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KARS RNA-Seq in HepG2



KARS      CRISPR in HepG2      Control:

General Information
RBPKARS
Cell_LineHepG2
MethodCRISPR
Exp_NameKARS-BGHcLV43-HepG2
ENCODE_series_ID
Batch_IDBGHcLV43
Pool IDPool-240723
Local_Set_Nameset74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1KARS-BGHcLV43-25
Rep2KARS-BGHcLV43-26
CN1NT-BGHcLV43-1
CN2NT-BGHcLV43-2
Rep1_qPCR83.4
Rep2_qPCR83.8
Rep1_WB77.9
Rep2_WB87.0
Antibody Cat#9990S
Antibody Lot#lot # 1
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1578




Experiment Information (Status: Sequenced)
BGHcLV43-25BGHcLV43-26
idx13931394
TRCN#_or_BGC#BGC#0001150BGC#0001150
shRNA_or_gRNA_sequenceGACGCCAGTTCCGGAATGAGGACGCCAGTTCCGGAATGAG
PAMGGGGGG
NameKARS_91KARS_91
Sample_IDBGHcLV43-25BGHcLV43-26
transduction_Date6/6/246/6/24
daysD6D6
RBP_nameKARSKARS
qPCR_result83.483.8
Ave_qPCR83.6
RT-qPCR_primer-Ftgtggcaaaagctgttgaat
RT-qPCR_primer-Rgccaaagggctcattatctg
protein_conc38072975
WB_result77.987.0
Ave_WB82.4
WB_DONE_date6/13/24
MW75kd
IP
antibody_Cat#9990Slot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID75987599




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
KARSProduct_ID: 9990S
Lot_ID: 1
Source: Cell Signaling Technology
Target Name: KARS-human		 KARS-HEPG2-CRISPR-9990S.png<br>Caption: Western blot following CRISPR against KARS in HepG2 whole cell lysate using KARS specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against KARS. KARS protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 CST_9990S_1_KARS.png<br>Caption: IP-WB analysis of 9990S whole cell lysate using the KARS specific antibody, 9990S. 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 KARS-specific antibody, 9990S. 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.
 KARS-K562-CRISPR-9990S.png<br>Caption: Western blot following CRISPR against KARS in K562 whole cell lysate using KARS specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against KARS. KARS protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGHcLV43-25BGHcLV43-26
Sample_IDBGHcLV43-25BGHcLV43-26
Sample Name
Sample NameKARS-BGHcLV43-25KARS-BGHcLV43-26
RBPKARSKARS
Cell_LineHepG2HepG2
Exp UID
StatusSequencedSequenced
Status_date2024-10-272024-10-27
ProjectENCORE2ENCORE2
Note
ID1324613247




Library-Prep Information
BGHcLV43-25BGHcLV43-26
Sample #1920
Sample NameKARS-BGHcLV43-25KARS-BGHcLV43-26
Sample_Name_Alias
Index Well PositionC08D08
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2024-07-222024-07-22
Lib_IDLib-240722Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp292298
Peak_Molarity97.0093.40
libSampleQC_DNA_WellDNA_Library_set74/set1/C3.pngDNA_Library_set74/set1/D3.png
RIN10.010.0
libSample_RNA_WellRNA_Library_set74/set1/G8.pngRNA_Library_set74/set1/H8.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-07-232024-07-23
Sample_IDBGHcLV43-25BGHcLV43-26
RBPKARSKARS
Batch_IDBGHcLV43BGHcLV43
WB_result77.90087.000
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID43784379




Sequencing Information
BGHcLV43-25BGHcLV43-26
Sample_IDBGHcLV43-25BGHcLV43-26
Sample NameKARS-BGHcLV43-25KARS-BGHcLV43-26
Pool IDPool-240723Pool-240723
LocalServer_folderset74set74
total_reads38,161,62641,073,207
total_aligned_reads33,339,97137,473,577
unique_aligned_reads31,352,81335,298,308
percent_uniqueAligned0.821580.85940
correlation_replicates0.9985160.998516
spikein_reads29,20622,008
percent_spikeins0.000770.00054
original_ReadLength101101
QC_StatusReadyToSubmitReadyToSubmit
ID32453246




Data Submission Information
DCC submission information was not avaliable




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