VASP RNA-Seq in K562

General Information


RBP	VASP
Cell_Line	K562
Method	CRISPR
Exp_Name	VASP-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	VASP-BGKcLV42-103
Rep2	VASP-BGKcLV42-104
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	45.0
Rep2_qPCR	49.6
Rep1_WB	98.7
Rep2_WB	97.4
Antibody Cat#	3132S
Antibody Lot#	lot # 5
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1567

Experiment Information (Status: Submitting)

	BGKcLV42-103	BGKcLV42-104
idx	0	0
TRCN#_or_BGC#	BGC#0001204	BGC#0001204
shRNA_or_gRNA_sequence	CGCGAAAGGAATTGGCCGTG	CGCGAAAGGAATTGGCCGTG
PAM	GGG	GGG
Name	VASP_96	VASP_96
Sample_ID	BGKcLV42-103	BGKcLV42-104
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	VASP	VASP
qPCR_result	45.0	49.6
Ave_qPCR	47.3
RT-qPCR_primer-F	caacctccacaccctcaagt
RT-qPCR_primer-R	gcaatttgctgctttgtgaa
protein_conc	2879	3411
WB_result	98.7	97.4
Ave_WB	98.1
WB_DONE_date	5/10/24
MW	46,50kd
IP
antibody_Cat#	3132S	lot # 5
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	5871	5872

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
VASP	Product_ID: 3132S Lot_ID: 5 Source: Cell Signaling Technology Target Name: VASP-human

Experiment Status

	BGKcLV42-103	BGKcLV42-104
Sample_ID	BGKcLV42-103	BGKcLV42-104
Sample Name
Sample Name	VASP-BGKcLV42-103	VASP-BGKcLV42-104
RBP	VASP	VASP
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13128	13129

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-103	BGKcLV42-104
Sample #	85	86
Sample Name	VASP-BGKcLV42-103	VASP-BGKcLV42-104
Sample_Name_Alias
Index Well Position	E11	F11
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	315	292
Peak_Molarity	86.10	85.80
libSampleQC_DNA_Well	DNA_Library_set73/set1/E11.png	DNA_Library_set73/set1/F11.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set73/set1/E11.png	RNA_Library_set73/set1/F11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-103	BGKcLV42-104
RBP	VASP	VASP
Batch_ID	BGKcLV42	BGKcLV42
WB_result	98.700	97.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4354	4355

Sequencing Information

	BGKcLV42-103	BGKcLV42-104
Sample_ID	BGKcLV42-103	BGKcLV42-104
Sample Name	VASP-BGKcLV42-103	VASP-BGKcLV42-104
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	41,801,857	30,100,370
total_aligned_reads	39,294,873	24,441,267
unique_aligned_reads	36,281,510	22,439,651
percent_uniqueAligned	0.86794	0.74549
correlation_replicates	0.994954	0.994954
spikein_reads	2,326	590
percent_spikeins	0.00006	0.00002
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3221	3222

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
VASP-BGKcLV42-103_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3221	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	30424
VASP-BGKcLV42-103_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3221	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	30514
VASP-BGKcLV42-103_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3221					GRCh38	V40	VASP-BGKcLV42-103_L001_R1_001.filtered.trimmed.paired.fastq.gz,VASP-BGKcLV42-103_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31356
VASP-BGKcLV42-103_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	3221					GRCh38	V40	VASP-BGKcLV42-103_Aligned.sortedByCoord.out.bam		ENCORE2	31446
VASP-BGKcLV42-103_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	3221					GRCh38	V40	VASP-BGKcLV42-103_Aligned.sortedByCoord.out.bam		ENCORE2	31536
VASP-BGKcLV42-103_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	3221					GRCh38	V40	VASP-BGKcLV42-103_Aligned.sortedByCoord.out.bam		ENCORE2	31626
VASP-BGKcLV42-103_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	3221					GRCh38	V40	VASP-BGKcLV42-103_Aligned.sortedByCoord.out.bam		ENCORE2	31716
VASP-BGKcLV42-103_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3221					GRCh38	V40	VASP-BGKcLV42-103_L001_R1_001.filtered.trimmed.paired.fastq.gz,VASP-BGKcLV42-103_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31806
VASP-BGKcLV42-104_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3222	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	30425
VASP-BGKcLV42-104_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3222	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	30515
VASP-BGKcLV42-104_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3222					GRCh38	V40	VASP-BGKcLV42-104_L001_R1_001.filtered.trimmed.paired.fastq.gz,VASP-BGKcLV42-104_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31357
VASP-BGKcLV42-104_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	3222					GRCh38	V40	VASP-BGKcLV42-104_Aligned.sortedByCoord.out.bam		ENCORE2	31447
VASP-BGKcLV42-104_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	3222					GRCh38	V40	VASP-BGKcLV42-104_Aligned.sortedByCoord.out.bam		ENCORE2	31537
VASP-BGKcLV42-104_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	3222					GRCh38	V40	VASP-BGKcLV42-104_Aligned.sortedByCoord.out.bam		ENCORE2	31627
VASP-BGKcLV42-104_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	3222					GRCh38	V40	VASP-BGKcLV42-104_Aligned.sortedByCoord.out.bam		ENCORE2	31717
VASP-BGKcLV42-104_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3222					GRCh38	V40	VASP-BGKcLV42-104_L001_R1_001.filtered.trimmed.paired.fastq.gz,VASP-BGKcLV42-104_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31807