title: TF ChIP-seq from whole organism (ENCSR633IKC)

summary:
ChIP-seq on transgenic flies expressing Ssrp-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR629OQQ)

status: Public on Feb 27 2024

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
ChIP-seq against ama-1 in L3 larva worms.

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: Control ChIP-seq from whole organism (ENCSR622TPD)

summary:
Input ChIP-seq in L1 larva worms.

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: Control ChIP-seq from whole organism (ENCSR616DAV)

summary:
This is the ChIP-seq control of transgenic worms expressing SPR-1-eGFP fusion proteins.

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 whole organism (ENCSR620IUW)

summary:
ChIP-seq on transgenic worms expressing zfp-3-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR626WON)

summary:
Input ChIP-seq in L4 larva worms.

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 whole organism (ENCSR932STL)

summary:
ChIP-seq on transgenic flies expressing Elba2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR739RAY)

summary:
This is the ChIP-seq control of transgenic worms expressing WAGO-9-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR729ROL)

summary:
Input ChIP-seq in worms.

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 whole organism (ENCSR726OQC)

summary:
ChIP-seq of transgenic worms expressing T02C12.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR417YYF)

summary:
ChIP-seq on transgenic worms expressing flt-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR733FVS)

summary:
ChIP-seq against AMA-1 in YA worms.

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 whole organism (ENCSR611XWP)

summary:
ChIP-seq on transgenic flies expressing chm-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR721CXH)

summary:
This is the ChIP-seq control of transgenic worms expressing ccch-3-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR608DYO)

summary:
Input ChIP-seq in L3 larva worms.

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: Control ChIP-seq from whole organism (ENCSR602WXH)

summary:
This is the ChIP-seq control of transgenic worms expressing B0019.2-eGFP fusion proteins.

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 whole organism (ENCSR607BSL)

summary:
ChIP-seq of transgenic worms expressing HIM-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR602FMN)

summary:
Input control for ChIP-seq on transgenic flies expressing esn-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR625AVD)

summary:
Input control for ChIP-seq on transgenic flies expressing Pif1A-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR917EGR)

summary:
Input ChIP-seq in late embryonic worms.

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 whole organism (ENCSR909HKS)

summary:
ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR411ODP)

summary:
This is the ChIP-seq control of transgenic worms expressing Y116A8C.19-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR404KWM)

summary:
Input control for ChIP-seq on transgenic flies expressing mam-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR903ZHS)

summary:
Input ChIP-seq in L1 larva worms.

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: Control ChIP-seq from whole organism (ENCSR892ECY)

summary:
This is the ChIP-seq control of transgenic worms expressing F49E8.2-eGFP fusion proteins.

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 whole organism (ENCSR412LYV)

summary:
ChIP-seq against ALY-2 in L4 larva worms.

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 whole organism (ENCSR907HKG)

summary:
ChIP-seq on transgenic flies expressing CG7839-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR896OQW)

summary:
ChIP-seq on transgenic flies expressing CG8632-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR904QAP)

summary:
Input control for ChIP-seq on transgenic flies expressing h-eGFP fusion proteins.

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 whole organism (ENCSR396ONU)

summary:
ChIP-seq on transgenic worms expressing C17E4.6-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR890EWP)

summary:
Input control for ChIP-seq on transgenic flies expressing Pif1B-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR583RLO)

summary:
Input control for ChIP-seq on transgenic flies expressing Bgb-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR877IXV)

summary:
Input control for ChIP-seq on transgenic flies expressing Nf-Yc-eGFP fusion proteins.

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 whole organism (ENCSR396LMJ)

summary:
ChIP-seq on transgenic flies expressing YL-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR592DAH)

summary:
ChIP-seq against eGFP-F16B12.6 in L1 larva worms.

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 whole organism (ENCSR876FER)

summary:
ChIP-seq on transgenic flies expressing Taf1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR875UKH)

summary:
Input control for ChIP-seq on transgenic flies expressing CG9705-eGFP fusion proteins.

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 whole organism (ENCSR589XWJ)

summary:
ChIP-seq on transgenic flies expressing Su(var)3-7-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR881KXY)

summary:
ChIP-seq against ama-1 in L1 larva worms.

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: Control ChIP-seq from whole organism (ENCSR589NOT)

summary:
Input ChIP-seq in L4 larva worms.

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 whole organism (ENCSR576YEP)

summary:
ChIP-seq on transgenic worms expressing C06A6.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR868TYN)

summary:
This is the ChIP-seq control of transgenic worms expressing pbrm-1-eGFP fusion proteins.

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 whole organism (ENCSR698RXJ)

summary:
ChIP-seq of transgenic worms expressing F55B11.4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR388YUZ)

summary:
ChIP-seq on transgenic flies expressing Jarid2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR387HSD)

summary:
ChIP-seq of transgenic worms expressing F13C5.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR867RUX)

summary:
ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR965GGK)

summary:
ChIP-seq on transgenic flies expressing CG32264-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR867JOP)

summary:
ChIP-seq on transgenic flies expressing Bgb-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR561RIA)

summary:
This is the ChIP-seq control of transgenic worms expressing RPC-1-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR568HWW)

summary:
This is the ChIP-seq control of transgenic worms expressing RBR-2-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR561OFJ)

summary:
Input control for ChIP-seq on transgenic flies expressing CG7556-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR581NPL)

summary:
This is the ChIP-seq control of transgenic worms expressing flt-1-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR385LHQ)

summary:
This is the ChIP-seq control of transgenic worms expressing REC-8-eGFP fusion proteins.

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 whole organism (ENCSR555GAJ)

summary:
ChIP-seq against ama-1 in L2 larva worms.

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 whole organism (ENCSR861XSB)

summary:
ChIP-seq on transgenic flies expressing mod(mdg4)-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR689UBU)

summary:
ChIP-seq of transgenic worms expressing REC-8-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR858MGR)

summary:
This is the ChIP-seq control of transgenic worms expressing Y53F4B.3-eGFP fusion proteins.

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 whole organism (ENCSR857HWD)

summary:
ChIP-seq on transgenic worms expressing F57A8.1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR380CVK)

summary:
ChIP-seq on transgenic flies expressing CG9705-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR851OBZ)

summary:
Input ChIP-seq in L3 larva worms.

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 whole organism (ENCSR856SZD)

summary:
Input control for ChIP-seq on transgenic flies expressing CG8290-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR851JOQ)

summary:
Input control for ChIP-seq on transgenic flies expressing corto-eGFP fusion proteins.

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 whole organism (ENCSR547IVT)

summary:
ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR684BMF)

summary:
Input control for ChIP-seq on transgenic flies expressing CG6175-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR280USI)

summary:
This is the ChIP-seq control of transgenic worms expressing T02C12.2-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR679UNL)

summary:
Input control for ChIP-seq on transgenic flies expressing Ravus-eGFP fusion proteins.

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 whole organism (ENCSR548OPZ)

summary:
ChIP-seq of transgenic worms expressing WAGO-9-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR378TOV)

summary:
ChIP-seq against eGFP-C34F6.9 in L2 larva worms.

