title: total RNA-seq from H1 (ENCSR712GOC)

summary:
h1_hesc

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from aorta (ENCSR185TQB)

status: Public on May 23 2021

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Expression profiling by high throughput sequencing

summary:
w61_aorta

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from mucosa of descending colon (ENCSR184LTL)

summary:
w80_mucosa_of_descending_colon

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from H9 (ENCSR712BRU)

summary:
H9 ESC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from A549 (ENCSR192PBJ)

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from A549 (ENCSR716SJK)

summary:
cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HCT116 (ENCSR698RPL)

summary:
HCT116_rep2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR184IQF)

summary:
eGFP-SHOX2 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from mucosa of descending colon (ENCSR674KHG)

summary:
w76_mucosa_of_descending_colon

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from SK-N-SH (ENCSR706OJM)

summary:
eGFP-POU6F1 ChIP-seq on human SK-N-SH

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from A549 (ENCSR174FJD)

summary:
EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR177DNR)

summary:
FIP1L1 ChIP-seq in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR663NFC)

summary:
eGFP-STAT5B ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from WTC11 (ENCSR673UKZ)

summary:
LRGASP_WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from A673 (ENCSR179SAO)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR172OSX)

summary:
eGFP-ZBTB12 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from PC-3 (ENCSR648KDM)

summary:
PC-3_rep2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from pancreas (ENCSR165QTZ)

summary:
w80_pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from A549 (ENCSR167QIJ)

summary:
EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR643JRH)

summary:
eGFP-MAZ ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from left cardiac atrium (ENCSR652PHZ)

summary:
w73_left_cardiac_atrium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR172XJS)

summary:
eGFP-ZNF165 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from WTC11 (ENCSR166IFS)


title: Histone ChIP-seq from RWPE2 (ENCSR161GUA)

summary:
H3K4me1 ChIP-seq on human RWPE2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from ovary (ENCSR146ZLV)

summary:
w73_ovary

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from ovary (ENCSR140DCD)

summary:
W72_ovary

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from posterior vena cava (ENCSR149AHS)

summary:
w73_posterior_vena_cava

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from Right ventricle myocardium superior (ENCSR132VGJ)

summary:
w78_right_ventricle_myocardium_superior

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from right lobe of liver (ENCSR135IAL)

summary:
w61_right_lobe_of_liver

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from sciatic nerve (ENCSR631NUQ)

summary:
w61_sciatic_nerve

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM12878 (ENCSR151NGC)

summary:
GM12878_rep2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from T-cell (ENCSR631FXT)

summary:
Allcells15824 inactive T-cells

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from NCI-H929 (ENCSR634OAQ)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR156APP)

summary:
PTBP1 ChIP-seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from GM23248 (ENCSR131FFJ)


title: TF ChIP-seq from K562 (ENCSR630KQP)

summary:
eGFP-ZNF250 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from Panc1 (ENCSR128CYL)

summary:
Panc1_rep2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from posterior vena cava (ENCSR130TZW)

summary:
w71_posterior_vena_cava

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR125YGM)

summary:
eGFP-ID3 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from SU-DHL-6 (ENCSR125DKL)


title: Histone ChIP-seq from KOPT-K1 (ENCSR630IBN)


title: total RNA-seq from activated T-cell (ENCSR111PSY)

summary:
Allcells6054 activated T-cells

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from A549 (ENCSR628MQN)

summary:
cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from SK-N-SH (ENCSR106GVM)

summary:
eGFP-SNAI2 ChIP-seq on human SK-N-SH

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR109SJT)

summary:
eGFP-SMAD4 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from A549 (ENCSR110UPH)

summary:
cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR624GNZ)

summary:
SRSF9 ChIP-seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from right cardiac atrium (ENCSR622PIH)

summary:
w73_cardiac_right_atrium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from GM23248 (ENCSR096KPA)


title: TF ChIP-seq from K562 (ENCSR112RNT)

summary:
HNRNPLL ChIP-seq in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from spleen (ENCSR096LTX)

summary:
w80_spleen

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from spleen (ENCSR621PZI)

summary:
w61_spleen

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR625ORP)

summary:
SYNCRIP ChIP-seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from neural cell (ENCSR076NBJ)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR075PWK)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR099MNR)

summary:
eGFP-ZNF75A ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from spleen (ENCSR074FTH)

summary:
w64_spleen

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR623RFC)


title: TF ChIP-seq from A549 (ENCSR070VXO)

summary:
GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from K562 (ENCSR615EEK)

summary:
K562_rep2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from pancreas (ENCSR071DYD)

summary:
w62_pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HEK293 (ENCSR618HNF)

summary:
TRIM28 ChIP-seq on human HEK293

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from WERI-Rb-1 (ENCSR614NUF)

summary:
H3K4me1 ChIP-seq on human WERI-Rb-1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from A549 (ENCSR604CKQ)

summary:
cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from MCF-7 (ENCSR059ICA)


title: TF ChIP-seq from A549 (ENCSR044IFH)

summary:
EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from lung (ENCSR045GTF)

summary:
W71_lung

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR696MBC)

summary:
SRSF4 ChIP-seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR052PTN)

summary:
PCBP1 ChIP-seq in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from MCF-7 (ENCSR610IYQ)


title: TF ChIP-seq from K562 (ENCSR603REQ)

summary:
PCBP2 ChIP-seq in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from foreskin keratinocyte (ENCSR034RPU)

summary:
RiboZero RNA-seq on primary keratinocytes in day 0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from pancreas (ENCSR579BDN)

summary:
w61_pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from SK-N-SH (ENCSR602QEJ)

summary:
eGFP-PPARA ChIP-seq on human SK-N-SH

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from psoas muscle (ENCSR574PFY)

summary:
w61_psoas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from upper lobe of left lung (ENCSR589EBT)

summary:
W80_upper_lobe_of_left_lung

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from SK-N-SH (ENCSR581GUY)

summary:
eGFP-ZFP3 ChIP-seq on human SK-N-SH

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from thyroid gland (ENCSR582PKH)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from testis (ENCSR561MYM)


title: TF ChIP-seq from K562 (ENCSR590FLL)

summary:
eGFP-ZNF347 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from foreskin keratinocyte (ENCSR036EGV)

summary:
CTCF ChIP-seq on primary keratinocytes in day 3 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from psoas muscle (ENCSR563VMC)

summary:
w80_psoas_muscle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from endodermal cell (ENCSR559HWG)

summary:
h1_endoderm

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Functional roles of the chromatin remodeler SMARCA5(SNF2H) in mouse and bovine preimplantation embryos

status: Public on May 31 2021

city: Hangzhou

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

country: China

institute: Zhejiang University

summary: Upon fertilization, extensive chromatin reprogramming occurs during preimplantation development. Growing evidence reveals species-dependent regulations of this process in mammals. ATP-dependent chromatin remodeling factor SMARCA5 (also known as SNF2H) is required for peri-implantation development in mice. However, the specific functional role of SMARCA5 in preimplantation development and if it is conserved among species remain unclear. Herein, comparative analysis of public RNA-seq datasets reveals that SMARCA5 is universally expressed during oocyte maturation and preimplantation development in mice, cattle, humans and pigs with species-specific patterns. Immunostaining analysis further describes the temporal and spatial changes of SMARCA5 in both mouse and bovine models. siRNA-mediated SMARCA5 depletion reduces the developmental capability and compromises the specification and differentiation of inner cell mass in mouse preimplantation embryos. Indeed, OCT4 is not restricted into the inner cell mass and the formation of epiblast and primitive endoderm disturbed with reduced NANOG and SOX17 in SMARCA5-deficient blastocysts. RNA-seq analysis shows SMARCA5 depletion causes limited effects on the transcriptomics at the morula stage, however, dysregulates 402 genes, including genes involved in transcription regulation and cell proliferation at the blastocyst stage in mice. By comparison, SMARCA5 depletion does not affect the development through the blastocyst stage but significantly compromises the blastocyst quality in cattle. Primitive endoderm formation is greatly disrupted with reduced GATA6 in bovine blastocysts. Overall, our studies demonstrate the importance of SMARCA5 in fostering the preimplantation development in mice and cattle while there are species-specific effects.

overall_design: Mouse embryos were obtained at E3.75 and E4.25 from NC and KD groups (n=2; 20 embryos per group per replicate). RNA isolation was performed by using Arcturus PicoPureRNA Isolation Kit (Applied Biosystems, Foster City, CA) based on the manufacturer's instructions. The separation of mRNAs was completed by using oligo(dT)25 beads. Sequencing libraries were constructed by using NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) according to the instructions. In brief, mRNAs were fragmented and reverse transcribed. Then, the cDNA library went through end repair, poly(A)-tailing, adaptor ligation, and PCR amplification for 12-15 cycles. Sequencing was conducted with paired-end 150 by Novogene (Beijing, China).

