SYMPK RNA-Seq in K562

General Information


RBP	SYMPK
Cell_Line	K562
Method	CRISPR
Exp_Name	SYMPK-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	SYMPK-BGKcLV42-91
Rep2	SYMPK-BGKcLV42-92
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	need discussion
Rep2_WB
Antibody Cat#	13071S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1562

Experiment Information (Status: Submitting)

	BGKcLV42-91	BGKcLV42-92
idx	0	0
TRCN#_or_BGC#	BGC#0001190	BGC#0001190
shRNA_or_gRNA_sequence	ACTGTGATGCCACGCTCCGA	ACTGTGATGCCACGCTCCGA
PAM	CGG	CGG
Name	SYMPK_95b	SYMPK_95b
Sample_ID	BGKcLV42-91	BGKcLV42-92
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	SYMPK	SYMPK
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	CGAAAATTTGTCATCGGCTT
RT-qPCR_primer-R	TCACCACGTTCACATTCTCG
protein_conc	2098	2580
WB_result	need discussion
Ave_WB
WB_DONE_date	5/10/24
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	check result befor release	check result befor release
ID	5859	5860

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV42-91	BGKcLV42-92
Sample_ID	BGKcLV42-91	BGKcLV42-92
Sample Name
Sample Name	SYMPK-BGKcLV42-91	SYMPK-BGKcLV42-92
RBP	SYMPK	SYMPK
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13118	13119

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-91	BGKcLV42-92
Sample #	75	76
Sample Name	SYMPK-BGKcLV42-91	SYMPK-BGKcLV42-92
Sample_Name_Alias
Index Well Position	C10	D10
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	322	324
Peak_Molarity	100.00	105.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/C10.png	DNA_Library_set73/set1/D10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/C10.png	RNA_Library_set73/set1/D10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-91	BGKcLV42-92
RBP	SYMPK	SYMPK
Batch_ID	BGKcLV42	BGKcLV42
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4344	4345

Sequencing Information

	BGKcLV42-91	BGKcLV42-92
Sample_ID	BGKcLV42-91	BGKcLV42-92
Sample Name	SYMPK-BGKcLV42-91	SYMPK-BGKcLV42-92
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	39,241,468	45,250,524
total_aligned_reads	36,961,680	42,756,531
unique_aligned_reads	34,136,184	39,585,648
percent_uniqueAligned	0.86990	0.87481
correlation_replicates	0.997112	0.997112
spikein_reads	248	2,050
percent_spikeins	0.00001	0.00005
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3211	3212

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-BGKcLV42-91_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3211	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	30414
SYMPK-BGKcLV42-91_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3211	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	30504
SYMPK-BGKcLV42-91_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3211					GRCh38	V40	SYMPK-BGKcLV42-91_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGKcLV42-91_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31346
SYMPK-BGKcLV42-91_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	3211					GRCh38	V40	SYMPK-BGKcLV42-91_Aligned.sortedByCoord.out.bam		ENCORE2	31436
SYMPK-BGKcLV42-91_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	3211					GRCh38	V40	SYMPK-BGKcLV42-91_Aligned.sortedByCoord.out.bam		ENCORE2	31526
SYMPK-BGKcLV42-91_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	3211					GRCh38	V40	SYMPK-BGKcLV42-91_Aligned.sortedByCoord.out.bam		ENCORE2	31616
SYMPK-BGKcLV42-91_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	3211					GRCh38	V40	SYMPK-BGKcLV42-91_Aligned.sortedByCoord.out.bam		ENCORE2	31706
SYMPK-BGKcLV42-91_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3211					GRCh38	V40	SYMPK-BGKcLV42-91_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGKcLV42-91_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31796
SYMPK-BGKcLV42-92_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3212	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	30415
SYMPK-BGKcLV42-92_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3212	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	30505
SYMPK-BGKcLV42-92_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3212					GRCh38	V40	SYMPK-BGKcLV42-92_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGKcLV42-92_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31347
SYMPK-BGKcLV42-92_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	3212					GRCh38	V40	SYMPK-BGKcLV42-92_Aligned.sortedByCoord.out.bam		ENCORE2	31437
SYMPK-BGKcLV42-92_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	3212					GRCh38	V40	SYMPK-BGKcLV42-92_Aligned.sortedByCoord.out.bam		ENCORE2	31527
SYMPK-BGKcLV42-92_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	3212					GRCh38	V40	SYMPK-BGKcLV42-92_Aligned.sortedByCoord.out.bam		ENCORE2	31617
SYMPK-BGKcLV42-92_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	3212					GRCh38	V40	SYMPK-BGKcLV42-92_Aligned.sortedByCoord.out.bam		ENCORE2	31707
SYMPK-BGKcLV42-92_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3212					GRCh38	V40	SYMPK-BGKcLV42-92_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGKcLV42-92_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31797