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: Control ChIP-seq from whole organism (ENCSR276KDH)

summary:
This is the ChIP-seq control of transgenic worms expressing F55B11.4-eGFP fusion proteins.

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 whole organism (ENCSR845XRR)

summary:
ChIP-seq against LIN-35 in YA worms.

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: Control ChIP-seq from whole organism (ENCSR280QNW)

summary:
This is the ChIP-seq control of transgenic worms expressing T26A8.4-eGFP fusion proteins.

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 whole organism (ENCSR537QPX)

summary:
ChIP-seq of transgenic worms expressing T26A5.8-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR269LRI)

summary:
Input ChIP-seq in L1 larva worms.

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: Control ChIP-seq from whole organism (ENCSR368HRR)

summary:
Input ChIP-seq in YA worms.

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: Control ChIP-seq from whole organism (ENCSR268WXK)

summary:
This is the ChIP-seq control of transgenic worms expressing C17E4.6-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR264BNK)

summary:
Input control for ChIP-seq on transgenic flies expressing CG9139-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR371KOI)

summary:
Input control for ChIP-seq on transgenic flies expressing gro-eGFP fusion proteins.

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 whole organism (ENCSR272DEA)

summary:
ChIP-seq on transgenic flies expressing Lhr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR860DSL)

summary:
Input control for ChIP-seq on transgenic flies expressing Ada2b-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR260YDC)

summary:
Input control for ChIP-seq on transgenic flies expressing Su(var)3-7-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR366FCQ)

summary:
Input control for ChIP-seq on transgenic flies expressing ADD1-eGFP fusion proteins.

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 whole organism (ENCSR274WQG)

summary:
ChIP-seq of transgenic worms expressing RBR-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR260AKX)

summary:
ChIP-seq on transgenic worms expressing tbp1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR364IJK)

summary:
ChIP-seq against ama-1 in L4 larva worms.

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 whole organism (ENCSR356MVJ)

summary:
ChIP-seq on transgenic worms expressing mdt-29-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR098GAV)

summary:
ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR346UOK)


title: Control ChIP-seq from whole organism (ENCSR349TJN)

summary:
Input control for ChIP-seq on transgenic flies expressing Hmr-eGFP fusion proteins.

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 whole organism (ENCSR097DMR)

summary:
ChIP-seq on transgenic flies expressing Chrac-16-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR338IOQ)


title: Control ChIP-seq from whole organism (ENCSR089YGV)

summary:
Input control for ChIP-seq on transgenic flies expressing Jarid2-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR072UGA)

summary:
Input control for ChIP-seq on transgenic flies expressing nmo-eGFP fusion proteins.

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 whole organism (ENCSR252BZF)

summary:
ChIP-seq against rpc-1 in young adult worms.

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 whole organism (ENCSR342YUI)

summary:
Input control for ChIP-seq on transgenic flies expressing ash1-eGFP fusion proteins.

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 whole organism (ENCSR069JDM)

summary:
ChIP-seq on transgenic flies expressing CG34422-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR082FZF)

summary:
ChIP-seq on transgenic flies expressing CG2875-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR182GCE)

summary:
This is the ChIP-seq control of transgenic worms expressing C06A6.2-eGFP fusion proteins.

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 whole organism (ENCSR245QIG)


title: TF ChIP-seq from whole organism (ENCSR181RJW)

summary:
ChIP-seq on transgenic worms expressing isw-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR334YYP)

summary:
ChIP-seq of transgenic worms expressing Y116A8C.19-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR336MGM)

summary:
Input control for ChIP-seq on transgenic flies expressing BEAF-32-eGFP fusion proteins.

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 whole organism (ENCSR256CRR)

summary:
ChIP-seq of transgenic worms expressing SPR-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR327NRA)

summary:
ChIP-seq of transgenic worms expressing XND-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR254SSJ)

summary:
ChIP-seq against eGFP-aly-2 in L2 larva worms.

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 whole organism (ENCSR162EDN)

summary:
ChIP-seq on transgenic worms expressing B0019.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR345LWU)

summary:
Input control for ChIP-seq on transgenic flies expressing Dad-eGFP fusion proteins.

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 whole organism (ENCSR166XCH)

summary:
ChIP-seq on transgenic flies expressing corto-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR049FHU)

summary:
ChIP-seq on transgenic worms expressing tlf-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR157EWZ)

summary:
Input control for ChIP-seq on transgenic flies expressing chif-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR231NHQ)

summary:
Input control for ChIP-seq on transgenic flies expressing chm-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR183OHH)

summary:
This is the ChIP-seq control of transgenic worms expressing mdt-29-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR066HHD)


title: Control ChIP-seq from whole organism (ENCSR041LTG)

summary:
This is the ChIP-seq control of transgenic worms expressing C06A8.2-eGFP fusion proteins.

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 whole organism (ENCSR324QVN)

summary:
ChIP-seq on transgenic flies expressing Hmr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR040FYF)

summary:
This is the ChIP-seq control of transgenic worms expressing XND-1-eGFP fusion proteins.

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 whole organism (ENCSR042FCJ)

summary:
ChIP-seq on transgenic flies expressing CG7556-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR225ALY)

summary:
This is the ChIP-seq control of transgenic worms expressing DAO-5-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR224PPR)

summary:
Input control for ChIP-seq on transgenic flies expressing Elba2-eGFP fusion proteins.

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 whole organism (ENCSR154LSU)

summary:
ChIP-seq on transgenic worms expressing akir-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR147WAA)

summary:
ChIP-seq on transgenic worms expressing snpc-1.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR226MOG)

summary:
ChIP-seq on transgenic flies expressing CG10565-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR145MWJ)

summary:
Input ChIP-seq in L1 larva worms.

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: Control ChIP-seq from whole organism (ENCSR219ATU)

summary:
This is the ChIP-seq control of transgenic worms expressing CEY-2-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR317QFT)

summary:
Input control for ChIP-seq on transgenic flies expressing YL-1-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR235ERJ)

summary:
ChIP-seq on transgenic flies expressing CG8290-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR048CGN)

summary:
This is the ChIP-seq control of transgenic worms expressing hmg-1.2-eGFP fusion proteins.

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 whole organism (ENCSR049CFS)

summary:
ChIP-seq on transgenic worms expressing T26A8.4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR219AHM)

summary:
ChIP-seq on transgenic flies expressing CG9139-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR142HMN)

summary:
Input control for ChIP-seq on transgenic flies expressing CG12659-eGFP fusion proteins.

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 whole organism (ENCSR312RCJ)

summary:
ChIP-seq on transgenic flies expressing CG8216-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR139RMN)

summary:
Input control for ChIP-seq on transgenic flies expressing Lpt-eGFP fusion proteins.

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 whole organism (ENCSR135QZY)

summary:
ChIP-seq on transgenic worms expressing set-16-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR142DMI)

summary:
Input ChIP-seq in young adult worms.

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 whole organism (ENCSR213XFQ)

summary:
ChIP-seq of transgenic worms expressing DAO-5-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR032HMJ)

summary:
ChIP-seq on transgenic flies expressing E(z)-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR032CWX)

summary:
ChIP-seq of transgenic worms expressing C06A8.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR223SII)

summary:
This is the ChIP-seq control of transgenic worms expressing F13C5.2-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR029WBT)

summary:
Input ChIP-seq in YA worms.