first: Yan

last: Shi


title: TF ChIP-seq from A549 (ENCSR602BTS)

summary:
EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from excitatory neuron (ENCSR595YCU)


title: Histone ChIP-seq from A549 (ENCSR027BPE)

summary:
H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR555ZMV)

summary:
AGO1 ChIP-seq in HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from SK-N-SH (ENCSR023KKB)

summary:
eGFP-ESRRG ChIP-seq on human SK-N-SH

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from A549 (ENCSR022WVP)

summary:
cJun ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from Right ventricle myocardium inferior (ENCSR015PUN)

summary:
w78_right_ventricle_myocardium_inferior

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR014RCS)

summary:
HNRNPK ChIP-seq in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from WTC11 (ENCSR547WSB)

summary:
eGFP-TRERF1 ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR008DOU)

summary:
eGFP-SNAPC5 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from foreskin keratinocyte (ENCSR527SSD)

summary:
RiboZero RNA-seq on primary keratinocytes in day 6 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from pancreas (ENCSR523RGW)

summary:
W71_pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR005WGY)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from WTC11 (ENCSR004HEA)

summary:
eGFP-OTX2 ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from adrenal gland (ENCSR003BTD)

summary:
W71_adrenal_gland

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from colonic mucosa (ENCSR516BJM)

summary:
W62_colonic_mucosa

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR519QAA)

summary:
HNRNPK ChIP-seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from left ventricle myocardium inferior (ENCSR516TTH)

summary:
w78_left_ventricle_myocardium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR517HGZ)


title: Histone ChIP-seq from HEK293 (ENCSR000FCJ)

summary:
H3K9me3 HEK293 ChIP-Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: RNA-seq access dataset for epigenomics landscape of colorectal cancer

status: Public on May 22 2021

city: Cambridge

first: Ayush

middle: T

last: Raman

state: MA

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

summary: Enhancer aberrations are beginning to emerge as a key feature of colorectal cancers, however, we have limited understanding of epigenomic patterns that distinguish tumors and underlying heterogeneity between tumors. Here, using epigenomic profiling of colorectal tumors, adenomas and normal colon tissues, we identify unique pattern of regulatory elements in colorectal cancer, which could reliably distinguish tumors from normal colon specimens. We define shared and unique enhancer elements during colorectal cancer progression using normal adjacent colon, adenomas and adenocarcinomas. We validate the functional nature of tumor-specific enhancers for important oncogenes such as ASCL2 and Fzd10. NMF clustering identified 4 epigenetic (EPIC) subtypes in colorectal cancer, which mimics consensus molecular subtypes (CMS)1, with an advantage of introducing a novel epigenetically-identifiable subtype with poor prognosis and survival. Based on this correlation, we defined and validated a combination therapeutic strategy of enhancer-blocking BETi with pathway specific inhibitor for 3 CMS subtypes. In conclusion, by comprehensive characterization of chromatin state patterns in colorectal tumors, we define epigenomic patterns during tumor evolution, heterogeneity of enhancers among patients and a combination therapy strategy for CMS-subgroups.

overall_design: There are 12 samples with 7 tumor samples and 5 normal samples.

first: Elias

last: Orouji

first: Anand

middle: K

last: Singh

first: Kunal

last: Rai


title: XCR1+ type 1 conventional dendritic cells drive liver pathology in Non-Alcoholic Steatohepatitis [10x scRNA-seq]

status: Public on May 21 2021

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) are prevalent liver conditions, which underlie the development of life-threatening cirrhosis, liver failure and liver cancer. Chronic necro-inflammation is a critical factor in development of NASH, yet the cellular and molecular mechanisms of immune dysregulation in this disease are poorly understood. Here, using single cell transcriptomic analysis, we comprehensively profiled the immune composition of the mouse liver during NASH. We identified a significant pathology-associated increase in hepatic conventional dendritic cells (cDC), and further defined their source as NASH-induced boost in cycling of cDC progenitors in the bone marrow. Analysis of blood and liver from patients on the NALFD/NASH spectrum showed that cDC type 1 (cDC1) were more abundant and activated in disease. Genomic analysis of cDC-T pairs in liver draining lymph nodes revealed that cDCs in NASH promote inflammatory T cell reprogramming, previously associated with NASH worsening. Finally, depletion of cDC1 in XCR1DTA mice or using anti-XCL1 blocking antibody attenuated liver pathology in NASH mouse models. Overall, our study provides a comprehensive characterization of cDC biology in NASH, and identifies XCR1+ cDC1 as an important driver of liver pathology.

overall_design: Liver biopsies from bariatric surgery patients were collected in RPMI (Supplemented with 10%FBS) and immediately transported on ice to the laboratory. A section of tissue was formalin fixed for histopathological evaluation; however, the bulk of the tissue was digested using Miltenyi Tumor dissociation Kit (cat no. 130-095-929) as per the manufacturer’s instructions. Single cell suspensions thus generated were stored in Liquid nitrogen in FBS+20% DMSO until further processing. For sorting and scRNAseq of DCs obtained from control and NASH livers, the stored cells were thawed in a 37oC water bath, washed once with complete media and once with FACS buffer (PBS+2% FBS). After FC blocking, cells were stained for 30 min and washed once with FACS buffer and once with sorting buffer (PBS+0.5mM EDTA). Sorting was carried out at DKFZ cytometry facility using BD FACS Aria. Bulk-sorted CD45+ Lin- CD11c+ were then processed for 10X (10X Genomics).

first: Aleksandra

last: Deczkowska

first: Eyal

last: David

first: Pierluigi

last: Ramadori

first: Dominik

last: Pfister

first: Michal

last: Safran

first: Baoguo

last: Li

first: Amir

last: Giladi

first: Diego

middle: A

last: Jaitin

first: Oren

last: Barboy

first: Merav

last: Cohen

last: Yofe

first: Chamutal

last: Gur

first: Shir

last: Shlomi-Loubaton

first: Sandrine

last: Henri

first: Yousuf

last: Suhail

first: Mengjie

last: Qiu

first: Shing

last: Kam

first: Hila

last: Hermon

first: Eylon

last: Lahat

first: Gil

last: Ben-Yakov

first: Oranit

last: Cohen-Ezra

first: Yana

last: Davidov

first: Mariya

last: Likhter

first: David

last: Goitein

first: Susanne

last: Roth

first: Achim

last: Weber

first: Bernard

last: Malissen

first: Assaf

last: Weiner

first: Ziv

last: Ben-Ari

first: Mathias

last: Heikenwälder

first: Eran

last: Elinav


title: AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency (ChIP-Seq)

first: Helen

middle: M

last: Blau

address: 269 Campus Dr

department: Baxter Laboratories

institute: Stanford University

summary: Somatic cell transcription factors are critical to maintaining cellular identity and constitute a barrier to human somatic cell reprogramming, yet a comprehensive understanding of the mechanism of action is lacking. To gain insight, we examined epigenome remodeling at the onset of human nuclear reprogramming by profiling human fibroblasts after fusion with murine embryonic stem cells. By ATAC-seq and ChIP-seq we identified enrichment for the AP-1 transcription factor c Jun at regions of early transient accessibility at fibroblast-specific enhancers. Expression of a dominant negative AP-1 mutant (dnAP 1) reduced accessibility and expression of fibroblast genes, overcoming the barrier to reprogramming. Remarkably, efficient reprogramming of human fibroblasts to iPSC was achieved by transduction with vectors expressing SOX2, KLF4, and inducible dnAP 1 demonstrating that dnAP-1 can substitute for exogenous human OCT4. Mechanistically, we show that the AP-1 component c-Jun has two unexpected temporally distinct functions in human reprogramming: i) to potentiate fibroblast enhancer accessibility and fibroblast-specific gene expression and ii) to bind to and repress OCT4 as a complex with MBD3. Our findings highlight AP-1 as a previously unrecognized potent dual gatekeeper of the somatic cell state.

overall_design: Chip-seq by ChIPmentation in cultured human fibroblasts

first: Glenn

middle: J

last: Markov

first: Thach

last: Mai

first: Surag

last: Nair

first: Anna

last: Shcherbina

first: Yu

middle: X

last: Wang

last: Burns

first: Anshul

last: Kundaje


title: Epigenomics landscape of colorectal cancer

first: Ayush

last: Raman

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Histone ChIP-seq from HEK293 (ENCSR000FCH)

first: ENCODE

last: DCC

summary:
H3K27Ac HEK293 ChIP-Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from HEK293 (ENCSR000FCK)

summary:
H3K36me3 HEK293 ChIP-Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: XCR1+ type 1 conventional dendritic cells drive liver pathology in Non-Alcoholic Steatohepatitis [scRNA-seq]

first: Ido

last: Amit

overall_design:
Indicated cell types were isolated by sorting from bone marrow/blood/liver/liver lymph nodes from mice kept on normal diet (ND) or methionine and choline deficient diet (MCDD) for two weeks (unless indicated otherwise).
Please note that [1]  the second read contained only cell and molecule barcodes. This information was appended to the fastq entry header. [2] *_metadata_s.txt file is meta data file associating each single cell with its amplification batch and index sorting readouts.

