set.submission.txt

library_source: transcriptomic

data_processing:
Read were aligned to the UCSC hg19 transcriptomee using Bowtie v0.12.7
Expression levels were quantified using RSEM v1.2.1 (TPM values)
UCSC genome table browser was used to map UCSC gene ID (kgID) and the gene name (geneSymbol) for all genes in hg19
If multiple UCSC gene IDs are assigned to the same geneSymbol, the TPM values of all kgIDs that share the same geneSymbol are summed
Genome_build: hg19
Supplementary_files_format_and_content: Text file with tab delimiters

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Enriched immune cell fractions isolated from healthy blood PBMCs were FACS sorted in 96-well plates (single cell sorted) containing lysis buffer (TCL together with 1% of 2-Mercaptoethanol).
Smart-seq2 (Picelli et al., Nature Methods, 2014)
Full-length RNA-sequencing


title: Mono_nonclassical_S11


title: Mono_nonclassical_S110


title: Mono_nonclassical_S122


title: Mono_nonclassical_S12


title: Mono_nonclassical_S117


title: Mono_nonclassical_S111


title: Mono_nonclassical_S105


title: Mono_nonclassical_S116


title: Mono_nonclassical_S100


title: Mono_nonclassical_S113


title: Mono_nonclassical_S1


title: Mono_nonclassical_S112


title: Mono_nonclassical_S119


title: Mono_nonclassical_S109


title: Mono_nonclassical_S10


title: Mono_nonclassical_S107


title: Mono_nonclassical_S103


title: Mono_intermediate_S99


title: Mono_nonclassical_S108


title: Mono_intermediate_S98


title: Mono_intermediate_S97


title: Mono_nonclassical_S101


title: Mono_intermediate_S95


title: Mono_nonclassical_S104


title: Mono_nonclassical_S106


title: Mono_nonclassical_S102


title: Mono_intermediate_S94


title: Mono_intermediate_S91


title: Mono_intermediate_S96


title: Mono_intermediate_S93


title: Mono_intermediate_S92


title: Mono_intermediate_S90


title: Mono_intermediate_S9


title: Mono_intermediate_S89


title: Mono_intermediate_S88


title: Mono_intermediate_S84


title: Mono_intermediate_S86


title: Mono_intermediate_S83


title: Mono_intermediate_S85


title: Mono_intermediate_S80


title: Mono_intermediate_S81


title: Mono_intermediate_S82


title: Mono_intermediate_S78


title: Mono_intermediate_S8


title: Mono_intermediate_S79


title: Mono_intermediate_S75


title: Mono_intermediate_S72


title: Mono_intermediate_S76


title: Mono_intermediate_S77


title: Mono_intermediate_S74


title: Mono_intermediate_S70


title: Mono_intermediate_S87


title: Mono_intermediate_S73


title: Mono_intermediate_S69


title: Mono_intermediate_S7


title: Mono_intermediate_S68


title: Mono_intermediate_S67


title: Mono_intermediate_S62


title: Mono_intermediate_S66


title: Mono_intermediate_S64


title: Mono_intermediate_S63


title: Mono_intermediate_S65


title: Mono_intermediate_S61


title: Mono_intermediate_S71


title: Mono_intermediate_S58


title: Mono_intermediate_S59


title: Mono_intermediate_S54


title: Mono_intermediate_S60


title: Mono_intermediate_S6


title: Mono_intermediate_S57


title: Mono_intermediate_S56


title: Mono_intermediate_S45


title: Mono_intermediate_S48


title: Mono_intermediate_S49


title: Mono_intermediate_S43


title: Mono_intermediate_S42


title: Mono_intermediate_S4


title: Mono_intermediate_S55


title: Mono_intermediate_S53


title: Mono_intermediate_S52


title: Mono_intermediate_S50


title: Mono_intermediate_S47


title: Mono_intermediate_S35


title: Mono_intermediate_S51


title: Mono_intermediate_S5


title: Mono_intermediate_S34


title: Mono_intermediate_S37


title: Mono_intermediate_S46


title: Mono_intermediate_S44


title: Mono_intermediate_S30


title: Mono_intermediate_S3


title: Mono_intermediate_S40


title: Mono_intermediate_S39


title: Mono_intermediate_S32


title: Mono_intermediate_S41


title: Mono_intermediate_S38


title: Mono_intermediate_S24


title: Mono_intermediate_S27


title: Mono_intermediate_S22


title: Mono_intermediate_S36


title: Mono_intermediate_S26


title: Mono_intermediate_S33


title: Mono_intermediate_S31


title: Mono_intermediate_S17


title: Mono_intermediate_S29


title: Mono_intermediate_S16


title: Mono_intermediate_S2


title: Mono_intermediate_S13


title: Mono_intermediate_S25


title: Mono_intermediate_S14


title: Mono_intermediate_S28


title: Mono_intermediate_S21


title: Mono_intermediate_S120


title: Mono_intermediate_S12


title: Mono_intermediate_S119


title: Mono_intermediate_S118


title: Mono_intermediate_S23


title: Mono_intermediate_S20


title: Mono_intermediate_S116


title: Mono_intermediate_S115


title: Mono_intermediate_S114


title: Mono_intermediate_S19


title: Mono_intermediate_S18


title: Mono_intermediate_S124


title: Mono_intermediate_S15


title: Mono_intermediate_S117


title: Mono_intermediate_S111


title: Mono_intermediate_S121


title: Mono_intermediate_S113


title: Mono_intermediate_S109


title: Mono_intermediate_S123


title: Mono_intermediate_S112


title: Mono_intermediate_S105


title: Mono_intermediate_S104


title: Mono_intermediate_S110


title: Mono_intermediate_S102


title: Mono_intermediate_S122


title: Mono_intermediate_S108


title: Mono_intermediate_S101


title: Mono_intermediate_S106


title: Mono_intermediate_S107


title: Mono_intermediate_S11


title: Mono_intermediate_S103


title: Mono_intermediate_S10


title: Mono_intermediate_S100


title: Mono_intermediate_S1


title: Mono_classical_S98


title: Mono_classical_S99


title: Mono_classical_S96


title: Mono_classical_S95


title: Mono_classical_S97


title: Mono_classical_S90


title: Mono_classical_S92


title: Mono_classical_S94


title: Mono_classical_S93


title: Mono_classical_S91


title: Mono_classical_S89


title: Mono_classical_S9


title: Mono_classical_S88


title: Mono_classical_S87


title: Mono_classical_S86


title: Mono_classical_S81


title: Mono_classical_S83


title: Mono_classical_S82


title: Mono_classical_S8


title: Mono_classical_S84


title: Mono_classical_S79


title: Mono_classical_S85


title: Mono_classical_S80


title: Mono_classical_S77


title: Mono_classical_S78


title: Mono_classical_S75


title: Mono_classical_S74


title: Mono_classical_S73


title: Mono_classical_S76


title: Mono_classical_S71


title: Mono_classical_S72


title: Mono_classical_S7


title: Mono_classical_S69


title: Mono_classical_S70


title: Mono_classical_S64


title: Mono_classical_S67


title: Mono_classical_S66


title: Mono_classical_S65


title: Mono_classical_S68


title: Mono_classical_S61


title: Mono_classical_S60


title: Mono_classical_S62


title: Mono_classical_S6


title: Mono_classical_S63


title: Mono_classical_S59


title: Mono_classical_S58


title: Mono_classical_S55


title: Mono_classical_S56


title: Mono_classical_S53


title: Mono_classical_S54


title: Mono_classical_S51


title: Mono_classical_S57


title: Mono_classical_S49


title: Mono_classical_S5


title: Mono_classical_S52


title: Mono_classical_S47


title: Mono_classical_S50


title: Mono_classical_S48


title: Mono_classical_S46


title: Mono_classical_S44


title: Mono_classical_S43


title: Mono_classical_S45


title: Mono_classical_S39


title: Mono_classical_S41


title: Mono_classical_S42


title: Mono_classical_S4


title: Mono_classical_S37


title: Mono_classical_S38


title: Mono_classical_S40


title: Mono_classical_S34


title: Mono_classical_S33


title: Mono_classical_S36


title: Mono_classical_S35


title: Mono_classical_S32


title: Mono_classical_S30


title: Mono_classical_S3


title: Mono_classical_S27


title: Mono_classical_S31


title: Mono_classical_S25


title: Mono_classical_S29


title: Mono_classical_S24


title: Mono_classical_S21


title: Mono_classical_S26


title: Mono_classical_S23


title: Mono_classical_S20


title: Mono_classical_S2


title: Mono_classical_S16


title: Mono_classical_S17


title: Mono_classical_S22


title: Mono_classical_S18


title: Mono_classical_S19


title: Mono_classical_S15


title: Mono_classical_S13


title: Mono_classical_S122


title: Mono_classical_S121


title: Mono_classical_S124


title: Mono_classical_S14


title: Mono_classical_S123


title: Mono_classical_S120


title: Mono_classical_S118


title: Mono_classical_S12


title: Mono_classical_S28


title: Mono_classical_S116


title: Mono_classical_S119


title: Mono_classical_S117


title: Mono_classical_S115


title: Mono_classical_S113


title: Mono_classical_S114


title: Mono_classical_S112


title: Mono_classical_S110


title: Mono_classical_S108


title: Mono_classical_S11


title: Mono_classical_S111


title: Mono_classical_S109


title: Mono_classical_S104


title: Mono_classical_S106


title: Mono_classical_S105


title: Mono_classical_S107


title: Mono_classical_S103


title: Mono_classical_S100


title: Mono_classical_S102


title: Mono_classical_S101


title: Mono_classical_S1


title: Mono_classical_S10


title: DoubleNeg_P9_S71


title: DoubleNeg_P9_S72


title: DoubleNeg_P9_S68


title: DoubleNeg_P9_S70


title: DoubleNeg_P9_S66


title: DoubleNeg_P9_S67


title: DoubleNeg_P9_S69


title: DoubleNeg_P9_S65


title: DoubleNeg_P9_S63


title: DoubleNeg_P9_S62


title: DoubleNeg_P9_S60


title: DoubleNeg_P9_S64


title: DoubleNeg_P9_S61


title: DoubleNeg_P9_S59


title: DoubleNeg_P9_S57


title: DoubleNeg_P9_S55


title: DoubleNeg_P9_S54


title: DoubleNeg_P9_S58


title: DoubleNeg_P9_S53


title: DoubleNeg_P9_S50


title: DoubleNeg_P9_S52


title: DoubleNeg_P9_S49


title: DoubleNeg_P8_S47


title: DoubleNeg_P8_S48


title: DoubleNeg_P8_S44


title: DoubleNeg_P8_S45


title: DoubleNeg_P8_S42


title: DoubleNeg_P8_S36


title: DoubleNeg_P8_S35


title: DoubleNeg_P8_S39


title: DoubleNeg_P8_S34


title: DoubleNeg_P8_S38


title: DoubleNeg_P8_S33


title: DoubleNeg_P8_S31


title: DoubleNeg_P9_S56


title: DoubleNeg_P8_S27


title: DoubleNeg_P8_S32


title: DoubleNeg_P9_S51


title: DoubleNeg_P8_S46


title: DoubleNeg_P7_S9


title: DoubleNeg_P8_S25


title: DoubleNeg_P8_S43


title: DoubleNeg_P8_S40


title: DoubleNeg_P8_S41


title: DoubleNeg_P7_S7


title: DoubleNeg_P8_S28


title: DoubleNeg_P8_S37


title: DoubleNeg_P7_S3


title: DoubleNeg_P7_S5


title: DoubleNeg_P7_S4


title: DoubleNeg_P7_S20


title: DoubleNeg_P7_S21


title: DoubleNeg_P8_S30


title: DoubleNeg_P8_S29


title: DoubleNeg_P7_S18


title: DoubleNeg_P8_S26


title: DoubleNeg_P7_S16


title: DoubleNeg_P7_S8


title: DoubleNeg_P7_S13


title: DoubleNeg_P7_S24


title: DoubleNeg_P7_S6


title: DoubleNeg_P7_S10


title: DoubleNeg_P7_S23


title: DoubleNeg_P7_S12


title: DoubleNeg_P7_S1


title: DoubleNeg_P4_S47


title: DoubleNeg_P7_S2


title: DoubleNeg_P4_S44


title: DoubleNeg_P7_S22


title: DoubleNeg_P7_S19


title: DoubleNeg_P7_S17


title: DoubleNeg_P4_S39


title: DoubleNeg_P4_S38


title: DoubleNeg_P7_S15


title: DoubleNeg_P4_S37


title: DoubleNeg_P4_S35


title: DoubleNeg_P7_S11


title: DoubleNeg_P4_S34


title: DoubleNeg_P4_S46


title: DoubleNeg_P4_S32


title: DoubleNeg_P4_S45


title: DoubleNeg_P4_S48


title: DoubleNeg_P4_S31


title: DoubleNeg_P4_S41


title: DoubleNeg_P4_S28


title: DoubleNeg_P4_S30


title: DoubleNeg_P4_S27


title: DoubleNeg_P4_S42


title: DoubleNeg_P4_S26


title: DoubleNeg_P3_S9


title: DoubleNeg_P4_S25


title: DoubleNeg_P3_S7


title: DoubleNeg_P3_S6


title: DoubleNeg_P3_S8


title: DoubleNeg_P4_S40


title: DoubleNeg_P4_S36


title: DoubleNeg_P4_S43


title: DoubleNeg_P3_S5


title: DoubleNeg_P3_S3


title: DoubleNeg_P3_S4


title: DoubleNeg_P3_S23


title: DoubleNeg_P4_S33


title: DoubleNeg_P3_S22


title: DoubleNeg_P3_S24


title: DoubleNeg_P4_S29


title: DoubleNeg_P3_S20


title: DoubleNeg_P3_S21


title: DoubleNeg_P3_S2


title: DoubleNeg_P3_S17


title: DoubleNeg_P3_S16


title: DoubleNeg_P3_S18


title: DoubleNeg_P3_S14


title: DoubleNeg_P3_S19


title: DoubleNeg_P3_S15


title: DoubleNeg_P3_S12


title: DoubleNeg_P3_S11


title: DoubleNeg_P3_S13


title: DoubleNeg_P14_S96


title: DoubleNeg_P3_S1


title: DoubleNeg_P14_S93


title: DoubleNeg_P14_S88


title: DoubleNeg_P14_S95


title: DoubleNeg_P14_S90


title: DoubleNeg_P14_S89


title: DoubleNeg_P14_S94


title: DoubleNeg_P14_S87


title: DoubleNeg_P14_S86


title: DoubleNeg_P14_S85


title: DoubleNeg_P3_S10


title: DoubleNeg_P14_S83


title: DoubleNeg_P14_S81


title: DoubleNeg_P14_S80


title: DoubleNeg_P14_S92


title: DoubleNeg_P14_S82


title: DoubleNeg_P14_S91


title: DoubleNeg_P14_S84


title: DoubleNeg_P14_S79


title: DoubleNeg_P14_S78


title: DoubleNeg_P14_S76


title: DoubleNeg_P14_S75


title: DoubleNeg_P14_S74


title: DoubleNeg_P14_S77


title: DoubleNeg_P14_S73


title: DoubleNeg_P13_S72


title: DoubleNeg_P13_S71


title: DoubleNeg_P13_S70


title: DoubleNeg_P13_S66


title: DoubleNeg_P13_S64


title: DoubleNeg_P13_S61


title: DoubleNeg_P13_S67


title: DoubleNeg_P13_S65


title: DoubleNeg_P13_S62


title: DoubleNeg_P13_S69


title: DoubleNeg_P13_S68


title: DoubleNeg_P13_S59


title: DoubleNeg_P13_S63


title: DoubleNeg_P13_S58


title: DoubleNeg_P13_S60


title: DoubleNeg_P13_S56


title: DoubleNeg_P13_S57


title: DoubleNeg_P13_S55


title: DoubleNeg_P13_S54


title: DoubleNeg_P10_S96


title: DoubleNeg_P13_S53


title: DoubleNeg_P13_S49


title: DoubleNeg_P10_S95


title: DoubleNeg_P13_S51


title: DoubleNeg_P13_S52


title: DoubleNeg_P10_S92


title: DoubleNeg_P13_S50


title: DoubleNeg_P10_S90


title: DoubleNeg_P10_S91


title: DoubleNeg_P10_S94


title: DoubleNeg_P10_S85


title: DoubleNeg_P10_S84


title: DoubleNeg_P10_S88


title: DoubleNeg_P10_S93


title: DoubleNeg_P10_S89


title: DoubleNeg_P10_S87


title: DoubleNeg_P10_S86


title: DoubleNeg_P10_S79


title: DoubleNeg_P10_S81


title: DoubleNeg_P10_S76


title: DoubleNeg_P10_S82


title: DoubleNeg_P10_S77


title: DoubleNeg_P10_S74


title: DoubleNeg_P10_S78


title: DoubleNeg_P10_S75


title: DoubleNeg_P10_S80


title: DoubleNeg_P10_S73


title: DoubleNeg_P10_S83


title: CD1C_P9_S72


title: CD1C_P9_S71


title: CD1C_P9_S70


title: CD1C_P9_S65


title: CD1C_P9_S67


title: CD1C_P9_S69


title: CD1C_P9_S66


title: CD1C_P9_S68


title: CD1C_P9_S63


title: CD1C_P9_S62


title: CD1C_P9_S64


title: CD1C_P9_S59


title: CD1C_P9_S60


title: CD1C_P9_S58


title: CD1C_P9_S57


title: CD1C_P9_S55


title: CD1C_P9_S56


title: CD1C_P9_S54


title: CD1C_P9_S53


title: CD1C_P9_S52


title: CD1C_P9_S49


title: CD1C_P9_S51


title: CD1C_P8_S44


title: CD1C_P9_S50


title: CD1C_P8_S42


title: CD1C_P8_S48


title: BPDCN4_S5_S55

description:
paired-end RNA-seq data
processed data file:
raw.expMatrix_deeper.characterization.set.submission.txt