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 whole organism (ENCSR125NWX)

summary:
ChIP-seq on transgenic flies expressing nmo-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR303EBD)

summary:
ChIP-seq on transgenic flies expressing Lpt-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR032CDC)

summary:
ChIP-seq on transgenic flies expressing chif-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR111NKF)

summary:
This is the ChIP-seq control of transgenic worms expressing SDC-2-eGFP fusion proteins.

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: Control ChIP-seq from whole organism (ENCSR316CFG)

summary:
Input ChIP-seq in L2 larva worms.

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 whole organism (ENCSR192NDP)

summary:
ChIP-seq of transgenic worms expressing F08F3.9-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR111IAZ)

summary:
ChIP-seq on transgenic worms expressing pbrm-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR110CKX)

summary:
ChIP-seq of transgenic worms expressing HIM-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR191TAJ)

summary:
This is the ChIP-seq control of transgenic worms expressing F08F3.9-eGFP fusion proteins.

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 whole organism (ENCSR010MNU)

summary:
ChIP-seq of transgenic worms expressing CHD-7-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR101QFW)

summary:
ChIP-seq of transgenic worms expressing C08G9.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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 whole organism (ENCSR027AMS)

summary:
ChIP-seq on transgenic flies expressing CG12659-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Nova-ST: Nano-Patterned Ultra-Dense platform for spatial transcriptomics [Nova-ST]

status: Public on Feb 22 2024

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

summary: Spatial transcriptomics workflows using barcoded capture arrays are commonly used for resolving gene expression in tissues. However, existing techniques are either limited by capture array density or are cost prohibitive for large scale atlasing. We present Nova-ST, a dense nano-patterned spatial transcriptomics technique derived from randomly barcoded Illumina sequencing flow cells. Nova-ST enables customized, low cost, flexible, and high-resolution spatial profiling of large tissue sections. Benchmarking on mouse brain sections demonstrates significantly higher sensitivity compared to existing methods, at reduced cost.

overall_design: 6-8 week old C57BL/6J mice were used for these experiments. Five coronal brain sections were taken and Nova-ST spatial transcriptomics libraries were created

first: Suresh

last: Poovathingal

first: Lars

middle: E

last: Borm

first: Roel

last: Vandepoel

first: Nicholas

last: Poulvellarie

first: Annelien

last: Verfaillie

first: Nikky

last: Corthout

first: Stein

last: Aerts


title: Nova-ST: Nano-Patterned Ultra-Dense platform for spatial transcriptomics [Stereo-Seq]

overall_design: 6-8 week old C57BL/6J mice were used for these experiments. One coronal brain section was taken and a Stereo-seq spatial transcriptomics library was created


title: High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labelling [bulk RNA-seq]

status: Public on Feb 25 2024

city: Shanghai

first: Yuejun

last: Chen

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: Deciphering patterns of connectivity between neurons in the mammalian brain is a critical step toward understanding brain function. Conventional imaging based neuroanatomical tracing methods identify area-to-area or sparse neuron-to-neuron connectivity patterns, but with extremely limited throughput. Recently developed barcode-based connectomics methods can efficiently map large numbers of single-neuron projections, but linking these data to single-cell transcriptomics remains a challenge. Here, we established a retro-AAV barcode-based multiplexed tracing method called MERGE-seq (Multiplexed projection neuRons retroGrade barcodE sequencing), which is capable of simultaneously characterizing the projectome and transcriptome at the single neuron level. We uncovered dedicated and collateral projection patterns of ventromedial prefrontal cortex (vmPFC) neurons to five downstream targets (AI, DMS, BLA, MD and LH). We found that projection-defined vmPFC neurons are molecularly heterogeneous, which are composed of different neuronal subtypes. We further identified transcriptional signatures of various dedicated and bifurcated vmPFC neurons, and verified Pou3f1 as the marker gene of neurons sending collateral axons to DMS and LH. Finally, we fitted our single-neuron connectome/transcriptome data into a machine learning-based model and revealed groups of genes that were predictive of certain projection pattern. In summary, we have developed a new multiplexed technique whose paired connectome and gene expression data can help reveal organizational principles that form neural circuits and process information.

overall_design: Male adult C57BL/6 mice (8 weeks of age) were anesthetized intraperitoneally using pentobarbital sodium (10 mg/mL, 120 mg/kg b.w.) and unilaterally injected with rAAV-EGFP-BARCODE virus into five projection targets simultaneously.  Barcode 0 sequences representing the AI target is: CTGCACCGACGCATT; barcode 1 sequences representing the DMS target is: GAAGGCACAGACTTT; barcode 2 sequences representing the MD target is: GTTGGCTGCAATCCA; barcode 3 sequences representing the BLA target is: AAGACGCCGTCGCAA; barcode 4 sequences representing the LH target is: TATTCGGAGGACGAC.  3 mice were performed scRNA-seq without FAC-sorting, cell pellets were resuspended and 48,000 cells were loaded into 3 lanes to perform 10X Genomics sequencingperformed scRNA. 3 mice with sorting and pooled together for scRNA-seq. Chromium Single Cell 3' Reagent Kits (v3) were used for transcriptome library preparation (10X Genomics). Libraries were sequenced on an Illumina Novaseq 6000 system.  Parallel PCR reactions were performed containing 50 ng of post cDNA amplification reaction cleanup material as a template. P5-Read1 (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC) and P7-index-Read2-EGFP (CAAGCAGAAGACGGCATACGAGATAGGATTCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGgCATGGACGAGCTGTACAAG) (200 nM each) were used as primers with the NEBNext Ultra II Q5 Master Mix (NEB, Cat #M0544L). Amplification was performed using the following PCR protocol: (1) 33°C for 1 min, (2) 98° for 10 s, then 65°C for 75 s (20-24 cycles), (3) 75°C for 5 min. Reactions were re-pooled during 1X SPRI selection (Beckman, Cat #B23317), which harvested virus projection barcodes library. 431-437bp (with 120bp adaptors) projectome libraries were sequenced using Illumina HiSeq X Ten.

first: Peibo

last: Xu

first: Jian

last: Peng

first: Tingli

last: Yuan

first: Zhaoqin

first: Ziyan

last: Wu

first: Chengyu

middle: T

last: Li

first: Zhen-Ge

last: Luo


title: TF ChIP-seq from whole organism (ENCSR105OGL)

first: ENCODE

summary:
ChIP-seq on transgenic flies expressing pum-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Control ChIP-seq from whole organism (ENCSR007JPR)

summary:
This is the ChIP-seq control of transgenic worms expressing REC-8-eGFP fusion proteins.