first: Aleksandra

last: Deczkowska

first: Eyal

last: David

first: Pierluigi

last: Ramadori

first: Dominik

last: Pfister

first: Michal

last: Safran

first: Baoguo

last: Li

first: Amir

last: Giladi

first: Diego

last: Jaitin

first: Oren

last: Barboy

first: Merav

last: Cohen

last: Yofe

first: Chamutal

last: Gur

first: Shir

last: Shlomi-Loubaton

first: Sandrine

last: Henri

first: Yousuf

last: Suhail

first: Mengjie

last: Qiu

first: Shing

last: Kam

first: Hila

last: Hermon

first: Eylon

last: Lahat

first: Gil

last: Ben-Yakov

first: Oranit

last: Cohen-Ezra

first: Yana

last: Davidov

first: Mariya

last: Likhter

first: David

last: Goitein

last: Roth


title: MicroRNA in combination with HER2-targeting drugs reduces breast cancer cell viability in vitro

city: Drammen

first: Lisa

middle: Svartdal

last: Normann

address: Wergelands gate 10

department: Department of Research and Innovation

country: Norway

institute: Vestre Viken Health Trust

summary: HER2-positive (HER2+) breast cancer patients that do not respond to targeted treatment have a poor prognosis. The effects of targeted treatment on endogenous microRNA (miRNA) expression levels are unclear. We report that responsive HER2+ breast cancer cell lines had a higher number of miRNAs with altered expression after treatment with trastuzumab and lapatinib compared to poorly responsive cell lines. To evaluate whether miRNAs can sensitize HER2+ cells to treatment, we performed a high-throughput screen of 1626 miRNA mimics and inhibitors in combination with trastuzumab and lapatinib in HER2+ breast cancer cells. We identified eight miRNA mimics sensitizing cells to targeted treatment, miR-101-5p, mir-518a-5p, miR-19b-2-5p, miR-1237-3p, miR-29a-3p, miR-29c-3p, miR-106a-5p, and miR-744-3p. A higher expression of miR-101-5p predicted better prognosis in patients with HER2+ breast cancer (OS: p=0.0392; BCSS: p=0.0125), supporting the tumor-suppressing role of this miRNA. In conclusion, we have identified miRNAs that sensitize HER2+ breast cancer cells to targeted therapy. This indicates the potential of combining targeted drugs with miRNAs to improve current treatments for HER2+ breast cancers.

overall_design: Four HER2 positive breast cancer cell lines (SKBR3, BT-474, KPL4 and SUM190PT) were treated with trastuzumab (10 µg/mL), lapatinib (100 nM) or trastuzumab plus lapatinib for 24 hours. miRNA expression levels were measured in untreated and treated cells using the one-color microarray SurePrint Human miRNA Microarray with design ID 031181, release 16.0, 8 x 60K (Agilent Technologies, Santa Clara, CA, USA) according to the protocol supplied by the manufacturer (miRNA Microarray System v2.3). Scanning was performed on Agilent Scanner G2565B. Samples were processed using Feature Extraction (FE) version 10.7.3.1 (Agilent Technologies). Quality was assessed by the quality control parameters in FE. The data were log2-transformed and for each sample, considering only expressed miRNAs, the data were median centered. All non-expressed miRNAs across samples were set to a common minimum value.

last: Svartdal Normann

first: Miriam

last: Ragle Aure

first: Suvi-Katri

last: Leivonen

first: Mads

last: Haugland Haugen

first: Vesa

last: Hongisto

first: Vessela

middle: N

last: Kristensen

first: Gunhild

last: Mari Mælandsmo

first: Kristine

last: Kleivi Sahlberg


title: Hi-ChIP dataset for epigenomics landscape of colorectal cancer

first: Ayush

last: Raman

overall_design: H3K27Ac HiChIP data for four colorectal cancer cell lines were generated with deep sequencing using the HiSeq4000 sequencer.

first: Anand

last: Singh

first: Elias

last: Orouji

first: Kunal

last: Rai


title: Next generation sequencing of neutrophils from WT, PyMT and PyMT-Cxcr2-/- mice

city: Montpellier

first: Gwendal

last: Lazennec

address: 1682 rue de la valsiere

country: France

institute: CNRS

summary: We report the comparison of gene expression of neutrophils  in the mammary gland of PyMT and PyMT-Cxcr2-/- animals as well as the one of WT bone marrow

overall_design: mRNA profile was generated by deep sequencing using Novaseq 6000 SP Illumina.


title: Expression data from EML4-ALK overexpression in HEK293 cell line and EML4-ALK knockdown in H2228 lung cancer cell line.

status: Public on May 20 2021

city: Tianjin

first: Yongwen

last: Li

address: No.154, Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

summary:
We demonstrate that EML4-ALK siRNAs significantly reduced cell viability in EML4-ALK postive lung cancer cell lines,while overexpression of EML4-ALK  increased cell viability in HEK293 cells in vitro.
The aim of this study was to analyze the EML4-ALK regulated gene expression in lung cancer.

overall_design: H2228 and HEK293 cells transfected with EML4-ALK  siRNAs or EML4-ALK V3 plasimd for 48 hours were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Ying

last: li

first: Hongyu

last: Liu

first: Jun

last: Chen


title: Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

summary: ARH3/ADPRHL2 and PARG are the major enzymes reversing ADP-ribosylation in vertebrates, yet their functions in vivo remain unclear. ARH3 is the only hydrolase able to removes serine-linked mono(ADP-ribose) (MAR), but is much less efficient than PARG against poly(ADP-ribose) (PAR) chains in vitro. Here, by utilizing ARH3-deficient cells, we demonstrate that endogenous MARylation persists on chromatin throughout the cell cycle including mitosis, and is, surprisingly, well tolerated. Conversely, persistent PARylation is highly toxic and has distinct physiological effects, in particular on active transcription histone marks such as H3K9ac and H3K27ac. Furthermore, we reveal a synthetic lethal interaction between ARH3 and PARG, and identify loss of ARH3 as a mechanism of PARP inhibitor resistance, both of which can be exploited in cancer therapy. Finally, we extend our findings to neurodegeneration, suggesting that patients with inherited ARH3 deficiency suffer from stress-induced pathogenic increase in PARylation that can be mitigated by PARP inhibition.

overall_design: RNA-seq in biological triplicates of U2OS ADPRS KO cells treated with either DMSO or PARGi

first: Evgeniia

last: Prokhorova

first: Thomas

last: Agnew

first: Anne

middle: R

last: Wondisford

first: Nicole

last: Kaminski

first: Danique

last: Beijer

first: James

last: Holder

first: Josephine

last: Groslambert

first: Marcin

last: Suskiewicz

first: Kang

last: Zhu

first: Julia

last: Reber

first: Sarah

middle: C

last: Krassnig

first: Luca

last: Palazzo

first: Shona

last: Murphy

middle: L

last: Nielsen

first: Aswin

last: Mangerich

first: Dragana

last: Ahel

first: Roderick

last: O’Sullivan

first: Jonathan

last: Baets

first: Ivan


title: A spatial vascular transcriptomic, proteomic and phosphoproteomic atlas unveils an angiocrine Tie Wnt signaling axis in the liver

city: Heidelberg

first: Jingjing

last: Shi

state: Baden-Wuerttemberg

address: Im Neuenheimer Feld 280

department: Vascular Oncology and Metastasis

country: Germany

institute: German Cancer Research Center

summary: Single cell transcriptomic analyses (scRNAseq) of hepatocytes and liver endothelial cells (L-EC) have revolutionized the understanding of the spatial architecture of liver structure and function. The spatial alignment of L-EC and hepatocytes is pivotal for liver function in health and disease given that L-EC act as instructive gatekeeper of nearby hepatocytes including the maintenance of liver metabolic zonation in a Wnt-dependent manner. Advancing liver biology beyond the ’transcript-centric’ view of scRNAseq analyses is presently restricted by the limited resolution of proteomics and genome-wide techniques to analyse post-translational modifications. Here, by combining spatial cell sorting methodology with transcriptomic and quantitative proteomic/phospho-proteomic analyses, we established the first functionally and spatially-resolved proteome landscape of the liver endothelium, yielding deep mechanistic insight into zonated vascular signalling mechanisms. Phosphorylation of receptor tyrosine kinases (RTK) was detected preferentially in the central vein area resulting in an atypical enrichment of tyrosine phosphorylation. Prototypic biological validation of the identified strong phosphorylation gradient of the vascular RTK Tie1 by blockade resulted in the rapid peri-central dysregulation of the L-EC transcriptome. Notably, the expression of Wnt9b in L-EC was discovered as Tie receptor controlled with reciprocal regulation by FoxO1 and STAT3 transcription factors. Genetic inactivation of Tie1 in L-EC or antibody blockade resulted in reduced liver regeneration following partial hepatectomy with reduced Wnt ligand and Wnt target gene expression, including Sox9, Tbx3 and Lgr5. Taken together, the study has yielded unparalleled insight into the spatial organization of L EC signalling and discovered a vascular Tie/Wnt signalling axis as regulator of liver function. The employed spatial sorting technique followed by phospho-proteomic analysis may be employed as a universally adaptable strategy for the spatial phosphoproteomic analysis of scRNAseq data-defined relevant cellular (sub)-populations.

