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DDX41 RNA-Seq in HepG2



DDX41      CRISPR in HepG2      Control:

General Information
RBPDDX41
Cell_LineHepG2
MethodCRISPR
Exp_NameDDX41-BGHcLV43-HepG2
ENCODE_series_ID
Batch_IDBGHcLV43
Pool IDPool-240723
Local_Set_Nameset74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1DDX41-BGHcLV43-13
Rep2DDX41-BGHcLV43-14
CN1NT-BGHcLV43-1
CN2NT-BGHcLV43-2
Rep1_qPCR78.1
Rep2_qPCR75.7
Rep1_WB85.0
Rep2_WB84.2
Antibody Cat#15076S
Antibody Lot#lot # 1
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1573




Experiment Information (Status: Sequenced)
BGHcLV43-13BGHcLV43-13BGHcLV43-14BGHcLV43-14
idx1381138113821382
TRCN#_or_BGC#BGC#0001126BGC#0001126BGC#0001126BGC#0001126
shRNA_or_gRNA_sequenceGACATGCTCAGAACATAACGGACATGCTCAGAACATAACGGACATGCTCAGAACATAACGGACATGCTCAGAACATAACG
PAMGGGGGGGGGGGG
NameDDX41_90DDX41_90DDX41_90DDX41_90
Sample_IDBGHcLV43-13BGHcLV43-13BGHcLV43-14BGHcLV43-14
transduction_Date6/6/246/6/246/6/246/6/24
daysD6D6D6D6
RBP_nameDDX41DDX41DDX41DDX41
qPCR_result78.178.175.775.7
Ave_qPCR76.976.9
RT-qPCR_primer-FTGCTGCAGGTGCTGCATTTGCTGCAGGTGCTGCATT
RT-qPCR_primer-RAGTCAGTGATCCGATGACCCAGTCAGTGATCCGATGACCC
protein_conc3099309929072907
WB_result85.067.784.272.6535
Ave_WB84.670.2
WB_DONE_date6/13/246/28/24
MW75KD75KD
IP
antibody_Cat#15076SA301-050Alot # 1lot # 2
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM0000
Rep2_TPM0000
ActionReadyReady
Library_start_date
repeat_library
Note
ID7584758675857587




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
DDX41Product_ID: 15076S
Lot_ID: 1
Source: Cell Signaling Technology
Target Name: DDX41-human		 DDX41-HEPG2-CRISPR-15076S.png<br>Caption: Western blot following CRISPR against DDX41 in HepG2 whole cell lysate using DDX41 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against DDX41. DDX41 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 CST_15076S_1_DDX41.png<br>Caption: IP-WB analysis of 15076S whole cell lysate using the DDX41 specific antibody, 15076S. 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 DDX41-specific antibody, 15076S. 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.
 DDX41-K562-CRISPR-15076S.png<br>Caption: Western blot following CRISPR against DDX41 in K562 whole cell lysate using DDX41 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against DDX41. DDX41 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
DDX41Product_ID: A301-050A
Lot_ID: 2
Source: Bethyl Labs
Target Name: DDX41-human		 DDX41-HEPG2-CRISPR-A301-050A.png<br>Caption: Western blot following CRISPR against DDX41 in HepG2 whole cell lysate using DDX41 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against DDX41. DDX41 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 DDX41-K562-CRISPR-A301-050A.png<br>Caption: Western blot following CRISPR against DDX41 in K562 whole cell lysate using DDX41 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against DDX41. DDX41 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGHcLV43-13BGHcLV43-13BGHcLV43-14BGHcLV43-14
Sample_IDBGHcLV43-13BGHcLV43-13BGHcLV43-14BGHcLV43-14
Sample Name
Sample NameDDX41-BGHcLV43-13DDX41-BGHcLV43-14
RBPDDX41DDX41DDX41DDX41
Cell_LineHepG2HepG2HepG2HepG2
Exp UID
StatusSequencedNotSatisfiedSequencedNotSatisfied
Status_date2024-10-272024-07-162024-10-272024-07-16
ProjectENCORE2ENCORE2ENCORE2ENCORE2
Note
ID13236132861323713287




Library-Prep Information
BGHcLV43-13BGHcLV43-14
Sample #910
Sample NameDDX41-BGHcLV43-13DDX41-BGHcLV43-14
Sample_Name_Alias
Index Well PositionA07B07
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2024-07-222024-07-22
Lib_IDLib-240722Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp321313
Peak_Molarity122.0094.40
libSampleQC_DNA_WellDNA_Library_set74/set1/A2.pngDNA_Library_set74/set1/B2.png
RIN10.010.0
libSample_RNA_WellRNA_Library_set74/set1/E7.pngRNA_Library_set74/set1/F7.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-07-232024-07-23
Sample_IDBGHcLV43-13BGHcLV43-14
RBPDDX41DDX41
Batch_IDBGHcLV43BGHcLV43
WB_result85.00084.200
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID43684369




Sequencing Information
BGHcLV43-13BGHcLV43-14
Sample_IDBGHcLV43-13BGHcLV43-14
Sample NameDDX41-BGHcLV43-13DDX41-BGHcLV43-14
Pool IDPool-240723Pool-240723
LocalServer_folderset74set74
total_reads58,992,01248,455,481
total_aligned_reads56,138,48645,266,235
unique_aligned_reads52,865,18842,595,609
percent_uniqueAligned0.896140.87907
correlation_replicates0.9912380.991238
spikein_reads26,64415,566
percent_spikeins0.000450.00032
original_ReadLength101101
QC_StatusReadyToSubmitReadyToSubmit
ID32353236




Data Submission Information
DCC submission information was not avaliable




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