VARS RNA-Seq in HepG2

General Information


RBP	VARS
Cell_Line	HepG2
Method	CRISPR
Exp_Name	VARS-BGHcLV36-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV36
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	VARS-BGHcLV36-55
Rep2	VARS-BGHcLV36-56
CN1	NT-BGHcLV36-1
CN2	NT-BGHcLV36-2
Rep1_qPCR	9.0
Rep2_qPCR	0.0
Rep1_WB	52.1
Rep2_WB	51.3
Antibody Cat#	A304-776A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1047

Experiment Information (Status: Submitting)

	BGHcLV36-55	BGHcLV36-56
idx	1186	1187
TRCN#_or_BGC#	BGC#0001073	BGC#0001073
shRNA_or_gRNA_sequence	GTGGGTCAGTTACGCCGACA	GTGGGTCAGTTACGCCGACA
PAM	CGG	CGG
Name	VARS_98	VARS_98
Sample_ID	BGHcLV36-55	BGHcLV36-56
transduction_Date	8/2/22	8/2/22
days	D6	D6
RBP_name	VARS	VARS
qPCR_result	9.0	0.0
Ave_qPCR	4.5
RT-qPCR_primer-F	cttgttccggtttcagagga
RT-qPCR_primer-R	gcaacgacactggtttatgg
protein_conc	4364	4790
WB_result	52.1	51.3
Ave_WB	51.7
WB_DONE_date	9/6/22,9/12/22	Jess
MW	140kd
IP
antibody_Cat#	A304-776A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/9/24
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7369	7370

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

	BGHcLV36-55	BGHcLV36-56
Sample_ID	BGHcLV36-55	BGHcLV36-56
Sample Name
Sample Name	VARS-BGHcLV36-55	VARS-BGHcLV36-56
RBP	VARS	VARS
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10956	10957

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV36-55	BGHcLV36-56
Sample #	15	16
Sample Name	VARS-BGHcLV36-55	VARS-BGHcLV36-56
Sample_Name_Alias
Index Well Position	G02	H02
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	296	288
Peak_Molarity	47.50	23.90
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/G2.png	DNA_Library_set54-56/set1/H2.png
RIN	10.0	9.7
libSample_RNA_Well	RNA_Library_set54-56/set1/G2.png	RNA_Library_set54-56/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGHcLV36-55	BGHcLV36-56
RBP	VARS	VARS
Batch_ID	BGHcLV36	BGHcLV36
WB_result	52.100	51.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3386	3387

Sequencing Information

	BGHcLV36-55	BGHcLV36-56
Sample_ID	BGHcLV36-55	BGHcLV36-56
Sample Name	VARS-BGHcLV36-55	VARS-BGHcLV36-56
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	47,726,624	38,513,433
total_aligned_reads	42,253,126	34,624,635
unique_aligned_reads	40,066,744	32,925,324
percent_uniqueAligned	0.83951	0.85490
correlation_replicates	0.967608	0.967608
spikein_reads	4,522	4,814
percent_spikeins	0.00009	0.00012
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2259	2260

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-BGHcLV36-55_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2259	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8422
VARS-BGHcLV36-55_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2259	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8472
VARS-BGHcLV36-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2259					GRCh38	V40	VARS-BGHcLV36-55_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,VARS-BGHcLV36-55_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25663
VARS-BGHcLV36-55_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	2259					GRCh38	V40	VARS-BGHcLV36-55/Aligned.sortedByCoord.out.bam		ENCORE2	25713
VARS-BGHcLV36-55_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	2259					GRCh38	V40	VARS-BGHcLV36-55/Aligned.sortedByCoord.out.bam		ENCORE2	25763
VARS-BGHcLV36-55_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	2259					GRCh38	V40	VARS-BGHcLV36-55/Aligned.sortedByCoord.out.bam		ENCORE2	25813
VARS-BGHcLV36-55_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	2259					GRCh38	V40	VARS-BGHcLV36-55/Aligned.sortedByCoord.out.bam		ENCORE2	25863
VARS-BGHcLV36-55_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2259					GRCh38	V40	VARS-BGHcLV36-55_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,VARS-BGHcLV36-55_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25913
VARS-BGHcLV36-56_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2260	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8423
VARS-BGHcLV36-56_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2260	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8473
VARS-BGHcLV36-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2260					GRCh38	V40	VARS-BGHcLV36-56_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,VARS-BGHcLV36-56_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25664
VARS-BGHcLV36-56_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	2260					GRCh38	V40	VARS-BGHcLV36-56/Aligned.sortedByCoord.out.bam		ENCORE2	25714
VARS-BGHcLV36-56_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	2260					GRCh38	V40	VARS-BGHcLV36-56/Aligned.sortedByCoord.out.bam		ENCORE2	25764
VARS-BGHcLV36-56_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	2260					GRCh38	V40	VARS-BGHcLV36-56/Aligned.sortedByCoord.out.bam		ENCORE2	25814
VARS-BGHcLV36-56_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	2260					GRCh38	V40	VARS-BGHcLV36-56/Aligned.sortedByCoord.out.bam		ENCORE2	25864
VARS-BGHcLV36-56_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2260					GRCh38	V40	VARS-BGHcLV36-56_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,VARS-BGHcLV36-56_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25914