Notice: Undefined offset: 1 in /website/encore_alpha/gene/index.php on line 599
DDX41 RNA-Seq in K562



DDX41      CRISPR in K562      Control:

General Information
RBPDDX41
Cell_LineK562
MethodCRISPR
Exp_NameDDX41-BGKcLV42-K562
ENCODE_series_ID
Batch_IDBGKcLV42
Pool IDPool-240715
Local_Set_Nameset73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1DDX41-BGKcLV42-21
Rep2DDX41-BGKcLV42-22
CN1NT-BGKcLV42-1
CN2NT-BGKcLV42-2
Rep1_qPCR79.5
Rep2_qPCR71.4
Rep1_WB88.2
Rep2_WB88.0
Antibody Cat#15076S
Antibody Lot#lot # 1
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1534




Experiment Information (Status: Sequenced)
BGKcLV42-21BGKcLV42-21BGKcLV42-22BGKcLV42-22
idx0000
TRCN#_or_BGC#BGC#0001124BGC#0001124BGC#0001124BGC#0001124
shRNA_or_gRNA_sequenceGACATGCTCAGAACATAACGGACATGCTCAGAACATAACGGACATGCTCAGAACATAACGGACATGCTCAGAACATAACG
PAMGGGGGGGGGGGG
NameDDX41_90DDX41_90DDX41_90DDX41_90
Sample_IDBGKcLV42-21BGKcLV42-21BGKcLV42-22BGKcLV42-22
transduction_Date4/23/244/23/244/23/244/23/24
daysD6D6D6D6
RBP_nameDDX41DDX41DDX41DDX41
qPCR_result79.579.571.471.4
Ave_qPCR75.475.475.4
RT-qPCR_primer-Faggagatggctaagggcattaggagatggctaagggcatt
RT-qPCR_primer-Rcagaacataacggggtggagcagaacataacggggtggag
protein_conc1836183610701070
WB_result88.250.288.058.0838
Ave_WB88.154.1
WB_DONE_date5/6/246/24/24,6/28/24
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
ID5779578157805782




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
BGKcLV42-21BGKcLV42-22
Sample_IDBGKcLV42-21BGKcLV42-22
Sample Name
Sample NameDDX41-BGKcLV42-21DDX41-BGKcLV42-22
RBPDDX41DDX41
Cell_LineK562K562
Exp UID
StatusSequencedSequenced
Status_date2024-10-272024-10-27
ProjectENCORE2ENCORE2
Note
ID1306213063




Library-Prep Information
BGKcLV42-21BGKcLV42-22
Sample #1920
Sample NameDDX41-BGKcLV42-21DDX41-BGKcLV42-22
Sample_Name_Alias
Index Well PositionC03D03
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2024-06-212024-06-21
Lib_IDLib-240621Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp287289
Peak_Molarity113.0082.00
libSampleQC_DNA_WellDNA_Library_set73/set1/C3.pngDNA_Library_set73/set1/D3.png
RIN10.010.0
libSample_RNA_WellRNA_Library_set73/set1/C3.pngRNA_Library_set73/set1/D3.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-07-152024-07-15
Sample_IDBGKcLV42-21BGKcLV42-22
RBPDDX41DDX41
Batch_IDBGKcLV42BGKcLV42
WB_result88.20088.000
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID42884289




Sequencing Information
BGKcLV42-21BGKcLV42-22
Sample_IDBGKcLV42-21BGKcLV42-22
Sample NameDDX41-BGKcLV42-21DDX41-BGKcLV42-22
Pool IDPool-240715Pool-240715
LocalServer_folderset73set73
total_reads38,418,89530,505,219
total_aligned_reads32,117,20626,153,579
unique_aligned_reads29,672,11724,314,631
percent_uniqueAligned0.772330.79706
correlation_replicates0.9964250.996425
spikein_reads4,4201,544
percent_spikeins0.000120.00005
original_ReadLength101101
QC_StatusReadyToSubmitReadyToSubmit
ID31553156




Data Submission Information
DCC submission information was not avaliable




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