overall_design: Liver endothelial cells from C57BL/6 mice spatially sorted into 4 subpopulations (PN, PP, PC, CV), each containing 4 replicates. And Liver endothelial cells from Tie-1 treated mice spatially sorted into 4 subpopulations (PN, PP, PC, CV), each containing 4 replicates.

first: Donato

last: Inverso

first: Hellmut

middle: G

last: Augustin


title: N6-methyladenosine mRNA methylomes in the MTA RNAi strawberry fruits and the controls

city: Beijing

first: Leilei

last: Zhou

state: Beijing

address: No. 20 Nanxincun, Xiangshan, Haidian District

department: Institute of botany

institute: Chinese Academy of Sciences

summary: For exploring the influence of the m6A methyltransferase gene MTA silencing in the global m6A mRNA methylomes of strawberry fruits, we performed m6A-seq in the MTA RNAi strawberry fruits (RNAi-MTA) and the controls with three independently biological replicates. Results showed that MTA silencing induces the m6A hypomethylation of thousands of transcripts, including those of ripening and ABA pathway genes.

overall_design: mRNA m6A methylomes profiled in octoploid cultivated strawberry with the MTA silencing, as well as the controls, were generated by m6A-seq, in triplicate, using Illumina Hiseq X.

first: Guozheng

last: Qin

first: Renkun

last: Tang


title: Global transcriptional analysis of Cr(VI)-adapted cells of Klebsiella sp. AqSCr

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: Hexavalent chromium (Cr(VI)) is a highly toxic contaminant, some bacteria are able to transform it to less toxic and less soluble trivalent chromium (Cr(III)).  Klebsiella sp. strain AqSCr, isolated from Cr(VI)-polluted groundwater, reduces Cr(VI) both aerobically and anaerobically, and resists up 35 mM of Cr(VI);  Subculturing of AqSCr in the presence of Cr(VI) conduces to adaptation. In this study, we performed RNA-Seq of Cr(VI) adapted stage, finding 255 genes upregulated and 240 downregulated with respect to controls without Cr(VI). Genes differentially expressed are mostly associated with oxidative stress response, DNA repair and replication, sulfur starvation response, envelope-osmotic stress response, fatty acid metabolism, ribosomal subunits and energy metabolism. Among them, genes not previously associated with chromium resistance as cybB, encoding a putative superoxide oxidase, gltA2, encoding an alternative citrate synthase, and des, encoding a fatty acid desaturase were upregulated. The alternative sigma factors fecl, rpoE and rpoS were upredgulated in Cr(VI) adapted cells, then they participate in orchestate the Cr(VI)-resistance mechanisms in AqSCr strain

overall_design: mRNA profiles of Klebsiella sp. AqSCr grown in  LB medium pH 8 with and without Cr(VI) 11mM, in triplicate, using Illumina Genome Analyzer Iix

first: Lara

last: Paloma

first: Vega-Alvarado

last: Leticia

first: Morett

last: Enrique

first: Juárez

last: Katy


title: Transcription shapes DNA replication initiation to preserve genome integrity

first: Chen

last: Ai

address: Yiheyuan Road No.5

institute: Peking University

summary: We develop a high-throughput nucleoside analog incorporation sequencing assay and identify thousands of early replication initiation zones (ERIZs) in both mouse and human cells. The identified ERIZs fall in open chromatin compartments while are mutually exclusive with transcription elongation and occupy mainly non-transcribed regions adjacent to transcribed regions. Furthermore, we reveal that RNA polymerase II actively redistributes the chromatin-encircled mini-chromosome maintenance (MCM) complex but not the origin-recognition complex (ORC) to actively restrict early DNA replication initiation outside of transcribed regions. The coupling of RNA polymerase II and MCM is further validated by detected MCM accumulation and DNA replication initiation after RNA polymerase II stalling via anchoring nuclease-dead Cas9 at the transcribed genes. Importantly, we also find that the orchestration of DNA replication initiation by transcription can efficiently prevent gross DNA damage.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We have finished the NAIL-seq with EdU and BrdU dual labeling replicating DNA with K562/GM12878 cell line, NAIL-seq with EdU label only under HU treatment(EdU/HU) of K562/GM12878/mESC/mSB cells. We have finished NAIL-seq EdU/HU in K562 cells under transcription inhibition via a-amanitin/DRB, NAIL-seq EdU/HU in mouse spleenic B cells under a-amanitin, NAIL-seq EdU/HU in mESC RNA Pol2 degron system. We have finished ORC2 ChIP-seq and MCM5 ChIP-seq in both untreated cells and cells under transcription inhibition.

first: Yang

last: Liu

first: Tingting

last: Gan

first: Jiazhi

last: Hu


title: Role of GR in protection of podocyte

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

summary: In order to understand the protection role of GR in hPC, we captured the GR binding sites and H3K27ac profiles with or without DEX treatment. As GR generally bound far away from TSS, we further generated chromatin interaction map with HiChIP to disect the mechanism of GR regulated transcriptome.

overall_design: Cells with or without DEX treatment were subjected to ChIP-seq, RNA-seq and HiChIP

first: Hong

last: Wang

first: Aiping

last: Duan


title: Histone ChIP-seq from HEK293 (ENCSR000FCG)

first: ENCODE

last: DCC

summary:
H3K4me1 HEK293 ChIP-Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: A multi-omics investigation on the composition and physiological function of extracellular vesicles along the temporal trajectory of COVID-19

status: Public on May 19 2021

city: BEIJING

first: Guanghou

last: Shui

address: Bei Chen Road(west)

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: RNA seq analysis

overall_design: mRNA profiles of A549 and HepG2 cell lines incubated with EVs isolated from healthy controls (HC), as well as presymptomatic S1, hyperinflammatory S2, convalescent S3 and resolution S4 phases of COVID-19.

first: Sin

last: Lam

first: Jun

first: Jiabao

last: Cao


title: TF ChIP-seq from neural cell (ENCSR511CUH)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Expression data from IL4 treatment in EML4-ALK-positive lung cancer cells.

first: Yongwen

last: Li

summary:
We demonstrate that STAT3 and STAT6 significantly activated after IL4 treatment in EML4-ALK postive lung cancer cell lines
The aim of this study was to explore whether IL4 could activate the JAK2-STAT pathway in EML4-ALK-positive cells.

overall_design: H2228 cells treated with 100ng/mL IL4 for 30 mins were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Ying

first: Hongyu

last: Chen


title: XCR1+ type 1 conventional dendritic cells drive liver pathology in Non-Alcoholic Steatohepatitis.

first: Ido

last: Amit


title: TRAP-seq of VMH Nr5a1 neurons

city: Ann Arbor

first: Martin

last: Myers Jr

state: MI

address: 1000 Wall St

institute: University of Michigan

summary: To identify transcripts enriched in ventomedial hypothalamus (VMH) neurons, we used translating affinity ribosome purification combined with RNA-seq (TRAP-seq) from Nr5a1-Cre mice.

overall_design: Nr5a1-Cre mice were crossed to a ROSA26 Cre-dependent EGFP-L10a line. The VMH was microdissected and ribosomes were isolated using an anti-GFP-coated beads. RNA was isolated from the beads and the supernatant and converted to cDNA. Illumina libraries were prepared and sequenced on an Illumina HiSeq machine for 52 cycles.

first: Alan

last: Rupp


title: Single nucleus RNA-seq atlas of mouse ventromedial hypothalamus

summary: To uncover the cellular architecture of the mouse ventromedial hypothalamus (VMH), we used single nucleus RNA-seq (snRNA-seq) from wild-type mice.

overall_design: Mice were maintained on ad libitum chow prior to microdissection of the VMH. We then isolated nuclei and subjected these nuclei to snRNA-seq using the 10x Genomics 3’ gene expression platform.


title: Human vascular smooth muscle cells undergoing cell senescence

status: Public on May 18 2021

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Vascular smooth muscle cells (VSMCs) undergo cell senescence in a number of diseases, both due to stress and loss of replication. Here we have cultured human VSMCs to replicative senescence, or induced stress-induced premature senescence (SIPS), and compared their transcriptome with cells treated with doxorubicin for 1d or control cells

overall_design: Bulk RNAseq from primary human VSMCs undergoing (1) doxorubicin-induced SIPs (dox 1d+21d), (2) replicative senescence (RS), (3) Doxorubicin treatment for 1d (dox1d), or control cells (Ctr)

first: Abel

last: Garrido

first: Anuradha

last: Kaistha

first: Mandy

last: Grootaert

first: Anna

last: Uryga

last: Bennett

first: Sebnem

last: Oc


title: TRAP-seq of VMH Lepr neurons

summary: To identify transcripts enriched in ventomedial hypothalamus (VMH) Lepr neurons, we used translating affinity ribosome purification combined with RNA-seq (TRAP-seq) from Lepr-Cre mice.

overall_design: Lepr-Cre mice were crossed to a ROSA26 Cre-dependent EGFP-L10a line and treated with PBS or leptin. The VMH was microdissected and ribosomes were isolated using an anti-GFP-coated beads. RNA was isolated from the beads and the supernatant and converted to cDNA. Illumina libraries were prepared and sequenced on an Illumina HiSeq machine for 52 cycles.


