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USP39 RNA-Seq in K562



USP39      CRISPR in K562      Control:

General Information
RBPUSP39
Cell_LineK562
MethodCRISPR
Exp_NameUSP39-BGKcLV42-K562
ENCODE_series_ID
Batch_IDBGKcLV42
Pool IDPool-240715
Local_Set_Nameset73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1USP39-BGKcLV42-101
Rep2USP39-BGKcLV42-102
CN1NT-BGKcLV42-1
CN2NT-BGKcLV42-2
Rep1_qPCR50.9
Rep2_qPCR53.0
Rep1_WB89.4
Rep2_WB88.5
Antibody Cat#23303S
Antibody Lot#lot # 1
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1566




Experiment Information (Status: Sequenced)
BGKcLV42-101BGKcLV42-102
idx00
TRCN#_or_BGC#BGC#0001202BGC#0001202
shRNA_or_gRNA_sequenceCACCGTGATATCCTCCAATGCACCGTGATATCCTCCAATG
PAMAGGAGG
NameUSP39_90USP39_90
Sample_IDBGKcLV42-101BGKcLV42-102
transduction_Date4/23/244/23/24
daysD6D6
RBP_nameUSP39USP39
qPCR_result50.953.0
Ave_qPCR51.9
RT-qPCR_primer-Fcaacctccacaccctcaagt
RT-qPCR_primer-Rgcaatttgctgctttgtgaa
protein_conc25022571
WB_result89.488.5
Ave_WB88.9
WB_DONE_date5/10/24
MW65kd
IP
antibody_Cat#23303Slot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID58675868




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
USP39Product_ID: 23303S
Lot_ID: 1
Source: Cell Signaling Technology
Target Name: USP39-human		 CST_23303S_1_USP39.png<br>Caption: IP-WB analysis of 23303S whole cell lysate using the USP39 specific antibody, 23303S. 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 USP39-specific antibody, 23303S. 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.
 USP39-K562-CRISPR-23303S.png<br>Caption: Western blot following CRISPR against USP39 in K562 whole cell lysate using USP39 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against USP39. USP39 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGKcLV42-101BGKcLV42-102
Sample_IDBGKcLV42-101BGKcLV42-102
Sample Name
Sample NameUSP39-BGKcLV42-101USP39-BGKcLV42-102
RBPUSP39USP39
Cell_LineK562K562
Exp UID
StatusSequencedSequenced
Status_date2024-10-272024-10-27
ProjectENCORE2ENCORE2
Note
ID1312613127




Library-Prep Information
BGKcLV42-101BGKcLV42-102
Sample #8384
Sample NameUSP39-BGKcLV42-101USP39-BGKcLV42-102
Sample_Name_Alias
Index Well PositionC11D11
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2024-06-212024-06-21
Lib_IDLib-240621Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp309309
Peak_Molarity107.00101.00
libSampleQC_DNA_WellDNA_Library_set73/set1/C11.pngDNA_Library_set73/set1/D11.png
RIN9.910.0
libSample_RNA_WellRNA_Library_set73/set1/C11.pngRNA_Library_set73/set1/D11.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-07-152024-07-15
Sample_IDBGKcLV42-101BGKcLV42-102
RBPUSP39USP39
Batch_IDBGKcLV42BGKcLV42
WB_result89.40088.500
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID43524353




Sequencing Information
BGKcLV42-101BGKcLV42-102
Sample_IDBGKcLV42-101BGKcLV42-102
Sample NameUSP39-BGKcLV42-101USP39-BGKcLV42-102
Pool IDPool-240715Pool-240715
LocalServer_folderset73set73
total_reads31,311,62050,717,531
total_aligned_reads28,301,42946,648,858
unique_aligned_reads26,107,88543,161,740
percent_uniqueAligned0.833810.85102
correlation_replicates0.9990170.999017
spikein_reads1,054254
percent_spikeins0.000030.00001
original_ReadLength101101
QC_StatusReadyToSubmitReadyToSubmit
ID32193220




Data Submission Information
DCC submission information was not avaliable




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