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 whole organism (ENCSR012MXT)

summary:
ChIP-seq on transgenic flies expressing Nf-YC-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labelling

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

overall_design: Refer to individual Series


title: TF ChIP-seq from whole organism (ENCSR013JXG)

summary:
ChIP-seq of transgenic worms expressing F49E8.2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Transcriptomic changes following NR1D1 modulation in thyroid cancer cell lines

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

summary: Nuclear receptor subfamily 1 group D member 1 (NR1D1), also known as Rev-Erbα, is a circadian clock component that functions as a transcriptional repressor which coordinates circadian rhythm and cell metabolism. Altered circadian clock characteristics have been shown in malignant thyroid neoplasms, and NR1D1 is one of the recurrence-associated genes in papillary thyroid cancer. We aimed to investigate the biological role of NR1D1 in thyroid cancer cells.

overall_design: Human thyroid cancer cell lines 8505C and CAL-62 were transfected with either a siRNA against NR1D1 or a control siRNA, whereas TPC-1 and FTC-133 cells were transfected with either an NR1D1-overexpressing vector or an empty vector. Cellular RNA was subjected to RNA sequencing.


title: The effect of anti-Gremlin-1 treatment on human cirrhotic precision-cut liver slices

status: Public on Feb 21 2024

city: Berlin

first: Paul

last: Horn

address: Augustenburger Platz 1

department: Department of Hepatology and Gastroenterology

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: Gremlin-1 has been implicated in liver fibrosis in metabolic dysfunction-associated steatohepatitis (MASH) via inhibition of bone-morphogenetic protein (BMP) signalling and has thereby been identified as a potential therapeutic target. Using human cirrhotic precision-cut liver slices (PCLS) as an ex vivo model systems of MASH fibrosis, we show that neutralisation of Gremlin-1 activity with monoclonal therapeutic antibodies does not reduce liver inflammation or liver fibrosis. Overall, our findings suggest a redundant role for Gremlin-1 in the pathogenesis of liver fibrosis, which is unamenable to therapeutic targeting.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PCLS treated with anti-Gremlin-1 or Isotype control antibodies.

first: Chris

middle: J

last: Weston

first: Philip

middle: N

last: Newsome


title: Control ChIP-seq from whole organism (ENCSR010TXY)

last: DCC

summary:
ChIP-seq on transgenic flies expressing ash1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.

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: Analysis of the stress response after induction of the dormancy-inducing membrane toxin TisB in Escherichia coli

status: Public on Feb 20 2024

city: Giessen

first: Bork

middle: A.

last: Berghoff

address: Heinrich-Buff-Ring 26-32

institute: University of Giessen

summary: We assume that adaptation to tisB expression is driven by cellular stress responses. It has already been observed that expression of type I toxins leads to up-regulation of several stress-related genes. To reveal the response to TisB on a global scale, transcriptome analysis of MG1655 p0SD-tisB was performed.

overall_design:
Wild type MG1655, harboring the p0SD-tisB plasmid, was treated with L-ara for tisB induction during exponential phase for 30 min.
RNA samples of biological triplicates were extracted before (exp) and after L-ara treatment (0ATG), and after 1 hour (rec1h) and 2 hours (rec2h) of recovery.

first: Florian

middle: H

last: Leinberger

first: Daniel

last: Edelmann

first: Nicole

last: Schmid

first: Patrick

last: Blumenkamp

middle: A


title: Denaturing purifications demonstrate that PRC2 and other widely-reported chromatin proteins do not appear to bind directly to RNA in vivo

city: Pasadena

first: Jimmy

middle: K

last: Guo

address: 1200 E California Blvd

institute: Caltech

sample_organism:
Homo sapiens
Mus
Mus musculus

platform_organism:
Homo sapiens
Mus
Mus musculus


title: Brain endothelial GSDMD activation mediates inflammatory BBB breakdown

city: Beijing

first: Minmin

address: 7 Science Park Road, ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

summary: The blood-brain barrier (BBB) protects the central nervous system (CNS) from external assaults by pathogenic or harmful substances. BBB impairment frequently occurs during infection, inflammatory, or other pathological conditions, which causes or exacerbates a wide range of CNS diseases. Using single cell transcriptomics, we show in this study that during systemic LPS challenges, brain endothelial cells undergo Gsdmd-mediated pyroptosis and impair the integrity of the BBB, leading to profound changes in the transcriptomic landscape of brain parenchymal populations. Analyses of the scRNA-seq dataset reveal that brain endothelial cells responded strongly to systemic LPS challenge. Further analyses of the transcriptional signatures revealed that the brain parenchymal populations displayed heterogeneous responses to BBB leakage accompanied by systemic inflammation.

overall_design: Adult (6~8w) wild type or Gsdmd-/- mice were subjected to either Dulbecco's phosphate buffer saline (Ctrl) or 40mg/kg lipopolysaccharide (LPS) for ~8 hours, from the parenteral route (i.p.). Single cells from the motor cortex were dissociated and collected for scRNA-seq and sequenced using the 10X Genomics Chromium platform.

first: Chao

last: Wei

first: Wei

last: Jiang

first: Ruiyu

last: Wang

first: Li

last: Zhang

first: Feng

last: Shao


title: Monocyte mRNA following incubation for 4 hrs with adult or P7 platelets

status: Public on Feb 15 2024

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: We seek to define how neonatal and adult platelets differentially mediate monocyte immune differentiation

overall_design: Adult monocytes were incubated with control buffer, adult plateltes or P7 platelets.  After 4hrs monocytes were washed and mRNA isolated for RNA-seq

first: Craig

last: Morrell

first: Preeti

last: Maurya


title: P7 and Adult mouse platelet RNA-seq

summary: We seek to compare the mRNA profile of neonatal and adult platelets in mice

overall_design: Platelets isolated from P7 and adult mice, mRNA isolated

first: Kathleen

last: McGrath

first: James

last: Palis


title: Control ChIP-seq from whole organism (ENCSR107LHB)

first: ENCODE

last: DCC

summary:
This is the ChIP-seq control of transgenic worms expressing HIM-1-eGFP fusion proteins.

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: Conserved regulation of ZC3H14/Nab2 in circRNA biogenesis

status: Public on Feb 10 2024

city: Hefei

first: Xiaolin

address: Huangshan Road

institute: USTC

summary: Circular RNAs (circRNAs) are natural outputs of eukaryotic transcription and RNA processing and have emerged as critical regulators in physiology and human diseases. Although a series of cis-elements and trans-factors are reported to globally regulate circRNA biogenesis, most of these regulations are unconserved or at most mammalian conserved. Here, using a genome-wide CRISPR knockout screen, we have identified an evolutionarily conserved polyadenosine RNA-binding protein ZC3H14 to regulate circRNA biogenesis in eukaryotes. Mechanistically, ZC3H14 associates with spliceosome to bind to 3' and 5' exon-intron boundaries of circularized exons, and forms a dimer to promote circRNA biogenesis. ZC3H14 knockout mice exhibit disrupted spermatogenesis and reduced testicular circRNA levels. Additionally, human ZC3H14 is associated with male infertility. Our findings reveal a conserved requirement for ZC3H14/Nab2 in the modulation of eukaryotic backsplicing and link ZC3H14 along with circRNAs to mammalian testicular disorders.

sample_organism:
Schizosaccharomyces pombe
Homo sapiens
Mus musculus

overall_design:
To investigate direct and specific regulators of backsplicing, we set out to establish a circReporter system with an unbiased genome-wide CRISPR-Cas9 knockout screen, and identified an evolutionarily conserved polyadenosine-binding protein ZC3H14 to regulate circRNA biogenesis.
Then, we performed circRNA profiles in human HEK293 cells or mouse testes when ZC3H14 was knocked down or knockout.
We also performed the individual-nucleotide resolution crosslink immunoprecipitation (iCLIP) followed by RNA-seq of the endogenous ZC3H14 in HEK293 cells in duplicates and in mouse germ cells

Please note that each processed data file was generated from 2-3 samples together as indicated in the corresponding sample description field.

first: Qiqi

last: Li


title: Control ChIP-seq from whole organism (ENCSR111HDC)

summary:
Input ChIP-seq in starved L1 larva worms.

