ZNF574 RNA-Seq in K562

General Information


RBP	ZNF574
Cell_Line	K562
Method	CRISPR
Exp_Name	ZNF574-BGKcLV17-K562
ENCODE_series_ID	ENCSR959ALJ
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR064VKV
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	ZNF574-BGKcLV17-59
Rep2	ZNF574-BGKcLV17-60
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	84.7
Rep2_qPCR	93.2
Rep1_WB	64.5
Rep2_WB	79.9
Antibody Cat#	PA5-54719
Antibody Lot#	lot# UC2731463
Antibody DCC ID	ENCAB743ZXI
Status	Released
Project	ENCODE4
ID	97

Experiment Information (Status: Released)

	BGKcLV17-59	BGKcLV17-60
idx	668	669
TRCN#_or_BGC#	BGC#0000449	BGC#0000449
shRNA_or_gRNA_sequence	TGTGGAGCACTCATACCGAA	TGTGGAGCACTCATACCGAA
PAM	AGG	AGG
Name	ZNF574_96	ZNF574_96
Sample_ID	BGKcLV17-59	BGKcLV17-60
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	ZNF574	ZNF574
qPCR_result	84.7	93.2
Ave_qPCR	88.9
RT-qPCR_primer-F	caggacggaggcttggag
RT-qPCR_primer-R	gcactcagagcagacatagc
protein_conc	5247	5491
WB_result	64.5	79.9
Ave_WB	72.2
WB_DONE_date	7/22/19	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	5.7	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4788	4789

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

	BGKcLV17-59	BGKcLV17-60
Sample_ID	BGKcLV17-59	BGKcLV17-60
Sample Name
Sample Name	ZNF574-BGKcLV17-59	ZNF574-BGKcLV17-60
RBP	ZNF574	ZNF574
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5527	5528

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-59	BGKcLV17-60
Sample #	117	118
Sample Name	ZNF574-BGKcLV17-59	ZNF574-BGKcLV17-60
Sample_Name_Alias
Index Well Position	A03	B03
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-A1	3-B1
Tecan	25.82	33.02
Tecan_date	2019-12-16	2019-12-16
Size_bp	276	276
Peak_Molarity	30.10	23.70
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/A11.png	DNA_Library_set43-44/set1/B11.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set43-44/set4/A6.png	RNA_Library_set43-44/set4/B6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-59	BGKcLV17-60
RBP	ZNF574	ZNF574
Batch_ID	BGKcLV17	BGKcLV17
WB_result	64.500	79.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	693	694

Sequencing Information

	BGKcLV17-59	BGKcLV17-60
Sample_ID	BGKcLV17-59	BGKcLV17-60
Sample Name	ZNF574-BGKcLV17-59	ZNF574-BGKcLV17-60
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	124,010,564	126,398,798
total_aligned_reads	123,115,076	124,420,578
unique_aligned_reads	112,336,572	113,133,876
percent_uniqueAligned	0.90586	0.89505
correlation_replicates	0.998013	0.998013
spikein_reads	21,436	13,720
percent_spikeins	0.00017	0.00011
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	199	200