title: BPDCN4_S8_S8


title: CD1C_P8_S41


title: BPDCN4_S4_S43


title: BPDCN4_S9_S20


title: CD1C_P8_S47


title: CD1C_P8_S46


title: BPDCN4_S47_S96


title: DoubleNeg_P7_S14


title: CD1C_P8_S38


title: CD1C_P8_S45


title: CD1C_P8_S37


title: CD1C_P8_S43


title: BPDCN4_S7_S79


title: BPDCN4_S6_S67


title: CD1C_P8_S40


title: BPDCN4_S42_S36


title: BPDCN4_S46_S84


title: CD1C_P8_S39


title: BPDCN4_S45_S72


title: CD1C_P8_S32


title: BPDCN4_S44_S60


title: BPDCN4_S43_S48


title: CD1C_P8_S34


title: BPDCN4_S38_S83


title: BPDCN4_S41_S24


title: CD1C_P8_S27


title: CD1C_P8_S33


title: BPDCN4_S36_S59


title: BPDCN4_S37_S71


title: BPDCN4_S35_S47


title: CD1C_P8_S29


title: BPDCN4_S3_S31


title: BPDCN4_S40_S12


title: CD1C_P8_S36


title: CD1C_P8_S30


title: BPDCN4_S39_S95


title: CD1C_P8_S28


title: CD1C_P8_S25


title: BPDCN4_S32_S11


title: CD1C_P7_S9


title: BPDCN4_S33_S23


title: BPDCN4_S34_S35


title: CD1C_P7_S8


title: BPDCN4_S30_S82


title: BPDCN4_S31_S94


title: CD1C_P7_S6


title: BPDCN4_S2_S19


title: CD1C_P8_S26


title: CD1C_P7_S5


title: BPDCN4_S27_S46


title: CD1C_P7_S24


title: CD1C_P7_S4


title: BPDCN4_S29_S70


title: BPDCN4_S26_S34


title: CD1C_P7_S22


title: CD1C_P7_S23


title: CD1C_P7_S20


title: BPDCN4_S28_S58


title: BPDCN4_S23_S93


title: CD1C_P7_S7


title: BPDCN4_S25_S22


title: BPDCN4_S20_S57


title: CD1C_P7_S3


title: CD1C_P9_S61


title: BPDCN4_S24_S10


title: CD1C_P7_S21


title: CD1C_P7_S2


title: BPDCN4_S22_S81


title: BPDCN4_S21_S69


title: CD1C_P7_S19


title: CD1C_P7_S17


title: CD1C_P7_S13


title: CD1C_P7_S15


title: CD1C_P7_S16


title: BPDCN4_S1_S7


title: CD1C_P7_S18


title: BPDCN4_S19_S45


title: CD1C_P8_S31


title: BPDCN4_S14_S80


title: CD1C_P7_S10


title: CD1C_P7_S14


title: BPDCN4_S18_S33


title: CD1C_P4_S48


title: CD1C_P8_S35


title: BPDCN4_S16_S9


title: BPDCN4_S17_S21


title: BPDCN4_S15_S92


title: CD1C_P7_S12


title: CD1C_P4_S46


title: CD1C_P7_S11


title: BPDCN4_S13_S68


title: BPDCN4_S12_S56


title: CD1C_P7_S1


title: BPDCN3_S9_S14


title: BPDCN4_S11_S44


title: BPDCN3_S4_S37


title: BPDCN4_S10_S32


title: BPDCN3_S5_S49


title: BPDCN3_S8_S2


title: CD1C_P4_S45


title: CD1C_P4_S47


title: BPDCN3_S7_S73


title: CD1C_P4_S40


title: CD1C_P4_S44


title: BPDCN3_S6_S61


title: CD1C_P4_S43


title: CD1C_P4_S37


title: CD1C_P4_S41


title: CD1C_P4_S42


title: BPDCN3_S47_S90


title: BPDCN3_S43_S42


title: CD1C_P4_S36


title: BPDCN3_S46_S78


title: BPDCN3_S44_S54


title: CD1C_P4_S35


title: BPDCN3_S41_S18


title: CD1C_P4_S38


title: BPDCN3_S45_S66


title: CD1C_P4_S39


title: BPDCN3_S42_S30


title: BPDCN3_S40_S6


title: CD1C_P4_S34


title: CD1C_P4_S31


title: BPDCN3_S39_S89


title: CD1C_P4_S33


title: CD1C_P4_S32


title: CD1C_P4_S30


title: BPDCN3_S38_S77


title: CD1C_P4_S29


title: BPDCN3_S36_S53


title: CD1C_P4_S28


title: CD1C_P4_S27


title: BPDCN3_S31_S88


title: CD1C_P4_S26


title: CD1C_P3_S9


title: BPDCN3_S33_S17


title: BPDCN3_S32_S5


title: BPDCN3_S3_S25


title: BPDCN3_S29_S64


title: CD1C_P3_S5


title: BPDCN3_S30_S76


title: BPDCN3_S2_S13


title: CD1C_P3_S4


title: CD1C_P3_S3


title: BPDCN3_S37_S65


title: CD1C_P3_S22


title: BPDCN3_S34_S29


title: CD1C_P3_S24


title: BPDCN3_S22_S75


title: BPDCN3_S23_S87


title: CD1C_P3_S7


title: BPDCN3_S35_S41


title: BPDCN3_S20_S51


title: CD1C_P3_S2


title: BPDCN3_S25_S16


title: CD1C_P4_S25


title: CD1C_P3_S6


title: CD1C_P3_S8


title: BPDCN3_S28_S52


title: BPDCN3_S19_S39


title: BPDCN3_S1_S1


title: BPDCN3_S17_S15


title: BPDCN3_S21_S63


title: CD1C_P3_S15


title: CD1C_P3_S21


title: CD1C_P3_S12


title: BPDCN3_S26_S28


title: CD1C_P3_S20


title: CD1C_P3_S19


title: CD1C_P3_S23


title: BPDCN3_S27_S40


title: CD1C_P3_S1


title: CD1C_P14_S96


title: BPDCN3_S24_S4


title: CD1C_P3_S14


title: BPDCN3_S15_S86


title: CD1C_P3_S13


title: BPDCN3_S14_S74


title: BPDCN3_S13_S62


title: BPDCN3_S12_S50


title: BPDCN2_S95_S95


title: BPDCN3_S11_S38


title: BPDCN3_S18_S27


title: CD1C_P3_S17


title: CD1C_P14_S93


title: BPDCN3_S16_S3


title: CD1C_P3_S16


title: BPDCN3_S10_S26


title: BPDCN2_S93_S93


title: CD1C_P14_S95


title: CD1C_P14_S91


title: CD1C_P3_S11


title: BPDCN2_S9_S9


title: BPDCN2_S91_S91


title: CD1C_P14_S90


title: CD1C_P14_S94


title: BPDCN2_S94_S94


title: CD1C_P3_S10


title: CD1C_P14_S88


title: CD1C_P14_S92


title: BPDCN2_S96_S96


title: BPDCN2_S8_S8


title: CD1C_P14_S89


title: BPDCN2_S92_S92


title: BPDCN2_S90_S90


title: CD1C_P14_S86


title: CD1C_P14_S85


title: CD1C_P14_S87


title: CD1C_P14_S84


title: BPDCN2_S87_S87


title: CD1C_P14_S83


title: BPDCN2_S88_S88


title: BPDCN2_S85_S85


title: BPDCN2_S83_S83


title: CD1C_P14_S82


title: BPDCN2_S86_S86


title: BPDCN2_S82_S82


title: CD1C_P14_S79


title: CD1C_P14_S81


title: BPDCN2_S81_S81


title: CD1C_P3_S18


title: CD1C_P14_S78


title: BPDCN2_S80_S80


title: BPDCN2_S89_S89


title: CD1C_P14_S77


title: CD1C_P14_S76


title: BPDCN2_S79_S79


title: CD1C_P14_S75


title: BPDCN2_S78_S78


title: BPDCN2_S84_S84


title: BPDCN2_S77_S77


title: CD1C_P14_S74


title: BPDCN2_S7_S7


title: CD1C_P14_S73


title: BPDCN2_S75_S75


title: BPDCN2_S76_S76


title: CD1C_P14_S80


title: CD1C_P13_S72


title: BPDCN2_S73_S73


title: BPDCN2_S74_S74


title: BPDCN2_S72_S72


title: CD1C_P13_S71


title: CD1C_P13_S69


title: CD1C_P13_S70


title: BPDCN2_S71_S71


title: CD1C_P13_S68


title: CD1C_P13_S67


title: BPDCN2_S70_S70


title: BPDCN2_S69_S69


title: BPDCN2_S68_S68


title: BPDCN2_S67_S67


title: CD1C_P13_S61


title: CD1C_P13_S63


title: CD1C_P13_S65


title: BPDCN2_S66_S66


title: CD1C_P13_S66


title: CD1C_P13_S60


title: CD1C_P13_S62


title: BPDCN2_S64_S64


title: BPDCN2_S5_S5


title: BPDCN2_S61_S61


title: CD1C_P13_S64


title: BPDCN2_S59_S59


title: BPDCN2_S62_S62


title: CD1C_P13_S59


title: CD1C_P13_S58


title: CD1C_P13_S57


title: CD1C_P13_S55


title: BPDCN2_S58_S58


title: BPDCN2_S56_S56


title: CD1C_P13_S54


title: BPDCN2_S55_S55


title: BPDCN2_S57_S57


title: CD1C_P13_S56


title: CD1C_P13_S53


title: CD1C_P13_S52


title: CD1C_P13_S51


title: BPDCN2_S52_S52


title: BPDCN2_S53_S53


title: BPDCN2_S51_S51


title: CD1C_P13_S50


title: BPDCN2_S48_S48


title: CD1C_P13_S49


title: CD1C_P10_S96


title: BPDCN2_S4_S4


title: BPDCN2_S50_S50


title: CD1C_P10_S95


title: CD1C_P10_S94


title: BPDCN2_S44_S44


title: CD1C_P10_S92


title: BPDCN2_S46_S46


title: BPDCN2_S47_S47


title: BPDCN2_S41_S41


title: CD1C_P10_S93


title: BPDCN2_S40_S40


title: CD1C_P10_S91


title: BPDCN2_S43_S43


title: CD1C_P10_S88


title: CD1C_P10_S89


title: CD1C_P10_S90


title: CD1C_P10_S87


title: BPDCN2_S39_S39


title: BPDCN2_S37_S37


title: BPDCN2_S3_S3


title: CD1C_P10_S86


title: CD1C_P10_S83


title: CD1C_P10_S84


title: BPDCN2_S35_S35


title: BPDCN2_S36_S36


title: CD1C_P10_S85


title: CD1C_P10_S80


title: BPDCN2_S33_S33


title: CD1C_P10_S82


title: BPDCN2_S31_S31


title: CD1C_P10_S81


title: BPDCN2_S32_S32


title: BPDCN2_S30_S30


title: CD1C_P10_S79


title: CD1C_P10_S78


title: BPDCN2_S27_S27


title: CD1C_P10_S77


title: BPDCN2_S26_S26


title: BPDCN2_S28_S28


title: BPDCN2_S2_S2


title: CD1C_P10_S76


title: CD1C_P10_S75


title: BPDCN2_S24_S24


title: BPDCN2_S22_S22


title: CD1C_P10_S73


title: CD141_P9_S72


title: BPDCN2_S38_S38


title: CD1C_P10_S74


title: BPDCN2_S19_S19


title: BPDCN2_S18_S18


title: CD141_P9_S71


title: BPDCN2_S20_S20


title: BPDCN2_S14_S14


title: BPDCN2_S17_S17


title: BPDCN2_S12_S12


title: CD141_P9_S67


title: BPDCN2_S11_S11


title: CD141_P9_S68


title: CD141_P9_S70


title: CD141_P9_S69


title: BPDCN2_S13_S13


title: CD141_P9_S65


title: BPDCN2_S10_S10


title: CD141_P9_S66


title: BPDCN1_S95_S96


title: CD141_P9_S62


title: CD141_P9_S64


title: CD141_P9_S63


title: BPDCN1_S9_S9