title: RNAseq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16

city: Cologne

first: Ludwig

last: Eichinger

state: NRW

address: Joseph-Stelzmann-Str. 52

department: Biochemistry Medical Faculty

institute: Centre for Biochemistry Medical Faculty University of Cologne

summary: Purpose: Global survey of the transcriptome and comparison to the proteome in autophagy-deficient strains of D. discoideum. Results: Our RNAseq analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells revealed major transcriptional changes in a large number of genes in comparison to AX2. Conclusions: Our study provides the first combined transcriptome and proteome analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells and adds to our knowledge of functions of these proteins in Dictyostelium discoideum.

overall_design: Total RNA from vegetative Dictyostelium discoideum cells (AX2 wild-type and ATG9‾, ATG16‾, ATG9‾/16‾ mutant strains) was isolated; sequencing and analysis was as described in Karow et al. Cells, 9(5), E1179. n=9, Illumina Genome Analyzer IIx

first: Qiuhong

last: Xiong

first: Ning

last: Song

first: Ping

last: LI

first: Sarah

last: Fischer

first: Roman

last: Konertz

first: Prerana

last: Wagle

first: Gernot

last: Glöckner

first: Changxin

last: Wu


title: AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency

first: Helen

last: Blau

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Glenn

last: Markov

first: Thach

last: Mai

first: Surag

last: Nair

last: Shcherbina

first: Yu

last: Wang

first: David

last: Burns

first: Anshul

last: Kundaje


title: Single nucleus RNA-seq atlas of macaque ventromedial and dorsomedial hypothalamus

first: Martin

last: Myers Jr

summary: To uncover the cellular architecture of the macaque ventromedial (VMH) and dorsomedial hypothalamus (DMH), we used single nucleus RNA-seq (snRNA-seq) from a Rhesus macaque

overall_design: A 6.1 year-old Rhesus macaque had been maintained on chow prior to sacrifice and microdissection of the VMH and DMH. The VMH and DMH were then combined prior to nuclei isolation and snRNA-seq using the 10x Genomics 3’ gene expression platform.

first: Alan

last: Rupp

first: Paul

last: Kievit


title: Cross-Species Analysis Defines the Conservation of Anatomically-Segregated VMH Neuron Populations

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus


title: TRAP-seq of VMH Lepr∩Slc17a6 neurons

summary: To identify transcripts enriched in ventomedial hypothalamus (VMH) neurons that contain both Lepr and Slc17a6, we used translating affinity ribosome purification combined with RNA-seq (TRAP-seq) from Lepr-Cre;Slc17a6-Flpo mice.

overall_design: Lepr-Cre;Slc17a6-Flpo mice were crossed to a ROSA26 Cre- and Flp-dependent EGFP-L10a line. The VMH was microdissected and ribosomes were isolated using an anti-GFP-coated beads. RNA was isolated from the beads and the supernatant and converted to cDNA. Illumina libraries were prepared and sequenced on an Illumina HiSeq machine for 52 cycles.


title: AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency (ATAC-Seq)

summary: Somatic cell transcription factors are critical to maintaining cellular identity and constitute a barrier to human somatic cell reprogramming, yet a comprehensive understanding of the mechanism of action is lacking. To gain insight, we examined epigenome remodeling at the onset of human nuclear reprogramming by profiling human fibroblasts after fusion with murine embryonic stem cells. By ATAC-seq and ChIP-seq we identified enrichment for the AP-1 transcription factor c Jun at regions of early transient accessibility at fibroblast-specific enhancers. Expression of a dominant negative AP-1 mutant (dnAP 1) reduced accessibility and expression of fibroblast genes, overcoming the barrier to reprogramming. Remarkably, efficient reprogramming of human fibroblasts to iPSC was achieved by transduction with vectors expressing SOX2, KLF4, and inducible dnAP 1 demonstrating that dnAP-1 can substitute for exogenous human OCT4. Mechanistically, we show that the AP-1 component c-Jun has two unexpected temporally distinct functions in human reprogramming: i) to potentiate fibroblast enhancer accessibility and fibroblast-specific gene expression and ii) to bind to and repress OCT4 as a complex with MBD3. Our findings highlight AP-1 as a previously unrecognized potent dual gatekeeper of the somatic cell state.

overall_design: Human fibroblasts are fused with mouse embryonic stem cells (mESCs) with or without induction of dominant negative AP-1 (dnAP-1) to make heterokaryons. Heterokaryons are sorted at the specified timepoint post-fusion. Fibroblasts alone, fibroblasts co-cultured with mESCs (co-culture), and fibroblasts fused with each other (homokaryon) are used as controls.

first: Anna


title: AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency (RNA-Seq)

overall_design: Human fibroblasts are fused with mouse embryonic stem cells (mESCs) with or without induction of dominant negative AP-1 (dnAP-1) to make heterokaryons. Heterokaryons are sorted at the specified timepoint post-fusion. Fibroblasts alone, fibroblasts co-cultured with mESCs (co-culture), and fibroblasts fused with each other (homokaryon) are used as controls. RNA is extracted for RNA-seq library preparation and sequencing.


title: Mutant SETBP1 enhances NRAS-driven MAPK pathway activation to promote aggressive leukemia

city: Portland

middle: Ann

last: Carratt

state: Oregon

address: 3181 S.W. Sam Jackson Park Road, Mail Code KR-HEM

institute: OHSU

summary: Mutations in SET binding protein 1 (SETBP1) are associated with poor outcomes in myeloid leukemias. In the Ras-driven leukemia, juvenile myelomonocytic leukemia, SETBP1 mutations are enriched in relapsed disease. We demonstrate that SETBP1 enhances the NRAS gene expression signature, driving upregulation of mitogen-activated protein kinase (MAPK) signaling and downregulation of differentiation pathways.

overall_design: Comparison of gene expression in mouse bone marrow cells retrovirally expressing mutant SETBP1 and/or NRAS

first: Julia

middle: E

last: Maxson


title: Effect of methanol fixation on single-cell RNA sequencing data

city: Hong Kong

first: Xinlei

state: Hong Kong

address: Clear Water Bay, Sai Kung,

department: LIFS

institute: HKUST

summary: We report how methanol fixation influences transcriptome profile in single cell RNA-seq. We generatad Smart-seq2 data from two cell lines, and both live  and fixed cells from each cell line were processed and analyzed to illustrate fixaiton effect.

overall_design: We used Smart-seq2 to generate single cell RNA-seq data from two cell lines: HCT-116 and HepG2. Both live and fixed cells were generated from each cell line.


title: Hippocampal gene expression profiling in mice treated with stigmasterol or beta-sitosterol

first: Mike

last: Fainzilber

address: 234 Herzl Street

department: Department of Biomolecular Sciences

institute: Weizmann Institute of Science


title: Hippocampal gene expression profiling in mice treated with beta-sitosterol

summary: Anxiety and stress-related conditions represent a significant health burden in modern society. Unfortunately, most of the drugs currently used in the clinic modulate neurotransmission and are prone to side effects, limiting their long-term use. We used bioinformatics screening to find small molecules mimicking the transcriptional profile  recently reported in hippocampi of importin α5 mutant anxiolytic mice, identifying the plant sterol β-sitosterol as a top candidate. Behavioral analyses confirmed anxiolytic properties of β-sitosterol. The present RNA-seq experiment characterizes the hippocampal transcriptome in mice 1 hr and 6 hrs after intraperitoneal injection of 100 mg/kg β-sitosterol or vehicle.

overall_design: RNA-seq performed on: 2 treatment groups (beta-sitosterol; vehicle), 2 time points per treatment (1hr; 6hrs), 4 animals per each group and replicate

first: Nicolas

last: Panayotis


title: Perinatal exposure to nicotine alters spermatozoal DNA methylation near genes controlling nicotine action

status: Public on May 17 2021

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

type: Methylation profiling by high throughput sequencing

summary: Perinatal smoke/nicotine exposure alters lung development and causes asthma in exposed offspring, transmitted transgenerationally. The mechanism underlying the transgenerational inheritance of perinatal smoke/nicotine-induced asthma remains unknown, but germline epigenetic modulations may play a role. Using a well-established rat model of perinatal nicotine-induced asthma, we determined the DNA methylation pattern of spermatozoa of F1 rats exposed perinatally to nicotine in F0 gestation. To identify differentially methylated regions (DMRs), reduced representation bisulfite sequencing was performed on spermatozoa of F1 litters.  The top regulated gene body and promoter DMRs were tested for lung gene expression levels, and key proteins involved in lung development and repair were determined. The overall CpG methylation in F1 sperms across gene bodies, promoters, 5’UTRs, exons, introns, and 3’UTRs was not affected by nicotine exposure. However, the methylation levels were different between the different genomic regions. 81 CpG sites, 16 gene bodies, and 3 promoter regions were differentially methylated. Gene enrichment analysis of DMRs revealed pathways involved in oxidative stress, nicotine response, alveolar and brain development, and cellular signaling. Among the DMRs, Dio1 and Nmu were the most hypermethylated and hypomethylated genes, respectively. Gene expression analysis showed that the mRNA expression and DNA methylation were incongruous. Key proteins involved in lung development and repair were significantly different (FDR < 0.05) between the nicotine and placebo-treated groups. Our data show that DNA methylation is remodeled in offspring spermatozoa upon perinatal nicotine exposure. These epigenetic alterations may play a role in transgenerational inheritance of perinatal smoke/nicotine induced asthma.

