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YTHDF2 RNA-Seq in K562



YTHDF2      CRISPR in K562      Control:

General Information
RBPYTHDF2
Cell_LineK562
MethodCRISPR
Exp_NameYTHDF2-BGKcLV42-K562
ENCODE_series_ID
Batch_IDBGKcLV42
Pool IDPool-240715
Local_Set_Nameset73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1YTHDF2-BGKcLV42-107
Rep2YTHDF2-BGKcLV42-108
CN1NT-BGKcLV42-1
CN2NT-BGKcLV42-2
Rep1_qPCR63.1
Rep2_qPCR72.7
Rep1_WB58.2
Rep2_WB69.2
Antibody Cat#71283S
Antibody Lot#lot # 1
Antibody DCC ID
StatusSubmitted
ProjectENCORE2
ID1569




Experiment Information (Status: Sequenced)
BGKcLV42-107BGKcLV42-108
idx00
TRCN#_or_BGC#BGC#0001213BGC#0001213
shRNA_or_gRNA_sequenceTGTAGGAACGTCAAGGTCGTTGTAGGAACGTCAAGGTCGT
PAMGGGGGG
NameYTHDF2_94YTHDF2_94
Sample_IDBGKcLV42-107BGKcLV42-108
transduction_Date4/23/244/23/24
daysD6D6
RBP_nameYTHDF2YTHDF2
qPCR_result63.172.7
Ave_qPCR67.9
RT-qPCR_primer-Fgagaaacgccaagaggaaga
RT-qPCR_primer-Rctgccttttatttcccacga
protein_conc33183032
WB_result58.269.2
Ave_WB63.7
WB_DONE_date5/14/24
MW65kd
IP
antibody_Cat#71283Slot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date
repeat_library
Note
ID58735874




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
YTHDF2Product_ID: 71283S
Lot_ID: 1
Source: Cell Signaling Technology
Target Name: YTHDF2-human		 YTHDF2-HEPG2-CRISPR-71283S.png<br>Caption: Western blot following CRISPR against YTHDF2 in HepG2 whole cell lysate using YTHDF2 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against YTHDF2. YTHDF2 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 CST_71283S_1_YTHDF2.png<br>Caption: IP-WB analysis of 71283S whole cell lysate using the YTHDF2 specific antibody, 71283S. 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 YTHDF2-specific antibody, 71283S. 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.
 YTHDF2-K562-CRISPR-71283S.png<br>Caption: Western blot following CRISPR against YTHDF2 in K562 whole cell lysate using YTHDF2 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against YTHDF2. YTHDF2 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGKcLV42-107BGKcLV42-108
Sample_IDBGKcLV42-107BGKcLV42-108
Sample Name
Sample NameYTHDF2-BGKcLV42-107YTHDF2-BGKcLV42-108
RBPYTHDF2YTHDF2
Cell_LineK562K562
Exp UID
StatusSequencedSequenced
Status_date2024-10-272024-10-27
ProjectENCORE2ENCORE2
Note
ID1313213133




Library-Prep Information
BGKcLV42-107BGKcLV42-108
Sample #8990
Sample NameYTHDF2-BGKcLV42-107YTHDF2-BGKcLV42-108
Sample_Name_Alias
Index Well PositionA12B12
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2024-06-212024-06-21
Lib_IDLib-240621Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp296276
Peak_Molarity92.5071.70
libSampleQC_DNA_WellDNA_Library_set73/set1/A12.pngDNA_Library_set73/set1/B12.png
RIN9.89.3
libSample_RNA_WellRNA_Library_set73/set1/A12.pngRNA_Library_set73/set1/B12.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2024-07-152024-07-15
Sample_IDBGKcLV42-107BGKcLV42-108
RBPYTHDF2YTHDF2
Batch_IDBGKcLV42BGKcLV42
WB_result58.20069.200
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCORE2ENCORE2
ID43584359




Sequencing Information
BGKcLV42-107BGKcLV42-108
Sample_IDBGKcLV42-107BGKcLV42-108
Sample NameYTHDF2-BGKcLV42-107YTHDF2-BGKcLV42-108
Pool IDPool-240715Pool-240715
LocalServer_folderset73set73
total_reads37,204,17122,375,434
total_aligned_reads30,892,94316,982,361
unique_aligned_reads28,504,55115,562,509
percent_uniqueAligned0.766170.69552
correlation_replicates0.9909320.990932
spikein_reads1,010624
percent_spikeins0.000030.00003
original_ReadLength101101
QC_StatusReadyToSubmitReadyToSubmit
ID32253226




Data Submission Information
DCC submission information was not avaliable




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