YTHDF2 RNA-Seq in K562

General Information


RBP	YTHDF2
Cell_Line	K562
Method	CRISPR
Exp_Name	YTHDF2-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	YTHDF2-BGKcLV42-107
Rep2	YTHDF2-BGKcLV42-108
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	63.1
Rep2_qPCR	72.7
Rep1_WB	58.2
Rep2_WB	69.2
Antibody Cat#	71283S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1569

Experiment Information (Status: Submitting)

	BGKcLV42-107	BGKcLV42-108
idx	0	0
TRCN#_or_BGC#	BGC#0001213	BGC#0001213
shRNA_or_gRNA_sequence	TGTAGGAACGTCAAGGTCGT	TGTAGGAACGTCAAGGTCGT
PAM	GGG	GGG
Name	YTHDF2_94	YTHDF2_94
Sample_ID	BGKcLV42-107	BGKcLV42-108
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	YTHDF2	YTHDF2
qPCR_result	63.1	72.7
Ave_qPCR	67.9
RT-qPCR_primer-F	gagaaacgccaagaggaaga
RT-qPCR_primer-R	ctgccttttatttcccacga
protein_conc	3318	3032
WB_result	58.2	69.2
Ave_WB	63.7
WB_DONE_date	5/14/24
MW	65kd
IP
antibody_Cat#	71283S	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5875	5876

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
YTHDF2	Product_ID: 71283S Lot_ID: 1 Source: Cell Signaling Technology Target Name: YTHDF2-human

Experiment Status

	BGKcLV42-107	BGKcLV42-108
Sample_ID	BGKcLV42-107	BGKcLV42-108
Sample Name
Sample Name	YTHDF2-BGKcLV42-107	YTHDF2-BGKcLV42-108
RBP	YTHDF2	YTHDF2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13132	13133

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-107	BGKcLV42-108
Sample #	89	90
Sample Name	YTHDF2-BGKcLV42-107	YTHDF2-BGKcLV42-108
Sample_Name_Alias
Index Well Position	A12	B12
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	296	276
Peak_Molarity	92.50	71.70
libSampleQC_DNA_Well	DNA_Library_set73/set1/A12.png	DNA_Library_set73/set1/B12.png
RIN	9.8	9.3
libSample_RNA_Well	RNA_Library_set73/set1/A12.png	RNA_Library_set73/set1/B12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-107	BGKcLV42-108
RBP	YTHDF2	YTHDF2
Batch_ID	BGKcLV42	BGKcLV42
WB_result	58.200	69.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4358	4359

Sequencing Information

	BGKcLV42-107	BGKcLV42-108
Sample_ID	BGKcLV42-107	BGKcLV42-108
Sample Name	YTHDF2-BGKcLV42-107	YTHDF2-BGKcLV42-108
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	37,204,171	22,375,434
total_aligned_reads	30,892,943	16,982,361
unique_aligned_reads	28,504,551	15,562,509
percent_uniqueAligned	0.76617	0.69552
correlation_replicates	0.990932	0.990932
spikein_reads	1,010	624
percent_spikeins	0.00003	0.00003
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3225	3226

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
YTHDF2-BGKcLV42-107_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3225	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30428
YTHDF2-BGKcLV42-107_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3225	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30518
YTHDF2-BGKcLV42-107_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3225					GRCh38	V40	YTHDF2-BGKcLV42-107_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF2-BGKcLV42-107_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31360
YTHDF2-BGKcLV42-107_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3225					GRCh38	V40	YTHDF2-BGKcLV42-107_Aligned.sortedByCoord.out.bam		ENCORE2	31450
YTHDF2-BGKcLV42-107_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3225					GRCh38	V40	YTHDF2-BGKcLV42-107_Aligned.sortedByCoord.out.bam		ENCORE2	31540
YTHDF2-BGKcLV42-107_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3225					GRCh38	V40	YTHDF2-BGKcLV42-107_Aligned.sortedByCoord.out.bam		ENCORE2	31630
YTHDF2-BGKcLV42-107_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3225					GRCh38	V40	YTHDF2-BGKcLV42-107_Aligned.sortedByCoord.out.bam		ENCORE2	31720
YTHDF2-BGKcLV42-107_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3225					GRCh38	V40	YTHDF2-BGKcLV42-107_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF2-BGKcLV42-107_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31810
YTHDF2-BGKcLV42-108_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3226	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30429
YTHDF2-BGKcLV42-108_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3226	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30519
YTHDF2-BGKcLV42-108_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3226					GRCh38	V40	YTHDF2-BGKcLV42-108_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF2-BGKcLV42-108_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31361
YTHDF2-BGKcLV42-108_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3226					GRCh38	V40	YTHDF2-BGKcLV42-108_Aligned.sortedByCoord.out.bam		ENCORE2	31451
YTHDF2-BGKcLV42-108_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3226					GRCh38	V40	YTHDF2-BGKcLV42-108_Aligned.sortedByCoord.out.bam		ENCORE2	31541
YTHDF2-BGKcLV42-108_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3226					GRCh38	V40	YTHDF2-BGKcLV42-108_Aligned.sortedByCoord.out.bam		ENCORE2	31631
YTHDF2-BGKcLV42-108_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3226					GRCh38	V40	YTHDF2-BGKcLV42-108_Aligned.sortedByCoord.out.bam		ENCORE2	31721
YTHDF2-BGKcLV42-108_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3226					GRCh38	V40	YTHDF2-BGKcLV42-108_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF2-BGKcLV42-108_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31811