BAZ1A RNA-Seq in K562

General Information


RBP	BAZ1A
Cell_Line	K562
Method	CRISPR
Exp_Name	BAZ1A-BGKcLV17-K562
ENCODE_series_ID	ENCSR885KER
Batch_ID	BGKcLV17
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR825EPB
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	BAZ1A-BGKcLV17-3
Rep2	BAZ1A-BGKcLV17-4
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	98.7
Rep2_qPCR	98.7
Rep1_WB	95.5
Rep2_WB	96.6
Antibody Cat#	PA5-51736
Antibody Lot#	lot# UC2743813B
Antibody DCC ID	ENCAB850VOO
Status	Released
Project	ENCODE4
ID	140

Experiment Information (Status: Released)

	BGKcLV17-3	BGKcLV17-4
idx	610	611
TRCN#_or_BGC#	BGC#0000453	BGC#0000453
shRNA_or_gRNA_sequence	CCGGCTCTTACTCGTAGTGG	CCGGCTCTTACTCGTAGTGG
PAM	CGG	CGG
Name	BAZ1A_95	BAZ1A_95
Sample_ID	BGKcLV17-3	BGKcLV17-4
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	BAZ1A	BAZ1A
qPCR_result	98.7	98.7
Ave_qPCR	98.7
RT-qPCR_primer-F	AACGAGATCTTCCGCCACTAC
RT-qPCR_primer-R	CAGCACAACTCCACACAAGG
protein_conc	4530	4124
WB_result	95.5	96.6
Ave_WB	96.1
WB_DONE_date	7/10/19	WES
MW	179KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-51736	lot# UC2743813B
Antibody DCC ID	ENCAB850VOO
submitted_to_DCC_date	11/16/20
Rep1_TPM	34.1	0
Rep2_TPM	36	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4722	4723

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BAZ1A	Product_ID: PA5-51736 Lot_ID: UC2743813B Source: Thermo Fisher Target Name: BAZ1A-human

Experiment Status

	BGKcLV17-3	BGKcLV17-4
Sample_ID	BGKcLV17-3	BGKcLV17-4
Sample Name	BAZ1A-BGKcLV17-3	BAZ1A-BGKcLV17-4
Sample Name	BAZ1A-BGKcLV17-3	BAZ1A-BGKcLV17-4
RBP	BAZ1A	BAZ1A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5487	5488

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-3	BGKcLV17-4
Sample #	77	78
Sample Name	BAZ1A-BGKcLV17-3	BAZ1A-BGKcLV17-4
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-C1	1-D1
Tecan	31.98	38.43
Tecan_date	2019-12-10	2019-12-10
Size_bp	271	275
Peak_Molarity	24.20	34.10
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C6.png	DNA_Library_set43-44/set1/D6.png
RIN	9.2	9.4
libSample_RNA_Well	RNA_Library_set43-44/set4/C1.png	RNA_Library_set43-44/set4/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-3	BGKcLV17-4
RBP	BAZ1A	BAZ1A
Batch_ID	BGKcLV17	BGKcLV17
WB_result	95.500	96.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	653	654

Sequencing Information

	BGKcLV17-3	BGKcLV17-4
Sample_ID	BGKcLV17-3	BGKcLV17-4
Sample Name	BAZ1A-BGKcLV17-3	BAZ1A-BGKcLV17-4
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	242,527,898	101,110,548
total_aligned_reads	222,720,678	94,993,832
unique_aligned_reads	201,624,632	86,324,838
percent_uniqueAligned	0.83135	0.85377
correlation_replicates	0.998233	0.998233
spikein_reads	58,286	26,862
percent_spikeins	0.00024	0.00027
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	155	156