Data Submission Information

	BGKcLV17-59	BGKcLV17-59	BGKcLV17-59	BGKcLV17-59	BGKcLV17-59	BGKcLV17-59	BGKcLV17-60	BGKcLV17-60	BGKcLV17-60	BGKcLV17-60
ENCODE_alias	brenton-graveley:ZNF574-BGKcLV17	brenton-graveley:ZNF574-BGKcLV17-59	brenton-graveley:L-ZNF574-BGKcLV17-59	brenton-graveley:ZNF574-BGKcLV17-59_S27_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF574-BGKcLV17-59_S27_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF574-BGKcLV17-K562	brenton-graveley:ZNF574-BGKcLV17-60	brenton-graveley:L-ZNF574-BGKcLV17-60	brenton-graveley:ZNF574-BGKcLV17-60_S28_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF574-BGKcLV17-60_S28_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR064VKV	ENCBS357BKM	ENCLB950IDL	ENCFF791IBG	ENCFF659GSL	ENCSR959ALJ	ENCBS584XDN	ENCLB855VYU	ENCFF148VPO	ENCFF925UOU
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	BGKcLV17-59	BGKcLV17-59	BGKcLV17-59	BGKcLV17-59	BGKcLV17-59	BGKcLV17-59	BGKcLV17-60	BGKcLV17-60	BGKcLV17-60	BGKcLV17-60
Sample Name	ZNF574-BGKcLV17-59	ZNF574-BGKcLV17-59	ZNF574-BGKcLV17-59	ZNF574-BGKcLV17-59	ZNF574-BGKcLV17-59	ZNF574-BGKcLV17-59	ZNF574-BGKcLV17-60	ZNF574-BGKcLV17-60	ZNF574-BGKcLV17-60	ZNF574-BGKcLV17-60
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
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		ZNF574-BGKcLV17-59.pdf	L-ZNF574-BGKcLV17-59.pdf				ZNF574-BGKcLV17-60.pdf	L-ZNF574-BGKcLV17-60.pdf
ID	83	246	412	714	744	7372	247	413	715	745

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-BGKcLV17-59_S27_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	199	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	301
ZNF574-BGKcLV17-59_S27_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	199	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	331
ZNF574-BGKcLV17-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	199					GRCh38	V40	ZNF574-BGKcLV17-59_S27_R1_001.filtered.trimmed.paired.fastq.gz,ZNF574-BGKcLV17-59_S27_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24697
ZNF574-BGKcLV17-59_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	199					GRCh38	V40	ZNF574-BGKcLV17-59/Aligned.sortedByCoord.out.bam		ENCORE2	24727
ZNF574-BGKcLV17-59_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	199					GRCh38	V40	ZNF574-BGKcLV17-59/Aligned.sortedByCoord.out.bam		ENCORE2	24757
ZNF574-BGKcLV17-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	199					GRCh38	V40	ZNF574-BGKcLV17-59/Aligned.sortedByCoord.out.bam		ENCORE2	24787
ZNF574-BGKcLV17-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	199					GRCh38	V40	ZNF574-BGKcLV17-59/Aligned.sortedByCoord.out.bam		ENCORE2	24817
ZNF574-BGKcLV17-59_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	199					GRCh38	V40	ZNF574-BGKcLV17-59_S27_R1_001.filtered.trimmed.paired.fastq.gz,ZNF574-BGKcLV17-59_S27_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24847
ZNF574-BGKcLV17-60_S28_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	200	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	302
ZNF574-BGKcLV17-60_S28_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	200	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	332
ZNF574-BGKcLV17-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	200					GRCh38	V40	ZNF574-BGKcLV17-60_S28_R1_001.filtered.trimmed.paired.fastq.gz,ZNF574-BGKcLV17-60_S28_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24698
ZNF574-BGKcLV17-60_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	200					GRCh38	V40	ZNF574-BGKcLV17-60/Aligned.sortedByCoord.out.bam		ENCORE2	24728
ZNF574-BGKcLV17-60_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	200					GRCh38	V40	ZNF574-BGKcLV17-60/Aligned.sortedByCoord.out.bam		ENCORE2	24758
ZNF574-BGKcLV17-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	200					GRCh38	V40	ZNF574-BGKcLV17-60/Aligned.sortedByCoord.out.bam		ENCORE2	24788
ZNF574-BGKcLV17-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	200					GRCh38	V40	ZNF574-BGKcLV17-60/Aligned.sortedByCoord.out.bam		ENCORE2	24818
ZNF574-BGKcLV17-60_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	200					GRCh38	V40	ZNF574-BGKcLV17-60_S28_R1_001.filtered.trimmed.paired.fastq.gz,ZNF574-BGKcLV17-60_S28_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24848