overall_design: Placebo (Ctrl) and nicotine (Nico) treated F0 mothers. Sperm cells are isolated from F1 generation (n = 10 per group).

last: Altıntaş

first: Jie

last: Liu

first: Odile

last: Fabre

first: Tsai-Der

last: Chuang

first: Ying

first: Reiko

last: Sakurai

first: Galal

last: Nazih Chehabi

first: Romain

last: Barrès

first: Virender

last: Rehan


title: RegAB Two-Component System Homolog of Burkholderia pseudomallei is the Master Regulator of Redox Control and involved in Virulence.

city: Greifswald

first: Christian

last: Kohler

address: Ferdinand Sauerbruch Strasse 1

department: Friedrich Loeffler Institue of Medical Microbiology

institute: University Medicine Greifswald

type: Expression profiling by genome tiling array

summary: Burkholderia pseudomallei, the etiological agent of melioidosis in humans and animals, often occupies environmental niches and infection sites characterized by limited concentrations of oxygen. Versatile genomic features enable this pathogen to maintain its physiology and virulence under hypoxia, but the crucial regulatory networks employed to switch from oxygen dependent respiration to alternative terminal electron acceptors (TEA) like nitrate, remains poorly understood. Here, we combined a Tn5 transposon mutagenesis screen and an anaerobic growth screen to identify a two-component signal transduction system with homology to RegAB. We show that RegAB is not only essential for anaerobic growth, but also for full virulence in cell lines and a mouse infection model. Further investigations of the RegAB regulon, using a global transcriptomic approach, identified 20 additional regulators under transcriptional control of RegAB, indicating a superordinate role of RegAB in the B. pseudomallei anaerobiosis regulatory network. Of the 20 identified regulators, NarX/L and a FNR homolog were selected for further analyses and a role in adaptation to anaerobic conditions was demonstrated. Growth experiments identified nitrate and intermediates of the denitrification process as the likely signal activateing RegAB, NarX/L, and probably of the downstream regulators Dnr or NsrR homologs. While deletions of individual genes involved in the denitrification process demonstrated their important role in anaerobic fitness, they showed no effect on virulence. This further highlights the central role of RegAB as the master regulator of anaerobic metabolism in B. pseudomallei and that the complete RegAB-mediated response is required to achieve full virulence. In summary, our analysis of the RegAB-dependent modulon and its interconnected regulons revealed a key role for RegAB of B. pseudomallei in the coordination of the response to hypoxic conditions and virulence, in the environment and the host.

overall_design: The transcriptome profiles of Burkholderia pseudomallei wild type strain E8 and corresponding mutant strains (DregA, DnarL, Dfnr) exposed to several growth conditions (Lysogeny broth (LB) exponential growth, aerobic and anaerobic conditions w/ and /or w/o nitrate) were captured and compared using a custom-designed tiling microarray to elucidate the RegAB, NarXL and FNR dependent regulons. Three biological replicates per strain and condition were used.

last: Phenn


title: N6-methyladenosine RNA methylomes in woodland strawberry fruit at three different development stages.

first: Leilei

last: Zhou

summary: For exploring whether mRNA m6A modification participates in the regulation of strawberry fruit ripening, we performed m6A-seq in woodland strawberry fruit at three different development stages, including the S6 stage (almost 15 days post-anthsis (DPA)), the RS1 stage (21 DPA), and the RS3 stage (27 DPA), with three biological replicates. mRNA methylome analysis reveals that m6A methylation prevalently distributes in the strawberry transcriptome and highly enrichs in the coding sequence, stop codon and 3’ untranslated region.

overall_design: mRNA m6A methylomes profiled in woodland strawberry fruit at S6, RS1, and RS3 stages were generated by m6A-seq, in triplicate, using Illumina Hiseq X.

first: Guozheng

last: Qin

first: Renkun

last: Tang


title: RNA-seq strategy to study Mycobacterium ulcerans adaptation within our original mouse model of spontaneous healing.

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Mycobacterium ulcerans is the causal agent of Buruli ulcer, a chronic infectious disease and the third most common mycobacterial disease worldwide. Without early treatment, M. ulcerans provokes massive skin ulcers, caused by the mycolactone toxin, its main virulence factor. However, spontaneous healing may occur in Buruli ulcer patients several months or years after the disease onset. We have shown, in an original mouse model, that bacterial load remains high and viable in spontaneously healed tissues, suggesting that M. ulcerans switches to low levels of mycolactone production, adapting its strategy to survive in such a hostile environment. We investigated the regulation of mycolactone production, by using an RNA-seq strategy to study bacterial adaptation within our original mouse model of spontaneous healing. Pathway analysis and characterization of the tissue environment showed that the bacillus adapted to its new environment by modifying its metabolic activity and switching nutrient sources. Thus, M. ulcerans ensures its survival in healing tissues by reducing its secondary metabolism, leading to an inhibition of mycolactone synthesis and changes in cell wall composition. These findings shed new light on mycolactone regulation and pave the way for new therapeutic strategies.

sample_organism:
Mycobacterium ulcerans
Mus musculus

platform_organism:
Mycobacterium ulcerans
Mus musculus

overall_design: We used an optimized method, based on differential lysis, for the analysis of the whole transcriptome of Mycobacterium ulcerans. RNA was extracted from infected tail skin at the edema stage (30 days post-infection) and at the healing stage (60-75 days post-infection). We performed a comparative transcriptomic analysis of M. ulcerans using RNA-sequencing method.

first: Marie

last: Robbe-Saule

last: Sismeiro

first: Hugo

last: Varet

first: Estelle

last: Marion

first: Laurent

last: Marsollier


title: Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transition

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology


title: Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transition [ChIP-seq]

summary: We performed ChIP-seq ananlysis on HDAC1 in MiaPaCa2 using two different antibodies (Santa Cruz Biotechnologies sc-81598 HDAC1(10E2) and Invitrogen HDAC1 Polyclonal Antibody PA1-860), two non-targeting scrableled sgRNA controls and two replicates for each.

overall_design: ChIP-seq data in both control and HDAC1 over expressed MiaPaCa2 cell lines were produced using standard ENCODE protocols ( https://www.encodeproject.org/documents/73c95206-fc02-41ea-93e0-a929a6939aaf/ )

first: Richard

last: Myers


title: Hippocampal gene expression profiling in mice treated with stigmasterol

city: Rehovot

first: Mike

last: Fainzilber

summary: Anxiety and stress-related conditions represent a significant health burden in modern society. Unfortunately, most of the drugs currently used in the clinic modulate neurotransmission and are prone to side effects, limiting their long-term use. We used bioinformatics screening to find small molecules mimicking the transcriptional profile recently reported in hippocampi of importin α5 mutant anxiolytic mice, identifying the plant sterol β-sitosterol as a top candidate. Behavioral analyses confirmed anxiolytic properties of β-sitosterol, but did not show anxiolytic activity for stigmasterol, a related plant sterol. The present RNA-seq experiment characterizes the hippocampal transcriptome in mice 1 hr and 6 hrs after after intraperitoneal injection of 100 mg/kg stigmasterol or vehicle.

overall_design: RNA-seq performed on: 2 treatment groups (stigmasterol; vehicle), 2 time points per treatment (1hr; 6hrs), 3 animals per each group and replicate

first: Nicolas

last: Panayotis


title: Cadherin-13 is a critical regulator of GABAergic modulation in human stem-cell-derived neuronal networks

city: Nijmegen

first: Nael

last: Nadif Kasri

address: Geert Grooteplein Zuid 10

department: Department of Human Genetics

country: Netherlands

institute: Radboudumc

summary: Activity in the healthy brain relies on a concerted interplay of excitation (E) and inhibition (I) via balanced synaptic communication between glutamatergic and GABAergic neurons. A growing number of studies imply that disruption of this E/I balance is a commonality in many brain disorders; however, obtaining mechanistic insight into these disruptions, with translational value for the patient, has typically been hampered by methodological limitations. Cadherin-13 (CDH13) has been associated with autism and attention-deficit/hyperactivity disorder. CDH13 localizes at inhibitory presynapses, specifically of parvalbumin (PV) and somatostatin (SST) expressing GABAergic neurons. However, the mechanism by which CDH13 regulates the function of inhibitory synapses in human neurons remains unknown. Starting from humaninduced pluripotent stem cells, we established a robust method to generate a homogenous population of SST and MEF2C (PV-precursor marker protein) expressing GABAergic neurons (iGABA) in vitro, and co-cultured these with glutamatergic neurons at defined E/I ratios on micro-electrode arrays. We identified functional network parameters that are most reliably affected by GABAergic modulation as such, and through alterations of E/I balance by reduced expression of CDH13 in iGABAs. We found that CDH13 deficiency in iGABAs decreased E/I balance by means of increased inhibition. Moreover, CDH13 interacts with Integrin-β1 and Integrin-β3, which play opposite roles in the regulation of inhibitory synaptic strength via this interaction. Taken together, this model allows for standardized investigation of the E/I balance in a human neuronal background and can be deployed to dissect the cell-type-specific contribution of disease genes to the E/I balance.