Data Submission Information

	BGKcLV17-3	BGKcLV17-3	BGKcLV17-3	BGKcLV17-3	BGKcLV17-3	BGKcLV17-3	BGKcLV17-4	BGKcLV17-4	BGKcLV17-4	BGKcLV17-4
ENCODE_alias	brenton-graveley:BAZ1A-BGKcLV17	brenton-graveley:BAZ1A-BGKcLV17-3	brenton-graveley:L-BAZ1A-BGKcLV17-3	brenton-graveley:BAZ1A-BGKcLV17-3_S73_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BAZ1A-BGKcLV17-3_S73_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BAZ1A-BGKcLV17-K562	brenton-graveley:BAZ1A-BGKcLV17-4	brenton-graveley:L-BAZ1A-BGKcLV17-4	brenton-graveley:BAZ1A-BGKcLV17-4_S74_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BAZ1A-BGKcLV17-4_S74_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR825EPB	ENCBS089LHN	ENCLB231CGP	ENCFF062RGF	ENCFF445YQF	ENCSR885KER	ENCBS287JVX	ENCLB150APE	ENCFF096SYL	ENCFF653TSE
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	BGKcLV17-3	BGKcLV17-3	BGKcLV17-3	BGKcLV17-3	BGKcLV17-3	BGKcLV17-3	BGKcLV17-4	BGKcLV17-4	BGKcLV17-4	BGKcLV17-4
Sample Name	BAZ1A-BGKcLV17-3	BAZ1A-BGKcLV17-3	BAZ1A-BGKcLV17-3	BAZ1A-BGKcLV17-3	BAZ1A-BGKcLV17-3	BAZ1A-BGKcLV17-3	BAZ1A-BGKcLV17-4	BAZ1A-BGKcLV17-4	BAZ1A-BGKcLV17-4	BAZ1A-BGKcLV17-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		BAZ1A-BGKcLV17-3.pdf	L-BAZ1A-BGKcLV17-3.pdf				BAZ1A-BGKcLV17-4.pdf	L-BAZ1A-BGKcLV17-4.pdf
ID	37	156	320	518	570	7100	157	321	519	571

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
BAZ1A-BGKcLV17-3_S73_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	155	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	65
BAZ1A-BGKcLV17-3_S73_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	155	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	117
BAZ1A-BGKcLV17-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	155					GRCh38	V40	BAZ1A-BGKcLV17-3_S73_R1_001.filtered.trimmed.paired.fastq.gz,BAZ1A-BGKcLV17-3_S73_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24356
BAZ1A-BGKcLV17-3_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	155					GRCh38	V40	BAZ1A-BGKcLV17-3/Aligned.sortedByCoord.out.bam		ENCORE2	24408
BAZ1A-BGKcLV17-3_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	155					GRCh38	V40	BAZ1A-BGKcLV17-3/Aligned.sortedByCoord.out.bam		ENCORE2	24460
BAZ1A-BGKcLV17-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	155					GRCh38	V40	BAZ1A-BGKcLV17-3/Aligned.sortedByCoord.out.bam		ENCORE2	24512
BAZ1A-BGKcLV17-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	155					GRCh38	V40	BAZ1A-BGKcLV17-3/Aligned.sortedByCoord.out.bam		ENCORE2	24564
BAZ1A-BGKcLV17-3_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	155					GRCh38	V40	BAZ1A-BGKcLV17-3_S73_R1_001.filtered.trimmed.paired.fastq.gz,BAZ1A-BGKcLV17-3_S73_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24616
BAZ1A-BGKcLV17-4_S74_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	156	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	66
BAZ1A-BGKcLV17-4_S74_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	156	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	118
BAZ1A-BGKcLV17-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	156					GRCh38	V40	BAZ1A-BGKcLV17-4_S74_R1_001.filtered.trimmed.paired.fastq.gz,BAZ1A-BGKcLV17-4_S74_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24357
BAZ1A-BGKcLV17-4_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	156					GRCh38	V40	BAZ1A-BGKcLV17-4/Aligned.sortedByCoord.out.bam		ENCORE2	24409
BAZ1A-BGKcLV17-4_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	156					GRCh38	V40	BAZ1A-BGKcLV17-4/Aligned.sortedByCoord.out.bam		ENCORE2	24461
BAZ1A-BGKcLV17-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	156					GRCh38	V40	BAZ1A-BGKcLV17-4/Aligned.sortedByCoord.out.bam		ENCORE2	24513
BAZ1A-BGKcLV17-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	156					GRCh38	V40	BAZ1A-BGKcLV17-4/Aligned.sortedByCoord.out.bam		ENCORE2	24565
BAZ1A-BGKcLV17-4_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	156					GRCh38	V40	BAZ1A-BGKcLV17-4_S74_R1_001.filtered.trimmed.paired.fastq.gz,BAZ1A-BGKcLV17-4_S74_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24617