title: BPDCN1_S94_S95


title: CD141_P9_S60


title: CD141_P9_S61


title: BPDCN1_S93_S94


title: BPDCN1_S92_S93


title: CD141_P9_S59


title: BPDCN1_S91_S92


title: CD141_P9_S58


title: BPDCN1_S90_S91


title: CD141_P9_S57


title: CD141_P9_S56


title: CD141_P9_S55


title: BPDCN1_S89_S90


title: BPDCN1_S88_S89


title: BPDCN1_S87_S88


title: BPDCN1_S85_S86


title: BPDCN1_S86_S87


title: BPDCN1_S84_S84


title: CD141_P9_S53


title: CD141_P9_S54


title: CD141_P9_S50


title: CD141_P9_S51


title: CD141_P8_S48


title: BPDCN1_S81_S81


title: BPDCN1_S82_S82


title: CD141_P9_S52


title: BPDCN1_S80_S80


title: BPDCN1_S83_S83


title: CD141_P8_S47


title: CD141_P9_S49


title: BPDCN1_S7_S7


title: CD141_P8_S45


title: CD141_P8_S46


title: CD141_P8_S44


title: BPDCN1_S79_S79


title: CD141_P8_S43


title: BPDCN1_S78_S78


title: BPDCN1_S77_S77


title: CD141_P8_S42


title: BPDCN1_S76_S76


title: BPDCN1_S75_S75


title: CD141_P8_S39


title: CD141_P8_S40


title: CD141_P8_S41


title: BPDCN1_S74_S74


title: BPDCN1_S73_S73


title: CD141_P8_S37


title: BPDCN1_S8_S8


title: CD141_P8_S38


title: BPDCN1_S6_S6


title: BPDCN1_S72_S72


title: BPDCN1_S70_S70


title: CD141_P8_S34


title: BPDCN1_S69_S69


title: CD141_P8_S33


title: CD141_P8_S32


title: BPDCN1_S71_S71


title: CD141_P8_S36


title: BPDCN1_S68_S68


title: CD141_P8_S35


title: BPDCN1_S67_S67


title: CD141_P8_S31


title: CD141_P8_S30


title: CD141_P8_S29


title: BPDCN1_S66_S66


title: BPDCN1_S64_S64


title: BPDCN1_S65_S65


title: BPDCN1_S63_S63


title: CD141_P8_S27


title: CD141_P8_S28


title: CD141_P8_S26


title: BPDCN1_S61_S61


title: BPDCN1_S60_S60


title: CD141_P7_S8


title: CD141_P7_S9


title: BPDCN1_S62_S62


title: CD141_P8_S25


title: BPDCN1_S59_S59


title: BPDCN1_S5_S5


title: BPDCN1_S58_S58


title: BPDCN1_S54_S54


title: BPDCN1_S57_S57


title: CD141_P7_S3


title: CD141_P7_S5


title: CD141_P7_S6


title: CD141_P7_S4


title: CD141_P7_S23


title: CD141_P7_S7


title: CD141_P7_S24


title: CD141_P7_S20


title: BPDCN1_S55_S55


title: BPDCN1_S51_S51


title: BPDCN1_S52_S52


title: CD141_P7_S22


title: BPDCN1_S49_S49


title: BPDCN1_S4_S4


title: CD141_P7_S21


title: BPDCN1_S56_S56


title: BPDCN1_S47_S47


title: CD141_P7_S18


title: CD141_P7_S17


title: BPDCN1_S50_S50


title: CD141_P7_S19


title: BPDCN1_S53_S53


title: BPDCN1_S45_S45


title: CD141_P7_S16


title: BPDCN1_S43_S43


title: CD141_P7_S14


title: CD141_P7_S12


title: BPDCN1_S42_S42


title: CD141_P7_S11


title: CD141_P4_S48


title: BPDCN1_S41_S41


title: BPDCN1_S46_S46


title: CD141_P7_S2


title: CD141_P4_S47


title: BPDCN1_S40_S40


title: BPDCN1_S38_S38


title: CD141_P4_S46


title: CD141_P7_S10


title: CD141_P7_S1


title: BPDCN1_S3_S3


title: BPDCN1_S44_S44


title: BPDCN1_S48_S48


title: CD141_P7_S13


title: CD141_P4_S43


title: BPDCN1_S37_S37


title: CD141_P4_S45


title: CD141_P4_S44


title: BPDCN1_S39_S39


title: CD141_P7_S15


title: CD141_P4_S42


title: BPDCN1_S31_S31


title: CD141_P4_S41


title: BPDCN1_S36_S36


title: CD141_P4_S38


title: CD141_P4_S39


title: BPDCN1_S29_S29


title: BPDCN1_S35_S35


title: BPDCN1_S27_S27


title: CD141_P4_S34


title: CD141_P4_S33


title: BPDCN1_S33_S33


title: BPDCN1_S25_S25


title: BPDCN1_S34_S34


title: BPDCN1_S24_S24


title: BPDCN1_S32_S32


title: CD141_P4_S40


title: CD141_P4_S32


title: BPDCN1_S30_S30


title: CD141_P4_S31


title: BPDCN1_S21_S21


title: BPDCN1_S22_S22


title: CD141_P4_S30


title: BPDCN1_S2_S2


title: CD141_P4_S37


title: BPDCN1_S1_S1


title: BPDCN1_S19_S19


title: BPDCN1_S28_S28


title: BPDCN1_S26_S26


title: BPDCN1_S18_S18


title: CD141_P4_S35


title: CD141_P4_S25


title: CD141_P4_S36


title: CD141_P4_S27


title: CD141_P4_S26


title: CD141_P3_S9


title: BPDCN1_S15_S15


title: CD141_P3_S6


title: CD141_P3_S8


title: BPDCN1_S14_S14


title: BPDCN1_S16_S16


title: BPDCN1_S13_S13


title: BPDCN1_S23_S23


title: BPDCN1_S11_S11


title: BPDCN1_S20_S20


title: CD141_P3_S4


title: BPDCN1_S12_S12


title: CD141_P4_S29


title: CD141_P3_S3


title: CD141_P3_S7


title: CD141_P3_S5


title: CD141_P4_S28


title: CD141_P3_S23


title: BPDCN1_S10_S10


title: CD141_P3_S24


title: CD1C_CD36CD163_S8_S8


title: CD1C_CD36CD163_S7_S7


title: CD141_P3_S20


title: CD141_P3_S21


title: CD1C_CD36CD163_S9_S9


title: CD141_P3_S2


title: CD1C_CD36CD163_S5_S5


title: BPDCN1_S17_S17


title: CD141_P3_S22


title: CD1C_CD36CD163_S4_S4


title: CD1C_CD36CD163_S6_S6


title: CD141_P3_S18


title: CD1C_CD36CD163_S47_S48


title: CD141_P3_S19


title: CD1C_CD36CD163_S46_S47


title: CD1C_CD36CD163_S43_S44


title: CD1C_CD36CD163_S42_S43


title: CD1C_CD36CD163_S45_S46


title: CD1C_CD36CD163_S41_S42


title: CD141_P3_S16


title: CD141_P3_S17


title: CD141_P3_S12


title: CD141_P3_S13


title: CD141_P3_S15


title: CD141_P3_S10


title: CD1C_CD36CD163_S40_S41


title: CD141_P3_S11


title: CD1C_CD36CD163_S3_S3


title: CD141_P14_S95


title: CD1C_CD36CD163_S38_S39


title: CD1C_CD36CD163_S39_S40


title: CD1C_CD36CD163_S37_S38


title: CD141_P14_S96


title: CD141_P3_S1


title: CD1C_CD36CD163_S44_S45


title: CD1C_CD36CD163_S36_S36


title: CD141_P3_S14


title: CD1C_CD36CD163_S35_S35


title: CD141_P14_S92


title: CD141_P14_S94


title: CD141_P14_S93


title: CD1C_CD36CD163_S34_S34


title: CD141_P14_S91


title: CD1C_CD36CD163_S33_S33


title: CD1C_CD36CD163_S32_S32


title: CD141_P14_S87


title: CD141_P14_S90


title: CD141_P14_S82


title: CD1C_CD36CD163_S31_S31


title: CD1C_CD36CD163_S26_S26


title: CD1C_CD36CD163_S30_S30


title: CD1C_CD36CD163_S27_S27


title: CD141_P14_S84


title: CD141_P14_S85


title: CD141_P14_S89


title: CD141_P14_S83


title: CD141_P14_S88


title: CD1C_CD36CD163_S2_S2


title: CD141_P14_S86


title: CD141_P14_S80


title: CD1C_CD36CD163_S29_S29


title: CD1C_CD36CD163_S25_S25


title: CD1C_CD36CD163_S24_S24


title: CD141_P14_S81


title: CD1C_CD36CD163_S20_S20


title: CD1C_CD36CD163_S22_S22


title: CD1C_CD36CD163_S23_S23


title: CD141_P14_S79


title: CD1C_CD36CD163_S21_S21


title: CD1C_CD36CD163_S19_S19


title: CD141_P14_S76


title: CD141_P14_S77


title: CD141_P14_S75


title: CD141_P14_S78


title: CD1C_CD36CD163_S1_S1


title: CD1C_CD36CD163_S17_S17


title: CD141_P14_S73


title: CD1C_CD36CD163_S28_S28


title: CD1C_CD36CD163_S18_S18


title: CD141_P14_S74


title: CD141_P13_S71


title: CD1C_CD36CD163_S16_S16


title: CD1C_CD36CD163_S13_S13


title: CD141_P13_S69


title: CD141_P13_S70


title: CD1C_CD36CD163_S15_S15


title: CD1C_CD36CD163_S14_S14


title: CD1C_CD36CD163_S11_S11


title: CD1C_CD32B_S9_S57


title: CD141_P13_S68


title: CD1C_CD36CD163_S10_S10


title: CD141_P13_S65


title: CD1C_CD36CD163_S12_S12


title: CD141_P13_S66


title: CD1C_CD32B_S8_S56


title: CD141_P13_S67


title: CD141_P13_S72


title: CD1C_CD32B_S7_S55


title: CD1C_CD32B_S6_S54


title: CD141_P13_S64


title: CD141_P13_S63


title: CD1C_CD32B_S5_S53


title: CD1C_CD32B_S4_S52


title: CD1C_CD32B_S47_S96


title: CD1C_CD32B_S45_S94


title: CD141_P13_S61


title: CD1C_CD32B_S43_S92


title: CD141_P13_S60


title: CD141_P13_S62


title: CD1C_CD32B_S46_S95


title: CD1C_CD32B_S44_S93


title: CD1C_CD32B_S40_S89


title: CD1C_CD32B_S39_S88


title: CD1C_CD32B_S42_S91


title: CD141_P13_S57


title: mock, 24h after treatment, biological replicate 2

type: RNA

city: Horsholm

first: Peter

middle: H

last: Hagedorn

state: Danmark

address: Fremtidsvej 3

department: Research

country: Denmark

institute: Roche Innovation Center Copenhagen A/S

hyb_protocol: Following fragmentation, 5 ug of cDNA were prepared and hybridized using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix)

scan_protocol: GCS3000 (Affymetrix)

data_processing: The raw cel files were converted into probeset-specific expression values using Robust Multiarray Averaging (Bioconductor package Affy) with summarization method using custom cdf annotations.