overall_design: RNA-seq performed on 3 replicates of excitatory/inhibitory co-culture samples of iPSC-derived neurons (DIV49) from a healthy control

first: Britt

last: Mossink

first: Anouk

middle: H

last: Verboven

first: Hans

last: van Bokhoven

first: Dirk

last: Schubert


title: Expanding highly homogenous population of human primordial germ cell like cells in long-term and feeder-free culture condition

status: Public on May 15 2021

city: Charlestown

first: Mutsumi

last: Kobayashi

state: Massachusetts

address: Building 147, 13th street, Rm# 7103

institute: MGH, center for cancer reserch


title: Single-cell RNA sequencing of SH-SY5Y untreated cells

status: Public on May 14 2021

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

summary: Single-cell transcriptome phenotyping of untreated SH-SY5Y neuroblastoma cells

overall_design: Untreated SH-SY5Y cells at about 70% confluence from two flasks are harvested and scRNA-seq performed

first: Nicola

last: Balboni

first: Francesca

last: De Giorgio

first: Emanuela

last: Aleo

first: Caterina

last: Garone

first: Federico

last: Giorgi


title: Pulsed cisplatin treatment of A549 lung adenocarcinoma cells

city: Concord, NSW

first: Kaitao

last: Lai

state: New South Wales

address: ANZAC Research Institute, Hospital Rd, Concord

department: Faculty of Medicine and Health

country: Australia

institute: Anzac Research Institute, The University Of Sydney

summary: A549 lung adenocarcinoma cells were pulsed for 2h with cisplatin and allowed to recover for 3 days. Cells were then FACS sorted based on size and enriched populations analysed for RNAseq.

overall_design: Next-generation RNAseq analysis of cisplatin pulsed A549 lung adenocarcinoma cells pre and post FACS sorting for cell size, in biological triplicate.

first: Andrew

last: Burgess

first: Alvaro

last: Gonzalez-Rajal


title: Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transition [RNA-Seq]

first: Sara

last: Cooper

summary: Over expression of co-repressor complexes implicated as a cause of multiple drug resistance in pancreatic cancer.

overall_design: Genome-wide CRISPR activation and knockout screen in pancreatic cancer cell lines

first: Richard

last: Myers


title: Transcriptome Analysis of Gene Expression involving C/EBPβ and Olaparib Resistance

city: WuHan

first: Zheng

last: Xu

address: 13 HangKong road, HanKou, WuHan city, HuBei province, China

institute: Hua Zhong University of Science and Technology

summary: Poly(ADP-ribose) polymerase inhibitors (PARPi) are now widely used in treating ovarian cancer. However, PARPi resistance emerges gradually. To investigate the change of gene expression during the transition, we have induced a stable resistant cell strain by culturing A2780 in the continued presence of olaparib.  We then performed RNA-seq of the resistant strain and its parent line A2780. We found that C/EBPβ was strongly correlated with PARPi resistance. RNA-seq of C13* after C/EBPβ knockdown was also performed.

overall_design: Examination of differentially expressed genes in A2780 Olaparib-resistant cell line and its parent line A2780 and in C13* cells after C/EBPβ knockdown

first: Jiahong

last: Tan

first: Xu

last: Zheng

first: Mengchen

last: Li

first: Qinglei

last: Gao


title: Repression of endogenous retroviruses is required for mammary gland development and homeostasis

city: Barcelona

first: Laudanna

last: Carmelo

state: Barcelona

address: Baldiri i Reixac, 10

department: Aging and Metabolism

country: Spain

institute: Institute for Research in Biomedicine (IRB-Barcelona)

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Stable epigenetic programming of effector and central memory CD4 T cells occurs within 7 days of antigen exposure in vivo (ATAC-seq)

city: Birmingham

first: Csilla

last: Varnai

address: Haworth Building

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

summary: T cell immunological memory is established within days of an infection but little is known about the in vivo changes in gene regulatory networks which account for the ability of memory T cells to respond more efficiently to secondary infections. To decipher the timing and nature of immunological memory we performed genome-wide analyses of epigenetic and transcriptional changes in a mouse model generating antigen-specific T cells.

overall_design: ATAC-seq of naïve CD4 T cells, in vivo generated antigen specific Th1 cells 7, 28 and 56 dpi and and antigen specific Tcm and Tem cells 7 dpi

first: Sarah

last: Bevington

first: Remi

last: Fiancette

first: Dominika

middle: W

last: Gajdasik

first: Jake

last: Soley

first: Peter

last: Keane

first: Daniel

last: Coleman

first: David

last: Withers

last: Cockerill


title: Stable epigenetic programming of effector and central memory CD4 T cells occurs within 7 days of antigen exposure in vivo


title: The effect of STAG2 loss in Ewing sarcoma [RNA-Seq]

city: Cambridge

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

summary: Ewing sarcoma is an aggressive malignancy characterized by oncogenic rearrangements of the EWS gene with an ETS-family transcription factor, most commonly FLI. Recent comprehensive next-generation sequencing efforts have revealed few other highly recurrent mutations in this disease apart from loss-of-function mutations in STAG2 which occur in 15-20% of tumors. STAG2 is a member of the cohesin complex, which regulates sister chromatid alignment during mitosis and epigenetic regulation of gene expression. While some studies suggest that loss of STAG2 is associated with the development of aneuploidy, this is not the case in Ewing sarcoma. To investigate whether STAG2 loss effects epigenetic regulation of gene expression in Ewing sarcoma, we developed isogenic Ewing sarcoma cell lines with STAG2 knockout. We found that Ewing sarcoma cells engineered for loss of STAG2 maintain an intact cohesion complex that alternately incorporates STAG1.

overall_design: RNA-seq transcriptome profiling of A673 cells with and without STAG2 loss as well as isogenic clonally-selected TC71 Ewing sarcoma cell lines treated with STAG2 targeting CRISPR Cas9. STAG2 knockout clones were labeled "STAG2 KO", STAG2 wild-type clones were labeled as "STAG2 WT".

first: Kimberly

last: Stegmaier


title: Psuedouridine sequencing rRNA in Rnmt cKO CD4 T cells

status: Public on May 13 2021

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

institute: Beatson CRUK

type: Non-coding RNA profiling by high throughput sequencing

summary: We investigated the role of RNMT in T cells using an Rnmt conditional knockout mouse model. We report that the mRNA cap methyltransferase, RNMT, supports naïve T cell survival and activation-induced proliferation. We demonstrate that RNMT has gene-specific impacts in T cells, selectively regulating expression of terminal polypyrimidine tract (TOP) mRNAs and small RNAs including snoRNAs. To deterine if had any effect on ribosomal RNA modification we carried out pseudoridine sequencing.

overall_design: Sequencing of total RNA either CMC treated (to form aducts on pseudouridine) or mock treated from 20 hour activated CD4 T cells from Rnmt fl/fl CD4cre (Rnmt cKO) and Rnmt fl/fl (control) mice.

first: Victoria

last: Cowling


title: RNMT regulates the CD4 T cell transcriptome and translatome


title: RNMT regulates the activated CD4 T cell transcriptome and translatome [Ribo-Seq]

summary: We investigated the role of RNMT in T cells using an Rnmt conditional knockout mouse model. We report that the mRNA cap methyltransferase, RNMT, supports naïve T cell survival and activation-induced proliferation. We demonstrate that RNMT has gene-specific impacts in T cells, selectively regulating expression of terminal polypyrimidine tract (TOP) mRNAs which are targets of the m7G-cap binding protein LARP1. These ribosome footprinting experiments investigate the effect of Rnmt cKO on the activated CD4 T cell transcriptome and translatome.

overall_design: Sequencing of rRNA-depleted RNA and ribosome protected fragments from 20 hour activated CD4 T cells from Rnmt fl/fl CD4cre (Rnmt cKO) and Rnmt fl/fl (control) mice.


title: Global Chromatin Changes resulting from Single Gene Inactivation – the Role of SMARCB1 in Malignant Rhabdoid Tumor

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Human cancer typically results from the stochastic accumulation of multiple oncogene-activating and tumors suppressor gene inactivating mutations, however this process takes time and especially in the context of certain pediatric cancer, fewer but more ‘impactful’ mutations may in short order produce the full-blown cancer phenotype. This is well-exemplified by the highly aggressive malignant rhabdoid tumor (MRT), where the only gene classically showing recurrent inactivation is SMARCB1, a subunit member of the BAF chromatin remodeling complex. This is true of all three presentations of MRT including MRT of kidney (MRTK), MRT of the central nervous system (Atypical Teratoid Rhabdoid Tumor – ATRT) and Extracranial, Extrarenal Rhabdoid Tumor (EERT). Our reverse modeling of rhabdoid tumors with isogenic cell lines, either induced or not induced, to express SMARCB1 showed widespread differential chromatin remodeling indicative of altered BAF complex activity with ensuant histone modifications when tested by chromatin immunoprecipitation followed by sequencing (ChIP-seq). The changes due to reintroduction of SMARCB1 were preponderantly at typical enhancers with tandem BAF complex occupancy at these sites and related gene activation, as substantiated also by transcriptomic data. Indeed, for both MRTK and ATRT cells, there is evidence of an overlap between SMARCB1-dependent enhancer activation and tissue-specific lineage determining genes. These genes are inactive in the tumor state, conceivably arresting the cells in a primitive/undifferentiated state. This epigenetic dysregulation from inactivation of a chromatin remodeling complex subunit contributes to an improved understanding of the complex pathophysiological basis of MRT, one of the most lethal and aggressive human cancers.

