VARS RNA-Seq in K562

General Information


RBP	VARS
Cell_Line	K562
Method	CRISPR
Exp_Name	VARS-BGKcLV37-K562
ENCODE_series_ID
Batch_ID	BGKcLV37
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	VARS-BGKcLV37-57
Rep2	VARS-BGKcLV37-58
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	0.8
Rep2_qPCR	8.1
Rep1_WB	57.4
Rep2_WB	51.1
Antibody Cat#	A304-776A
Antibody Lot#	lot # 1
Antibody DCC ID	NO id
Status	Submitted
Project	ENCORE2
ID	1063

Experiment Information (Status: Submitting)

	BGKcLV37-57	BGKcLV37-58
idx	1409	1410
TRCN#_or_BGC#	BGC#0001073	BGC#0001073
shRNA_or_gRNA_sequence	GTGGGTCAGTTACGCCGACA	GTGGGTCAGTTACGCCGACA
PAM	CGG	CGG
Name	VARS_98	VARS_98
Sample_ID	BGKcLV37-57	BGKcLV37-58
transduction_Date	9/20/22	9/20/22
days	D6	D6
RBP_name	VARS	VARS
qPCR_result	0.8	8.1
Ave_qPCR	4.4
RT-qPCR_primer-F	cttgttccggtttcagagga
RT-qPCR_primer-R	gcaacgacactggtttatgg
protein_conc	1495	1692
WB_result	57.4	51.1
Ave_WB	54.3
WB_DONE_date	9/27/22,9/28/22,9/29	JESS,Licor
MW	140kd
IP
antibody_Cat#	A304-776A	lot # 1
Antibody DCC ID	NO id
submitted_to_DCC_date	8/29/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5571	5572

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
VARS	Product_ID: A304-776A Lot_ID: 1 Source: Bethyl Labs Target Name: VARS-human

Experiment Status

	BGKcLV37-57	BGKcLV37-58
Sample_ID	BGKcLV37-57	BGKcLV37-58
Sample Name
Sample Name	VARS-BGKcLV37-57	VARS-BGKcLV37-58
RBP	VARS	VARS
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11110	11111

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-57	BGKcLV37-58
Sample #	49	50
Sample Name	VARS-BGKcLV37-57	VARS-BGKcLV37-58
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	291	297
Peak_Molarity	79.80	53.70
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/A7.png	DNA_Library_set54-56/set1/B7.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/A7.png	RNA_Library_set54-56/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-57	BGKcLV37-58
RBP	VARS	VARS
Batch_ID	BGKcLV37	BGKcLV37
WB_result	57.400	51.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3420	3421

Sequencing Information

	BGKcLV37-57	BGKcLV37-58
Sample_ID	BGKcLV37-57	BGKcLV37-58
Sample Name	VARS-BGKcLV37-57	VARS-BGKcLV37-58
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	34,116,153	44,560,856
total_aligned_reads	32,051,328	42,080,496
unique_aligned_reads	29,773,626	39,099,085
percent_uniqueAligned	0.87271	0.87743
correlation_replicates	0.994661	0.994661
spikein_reads	7,354	5,136
percent_spikeins	0.00022	0.00012
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2293	2294

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
VARS-BGKcLV37-57_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2293	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8424
VARS-BGKcLV37-57_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2293	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8474
VARS-BGKcLV37-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2293					GRCh38	V40	VARS-BGKcLV37-57_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,VARS-BGKcLV37-57_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25665
VARS-BGKcLV37-57_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2293					GRCh38	V40	VARS-BGKcLV37-57/Aligned.sortedByCoord.out.bam		ENCORE2	25715
VARS-BGKcLV37-57_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2293					GRCh38	V40	VARS-BGKcLV37-57/Aligned.sortedByCoord.out.bam		ENCORE2	25765
VARS-BGKcLV37-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2293					GRCh38	V40	VARS-BGKcLV37-57/Aligned.sortedByCoord.out.bam		ENCORE2	25815
VARS-BGKcLV37-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2293					GRCh38	V40	VARS-BGKcLV37-57/Aligned.sortedByCoord.out.bam		ENCORE2	25865
VARS-BGKcLV37-57_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2293					GRCh38	V40	VARS-BGKcLV37-57_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,VARS-BGKcLV37-57_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25915
VARS-BGKcLV37-58_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2294	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8425
VARS-BGKcLV37-58_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2294	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8475
VARS-BGKcLV37-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2294					GRCh38	V40	VARS-BGKcLV37-58_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,VARS-BGKcLV37-58_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25666
VARS-BGKcLV37-58_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2294					GRCh38	V40	VARS-BGKcLV37-58/Aligned.sortedByCoord.out.bam		ENCORE2	25716
VARS-BGKcLV37-58_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2294					GRCh38	V40	VARS-BGKcLV37-58/Aligned.sortedByCoord.out.bam		ENCORE2	25766
VARS-BGKcLV37-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2294					GRCh38	V40	VARS-BGKcLV37-58/Aligned.sortedByCoord.out.bam		ENCORE2	25816
VARS-BGKcLV37-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2294					GRCh38	V40	VARS-BGKcLV37-58/Aligned.sortedByCoord.out.bam		ENCORE2	25866
VARS-BGKcLV37-58_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2294					GRCh38	V40	VARS-BGKcLV37-58_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,VARS-BGKcLV37-58_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25916