BAZ1A RNA-Seq in HepG2

General Information


RBP	BAZ1A
Cell_Line	HepG2
Method	CRISPR
Exp_Name	BAZ1A-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR961SJX
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR197XHV
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	BAZ1A-BGHcLV18-3
Rep2	BAZ1A-BGHcLV18-4
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	97.2
Rep2_qPCR	96.9
Rep1_WB	95.2
Rep2_WB	98.8
Antibody Cat#	PA5-51736
Antibody Lot#	lot# UC2743813B
Antibody DCC ID	ENCAB850VOO
Status	Released
Project	ENCODE4
ID	99

Experiment Information (Status: Released)

	BGHcLV18-3	BGHcLV18-4
idx	496	497
TRCN#_or_BGC#	BGC#0000453	BGC#0000453
shRNA_or_gRNA_sequence	CCGGCTCTTACTCGTAGTGG	CCGGCTCTTACTCGTAGTGG
PAM	CGG	CGG
Name	BAZ1A_95	BAZ1A_95
Sample_ID	BGHcLV18-3	BGHcLV18-4
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	BAZ1A	BAZ1A
qPCR_result	97.2	96.9
Ave_qPCR	97.1
RT-qPCR_primer-F	AACGAGATCTTCCGCCACTAC
RT-qPCR_primer-R	CAGCACAACTCCACACAAGG
protein_conc	4038	3528
WB_result	95.2	98.8
Ave_WB	97.0
WB_DONE_date	10/2/20	JESS
MW	179KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-51736	lot# UC2743813B
Antibody DCC ID	ENCAB850VOO
submitted_to_DCC_date
Rep1_TPM	34	0
Rep2_TPM	42	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6647	6648

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

	BGHcLV18-3	BGHcLV18-4
Sample_ID	BGHcLV18-3	BGHcLV18-4
Sample Name	BAZ1A-BGHcLV18-3	BAZ1A-BGHcLV18-4
Sample Name	BAZ1A-BGHcLV18-3	BAZ1A-BGHcLV18-4
RBP	BAZ1A	BAZ1A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5615	5616

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-3	BGHcLV18-4
Sample #	121	122
Sample Name	BAZ1A-BGHcLV18-3	BAZ1A-BGHcLV18-4
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	3-E1	3-F1
Tecan	37.43	38.89
Tecan_date	2019-12-16	2019-12-16
Size_bp	261	298
Peak_Molarity	28.10	22.20
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/C5.png	DNA_Library_set43-44/set2/D5.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/G6.png	RNA_Library_set43-44/set4/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-3	BGHcLV18-4
RBP	BAZ1A	BAZ1A
Batch_ID	BGHcLV18	BGHcLV18
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	697	698

Sequencing Information

	BGHcLV18-3	BGHcLV18-4
Sample_ID	BGHcLV18-3	BGHcLV18-4
Sample Name	BAZ1A-BGHcLV18-3	BAZ1A-BGHcLV18-4
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	157,772,416	190,931,540
total_aligned_reads	152,342,914	183,083,104
unique_aligned_reads	142,647,530	171,483,202
percent_uniqueAligned	0.90413	0.89814
correlation_replicates	0.998360	0.998360
spikein_reads	258,932	293,722
percent_spikeins	0.00164	0.00154
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	203	204