label: biotin

molecule: total RNA

source_name: HuH7 cells transfected with mock and measured after 24h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: HuH7 cells were seeded in 6 well plates with 2,5x10^5 cells/ml in 2ml

extract_protocol: Cells were homogenized in Trizol and RNA was extracted according to standard protocols.

treatment_protocol: 24h after seeding (50%-70% confluence) HuH7 cells were transfected with 5nM antisense oligonucleotide or mock in 6 well plates using lipofectamine (5 ug/ml). After 4 hours media was changed and cells incubated for 6h or 20h without antisense oligonucleotide or mock.

tag: treatment

value: mock

tag: time


title: CD1C_CD32B_S36_S84


title: CD141_P13_S59


title: CD1C_CD32B_S41_S90


title: mock, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with mock and measured after 10h


title: mock, 24h after treatment, biological replicate 1


title: mock, 10h after treatment, biological replicate 1


title: CD1C_CD32B_S3_S51


title: CD141_P13_S58


title: CD1C_CD32B_S33_S81


title: CD1C_CD32B_S32_S80


title: CD1C_CD32B_S38_S87


title: CD1C_CD32B_S31_S79


title: SPC4402, 24h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4402 and measured after 24h


title: CD1C_CD32B_S37_S86


title: CD141_P13_S53


title: CD1C_CD32B_S35_S83


title: CD141_P13_S56


title: CD141_P13_S55


title: CD1C_CD32B_S34_S82


title: CD141_P13_S54


title: SPC4399, 24h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4399 and measured after 24h


title: SPC4402, 24h after treatment, biological replicate 1


title: CD1C_CD32B_S30_S78


title: CD141_P13_S52


title: CD1C_CD32B_S2_S50


title: SPC4399, 24h after treatment, biological replicate 1


title: SPC4401, 24h after treatment, biological replicate 1

source_name: HuH7 cells transfected with SPC4401 and measured after 24h


title: SPC4401, 24h after treatment, biological replicate 2


title: CD1C_CD32B_S25_S73


title: CD1C_CD32B_S29_S77


title: CD1C_CD32B_S28_S76


title: CD141_P13_S51


title: SPC4398, 24h after treatment, biological replicate 1

source_name: HuH7 cells transfected with SPC4398 and measured after 24h


title: CD1C_CD32B_S27_S75


title: CD1C_CD32B_S26_S74


title: CD1C_CD32B_S24_S72


title: CD141_P13_S50


title: CD1C_CD32B_S23_S71


title: CD141_P13_S49


title: CD1C_CD32B_S21_S69


title: CD141_P10_S96


title: CD1C_CD32B_S22_S70


title: SPC4395, 24h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4395 and measured after 24h


title: CD1C_CD32B_S20_S68


title: SPC4398, 24h after treatment, biological replicate 2


title: SPC4396, 24h after treatment, biological replicate 1

source_name: HuH7 cells transfected with SPC4396 and measured after 24h


title: CD1C_CD32B_S1_S49


title: CD141_P10_S95


title: CD1C_CD32B_S19_S67


title: SPC4396, 24h after treatment, biological replicate 2


title: SPC4394, 24h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4394 and measured after 24h


title: SPC4395, 24h after treatment, biological replicate 1


title: CD1C_CD32B_S18_S66


title: CD1C_CD32B_S16_S64


title: CD1C_CD32B_S17_S65


title: CD1C_CD32B_S15_S63


title: CD141_P10_S93


title: CD141_P10_S92


title: CD141_P10_S94


title: CD1C_CD32B_S14_S62


title: CD1C_CD32B_S13_S61


title: CD1C_CD32B_S12_S60


title: CD141_P10_S91


title: CD1C_CD32B_S11_S59


title: SPC4392, 24h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4392 and measured after 24h


title: SPC4394, 24h after treatment, biological replicate 1


title: CD1C_CD32B_S10_S58


title: SPC4392, 24h after treatment, biological replicate 1


title: CD141_P10_S90


title: CD141_P10_S89


title: SPC4391, 24h after treatment, biological replicate 1

source_name: HuH7 cells transfected with SPC4391 and measured after 24h


title: SPC4391, 24h after treatment, biological replicate 2


title: CD141_P10_S88


title: CD1C_CD163_S6_S6


title: CD1C_CD163_S9_S9


title: CD1C_CD163_S7_S7


title: CD1C_CD163_S8_S8


title: CD1C_CD163_S4_S4


title: SPC4390, 24h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4390 and measured after 24h


title: CD1C_CD163_S5_S5


title: CD1C_CD163_S31_S32


title: CD1C_CD163_S2_S2


title: CD1C_CD163_S29_S30


title: CD141_P10_S87


title: CD141_P10_S85


title: CD1C_CD163_S30_S31


title: CD1C_CD163_S3_S3


title: CD141_P10_S86


title: CD1C_CD163_S28_S29


title: CD141_P10_S84


title: CD1C_CD163_S27_S28


title: CD141_P10_S83


title: CD1C_CD163_S25_S26


title: SPC4388, 24h after treatment, biological replicate 1

source_name: HuH7 cells transfected with SPC4388 and measured after 24h


title: SPC4390, 24h after treatment, biological replicate 1


title: CD141_P10_S82


title: CD1C_CD163_S24_S25


title: CD1C_CD163_S21_S22


title: CD1C_CD163_S23_S24


title: CD1C_CD163_S1_S1


title: CD1C_CD163_S22_S23


title: SPC4388, 24h after treatment, biological replicate 2


title: SPC3744, 24h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC3744 and measured after 24h


title: CD141_P10_S80


title: CD1C_CD163_S18_S19


title: SPC4316, 24h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4316 and measured after 24h


title: SPC4316, 24h after treatment, biological replicate 1


title: CD1C_CD163_S20_S21


title: SPC3372, 24h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC3372 and measured after 24h


title: SPC3744, 24h after treatment, biological replicate 1


title: CD1C_CD163_S19_S20

source_name: PBMC


title: CD141_P10_S81


title: CD1C_CD163_S26_S27


title: CD1C_CD163_S14_S15


title: CD1C_CD163_S15_S16


title: CD1C_CD163_S13_S14


title: CD141_P10_S76


title: CD141_P10_S77


title: SPC4402, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4402 and measured after 10h


title: CD1C_CD163_S11_S11


title: SPC3372, 24h after treatment, biological replicate 1


title: CD141_P10_S78


title: CD1C_CD163_S17_S18


title: CD1C_CD163_S10_S10


title: C100C34int_S9_S9


title: SPC4401, 10h after treatment, biological replicate 1

source_name: HuH7 cells transfected with SPC4401 and measured after 10h


title: SPC4402, 10h after treatment, biological replicate 1


title: CD141_P10_S79


title: CD1C_CD163_S12_S12


title: SPC4401, 10h after treatment, biological replicate 2


title: CD141_P10_S75


title: CD1C_CD163_S16_S17


title: C100C34int_S95_S95


title: C100C34int_S93_S93


title: C100C34int_S96_S96


title: SPC4398, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4398 and measured after 10h


title: C100C34int_S94_S94


title: SPC4399, 10h after treatment, biological replicate 1

source_name: HuH7 cells transfected with SPC4399 and measured after 10h


title: CD141_P10_S73


title: C100C34int_S92_S92


title: pDC_P9_S72

value: pDC


title: C100C34int_S88_S88


title: pDC_P9_S71


title: CD141_P10_S74


title: C100C34int_S8_S8


title: C100C34int_S90_S90


title: SPC4396, 10h after treatment, biological replicate 1

source_name: HuH7 cells transfected with SPC4396 and measured after 10h


title: SPC4398, 10h after treatment, biological replicate 1


title: C100C34int_S89_S89


title: pDC_P9_S69


title: pDC_P9_S68


title: C100C34int_S85_S85


title: C100C34int_S83_S83


title: SPC4396, 10h after treatment, biological replicate 2


title: pDC_P9_S67


title: C100C34int_S91_S91


title: SPC4395, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4395 and measured after 10h


title: SPC4394, 10h after treatment, biological replicate 1

source_name: HuH7 cells transfected with SPC4394 and measured after 10h


title: C100C34int_S81_S81


title: SPC4395, 10h after treatment, biological replicate 1


title: pDC_P9_S70


title: pDC_P9_S66


title: C100C34int_S80_S80


title: C100C34int_S87_S87


title: C100C34int_S7_S7


title: C100C34int_S86_S86


title: C100C34int_S84_S84


title: C100C34int_S78_S78


title: SPC4391, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4391 and measured after 10h


title: C100C34int_S77_S77


title: pDC_P9_S63


title: SPC4394, 10h after treatment, biological replicate 2


title: C100C34int_S82_S82


title: C100C34int_S76_S76


title: pDC_P9_S62


title: C100C34int_S74_S74


title: C100C34int_S73_S73


title: pDC_P9_S61


title: C100C34int_S71_S71


title: SPC4392, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4392 and measured after 10h


title: SPC4392, 10h after treatment, biological replicate 1


title: C100C34int_S72_S72


title: SPC4390, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4390 and measured after 10h


title: pDC_P9_S60


title: SPC4391, 10h after treatment, biological replicate 1


title: C100C34int_S79_S79


title: pDC_P9_S64


title: pDC_P9_S59


title: C100C34int_S69_S69


title: C100C34int_S75_S75


title: SPC4388, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4388 and measured after 10h


title: pDC_P9_S58


title: C100C34int_S68_S68


title: C100C34int_S66_S66


title: pDC_P9_S57


title: C100C34int_S70_S70


title: pDC_P9_S56


title: SPC4316, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC4316 and measured after 10h


title: pDC_P9_S55


title: C100C34int_S63_S63


title: C100C34int_S62_S62


title: SPC4390, 10h after treatment, biological replicate 1


title: C100C34int_S60_S60


title: C100C34int_S6_S6


title: SPC4316, 10h after treatment, biological replicate 1


title: C100C34int_S5_S5


title: C100C34int_S59_S59


title: SPC4388, 10h after treatment, biological replicate 1


title: C100C34int_S58_S58


title: C100C34int_S67_S67


title: SPC3744, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC3744 and measured after 10h