overall_design: Examination of various histone modifications and subunits of chromatin remodelling complexes in MRTK and ATRT cells (G401 and BT16).

first: Colin

last: Kenny

first: Maureen

last: O'Sullivan


title: Low miR-214-5p expression correlates with aggressive subtypes of pediatric ALCL with non-common histology

status: Public on May 12 2021

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

summary: The small RNA landscape of pediatric ALK-positive ALCL was defined by RNA sequencing. Overall, 121 miRNAs were significantly dysregulated in ALCL compared to non-neoplastic lymph nodes. The most up-regulated miRNA was miR-21-5p, while miR-19a-3p and miR-214-5p were reduced in ALCL. Characterization of miRNA expression in cases that relapsed after first line therapy disclosed a significant association between miR-214-5p down-regulation and aggressive non-common histology.

overall_design: Tumor biopsies from ALCL pediatric patients; reactive lymph nodes from healthy donors.

first: Piero

last: Di Battista

first: Federica

last: Lovisa

first: Enrico

last: Gaffo

first: Ilaria

last: Gallingani

first: Carlotta

last: Damanti

first: Anna

last: Garbin

first: Elisa

last: Carraro

first: Marta

last: Pillon

first: Luca

last: Lo Nigro

first: Rossella

last: Mura

first: Marco

last: Pizzi

first: Vincenza

last: Guzzardo

first: Angelo

middle: P

last: Dei Tos

first: Alessandra

last: Biffi

first: Lara

last: Mussolin


title: RNA-sequencing analysis of the effect of progesterone on T cell activation

city: Linköping

first: Sandra

last: Hellberg

address: Universitetssjukhuset

country: Sweden

institute: Linköping University

summary: The changes in progesterone (P4) levels during and after pregnancy coincide with the temporary improvement and worsening of several autoimmune diseases like multiple sclerosis (MS) and rheumatoid arthritis (RA). Most likely immune-endocrine interactions play a major role in these pregnancy-induced effects. In this study, we used next generation sequencing to investigate the direct effects of P4 on CD4+ T cell activation, of central importance in pregnancy and disease. We found that P4 had a profound dampening effect on T cell activation, altering the gene and protein expression profile and reversing many of the changes induced during the activation. The transcriptomic changes induced by P4 were significantly enriched for genes associated with diseases known to be modulated during pregnancy such as MS, RA and psoriasis. The TH1-and TH17-associated transcription factors STAT1 and STAT3 were significantly downregulated by P4 and their downstream targets were significantly enriched among the diseases-associated genes. Several of these genes included well-known and disease-relevant cytokines, such as IL-12β, CXCL10 and OSM, that were further validated also at the protein level using proximity extension assay. Our results extend the previous knowledge of P4 as an immune regulatory hormone and support its importance during pregnancy for regulating potentially detrimental immune responses towards the semi-allogenic fetus. Further, our results also point toward a potential role for P4 in the pregnancy-induced disease immunomodulation, suggestively through dampening of TH1 and TH17-associated immune responses and highlight the need for further studies evaluating P4 as a future treatment option.

overall_design: Blood was collected in sodium-heparin tubes from healthy female controls (n=8). CD4+ T cells were isolated using positive immunomagnetic sorting and pre-incubated for 20 hrs with or without 50 uM of progesterone. Following pre-incubation, the cells were cultured unactivated or activated by plate-bound anti-CD3 and anti-CD28 antibodies in the presence or absence of 50 uM progesterone for 6 and 24 hrs.

first: Johanna

last: Raffetseder

first: Olof

last: Rundquist

first: Rasmus

last: Magnusson

first: Georgia

last: Papapavlou

first: Maria

last: Jenmalm

first: Jan

last: Ernerudh

first: Mika

last: Gustafsson


title: Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing

city: Bethesda

first: Daniel

last: Larson

address: 41 Medlar Dr.

institute: NIH

summary: The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. We find that all observed genes show transcriptional bursting. We also observe large kinetic variation in intron removal for single introns in single cells which is inconsistent with deterministic splice site selection. Transcriptome-wide footprinting of the U2AF complex further reveals widespread splice site selection within introns. We propose and validate a unified theoretical model for transcription and splicing based on pervasive stochastic recursive splicing.

first: Yihan

last: Wan

first: Dimitrios

last: Anastasakis

first: Markus

last: Hafner


title: IL-4 signals interfere with regulatory T cell polarization in vitro by controlling their genome-wide chromatin accessibility

city: Wuhan

first: Jie

last: Wu

state: Hubei

address: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1277

department: Department of Cardiovascular Surgery

overall_design: ATAC-sequencing of regulatory T cell in vitro polarization with or without mouse IL-4 for 48 h

first: Jikai

last: Cui

first: Heng

last: Xu


title: smORFer: a modular algorithm to detect small ORFs in prokaryotes

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

summary: We developed a novel algorithm, smORFer, detecting smORFs (e.g. <50 codons) which performs with higher accuracy in prokaryotic organisms. smORFer considers structural features of genetic sequence along with in-register translation and using Fourier transform converts them into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way and dependent on the data available different modules can be tested.

overall_design: Ribosome profiling of Staphylococcus aureus cultured in complex TBS medium

first: Alexander

last: Bartholomäus

first: Baban

last: Kolte

first: Ayten

last: Mustafayeva

first: Ingrid

last: Goebel

first: Susanne

last: Engelmann


title: The effect of STAG2 loss in Ewing sarcoma [ChIP-seq]

first: Gabriela

last: Alexe

overall_design:
ChIP-Seq profiling was performed as follows:
(i) EWS/FLI1, SMC1A, STAG1, STAG2, H3K27me3, H3K27ac and Input on isogenic clonally-selected A673 cells treated with STAG2 targeting CRISPR Cas9, and on A673 cells with STAG2 wild-type.
(ii) EWS/FLI1 and Input on A673 untreated clones.
(iii) H3K4me3 on A673 clones with STAG2 wild-type.
For each mark, the reads mapped on the STAG2 wild-type clones A673.sgNT-1c4 and A673.sgNT-2c3 were merged and labeled as "STAG2 WT". Similarly, for each mark, the reads mapped on the STAG2 knockout clones A673.sgSTAG2-1c6, A673.sgSTAG2-4c5 were merged and labeled as "STAG2 KO" with the exception of H3K27me3 for which only the A673.sgSTAG2-1c6 clone was available and labeled as "STAG2 sg1KO".
Drosophila melanogaster (Active Motif) was used as a spike-in control for all non-input samples profiled on both the  STAG2 knockout and STAG2 wild-type clones, with the exception of H3K27ac. The Active Motif Spike-in Normalization protocol was applied to each sample by multiplying the human tag counts with the normalization factors derived from the uniquely mapped Drosophila reads vs. the dm6 counts for that sample. The dm6 normalization factors for individual clones and for the merged clones were very close to 1.

first: Kimberly

last: Stegmaier


title: A transcriptomic analysis of SH-SY5Y cells with Varicella-Zoster Virus-Infected

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

summary: In this study, we screened the differentially expressed genes (DEGs) in SH-SY5Y cells  with Varicella-Zoster Virus-Infected using RNAseq technique to explore the molecular mechanisms of Herpes zoster pain

first: Shaomin

last: Yang


title: Stable epigenetic programming of effector and central memory CD4 T cells occurs within 7 days of antigen exposure in vivo (RNA-seq)

first: Csilla

last: Varnai

overall_design: RNA-seq of naïve CD4 T cells, in vivo generated antigen specific Th1 cells 28 and 56 dpi and and antigen specific Tcm and Tem cells 7 dpi

first: Sarah

last: Bevington

first: Remi

last: Fiancette

first: Dominika

last: Gajdasik

first: Jake

middle: K

last: Soley

first: Peter

last: Keane

first: Daniel

last: Coleman

first: David

last: Withers

last: Cockerill


title: The effect of STAG2 loss in Ewing sarcoma [ATAC-Seq]

overall_design: ATAC-seq  on isogenic clonally-selected   A673 cells treated with STAG2 targeting CRISPR Cas9,  and on  A673 cells with STAG2 wild-type. Reads mapped on the STAG2 wild-type clones (A673.sgNT-1c4 and  A673.sgNT-2c3) were merged  and labeled  “STAG2 WT”. Reads mapped on the STAG2 knockout clones (A673.sgSTAG2-1c6, A673.sgSTAG2-4c5) were merged and labeled  “STAG2 null”.