Data Submission Information

	BGHcLV18-3	BGHcLV18-3	BGHcLV18-3	BGHcLV18-3	BGHcLV18-3	BGHcLV18-3	BGHcLV18-4	BGHcLV18-4	BGHcLV18-4	BGHcLV18-4
ENCODE_alias	brenton-graveley:BAZ1A-BGHcLV18	brenton-graveley:BAZ1A-BGHcLV18-3	brenton-graveley:L-BAZ1A-BGHcLV18-3	brenton-graveley:BAZ1A-BGHcLV18-3_S37_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BAZ1A-BGHcLV18-3_S37_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BAZ1A-BGHcLV18-HepG2	brenton-graveley:BAZ1A-BGHcLV18-4	brenton-graveley:L-BAZ1A-BGHcLV18-4	brenton-graveley:BAZ1A-BGHcLV18-4_S38_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BAZ1A-BGHcLV18-4_S38_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR197XHV	ENCBS257VCX	ENCLB120XZV	ENCFF973FJR	ENCFF345NOB	ENCSR961SJX	ENCBS128GTR	ENCLB425ZLV	ENCFF953VMN	ENCFF965YDC
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	BGHcLV18-3	BGHcLV18-3	BGHcLV18-3	BGHcLV18-3	BGHcLV18-3	BGHcLV18-3	BGHcLV18-4	BGHcLV18-4	BGHcLV18-4	BGHcLV18-4
Sample Name	BAZ1A-BGHcLV18-3	BAZ1A-BGHcLV18-3	BAZ1A-BGHcLV18-3	BAZ1A-BGHcLV18-3	BAZ1A-BGHcLV18-3	BAZ1A-BGHcLV18-3	BAZ1A-BGHcLV18-4	BAZ1A-BGHcLV18-4	BAZ1A-BGHcLV18-4	BAZ1A-BGHcLV18-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		BAZ1A-BGHcLV18-3.pdf	L-BAZ1A-BGHcLV18-3.pdf				BAZ1A-BGHcLV18-4.pdf	L-BAZ1A-BGHcLV18-4.pdf
ID	46	172	338	588	640	7099	173	339	589	641

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-BGHcLV18-3_S37_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	203	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	169
BAZ1A-BGHcLV18-3_S37_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	203	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	221
BAZ1A-BGHcLV18-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	203					GRCh38	V40	BAZ1A-BGHcLV18-3_S37_R1_001.filtered.trimmed.paired.fastq.gz,BAZ1A-BGHcLV18-3_S37_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24889
BAZ1A-BGHcLV18-3_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	203					GRCh38	V40	BAZ1A-BGHcLV18-3/Aligned.sortedByCoord.out.bam		ENCORE2	24941
BAZ1A-BGHcLV18-3_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	203					GRCh38	V40	BAZ1A-BGHcLV18-3/Aligned.sortedByCoord.out.bam		ENCORE2	24993
BAZ1A-BGHcLV18-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	203					GRCh38	V40	BAZ1A-BGHcLV18-3/Aligned.sortedByCoord.out.bam		ENCORE2	25045
BAZ1A-BGHcLV18-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	203					GRCh38	V40	BAZ1A-BGHcLV18-3/Aligned.sortedByCoord.out.bam		ENCORE2	25097
BAZ1A-BGHcLV18-3_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	203					GRCh38	V40	BAZ1A-BGHcLV18-3_S37_R1_001.filtered.trimmed.paired.fastq.gz,BAZ1A-BGHcLV18-3_S37_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25149
BAZ1A-BGHcLV18-4_S38_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	204	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	170
BAZ1A-BGHcLV18-4_S38_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	204	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	222
BAZ1A-BGHcLV18-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	204					GRCh38	V40	BAZ1A-BGHcLV18-4_S38_R1_001.filtered.trimmed.paired.fastq.gz,BAZ1A-BGHcLV18-4_S38_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24890
BAZ1A-BGHcLV18-4_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	204					GRCh38	V40	BAZ1A-BGHcLV18-4/Aligned.sortedByCoord.out.bam		ENCORE2	24942
BAZ1A-BGHcLV18-4_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	204					GRCh38	V40	BAZ1A-BGHcLV18-4/Aligned.sortedByCoord.out.bam		ENCORE2	24994
BAZ1A-BGHcLV18-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	204					GRCh38	V40	BAZ1A-BGHcLV18-4/Aligned.sortedByCoord.out.bam		ENCORE2	25046
BAZ1A-BGHcLV18-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	204					GRCh38	V40	BAZ1A-BGHcLV18-4/Aligned.sortedByCoord.out.bam		ENCORE2	25098
BAZ1A-BGHcLV18-4_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	204					GRCh38	V40	BAZ1A-BGHcLV18-4_S38_R1_001.filtered.trimmed.paired.fastq.gz,BAZ1A-BGHcLV18-4_S38_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25150