title: C100C34int_S57_S57


title: SPC3744, 10h after treatment, biological replicate 1


title: pDC_P9_S54


title: SPC3372, 10h after treatment, biological replicate 2

source_name: HuH7 cells transfected with SPC3372 and measured after 10h


title: pDC_P9_S53


title: C100C34int_S65_S65


title: pDC_P9_S52


title: C100C34int_S56_S56


title: C100C34int_S64_S64


title: pDC_P9_S51


title: C100C34int_S55_S55


title: C100C34int_S61_S61


title: C100C34int_S54_S54


title: C100C34int_S53_S53


title: C100C34int_S51_S51


title: pDC_P8_S48


title: C100C34int_S50_S50


title: C100C34int_S52_S52


title: C100C34int_S4_S4


title: C100C34int_S49_S49


title: pDC_P9_S49


title: pDC_P9_S50


title: C100C34int_S47_S47


title: C100C34int_S48_S48


title: C100C34int_S46_S46


title: pDC_P8_S47


title: C100C34int_S45_S45


title: C100C34int_S42_S42


title: pDC_P8_S45


title: pDC_P8_S44


title: C100C34int_S44_S44


title: pDC_P8_S46


title: C100C34int_S43_S43


title: C100C34int_S41_S41


title: C100C34int_S40_S40


title: SPC3372, 10h after treatment, biological replicate 1


title: pDC_P8_S43


title: C100C34int_S37_S37


title: C100C34int_S36_S36


title: C100C34int_S35_S35


title: C100C34int_S3_S3


title: C100C34int_S39_S39


title: pDC_P8_S42


title: pDC_P8_S40


title: C100C34int_S38_S38


title: C100C34int_S33_S33


title: C100C34int_S32_S32


title: pDC_P8_S39


title: pDC_P8_S41


title: C100C34int_S2_S2


title: pDC_P8_S37


title: pDC_P8_S36


title: C100C34int_S31_S31


title: pDC_P8_S34


title: pDC_P8_S38


title: C100C34int_S30_S30


title: C100C34int_S29_S29


title: C100C34int_S27_S27


title: C100C34int_S26_S26


title: C100C34int_S28_S28


title: C100C34int_S25_S25


title: pDC_P8_S35


title: C100C34int_S34_S34


title: C100C34int_S24_S24


title: C100C34int_S20_S20


title: C100C34int_S23_S23


title: C100C34int_S19_S19


title: pDC_P8_S31


title: C100C34int_S21_S21


title: C100C34int_S18_S18


title: pDC_P8_S33


title: pDC_P8_S32


title: C100C34int_S15_S15


title: C100C34int_S17_S17


title: C100C34int_S14_S14


title: C100C34int_S1_S1


title: C100C34int_S22_S22


title: C100C34int_S16_S16


title: pDC_P8_S28


title: pDC_P8_S30


title: C100C34int_S13_S13


title: pDC_P8_S29


title: C100C34int_S12_S12


title: C100C34int_S11_S11


title: pDC_P8_S27


title: AXLSIGLEC6_Bin8_S8_S96


title: AXLSIGLEC6_Bin8_S7_S95


title: AXLSIGLEC6_Bin8_S5_S93


title: pDC_P8_S26


title: AXLSIGLEC6_Bin8_S9_S85


title: C100C34int_S10_S10


title: pDC_P7_S9


title: pDC_P8_S25


title: AXLSIGLEC6_Bin8_S6_S94


title: AXLSIGLEC6_Bin8_S3_S91


title: AXLSIGLEC6_Bin8_S20_S96


title: AXLSIGLEC6_Bin8_S4_S92


title: pDC_P7_S8


title: AXLSIGLEC6_Bin8_S2_S90


title: pDC_P7_S7


title: pDC_P7_S5


title: AXLSIGLEC6_Bin8_S14_S90


title: pDC_P7_S6


title: pDC_P7_S4


title: AXLSIGLEC6_Bin8_S19_S95


title: AXLSIGLEC6_Bin8_S18_S94


title: AXLSIGLEC6_Bin8_S17_S93


title: AXLSIGLEC6_Bin8_S15_S91


title: AXLSIGLEC6_Bin8_S16_S92


title: AXLSIGLEC6_Bin8_S13_S89


title: AXLSIGLEC6_Bin8_S12_S88


title: AXLSIGLEC6_Bin8_S1_S89


title: AXLSIGLEC6_Bin8_S11_S87


title: pDC_P7_S23


title: AXLSIGLEC6_Bin8_S10_S86


title: pDC_P7_S22


title: pDC_P7_S3


title: pDC_P7_S24


title: AXLSIGLEC6_Bin7_S4_S80


title: AXLSIGLEC6_Bin7_S8_S84


title: AXLSIGLEC6_Bin7_S9_S73


title: AXLSIGLEC6_Bin7_S6_S82


title: AXLSIGLEC6_Bin7_S5_S81


title: pDC_P7_S21


title: AXLSIGLEC6_Bin7_S3_S79


title: AXLSIGLEC6_Bin7_S19_S83


title: pDC_P9_S65


title: pDC_P7_S2


title: AXLSIGLEC6_Bin7_S18_S82


title: AXLSIGLEC6_Bin7_S2_S78


title: pDC_P7_S18


title: AXLSIGLEC6_Bin7_S16_S80


title: AXLSIGLEC6_Bin7_S14_S78


title: pDC_P7_S17


title: AXLSIGLEC6_Bin7_S13_S77


title: AXLSIGLEC6_Bin7_S12_S76


title: AXLSIGLEC6_Bin7_S17_S81


title: AXLSIGLEC6_Bin7_S11_S75


title: pDC_P7_S16


title: AXLSIGLEC6_Bin6_S9_S61


title: AXLSIGLEC6_Bin7_S1_S77


title: AXLSIGLEC6_Bin7_S10_S74


title: AXLSIGLEC6_Bin6_S8_S72


title: pDC_P7_S15


title: AXLSIGLEC6_Bin6_S7_S71


title: pDC_P7_S14


title: AXLSIGLEC6_Bin7_S7_S83


title: pDC_P7_S13


title: pDC_P7_S20


title: AXLSIGLEC6_Bin6_S6_S70


title: AXLSIGLEC6_Bin6_S5_S69


title: pDC_P7_S12


title: AXLSIGLEC6_Bin6_S4_S68


title: pDC_P7_S19


title: AXLSIGLEC6_Bin6_S3_S67


title: pDC_P7_S11


title: AXLSIGLEC6_Bin6_S20_S72


title: pDC_P7_S10


title: AXLSIGLEC6_Bin6_S2_S66


title: pDC_P7_S1


title: AXLSIGLEC6_Bin6_S16_S68


title: AXLSIGLEC6_Bin6_S18_S70


title: AXLSIGLEC6_Bin6_S17_S69


title: AXLSIGLEC6_Bin6_S15_S67


title: pDC_P4_S48


title: AXLSIGLEC6_Bin6_S12_S64


title: pDC_P4_S47


title: AXLSIGLEC6_Bin6_S14_S66


title: AXLSIGLEC6_Bin7_S15_S79


title: AXLSIGLEC6_Bin7_S20_S84


title: pDC_P4_S46


title: AXLSIGLEC6_Bin6_S13_S65


title: AXLSIGLEC6_Bin6_S11_S63


title: AXLSIGLEC6_Bin6_S19_S71


title: AXLSIGLEC6_Bin6_S10_S62


title: AXLSIGLEC6_Bin6_S1_S65


title: pDC_P4_S45


title: AXLSIGLEC6_Bin5_S9_S49


title: pDC_P4_S44


title: AXLSIGLEC6_Bin5_S8_S60


title: AXLSIGLEC6_Bin5_S7_S59


title: AXLSIGLEC6_Bin5_S5_S57


title: pDC_P4_S43


title: AXLSIGLEC6_Bin5_S6_S58


title: AXLSIGLEC6_Bin5_S20_S60


title: pDC_P4_S41


title: pDC_P4_S42


title: AXLSIGLEC6_Bin5_S4_S56


title: AXLSIGLEC6_Bin5_S3_S55


title: pDC_P4_S40


title: AXLSIGLEC6_Bin5_S18_S58


title: AXLSIGLEC6_Bin5_S19_S59


title: pDC_P4_S39


title: AXLSIGLEC6_Bin5_S17_S57


title: pDC_P4_S38


title: AXLSIGLEC6_Bin5_S16_S56


title: pDC_P4_S37


title: AXLSIGLEC6_Bin5_S14_S54


title: pDC_P4_S36


title: AXLSIGLEC6_Bin5_S11_S51


title: pDC_P4_S35


title: AXLSIGLEC6_Bin5_S15_S55


title: AXLSIGLEC6_Bin5_S10_S50


title: pDC_P4_S34


title: AXLSIGLEC6_Bin4_S9_S37


title: AXLSIGLEC6_Bin4_S8_S48


title: AXLSIGLEC6_Bin4_S7_S47


title: AXLSIGLEC6_Bin4_S6_S46


title: pDC_P4_S33


title: AXLSIGLEC6_Bin5_S1_S53


title: AXLSIGLEC6_Bin4_S5_S45


title: AXLSIGLEC6_Bin5_S2_S54


title: AXLSIGLEC6_Bin4_S4_S44


title: pDC_P4_S31


title: AXLSIGLEC6_Bin4_S3_S43


title: pDC_P4_S30


title: AXLSIGLEC6_Bin4_S2_S42


title: AXLSIGLEC6_Bin5_S13_S53


title: AXLSIGLEC6_Bin5_S12_S52


title: AXLSIGLEC6_Bin4_S18_S46


title: pDC_P4_S29


title: AXLSIGLEC6_Bin4_S17_S45


title: AXLSIGLEC6_Bin4_S15_S43


title: pDC_P4_S28


title: AXLSIGLEC6_Bin4_S16_S44


title: AXLSIGLEC6_Bin4_S14_S42


title: AXLSIGLEC6_Bin4_S12_S40


title: AXLSIGLEC6_Bin4_S13_S41


title: pDC_P4_S26


title: AXLSIGLEC6_Bin4_S11_S39


title: AXLSIGLEC6_Bin4_S10_S38


title: AXLSIGLEC6_Bin4_S1_S41


title: pDC_P4_S25


title: AXLSIGLEC6_Bin3_S9_S25


title: pDC_P3_S9


title: AXLSIGLEC6_Bin3_S7_S35


title: pDC_P3_S8


title: AXLSIGLEC6_Bin4_S20_S48


title: AXLSIGLEC6_Bin3_S5_S33


title: AXLSIGLEC6_Bin4_S19_S47


title: AXLSIGLEC6_Bin3_S4_S32


title: AXLSIGLEC6_Bin3_S3_S31


title: pDC_P3_S7


title: pDC_P3_S6


title: AXLSIGLEC6_Bin3_S20_S36


title: pDC_P4_S27


title: pDC_P3_S5


title: pDC_P3_S4


title: AXLSIGLEC6_Bin3_S16_S32


title: AXLSIGLEC6_Bin3_S17_S33


title: pDC_P3_S3


title: AXLSIGLEC6_Bin3_S15_S31


title: AXLSIGLEC6_Bin3_S14_S30


title: pDC_P3_S24


title: AXLSIGLEC6_Bin3_S13_S29


title: AXLSIGLEC6_Bin3_S8_S36


title: pDC_P3_S23


title: AXLSIGLEC6_Bin3_S11_S27


title: AXLSIGLEC6_Bin3_S6_S34


title: AXLSIGLEC6_Bin3_S10_S26


title: AXLSIGLEC6_Bin3_S1_S29


title: pDC_P3_S21


title: AXLSIGLEC6_Bin3_S2_S30


title: AXLSIGLEC6_Bin2_S8_S24


title: AXLSIGLEC6_Bin3_S18_S34


title: pDC_P3_S2


title: AXLSIGLEC6_Bin2_S6_S22


title: AXLSIGLEC6_Bin3_S19_S35


title: AXLSIGLEC6_Bin2_S4_S20


title: pDC_P3_S19


title: AXLSIGLEC6_Bin2_S3_S19


title: AXLSIGLEC6_Bin3_S12_S28


title: AXLSIGLEC6_Bin2_S18_S22


title: pDC_P3_S18


title: AXLSIGLEC6_Bin2_S19_S23


title: pDC_P3_S17


title: AXLSIGLEC6_Bin2_S17_S21


title: AXLSIGLEC6_Bin2_S16_S20


title: pDC_P3_S22


title: AXLSIGLEC6_Bin2_S9_S13


title: AXLSIGLEC6_Bin2_S15_S19


title: AXLSIGLEC6_Bin2_S14_S18


title: AXLSIGLEC6_Bin2_S13_S17


title: AXLSIGLEC6_Bin2_S5_S21


title: pDC_P3_S20


title: pDC_P3_S14


title: AXLSIGLEC6_Bin2_S12_S16


title: AXLSIGLEC6_Bin2_S7_S23


title: pDC_P3_S13


title: pDC_P3_S12


title: AXLSIGLEC6_Bin2_S11_S15


title: AXLSIGLEC6_Bin2_S10_S14


title: AXLSIGLEC6_Bin2_S1_S17


title: pDC_P3_S11


title: AXLSIGLEC6_Bin2_S20_S24


title: AXLSIGLEC6_Bin2_S2_S18


title: pDC_P3_S10


title: AXLSIGLEC6_Bin1_S9_S1


title: pDC_P3_S15


title: pDC_P3_S1


title: AXLSIGLEC6_Bin1_S5_S9


title: AXLSIGLEC6_Bin1_S4_S8


title: pDC_P14_S92


title: pDC_P14_S93


title: AXLSIGLEC6_Bin1_S3_S7


title: pDC_P14_S94


title: pDC_P14_S91


title: pDC_P14_S90


title: AXLSIGLEC6_Bin1_S20_S12


title: AXLSIGLEC6_Bin1_S2_S6


title: AXLSIGLEC6_Bin1_S19_S11


title: pDC_P14_S89


title: pDC_P14_S87


title: pDC_P3_S16


title: AXLSIGLEC6_Bin1_S17_S9


title: pDC_P14_S88


title: AXLSIGLEC6_Bin1_S18_S10


title: AXLSIGLEC6_Bin1_S15_S7


title: AXLSIGLEC6_Bin1_S16_S8


title: pDC_P14_S85


title: pDC_P14_S86


title: AXLSIGLEC6_Bin1_S7_S11


title: AXLSIGLEC6_Bin1_S6_S10


title: pDC_P14_S95


title: AXLSIGLEC6_Bin1_S8_S12


title: pDC_P14_S96


title: AXLSIGLEC6_Bin1_S14_S6


title: pDC_P14_S83


title: AXLSIGLEC6_Bin1_S13_S5


title: AXLSIGLEC6_Bin1_S12_S4


title: pDC_P14_S81


title: pDC_P14_S80


title: AXLSIGLEC6_Bin1_S11_S3


title: AXLSIGLEC6_Bin1_S10_S2


title: AXLSIGLEC6_Bin1_S1_S5


title: pDC_P14_S79


title: pDC_P14_S76


title: pDC_P14_S77


title: pDC_P14_S78


title: pDC_P14_S74


title: pDC_P14_S75


title: pDC_P13_S71


title: pDC_P14_S73


title: pDC_P14_S84


title: pDC_P13_S72


title: pDC_P13_S67


title: pDC_P13_S69


title: pDC_P13_S68


title: pDC_P13_S66


title: pDC_P13_S65


title: pDC_P13_S64


title: pDC_P14_S82


title: pDC_P13_S63


title: pDC_P13_S62


title: pDC_P13_S70


title: pDC_P13_S60


title: pDC_P13_S59


title: pDC_P13_S57


title: pDC_P13_S58


title: pDC_P13_S56


title: pDC_P13_S61


title: pDC_P13_S55


title: Brg1fl/fl-R1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from Brg1fl/fl-R1-E8.5-RNA

