ZNF574 RNA-Seq in HepG2

General Information


RBP	ZNF574
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ZNF574-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR713SJV
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR821GQN
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	ZNF574-BGHcLV18-53
Rep2	ZNF574-BGHcLV18-54
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	9.0
Rep2_qPCR	0.0
Rep1_WB	96.2
Rep2_WB	95.6
Antibody Cat#	PA5-54719
Antibody Lot#	lot# UC2731463
Antibody DCC ID	ENCAB743ZXI
Status	Released
Project	ENCODE4
ID	121

Experiment Information (Status: Released)

	BGHcLV18-53	BGHcLV18-54
idx	548	549
TRCN#_or_BGC#	BGC#0000449	BGC#0000449
shRNA_or_gRNA_sequence	TGTGGAGCACTCATACCGAA	TGTGGAGCACTCATACCGAA
PAM	AGG	AGG
Name	ZNF574_96	ZNF574_96
Sample_ID	BGHcLV18-53	BGHcLV18-54
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	ZNF574	ZNF574
qPCR_result	9.0	0.0
Ave_qPCR	4.5
RT-qPCR_primer-F	caggacggaggcttggag
RT-qPCR_primer-R	gcactcagagcagacatagc
protein_conc	4847	4314
WB_result	96.2	95.6
Ave_WB	95.9
WB_DONE_date	8/22/19	wes
MW	99KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-54719	lot# UC2731463
Antibody DCC ID	ENCAB743ZXI
submitted_to_DCC_date
Rep1_TPM	10	0
Rep2_TPM	3	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6703	6704

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ZNF574	Product_ID: PA5-54719 Lot_ID: UC2731463 Source: Thermo Fisher Target Name: ZNF574-human

Experiment Status

	BGHcLV18-53	BGHcLV18-54
Sample_ID	BGHcLV18-53	BGHcLV18-54
Sample Name
Sample Name	ZNF574-BGHcLV18-53	ZNF574-BGHcLV18-54
RBP	ZNF574	ZNF574
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5659	5660

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-53	BGHcLV18-54
Sample #	165	166
Sample Name	ZNF574-BGHcLV18-53	ZNF574-BGHcLV18-54
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	6-A1	6-B1
Tecan	39.17	33.72
Tecan_date	2019-12-16	2019-12-16
Size_bp	275	277
Peak_Molarity	32.70	25.90
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/C10.png	DNA_Library_set43-44/set2/D10.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/G11.png	RNA_Library_set43-44/set4/H11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-53	BGHcLV18-54
RBP	ZNF574	ZNF574
Batch_ID	BGHcLV18	BGHcLV18
WB_result	96.200	95.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	741	742

Sequencing Information

	BGHcLV18-53	BGHcLV18-54
Sample_ID	BGHcLV18-53	BGHcLV18-54
Sample Name	ZNF574-BGHcLV18-53	ZNF574-BGHcLV18-54
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	167,111,832	140,395,442
total_aligned_reads	162,906,608	135,522,490
unique_aligned_reads	152,707,542	127,086,648
percent_uniqueAligned	0.91380	0.90520
correlation_replicates	0.998995	0.998995
spikein_reads	270,092	182,474
percent_spikeins	0.00162	0.00130
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	247	248

