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PSMD4 RNA-Seq in HepG2



PSMD4      CRISPR in HepG2      Control:

General Information
RBPPSMD4
Cell_LineHepG2
MethodCRISPR
Exp_NamePSMD4-BGHcLV43-HepG2
ENCODE_series_ID
Batch_IDBGHcLV43
Pool IDPool-240723
Local_Set_Nameset74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1PSMD4-BGHcLV43-45
Rep2PSMD4-BGHcLV43-46
CN1NT-BGHcLV43-1
CN2NT-BGHcLV43-2
Rep1_qPCR73.0
Rep2_qPCR65.6
Rep1_WB69.6
Rep2_WB78.2
Antibody Cat#12441S
Antibody Lot#lot # 1
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1586




Experiment Information (Status: Sequenced)
BGHcLV43-45BGHcLV43-45BGHcLV43-46BGHcLV43-46
idx1413014140
TRCN#_or_BGC#BGC#0001177BGC#0001177BGC#0001177BGC#0001177
shRNA_or_gRNA_sequenceCTTCTGCACGGGCATCCGCGCTTCTGCACGGGCATCCGCGCTTCTGCACGGGCATCCGCGCTTCTGCACGGGCATCCGCG
PAMTGGTGGTGGTGG
NamePSMD4_88PSMD4_88PSMD4_88PSMD4_88
Sample_IDBGHcLV43-45BGHcLV43-45BGHcLV43-46BGHcLV43-46
transduction_Date6/6/246/6/246/6/246/6/24
daysD6D6D6D6
RBP_namePSMD4PSMD4PSMD4PSMD4
qPCR_result73.073.065.665.6
Ave_qPCR69.369.3
RT-qPCR_primer-Fatcattgcctttgtgggaagatcattgcctttgtgggaag
RT-qPCR_primer-Rtcttgaggcgtttagccagttcttgaggcgtttagccagt
protein_conc3350335037123712
WB_result69.673.078.271.8
Ave_WB73.972.4
WB_DONE_date6/17/246/25/24
MW50kd50kd
IP
antibody_Cat#12441S3336Slot # 1lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM0000
Rep2_TPM0000
ActionReadyReady
Library_start_date
repeat_library
Note
ID7618762076197621




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
PSMD4Product_ID: 12331S
Lot_ID: 1
Source: Cell Signaling
Target Name: PSMD4-human		 PSMD4-HEPG2-CRISPR-12331S.png<br>Caption: Western blot following CRISPR against PSMD4 in HepG2 whole cell lysate using PSMD4 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against PSMD4. PSMD4 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
PSMD4Product_ID: 3336S
Lot_ID: 1
Source: Cell Signaling Technology
Target Name: PSMD4-human		 PSMD4-HEPG2-CRISPR-3336S.png<br>Caption: Western blot following CRISPR against PSMD4 in HepG2 whole cell lysate using PSMD4 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against PSMD4. PSMD4 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 CST_3336S_1_PSMD4.png<br>Caption: IP-WB analysis of 3336S whole cell lysate using the PSMD4 specific antibody, 3336S. 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 PSMD4-specific antibody, 3336S. 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.




Experiment Status
BGHcLV43-45BGHcLV43-45BGHcLV43-46BGHcLV43-46
Sample_IDBGHcLV43-45BGHcLV43-45BGHcLV43-46BGHcLV43-46
Sample Name
Sample NamePSMD4-BGHcLV43-45PSMD4-BGHcLV43-46
RBPPSMD4PSMD4PSMD4PSMD4
Cell_LineHepG2HepG2HepG2HepG2
Exp UID
StatusSequencedNotSatisfiedSequencedNotSatisfied
Status_date2024-10-272024-07-162024-10-272024-07-16
ProjectENCORE2ENCORE2ENCORE2ENCORE2
Note
ID13262132941326313295




Library-Prep Information
BGHcLV43-45BGHcLV43-46
Sample #3536
Sample NamePSMD4-BGHcLV43-45PSMD4-BGHcLV43-46
Sample_Name_Alias
Index Well PositionC10D10
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2024-07-222024-07-22
Lib_IDLib-240722Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp302300
Peak_Molarity97.1092.00
libSampleQC_DNA_WellDNA_Library_set74/set1/C5.pngDNA_Library_set74/set1/D5.png
RIN10.010.0
libSample_RNA_WellRNA_Library_set74/set1/G10.pngRNA_Library_set74/set1/H10.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-07-232024-07-23
Sample_IDBGHcLV43-45BGHcLV43-46
RBPPSMD4PSMD4
Batch_IDBGHcLV43BGHcLV43
WB_result69.60078.200
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID43944395




Sequencing Information
BGHcLV43-45BGHcLV43-46
Sample_IDBGHcLV43-45BGHcLV43-46
Sample NamePSMD4-BGHcLV43-45PSMD4-BGHcLV43-46
Pool IDPool-240723Pool-240723
LocalServer_folderset74set74
total_reads51,571,24147,825,434
total_aligned_reads47,401,50844,758,035
unique_aligned_reads44,614,11942,214,373
percent_uniqueAligned0.865100.88268
correlation_replicates0.9978980.997898
spikein_reads46,29031,298
percent_spikeins0.000900.00065
original_ReadLength101101
QC_StatusReadyToSubmitReadyToSubmit
ID32613262




Data Submission Information
DCC submission information was not avaliable




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