YTHDC1 RNA-Seq in K562

General Information


RBP	YTHDC1
Cell_Line	K562
Method	CRISPR
Exp_Name	YTHDC1-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	YTHDC1-BGKcLV46-111
Rep2	YTHDC1-BGKcLV46-112
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	70.1
Rep2_WB	90.4
Antibody Cat#	81504S
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1656

Experiment Information (Status: Submitting)

	BGKcLV46-111	BGKcLV46-111	BGKcLV46-112	BGKcLV46-112
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001078	BGC#0001078	BGC#0001078	BGC#0001078
shRNA_or_gRNA_sequence	CATGGCGGCTGACAGTCGGG	CATGGCGGCTGACAGTCGGG	CATGGCGGCTGACAGTCGGG	CATGGCGGCTGACAGTCGGG
PAM	AGG	AGG	AGG	AGG
Name	YTHDC1_89	YTHDC1_89	YTHDC1_89	YTHDC1_89
Sample_ID	BGKcLV46-111	BGKcLV46-111	BGKcLV46-112	BGKcLV46-112
transduction_Date	12/20/24	12/20/24	12/20/24	12/20/24
days	D6	D6	D6	D6
RBP_name	YTHDC1	YTHDC1	YTHDC1	YTHDC1
qPCR_result	0.0	0.0	0.0	0.0
Ave_qPCR	0.0	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3982	3982	4140	4140
WB_result	70.1	80.4	90.4	81.6
Ave_WB
WB_DONE_date	1/23/25	1/31/25
MW	85kd	85kd
IP
antibody_Cat#	81504S	77422S	lot# 1	lot# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	6111	6113	6112	6114

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
YTHDC1	Product_ID: 81504S Lot_ID: 1 Source: Cell Signaling Technology Target Name: YTHDC1-human
YTHDC1	Product_ID: 77422S Lot_ID: 1 Source: Cell Signaling Technology Target Name: YTHDC1-human

Experiment Status

	BGKcLV46-111	BGKcLV46-111	BGKcLV46-112	BGKcLV46-112
Sample_ID	BGKcLV46-111	BGKcLV46-111	BGKcLV46-112	BGKcLV46-112
Sample Name
Sample Name	YTHDC1-BGKcLV46-111		YTHDC1-BGKcLV46-112
RBP	YTHDC1	YTHDC1	YTHDC1	YTHDC1
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-04-21	2025-02-10	2025-04-21	2025-02-10
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14068	14142	14069	14143

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-111	BGKcLV46-112
Sample #	47	48
Sample Name	YTHDC1-BGKcLV46-111	YTHDC1-BGKcLV46-112
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	301	300
Peak_Molarity	69.80	70.50
libSampleQC_DNA_Well	DNA_Library_set77/set1/G12.png	DNA_Library_set77/set1/H12.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set77/set1/G6.png	RNA_Library_set77/set1/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-111	BGKcLV46-112
RBP	YTHDC1	YTHDC1
Batch_ID	BGKcLV46	BGKcLV46
WB_result	70.100	90.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4706	4707

Sequencing Information

	BGKcLV46-111	BGKcLV46-112
Sample_ID	BGKcLV46-111	BGKcLV46-112
Sample Name	YTHDC1-BGKcLV46-111	YTHDC1-BGKcLV46-112
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	73,057,458	56,069,645
total_aligned_reads	68,873,052	52,458,006
unique_aligned_reads	63,426,739	48,310,234
percent_uniqueAligned	0.86818	0.86161
correlation_replicates	0.999014	0.999014
spikein_reads	73,992	105,252
percent_spikeins	0.00101	0.00188
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3409	3410

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
YTHDC1-BGKcLV46-111_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3409	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32196
YTHDC1-BGKcLV46-111_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3409	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32246
YTHDC1-BGKcLV46-111_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3409					GRCh38	V40	YTHDC1-BGKcLV46-111_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDC1-BGKcLV46-111_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32296
YTHDC1-BGKcLV46-111_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3409					GRCh38	V40	YTHDC1-BGKcLV46-111_Aligned.sortedByCoord.out.bam		ENCORE2	32346
YTHDC1-BGKcLV46-111_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3409					GRCh38	V40	YTHDC1-BGKcLV46-111_Aligned.sortedByCoord.out.bam		ENCORE2	32396
YTHDC1-BGKcLV46-111_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3409					GRCh38	V40	YTHDC1-BGKcLV46-111_Aligned.sortedByCoord.out.bam		ENCORE2	32446
YTHDC1-BGKcLV46-111_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3409					GRCh38	V40	YTHDC1-BGKcLV46-111_Aligned.sortedByCoord.out.bam		ENCORE2	32496
YTHDC1-BGKcLV46-111_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3409					GRCh38	V40	YTHDC1-BGKcLV46-111_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDC1-BGKcLV46-111_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32546
YTHDC1-BGKcLV46-112_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3410	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32197
YTHDC1-BGKcLV46-112_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3410	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32247
YTHDC1-BGKcLV46-112_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3410					GRCh38	V40	YTHDC1-BGKcLV46-112_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDC1-BGKcLV46-112_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32297
YTHDC1-BGKcLV46-112_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3410					GRCh38	V40	YTHDC1-BGKcLV46-112_Aligned.sortedByCoord.out.bam		ENCORE2	32347
YTHDC1-BGKcLV46-112_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3410					GRCh38	V40	YTHDC1-BGKcLV46-112_Aligned.sortedByCoord.out.bam		ENCORE2	32397
YTHDC1-BGKcLV46-112_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3410					GRCh38	V40	YTHDC1-BGKcLV46-112_Aligned.sortedByCoord.out.bam		ENCORE2	32447
YTHDC1-BGKcLV46-112_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3410					GRCh38	V40	YTHDC1-BGKcLV46-112_Aligned.sortedByCoord.out.bam		ENCORE2	32497
YTHDC1-BGKcLV46-112_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3410					GRCh38	V40	YTHDC1-BGKcLV46-112_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDC1-BGKcLV46-112_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32547