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

organism: Mus musculus

label_protocol: Starting with 250ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: RNA was prepared using the Qiagen RNA Purification kit following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tamoxifen was intraperitoneally injected to dam and embryos were harvested embryonic day (E)8.5

tag: tissue

value: whole embryo

tag: age

tag: genotype

value: Brg1fl/fl (Brg1 wildtype)


title: Brg1fl/fl-R2

description: Gene expression from Brg1fl/fl-R2-E8.5-RNA


title: Brg1fl/fl-R3

description: Gene expression from Brg1fl/fl-R3-E8.5-RNA


title: pDC_P4_S32


title: Brg1d/d-R1

description: Gene expression from Brg1d/d-R1-E8.5RNA

value: Brg1d/d (Brg1 CKO)


title: pDC_P13_S54


title: Brg1d/d-R2

description: Gene expression from Brg1d/d-R2-E8.5RNA


title: Brg1d/d-R3

description: Gene expression from Brg1d/d-R3-E8.5RNA


title: pDC_P13_S53


title: pDC_P13_S52


title: pDC_P13_S51


title: pDC_P13_S50


title: GRHL2 overexpressing SKOV3 clone OV2 vs control (CSov) SKOV3 clone - 2

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

country: Canada

institute: CHU-Q, Centre de recherche-HDQ

description: Cy5 label sample being the reference

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.
Normalized log10 ratio (Cy3/Cy5) representing test/reference for samples CA – KOA1, CA – KOA2, CS - sh-S2, CS - sh-S5, CSov - OV1 and CSov - OV2; normalized log10 ratio (Cy5/Cy3) representing test/reference for samples  KOA1 - CA, KOA2 - CA, sh-S2 - CS, sh-S5 - CS, OV1 - CSov and OV2 - CSov

source_name: SKOV3 sGRHL2 overexpressing clone OV2

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: A2780s and SKOV3 cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 (HyClone Europe Ltd, Cramlington, UK) supplemented with 10% heat-inactivated fetal calf serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 μg/ml streptomycin (all reagents were from HyClone Europe). Cells were grown as adherent cells in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: CRISPR/Cas9 mediated GRHL2 knockout in A2780s cells was done according to the manufacturer's guidelines (Santa Cruz Biotechnology, Inc), as previously described (PMID: 26871602). The shRNA-mediated GRHL2 knockdown in SKOV3 cells was performed, as previously described (PMID: 26871602). For GRHL2 ectopic expression, cDNA of the human GRHL2 gene cloned in the pCMV6 entry eukaryotic expression vector (pCMV-GRHL2) was purchased from OriGene Technologies, Inc. (Rockville, MD). Transfection with ExGen 500 (Fermentas Canada Inc., Burlington ON) was carried out according to the manufacturer’s guidelines, as previously described (PMID: 21856257).

tag: cell type

value: ovarian clear cell carcinoma  cell line

source_name: control CSov SKOV3 clone


title: GRHL2 overexpressing SKOV3 clone OV1 vs control (CSov) SKOV3 clone - 1

description: Cy5 label sample being the reference

source_name: SKOV3 sGRHL2 overexpressing clone OV1


title: shRNA-mediated GRHL2 knockdown SKOV3 clone sh-S5 vs control (CS) SKOV3 clone - 2

description: Cy5 label sample being the reference

source_name: SKOV3 sGRHL2 knockdown clone S5

source_name: control CS SKOV3 clone


title: GRHL2 overexpressing SKOV3 clone OV1 vs control (CSov) SKOV3 clone - 2

description: Cy5 label sample being the reference


title: shRNA-mediated GRHL2 knockdown SKOV3 clone sh-S5 vs control (CS) SKOV3 clone - 1

description: Cy5 label sample being the reference


title: shRNA-mediated GRHL2 knockdown SKOV3 clone sh-S2 vs control (CS) SKOV3 clone - 2

description: Cy5 label sample being the reference

source_name: SKOV3 sGRHL2 knockdown clone S2


title: GRHL2 overexpressing SKOV3 clone OV2 vs control (CSov) SKOV3 clone - 1

description: Cy5 label sample being the reference


title: shRNA-mediated GRHL2 knockdown SKOV3 clone sh-S2 vs control (CS) SKOV3 clone - 1

description: Cy5 label sample being the reference


title: pDC_P10_S96

source_name: PBMC


title: nRBC_term_ind5

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

hyb_protocol: Illumina HumanMethylation450 BeadChip protocol.

scan_protocol: Arrays were imaged using Illumina HiScan on a two-colour channel.

data_processing:
GenomeStudio 2011.1 software and R version 3.1.1.
Normalized by background subtraction in GenomeStudio, red-green colour bias correction (lumi, Bioconductor package), subset within-array quantile normalization (minfi, Bioconductor package).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: term cord blood, nRBC, 5

extract_protocol: Genomic DNA was purified using Qiagen's DNeasy Blood and Tissue kit followed by bisulphite conversion using Zymo's EZ DNA Methylation Kit following manufacturer's protocols.

value: term cord blood

value: nucleated red blood cells

tag: Sex

value: male

tag: gestational age

value: 38-40 weeks

tag: individual

tag: array chip

tag: array position


title: Monocyte_term_ind3

source_name: term cord blood, monocyte, 3

label_protocol: Illumina HumanMethylation450 BeadChip protocol.

value: monocytes

value: female


title: Tcell_term_ind5

source_name: term cord blood, T cell, 5

value: T cells


title: Tcell_term_ind4

source_name: term cord blood, T cell, 4


title: pDC_P10_S95


title: nRBC_term_ind4

source_name: term cord blood, nRBC, 4


title: Granulocyte_term_ind5

source_name: term cord blood, granulocyte, 5

value: granulocytes


title: nRBC_term_ind3

source_name: term cord blood, nRBC, 3


title: Granulocyte_term_ind3

source_name: term cord blood, granulocyte, 3


title: CRISPR/Cas9-mediated GRHL2 knockout A2780s clone KOA2 vs the control CA A2780s clone -1

description: Cy5 label sample being the reference

source_name: control CA A2780s  clone

value: ovarian endometrioid carcinoma  cell line

source_name: A270s knockout GRHL2 clone A2


title: pDC_P10_S94


title: Granulocyte_term_ind4

source_name: term cord blood, granulocyte, 4


title: pDC_P13_S49


title: Monocyte_term_ind5

source_name: term cord blood, monocyte, 5


title: CRISPR/Cas9-mediated GRHL2 knockout A2780s clone KOA1 vs the control CA A2780s clone - 2

description: Cy5 label sample being the reference

source_name: A2780s sGRHL2 knockout clone A1


title: Monocyte_term_ind4

source_name: term cord blood, monocyte, 4


title: CRISPR/Cas9-mediated GRHL2 knockout A2780s clone KOA1 vs the control CA A2780s clone - 1

description: Cy5 label sample being the reference

source_name: A270s knockout GRHL2 clone A1


title: pDC_P10_S92


title: Tcell_term_ind3

source_name: term cord blood, T cell, 3


title: nRBC_term_ind2

source_name: term cord blood, nRBC, 2


title: pDC_P10_S91

source_name: PBMC


title: Tcell_term_ind2

source_name: term cord blood, T cell, 2


title: pDC_P10_S90


title: pDC_P10_S89


title: pDC_P10_S88


title: Monocyte_term_ind2

source_name: term cord blood, monocyte, 2


title: nRBC_term_ind1

source_name: term cord blood, nRBC, 1


title: (Hes1)GFP-high cells, biological rep 3

city: Stanford

first: Julien

last: Sage

state: CA

address: 265 Campus Drive

department: Pediatrics and Genetics

institute: Stanford

description: Gene expression data from (Hes1)GFP-high cells in mouse SCLC tumors.

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16 hour (overnight) hybridization at 45°C at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using Robust Multichip Average (RMA) using Affymetrix default analysis settings and quantile as normalization method.

source_name: GFP-high cells isolated from pooled SCLC tumors from a mouse carrying a GFP-reporter allele for Hes1 expression.

label_protocol: Affymetrix WT Plus kit was used to generate ssDNA targets. Fragmentation and biotin-labeling were performed using Affymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: Rb/p53/p130 conditional knockout SCLC mice carrying a GFP reporter for Hes1 were given intratracheal administration of Adeno-Cre to induce tumor formation. SCLC tumors were isolated from the lungs of mice 5-6 months after Cre recombination.

extract_protocol: Total RNA was extracted using the Qiagen AllPrep DNA/RNA micro kit.

treatment_protocol: Pooled tumors from 3 mice were FACS sorted for GFP-negative or GFP-high cells, corresponding to low or high Hes1 expression respectively.

value: SCLC tumor

tag: (hes1) gfp expression status

value: high


title: Granulocyte_term_ind2

source_name: term cord blood, granulocyte, 2


title: CRISPR/Cas9-mediated GRHL2 knockout A2780s clone KOA2 vs the control CA A2780s clone - 2

description: Cy5 label sample being the reference

source_name: A2780s sGRHL2 knockout clone A2


title: (Hes1)GFP-high cells, biological rep 1


title: (Hes1)GFP-negative cells, biological rep 3

description: Gene expression data from (Hes1)GFP-negative cells in mouse SCLC tumors.

source_name: GFP-negative cells isolated from pooled SCLC tumors from a mouse carrying a GFP-reporter allele for Hes1 expression.

value: negative / low


title: pDC_P10_S87

value: pDC


title: Tcell_term_ind1

source_name: term cord blood, T cell, 1


title: (Hes1)GFP-negative cells, biological rep 1


title: pDC_P10_S86


title: Granulocyte_term_ind1

source_name: term cord blood, granulocyte, 1


title: Tcell_preterm_indE

source_name: preterm cord blood, T cell, E

value: preterm cord blood

value: 30 weeks

value: E


title: pDC_P10_S84


title: pDC_P10_S83


title: nRBC_preterm_indE

source_name: preterm cord blood, nRBC, E


title: pDC_P10_S85


title: pDC_P10_S82


title: pDC_P10_S81


title: (Hes1)GFP-high cells, biological rep 2


title: pDC_P10_S80


title: Monocyte_term_ind1

source_name: term cord blood, monocyte, 1


title: pDC_P10_S79


title: pDC_P10_S78


title: pDC_P10_S77


title: PBMCs from mice transplanted with BMTCD + R848-pretreated splenocytes

city: Thessaloniki

first: Nikolaos

last: Zogas

address: Exokhi

department: Hematology-BMT Unit

country: Greece

institute: George Papanicolaou Hospital

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://www.qiagen.com/gr/shop/genes-and-pathways/data-analysis-center-overview-page/
Raw data from each experimental condition (5 mice/condition, corresponding to 5x96-well plates) were uploaded in the web-based software as indicated above. The software calculates the average of the raw Ct values of each target gene per experimental condition.
For the normalization it uses the average of five housekeeping genes: B2m, Gusb, Hsp90ab1, Gapdh, Actb.
Target gene signals normalized to housekeeping genes; AVG Delta(Ct)  (Ct(target) - Ave Ct(HKG))
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. The threshold value was set at 0.05 for all independent experiments according to the manufacturer’s instructions.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., BMTCD/BMTCD + PBS-pretreated splenocytes) ratios.

label: SYBR Green

source_name: Peripheral blood

label_protocol: PCR arrays were performed using the Toll-like Receptor RT2 Profiler PCR Array panel (QIAGEN, Hilden, Germany) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (Qiagen). Quantitative real-time PCR was performed (ABI 7500, Applied Biosystems) according to Manufacturer's instructions.

extract_protocol: Total RNA was extracted with Qiamp RNA blood mini kit with on-column DNAse treatment with the RNase-Free DNase Set (Qiagen).

value: Peripheral blood mononuclear cells (PBMCs)

tag: agent to induce tolerance


title: PBMCs from mice transplanted with BMTCD + LPS-pretreated splenocytes

description: Test

value: high pure LPS


title: pDC_P10_S76


title: Tcell_preterm_indD

source_name: preterm cord blood, T cell, D

value: D


title: (Hes1)GFP-negative cells, biological rep 2


title: pDC_P10_S75


title: nRBC_preterm_indD

source_name: preterm cord blood, nRBC, D

value: nucleated red blood cells


title: PBMCs from mice transplanted with BMTCD + Pam3CSK4-pretreated splenocytes

description: Test


title: Monocyte_preterm_indE

source_name: preterm cord blood, monocyte, E

value: male


title: PBMCs from mice transplanted with BMTCD

description: Test


title: pDC_P10_S73

source_name: PBMC


title: pDC_P10_S74


title: PBMCs from mice transplanted with BMTCD + PBS-pretreated splenocytes

description: Control

value: PBS


title: pDC_P10_S93


title: TLR7-tolerant CD3+ T-cells from C57BL/6J mice

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://www.qiagen.com/gr/shop/genes-and-pathways/data-analysis-center-overview-page/
Raw data from each experimental condition (5 mice/condition, corresponding to 5x96-well plates) were uploaded in the web-based software as indicated above. The software calculates the average of the raw Ct values of each target gene per experimental condition.
For the normalization it uses the average of five housekeeping genes: B2m, Gusb, Hsp90ab1, Gapdh, Actb.
Target gene signals normalized to housekeeping genes; AVG Delta(Ct)  (Ct(target) - Ave Ct(HKG))
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. The threshold value was set at 0.05 for all independent experiments according to the manufacturer’s instructions.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., C57BL/6J R848-pretreated CD3+ T-cells/unmanipulated B6 TLR7 null CD3+ T-cells) ratios.

