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PKM RNA-Seq in HepG2



PKM      CRISPR in HepG2      Control:

General Information
RBPPKM
Cell_LineHepG2
MethodCRISPR
Exp_NamePKM-BGHcLV43-HepG2
ENCODE_series_ID
Batch_IDBGHcLV43
Pool IDPool-240723
Local_Set_Nameset74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1PKM-BGHcLV43-41
Rep2PKM-BGHcLV43-42
CN1NT-BGHcLV43-1
CN2NT-BGHcLV43-2
Rep1_qPCR82.9
Rep2_qPCR81.2
Rep1_WB83.5
Rep2_WB91.8
Antibody Cat#4053S
Antibody Lot#lot # 6
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1584




Experiment Information (Status: Sequenced)
BGHcLV43-41BGHcLV43-42
idx14091410
TRCN#_or_BGC#BGC#0001169BGC#0001169
shRNA_or_gRNA_sequenceTTGGACGGTGCAACCGAGCTTTGGACGGTGCAACCGAGCT
PAMGGGGGG
NamePKM_96PKM_96
Sample_IDBGHcLV43-41BGHcLV43-42
transduction_Date6/6/246/6/24
daysD6D6
RBP_namePKMPKM
qPCR_result82.981.2
Ave_qPCR82.0
RT-qPCR_primer-Fcgtggatgatgggcttattt
RT-qPCR_primer-Rggttcacacccttcttgctg
protein_conc38253470
WB_result83.591.8
Ave_WB87.6
WB_DONE_date6/17/24
MW60kd
IP
antibody_Cat#4053Slot # 6
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID76147615




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
PKMProduct_ID: 4053S
Lot_ID: 6
Source: Cell Signaling Technology
Target Name: PKM-human		 PKM-HEPG2-CRISPR-4053S.png<br>Caption: Western blot following CRISPR against PKM in HepG2 whole cell lysate using PKM specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against PKM. PKM protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 CST_4053S_6_PKM2.png<br>Caption: IP-WB analysis of 4053S whole cell lysate using the PKM2 specific antibody, 4053S. Lanes 1 and 2 are 2.5% of five million whole cell lysate input and 50% of IP enrichment, respectively, using a normal IgG antibody. Lane 3 is 50% of IP enrichment from five million whole cell lysate using the PKM2-specific antibody, 4053S. The same antibody was used to detect protein levels via Western blot. This antibody passes preliminary validation and will be further pursued for secondary validation. *NOTE* Protein sizes are taken from Genecards.org and are only estimates based on sequence. Actual protein size may differ based on protein characteristics and electrophoresis method used.
 PKM-K562-CRISPR-4053S.png<br>Caption: Western blot following CRISPR against PKM in K562 whole cell lysate using PKM specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against PKM. PKM protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGHcLV43-41BGHcLV43-42
Sample_IDBGHcLV43-41BGHcLV43-42
Sample Name
Sample NamePKM-BGHcLV43-41PKM-BGHcLV43-42
RBPPKMPKM
Cell_LineHepG2HepG2
Exp UID
StatusSequencedSequenced
Status_date2024-10-272024-10-27
ProjectENCORE2ENCORE2
Note
ID1325813259




Library-Prep Information
BGHcLV43-41BGHcLV43-42
Sample #3132
Sample NamePKM-BGHcLV43-41PKM-BGHcLV43-42
Sample_Name_Alias
Index Well PositionG09H09
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2024-07-222024-07-22
Lib_IDLib-240722Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp282280
Peak_Molarity89.8073.00
libSampleQC_DNA_WellDNA_Library_set74/set1/G4.pngDNA_Library_set74/set1/H4.png
RIN10.010.0
libSample_RNA_WellRNA_Library_set74/set1/C10.pngRNA_Library_set74/set1/D10.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-07-232024-07-23
Sample_IDBGHcLV43-41BGHcLV43-42
RBPPKMPKM
Batch_IDBGHcLV43BGHcLV43
WB_result83.50091.800
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID43904391




Sequencing Information
BGHcLV43-41BGHcLV43-42
Sample_IDBGHcLV43-41BGHcLV43-42
Sample NamePKM-BGHcLV43-41PKM-BGHcLV43-42
Pool IDPool-240723Pool-240723
LocalServer_folderset74set74
total_reads59,237,61050,565,586
total_aligned_reads53,771,07246,141,652
unique_aligned_reads50,596,33443,298,363
percent_uniqueAligned0.854130.85628
correlation_replicates0.9957890.995789
spikein_reads53,60442,140
percent_spikeins0.000900.00083
original_ReadLength101101
QC_StatusReadyToSubmitReadyToSubmit
ID32573258




Data Submission Information
DCC submission information was not avaliable




File Information
Files of the experiment was not avaliable in the database