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DEK RNA-Seq in K562



DEK      CRISPR in K562      Control:

General Information
RBPDEK
Cell_LineK562
MethodCRISPR
Exp_NameDEK-BGKcLV44-K562
ENCODE_series_ID
Batch_IDBGKcLV44
Pool IDPool-241015
Local_Set_Nameset75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1DEK-BGKcLV44-13
Rep2DEK-BGKcLV44-14
CN1NT-BGKcLV44-1
CN2NT-BGKcLV44-2
Rep1_qPCR58.9
Rep2_qPCR59.4
Rep1_WB72.0
Rep2_WB76.3
Antibody Cat#720215
Antibody Lot#SD249202
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1597




Experiment Information (Status: Sequenced)
BGKcLV44-13BGKcLV44-14
idx00
TRCN#_or_BGC#BGC#0000310BGC#0000310
shRNA_or_gRNA_sequenceGTTCTTTCTCGGACGCGGGCGTTCTTTCTCGGACGCGGGC
PAMtggtgg
NameDEK_97DEK_97
Sample_IDBGKcLV44-13BGKcLV44-14
transduction_Date7/30/247/30/24
daysD6D6
RBP_nameDEKDEK
qPCR_result58.959.4
Ave_qPCR59.2
RT-qPCR_primer-Fggtcagttcagtggctttcc
RT-qPCR_primer-Rtctccaaatcaagaacctcaca
protein_conc50484442
WB_result72.076.3
Ave_WB74.2
WB_DONE_date8/7/24,8/13/24
MW43kd
IP
antibody_Cat#720215SD249202
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID58885889




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
DEKProduct_ID: 720215
Lot_ID: SD249202
Source: Thermo Fisher
Target Name: DEK-human		 DEK-HEPG2-CRISPR-720215.png<br>Caption: Western blot following CRISPR against DEK in HepG2 whole cell lysate using DEK specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against DEK. DEK protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 ThermoFisher_720215_SD249202_DEK.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the DEK specific antibody, 720215. Lanes 1 and 3 are 2.5% of five million whole cell lysate input. Lanes 2 and 4 are 50% of IP enrichment from five million whole cell lysate using normal IgG antibody and the DEK-specific antibody, 720215. 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.
 DEK-K562-CRISPR-720215.png<br>Caption: Western blot following CRISPR against DEK in K562 whole cell lysate using DEK specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against DEK. DEK protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGKcLV44-13BGKcLV44-14
Sample_IDBGKcLV44-13BGKcLV44-14
Sample Name
Sample NameDEK-BGKcLV44-13DEK-BGKcLV44-14
RBPDEKDEK
Cell_LineK562K562
Exp UID
StatusSequencedSequenced
Status_date2024-11-062024-11-06
ProjectENCORE2ENCORE2
Note
ID1358613587




Library-Prep Information
BGKcLV44-13BGKcLV44-14
Sample #1516
Sample NameDEK-BGKcLV44-13DEK-BGKcLV44-14
Sample_Name_Alias
Index Well PositionG07H07
Index_tableIDT_UniqueDualIndex_96_V2IDT_UniqueDualIndex_96_V2
LibPrep_date2024-10-102024-10-10
Lib_IDLib-241010Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp285299
Peak_Molarity55.6057.80
libSampleQC_DNA_WellDNA_Library_set75/set1/G7.pngDNA_Library_set75/set1/H7.png
RIN10.010.0
libSample_RNA_WellRNA_Library_set75/set1/G1.pngRNA_Library_set75/set1/H1.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-10-152024-10-15
Sample_IDBGKcLV44-13BGKcLV44-14
RBPDEKDEK
Batch_IDBGKcLV44BGKcLV44
WB_result72.00076.300
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID45744575




Sequencing Information
BGKcLV44-13BGKcLV44-14
Sample_IDBGKcLV44-13BGKcLV44-14
Sample NameDEK-BGKcLV44-13DEK-BGKcLV44-14
Pool IDPool-241015Pool-241015
LocalServer_folderset75set75
total_reads50,167,96960,636,311
total_aligned_reads47,078,65457,996,396
unique_aligned_reads43,488,18953,520,041
percent_uniqueAligned0.866850.88264
correlation_replicates0.9946050.994605
spikein_reads72,266134,456
percent_spikeins0.001440.00222
original_ReadLength101101
QC_StatusReadyToSubmitReadyToSubmit
ID32853286




Data Submission Information
DCC submission information was not avaliable




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