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PKM RNA-Seq in K562



PKM      CRISPR in K562      Control:

General Information
RBPPKM
Cell_LineK562
MethodCRISPR
Exp_NamePKM-BGKcLV42-K562
ENCODE_series_ID
Batch_IDBGKcLV42
Pool IDPool-240715
Local_Set_Nameset73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1PKM-BGKcLV42-65
Rep2PKM-BGKcLV42-66
CN1NT-BGKcLV42-1
CN2NT-BGKcLV42-2
Rep1_qPCR42.0
Rep2_qPCR52.6
Rep1_WB98.6
Rep2_WB94.7
Antibody Cat#4053S
Antibody Lot#lot # 6
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1552




Experiment Information (Status: Sequenced)
BGKcLV42-65BGKcLV42-66
idx00
TRCN#_or_BGC#BGC#0001166BGC#0001166
shRNA_or_gRNA_sequenceGTGGTGAATCAATGTCCAGGGTGGTGAATCAATGTCCAGG
PAMCGGCGG
NamePKM_75PKM_75
Sample_IDBGKcLV42-65BGKcLV42-66
transduction_Date4/23/244/23/24
daysD6D6
RBP_namePKMPKM
qPCR_result42.052.6
Ave_qPCR47.3
RT-qPCR_primer-Fcgtggatgatgggcttattt
RT-qPCR_primer-Rggttcacacccttcttgctg
protein_conc24922528
WB_result98.694.7
Ave_WB96.7
WB_DONE_date5/8/24
MW60kd
IP
antibody_Cat#4053Slot # 6
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID58275828




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
BGKcLV42-65BGKcLV42-66
Sample_IDBGKcLV42-65BGKcLV42-66
Sample Name
Sample NamePKM-BGKcLV42-65PKM-BGKcLV42-66
RBPPKMPKM
Cell_LineK562K562
Exp UID
StatusSequencedSequenced
Status_date2024-10-272024-10-27
ProjectENCORE2ENCORE2
Note
ID1309813099




Library-Prep Information
BGKcLV42-65BGKcLV42-66
Sample #5556
Sample NamePKM-BGKcLV42-65PKM-BGKcLV42-66
Sample_Name_Alias
Index Well PositionG07H07
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2024-06-212024-06-21
Lib_IDLib-240621Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp298303
Peak_Molarity73.4068.60
libSampleQC_DNA_WellDNA_Library_set73/set1/G7.pngDNA_Library_set73/set1/H7.png
RIN10.010.0
libSample_RNA_WellRNA_Library_set73/set1/G7.pngRNA_Library_set73/set1/H7.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-07-152024-07-15
Sample_IDBGKcLV42-65BGKcLV42-66
RBPPKMPKM
Batch_IDBGKcLV42BGKcLV42
WB_result98.60094.700
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID43244325




Sequencing Information
BGKcLV42-65BGKcLV42-66
Sample_IDBGKcLV42-65BGKcLV42-66
Sample NamePKM-BGKcLV42-65PKM-BGKcLV42-66
Pool IDPool-240715Pool-240715
LocalServer_folderset73set73
total_reads49,573,35850,961,950
total_aligned_reads44,885,79346,681,964
unique_aligned_reads41,425,75243,148,050
percent_uniqueAligned0.835650.84667
correlation_replicates0.9950790.995079
spikein_reads5,0766,044
percent_spikeins0.000100.00012
original_ReadLength101101
QC_StatusReadyToSubmitReadyToSubmit
ID31913192




Data Submission Information
DCC submission information was not avaliable




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