BZW2 RNA-Seq in HepG2

General Information


RBP	BZW2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	BZW2-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR453EZZ
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR921IQU
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	BZW2-BGHcLV27-29
Rep2	BZW2-BGHcLV27-30
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	1.6
Rep2_qPCR	7.6
Rep1_WB	59.7
Rep2_WB	64.1
Antibody Cat#	A304-608A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB067UBG
Status	Released
Project	ENCODE4
ID	811

Experiment Information (Status: Released)

	BGHcLV27-29	BGHcLV27-30
idx	795	796
TRCN#_or_BGC#	BGC#0000653	BGC#0000653
shRNA_or_gRNA_sequence	GCTAAATACTTCACTGACGC	GCTAAATACTTCACTGACGC
PAM	AGG	AGG
Name	BZW2_94	BZW2_94
Sample_ID	BGHcLV27-29	BGHcLV27-30
transduction_Date	5/18/21	5/18/21
days	D6	D6
RBP_name	BZW2	BZW2
qPCR_result	1.6	7.6
Ave_qPCR	4.6
RT-qPCR_primer-F	ggaagcacatgttgctaaagg
RT-qPCR_primer-R	ttgtgcttgttgagccattt
protein_conc	1471	1467
WB_result	59.7	64.1
Ave_WB	61.9
WB_DONE_date	6/7/21	JESS
MW	48kDa
IP	Rabbit / I
antibody_Cat#	A304-608A	LOT# 1
Antibody DCC ID	ENCAB067UBG	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/03/21	09/03/21
repeat_library
Note
ID	6960	6961

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BZW2	Product_ID: A304-608A Lot_ID: 1 Source: Bethyl Labs Target Name: BZW2-human

Experiment Status

	BGHcLV27-29	BGHcLV27-30
Sample_ID	BGHcLV27-29	BGHcLV27-30
Sample Name
Sample Name	BZW2-BGHcLV27-29	BZW2-BGHcLV27-30
RBP	BZW2	BZW2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9685	9686

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-29	BGHcLV27-30
Sample #	89	90
Sample Name	BZW2-BGHcLV27-29	BZW2-BGHcLV27-30
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	328	300
Peak_Molarity	126.00	145.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/E8.png	DNA_Library_set48-49/set2/F8.png
RIN	9.9	9.6
libSample_RNA_Well	RNA_Library_set48-49/set1/G8.png	RNA_Library_set48-49/set1/H8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-29	BGHcLV27-30
RBP	BZW2	BZW2
Batch_ID	BGHcLV27	BGHcLV27
WB_result	59.700	64.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1648	1649

Sequencing Information

	BGHcLV27-29	BGHcLV27-30
Sample_ID	BGHcLV27-29	BGHcLV27-30
Sample Name	BZW2-BGHcLV27-29	BZW2-BGHcLV27-30
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	106,958,120	104,703,202
total_aligned_reads	95,580,610	95,833,304
unique_aligned_reads	89,863,862	90,289,344
percent_uniqueAligned	0.84018	0.86234
correlation_replicates	0.998774	0.998774
spikein_reads	23,876	39,644
percent_spikeins	0.00022	0.00038
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1799	1800