Data Submission Information

	BGHcLV18-53	BGHcLV18-53	BGHcLV18-53	BGHcLV18-53	BGHcLV18-53	BGHcLV18-53	BGHcLV18-54	BGHcLV18-54	BGHcLV18-54	BGHcLV18-54
ENCODE_alias	brenton-graveley:ZNF574-BGHcLV18	brenton-graveley:ZNF574-BGHcLV18-53	brenton-graveley:L-ZNF574-BGHcLV18-53	brenton-graveley:ZNF574-BGHcLV18-53_S77_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF574-BGHcLV18-53_S77_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF574-BGHcLV18-HepG2	brenton-graveley:ZNF574-BGHcLV18-54	brenton-graveley:L-ZNF574-BGHcLV18-54	brenton-graveley:ZNF574-BGHcLV18-54_S78_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF574-BGHcLV18-54_S78_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR821GQN	ENCBS278VDI	ENCLB117WMX	ENCFF215MPS	ENCFF825THF	ENCSR713SJV	ENCBS511OGB	ENCLB834JZQ	ENCFF481GUB	ENCFF515HGM
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	BGHcLV18-53	BGHcLV18-53	BGHcLV18-53	BGHcLV18-53	BGHcLV18-53	BGHcLV18-53	BGHcLV18-54	BGHcLV18-54	BGHcLV18-54	BGHcLV18-54
Sample Name	ZNF574-BGHcLV18-53	ZNF574-BGHcLV18-53	ZNF574-BGHcLV18-53	ZNF574-BGHcLV18-53	ZNF574-BGHcLV18-53	ZNF574-BGHcLV18-53	ZNF574-BGHcLV18-54	ZNF574-BGHcLV18-54	ZNF574-BGHcLV18-54	ZNF574-BGHcLV18-54
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		ZNF574-BGHcLV18-53.pdf	L-ZNF574-BGHcLV18-53.pdf				ZNF574-BGHcLV18-54.pdf	L-ZNF574-BGHcLV18-54.pdf
ID	68	216	382	632	684	7371	217	383	633	685

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
ZNF574-BGHcLV18-53_S77_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	247	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	219
ZNF574-BGHcLV18-53_S77_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	247	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	271
ZNF574-BGHcLV18-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	247					GRCh38	V40	ZNF574-BGHcLV18-53_S77_R1_001.filtered.trimmed.paired.fastq.gz,ZNF574-BGHcLV18-53_S77_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24939
ZNF574-BGHcLV18-53_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	247					GRCh38	V40	ZNF574-BGHcLV18-53/Aligned.sortedByCoord.out.bam		ENCORE2	24991
ZNF574-BGHcLV18-53_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	247					GRCh38	V40	ZNF574-BGHcLV18-53/Aligned.sortedByCoord.out.bam		ENCORE2	25043
ZNF574-BGHcLV18-53_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	247					GRCh38	V40	ZNF574-BGHcLV18-53/Aligned.sortedByCoord.out.bam		ENCORE2	25095
ZNF574-BGHcLV18-53_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	247					GRCh38	V40	ZNF574-BGHcLV18-53/Aligned.sortedByCoord.out.bam		ENCORE2	25147
ZNF574-BGHcLV18-53_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	247					GRCh38	V40	ZNF574-BGHcLV18-53_S77_R1_001.filtered.trimmed.paired.fastq.gz,ZNF574-BGHcLV18-53_S77_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25199
ZNF574-BGHcLV18-54_S78_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	248	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	220
ZNF574-BGHcLV18-54_S78_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	248	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	272
ZNF574-BGHcLV18-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	248					GRCh38	V40	ZNF574-BGHcLV18-54_S78_R1_001.filtered.trimmed.paired.fastq.gz,ZNF574-BGHcLV18-54_S78_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24940
ZNF574-BGHcLV18-54_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	248					GRCh38	V40	ZNF574-BGHcLV18-54/Aligned.sortedByCoord.out.bam		ENCORE2	24992
ZNF574-BGHcLV18-54_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	248					GRCh38	V40	ZNF574-BGHcLV18-54/Aligned.sortedByCoord.out.bam		ENCORE2	25044
ZNF574-BGHcLV18-54_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	248					GRCh38	V40	ZNF574-BGHcLV18-54/Aligned.sortedByCoord.out.bam		ENCORE2	25096
ZNF574-BGHcLV18-54_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	248					GRCh38	V40	ZNF574-BGHcLV18-54/Aligned.sortedByCoord.out.bam		ENCORE2	25148
ZNF574-BGHcLV18-54_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	248					GRCh38	V40	ZNF574-BGHcLV18-54_S78_R1_001.filtered.trimmed.paired.fastq.gz,ZNF574-BGHcLV18-54_S78_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25200