SYMPK RNA-Seq in K562

General Information


RBP	SYMPK
Cell_Line	K562
Method	CRISPR
Exp_Name	SYMPK-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	SYMPK-BGKcLV46-99
Rep2	SYMPK-BGKcLV46-100
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	10.8
Rep2_qPCR	27.3
Rep1_WB	71.7
Rep2_WB	83.8904
Antibody Cat#	13071S
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1654

Experiment Information (Status: Submitting)

	BGKcLV46-99	BGKcLV46-100
idx	0	0
TRCN#_or_BGC#	BGC#0001193	BGC#0001193
shRNA_or_gRNA_sequence	TGTCATCGGCTTCATCGAGG	TGTCATCGGCTTCATCGAGG
PAM	AGG	AGG
Name	SYMPK_91B	SYMPK_91B
Sample_ID	BGKcLV46-99	BGKcLV46-100
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	SYMPK	SYMPK
qPCR_result	10.8	27.3
Ave_qPCR	19.1
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4822	3922
WB_result	71.7	83.8904
Ave_WB
WB_DONE_date	1/31/25,1/13/25
MW	141kd
IP
antibody_Cat#	13071S	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	6097	6098

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SYMPK	Product_ID: 13071S Lot_ID: 1 Source: Cell Signaling Technology Target Name: SYMPK-human

Experiment Status

	BGKcLV46-99	BGKcLV46-100
Sample_ID	BGKcLV46-99	BGKcLV46-100
Sample Name
Sample Name	SYMPK-BGKcLV46-99	SYMPK-BGKcLV46-100
RBP	SYMPK	SYMPK
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14064	14065

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-99	BGKcLV46-100
Sample #	43	44
Sample Name	SYMPK-BGKcLV46-99	SYMPK-BGKcLV46-100
Sample_Name_Alias
Index Well Position	C06	D06
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	304	306
Peak_Molarity	71.60	68.50
libSampleQC_DNA_Well	DNA_Library_set77/set1/C12.png	DNA_Library_set77/set1/D12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/C6.png	RNA_Library_set77/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-99	BGKcLV46-100
RBP	SYMPK	SYMPK
Batch_ID	BGKcLV46	BGKcLV46
WB_result	71.700	83.890
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4702	4703

Sequencing Information

	BGKcLV46-99	BGKcLV46-100
Sample_ID	BGKcLV46-99	BGKcLV46-100
Sample Name	SYMPK-BGKcLV46-99	SYMPK-BGKcLV46-100
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	55,128,349	62,179,920
total_aligned_reads	49,379,371	58,203,409
unique_aligned_reads	45,283,547	53,684,755
percent_uniqueAligned	0.82142	0.86338
correlation_replicates	0.996143	0.996143
spikein_reads	75,674	47,500
percent_spikeins	0.00137	0.00076
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3405	3406

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
SYMPK-BGKcLV46-99_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3405	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	32193
SYMPK-BGKcLV46-99_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3405	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	32243
SYMPK-BGKcLV46-99_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3405					GRCh38	V40	SYMPK-BGKcLV46-99_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGKcLV46-99_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32293
SYMPK-BGKcLV46-99_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	3405					GRCh38	V40	SYMPK-BGKcLV46-99_Aligned.sortedByCoord.out.bam		ENCORE2	32343
SYMPK-BGKcLV46-99_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	3405					GRCh38	V40	SYMPK-BGKcLV46-99_Aligned.sortedByCoord.out.bam		ENCORE2	32393
SYMPK-BGKcLV46-99_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	3405					GRCh38	V40	SYMPK-BGKcLV46-99_Aligned.sortedByCoord.out.bam		ENCORE2	32443
SYMPK-BGKcLV46-99_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	3405					GRCh38	V40	SYMPK-BGKcLV46-99_Aligned.sortedByCoord.out.bam		ENCORE2	32493
SYMPK-BGKcLV46-99_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3405					GRCh38	V40	SYMPK-BGKcLV46-99_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGKcLV46-99_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32543
SYMPK-BGKcLV46-100_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3406	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	32192
SYMPK-BGKcLV46-100_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3406	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	32242
SYMPK-BGKcLV46-100_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3406					GRCh38	V40	SYMPK-BGKcLV46-100_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGKcLV46-100_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32292
SYMPK-BGKcLV46-100_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	3406					GRCh38	V40	SYMPK-BGKcLV46-100_Aligned.sortedByCoord.out.bam		ENCORE2	32342
SYMPK-BGKcLV46-100_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	3406					GRCh38	V40	SYMPK-BGKcLV46-100_Aligned.sortedByCoord.out.bam		ENCORE2	32392
SYMPK-BGKcLV46-100_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	3406					GRCh38	V40	SYMPK-BGKcLV46-100_Aligned.sortedByCoord.out.bam		ENCORE2	32442
SYMPK-BGKcLV46-100_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	3406					GRCh38	V40	SYMPK-BGKcLV46-100_Aligned.sortedByCoord.out.bam		ENCORE2	32492
SYMPK-BGKcLV46-100_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3406					GRCh38	V40	SYMPK-BGKcLV46-100_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGKcLV46-100_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32542