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ALYREF RNA-Seq in K562



ALYREF      CRISPR in K562      Control:

General Information
RBPALYREF
Cell_LineK562
MethodCRISPR
Exp_NameALYREF-BGKcLV44-K562
ENCODE_series_ID
Batch_IDBGKcLV44
Pool IDPool-241015
Local_Set_Nameset75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1ALYREF-BGKcLV44-3
Rep2ALYREF-BGKcLV44-4
CN1NT-BGKcLV44-1
CN2NT-BGKcLV44-2
Rep1_qPCR61.3
Rep2_qPCR61.2
Rep1_WB61.9
Rep2_WB70.0
Antibody Cat#12655S
Antibody Lot#lot # 1
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1595




Experiment Information (Status: Sequenced)
BGKcLV44-3BGKcLV44-4
idx00
TRCN#_or_BGC#BGC#0001108BGC#0001108
shRNA_or_gRNA_sequenceGCCGCGCGAGTGAATCGAGGGCCGCGCGAGTGAATCGAGG
PAMCGGCGG
NameALYREF_97ALYREF_97
Sample_IDBGKcLV44-3BGKcLV44-4
transduction_Date7/30/247/30/24
daysD6D6
RBP_nameALYREFALYREF
qPCR_result61.361.2
Ave_qPCR61.2
RT-qPCR_primer-FCTGAAGGCCATGAAGCAGTA
RT-qPCR_primer-RTCTGTGACGTGACAAGCTGA
protein_conc49815850
WB_result61.970.0
Ave_WB66.0
WB_DONE_date8/13/24
MW27KD
IP
antibody_Cat#12655Slot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID58785879




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
ALYREFProduct_ID: 12655S
Lot_ID: 1
Source: Cell Signaling Technology
Target Name: ALYREF-human		 ALYREF-HEPG2-CRISPR-12655S.png<br>Caption: Western blot following CRISPR against ALYREF in HepG2 whole cell lysate using ALYREF specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against ALYREF. ALYREF protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 CST_12655S_1_ALYREF.png<br>Caption: IP-WB analysis of 12655S whole cell lysate using the ALYREF specific antibody, 12655S. 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 ALYREF-specific antibody, 12655S. 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.
 ALYREF-K562-CRISPR-12655S.png<br>Caption: Western blot following CRISPR against ALYREF in K562 whole cell lysate using ALYREF specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against ALYREF. ALYREF protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGKcLV44-3BGKcLV44-4
Sample_IDBGKcLV44-3BGKcLV44-4
Sample Name
Sample NameALYREF-BGKcLV44-3ALYREF-BGKcLV44-4
RBPALYREFALYREF
Cell_LineK562K562
Exp UID
StatusSequencedSequenced
Status_date2024-11-062024-11-06
ProjectENCORE2ENCORE2
Note
ID1358213583




Library-Prep Information
BGKcLV44-3BGKcLV44-4
Sample #1112
Sample NameALYREF-BGKcLV44-3ALYREF-BGKcLV44-4
Sample_Name_Alias
Index Well PositionC07D07
Index_tableIDT_UniqueDualIndex_96_V2IDT_UniqueDualIndex_96_V2
LibPrep_date2024-10-102024-10-10
Lib_IDLib-241010Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp297291
Peak_Molarity96.9081.70
libSampleQC_DNA_WellDNA_Library_set75/set1/C7.pngDNA_Library_set75/set1/D7.png
RIN10.010.0
libSample_RNA_WellRNA_Library_set75/set1/C1.pngRNA_Library_set75/set1/D1.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-10-152024-10-15
Sample_IDBGKcLV44-3BGKcLV44-4
RBPALYREFALYREF
Batch_IDBGKcLV44BGKcLV44
WB_result61.90070.000
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID45704571




Sequencing Information
BGKcLV44-3BGKcLV44-4
Sample_IDBGKcLV44-3BGKcLV44-4
Sample NameALYREF-BGKcLV44-3ALYREF-BGKcLV44-4
Pool IDPool-241015Pool-241015
LocalServer_folderset75set75
total_reads66,148,71653,764,910
total_aligned_reads62,662,18550,836,462
unique_aligned_reads57,701,60446,763,766
percent_uniqueAligned0.872300.86978
correlation_replicates0.9942220.994222
spikein_reads135,55899,790
percent_spikeins0.002050.00186
original_ReadLength101101
QC_StatusReadyToSubmitReadyToSubmit
ID32813282




Data Submission Information
DCC submission information was not avaliable




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