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: Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription (RNA-Seq)

status: Public on Feb 09 2024

city: Austin

first: Qian

state: TX

address: 2515 Speedway

institute: The Unibersity of Texas at Austin

summary: The C-terminal domain of RPB1 (CTD) orchestrates transcription by recruiting regulators to RNA Pol II upon phosphorylation. Recent insights highlight CTD’s pivotal role in driving condensate formation on gene loci. Yet, the molecular mechanism behind how CTD-mediated recruitment of transcriptional regulators influences condensates formation remains unclear.  Our study unveils that phosphorylation reversibly dissolves phase separation induced by the unphosphorylated CTD. Phosphorylated CTD, upon specific association with transcription regulatory proteins, forms distinct condensates from unphosphorylated CTD. Function studies demonstrate CTD variants with diverse condensation properties in vitro exhibit difference in promoter binding and mRNA co-processing in cells. Notably, varying CTD lengths lead to alternative splicing outcomes impacting cellular growth, linking the evolution of CTD variation/length with the complexity of splicing from yeast to human. These findings provide compelling evidence for a model wherein post-translational modification enables the transition of functionally specialized condensates, highlighting a co-evolution link between CTD condensation and splicing.

overall_design: To investigate gene expression and RNA splicing of different CTD length, we overexpressed RPB1_52xCTD and RPB1_26xCTD in HEK 293T cells, upon α-amanitin administration, we then performed gene expression and alterative splicing profiling using data obtained from RNA-seq of 2 conditions (HEK 293T_RPB1_52xCTD vs HEK 293T RPB1_26xCTD) with 2 replicates respectively.

first: Wantae

last: Kim

first: Svetlana

last: Panina

first: Joshua

last: Mayfield

first: Bede

last: Portz

first: Y


title: Denaturing purifications demonstrate that PRC2 and other widely-reported chromatin proteins do not appear to bind directly to RNA in vivo [CLIP and CLAP]

first: Jimmy

last: Guo

summary: The Polycomb Repressive Complex 2 (PRC2) has been reported to bind to many RNAs and has become a central player in reports describing the mechanisms of how long non-coding RNAs (lncRNAs) regulate gene expression. Based largely on these observations of PRC2, many additional chromatin proteins have similarly been reported to bind RNA to enact their functions. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here we revisit the evidence supporting broad RNA binding by PRC2 and other chromatin proteins and show that many previously reported RNA-protein interactions do not represent in vivo interactions. We find that denaturing purification of in vivo crosslinked RNA-protein complexes leads to loss of detectable PRC2-RNA interactions. Similarly, we fail to detect in vivo RNA binding of other chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, WDR5, and others), despite accurately mapping bona fide RNA-protein binding sites across a range of proteins including several specific chromatin-associated proteins (SPEN, CHTOP, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.

overall_design: CLIP and CLAP were used to map direct RNA-protein interactions in HEK293T and mouse embryonic stem cells.

first: Mario

last: Blanco

first: Mitchell

last: Guttman


title: Multifaceted anti-tumor activity of a CDK9 inhibitor in prostate cancer [ChIP-seq]

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: Cyclin-dependent kinase 9 (CDK9) stimulates oncogenic transcriptional pathways in cancer. Here, we evaluate the activity of an orally bioavailable CDK9 inhibitor, CDKI-73, in prostate cancer, a disease characterized by aberrant activity of multiple transcriptional regulators. CDKI-73 caused inhibition of proliferation and cell death in diverse in vitro models of androgen receptor (AR)-driven and AR-independent models of castration-resistant prostate cancer (CRPC). The activity of CDKI-73 was validated in more clinically-relevant systems, including xenografts, patient-derived tumor explants and aggressive patient-derived CRPC organoids. Mechanistically, CDKI-73 inhibited CDK9-mediated phosphorylation of serine 2 on RNA polymerase II and serine 81 on AR. This resulted in reduced levels of anti-apoptotic factors and suppression of signaling pathways regulated by AR, MYC and BRD4, key drivers of dysregulated transcription in prostate cancer. CDKI-73 synergized with the BRD4 inhibitor AZD5153 in cell lines and organoid models of aggressive AR-driven and AR-independent disease. Collectively, our work provides new insights into CDK9’s oncogenic activity and reveals CDKI-73 as a promising therapeutic agent for prostate cancer, particularly aggressive, therapy-resistant subtypes.

overall_design: H3K27ac ChIP-seq in LNCaP cells following 48 hours of CDKI-73 treatment (150 nM) or DMSO control.


title: Evaluation and optimization of sequence-based gene regulatory deep learning models

status: Public on Feb 03 2024

city: Vancouver

first: Abdul Muntakim

last: Rafi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

summary: As training dataset for Random Promoter DREAM Challenge 2022, we generated ~6.7 million synthetic promoters (in yeast) comprised of random DNA (N80) and measured their expression by FACS (sorting into 18 bins). As test dataset for Random Promoter DREAM Challenge 2022, we generated ~71k synthetic promoters (in yeast) comprised of designed DNA (NBT) and measured their expression by FACS (sorting into 18 bins).

overall_design: Two promoter libraries (random N80 and designed NBT), embedded within a promoter scaffold with a distal poly-T and proximal poly-A tract (pTpA) regulating yellow flourescent protein (YFP) was tested in Chardonnay (Chard). The sequences flanking the random 80 bp oligo were as follows: the pTpA distal region was (pT) GCTAGCAGGAATGATGCAAAAGGTTCCCGATTCGAACTGCATTTTTTTCACATC and proximal region (pA) was GGTTACGGCTGTTTCTTAATTAAAAAAAGATAGAAAACATTAGGAGTGTAACACAAGACTTTCGGATCCTGAGCAGGCAAGATAAACGA (up to the theoretical TSS). In both cases, 80 Ns were inserted in between proximal and distal regions.

first: Carl

last: de Boer

first: Abdul

last: Muntakim Rafi


title: Transcriptional response of Gemmatimonas phototrophica to changing light regimes [AP64_LowLight]

status: Public on Feb 01 2024

city: Trebon

first: Karel

middle: Vaclav

last: Kopejtka

address: Novohradska

department: Centre Algatech

country: Czech Republic

institute: Institute of Microbiology Czech Acad. Sci.