source_name: Spleen

value: CD3+ T-cells


title: TLR7-tolerant splenocytes

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://www.qiagen.com/gr/shop/genes-and-pathways/data-analysis-center-overview-page/
Raw data from each experimental condition (6 mice/condition, corresponding to 6x96-well plates) were uploaded in the web-based software as indicated above. The software calculates the average of the raw Ct values of each target gene per experimental condition.
For the normalization it uses the average of five housekeeping genes: B2m, Gusb, Hsp90ab1, Gapdh, Actb.
Target gene signals normalized to housekeeping genes; AVG Delta(Ct)  (Ct(target) - Ave Ct(HKG))
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. The threshold value was set at 0.05 for all independent experiments according to the manufacturer’s instructions.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., Pam3CSK4-pretreated splenocytes/PBS-pretreated splenocytes) ratios.

value: splenocytes


title: Granulocyte_preterm_indE

source_name: preterm cord blood, granulocyte, E

value: granulocytes


title: Unmanipulated CD3+ T-cells from B6 TLR7 null mice

description: Control

value: control


title: TLR2-tolerant splenocytes

description: Test


title: Monocyte_preterm_indD

source_name: preterm cord blood, monocyte, D

value: monocytes

value: female


title: TLR4-tolerant splenocytes

description: Test


title: TLR7-tolerant CD3+ T-cells

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://www.qiagen.com/gr/shop/genes-and-pathways/data-analysis-center-overview-page/
Raw data from each experimental condition (5 mice/condition, corresponding to 5x96-well plates) were uploaded in the web-based software as indicated above. The software calculates the average of the raw Ct values of each target gene per experimental condition.
For the normalization it uses the average of five housekeeping genes: B2m, Gusb, Hsp90ab1, Gapdh, Actb.
Target gene signals normalized to housekeeping genes; AVG Delta(Ct)  (Ct(target) - Ave Ct(HKG))
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. The threshold value was set at 0.05 for all independent experiments according to the manufacturer’s instructions.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., R848-pretreated CD3+ T-cells/unmanipulated CD3+ T-cells) ratios.


title: Unmanipulated CD3+ T-cells

description: Control


title: Tcell_preterm_indB

source_name: preterm cord blood, T cell, B

value: T cells

value: 29 weeks

value: B


title: Tcell_preterm_indC

source_name: preterm cord blood, T cell, C

value: preterm cord blood

value: 30 weeks

value: C


title: SPC2996, biological rep1

hyb_protocol: The labeled sense strand DNA was hybridized to the Affymetrix GeneChip human Exon 1.0 ST arrays for 17hr at 45 C with constant rotation

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner

data_processing: The raw cel files were converted into probeset-specific expression values using Robust Multiarray Averaging (Bioconductor package Affy) with summarization method using Brainarray cdf annotations.

source_name: 518A2 cells transfected with SPC2996 and measured after 24h

label_protocol: RNA samples were labeled using the Whole Transcript Sense Target Labeling protocol described by Affymetrix and reagent from Affymetrix.

growth_protocol: 518A2 cells were seeded in 6 well plates with 2,5x10^5 cells/ml in 2ml

treatment_protocol: 24h after seeding (50%-70% confluence) 518A2 cells were transfected with 10nM antisense oligonucleotide or mock in 6 well plates using lipofectamine (5 ug/ml). After 4 hours media was changed and cells incubated for 3 days without antisense oligonucleotide or mock.


title: Mock, biological rep2

source_name: 518A2 cells transfected with mock and measured after 24h

value: mock


title: SPC2996, biological rep3


title: Mock, biological rep1


title: SPC2996, biological rep2


title: 5-2

status: Public on Apr 20 2017

city: Ningbo

first: liyun

last: fu

state: Zhejiang

address: ningbo xibei street No.41, zhejiang province

department: Department of Hepatology

country: China

institute: HwaMei Hospital, University of Chinese Academy of Sciences (Ningbo No.2 hospital)

description: This sample is paired paracancerous tissue from a patient with hepatocellular carcinoma

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5 µm/pixel resolution using a GenePix 4000B scanner piloted by GenePix Pro 6.0 software (Axon Instruments, Union City, CA). Scanned images were then imported into NimbleScan software (version 2.5) for grid alignment and raw intensity extraction.

data_processing: The raw microarray data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.

source_name: Paracancerous tissue

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using SuperScript ds-cDNA synthesis kit (Life Technologies, Inc., Carlsbad, CA, USA) in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA).

extract_protocol: Total RNA was extracted by using TRIzol (Life Technologies, Inc., Carlsbad, CA, USA) according to the manufacturer’s protocol.  circRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrohoresis.

value: Paracancerous


title: 4-2


title: 5-1

description: This sample is cancer tissue from a patient with hepatocellular carcinomar

source_name: hepatocellular carcinoma tissue

value: hepatocellular carcinoma


title: 3-2


title: 4-1


title: 3-1


title: Granulocyte_preterm_indB

source_name: preterm cord blood, granulocyte, B


title: nRBC_preterm_indA

source_name: preterm cord blood, nRBC, A

value: nucleated red blood cells

value: male

value: 26 weeks

value: A


title: Tcell_preterm_indA

source_name: preterm cord blood, T cell, A


title: Monocyte_preterm_indB

source_name: preterm cord blood, monocyte, B


title: Mock, biological rep3


title: 2-2


title: Monocyte_preterm_indC

source_name: preterm cord blood, monocyte, C


title: PBS-treated splenocytes

description: Control

value: splenocytes

value: PBS


title: Granulocyte_preterm_indC

source_name: preterm cord blood, granulocyte, C

value: granulocytes


title: nRBC_preterm_indC

source_name: preterm cord blood, nRBC, C


title: 1-2


title: 2-1


title: 1-1


title: hACs4_EPZ-5676

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Effective DOT1L inhibition by EPZ-5676 was confirmed by Western blot analysis of H3K79 methylation.

hyb_protocol: Following fragmentation, 12.5 microgram of cRNA were hybridized for 17 hr at 45°C and at 60 rounds/min on Affymetrix HG U133 Plus 2.0 arrays. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.40.0) of Bioconductor. Expression values are represented on a log2-scale.

source_name: Human articular chondrocytes from patient 4

label_protocol: Biotinylated cRNA were prepared according to the GeneChip 3' IVT express kit (Affymetrix) protocol from 100 nanogram total RNA.

growth_protocol: DMEM/F12, 10% fetal bovine serum (FBS), 1% (vol/vol) antibiotic/antimycotic and 1% L-glutamine (Detailed in Material and Methods: Cell culture)

extract_protocol: Nucleospin RNA II kit (Macherey-Nagel)

treatment_protocol: EPZ-5676 3 µM 4 days

value: articular cartilage from hip - no documented joint disease

value: 80 years

tag: gender

value: female


title: hACs2_vehicle

source_name: Human articular chondrocytes from patient 2

treatment_protocol: vehicle (DMSO) 4 days

value: 62 years


title: hACs1_vehicle

source_name: Human articular chondrocytes from patient 1

value: 74 years


title: hippocampus F2 methyldiet rep1

city: Bonn

first: Dan

last: ehninger

address: Sigmund-Freud-Straße 27

country: Germany

institute: German Center for Neurodegenerative Diseases

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Methyl_Diet_F2_Hippo_DNA_#1

hyb_protocol: Competitive sample hybridization and washing steps were performed according to the instructions provided by NimbleGen.

scan_protocol: Two-color scanning was performed with the MS 200 Microarray Scanner according to the Operator's Manual

data_processing:
Peak finding was performed using NimbleScan (v2.3) software according to the manufacturer's specifications by identifying peak positions from signal ratio data (MBP-IP vs. Input) in chromosomal bins of 500 bp yielding an average of peak numbers per bin. Differentially methylated regions (DMR) were defined as chromosomal loci where across the three treatment samples, or control samples there were 2 or more peaks whereas the other sample contained none.
Peaks were called using the NimbleGen NimbleScan (v2.3) software by identifying peak positions from signal ratio data (enriched vs input) in chromosomal bins of 500 bp yielding an average of peak numbers per bin in accordance with manufacturers guidelines. Differentially methylated regions (DMR) were defined as chromosomal loci where across the three treatment samples, or control samples there were 2 or more peaks whereas the other sample contained none.
Log2 ratio data contained in .gff files were calculated as the ratio of the input signals for the enriched (Cy5) and input (Cy3) samples and scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2 ratio values for all features on the array from each log2 ratio value

source_name: input from hippocampus, methyl diet, F2

label_protocol: MBD enriched and input samples were labeled with Cy5 and Cy3 dyes, respectively according to the NimbleGen Array kit instructions (v 7.2).

extract_protocol: DNA from sperm and hippocampus samples was prepared using Qiagen Triple Kits. Methylated DNA was immunoprecipitated using Invitrogen's MethylMiner kit (Catalog ME10025) according to the manufacturer protocol using 1 µg DNA. .

tag: strain background

value: C57BL/6J x 129S6/SvEv

tag: generation

value: F2 offspring

tag: diet

value: experimental methyl donor diet

value: hippocampus

source_name: MBD enriched from hippocampus, methyl diet, F2


title: hippocampus F2 controldiet rep2

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Control_Diet_F2_Hippo_DNA_#2

source_name: input from hippocampus, control diet, F2

value: control diet

source_name: MBD enriched from hippocampus, control diet, F2


title: hippocampus F2 methyldiet rep3

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Methyl_Diet_F2_Hippo_DNA_#3


title: hippocampus F2 methyldiet rep2

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Methyl_Diet_F2_Hippo_DNA_#2


title: hippocampus F2 controldiet rep3

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Control_Diet_F2_Hippo_DNA_#3


title: hACs4_vehicle


title: hACs5_EPZ-5676

source_name: Human articular chondrocytes from patient 5

value: 86 years


title: hACs1_EPZ-5676


title: hACs5_vehicle


title: hACs3_EPZ-5676

source_name: Human articular chondrocytes from patient 3

value: 75 years


title: hippocampus F2 controldiet rep1

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Control_Diet_F2_Hippo_DNA_#1


title: hippocampus F1 methyldiet rep3

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Hippocampus_DIET_Methyl#3

source_name: input from hippocampus, methyl diet, F1

value: F1 offspring

source_name: MBD enriched from hippocampus, methyl diet, F1


title: hACs3_vehicle


title: hACs2_EPZ-5676


title: hippocampus F1 methyldiet rep1

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Hippocampus_DIET_Methyl#1


title: hippocampus F1 methyldiet rep2

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Hippocampus_DIET_Methyl#2


title: hippocampus F1 controldiet rep3

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Hippocampus_DIET_Control#3

source_name: input from hippocampus, control diet, F1

source_name: MBD enriched from hippocampus, control diet, F1


title: hippocampus F1 controldiet rep2

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Hippocampus_DIET_Control#2


title: hippocampus_F2_methyldiet_rep3

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in a hybridization oven (Agilent) using the Mouse GE 4x44K v2 Microarray Kit (Cat. No. G4846A). Washing and staining of the arrays were performed according to the manufacturer’s recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 μm resolution. Scanned image files were inspected for artifacts and then analyzed.

data_processing: ntensity data were extracted using Agilent’s Feature Extraction (FE) software (version 9.5.3.1) including a quality control based on internal controls using Agilent’s protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma package of Bioconductor. The microarray data analysis consists of the following steps: 1. between-array normalization, 2. global clustering and PCA-analysis, 3. fitting the data to a linear model, 4. detection of differential gene expression and 5. over-representation analysis of differentially expressed genes. We applied quantile-normalization to the log2-transformed intensity values as a method for between-array normalization.

source_name: hippocampus of F2 offspring of methyl diet supplemented fathers

label_protocol: Cy3 labeled cRNA was prepared from 0.6 ug RNA using the Low RNA Input linear Amplification Kit Plus, One Color protocol (Agilent 5188-5339) and the Agilent One color RNA Spike-In Kit (Agilent 5188-5252) following the manufacturer's standard protocols.

extract_protocol: RNA was prepared using Qiagen RNeasy kits

treatment_protocol: F1 and F2 mice fed a control diet were derived from fathers or grandfathers, respectively fed a control diet (T.2918.12, Envigo) or an experimental methyl donor diet (3MS ZM) supplemented with 7.5 g l-methionine, 15 g choline, 15 g betaine, 15 mg folic acid, 1.5 mg vitamin B12 and 150 mg zinc for 6 weeks prior to mating.

