BZW2 RNA-Seq in K562

General Information


RBP	BZW2
Cell_Line	K562
Method	CRISPR
Exp_Name	BZW2-BGKcLV26-K562
ENCODE_series_ID	ENCSR908CFK
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR528OVC
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	BZW2-BGKcLV26-45
Rep2	BZW2-BGKcLV26-46
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	32.8
Rep2_qPCR	42.9
Rep1_WB	74.2
Rep2_WB	62.6
Antibody Cat#	A304-608A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB067UBG
Status	Released
Project	ENCODE4
ID	798

Experiment Information (Status: Released)

	BGKcLV26-45	BGKcLV26-46
idx	906	907
TRCN#_or_BGC#	BGC#0000653	BGC#0000653
shRNA_or_gRNA_sequence	GCTAAATACTTCACTGACGC	GCTAAATACTTCACTGACGC
PAM	AGG	AGG
Name	BZW2_94	BZW2_94
Sample_ID	BGKcLV26-45	BGKcLV26-46
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	BZW2	BZW2
qPCR_result	32.8	42.9
Ave_qPCR	37.8
RT-qPCR_primer-F	ggaagcacatgttgctaaagg
RT-qPCR_primer-R	ttgtgcttgttgagccattt
protein_conc	4753	4774
WB_result	74.2	62.6
Ave_WB	68.4
WB_DONE_date	5/18/21	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	09/01/21	09/01/21
repeat_library
Note
ID	5038	5039

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

	BGKcLV26-45	BGKcLV26-46
Sample_ID	BGKcLV26-45	BGKcLV26-46
Sample Name
Sample Name	BZW2-BGKcLV26-45	BZW2-BGKcLV26-46
RBP	BZW2	BZW2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9777	9778

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-45	BGKcLV26-46
Sample #	35	36
Sample Name	BZW2-BGKcLV26-45	BZW2-BGKcLV26-46
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	289	291
Peak_Molarity	127.00	141.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/C5.png	DNA_Library_set48-49/set1/D5.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_set48-49/set1/C5.png	RNA_Library_set48-49/set1/D5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-45	BGKcLV26-46
RBP	BZW2	BZW2
Batch_ID	BGKcLV26	BGKcLV26
WB_result	74.200	62.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1594	1595

Sequencing Information

	BGKcLV26-45	BGKcLV26-46
Sample_ID	BGKcLV26-45	BGKcLV26-46
Sample Name	BZW2-BGKcLV26-45	BZW2-BGKcLV26-46
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	75,109,954	53,329,188
total_aligned_reads	63,405,320	46,968,022
unique_aligned_reads	58,040,654	42,983,008
percent_uniqueAligned	0.77274	0.80599
correlation_replicates	0.999097	0.999097
spikein_reads	30,606	12,038
percent_spikeins	0.00041	0.00023
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1771	1772

Data Submission Information

	BGKcLV26-45	BGKcLV26-45	BGKcLV26-45	BGKcLV26-45	BGKcLV26-45	BGKcLV26-45	BGKcLV26-46	BGKcLV26-46	BGKcLV26-46	BGKcLV26-46
ENCODE_alias	brenton-graveley:BZW2-BGKcLV26	brenton-graveley:BZW2-BGKcLV26-45	brenton-graveley:L-BZW2-BGKcLV26-45	brenton-graveley:BZW2-BGKcLV26-45_S41_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BZW2-BGKcLV26-45_S41_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BZW2-BGKcLV26-K562	brenton-graveley:BZW2-BGKcLV26-46	brenton-graveley:L-BZW2-BGKcLV26-46	brenton-graveley:BZW2-BGKcLV26-46_S42_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BZW2-BGKcLV26-46_S42_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR528OVC	ENCBS972LHO	ENCLB008HEL	ENCFF289XPT	ENCFF591SFS	ENCSR908CFK	ENCBS652IYM	ENCLB651VVC	ENCFF440RYQ	ENCFF255BOJ
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	BGKcLV26-45	BGKcLV26-45	BGKcLV26-45	BGKcLV26-45	BGKcLV26-45	BGKcLV26-45	BGKcLV26-46	BGKcLV26-46	BGKcLV26-46	BGKcLV26-46
Sample Name	BZW2-BGKcLV26-45	BZW2-BGKcLV26-45	BZW2-BGKcLV26-45	BZW2-BGKcLV26-45	BZW2-BGKcLV26-45	BZW2-BGKcLV26-45	BZW2-BGKcLV26-46	BZW2-BGKcLV26-46	BZW2-BGKcLV26-46	BZW2-BGKcLV26-46
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
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		BZW2-BGKcLV26-45.pdf	L-BZW2-BGKcLV26-45.pdf				BZW2-BGKcLV26-46.pdf	L-BZW2-BGKcLV26-46.pdf
ID	3463	3560	3694	3828	3962	7106	3561	3695	3829	3963

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-BGKcLV26-45_S41_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1771	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3864
BZW2-BGKcLV26-45_S41_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1771	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3914
BZW2-BGKcLV26-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1771					GRCh38	V40	BZW2-BGKcLV26-45_S41_L003_R1_001.filtered.trimmed.paired.fastq.gz,BZW2-BGKcLV26-45_S41_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25551
BZW2-BGKcLV26-45_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1771					GRCh38	V40	BZW2-BGKcLV26-45_S41_L003_R1_001.filtered.trimmed.paired.fastq.gz,BZW2-BGKcLV26-45_S41_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25601
BZW2-BGKcLV26-45_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1771					GRCh38	V40	BZW2-BGKcLV26-45/Aligned.sortedByCoord.out.bam		ENCORE2	26567
BZW2-BGKcLV26-45_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1771					GRCh38	V40	BZW2-BGKcLV26-45/Aligned.sortedByCoord.out.bam		ENCORE2	26617
BZW2-BGKcLV26-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1771					GRCh38	V40	BZW2-BGKcLV26-45/Aligned.sortedByCoord.out.bam		ENCORE2	26667
BZW2-BGKcLV26-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1771					GRCh38	V40	BZW2-BGKcLV26-45/Aligned.sortedByCoord.out.bam		ENCORE2	26717
BZW2-BGKcLV26-46_S42_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1772	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3865
BZW2-BGKcLV26-46_S42_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1772	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3915
BZW2-BGKcLV26-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1772					GRCh38	V40	BZW2-BGKcLV26-46_S42_L003_R1_001.filtered.trimmed.paired.fastq.gz,BZW2-BGKcLV26-46_S42_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25552
BZW2-BGKcLV26-46_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1772					GRCh38	V40	BZW2-BGKcLV26-46_S42_L003_R1_001.filtered.trimmed.paired.fastq.gz,BZW2-BGKcLV26-46_S42_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25602
BZW2-BGKcLV26-46_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1772					GRCh38	V40	BZW2-BGKcLV26-46/Aligned.sortedByCoord.out.bam		ENCORE2	26568
BZW2-BGKcLV26-46_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1772					GRCh38	V40	BZW2-BGKcLV26-46/Aligned.sortedByCoord.out.bam		ENCORE2	26618
BZW2-BGKcLV26-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1772					GRCh38	V40	BZW2-BGKcLV26-46/Aligned.sortedByCoord.out.bam		ENCORE2	26668
BZW2-BGKcLV26-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1772					GRCh38	V40	BZW2-BGKcLV26-46/Aligned.sortedByCoord.out.bam		ENCORE2	26718