summary: In this study, we provide a time-series analysis of the transcriptional response of Gemmatimonas phototrophica AP64T during the dark-to-light transition under aerobic and semiaerobic conditions. By analysing its transcriptome, focussing especially on PS-related genes, we tested the hypothesis that G. phototrophica might constitute an example of an anoxygenic phototroph on its evolutionary pathway from anaerobic to aerobic life-style.

overall_design: G. phototrophica AP64T (= DSM 29774) was grown in an optimized liquid medium described earlier (Shivaramu et al., 2023) at 25°C. At the beginning of each experiment, the inoculum (approx. OD600 = 0.2) was diluted in 100 mL of a fresh medium to approx. OD600 = 0.03. Cultures were grown in triplicates aerobically in the dark until reaching approx. OD600 = 0.2. Then cultures were illuminated with photon flux density of 100 µmol photons m-2 s-1. Sampling was done 2, 4, and 8 hours after the light was switched on. Control cultures were kept in dark and sampled for each time point as a reference.

first: Jürgen

last: Tomasch

first: Sahana

last: Shivaranu

first: Mohit

last: Saini

first: David

last: Kaftan

first: Michal

last: Koblížek


title: RNAseq of 3LL-ΔΝRAS lung tumours treated with SHP2 or/and KRAS inhibitors

city: London

first: Miriam

last: Molina-Arcas

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Intravenous-induced 3LL-ΔNRAS tumour bearing mice were treated with RMC-4550 or/and RMC-4998 for 7 days and isolated for RNAseq.

overall_design: 4 groups of 3LL-ΔNRAS tumour bearing mice: Vehicle, RMC-4550, RMC-4998, RMC-4550+RMC-4998 treated daily for 7 days. RNA was extracted from isolated  lungs.

first: Panayiotis

last: Anastasiou

first: Julian

last: Downward

first: Robert

last: Goldstone


title: Coordination of rhythmic RNA synthesis and degradation orchestrates 24- and 12-h RNA expression patterns in mouse fibroblasts

status: Public on Jan 22 2024

city: Blacksburg

first: Benjamin

middle: Alex

last: Unruh

email: baunruh@vt.edu, skojima@vt.edu

state: Virginia

address: 1015 Life Science Cir

department: Biological Sciences

institute: Virginia Tech

summary: Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and post transcriptional mechanisms are considered important to drive rhythmic RNA expression, however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. We find that rhythmic RNA synthesis is the primary contributor of 24 hr RNA rhythms, while rhythmic degradation is more important for 12 hr RNA rhythms. These rhythms were predominantly regulated by Bmal1 and/or the core clock mechanism, and interplay between rhythmic synthesis and degradation has a significant impact in shaping rhythmic RNA expression patterns. Interestingly, core clock RNAs are regulated by multiple rhythmic processes and have the highest amplitude of synthesis and degradation, presumably critical to sustain robust rhythmicity of cell-autonomous circadian rhythms. Our study yields invaluable insights into the temporal dynamics of both 24 hr and 12 hr RNA rhythms in mouse fibroblasts.

overall_design: Total RNA or nascent 4sU labeled RNA were submitted to Azenta for RNA sequencing. rRNA depletion was performed and library prep with 150bp reads using standard Tru-seq adapters.

first: Douglas

last: Weidemann

first: Lin

last: Miao

first: Shihoko

last: Kojima


title: Endocrine disruptor-induced epimutagenesis in vitro: Insight into molecular mechanisms [RNA-Seq]

status: Public on Jan 31 2024

city: San Antonio

first: Jake

middle: Dean

last: Lehle

address: 16631 Vance Jackson Rd APT#1220

department: NDRB

institute: The University of Texas at San Antonio

summary: Endocrine disrupting chemicals (EDCs) such as bisphenol S (BPS) are xenobiotic compounds that can disrupt endocrine signaling following exposure due to steric similarities to endogenous hormones within the body. EDCs have been shown to induce disruptions in normal epigenetic programming (epimutations) that accompany dysregulation of normal gene expression patterns that appear to predispose disease states. Most interestingly, the prevalence of epimutations following exposure to many different EDCs often persists over multiple subsequent generations, even with no further exposure to the causative EDC. Many previous studies have described both the direct and prolonged effects of EDC exposure in animal models, but many questions remain about molecular mechanisms by which EDCs initially induce epimutations or contribute to the propagation of EDC-induced epimutations either within the exposed generation or to subsequent generations. Additional questions remain regarding the extent to which there may be differences in cell type-specific susceptibilities to various EDCs, and whether this susceptibility is correlative with expression of relevant hormone receptors and/or the location of relevant hormone response elements (HREs) in the genome. To address these questions, we exposed cultured mouse pluripotent (induced pluripotent stem [iPS]), somatic (Sertoli and granulosa), and germ (primordial germ cell like [PGCLCs]) cells to BPS and measured changes in DNA methylation levels at the epigenomic level and gene expression at the transcriptomic level. We found that there was indeed a difference in cell type-specific susceptibility to EDC-induced epimutagenesis and that this susceptibility correlated with differential expression of relevant hormone receptors and, in many cases, tended to generate epimutations near relevant HREs within the genome. Additionally, however, we also found that BPS can induce epimutations in a cell type that does not express relevant receptors and in genomic regions that do not contain relevant HREs, suggesting that both canonical and non-canonical signaling mechanisms can be disrupted by BPS exposure. Most interestingly, we found that when iPS cells were exposed to BPS and then induced to differentiate into PGCLCs, the prevalence of epimutations and differentially expressed genes (DEGs) initially induced in the iPSCs was largely retained in the resulting PGCLCs, however, >90% of the specific epimutations and DEGs were not conserved but were rather replaced by novel epimutations and DEGs following the iPSC to PGCLC transition. These results suggest a unique mechanism by which an EDC-induced epimutated state may be propagated transgenerationally following a single exposure to the causative EDC.

overall_design: To investigate cell type-specific differential susceptibility to BPS, we exposed cultured mouse pluripotent (induced pluripotent stem [iPS]), somatic (Sertoli and granulosa), and germ (primordial germ cell like [PGCLCs]) cells to BPS or vehicle alone and measured changes in gene expression at the transcriptomic level via RNA-seq.

middle: D

first: Yu-Huey

last: Lin

first: Amanda

last: Gomez

first: Laura

last: Chavez

first: John

middle: R

last: McCarrey


title: Endocrine disruptor-induced epimutagenesis in vitro: Insight into molecular mechanisms

type: Methylation profiling by genome tiling array

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


title: Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription

first: Qian

last: Zhang


title: ATAC-Seq experiment of humanized  liver mice with metabolic treatments

status: Public on Jan 23 2024

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary:
To make the human liver accessible to metabolic treatments, we employed a liver-specific humanized mouse model in which approximately 50% of the mouse hepatocytes were replaced by human ones.
For the dietary treatment, the humanized mice were allowed free access to food (AL, n=4 for donor1, n=3 for donor2) or subjected to a twenty-four hours food withdrawal (Fast, n=4 for donor1, n=3 for donor2). For the transcription factor agonist treatments, the humanized mice were injected with DMSO (n=4), fenofibrate (n=4, 50mg/kg, Sigma-Aldrich, Cat. F6020), rosiglitazone (n=4,10mg/kg, Sigma-Aldrich, Cat. R2408) and GW4064 (n=4, 30mg/kg, Sigma-Aldrich, Cat. G5172) by i.p. injection. The livers were collected after 6 hours fasting and stored in liquid nitrogen immediately after mice sacrificed.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The nuclei were isolated tissues from frozen livers and sent for ATAC-Seq library preparation.The ATAC-Seq DNA library generations were processed using Kaestner lab’s pipeline.The purified DNAs were amplified using TruSeq i7 index primers (Illumina) via PCR. The library quality and quantity were evaluated using Bioanalyzer and Qubit, and the final library was sequenced at NHLBI DNA Sequencing and Genomics Core.