Data Submission Information

	BGHcLV27-29	BGHcLV27-29	BGHcLV27-29	BGHcLV27-29	BGHcLV27-29	BGHcLV27-29	BGHcLV27-30	BGHcLV27-30	BGHcLV27-30	BGHcLV27-30
ENCODE_alias	brenton-graveley:BZW2-BGHcLV27	brenton-graveley:BZW2-BGHcLV27-29	brenton-graveley:L-BZW2-BGHcLV27-29	brenton-graveley:BZW2-BGHcLV27-29_S69_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BZW2-BGHcLV27-29_S69_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BZW2-BGHcLV27-HepG2	brenton-graveley:BZW2-BGHcLV27-30	brenton-graveley:L-BZW2-BGHcLV27-30	brenton-graveley:BZW2-BGHcLV27-30_S70_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BZW2-BGHcLV27-30_S70_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR921IQU	ENCBS219MYC	ENCLB195HWZ	ENCFF291EKK	ENCFF259KZM	ENCSR453EZZ	ENCBS376DUX	ENCLB376FDM	ENCFF946ZAL	ENCFF396KVG
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV27-29	BGHcLV27-29	BGHcLV27-29	BGHcLV27-29	BGHcLV27-29	BGHcLV27-29	BGHcLV27-30	BGHcLV27-30	BGHcLV27-30	BGHcLV27-30
Sample Name	BZW2-BGHcLV27-29	BZW2-BGHcLV27-29	BZW2-BGHcLV27-29	BZW2-BGHcLV27-29	BZW2-BGHcLV27-29	BZW2-BGHcLV27-29	BZW2-BGHcLV27-30	BZW2-BGHcLV27-30	BZW2-BGHcLV27-30	BZW2-BGHcLV27-30
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48H_biosample_protocol	LV48H_library_protocol				LV48H_biosample_protocol	LV48H_library_protocol
protocol_URL		BZW2-BGHcLV27-29.pdf	L-BZW2-BGHcLV27-29.pdf				BZW2-BGHcLV27-30.pdf	L-BZW2-BGHcLV27-30.pdf
ID	3439	3512	3646	3780	3914	7105	3513	3647	3781	3915

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
BZW2-BGHcLV27-29_S69_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1799	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3790
BZW2-BGHcLV27-29_S69_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1799	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3816
BZW2-BGHcLV27-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1799					GRCh38	V40	BZW2-BGHcLV27-29_S69_L003_R1_001.filtered.trimmed.paired.fastq.gz,BZW2-BGHcLV27-29_S69_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25477
BZW2-BGHcLV27-29_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1799					GRCh38	V40	BZW2-BGHcLV27-29_S69_L003_R1_001.filtered.trimmed.paired.fastq.gz,BZW2-BGHcLV27-29_S69_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25503
BZW2-BGHcLV27-29_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1799					GRCh38	V40	BZW2-BGHcLV27-29/Aligned.sortedByCoord.out.bam		ENCORE2	26441
BZW2-BGHcLV27-29_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1799					GRCh38	V40	BZW2-BGHcLV27-29/Aligned.sortedByCoord.out.bam		ENCORE2	26467
BZW2-BGHcLV27-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1799					GRCh38	V40	BZW2-BGHcLV27-29/Aligned.sortedByCoord.out.bam		ENCORE2	26493
BZW2-BGHcLV27-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1799					GRCh38	V40	BZW2-BGHcLV27-29/Aligned.sortedByCoord.out.bam		ENCORE2	26519
BZW2-BGHcLV27-30_S70_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1800	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3791
BZW2-BGHcLV27-30_S70_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1800	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3817
BZW2-BGHcLV27-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1800					GRCh38	V40	BZW2-BGHcLV27-30_S70_L003_R1_001.filtered.trimmed.paired.fastq.gz,BZW2-BGHcLV27-30_S70_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25478
BZW2-BGHcLV27-30_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1800					GRCh38	V40	BZW2-BGHcLV27-30_S70_L003_R1_001.filtered.trimmed.paired.fastq.gz,BZW2-BGHcLV27-30_S70_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25504
BZW2-BGHcLV27-30_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1800					GRCh38	V40	BZW2-BGHcLV27-30/Aligned.sortedByCoord.out.bam		ENCORE2	26442
BZW2-BGHcLV27-30_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1800					GRCh38	V40	BZW2-BGHcLV27-30/Aligned.sortedByCoord.out.bam		ENCORE2	26468
BZW2-BGHcLV27-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1800					GRCh38	V40	BZW2-BGHcLV27-30/Aligned.sortedByCoord.out.bam		ENCORE2	26494
BZW2-BGHcLV27-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1800					GRCh38	V40	BZW2-BGHcLV27-30/Aligned.sortedByCoord.out.bam		ENCORE2	26520