VASP RNA-Seq in HepG2

General Information


RBP	VASP
Cell_Line	HepG2
Method	CRISPR
Exp_Name	VASP-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	VASP-BGHcLV43-63
Rep2	VASP-BGHcLV43-64
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	0.6
Rep2_qPCR	4.7
Rep1_WB	85.6
Rep2_WB	78.7
Antibody Cat#	3132S
Antibody Lot#	lot # 5
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1594

Experiment Information (Status: Submitting)

	BGHcLV43-63	BGHcLV43-64
idx	1431	1432
TRCN#_or_BGC#	BGC#0001205	BGC#0001205
shRNA_or_gRNA_sequence	GGTTGTGGTAGATCTGGACG	GGTTGTGGTAGATCTGGACG
PAM	CGG	CGG
Name	VASP_90	VASP_90
Sample_ID	BGHcLV43-63	BGHcLV43-64
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	VASP	VASP
qPCR_result	0.6	4.7
Ave_qPCR	2.7
RT-qPCR_primer-F	caacctccacaccctcaagt
RT-qPCR_primer-R	gcaatttgctgctttgtgaa
protein_conc	3552	4450
WB_result	85.6	78.7
Ave_WB	82.1
WB_DONE_date	6/21/24
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	9686	9687

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

	BGHcLV43-63	BGHcLV43-64
Sample_ID	BGHcLV43-63	BGHcLV43-64
Sample Name
Sample Name	VASP-BGHcLV43-63	VASP-BGHcLV43-64
RBP	VASP	VASP
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13278	13279

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-63	BGHcLV43-64
Sample #	51	52
Sample Name	VASP-BGHcLV43-63	VASP-BGHcLV43-64
Sample_Name_Alias
Index Well Position	C12	D12
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	297	298
Peak_Molarity	81.40	65.10
libSampleQC_DNA_Well	DNA_Library_set74/set2/C7.png	DNA_Library_set74/set2/D7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/G12.png	RNA_Library_set74/set1/H12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-63	BGHcLV43-64
RBP	VASP	VASP
Batch_ID	BGHcLV43	BGHcLV43
WB_result	85.600	78.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4410	4411

Sequencing Information

	BGHcLV43-63	BGHcLV43-64
Sample_ID	BGHcLV43-63	BGHcLV43-64
Sample Name	VASP-BGHcLV43-63	VASP-BGHcLV43-64
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	51,973,052	49,629,913
total_aligned_reads	49,109,626	46,413,493
unique_aligned_reads	46,181,267	43,567,196
percent_uniqueAligned	0.88856	0.87784
correlation_replicates	0.997795	0.997795
spikein_reads	48,068	13,520
percent_spikeins	0.00092	0.00027
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3277	3278

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-BGHcLV43-63_S141_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3277	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30570
VASP-BGHcLV43-63_S141_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3277	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30622
VASP-BGHcLV43-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3277					GRCh38	V40	VASP-BGHcLV43-63_S141_L003_R1_001.filtered.trimmed.paired.fastq.gz,VASP-BGHcLV43-63_S141_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30674
VASP-BGHcLV43-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3277					GRCh38	V40	VASP-BGHcLV43-63_Aligned.sortedByCoord.out.bam		ENCORE2	30726
VASP-BGHcLV43-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3277					GRCh38	V40	VASP-BGHcLV43-63_Aligned.sortedByCoord.out.bam		ENCORE2	30778
VASP-BGHcLV43-63_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3277					GRCh38	V40	VASP-BGHcLV43-63_Aligned.sortedByCoord.out.bam		ENCORE2	30830
VASP-BGHcLV43-63_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3277					GRCh38	V40	VASP-BGHcLV43-63_Aligned.sortedByCoord.out.bam		ENCORE2	30882
VASP-BGHcLV43-63_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3277					GRCh38	V40	VASP-BGHcLV43-63_S141_L003_R1_001.filtered.trimmed.paired.fastq.gz,VASP-BGHcLV43-63_S141_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30934
VASP-BGHcLV43-64_S142_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3278	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30571
VASP-BGHcLV43-64_S142_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3278	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30623
VASP-BGHcLV43-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3278					GRCh38	V40	VASP-BGHcLV43-64_S142_L003_R1_001.filtered.trimmed.paired.fastq.gz,VASP-BGHcLV43-64_S142_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30675
VASP-BGHcLV43-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3278					GRCh38	V40	VASP-BGHcLV43-64_Aligned.sortedByCoord.out.bam		ENCORE2	30727
VASP-BGHcLV43-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3278					GRCh38	V40	VASP-BGHcLV43-64_Aligned.sortedByCoord.out.bam		ENCORE2	30779
VASP-BGHcLV43-64_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3278					GRCh38	V40	VASP-BGHcLV43-64_Aligned.sortedByCoord.out.bam		ENCORE2	30831
VASP-BGHcLV43-64_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3278					GRCh38	V40	VASP-BGHcLV43-64_Aligned.sortedByCoord.out.bam		ENCORE2	30883
VASP-BGHcLV43-64_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3278					GRCh38	V40	VASP-BGHcLV43-64_S142_L003_R1_001.filtered.trimmed.paired.fastq.gz,VASP-BGHcLV43-64_S142_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30935