first: Chengfei

last: Jiang


title: The role of nucleosome dynamics during the monocyte to macrophage transition

status: Public on Feb 06 2024

city: Tallahassee

first: Jonathan

last: Dennis

state: FL

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

summary: We used MNase Transcription Start Site Sequence Capture (mTSS-seq) to map nucleosome distribution and sensitivity to MNase digestion over pol II promoters in THP-1 monocytes during phorbol 12-myristate 13-acetate (PMA) induced differentiation. We found that differentially expressed macrophage genes have stronger nucleosome positioning and greater occupancy prior to differentiation suggesting that these genes are poised for future expression. We found dynamic alterations in nucleosome sensitivity during early differentiation and the establishment of a new sensitivity profile in macrophages. We further observed that alterations in sensitivity corresponded to gains and losses of regulatory factor footprints within the promoter region.

overall_design:
Nucleosome mapping by micrococcal nuclease (MNase) digestion and DNA sequencing of promoter captured mononucleosomes from THP-1 monocytes before, during, and after PMA induced differentiation

UPDATE: [09-30-2024] The bigWig files for GSM8037120-GSM8037135 were replaced.

UPDATE: [10-08-2024] Additional bigwig files are included. The list of the additional files and their associated sample/raw files is included in the readme.txt.

first: Jane

middle: M

last: Benoit

first: Brandon

last: Buck

first: Hank

middle: W

last: Bass


title: Transcriptional response of Gemmatimonas phototrophica to changing light regimes [AP64_O2]

first: Karel

last: Kopejtka

summary: In this study, we provide a time-series analysis of the transcriptional response of Gemmatimonas phototrophica  AP64T during the dark-to-light transition under aerobic and semiaerobic conditions. By analysing its transcriptome, focussing especially on PS-related genes, we tested the hypothesis that G. phototrophica might constitute an example of an anoxygenic phototroph on its evolutionary pathway from anaerobic to aerobic life-style.

overall_design: G. phototrophica AP64T (= DSM 29774) was grown in an optimized liquid medium described earlier (Shivaramu et al., 2023) at 25°C. At the beginning of each experiment, the inoculum (approx. OD600 = 0.2) was diluted in 100 mL of a fresh medium to approx. OD600 = 0.03. Cultures were grown in triplicates aerobically (20% O2) or semiaerobically (10% O2) in the dark until reaching approx. OD600 = 0.2. Then cultures were illuminated with photon flux density of 100 µmol photons m-2 s-1. Sampling was done 2 and 8 hours after the light was switched on. Control set was sampled at dark.

first: Jürgen

last: Tomasch

first: Sahana

last: Shivaranu

first: Mohit

last: Saini

first: David

last: Kaftan

first: Michal

last: Koblížek


title: UBR5 mediates chemoresistance in colorectal cancer by attenuating ferroptosis via Lys11 ubiquitin-dependent stabilization of Smad3-SLC7A11 signaling

city: Guangzhou

first: Mei

last: Song

address: Zhongshan No.2 Road 1th, Nonglin Street

institute: Sun Yat-sen University

summary: To elucidate the mechanisms underlying UBR5 deficiency-enhanced cytotoxic effects of Oxaliplatin, we performed transcriptome profiling by RNA-seq to explore the signaling pathways affected by UBR5.

overall_design: Colorectal cancer cell SW1116 stably expressing shUBR5 or control shRNA were treated with DMSO or 25µM of oxaliplatin (Oxa) for 48hr. Afterward, cells were harvested for RNA preparation. Total RNA was extracted using TRIzol reagent and sequenced on Illumina Novaseq 6000 sequencing instrument (BGI, China). There were four experimental groups (shNC+DMSO, shNC+Oxa, shUBR5+DMSO, shUBR5+Oxa) with 3 replicates for each.


title: Transcriptomes of ex vivo grown spontaneous p53-R270H MYC murine ovarian and uterine cancers

city: Charleston

first: Joe

last: Delaney

state: SC

address: 173 Ashley Avenue

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: Genetically engineered mouse models (GEMM) have fundamentally changed how ovarian cancer etiology, early detection, and treatment is understood. However, previous GEMMs of high-grade serous ovarian cancer (HGSOC) have had to utilize genetics rarely or never found in human HGSOC to yield ovarian cancer within the lifespan of a mouse. MYC, an oncogene, is amongst the most amplified genes in HGSOC, but it has not previously been utilized to drive HGSOC GEMMs. We coupled Myc and dominant negative mutant p53-R270H with a fallopian tube epithelium-specific promoter Ovgp1 to generate a new GEMM of HGSOC. Female mice developed lethal cancer at an average of 15.1 months. Histopathological examination of mice revealed HGSOC characteristics including nuclear p53 and nuclear MYC in clusters of cells within the fallopian tube epithelium and ovarian surface epithelium. Unexpectedly, nuclear p53 and MYC clustered cell expression was also identified in the uterine luminal epithelium, possibly from intraepithelial metastasis from the fallopian tube epithelium (FTE). Extracted tumor cells exhibited strong loss of heterozygosity at the p53 locus, leaving the mutant allele. Copy number alterations in these cancer cells were prevalent, disrupting a large fraction of genes. Transcriptome profiles most closely matched human HGSOC and serous endometrial cancer. Taken together, these results demonstrate the Myc and Trp53-R270H transgene was able to recapitulate many phenotypic hallmarks of HGSOC through the utilization of strictly human-mimetic genetic hallmarks of HGSOC. This new mouse model enables further exploration of ovarian cancer pathogenesis, particularly in the 50% of HGSOC which lack homology directed repair mutations. Histological and transcriptomic findings are consistent with the hypothesis that serous uterine cancer may originate from the fallopian tube epithelium.

overall_design: To investigate the transcriptional profiles of cancer cells spontaneously arising in a Ovgp1-Trp53-R270H-Myc model, cells from gynecologic tract tissue were isolated and grown ex vivo until uniform and actively proliferating.