tag: strain

value: mixed C57BL/6J x 129S6/SvEv hybrids

tag: diet (for fathers or grandfathers)

value: experimental methyl donor diet (3MS ZM)


title: hippocampus_F2_methyldiet_rep6

tag: tissue


title: hippocampus_F2_methyldiet_rep4

tag: age


title: hippocampus_F2_methyldiet_rep1


title: hippocampus F1 controldiet rep1

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
Hippocampus_DIET_Control#1


title: hippocampus_F2_controldiet_rep6

source_name: hippocampus of F2 offspring of control diet fathers

value: control diet (T.2918.12, Envigo)


title: hippocampus_F2_methyldiet_rep2


title: sperm F0 methyldiet rep2

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
methyl_2

source_name: input from sperm, methyl diet, F0

value: sperm

source_name: MBD enriched from sperm, methyl diet, F0


title: hippocampus_F2_methyldiet_rep5


title: sperm F0 controldiet rep3

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
control_3

source_name: input from sperm, control diet, F0

source_name: MBD enriched from sperm, control diet, F0


title: sperm F0 methyldiet rep3

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
methyl_3


title: sperm F0 methyldiet rep1

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
methyl_1


title: hippocampus_F2_controldiet_rep4


title: hippocampus_F2_controldiet_rep5


title: sperm F0 controldiet rep2

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
control_2


title: sperm F0 controldiet rep1

description:
Methylated DNA immunoprecipitation followed by microarray to identify differentially methylated regions genome-wide
control_1


title: hippocampus_F2_controldiet_rep1


title: hippocampus_F2_controldiet_rep3


title: hippocampus_F1_methyldiet_rep6

source_name: hippocampus of F1 offspring of methyl diet supplemented fathers

value: congenic C57BL/6J x 129S6/SvEv hybrids


title: hippocampus_F1_controldiet_rep4

source_name: hippocampus of F1 offspring of control diet fathers


title: hippocampus_F1_controldiet_rep6


title: hippocampus_F1_methyldiet_rep4


title: hippocampus_F1_controldiet_rep5


title: hippocampus_F1_controldiet_rep2


title: hippocampus_F1_methyldiet_rep3


title: hippocampus_F2_controldiet_rep2


title: hippocampus_F1_methyldiet_rep5


title: hippocampus_F1_controldiet_rep3


title: hippocampus_F1_methyldiet_rep1


title: hippocampus_F1_methyldiet_rep2


title: hippocampus_F1_controldiet_rep1


title: Left ventricle_normal sodium_angiotensin II_replicate 1

city: Montpellier

first: Caroline

last: DESMETZ

address: 15 avenue Charles Flahault

department: Faculty of pharmacy

country: France

institute: Montpellier University

hyb_protocol: Hybridization procedure was performed using Agilent Gene Expression Hybridization kit. Briefly, 1.65µg Cy3-labeled fragmented cRNA was hybridized 17h at 65°C to Agilent Rat Gene Expression Microarray V3 4x44K using recommended manufacturer’s hybridization chambers and oven. The microarrays were then washed once with the Agilent Gene Expression Wash Buffer for 1 min at RT, and then washed with Agilent Gene Expression Wash buffer 2 at 37°C for 1 min.

scan_protocol: Fluorescence signals were detected using Agilent’s Microarray Scanner System and the Agilent Feature Extraction Software (version 11.0.1.1) to read out and process the microarray image files.

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Statistical analysis was performed using R software version 3.3.04 along with the Limma package. The method used for background correction was based on the normal-exponential convolution model with the saddle-point approximation to maximum likelihood. Normalization was performed using cyclic loess method. Only probes whose signal was considered as higher than background in at least four out of six replicates in at least one condition were selected for further analysis. Within-array replicate probes were replaced with their average. The assessment of differentially expressed mRNAs between NS diet and LS diet was performed using the limma GLM (Generalized Linear Model) method followed by Benjamini Hochberg correction for multiple testing. Genes with a corrected p-value lower than 0.1 were selected for further investigation.

organism: Rattus norvegicus

source_name: Left ventricle, normal sodium, angitoensin II, replicate 1

label_protocol: 200ng of each total RNA samples was used for amplification and labelling with the Agilent Low Input Quick amp Labelling kit, one color. Yields of cRNA and dye incorporation rate were measured using ND-1000 spectrometer (NanoDrop technologies, Peqlab biotechnologies GmbH, Erlangen, Germany).

growth_protocol: Sprague-Dawley rats were fed for 8 weeks 60% fructose diet with either a normal sodium (0.64% NaCl) or a low sodium content (<0.01% NaCl) (n=40 in each). After 4 weeks, rats were infused or not with angiotensin II (200 ng.kg-1.min-1, sc) for 4 weeks.

extract_protocol: Tissues were dissociated in RLT buffer using a Fast-Prep® homogeneizer (MP Biomedicals). Total RNA was extracted using RNeasy® Fibrous Tissue mini-kit (Qiagen). RNA quality and integrity were determined using the Agilent 2100 Bioanalyser (Agilent Technologies).

treatment_protocol: At the end of the experiment, heart left ventricles were collected in RNA later and frozen (-80°C) for further mRNA extraction

value: Sprague-Dawley

value: heart left ventricle

value: male

tag: sodium

value: normal sodium


title: Left ventricle_normal sodium_no angiotensin II_replicate 2

source_name: Left ventricle, normal sodium, no angiotensin II, replicate 2


title: Left ventricle_normal sodium_no angiotensin II_replicate 3

source_name: Left ventricle, normal sodium, no angiotensin II, replicate 3


title: Left ventricle_normal sodium_angiotensin II_replicate 3

source_name: Left ventricle, normal sodium, angitoensin II, replicate 3


title: Left ventricle_low sodium_angiotensin II_replicate 3

source_name: Left ventricle, low sodium, angiotensin II, replicate 3

value: low sodium


title: Left ventricle_low sodium_no angiotensin II_replicate 3

source_name: Left ventricle, low sodium, no angiotensin II, replicate 3


title: Left ventricle_low sodium_no angiotensin II_replicate 1

source_name: Left ventricle, low sodium, no angiotensin II, replicate 1


title: Left ventricle_low sodium_angiotensin II_replicate 1

source_name: Left ventricle, low sodium, angiotensin II, replicate 1


title: Left ventricle_normal sodium_no angiotensin II_replicate 1

source_name: Left ventricle, normal sodium, no angiotensin II, replicate 1


title: hsp30Δ 40°C

city: Delhi

first: Amitabha

last: Chakrabarti

state: Delhi

address: Lucknow Road

department: Molecular Biology

country: India

institute: Defence Institute of Physiology and Allied Sciences

description: Gene expression from exponentially growing Saccharomyces cerevisiae BY4741hsp30Δ cells following 30 min exposure at 40°C

hyb_protocol: As per standard Affymetrix protocol

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

data_processing: The CEL files obtained for each sample were processed through GC-RMA normalization which includes log transformation and quantile normalization.  For each probe set, present/marginal /absent calls were generated using MAS5 algorithm developed by Affymetrix.  The control probe set and probe sets that were considered absent in more than two samples were excluded from the analysis.

organism: Saccharomyces cerevisiae

label_protocol: As per standard Affymetrix protocol

growth_protocol: Saccharomyces cerevisiae BY4741 and BY4741hsp30Δ cells grown at 30°C and following exposure at 40°C for 30 min

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini kit

tag: genotype

tag: treatment

value: 30 min exposure at 40°C

tag: state

value: exponentially growing


title: BY4741 30°C

description: Gene expression from exponentially growing Saccharomyces cerevisiae BY4741 cells at 30°C

source_name: BY4741 cells at 30°C

growth_protocol: Saccharomyces cerevisiae BY4741 and BY4741hsp30Δ cells grown at 30°C and following exposure at 40°C for 30 min.

value: Matahis3Δ1leu2Δ0met15Δ0 ura3Δ0


title: hsp30Δ 30°C

description: Gene expression from exponentially growing Saccharomyces cerevisiae BY4741hsp30Δ cells at 30°C

source_name: BY4741hsp30Δ cells at 30°C


title: BY4741 40°C

description: Gene expression from exponentially growing Saccharomyces cerevisiae BY4741 cells following 30 min exposure at 40°C


title: Left ventricle_low sodium_no angiotensin II_replicate 2

source_name: Left ventricle, low sodium, no angiotensin II, replicate 2


title: Left ventricle_low sodium_angiotensin II_replicate 2

source_name: Left ventricle, low sodium, angiotensin II, replicate 2


title: ∆mtrB test replicate 2

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

institute: Bose Institute

description: Gene expression during log phase growth

hyb_protocol: Hybridization was done using Agilent’s In situ Hybridzation kit 5188-5242.

scan_protocol: Slides were scanned with Agilent SureScan Microarray Scanner G2600D. Agilent Scan Control software was used with default setting to scan a complete slide in 20 mins. Agilent Feature Extraction Software 11.5.1.1 version was used to extract signal intensity data from Image file.

data_processing: The normalization has been done using GeneSpring GX 13.0 Software. In intra array normalization, gProcessed signal (dye normalized background subtracted signal intensity) is log transformed and then for each of the array the 75th percentile value is calculated separately. In each sample the log transformed intensity values for each probe is subtracted by the calculated 75th percentile value of the respective array and expression values are obtained.

organism: Mycobacterium tuberculosis H37Rv

source_name: Total bacterial RNA

label_protocol: 500ng RNA was labelled with Agilent’s Quick-Amp labeling Kit (p/n5190-0442). T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis).

growth_protocol: Strains were grown to log phase in MB7H9 containing 10% ADC.

extract_protocol: RNA was extracted by homogenising in a bead beater (Prospec) and purified with Qiagen RNeasy kit.

treatment_protocol: No treatment.

tag: growth phase

value: log phase

value: mtrB KO


title: Left ventricle_normal sodium_angiotensin II_replicate 2

source_name: Left ventricle, normal sodium, angitoensin II, replicate 2


title: H37Rv control replicate 2

description: Gene expression during log phase growth

value: wild type


title: ∆mtrB test replicate 1

description: Gene expression during log phase growth


title: Scrb_HG_biological replicate 2

city: Ann Arbor

first: Zhuoxian

last: Meng

state: Michigan

address: 210 Washtenaw Ave

institute: University of Michigan

description: Gene expression data from C2C12 myotubes transduced with siScramble retrovirus and treated with 10 mM glucose for 12 h.

hyb_protocol: According to standard Affymetrix protocol.

data_processing: Data was analyzed using the affy Bioconductor packages implemented in the R-statistical environment. RMA was used to fit log2 expression values.

source_name: C2C12 mouse cell line

extract_protocol: Extraction of total RNA using Trizol method was performed according to the manufacturer's instructions.

treatment_protocol: C2C12 myoblasts were transduced with retroviruses expressing shRNAs targeting control or mouse Baf60c, differentiated into myotubes, and treated with 1mM or 10 mM glucose for 12 h, followed by RNA extraction.

tag: cell line

tag: protocol


title: SiBc_HG_biological replicate 1

description: Gene expression data from C2C12 myotubes transduced with siBaf60c retrovirus and treated with 10 mM glucose for 12 h.

scan_protocol: According to standard Affymetrix protocol.


title: SiBc_LG_biological replicate 2

description: Gene expression data from C2C12 myotubes transduced with siBaf60c retrovirus and treated with 1 mM glucose for 12 h.

label_protocol: According to standard Affymetrix protocol.


title: SiBc_LG_biological replicate 1

value: transduced with siBaf60c retrovirus and treated with 1 mM glucose for 12 h.


title: Scrb_HG_biological replicate 1

value: transduced with siScramble retrovirus and treated with 10 mM glucose for 12 h.


title: H37Rv control replicate 1

description: Gene expression during log phase growth


title: SiBc_HG_biological replicate 2

value: transduced with siBaf60c retrovirus and treated with 10 mM glucose for 12 h.


title: Scrb_LG_biological replicate 2

description: Gene expression data from C2C12 myotubes transduced with siScramble retrovirus and treated with 1 mM glucose for 12 h.


title: post_MBT_rep2

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol on GeneChip Scanner 3000.

data_processing: R/Bioconductor, rma normalization, default parameters.

organism: Xenopus tropicalis

source_name: post-MBT embryos

label_protocol: Standard Affymetrix protocol.

growth_protocol: Xenopus tropicalis eggs were collected, in vitro fertilized and cultivated following standard procedures. Embryos were staged according to Nieuwkoop and Faber (1967). After fertilization, we collected one sample in the 4-cell stage as negative GS17 control. For the preMBT time-point, we collected around the ~1000 cell stage and then every 20-25 minutes for approximately 60-100min. We choose 20-25 min breaks depending on how long the embryos need in average for the first cell divisions. 120-150 minutes after collecting the last preMBT sample, we started again to collect every 20-25 min samples until we observed dorsal lip formation. In order to find the preMBT sample closest to the MBT, we performed qPCR analysis with MBT-marker GS17. For the preMBT time-point, we took the last sample without GS17 expression. As postMBT, we choose the sample ~40min before upcoming of dorsal lip formation, because this timepoint is in accordance to the timepoint of the comparative microarray analysis.

extract_protocol: Total RNA of 10 embryos was extracted using Trizol (Ambion) and phenol/chloroform. The RNA was precipitated with 70% isopropanol and cleaned using the RNeasy Cleanup Kit (Qiagen) including DNaseI-on-column digestion.

value: embryos

tag: developmental stage

value: post midblastula transition (MBT)

tag: replicate


title: post_MBT_rep1


title: brg1_rep4

source_name: late blastula embryos, brg1 morpholino

growth_protocol: Xenopus tropicalis eggs were collected, in vitro fertilized, microinjected and cultivated following standard procedures. Embryos were staged according to Nieuwkoop and Faber (1967).

treatment_protocol: Radial injections were performed at the 2-4 cell stage with 30ng BRG1 morpholino (CCATTGGAGGGTCTGGGGTGGACAT) or 60ng control morpholino and cultivated until late blastula stage.

value: late blastula

tag: morpholino


title: brg1_rep2


title: pre_MBT_rep3

source_name: pre-MBT embryos

value: pre midblastula transition (MBT)


title: pre_MBT_rep2