first: Alexandra

last: Blackman

first: Silvia

last: Saenz

first: Martin

last: Romeo


title: MFSD7C protects hemolysis-induced lung impairments by inhibiting ferroptosis

status: Public on Feb 08 2024

city: JiNan

first: Kaige

last: Lyu

state: ShanDong

address: SCHOOL OF PHARMACY ROOM 612, NEW SCIENTIFIC RESEARCH BUILDING OF PHARMACY  NO.44 WENHUA XI ROAD JINAN SHANDONG 250012 CHINA

institute: ShanDong University

summary: Hemolysis drives susceptibility to lung injury and predicts poor outcomes in diseases, such as malaria and sickle cell disease (SCD). However, the underlying pathological mechanism remains unknown. Here, we report that major facilitator superfamily domain containing 7C (MFSD7C) protects the lung from hemolytic-induced damage by preventing ferroptosis. Mechanistically, MFSD7C deficiency leads to mitochondrial dysfunction and lipid remodeling caused by increased fatty acid uptake and decreased consumption, the excess accumulation of lipids sensitizes cells to peroxidation and ferroptosis. Moreover, systematic delivery of MFSD7C mRNA-loaded nanoparticles to the lungs effectively prevented lung injury in mice with hemolysis. These findings present the detailed link between hemolytic complications and ferroptosis, providing potential therapeutic targets for patients with hemolytic disorders.

overall_design: In the present work, we investigated the role and the underlying mechanism of MFSD7C in lung damage in a hemolytic mouse model. We found that MFSD7C protected the pulmonary cells from ferroptosis by stabilizing mitochondrial function and preventing lipid remodeling. MFSD7C knockout alleviated pulmonary inflammation and lung fibrosis by encouraging ferroptosis in the lung. The administration of MFSD7C mRNA-loaded nanoparticles effectively improved lung damage in hemolytic mice model.


title: RNA-Seq experiment of humanized mice with metabolic transcriptional factor activations

first: Haiming

last: Cao

summary:
To make the human liver accessible to metabolic treatments, we employed a liver-specific humanized mouse model in which approximately 50% of the mouse hepatocytes were replaced by human ones.
To capture transcriptomes reflecting pathophysiology and therapeutic development of metabolic diseases, we subjected the humanized mice to the key metabolic transcriptional factor agonist treatments.  We then performed gene expression profiling analysis using data obtained from RNA-seq of these humanized mice.

overall_design: The humanized mice were injected with DMSO (n=4), fenofibrate (n=4, 50mg/kg, Sigma-Aldrich, Cat. F6020), rosiglitazone (n=4,10mg/kg, Sigma-Aldrich, Cat. R2408) and GW4064 (n=4, 30mg/kg, Sigma-Aldrich, Cat. G5172) by i.p. injection. The livers were collected after 6 hours fasting and stored in liquid nitrogen immediately after mice sacrificed.The RNAs that have been extracted by Trizol were purified using the MagMAX RNA extraction kit (Thermo Fisher Scientific, Cat.AM1830). The strand-specific sequencing libraries were constructed using the TruSeq Stranded Total RNA Prep kit (Illumina). DNA sequencings were performed at the NHLBI DNA Sequencing and Genomics Core.

first: Chengfei

last: Jiang


title: Gene expression differences of alcohol use disorder in human brain

status: Public on Jan 19 2024

city: Research Triangle Park

first: Dana

last: Hancock

state: NC

address: 3040 E Cornwallis Rd

institute: RTI  International

summary: Excessive alcohol consumption is a leading cause of preventable death worldwide. Neurobiological mechanisms associated with alcohol use disorder (AUD) remain insufficiently understood. Here, we provide RNA-sequencing data generated in nucleus accumbent and dorsolateral prefrontal cortex, from 114 deceased individuals: 58 AUD cases, 56 non-AUD controls. DNA methylation data on many of these same individuals is available (see GEO accession number GSE252501).

overall_design: Bulk RNAseq data were measured in postmortem nucleus accumbens (NAc) and dorsolateral prefrontal cortex (DLPFC) brain tissue. Illumina TruSeq Total RNA Stranded RiboZero Gold was used for library prep.

first: Caryn

last: Willis


title: Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription (ChiP-Seq)

first: Qian

last: Zhang

summary: The C-terminal domain of RPB1 (CTD) orchestrates transcription by recruiting regulators to RNA Pol II upon phosphorylation. Recent insights highlight CTD’s pivotal role in driving condensate formation on gene loci. Yet, the molecular mechanism behind how CTD-mediated recruitment of transcriptional regulators influences condensates formation remains unclear.  Our study unveils that phosphorylation reversibly dissolves phase separation induced by the unphosphorylated CTD. Phosphorylated CTD, upon specific association with transcription regulatory proteins, forms distinct condensates from unphosphorylated CTD. Function studies demonstrate CTD variants with diverse condensation properties in vitro exhibit difference in promoter binding and mRNA co-processing in cells. Notably, varying CTD lengths lead to alternative splicing outcomes impacting cellular growth, linking the evolution of CTD variation/length with the complexity of splicing from yeast to human. These findings provide compelling evidence for a model wherein post-translational modification enables the transition of functionally specialized condensates, highlighting a co-evolution link between CTD condensation and splicing.

overall_design: To investigate genomic locations of RPB1 with different CTD length or charges, we overexpressed RPB1_52xCTD, RPB1_26xCTD or RPB1_26xCTD T4E/S7E mutants with YFP tag in HEK 293T cells, then performed Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) by GFP antibody with 2 replicates respectively. IP IgG from wild-type HEK 293T cells as control.

first: Wantae

last: Kim

first: Svetlana

last: Panina

first: Joshua

last: Mayfield

first: Bede

last: Portz

first: Y


title: Regulation of potassium homeostasis in Caulobacter crescentus [Tn-seq]

city: Namur

first: Regis

last: Hallez

address: 61 Rue de Bruxelles

institute: UNamur

summary: Potassium (K+) is an essential physiological element determining membrane potential, intracellular pH, osmotic/turgor pressure, and protein synthesis in cells. Nevertheless, K+ homeostasis remains poorly studied in bacteria. Here we describe the regulation of potassium uptake systems in the oligotrophic -proteobacterium Caulobacter crescentus known as a model for asymmetric cell division. We show that C. crescentus can grow in concentrations from the micromolar to the millimolar range by essentially using two K+ transporters to maintain potassium homeostasis, the low affinity Kup and the high affinity Kdp uptake systems. When K+ is not limiting, we found that the kup gene is essential while kdp inactivation does not impact the growth. In contrast, kdp becomes critical but not essential and kup dispensable for growth in K+-limited environments. However, in the absence of kdp, mutations in kup were selected to improve growth in K+-depleted conditions, likely by improving the affinity of Kup for K+. In addition, mutations in the KdpDE two-component system, which regulates kdpABC expression, suggest that the inner membrane sensor regulatory component KdpD works as a kinase in early stages of growth and as a phosphatase to regulate transition into stationary phase. Our data also show that KdpE is not only phosphorylated by KdpD but also by another non-cognate histidine kinase. On top of this, we determined the KdpE-dependent and independent K+ transcriptome and identified the direct targets of KdpE. Together, our work illustrates how an oligotrophic bacterium responds to fluctuation in K+ availability.

overall_design: Determination of genes essential for survival in minimal agar plate without exogenous source of K+

first: Alex

last: Quintero-Yanes

first: Loïc

last: Léger

first: Madeline

last: Collignon

first: Julien

last: Mignon

first: Aurélie

last: Mayard

first: Catherine

last: Michaux

first: Régis